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The Union of Biomarkers and Drug Development

The Union of Biomarkers and Drug Development

Author and Curator: Larry H. Bernstein, MD, FCAP

There has been consolidation going on for over a decade in both thr pharmaceutical and in the diagnostics industry, and at the same time the page is being rewritten for health care delivery.  I shall try to work through a clear picture of these not coincidental events.

Key notables:

  1. A growing segment of the US population is reaching Medicare age
  2. There is also a large underserved population in both metropolitan and nonurban areas and a fragmentation of the middle class after a growth slowdown in the economy since the 2008 deep recession.
  3. The deep recession affecting worldwide economies was only buffered by availability of oil or natural gas.
  4. In addition, there was a self-destructive strategy to cut spending on national scales that withdrew the support that would bolster support for infrastrucrue renewl.
  5. There has been a dramatic success in the clinical diagnostics industry, with a long history of being viewed as a loss leader, and this has been recently followed by the pharmaceutical industry faced with inability to introduce new products, leading to more competition in off-patent medications.
  6. The introduction of the Accountable Care Act has opened the opportunities for improved care, despite political opposition, and has probably sustained opportunity in the healthcare market.

Let’s take a look at this three headed serpent. – Pharma, Diagnostics, New Entity
?  The patient  ?
?  Insurance    ?
?  Physician    ?

Part I.   The Concept

When Illumina Buys Roche: The Dawning Of The Era Of Diagnostics Dominance

Robert J. Easton, Alain J. Gilbert, Olivier Lesueur, Rachel Laing, and Mark Ratner
http://PharmaMedtechBI.com    | IN VIVO: The Business & Medicine Report Jul/Aug 2014; 32(7).

  • With current technology and resources, a well-funded IVD company can create and pursue a strategy of information gathering and informatics application to create medical knowledge, enabling it to assume the risk and manage certain segments of patients
  • We see the first step in the process as the emergence of new specialty therapy companies coming from an IVD legacy, most likely focused in cancer, infection, or critical care

When Illumina Inc. acquired the regulatory consulting firm Myraqa, a specialist in in vitro diagnostics (IVD), in July, the press release announcement characterized the deal as one that would bolster illumina’s in-house capabilities for clinical readiness and help prepare for its next growth phase in regulated markets. That’s not surprising given the US Food and Drug Administration’s (FDA) approval a year and a half ago of its MiSeq next-generation sequencer for clinical use. But the deal could also suggest illumina is beginning to move along the path toward taking on clinical risk – that is, eventually

  • advising physicians and patients, which would mean facing regulators directly

Such a move – by illumina, another life sciences tools firm, or an information specialist from the high-tech universe – is inevitable given

  • the emerging power of diagnostics and traditional health care players’ reluctance to themselves take on such risk.

Alternatively, we believe that a well-funded diagnostics company could establish this position. either way, such a champion would establish dominion over and earn higher valuation than less-aggressive players who

  • only supply compartmentalized drug and device solutions.

Diagnostics companies have long been dogged by a fundamental issue:

  1. they are viewed and valued more along the lines of a commodity business than as firms that deliver a unique product or service
  2. diagnostics companies are in position to do just that today because they are now advantaged by having access to more data points.
  3. if they were to cobble together the right capabilities, diagnostics companies would have the ability to turn information into true medical knowledge

Example: PathGEN PathChip

nucleic-acid-based platform detects 296 viruses, bacteria, fungi & parasites

http://ow.ly/d/2GvQhttp://ow.ly/DSORV

This puts the diagnostics player in an unfamiliar realm where it can ask the question of what value they offer compared with a therapeutic. The key is that diagnostics can now offer unique information and potentially unique tools to capture that information. In order to do so, it has to create information from the data it generates, and then to supply that knowledge to users who will value and act on that knowledge. Complex genomic tests, as much as physical examination, may be the first meaningful touch point for physicians’ classification of disease.

Even if lab tests are more expensive, it is a cheaper means for deciding what to do first for a patient than the trial and error of prescribing medication without adequate information. Information is gaining in value as the amount of treatment data available on genomically characterizable subpopulations increases. In such a circumstance
it is the ability to perform that advisory function that will add tremendous value above what any test provides, the leverage of being able to apply a proprietary diagnostics platform – and importantly, the data it generates. It is the ability to perform that advisory function that will add tremendous value above what any test provides.

Integrated Diagnostics Inc. and Biodesix Inc. with mass spectrometry has the tools for unraveling disease processes, and numerous players are quite visibly in or are getting into the business of providing medical knowledge and clinical decision support in pursuit of a huge payout for those who actually solve important disease mysteries. Of course one has to ask whether MS/MS is sufficient for the assigned task, and also whether the technology is ready for the kind of workload experienced in a clinical service compared to a research vehicle.  My impression (as a reviewer) is that it is not now the time to take this seriously.

Roche has not realized its intent with Ventana: failing to deliver on the promise of boosting Roche’s pipeline, which was a significant factor in the high price Roche paid. The combined company was to be “uniquely positioned to further expand Ventana’s business globally and together develop more cost-efficient, differentiated, and targeted medicines.  On the other hand,  Biodesix decided to use Veristrat to look back and analyze important trial data to try to ascertain which patients would benefit from ficlatuzumab (subset). The predictive effect for the otherwise unimpressive trial results was observed in both progression-free survival and overall survival endpoints, and encouraged the companies to conduct a proof-of-concept study of ficlatuzumab in combination with Tarceva in advanced Non Small Cell Lung Cancer Patients (NSCLC) selected using the Veristrat test.

A second phase of IVD evolution will be far more challenging to pharma, when the most accomplished companies begin to assemble and integrate much broader data
sets, thereby gaining knowledge sufficient to actually manage patients and dictate therapy, including drug selection. No individual physician has or will have access to all of this information on thousands of patients, combined with the informatics to tease out from trillions of data points the optimal personalized medical approach. When the IVD-origin knowledge integrator amasses enough data and understanding to guide therapy decisions in large categories, particularly drug choices, it will become more valuable than any of the drug suppliers.

This is an apparent reversal of fortune. The pharmaceutical industry has been considered the valued provider, while the IVD manufacturer has been the low valued cousin. Now, it is by an ability to make kore accurate the drug administration that the IVD company can control the drug bill, to the detriment of drug developers, by finding algorithms that generate equal-to-innovative-drug outcomes using generics for most of the patients, thereby limiting the margins of drug suppliers and the upsides for new drug discovery/development.

It is here that there appears to be a misunderstanding of the whole picture of the development of the healthcare industry.  The pharmaceutical industry had a high value added only insofar it could replace market leaders for treatment before or at the time of patent expiration, which largely depended either introducing a new class of drug, or by relieving the current drug in its class of undesired toxicities or “side effects”.  Otherwise, the drug armamentarium was time limited to the expiration date. In other words, the value was dependent on a window of no competition.  In addition, as the regulation of healthcare costs were tightening under managed care, the introduction of new products that were deemed to be only marginally better, could be substitued by “off-patent” drug products.

The other misunderstanding is related to the IVD sector.  Laboratory tests in the 1950’s were manual, and they could be done by “technicians” who might not have completed a specialized training in clinical laboratory sciences.  The first sign of progress was the introduction of continuous flow chemistry, with a sampling probe, tubing to bring the reacting reagents into a photocell, and the timing of the reaction controlled by a coiled glass tubing before introducing the colored product into a uv-visible photometer.  In perhaps a decade, the Technicon SMA 12 and 6 instruments were introduced that could do up to 18 tests from a single sample.

Part 2. Emergence of an IVD Clinical Automated Diagnostics Industry

Why tests are ordered

  1. Screening
  2. Diagnosis
  3. Monitoring

Historical Perspective

Case in Point 1:  Outstanding Contributions in Clinical Chemistry. 1991. Arthur Karmen.

Dr. Karmen was born in New York City in 1930. He graduated from the Bronx High School of Science in 1946 and earned an A.B. and M.D. in 1950 and 1954, respectively, from New York University. In 1952, while a medical student working on a summer project at Memorial-Sloan Kettering, he used paper chromatography of amino acids to demonstrate the presence of glutamic-oxaloacetic and glutaniic-pyruvic ransaminases (aspartate and alanine aminotransferases) in serum and blood. In 1954, he devised the spectrophotometric method for measuring aspartate aminotransferase in serum, which, with minor modifications, is still used for diagnostic testing today. When developing this assay, he studied the reaction of NADH with serum and demonstrated the presence of lactate and malate dehydrogenases, both of which were also later used in diagnosis. Using the spectrophotometric method, he found that aspartate aminotransferase increased in the period immediately after an acute myocardial infarction and did the pilot studies that showed its diagnostic utility in heart and liver diseases.  This became as important as the EKG. It was replaced in cardiology usage by the MB isoenzyme of creatine kinase, which was driven by Burton Sobel’s work on infarct size, and later by the troponins.

Case in point 2: Arterial Blood Gases.  Van Slyke. National Academy of Sciences.

The test is used to determine the pH of the blood, the partial pressure of carbon dioxide and oxygen, and the bicarbonate level. Many blood gas analyzers will also report concentrations of lactate, hemoglobin, several electrolytes, oxyhemoglobin, carboxyhemoglobin and methemoglobin. ABG testing is mainly used in pulmonology and critical care medicine to determine gas exchange which reflect gas exchange across the alveolar-capillary membrane.

DONALD DEXTER VAN SLYKE died on May 4, 1971, after a long and productive career that spanned three generations of biochemists and physicians. He left behind not only a bibliography of 317 journal publications and 5 books, but also more than 100 persons who had worked with him and distinguished themselves in biochemistry and academic medicine. His doctoral thesis, with Gomberg at University of Michigan was published in the Journal of the American Chemical Society in 1907.  Van Slyke received an invitation from Dr. Simon Flexner, Director of the Rockefeller Institute, to come to New York for an interview. In 1911 he spent a year in Berlin with Emil Fischer, who was then the leading chemist of the scientific world. He was particularly impressed by Fischer’s performing all laboratory operations quantitatively —a procedure Van followed throughout his life. Prior to going to Berlin, he published the  classic nitrous acid method for the quantitative determination of primary aliphatic amino groups,  the first of the many gasometric procedures devised by Van Slyke, and made possible the determination of amino acids. It was the primary method used to study amino acid

composition of proteins for years before chromatography. Thus, his first seven postdoctoral years were centered around the development of better methodology for protein composition and amino acid metabolism.

With his colleague G. M. Meyer, he first demonstrated that amino acids, liberated during digestion in the intestine, are absorbed into the bloodstream, that they are removed by the tissues, and that the liver alone possesses the ability to convert the amino acid nitrogen into urea.  From the study of the kinetics of urease action, Van Slyke and Cullen developed equations that depended upon two reactions: (1) the combination of enzyme and substrate in stoichiometric proportions and (2) the reaction of the combination into the end products. Published in 1914, this formulation, involving two velocity constants, was similar to that arrived at contemporaneously by Michaelis and Menten in Germany in 1913.

He transferred to the Rockefeller Institute’s Hospital in 2013, under Dr. Rufus Cole, where “Men who were studying disease clinically had the right to go as deeply into its fundamental nature as their training allowed, and in the Rockefeller Institute’s Hospital every man who was caring for patients should also be engaged in more fundamental study”.  The study of diabetes was already under way by Dr. F. M. Allen, but patients inevitably died of acidosis.  Van Slyke reasoned that if incomplete oxidation of fatty acids in the body led to the accumulation of acetoacetic and beta-hydroxybutyric acids in the blood, then a reaction would result between these acids and the bicarbonate ions that would lead to a lower than-normal bicarbonate concentration in blood plasma. The problem thus became one of devising an analytical method that would permit the quantitative determination of bicarbonate concentration in small amounts of blood plasma.  He ingeniously devised a volumetric glass apparatus that was easy to use and required less than ten minutes for the determination of the total carbon dioxide in one cubic centimeter of plasma.  It also was soon found to be an excellent apparatus by which to determine blood oxygen concentrations, thus leading to measurements of the percentage saturation of blood hemoglobin with oxygen. This found extensive application in the study of respiratory diseases, such as pneumonia and tuberculosis. It also led to the quantitative study of cyanosis and a monograph on the subject by C. Lundsgaard and Van Slyke.

In all, Van Slyke and his colleagues published twenty-one papers under the general title “Studies of Acidosis,” beginning in 1917 and ending in 1934. They included not only chemical manifestations of acidosis, but Van Slyke, in No. 17 of the series (1921), elaborated and expanded the subject to describe in chemical terms the normal and abnormal variations in the acid-base balance of the blood. This was a landmark in understanding acid-base balance pathology.  Within seven years after Van moved to the Hospital, he had published a total of fifty-three papers, thirty-three of them coauthored with clinical colleagues.

In 1920, Van Slyke and his colleagues undertook a comprehensive investigation of gas and electrolyte equilibria in blood. McLean and Henderson at Harvard had made preliminary studies of blood as a physico-chemical system, but realized that Van Slyke and his colleagues at the Rockefeller Hospital had superior techniques and the facilities necessary for such an undertaking. A collaboration thereupon began between the two laboratories, which resulted in rapid progress toward an exact physico-chemical description of the role of hemoglobin in the transport of oxygen and carbon dioxide, of the distribution of diffusible ions and water between erythrocytes and plasma,
and of factors such as degree of oxygenation of hemoglobin and hydrogen ion concentration that modified these distributions. In this Van Slyke revised his volumetric gas analysis apparatus into a manometric method.  The manometric apparatus proved to give results that were from five to ten times more accurate.

A series of papers on the CO2 titration curves of oxy- and deoxyhemoglobin, of oxygenated and reduced whole blood, and of blood subjected to different degrees of oxygenation and on the distribution of diffusible ions in blood resulted.  These developed equations that predicted the change in distribution of water and diffusible ions between blood plasma and blood cells when there was a change in pH of the oxygenated blood. A significant contribution of Van Slyke and his colleagues was the application of the Gibbs-Donnan Law to the blood—regarded as a two-phase system, in which one phase (the erythrocytes) contained a high concentration of nondiffusible negative ions, i.e., those associated with hemoglobin, and cations, which were not freely exchaThe importance of Vanngeable between cells and plasma. By changing the pH through varying the CO2 tension, the concentration of negative hemoglobin charges changed in a predictable amount. This, in turn, changed the distribution of diffusible anions such as Cl” and HCO3″ in order to restore the Gibbs-Donnan equilibrium. Redistribution of water occurred to restore osmotic equilibrium. The experimental results confirmed the predictions of the equations.

As a spin-off from the physico-chemical study of the blood, Van undertook, in 1922, to put the concept of buffer value of weak electrolytes on a mathematically exact basis.
This proved to be useful in determining buffer values of mixed, polyvalent, and amphoteric electrolytes, and put the understanding of buffering on a quantitative basis. A
monograph in Medicine entitled “Observation on the Courses of Different Types of Bright’s Disease, and on the Resultant Changes in Renal Anatomy,” was a landmark that
related the changes occurring at different stages of renal deterioration to the quantitative changes taking place in kidney function. During this period, Van Slyke and R. M. Archibald identified glutamine as the source of urinary ammonia. During World War II, Van and his colleagues documented the effect of shock on renal function and, with R. A. Phillips, developed a simple method, based on specific gravity, suitable for use in the field.

Over 100 of Van’s 300 publications were devoted to methodology. The importance of Van Slyke’s contribution to clinical chemical methodology cannot be overestimated.
These included the blood organic constituents (carbohydrates, fats, proteins, amino acids, urea, nonprotein nitrogen, and phospholipids) and the inorganic constituents (total cations, calcium, chlorides, phosphate, and the gases carbon dioxide, carbon monoxide, and nitrogen). It was said that a Van Slyke manometric apparatus was almost all the special equipment needed to perform most of the clinical chemical analyses customarily performed prior to the introduction of photocolorimeters and spectrophotometers for such determinations.

The progress made in the medical sciences in genetics, immunology, endocrinology, and antibiotics during the second half of the twentieth century obscures at times the progress that was made in basic and necessary biochemical knowledge during the first half. Methods capable of giving accurate quantitative chemical information on biological material had to be painstakingly devised; basic questions on chemical behavior and metabolism had to be answered; and, finally, those factors that adversely modified the normal chemical reactions in the body so that abnormal conditions arise that we characterize as disease states had to be identified.

Viewed in retrospect, he combined in one scientific lifetime (1) basic contributions to the chemistry of body constituents and their chemical behavior in the body, (2) a chemical understanding of physiological functions of certain organ systems (notably the respiratory and renal), and (3) how such information could be exploited in the
understanding and treatment of disease. That outstanding additions to knowledge in all three categories were possible was in large measure due to his sound and broadly based chemical preparation, his ingenuity in devising means of accurate measurements of chemical constituents, and the opportunity given him at the Hospital of the Rockefeller Institute to study disease in company with physicians.

In addition, he found time to work collaboratively with Dr. John P. Peters of Yale on the classic, two-volume Quantitative Clinical Chemistry. In 1922, John P. Peters, who had just gone to Yale from Van Slyke’s laboratory as an Associate Professor of Medicine, was asked by a publisher to write a modest handbook for clinicians describing useful chemical methods and discussing their application to clinical problems. It was originally to be called “Quantitative Chemistry in Clinical Medicine.” He soon found that it was going to be a bigger job than he could handle alone and asked Van Slyke to join him in writing it. Van agreed, and the two men proceeded to draw up an outline and divide up the writing of the first drafts of the chapters between them. They also agreed to exchange each chapter until it met the satisfaction of both.At the time it was published in 1931, it contained practically all that could be stated with confidence about those aspects of disease that could be and had been studied by chemical means. It was widely accepted throughout the medical world as the “Bible” of quantitative clinical chemistry, and to this day some of the chapters have not become outdated.

History of Laboratory Medicine at Yale University.

The roots of the Department of Laboratory Medicine at Yale can be traced back to John Peters, the head of what he called the “Chemical Division” of the Department of Internal Medicine, subsequently known as the Section of Metabolism, who co-authored with Donald Van Slyke the landmark 1931 textbook Quantitative Clinical Chemistry (2.3); and to Pauline Hald, research collaborator of Dr. Peters who subsequently served as Director of Clinical Chemistry at Yale-New Haven Hospital for many years. In 1947, Miss Hald reported the very first flame photometric measurements of sodium and potassium in serum (4). This study helped to lay the foundation for modern studies of metabolism and their application to clinical care.

The Laboratory Medicine program at Yale had its inception in 1958 as a section of Internal Medicine under the leadership of David Seligson. In 1965, Laboratory Medicine achieved autonomous section status and in 1971, became a full-fledged academic department. Dr. Seligson, who served as the first Chair, pioneered modern automation and computerized data processing in the clinical laboratory. In particular, he demonstrated the feasibility of discrete sample handling for automation that is now the basis of virtually all automated chemistry analyzers. In addition, Seligson and Zetner demonstrated the first clinical use of atomic absorption spectrophotometry. He was one of the founding members of the major Laboratory Medicine academic society, the Academy of Clinical Laboratory Physicians and Scientists.

Davenport fig 10.jpg

Case in Point 3.  Nathan Gochman.  Developer of Automated Chemistries.

Nathan Gochman, PhD, has over 40 years of experience in the clinical diagnostics industry. This includes academic teaching and research, and 30 years in the pharmaceutical and in vitro diagnostics industry. He has managed R & D, technical marketing and technical support departments. As a leader in the industry he was President of the American Association for Clinical Chemistry (AACC) and the National Committee for Clinical Laboratory Standards (NCCLS, now CLSI). He is currently a Consultant to investment firms and IVD companies.

Nathan Gochman

Nathan Gochman

The clinical laboratory has become so productive, particularly in chemistry and immunology, and the labor, instrument and reagent costs are well determined, that today a physician’s medical decisions are 80% determined by the clinical laboratory.  Medical information systems have lagged far behind.  Why is that?  Because the decision for a MIS has historical been based on billing capture.  Moreover, the historical use of chemical profiles were quite good at validating healthy dtatus in an outpatient population, but the profiles became restricted under Diagnostic Related Groups.    Thus, it came to be that the diagnostics was considered a “commodity”.  In order to be competitive, a laboratory had to provide “high complexity” tests that were drawn in by a large volume of “moderate complexity”tests.

Part 3. Biomarkers in Medical Practice

Case in Point 1.

A Solid Prognostic Biomarker

HDL-C: Target of Therapy or Fuggedaboutit?

Steven E. Nissen, MD, MACC, Peter Libby, MD

DisclosuresNovember 06, 2014

Steven E. Nissen, MD, MACC: I am Steve Nissen, chairman of the Department of Cardiovascular Medicine at the Cleveland Clinic. I am here with Dr Peter Libby, chief of cardiology at the Brigham and Women’s Hospital and professor of medicine at Harvard Medical School. We are going to discuss high-density lipoprotein cholesterol (HDL-C), a topic that has been very controversial recently. Peter, HDL-C has been a pretty good biomarker. The question is whether it is a good target.

Peter Libby, MD: Since the early days in Berkley, when they were doing ultracentrifugation, and when it was reinforced and put on the map by the Framingham Study,[1] we have known that HDL-C is an extremely good biomarker of prospective cardiovascular risk with an inverse relationship with all kinds of cardiovascular events. That is as solid a finding as you can get in observational epidemiology. It is a very reliable prospective marker. It’s natural that the pharmaceutical industry and those of us who are interested in risk reduction would focus on HDL-C as a target. That is where the controversies come in.

Dr Nissen: It has been difficult. My view is that the trials that have attempted to modulate HDL-C or the drugs they used have been flawed. Although the results have not been promising, the jury is yet out. Torcetrapib, the cholesteryl ester transfer protein (CETP) inhibitor developed by Pfizer, had anoff-target toxicity.[2] Niacin is not very effective, and there are a lot of downsides to the drug. That has been an issue, but people are still working on this. We have done some studies. We did our ApoA-1 Milano infusion study[3]about a decade ago, which showed very promising results with respect to shrinking plaques in coronary arteries. I remain open to the possibility that the right drug in the right trial will work.

Dr Libby: What do you do with the genetic data that have come out in the past couple of years? Sekar Kathiresan masterminded and organized an enormous collaboration[4] in which they looked, with contemporary genetics, at whether HDL had the genetic markers of being a causal risk factor. They came up empty-handed.

Dr Nissen: I am cautious about interpreting those data, like I am cautious about interpreting animal studies of atherosclerosis. We have both lived through this problem in which something works extremely well in animals but doesn’t work in humans, or it doesn’t work in animals but it works in humans. The genetic studies don’t seal the fate of HDL. I have an open mind about this. Drugs are complex. They work by complex mechanisms. It is my belief that what we have to do is test these hypotheses in well-designed clinical trials, which are rigorously performed with drugs that are clean—unlike torcetrapib—and don’t have off-target toxicities.

An Unmet Need: High Lp(a) Levels

Dr Nissen: I’m going to push back on that and make a couple of points. The HPS2-THRIVE study was flawed. They studied the wrong people. It was not a good study, and AIM-HIGH[8] was underpowered. I am not putting people on niacin. What do you do with a patient whose Lp(a) is 200 mg/dL?

Dr Libby: I’m waiting for the results of the PCSK9 and anacetrapib studies. You can tell me about evacetrapib.[9]Reducing Lp(a) is an unmet medical need. We both care for kindreds with high Lp(a) levels and premature coronary artery disease. We have no idea what to do with them other than to treat them with statins and lower their LDL-C levels.

Dr Nissen: I have taken a more cautious approach with respect to taking people off of niacin. If I have patients who are doing well and tolerating it (depending on why it was started), I am discontinuing niacin in some people. I am starting very few people on the drug, but I worry about the quality of the trial.

Dr Libby: So you are of the “don’t start don’t stop” school?

Dr Nissen: Yes. It’s difficult when the trial is fatally flawed. There were 11,000 patients from China in this study. I have known for years that if you give niacin to people of Asiatic ethnic descent, they have terrible flushing and they won’t continue the drug. One question is, what was the adherence? The adverse events would have been tolerable had there been efficacy. The concern here is that this study was destined to fail because they studied a low LDL/high HDL population, a group of people for whom niacin just isn’t used.

Triglycerides and HDL: Do We Have It Backwards?

Dr Libby: What about the recent genetic[10] and epidemiologic data that support triglycerides, and apolipoprotein C3 in particular as a causal risk factor? Have we been misled through all of the generations in whom we have been adjusting triglycerides for HDL-C and saying that triglycerides are not a causal risk factor because once we adjust for HDL, the risk goes away? Do you think we got it backwards?

Dr Nissen: The tricky factor here is that because of this intimate inverse relationship between triglycerides and HDL, we may be talking about the same phenomenon. That is one of the reasons that I am not certain we are not going to be able to find a therapy. What if you had a therapy that lowered triglycerides and raised HDL-C? Could that work? Could that combination be favorable? I want answers from rigorous, well-designed clinical trials that ask the right questions in the right populations. I am disappointed, just as I have been disappointed by the fibrate trials.[11,12] There is a class of drugs that raises HDL-C a little and lowers triglycerides a lot.

Dr Nissen: But the gemfibrozil studies (VA-HIT[13] and Helsinki Heart[14]) showed benefit.

The Dyslipidemia Bar Has Been Raised

Dr Libby: Those studies were from the pre-statin era. We both were involved in trials in which patients were on high-dose statins at baseline. Do you think that this is too high a bar?

Dr Nissen: The bar has been raised, and for the pharmaceutical industry, the studies that we need to find out whether lowering triglycerides or raising HDL is beneficial are going to be large. We are doing a study with evacetrapib. It has 12,000 patients. It’s fully enrolled. Evacetrapib is a very clean-looking drug. It doesn’t have such a long biological half-life as anacetrapib, so I am very encouraged that it won’t have that baggage of being around for 2-4 years. We’ve got a couple of shots on goal here. Don’t forget that we have multiple ongoing studies of HDL-C infusion therapies that are still under development. Those have some promise too. The jury is still out.

Dr Libby: We agree on the need to do rigorous, large-scale endpoint trials. Do the biomarker studies, but don’t wait to start the endpoint trial because that’s the proof in the pudding.

Dr Nissen: Exactly. We have had a little controversy about HDL-C. We often agree, but not always, and we may have a different perspective. Thanks for joining me in this interesting discussion of what will continue to be a controversial topic for the next several years until we get the results of the current ongoing trials.

Case in Point 2.

NSTEMI? Honesty in Coding and Communication?

Melissa Walton-Shirley

November 07, 2014

The complaint at ER triage: Weakness, fatigue, near syncope of several days’ duration, vomiting, and decreased sensorium.

The findings: O2sat: 88% on room air. BP: 88 systolic. Telemetry: Sinus tachycardia 120 bpm. Blood sugar: 500 mg/dL. Chest X ray: atelectasis. Urinalysis: pyuria. ECG: T-wave-inversion anterior leads. Echocardiography: normal left ventricular ejection fraction (LVEF) and wall motion. Troponin I: 0.3 ng/mL. CT angiography: negative for pulmonary embolism (PE). White blood cell count: 20K with left shift. Blood cultures: positive for Gram-negative rods.

The treatment: Intravenous fluids and IV levofloxacin—changed to ciprofloxacin.

The communication at discharge: “You had a severe urinary-tract infection and grew bacteria in your bloodstream. Also, you’ve had a slight heart attack. See your cardiologist immediately upon discharge-no more than 5 days from now.”

The diagnoses coded at discharge: Urosepsis and non-ST segment elevation MI (NSTEMI) 410.1.

One year earlier: This moderately obese patient was referred to our practice for a preoperative risk assessment. The surgery planned was a technically simple procedure, but due to the need for precise instrumentation, general endotracheal anesthesia (GETA) was being considered. The patient was diabetic, overweight, and short of air. A stress exam was equivocal for CAD due to poor exercise tolerance and suboptimal imaging. Upon further discussion, symptoms were progressive; therefore, cardiac cath was recommended, revealing angiographically normal coronaries and a predictably elevated left ventricular end diastolic pressure (LVEDP) in the mid-20s range. The patient was given a diagnosis of diastolic dysfunction, a prescription for better hypertension control, and in-depth discussion on exercise and the Mediterranean and DASH diets for weight loss. Symptoms improved with a low dose of diuretic. The surgery was completed without difficulty. Upon follow-up visit, the patient felt well, had lost a few pounds, and blood pressure was well controlled.

Five days after ER workup: While out of town, the patient developed profound weakness and went to the ER as described above. Fast forward to our office visit in the designated time frame of “no longer than 5 days’ postdischarge,” where the patient and family asked me about the “slight heart attack” that literally came on the heels of a normal coronary angiogram.

But the patient really didn’t have a “heart attack,” did they? The cardiologist aptly stated that it was likely nonspecific troponin I leak in his progress notes. Yet the hospitalist framed the diagnosis of NSTEMI as item number 2 in the final diagnoses.

The motivations on behalf of personnel who code charts are largely innocent and likely a direct result of the lack of understanding of the coding system on behalf of us as healthcare providers. I have a feeling, though, that hospitals aren’t anxious to correct this misperception, due to an opportunity for increased reimbursement. I contacted a director of a coding department for a large hospital who prefers to remain anonymous. She explained that NSTEMI ICD9 code 410.1 falls in DRG 282 with a weight of .7562. The diagnosis of “demand ischemia,” code 411.89, a slightly less inappropriate code for a nonspecific troponin I leak, falls in DRG 311 with a weight of .5662. To determine reimbursement, one must multiply the weight by the average hospital Medicare base rate of $5370. Keep in mind that each hospital’s base rate and corresponding payment will vary. The difference in reimbursement for a large hospital bill between these two choices for coding is substantial, at over $1000 difference ($4060 vs $3040).

Although hospitals that are already reeling from shrinking revenues will make more money on the front end by coding the troponin leak incorrectly as an NSTEMI, when multiple unnecessary tests are generated to follow up on a nondiagnostic troponin leak, the amount of available Centers for Medicare & Medicaid Services (CMS) reimbursement pie shrinks in the long run. Furthermore, this inappropriate categorization generates extreme concern on behalf of patients and family members that is often never laid to rest. The emotional toll of a “heart-attack” diagnosis has an impact on work fitness, quality of life, cost of medication, and the cost of future testing. If the patient lived for another 100 years, they will likely still list a “heart attack” in their medical history.

As a cardiologist, I resent the loose utilization of one of “my” heart-attack codes when it wasn’t that at all. At discharge, we need to develop a better way of communicating what exactly did happen. Equally important, we need to communicate what exactly didn’t happen as well.

Case in Point 3.

Blood Markers Predict CKD Heart Failure 

Published: Oct 3, 2014 | Updated: Oct 3, 2014

Elevated levels of high-sensitivity troponin T (hsTnT) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) strongly predicted heart failure in patients with chronic kidney disease followed for a median of close to 6 years, researchers reported.

Compared with patients with the lowest blood levels of hsTnT, those with the highest had a nearly five-fold higher risk for developing heart failure and the risk was 10-fold higher in patients with the highest NT-proBNP levels compared with those with the lowest levels of the protein, researcher Nisha Bansal, MD, of the University of Washington in Seattle, and colleagues wrote online in the Journal of the American Society of Nephrology.

A separate study, published online in theJournal of the American Medical Association earlier in the week, also examined the comorbid conditions of heart and kidney disease, finding no benefit to the practice of treating cardiac surgery patients who developed acute kidney injury with infusions of the antihypertensive drug fenoldopam.

The study, reported by researcher Giovanni Landoni, MD, of the IRCCS San Raffaele Scientific Institute, Milan, Italy, and colleagues, was stopped early “for futility,” according to the authors, and the incidence of hypotension during drug infusion was significantly higher in patients infused with fenoldopam than placebo (26% vs. 15%; P=0.001).

Blood Markers Predict CKD Heart Failure

The study in patients with mild to moderate chronic kidney disease (CKD) was conducted to determine if blood markers could help identify patients at high risk for developing heart failure.

Heart failure is the most common cardiovascular complication among people with renal disease, occurring in about a quarter of CKD patients.

The two markers, hsTnT and NT-proBNP, are associated with overworked cardiac myocytes and have been shown to predict heart failure in the general population.

However, Bansal and colleagues noted, the markers have not been widely used in diagnosing heart failure among patients with CKD due to concerns that reduced renal excretion may raise levels of these markers, and therefore do not reflect an actual increase in heart muscle strain.

To better understand the importance of elevated concentrations of hsTnT and NT-proBNP in CKD patients, the researchers examined their association with incident heart failure events in 3,483 participants in the ongoing observational Chronic Renal Insufficiency Cohort (CRIC) study.

All participants were recruited from June 2003 to August 2008, and all were free of heart failure at baseline. The researchers used Cox regression to examine the association of baseline levels of hsTnT and NT-proBNP with incident heart failure after adjustment for demographic influences, traditional cardiovascular risk factors, makers of kidney disease, pertinent medication use, and mineral metabolism markers.

At baseline, hsTnT levels ranged from ≤5.0 to 378.7 pg/mL and NT-proBNP levels ranged from ≤5 to 35,000 pg/mL. Compared with patients who had undetectable hsTnT, those in the highest quartile (>26.5 ng/mL) had a significantly higher rate of heart failure (hazard ratio 4.77; 95% CI 2.49-9.14).

Compared with those in the lowest NT-proBNP quintile (<47.6 ng/mL), patients in the highest quintile (>433.0 ng/mL) experienced an almost 10-fold increase in heart failure risk (HR 9.57; 95% CI 4.40-20.83).

The researchers noted that these associations remained robust after adjustment for potential confounders and for the other biomarker, suggesting that while hsTnT and NT-proBNP are complementary, they may be indicative of distinct biological pathways for heart failure.

Even Modest Increases in NP-proBNP Linked to Heart Failure

The findings are consistent with an earlier analysis that included 8,000 patients with albuminuria in the Prevention of REnal and Vascular ENd-stage Disease (PREVEND) study, which showed that hsTnT was associated with incident cardiovascular events, even after adjustment for eGFR and severity of albuminuria.

“Among participants in the CRIC study, those with the highest quartile of detectable hsTnT had a twofold higher odds of left ventricular hypertrophy compared with those in the lowest quartile,” Bansal and colleagues wrote, adding that the findings were similar after excluding participants with any cardiovascular disease at baseline.

Even modest elevations in NT-proBNP were associated with significantly increased rates of heart failure, including in subgroups stratified by eGFR, proteinuria, and diabetic status.

“NT-proBNP regulates blood pressure and body fluid volume by its natriuretic and diuretic actions, arterial dilation, and inhibition of the renin-aldosterone-angiotensin system and increased levels of this marker likely reflect myocardial stress induced by subclinical changes in volume or pressure, even in persons without clinical disease,” the researchers wrote.

The researchers concluded that further studies are needed to develop and validate risk prediction tools for clinical heart failure in patients with CKD, and to determine the potential role of these two biomarkers in a heart failure risk prediction and prevention strategy.

Fenoldopam ‘Widely Promoted’ in AKI Cardiac Surgery Setting

The JAMA study examined whether the selective dopamine receptor D agonist fenoldopam mesylate can reduce the need for dialysis in cardiac surgery patients who develop acute kidney injury (AKI).

Fenoldopam induces vasodilation of the renal, mesenteric, peripheral, and coronary arteries, and, unlike dopamine, it has no significant affinity for D2 receptors, meaning that it theoretically induces greater vasodilation in the renal medulla than in the cortex, the researchers wrote.

“Because of these hemodynamic effects, fenoldopam has been widely promoted for the prevention and therapy of AKI in the United States and many other countries with apparent favorable results in cardiac surgery and other settings,” Landoni and colleagues wrote.

The drug was approved in 1997 by the FDA for the indication of in-hospital, short-term management of severe hypertension. It has not been approved for renal indications, but is commonly used off-label in cardiac surgery patients who develop AKI.

Although a meta analysis of randomized trials, conducted by the researchers, indicated a reduction in the incidence and progression of AKI associated with the treatment, Landoni and colleagues wrote that the absence of a definitive trial “leaves clinicians uncertain as to whether fenoldopam should be prescribed after cardiac surgery to prevent deterioration in renal function.”

To address this uncertainty, the researchers conducted a prospective, randomized, parallel-group trial in 667 patients treated at 19 hospitals in Italy from March 2008 to April 2013.

All patients had been admitted to ICUs after cardiac surgery with early acute kidney injury (≥50% increase of serum creatinine level from baseline or low output of urine for ≥6 hours). A total of 338 received fenoldopam by continuous intravenous infusion for a total of 96 hours or until ICU discharge, while 329 patients received saline infusions.

The primary end point was the rate of renal replacement therapy, and secondary end points included mortality (intensive care unit and 30-day mortality) and the rate of hypotension during study drug infusion.

Study Showed No Benefit, Was Stopped Early

Yale Lampoon – AA Liebow.   1954

Not As a Doctor
[Fourth Year]

These lyrics, sung by John Cole, Jack Gariepy and Ed Ransenhofer to music borrowed from Gilbert and Sullivan’s The Mikado, lampooned Averill Liebow, M.D., a pathologist noted for his demands on students. (CPC stands for clinical pathology conference.)

If you want to know what this is,
it’s a medical CPC
Where we give the house staff
the biz, for there’s no one so
wise as we!
We pathologists show them how,
Although it is too late now.
Our art is a sacred cow!

American physician, born 1911, Stryj in Galicia, Austria (now in Ukraine); died 1978.

Averill Abraham Liebow, born in Austria, was the “founding father” of pulmonary pathology in the United States. He started his career as a pathologist at Yale, where he remained for many years. In 1968 he moved to the University of California School of Medicine, San Diego, where he taught for 7 years as Professor and Chairman, Department of Pathology.

His studies include many classic studies of lung diseases. Best known of these is his famous classification of interstitial lung disease. He also published papers on sclerosing pneumocytoma, pulmonary alveolar proteinosis, meningothelial-like nodules, pulmonary hypertension, pulmonary veno-occlusive disease, lymphomatoid granulomatosis, pulmonary Langerhans cell histiocytosis, pulmonary epithelioid hemangioendothelioma and pulmonary hyalinizing granuloma .

As a Lieutenant Colonel in the US Army Medical Corps, He was a member of the Atomic Bomb Casualty Commission who studied the effects of the atomic bomb in Hiroshima and Nagasaki.

We thank Sanjay Mukhopadhyay, M.D., for information submitted.

As a resident at UCSD, Dr. Liebow held “Organ Recitals” every morning, including Mother’s day.  The organs had to be presented in specified order… heart, lung, and so forth.  On one occasion, we needed a heart for purification of human lactate dehydrogenase for a medical student project, so I presented the lung out of order.  Dr. Liebow asked where the heart was, and I told the group it was noprmal and I froze it for enzyme purification (smiles).  In the future show it to me first. He was generous to those who showed interest.  As I was also doing research in Nathan Kaplan’s laboratory, he made special arrangements for me to mentor Deborah Peters, the daughter of a pulmonary physician, and granddaughter of the Peters who collaborated with Van Slyke.  I mentored many students with great reward since then.  He could look at a slide and tell you what the x-ray looked like.  I didn’t encounter that again until he sent me to the Armed Forces Institute of Pathology, Washington, DC during the Vietnam War and Watergate, and I worked in Orthopedic Pathology with Lent C. Johnson.  He would not review a case without the x-ray, and he taught the radiologists.

Part 3

My Cancer Genome from Vanderbilt University: Matching Tumor Mutations to Therapies & Clinical Trials

Reporter: Aviva Lev-Ari, PhD, RN

My Cancer Genome from Vanderbilt University: Matching Tumor Mutations to Therapies & Clinical Trials


GenomOncology and Vanderbilt-Ingram Cancer Center (VICC) today announced a partnership for the exclusive commercial development of a decision support tool based on My Cancer Genome™, an online precision cancer medicine knowledge resource for physicians, patients, caregivers and researchers.

Through this collaboration, GenomOncology and VICC will enhance My Cancer Genome through the development of a new genomics content management tool. The MyCancerGenome.org website will remain free and open to the public. In addition, GenomOncology will develop a decision support tool based on My Cancer Genome™ data that will enable automated interpretation of mutations in the genome of a patient’s tumor, providing actionable results in hours versus days.

Vanderbilt-Ingram Cancer Center (VICC) launched My Cancer Genome™ in January 2011 as an integral part of their Personalized Cancer Medicine Initiative that helps physicians and researchers track the latest developments in precision cancer medicine and connect with clinical research trials. This web-based information tool is designed to quickly educate clinicians on the rapidly expanding list of genetic mutations that impact cancers and enable the research of treatment options based on specific mutations. For more information on My Cancer Genome™visit www.mycancergenome.org/about/what-is-my-cancer-genome.

Therapies based on the specific genetic alterations that underlie a patient’s cancer not only result in better outcomes but often have less adverse reactions

Up front fee

Nominal fee covers installation support, configuring the Workbench to your specification, designing and developing custom report(s) and training your team.

Per sample fee

GenomOncology is paid on signed-out clinical reports. This philosophy aligns GenomOncology with your Laboratory as we are incentivized to offer world-class support and solutions to differentiate your clinical NGS program. There is no annual license fee.

Part 4

Clinical Trial Services: Foundation Medicine & EmergingMed to Partner

Reporter: Aviva Lev-Ari, PhD, RN

Clinical Trial Services: Foundation Medicine & EmergingMed to Partner


Foundation Medicine and EmergingMed said today that they will partner to offer clinical trial navigation services for health care providers and their patients who have received one of Foundation Medicine’s tumor genomic profiling tests.

The firms will provide concierge services to help physicians

  • identify appropriate clinical trials for patients
  • based on the results of FoundationOne or FoundationOne Heme.

“By providing clinical trial navigation services, we aim to facilitate

  • timely and accurate clinical trial information and enrollment support services for physicians and patients,
  • enabling greater access to treatment options based on the unique genomic profile of a patient’s cancer

Currently, there are over 800 candidate therapies that target genomic alterations in clinical trials,

  • but “patients and physicians must identify and act on relevant options
  • when the patient’s clinical profile is aligned with the often short enrollment window for each trial.

These investigational therapies are an opportunity to engage patients with cancer whose cancer has progressed or returned following standard treatment in a most favorable second option after relapse.  The new service is unique in notifying when new clinical trials emerge that match a patient’s genomic and clinical profile.

Google signs on to Foundation Medicine cancer Dx by offering tests to employees

By Emily Wasserman

Diagnostics luminary Foundation Medicine ($FMI) is generating some upward momentum, fueled by growing revenues and the success of its clinical tests. Tech giant Google ($GOOG) has taken note and is signing onto the company’s cancer diagnostics by offering them to employees.

Foundation Medicine CEO Michael Pellini said during the company’s Q3 earnings call that Google will start covering its DNA tests for employees and their family members suffering from cancer as part of its health benefits portfolio, Reuters reports.

Both sides stand to benefit from the deal, as Google looks to keep a leg up on Silicon Valley competitors and Foundation Medicine expands its cancer diagnostics platform. Last month, Apple ($AAPL) and Facebook ($FB) announced that they would begin covering the cost of egg freezing for female employees. A diagnostics partnership and attractive health benefits could work wonders for Google’s employee retention rates and bottom line.

In the meantime, Cambridge, MA-based Foundation Medicine is charging full speed ahead with its cancer diagnostics platform after filing for an IPO in September 2013. The company chalked up 6,428 clinical tests during Q3 2014, an eye-popping 149% increase year over year, and brought in total revenue for the quarter of $16.4 million–a 100% leap from last year. Foundation Medicine credits the promising numbers in part to new diagnostic partnerships and extended coverage for its tests.

In January, the company teamed up with Novartis ($NVS) to help the drugmaker evaluate potential candidates for its cancer therapies. In April, Foundation Medicine announced that it would develop a companion diagnostic test for a Clovis Oncology ($CLVS) drug under development to treat patients with ovarian cancer, building on an ongoing collaboration between the two companies.

Foundation Medicine also has its sights set on China’s growing diagnostics market, inking a deal in October with WuXi PharmaTech ($WX) that allows the company to perform lab testing for its FoundationOne assay at WuXi’s Shanghai-based Genome Center.

a nod to the deal with Google during a corporate earnings call on Wednesday, according to a person who listened in. Pellini said Google employees were made aware of this new benefit last week.

Foundation Medicine teams with MD Anderson for new trial of cancer Dx

Second study to see if targeted therapy can change patient outcomes

August 15, 2014 | By   FierceDiagnostics

Foundation Medicine ($FMI) is teaming up with the MD Anderson Cancer Center in Texas for a new trial of the the Cambridge, MA-based company’s molecular diagnostic cancer test that targets therapies matched to individual patients.

The study is called IMPACT2 (Initiative for Molecular Profiling and Advanced Cancer Therapy) and is designed to build on results from the the first IMPACT study that found

  • 40% of the 1,144 patients enrolled had an identifiable genomic alteration.

The company said that

  • by matching specific gene alterations to therapies,
  • 27% of patients in the first study responded versus
  • 5% with an unmatched treatment, and
  • “progression-free survival” was longer in the matched group.

The FoundationOne molecular diagnostic test

  • combines genetic sequencing and data gathering
  • to help oncologists choose the best treatment for individual patients.

Costing $5,800 per test, FoundationOne’s technology can uncover a large number of genetic alterations for 200 cancer-related genes,

  • blending genomic sequencing, information and clinical practice.

“Based on the IMPACT1 data, a validated, comprehensive profiling approach has already been adopted by many academic and community-based oncology practices,” Vincent Miller, chief medical officer of Foundation Medicine, said in a release. “This study has the potential to yield sufficient evidence necessary to support broader adoption across most newly diagnosed metastatic tumors.”

The company got a boost last month when the New York State Department of Health approved Foundation Medicine’s two initial cancer tests: the FoundationOne test and FoundationOne Heme, which creates a genetic profile for blood cancers. Typically,

  • diagnostics companies struggle to win insurance approval for their tests
  • even after they gain a regulatory approval, leaving revenue growth relatively flat.

However, Foundation Medicine reported earlier this week its Q2 revenue reached $14.5 million compared to $5.9 million for the same period a year ago. Still,

  1. net losses continue to soar as the company ramps up
  2. its commercial and business development operation,
  • hitting $13.7 million versus a $10.1 million deficit in the second quarter of 2013.

Oncology

There has been a remarkable transformation in our understanding of

  • the molecular genetic basis of cancer and its treatment during the past decade or so.

In depth genetic and genomic analysis of cancers has revealed that

  • each cancer type can be sub-classified into many groups based on the genetic profiles and
  • this information can be used to develop new targeted therapies and treatment options for cancer patients.

This panel will explore the technologies that are facilitating our understanding of cancer, and

  • how this information is being used in novel approaches for clinical development and treatment.
Oncology _ Reprted by Dr. Aviva Lev-Ari, Founder, Leaders in Pharmaceutical Intelligence

Opening Speaker & Moderator:

Lynda Chin, M.D.
Department Chair, Department of Genomic Medicine
MD Anderson Cancer Center

  • Who pays for PM?
  • potential of Big data, analytics, Expert systems, so not each MD needs to see all cases, Profile disease to get same treatment
  • business model: IP, Discovery, sharing, ownership — yet accelerate therapy
  • security of healthcare data
  • segmentation of patient population
  • management of data and tracking innovations
  • platforms to be shared for innovations
  • study to be longitudinal,
  • How do we reconcile course of disease with PM
  • phinotyping the disease vs a Patient in wait for cure/treatment

Panelists:

Roy Herbst, M.D., Ph.D.
Ensign Professor of Medicine and Professor of Pharmacology;
Chief of Medical Oncology, Yale Cancer Center and Smilow Cancer Hospital

Development new drugs to match patient, disease and drug – finding the right patient for the right Clinical Trial

  • match patient to drugs
  • partnerships: out of 100 screened patients, 10 had the gene, 5 were able to attend the trial — without the biomarker — all 100 patients would participate for the WRONG drug for them (except the 5)
  • patients wants to participate in trials next to home NOT to have to travel — now it is in the protocol
  • Annotated Databases – clinical Trial informed consent – adaptive design of Clinical Trial vs protocol
  • even Academic MD can’t read the reports on Genomics
  • patients are treated in the community — more training to MDs
  • Five companies collaborating – comparison og 6 drugs in the same class
  • if drug exist and you have the patient — you must apply PM

Summary and Perspective:

The current changes in Biotechnology have been reviewed with an open question about the relationship of In Vitro Diagnostics to Biopharmaceuticals switching, with the potential, particularly in cancer and infectious diseases, to added value in targeted therapy by matching patients to the best potential treatment for a favorable outcome.

This reviewer does not see the movement of the major diagnostics leaders entering into the domain of direct patient care, even though there are signals in that direction.  The Roche example is perhaps the most interesting because Roche already became the elephant in the room after the introduction of Valium,  subsequently bought out Boehringer Mannheim Diagnostics to gain entry into the IVD market, and established a huge presence in Molecular Diagnostics early.  If it did anything to gain a foothold in the treatment realm, it would more likely forge a relationship with Foundation Medicine.  Abbott Laboratories more than a decade ago was overextended, and it had become the leader in IVD as a result of the specialty tests, but it fell into difficulties with quality control of its products in the high volume testing market, and acceeded to Olympus, Roche, and in the mid volume market to Beckman and Siemens.  Of course, Dupont and Kodak, pioneering companies in IVD, both left the market.

The biggest challenge in the long run is identified by the ability to eliminate many treatments that would be failures for a large number of patients. That has already met the proof of concept.  However, when you look at the size of the subgroups, we are not anywhere near a large scale endeavor.  In addition, there is a lot that has to be worked out that is not related to genomic expression by the “classic” model, but has to take into account the emrging knowledge and greater understanding of regulation of cell metabolism, not only in cancer, but also in chronic inflammatory diseases.

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The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

Curator: Stephen J. Williams, Ph.D

Article ID #163: The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC. Published on 12/10/2014

WordCloud Image Produced by Adam Tubman

I am intending to do a series of posts highlighting interviews with Philadelphia area biotech startup CEO’s and show how a vibrant biotech startup scene is evolving in the city as well as the Delaware Valley area. Philadelphia has been home to some of the nation’s oldest biotechs including Cephalon, Centocor, hundreds of spinouts from a multitude of universities as well as home of the first cloned animal (a frog), the first transgenic mouse, and Nobel laureates in the field of molecular biology and genetics. Although some recent disheartening news about the fall in rankings of Philadelphia as a biotech hub and recent remarks by CEO’s of former area companies has dominated the news, biotech incubators like the University City Science Center and Bucks County Biotechnology Center as well as a reinvigorated investment community (like PCCI and MABA) are bringing Philadelphia back. And although much work is needed to bring the Philadelphia area back to its former glory days (including political will at the state level) there are many bright spots such as the innovative young companies as outlined in these posts.

First up I got to talk with Florian Schodel, M.D., Ph.D., CEO of Philimmune, which provides expertise in medicine, clinical and regulatory development and analytical sciences to support successful development and registration of vaccines and biologics. Before founding Philimmune, Dr. Schodel was VP in Vaccines Clinical Research of Merck Research Laboratories and has led EU vaccine clinical trials and the clinical development of rotavirus, measles, mumps, hepatitis B, and rubella vaccines. In addition Dr. Schodel and Philimmune consult on several vaccine development efforts at numerous biotech companies including:

 

\His specialties and services include: vaccines and biologics development strategy, clinical development, clinical operations, strategic planning and alliances, international collaborations, analytical and assay development, project and portfolio integration and leadership.

Successful development of vaccines and biologics poses some unique challenges: including sterile manufacturing and substantial early capital investment before initiated clinical trials, assay development for clinical trial support, and unique trail design. Therefore vaccines and biologics development is a highly collaborative process between several disciplines.

The Philadelphia area has a rich history in vaccine development including the discovery and development of the rubella, cytomegaolovirus, a rabies, and the oral polio vaccine at the Wistar Institute. Dr. Schodel answered a few questions on the state of vaccine development and current efforts in the Philadelphia area, including recent efforts by companies such as GSK’s efforts and Inovio’s efforts developing an Ebola vaccine.

In his opinion, Dr. Schodel believes our biggest hurdle in vaccine development in a societal issue, not a preclinic development issue. Great advances have been made to speed the discovery process and enhance quality assurance of manufacture capabilities like

however there has not been a great history or support for developing vaccines for the plethora of infectious diseases seen in the developing world. As Dr. Schodel pointed out, there are relatively few players in the field, and tough to get those few players excited for investing in new targets.

 

However, some companies are rapidly expanding their vaccine portfolios including

 

 

Why haven’t 3rd world countries developed their own vaccine programs?

 

  1. Hard to find partners willing to invest and support development
  2. Developing nations don’t have the money or infrastructure to support health programs
  3. Doctors in these countries need to be educated on how to conduct trials, conduct vaccine programs like Gates Foundation does. For more information see Nature paper on obstacles to vaccine introduction in third world countries.

 

Lastly, Dr. Schodel touched on a growing area, cancer vaccine development. Recent advances in bladder cancer vaccine, cervical, and promising results in an early phase metastatic breast cancer vaccine trial and phase I oral cancer vaccine trial have reinvigorated this field of cancer vaccinology.

 

Historic Timeline of Vaccine Development

vaccine development timeline

Graphic from http://en.pedaily.cn/Item.aspx?id=194125

 

Other posts on this site related to Biotech Startups in Philadelphia and some additional posts on infectious disease include:

 

RAbD Biotech Presents at 1st Pitch Life Sciences-Philadelphia

LytPhage Presents at 1st Pitch Life Sciences-Philadelphia

Hastke Inc. Presents at 1st Pitch Life Sciences-Philadelphia

1st Pitch Life Science- Philadelphia- What VCs Really Think of your Pitch

The History of Infectious Diseases and Epidemiology in the late 19th and 20th Century

 

 

 

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The History of Infectious Diseases and Epidemiology in the late 19th and 20th Century

Curator: Larry H Bernstein, MD, FCAP

 

Infectious diseases are a part of the history of English, French, and Spanish Colonization of the Americas, and of the Slave Trade.  The many plagues in the new and old world that have effected the course of history from ancient to modern times were known to the Egyptians, Greeks, Chinese, crusaders, explorers, Napoleon, and had familiar ties of war, pestilence, and epidemic. Our coverage is mainly concerned with the scientific and public health consequences of these events that preceded WWI and extended to the Vietnam War, and is highlighted by the invention of a public health system world wide.

The Armed Forces Institute of Pathology (AFIP) closed its’ doors on September 15, 2011. It was founded as the Army Medical Museum on May 21, 1862, to collect pathological specimens along with their case histories.

The information from the case files of the pathological specimens from the Civil War was compared with Army pensions records and compiled into the six-volume Medical and Surgical History of the War of the Rebellion, an early study of wartime medicine.

In 1900, museum curator Walter Reed led the commission which proved that a mosquito was the vector for Yellow Fever, beginning the mosquito eradication campaigns throughout most of the twentieth century.

WalterReed

WalterReed

Another museum curator, Frederick Russell, conducted clinical trials on the typhoid vaccine in 1907, resulting in the U.S. Army to be the first Army vaccinated against typhoid.

Increased emphasis on pathology during the twentieth century turned the museum, renamed the Armed Forces Institute of Pathology in 1949, into an international resource for pathology and the study of disease. AFIP’s pathological collections have been used, for example, in the characterization of the 1918-influenza virus in 1997.

Prior to moving to the Walter Reed Army Medical Center, the AFIP was located at the Army Medical Museum and Library on the Mall (1887-1969), and earlier as Army Medical Museum in Ford’s Theatre (1867-1886).

Army Medical Museum and Library on the Mall

Army Medical Museum and Library on the Mall

This institution, originally the Library of the Surgeon General’s Office (U.S. Army), gained its present name and was transferred from the Army to the Public Health Service in 1956. In 1962, it moved to its own Bethesda site after sharing space for nearly 100 years with other Army units, first at the former Ford’s Theatre building and then at the Army Medical Museum and Library on the Mall. Rare books and other holdings that had been sent to Cleveland for safekeeping during World War II were also reunited with the main collection at that time.

The National Museum of Health and Medicine, established in 1862, inspires interest in and promotes the understanding of medicine — past, present, and future — with a special emphasis on tri-service American military medicine. As a National Historic Landmark recognized for its ongoing value to the health of the military and to the nation, the Museum identifies, collects, and preserves important and unique resources to support a broad agenda of innovative exhibits, educational programs, and scientific, historical, and medical research. NMHM is a headquarters element of the U.S. Army Medical Research and Materiel Command. NMHM’s newest exhibit installations showcase the institution’s 25-million object collection, focusing on topics as diverse as innovations in military medicine, traumatic brain injury, anatomy and pathology, military medicine during the Civil War, the assassination of Abraham Lincoln (including the bullet that killed him), human identification and a special exhibition on the Museum’s own major milestone—the 150th anniversary of the founding of the Army Medical Museum. Objects on display will include familiar artifacts and specimens: the bullet that killed Lincoln and a leg showing the effects of elephantiasis, as well as recent finds in the collection—all designed to astound visitors to the new Museum.

Today, the National Library of Medicine houses the largest collection of print and non-print materials in the history of the health sciences in the United States, and maintains an active program of exhibits and public lectures. Most of the archival and manuscript material dates from the 17th century; however, the Library owns about 200 pre-1601 Western and Islamic manuscripts. Holdings include pre-1914 books, pre-1871 journals, archives and modern manuscripts, medieval and Islamic manuscripts, a collection of printed books, manuscripts, and visual material in Japanese, Chinese, and Korean; historical prints, photographs, films, and videos; pamphlets, dissertations, theses, college catalogs, and government documents.

The oldest item in the Library is an Arabic manuscript on gastrointestinal diseases from al-Razi’s The Comprehensive Book on Medicine (Kitab al-Hawi fi al-tibb) dated 1094. Significant modern collections include the papers of U.S. Surgeons General, including C. Everett Koop, and the papers of Nobel Prize-winning scientists, particularly those connected with NIH.

As part of its Profiles in Science project, the National Library of Medicine has collaborated with the Churchill Archives Centre to digitize and make available over the World Wide Web a selection of the Rosalind Franklin Papers for use by educators and researchers. This site provides access to the portions of the Rosalind Franklin Papers, which range from 1920 to 1975. The collection contains photographs, correspondence, diaries, published articles, lectures, laboratory notebooks, and research notes.

Rosalind Franklin

Rosalind Franklin

Rosalind Franklin

Rosalind Franklin

Rosalind Franklin

“Science and everyday life cannot and should not be separated. Science, for me, gives a partial explanation of life. In so far as it goes, it is based on fact, experience, and experiment. . . . I agree that faith is essential to success in life, but I do not accept your definition of faith, i.e., belief in life after death. In my view, all that is necessary for faith is the belief that by doing our best we shall come nearer to success and that success in our aims (the improvement of the lot of mankind, present and future) is worth attaining.”

–Rosalind Franklin in a letter to Ellis Franklin, ca. summer 1940

Smallpox

Although some disliked mandatory smallpox vaccination measures, coordinated efforts against smallpox went on in the United States after 1867, and the disease continued to diminish in the wealthy countries. By 1897, smallpox had largely been eliminated from the United States. In Northern Europe a number of countries had eliminated smallpox by 1900, and by 1914, the incidence in most industrialized countries had decreased to comparatively low levels. Vaccination continued in industrialized countries, until the mid to late 1970s as protection against reintroduction. Australia and New Zealand are two notable exceptions; neither experienced endemic smallpox and never vaccinated widely, relying instead on protection by distance and strict quarantines.

In 1966 an international team, the Smallpox Eradication Unit, was formed under the leadership of an American, Donald Henderson. In 1967, the World Health Organization intensified the global smallpox eradication by contributing $2.4 million annually to the effort, and adopted the new disease surveillance method promoted by Czech epidemiologist Karel Raška. Two-year old Rahima Banu of Bangladesh (pictured) was the last person infected with naturally occurring Variola major, in 1975

The global eradication of smallpox was certified, based on intense verification activities in countries, by a commission of eminent scientists on 9 December 1979 and subsequently endorsed by the World Health Assembly on 8 May 1980. The first two sentences of the resolution read:

Having considered the development and results of the global program on smallpox eradication initiated by WHO in 1958 and intensified since 1967 … Declares solemnly that the world and its peoples have won freedom from smallpox, which was a most devastating disease sweeping in epidemic form through many countries since earliest time, leaving death, blindness and disfigurement in its wake and which only a decade ago was rampant in Africa, Asia and South America.

—World Health Organization, Resolution WHA33.3

Anthrax

Anthrax is an acute disease caused by the bacterium Bacillus anthracis. Most forms of the disease are lethal, and it affects both humans and other animals. Effective vaccines against anthrax are now available, and some forms of the disease respond well to antibiotic treatment.

Like many other members of the genus Bacillus, B. anthracis can form dormant endospores (often referred to as “spores” for short, but not to be confused with fungal spores) that are able to survive in harsh conditions for decades or even centuries. Such spores can be found on all continents, even Antarctica. When spores are inhaled, ingested, or come into contact with a skin lesion on a host, they may become reactivated and multiply rapidly.

Anthrax commonly infects wild and domesticated herbivorous mammals that ingest or inhale the spores while grazing. Ingestion is thought to be the most common route by which herbivores contract anthrax. Carnivores living in the same environment may become infected by consuming infected animals. Diseased animals can spread anthrax to humans, either by direct contact (e.g., inoculation of infected blood to broken skin) or by consumption of a diseased animal’s flesh.

Anthrax does not spread directly from one infected animal or person to another; it is spread by spores. These spores can be transported by clothing or shoes. The body of an animal that had active anthrax at the time of death can also be a source of anthrax spores. Owing to the hardiness of anthrax spores, and their ease of production in vitro, they are extraordinarily well suited to use (in powdered and aerosol form) as biological weapons.

Bacillus anthracis is a rod-shaped, Gram-positive, aerobic bacterium about 1 by 9 μm in size. It was shown to cause disease by Robert Koch in 1876 when he took a blood sample from an infected cow, isolated the bacteria and put them into a mouse. The bacterium normally rests in endospore form in the soil, and can survive for decades in this state. Once ingested or placed in an open wound, the bacterium begins multiplying inside the animal or human and typically kills the host within a few days or weeks. The endospores germinate at the site of entry into the tissues and then spread by the circulation to the lymphatics, where the bacteria multiply.

Robert Koch

Robert Koch

Veterinarians can often tell a possible anthrax-induced death by its sudden occurrence, and by the dark, nonclotting blood that oozes from the body orifices. Bacteria that escape the body via oozing blood or through the opening of the carcass may form hardy spores. One spore forms per one vegetative bacterium. Once formed, these spores are very hard to eradicate.

The lethality of the anthrax disease is due to the bacterium’s two principal virulence factors: the poly-D-glutamic acid capsule, which protects the bacterium from phagocytosis by host neutrophils, and the tripartite protein toxin, called anthrax toxin. Anthrax toxin is a mixture of three protein components: protective antigen (PA), edema factor (EF), and lethal factor (LF). PA plus LF produces lethal toxin, and PA plus EF produces edema toxin. These toxins cause death and tissue swelling (edema), respectively.

To enter the cells, the edema and lethal factors use another protein produced by B. anthracis called protective antigen, which binds to two surface receptors on the host cell. A cell protease then cleaves PA into two fragments: PA20 and PA63. PA20 dissociates into the extracellular medium, playing no further role in the toxic cycle. PA63 then oligomerizes with six other PA63 fragments forming a heptameric ring-shaped structure named a prepore.

Once in this shape, the complex can competitively bind up to three EFs or LFs, forming a resistant complex. Receptor-mediated endocytosis occurs next, providing the newly formed toxic complex access to the interior of the host cell. The acidified environment within the endosome triggers the heptamer to release the LF and/or EF into the cytosol.

Edema factor is a calmodulin-dependent adenylate cyclase. Adenylate cyclase catalyzes the conversion of ATP into cyclic AMP (cAMP) and pyrophosphate. The complexation of adenylate cyclase with calmodulin removes calmodulin from stimulating calcium-triggered signaling. LF inactivates neutrophils so they cannot phagocytose bacteria. Anthrax causes vascular leakage of fluid and cells, and ultimately hypovolemic shock and septic shock.

Occupational exposure to infected animals or their products (such as skin, wool, and meat) is the usual pathway of exposure for humans. Workers who are exposed to dead animals and animal products are at the highest risk, especially in countries where anthrax is more common. Anthrax in livestock grazing on open range where they mix with wild animals still occasionally occurs in the United States and elsewhere. Many workers who deal with wool and animal hides are routinely exposed to low levels of anthrax spores, but most exposure levels are not sufficient to develop anthrax infections. The body’s natural defenses presumably can destroy low levels of exposure. These people usually contract cutaneous anthrax if they catch anything.

Throughout history, the most dangerous form of inhalational anthrax was called woolsorters’ disease because it was an occupational hazard for people who sorted wool. Today, this form of infection is extremely rare, as almost no infected animals remain. The last fatal case of natural inhalational anthrax in the United States occurred in California in 1976, when a home weaver died after working with infected wool imported from Pakistan. Gastrointestinal anthrax is exceedingly rare in the United States, with only one case on record, reported in 1942, according to the Centers for Disease Control and Prevention.

Various techniques are used for the direct identification of B. anthracis in clinical material. Firstly, specimens may be Gram stained. Bacillus spp. are quite large in size (3 to 4 μm long), they grow in long chains, and they stain Gram-positive. To confirm the organism is B. anthracis, rapid diagnostic techniques such as polymerase chain reaction-based assays and immunofluorescence microscopy may be used.

All Bacillus species grow well on 5% sheep blood agar and other routine culture media. Polymyxin-lysozyme-EDTA-thallous acetate can be used to isolate B. anthracis from contaminated specimens, and bicarbonate agar is used as an identification method to induce capsule formation. Bacillus spp. usually grow within 24 hours of incubation at 35 °C, in ambient air (room temperature) or in 5% CO2. If bicarbonate agar is used for identification, then the medium must be incubated in 5% CO2.

  1. anthracis colonies are medium-large, gray, flat, and irregular with swirling projections, often referred to as having a “medusa head” appearance, and are not hemolytic on 5% sheep blood agar. The bacteria are not motile, susceptible to penicillin, and produce a wide zone of lecithinase on egg yolk agar. Confirmatory testing to identify B. anthracis includes gamma bacteriophage testing, indirect hemagglutination, and enzyme linked immunosorbent assay to detect antibodies. The best confirmatory precipitation test for anthrax is the Ascoli test.

Vaccines against anthrax for use in livestock and humans have had a prominent place in the history of medicine, from Pasteur’s pioneering 19th-century work with cattle (the second effective vaccine ever) to the controversial 20th century use of a modern product (BioThrax) to protect American troops against the use of anthrax in biological warfare. Human anthrax vaccines were developed by the Soviet Union in the late 1930s and in the US and UK in the 1950s. The current FDA-approved US vaccine was formulated in the 1960s.

If a person is suspected as having died from anthrax, every precaution should be taken to avoid skin contact with the potentially contaminated body and fluids exuded through natural body openings. The body should be put in strict quarantine and then incinerated. A blood sample should then be collected and sealed in a container and analyzed in an approved laboratory to ascertain if anthrax is the cause of death. Microscopic visualization of the encapsulated bacilli, usually in very large numbers, in a blood smear stained with polychrome methylene blue (McFadyean stain) is fully diagnostic, though culture of the organism is still the gold standard for diagnosis.

Full isolation of the body is important to prevent possible contamination of others. Protective, impermeable clothing and equipment such as rubber gloves, rubber apron, and rubber boots with no perforations should be used when handling the body. Disposable personal protective equipment and filters should be autoclaved, and/or burned and buried.

Anyone working with anthrax in a suspected or confirmed victim should wear respiratory equipment capable of filtering this size of particle or smaller. The US National Institute for Occupational Safety and Health – and Mine Safety and Health Administration-approved high-efficiency respirator, such as a half-face disposable respirator with a high-efficiency particulate air filter, is recommended.

All possibly contaminated bedding or clothing should be isolated in double plastic bags and treated as possible biohazard waste. The victim should be sealed in an airtight body bag. Dead victims who are opened and not burned provide an ideal source of anthrax spores. Cremating victims is the preferred way of handling body disposal.

Until the 20th century, anthrax infections killed hundreds of thousands of animals and people worldwide each year. French scientist Louis Pasteur developed the first effective vaccine for anthrax in 1881.

louis-pasteur

louis-pasteur

As a result of over a century of animal vaccination programs, sterilization of raw animal waste materials, and anthrax eradication programs in United States, Canada, Russia, Eastern Europe, Oceania, and parts of Africa and Asia, anthrax infection is now relatively rare in domestic animals. Anthrax is especially rare in dogs and cats, as is evidenced by a single reported case in the United States in 2001.

Anthrax outbreaks occur in some wild animal populations with some regularity. The disease is more common in countries without widespread veterinary or human public health programs. In the 21st century, anthrax is still a problem in less developed countries.

  1. anthracis bacterial spores are soil-borne. Because of their long lifespan, spores are present globally and remain at the burial sites of animals killed by anthrax for many decades. Disturbed grave sites of infected animals have caused reinfection over 70 years after the animal’s interment.

Cholera

This is an acute diarrheal infection that can kill within a matter of hours if untreated. Oral rehydration therapy — drinking water mixed with salts and sugar. But researchers at EPFL — the Swiss Federal Institute of Technology in Lausanne — say using rice starch instead of sugar with the rehydration salts could reduce bacterial toxicity by almost 75 percent. That would make the microbe less likely to infect a patient’s family and friends if they are exposed to any body fluids.

The World Health Organization says cholera, a water-borne bacterium, infects three to five million people every year, and the severe dehydration it causes leads to as many as 120,000 deaths.

Cholera is an acute diarrheal disease caused by the water borne bacteria Vibrio cholerae O1 or O139 (V. cholerae). Infection is mainly through ingestion of contaminated water or food. The V cholerae passes through the stomach, colonizes the upper part of the small intestine, penetrates the mucus layer, and secretes cholera toxin which affects the small intestine.

Clinically, the majority of cholera episodes are characterized by a sudden onset of massive diarrhea and vomiting accompanied by the loss of profuse amounts of protein-free fluid with electrolytes. The resulting dehydration produces tachycardia, hypotension, and vascular collapse, which can lead to sudden death. The diagnosis of cholera is commonly established by isolating the causative organism from the stools of infected individuals

There are an estimated 3–5 million cholera cases and 100 000–120 000 deaths due to cholera every year.

Up to 80% of cases can be successfully treated with oral rehydration salts.

Effective control measures rely on prevention, preparedness and response.

Provision of safe water and sanitation is critical in reducing the impact of cholera and other waterborne diseases.

Oral cholera vaccines are considered an additional means to control cholera, but should not replace conventional control measures.

During the 19th century, cholera spread across the world from its original reservoir in the Ganges delta in India. Six subsequent pandemics killed millions of people across all continents. The current (seventh) pandemic started in South Asia in 1961, and reached Africa in 1971 and the Americas in 1991. Cholera is now endemic in many countries.

INDIA-ENVIRONMENT-POLUTION

INDIA-ENVIRONMENT-POLUTION

In its extreme manifestation, cholera is one of the most rapidly fatal infectious illnesses known. Within 3–4 hours of onset of symptoms, a previously healthy person may become severely dehydrated and if not treated may die within 24 hours (WHO, 2010). The disease is one of the most researched in the world today; nevertheless, it is still an important public health problem despite more than a century of study, especially in developing tropical countries. Cholera is currently listed as one of three internationally quarantinable diseases by the World Health Organization (WHO), along with plague and yellow fever (WHO, 2000a).

Two serogroups of V. cholerae – O1 and O139 – cause outbreaks. V. cholerae O1 causes the majority of outbreaks, while O139 – first identified in Bangladesh in 1992 – is confined to South-East Asia.

Non-O1 and non-O139 V. cholerae can cause mild diarrhoea but do not generate epidemics.

The main reservoirs of V. cholerae are people and aquatic sources such as brackish water and estuaries, often associated with algal blooms. Recent studies indicate that global warming creates a favorable environment for the bacteria.

Socioeconomic and demographic factors enhance the vulnerability of a population to infection and contribute to epidemic spread. Such factors also mandate the extent to which the disease will reach epidemic proportions and also modulate the size of the epidemic.Known population level (local-level) risk factors of cholera include poverty, lack of development, high population density, low education, and lack of previous exposure. Cholera diffuses rapidly in environments that lack basic infrastructure with regard to access to safe water and proper sanitation. The cholera vibrios can survive and multiply outside the human body and can spread rapidly in environments where living conditions are overcrowded and where there is no safe disposal of solid waste, liquid waste, and human feces.

Mapping the locations of cholera victims, John Snow was able to trace the cause of the disease to a contaminated water source. Surprisingly, this was done 20 years before Koch and Pasteur established the beginnings of microbiology (Koch, 1884).

John Snow's  map

John Snow’s map

Yellow Fever

Yellow fever virus was probably introduced into the New World via ships carrying slaves from West Africa. Throughout the 18th and 19th centuries, regular and devastating epidemics of yellow fever occurred across the Caribbean, Central and South America, the southern United States and Europe. The Yellow Fever Commission, founded as a consequence of excessive disease mortality during the Spanish– American War (1898), concluded that the best way to control the disease was to control the mosquito. William Gorgas successfully eradicated yellow fever from Havana by destroying larval breeding sites and this strategy of source reduction was then successfully used to reduce disease problems and thus finally permit the construction of the Panama Canal in 1904. Success was due largely to a top-down, military approach involving strict supervision and discipline (Gorgas, 1915). In 1946, an intensive Aedes aegypti eradication campaign was initiated in the Americas, which succeeded in reducing vector populations to undetectable levels throughout most of its range.

The production of an effective vaccine in the 1930s led to a change of emphasis from vector control to vaccination for the control of yellow fever. Vaccination campaigns almost eliminated urban yellow fever but incomplete coverage, as with incomplete anti-vectorial measures previously, meant the disease persisted, and outbreaks occurred in remote forest areas.

It was acknowledged by the Health Organization of the League of Nations (the forerunner to the World Health Organization (WHO)) that yellow fever was a severe burden on endemic countries. The work of Soper and the Brazilian Cooperative Yellow Fever Service (Soper, 1934, 1935a, b) began to determine the geographical extent of the disease, specifically in Brazil. Regional maps of disease outbreaks were published by Sawyer (1934), but it was not until after the formation of the WHO that a global map of yellow fever endemicity was first constructed (van Rooyen and Rhodes, 1948). This map was based on expert opinion (United Nations Relief and Rehabilitation Administration/Expert Commission on Quarantine) and serological surveys. The present-day distribution map for yellow fever is still essentially a modified version of this map.

global yellow fever risk map

global yellow fever risk map

Yellow fever is conspicuously absent from Asia. Although there is some evidence that other flaviviruses may offer cross-protection against yellow fever (Gordon-Smith et al., 1962), why yellow fever does not occur in Asia is still unexplained.

It has been estimated that the currently circulating strains of YFV arose in Africa within the last 1,500 years and emerged in the Americas following the slave trade approximately 300–400 years ago. These viruses then spread westwards across the continent and persist there to this day in the jungles of South America.

The 17D live-attenuated vaccine still in use today was developed in 1936, and a single dose confers immunity for at least ten years in 95% of the cases. In a bid to contain the spread of the disease, travellers to countries within endemic areas or those thought to be ‘at risk’ require a certificate of vaccination. The yellow fever certificate is the only internationally regulated certification supported by the WHO. The effectiveness of the vaccine reduces the need for anti-vectorial campaigns directed specifically against yellow fever. As the same major vector is involved, control of Aedes aegypti for dengue reduction will also reduce yellow fever transmission where both diseases co-occur, especially within urban settings.

Dengue

Probable epidemics of dengue fever have been recorded from Africa, Asia, Europe and the Americas since the early 19th century (Armstrong, 1923). Although it is rarely fatal, up to 90% of the

population of an infected area can be incapacitated during the course of an epidemic (Armstrong, 1923; Siler et al., 1926). Widespread movements of troops and refugees during and after World War II introduced vectors and viruses into many new areas. Dengue fever has unsurprisingly been mistaken for yellow fever as well as other diseases including influenza, measles, typhoid and malaria. It is rarely fatal and survivors appear to have lifelong immunity to the homologous serotype.

Far more serious is dengue haemorrhagic fever (DHF), where additional symptoms develop, including haemorrhaging and shock. The mortality from DHF can exceed 30% if appropriate care is unavailable. The most significant risk factor for DHF is when secondary infection with a different serotype occurs in people who have already had, and recovered from, a primary dengue infection.

Dengue has adapted to changes in human demography very effectively. The main vector of dengue is the anthropophilic Aedes aegypti, which is found in close association with human settlements throughout the tropics, breeding mainly in containers in and around, and feeding almost exclusively on humans. As a result, dengue is essentially a disease of tropical urban areas. Before 1970, only nine countries had experienced DHF epidemics, but by 1995 this number had increased fourfold (WHO, 2001). Dengue case numbers have increased considerably since the 1960s; by the end of the 20th century an estimated 50 million cases of dengue fever and 500 000 cases of DHF were occurring every year (WHO, 2001).

The appearance of DHF stimulated large amounts of dengue research, which established the existence of the four serotypes and the range of competent vectors, and led to the adoption of Aedes aegypti control programs in some areas (particularly South-East Asia) (Kilpatrick et al., 1970).

There have been several attempts to estimate the economic impact of dengue: the 1977 epidemic in Puerto Rico was thought to have cost between $6.1 and $15.6 million ($26–$31 per clinical case) (Von Allmen et al., 1979), while the 1981 Cuban epidemic (with a total of 344 203 reported cases) cost about $103 million (around $299 per case) (Kouri et al., 1989).

There is no cure for dengue fever or for DHF. Currently, the only treatment is symptomatic, but this can reduce mortality from DHF to less than 1% (WHO, 2002). Unfortunately, the extent of dengue epidemics means that local public health services are often overwhelmed by the demands for treatment.

Malaria

Malaria is a serious and sometimes fatal disease caused by a parasite that infects a mosquito. People who get malaria are typically very sick with high fevers, shaking chills, and flu-like illness. About 1,500 cases of malaria are diagnosed in the United States each year. The vast majority of cases in the United States are in travelers and immigrants returning from countries where malaria transmission occurs, many from sub-Saharan Africa and South Asia. Malaria has been noted for more than 4,000 years. It became widely recognized in Greece by the 4th century BCE, and it was responsible for the decline of many of the city-state populations. Hippocrates noted the principal symptoms. In the Susruta, a Sanskrit medical treatise, the symptoms of malarial fever were described and attributed to the bites of certain insects. A number of Roman writers attributed malarial diseases to the swamps.

Following their arrival in the New World, Spanish Jesuit missionaries learned from indigenous Indian tribes of a medicinal bark used for the treatment of fevers. With this bark, the Countess of Chinchón, the wife of the Viceroy of Peru, was cured of her fever. The bark from the tree was then called Peruvian bark and the tree was named Cinchona after the countess. The medicine from the bark is now known as the antimalarial, quinine. Along with artemisinins, quinine is one of the most effective antimalarial drugs available today.

quinquin acalisaya

quinquin acalisaya

Cinchona officinalis is a medicinal plant, one of several Cinchona species used for the production of quinine, which is an anti-fever agent. It is especially useful in the prevention and treatment of malaria. Cinchona calisaya is the tree most cultivated for quinine production.

There are a number of other alkaloids that are extracted from this tree. They include cinchonine, cinchonidine and quinidine  (Wikipedia)

Charles Louis Alphonse Laveran, a French army surgeon stationed in Constantine, Algeria, was the first to notice parasites in the blood of a patient suffering from malaria in 1880. Laveran was awarded the Nobel Prize in 1907.

Alphonse Laveran

Alphonse Laveran

Camillo Golgi, an Italian neurophysiologist, established that there were at least two forms of the disease, one with tertian periodicity (fever every other day) and one with quartan periodicity (fever every third day). He also observed that the forms produced differing numbers of merozoites (new parasites) upon maturity and that fever coincided with the rupture and release of merozoites into the blood stream. He was awarded a Nobel Prize in Medicine for his discoveries in neurophysiology in 1906.

malaria_lifecycle.

malaria_lifecycle.

Ookinete,_sporozoite,_merozoite

Ookinete,_sporozoite,_merozoite

The Italian investigators Giovanni Batista Grassi and Raimondo Filetti first introduced the names Plasmodium vivax and P. malariae for two of the malaria parasites that affect humans in 1890. Laveran had believed that there was only one species, Oscillaria malariae. William H. Welch, reviewed the subject and, in 1897, he named the malignant tertian malaria parasite P. falciparum. In 1922, John William Watson Stephens described the fourth human malaria parasite, P. ovale. P. knowlesi was first described by Robert Knowles and Biraj Mohan Das Gupta in 1931 in a long-tailed macaque, but the first documented human infection with P. knowlesi was in 1965.

Anopheles mosquito

Anopheles mosquito

Ronald Ross, a British officer in the Indian Medical Service, was the first to demonstrate that malaria parasites could be transmitted from infected patients to mosquitoes in 1997. In further work with bird malaria, Ross showed that mosquitoes could transmit malaria parasites from bird to bird. This necessitated a sporogonic cycle (the time interval during which the parasite developed in the mosquito). Ross was awarded the Nobel Prize in 1902.

Ronald Ross_1899

Ronald Ross_1899

A team of Italian investigators led by Giovanni Batista Grassi, collected Anopheles claviger mosquitoes and fed them on malarial patients. The complete sporogonic cycle of Plasmodium falciparum, P. vivax, and P. malariae were demonstrated. Mosquitoes infected by feeding on a patient in Rome were sent to London in 1999, where they fed on two volunteers, both of whom developed malaria.

The construction of the Panama Canal was made possible only after yellow fever and malaria were controlled in the area. These two diseases were a major cause of death and disease among workers in the area. In 1906, there were over 26,000 employees working on the Canal. Of these, over 21,000 were hospitalized for malaria at some time during their work. By 1912, there were over 50,000 employees, and the number of hospitalized workers had decreased to approximately 5,600. Through the leadership and efforts of William Crawford Gorgas, Joseph Augustin LePrince, and Samuel Taylor Darling, yellow fever was eliminated and malaria incidence markedly reduced through an integrated program of insect and malaria control.

Gorgas-William-Crawford, MD

Gorgas-William-Crawford, MD

During the U.S. military occupation of Cuba and the construction of the Panama Canal at the turn of the 20th century, U.S. officials made great strides in the control of malaria and yellow fever. In 1914 Henry Rose Carter and Rudolph H. von Ezdorf of the USPHS requested and received funds from the U.S. Congress to control malaria in the United States. Various activities to investigate and combat malaria in the United States followed from this initial request and reduced the number of malaria cases in the United States. USPHS established malaria control activities around military bases in the malarious regions of the southern United States to allow soldiers to train year round.

U.S. President Franklin D. Roosevelt signed a bill that created the Tennessee Valley Authority (TVA) on May 18, 1933. The law gave the federal government a centralized body to control the Tennessee River’s potential for hydroelectric power and improve the land and waterways for development of the region. An organized and effective malaria control program stemmed from this new authority in the Tennessee River valley. Malaria affected 30 percent of the population in the region when the TVA was incorporated in 1933. The Public Health Service played a vital role in the research and control operations and by 1947, the disease was essentially eliminated. Mosquito breeding sites were reduced by controlling water levels and insecticide applications.

Chloroquine was discovered by a German, Hans Andersag, in 1934 at Bayer I.G. Farbenindustrie A.G. laboratories in Eberfeld, Germany. He named his compound resochin. Through a series of lapses and confusion brought about during the war, chloroquine was finally recognized and established as an effective and safe antimalarial in 1946 by British and U.S. scientists.

Felix Hoffmann, Gerhard Domagk, Hermann Schnell_BAYER

Felix Hoffmann, Gerhard Domagk, Hermann Schnell_BAYER

A German chemistry student, Othmer Zeidler, synthesized DDT in 1874, for his thesis. The insecticidal property of DDT was not discovered until 1939 by Paul Müller in Switzerland. Various militaries in WWII utilized the new insecticide initially for control of louse-borne typhus. DDT was used for malaria control at the end of WWII after it had proven effective against malaria-carrying mosquitoes by British, Italian, and American scientists. Müller won the Nobel Prize for Medicine in 1948.

Paul Muller

Paul Muller

Malaria Control in War Areas (MCWA) was established to control malaria around military training bases in the southern United States and its territories, where malaria was still problematic. Many of the bases were established in areas where mosquitoes were abundant. MCWA aimed to prevent reintroduction of malaria into the civilian population by mosquitoes that would have fed on malaria-infected soldiers, in training or returning from endemic areas. During these activities, MCWA also trained state and local health department officials in malaria control techniques and strategies.

The National Malaria Eradication Program, a cooperative undertaking by state and local health agencies of 13 Southeastern states and the CDC, originally proposed by Louis Laval Williams, commenced operations on July 1, 1947. By the end of 1949, over 4,650,000 housespray applications had been made. In 1947, 15,000 malaria cases were reported. By 1950, only 2,000 cases were reported. By 1951, malaria was considered eliminated from the United States.

With the success of DDT, the advent of less toxic, more effective synthetic antimalarials, and the enthusiastic and urgent belief that time and money were of the essence, the World Health Organization (WHO) submitted at the World Health Assembly in 1955 an ambitious proposal for the eradication of malaria worldwide. Eradication efforts began and focused on house spraying with residual insecticides, antimalarial drug treatment, and surveillance, and would be carried out in 4 successive steps: preparation, attack, consolidation, and maintenance. Successes included elimination in nations with temperate climates and seasonal malaria transmission.

Some countries such as India and Sri Lanka had sharp reductions in the number of cases, followed by increases to substantial levels after efforts ceased, while other nations had negligible progress (such as Indonesia, Afghanistan, Haiti, and Nicaragua), and still others were excluded completely from the eradication campaign(sub-Saharan Africa). The emergence of drug resistance, widespread resistance to available insecticides, wars and massive population movements, difficulties in obtaining sustained funding from donor countries, and lack of community participation made the long-term maintenance of the effort untenable.

The goal of most current National Malaria Prevention and Control Programs and most malaria activities conducted in endemic countries is to reduce the number of malaria-related cases and deaths. To reduce malaria transmission to a level where it is no longer a public health problem is the goal of what is called malaria “control.”

The natural ecology of malaria involves malaria parasites infecting successively two types of hosts: humans and female Anopheles mosquitoes. In humans, the parasites grow and multiply first in the liver cells and then in the red cells of the blood. In the blood, successive broods of parasites grow inside the red cells and destroy them, releasing daughter parasites (“merozoites”) that continue the cycle by invading other red cells.

Anopheles mosquito

Anopheles mosquito

The blood stage parasites are those that cause the symptoms of malaria. When certain forms of blood stage parasites (“gametocytes”) are picked up by a female Anopheles mosquito during a blood meal, they start another, different cycle of growth and multiplication in the mosquito.

After 10-18 days, the parasites are found (as “sporozoites”) in the mosquito’s salivary glands. When the Anopheles mosquito takes a blood meal on another human, the sporozoites are injected with the mosquito’s saliva and start another human infection when they parasitize the liver cells.

Malaria. Wikipedia

Malaria. Wikipedia

A Plasmodium from the saliva of a female mosquito moving across a mosquito cell

Thus the mosquito carries the disease from one human to another (acting as a “vector”). Differently from the human host, the mosquito vector does not suffer from the presence of the parasites.

All the clinical symptoms associated with malaria are caused by the asexual erythrocytic or blood stage parasites. When the parasite develops in the erythrocyte, numerous known and unknown waste substances such as hemozoin pigment and other toxic factors accumulate in the infected red blood cell. These are dumped into the bloodstream when the infected cells lyse and release invasive merozoites. The hemozoin and other toxic factors such as glucose phosphate isomerase (GPI) stimulate macrophages and other cells to produce cytokines and other soluble factors which act to produce fever and rigors associated with malaria.

Ookinete,_sporozoite,_merozoite

Ookinete,_sporozoite,_merozoite

Plasmodium falciparum-infected erythrocytes, particularly those with mature trophozoites, adhere to the vascular endothelium of venular blood vessel walls and when they become sequestered in the vessels of the brain it is a factor in causing the severe disease syndrome known as cerebral malaria, which is associated with high mortality.

Following the infective bite by the Anopheles mosquito, a period of time (the “incubation period”) goes by before the first symptoms appear. The incubation period in most cases varies from 7 to 30 days. The shorter periods are observed most frequently with P. falciparum and the longer ones with P. malariae.

malaria_lifecycle.

malaria_lifecycle.

Antimalarial drugs taken for prophylaxis by travelers can delay the appearance of malaria symptoms by weeks or months, long after the traveler has left the malaria-endemic area. (This can happen particularly with P. vivax and P. ovale, both of which can produce dormant liver stage parasites; the liver stages may reactivate and cause disease months after the infective mosquito bite.)

The Influenza Pandemic of 1918

The Nation’s Health

If you had lived in the early twentieth century, your life expectancy would
have been much shorter than it is today. Today, life expectancy for men is 75 years;
for women, it is 80 years. In 1918, life expectancy for men was only 53 years.

Women’s life expectancy at 54 was only marginally better.

Why was life expectancy so much shorter?

During the early twentieth century, communicable diseases—that is diseases
which can spread from person to person—were widespread. Influenza and
pneumonia along with tuberculosis and gastrointestinal infections such
as diarrhea killed Americans at an alarming rate but
non-communicable diseases such as cancer and heart disease also
exacted a heavy toll. Accidents, especially in the nation’s unregulated factories
and workshops, were also responsible for maiming and killing many workers.

High infant mortality further shortened life expectancy. In 1918, one in
five American children did not live beyond their fifth birthday. In some
cities, the situation was even worse, with thirty percent of all infants dying
before their first birthday. Childhood diseases such as diphtheria, measles,
scarlet fever and whooping cough contributed significantly to these high
death rates.

osler_at_a_bedside

osler_at_a_bedside

By 1900, an increasing number of physicians were receiving clinical
training. This training provided doctors with new insights into disease
and specific types of diseases. [Credit: National Library of Medicine]

scarlet_fever

scarlet_fever

Quarantine signs such as this one warned visitors away from homes
with scarlet fever and other infectious diseases. [Credit: National
Library of Medicine]

Rat Proofing

Cities often sponsored Clean-Up Days. Here, Public Health Service
employees clean up San Francisco’s streets in a campaign to
eradicate bubonic plague. [Credit: Office of the Public Health
Service Historian]

cleanup days

cleanup days

A young woman is seated with a baby on her lap in the center
of the photo.  On the right are two young children.  One child is
standing.  The other is seated in a crib.  A woman in a long
white apron stands by the stove on the left side of the photo.
She is pulling a bottle out of a pan on the stove.

nurse_helps_with_baby_formula

nurse_helps_with_baby_formula

A public health nurse teaches a young mother how to sterilize
a bottle. [Credit: National Library of Medicine]

Seeking Medical Care

Feeling Sick in 1918?

If you became sick in nineteenth-century America, you might consult
a doctor, a druggist, a midwife, a folk healer, a nurse or even
your neighbor. Most of these practitioners would visit you in your home.

By 1918, these attitudes toward health care were beginning to
change. Some physicians had begun to set up offices where patients
could receive medical care and hospitals, which emphasized sterilization
and isolation, were also becoming popular.

However, these changes were not yet universal and many Americans
still lived their entire lives without visiting a doctor.

How Did Ordinary People View Disease?

Folk Medicine:

In 1918, folk healers could be found all over America. Some of these
healers believed that diseases had a physical cause such as cold
weather but others believed it had a supernatural cause such as a curse.

Treatments advocated by these healers ran the gamut. Herbal remedies
were especially popular. Other popular remedies included cupping,
which entailed attaching a heated cup to the surface of the skin,
and acupuncture. Many people also wore magical objects which they
believed protected the wearer from illness.

During the influenza pandemic of 1918 when scientific medicine
failed to provide Americans with a cure or preventative, many people
turned to folk remedies and treatments.

Scientific Medicine

In the 1880s, building on developments which had been in the
making since the 1830s, a growing number of scientists and
physicians came to believe that disease was spread by
minute pathogenic organisms or germs.

Often called the bacteriological revolution, this new theory
radically transformed the practice of medicine. But while this was a
major step forward in understanding disease, doctors and scientists
continued to have only a rudimentary understanding of the differences
between different types of microbes. Many practicing physicians
did not understand the differences between bacteria and viruses
and this sharply limited their ability to understand disease
causation and disease prevention.

Drugs and Druggists:

Although the early twentieth century witnessed growing attempts
to regulate the practice of medicine, many druggists assumed
duties we associate today with physicians. Some druggists, for
example, diagnosed and prescribed treatments which they
then sold to the patient. Some of these treatments included opiates;
few actually cured diseases.

Desperate times called for desperate remedies and during the
influenza pandemic, many patients turned to these and other drugs
in the hopes that they would provide a cure.

Nurses:

Between 1890 and 1920, nursing schools multiplied and trained
nurses began to replace practical nurses. Isolation practices
sterility, and strict routines, practices associated with professionally
trained nurses, increasingly became standard during this period. In 1918, nurses served as the physician’s hand, assisting doctors as
they made the rounds. During the pandemic, many nurses acted
independently of doctors, treating and prescribing for patients.

Physicians:

Throughout the eighteenth and much of the nineteenth centuries,
pretty much anyone had the right to call oneself a physician. By the
late nineteenth century, growing calls for reform had begun to
transform the profession.

In 1900, every state in the Union had some type of medical registration
law with about half of all states requiring physicians to possess a
medical diploma and pass an exam before they received a license
to practice. However, grandfather clauses which exempted many older
physicians meant that many physicians who practiced in 1918
had been poorly trained.

quack_doctor

quack_doctor

Poor training and loose regulations meant that some doctors were
little more than quacks. [Credit: National Library of Medicine]

drug_ad

drug_ad

Drug advertisers routinely promised quick and painless cures.
[Credit: National Library of Medicine]

While access to the profession was tightening, women and minorities,
including African-Americans, entered the profession in growing
numbers during the early twentieth century.

What Did Doctors Really Know?

Growing understanding of bacteriology enabled early twentieth-
century physicians to diagnose diseases more effectively than their
predecessors but diagnosis continued to be difficult. Influenza was
especially tricky to diagnose and many physicians may have incorrectly
diagnosed their patients, especially in the early stages of the pandemic.

Bacteriology did not revolutionize the treatment of disease. In the
pre-antibiotic era of 1918, physicians continued to rely heavily
on traditional therapeutics. During the pandemic, many physicians
used traditional treatments such as sweating which had their
roots in humoral medicine.

Reflecting the uneven structure of medical education, the level and
quality of care which physicians provided varied wildly.

The Public Health Service

Founded in 1798, the Marine Hospital Service originally provided
health care for sick and disabled seaman. By the late nineteenth
century, the growth of trade, travel and immigration networks
had led the Service to expand its mission to include protecting
the health of all Americans.

In a nation where federal and state authorities had consistently
battled for supremacy, the powers of the Public Health Service
were limited. Viewed with suspicion by many state and local
authorities, PHS officers often found themselves fighting state
and local authorities as well as epidemics—even when they had
been called in by these authorities.

chelsea marine hospital in 1918

chelsea marine hospital in 1918

A network of hospitals in the nation’s ports provided seamen with
access to healthcare. [Credit: Office of the Public Health Service Historian]

In 1918, there were fewer than 700 commissioned officers in the PHS.
Charged with the daunting task of protecting the health of some
106 million Americans, PHS officers were stationed in not only
the United States but also abroad.

Because few diseases could be cured, the prevention of disease
was central to the PHS mission. Under the leadership of Surgeon
General Rupert Blue, the PHS advocated the use of scientific
research, domestic and foreign quarantine, marine hospitals
and statistics to accomplish this mission. hen an epidemic emerged,
the Public Health Service’s epidemiologists tracked the disease,
house by house. The 1918 influenza pandemic occurred too
rapidly for the PHS to develop a detailed study of the pandemic.

typhoid_map

typhoid_map

This map was used to trace a smaller typhoid epidemic which erupted in
Washington, DC in 1906. [Credit: Office of the Public Health Service Historian]

The spread of disease within the US was a serious concern. However,
PHS officers were most concerned about the importation of disease into
the United States. To prevent this, ships could be, and often were,
quarantined by the PHS.

fever-quaranteen-station-1880

fever-quaranteen-station-1880

Travelers and immigrants to the United States were also required
to undergo a medical exam when entering the country. In 1918 alone,
700,000 immigrants underwent a medical exam at the hands of PHS
officers. Within the United States, PHS officers worked directly with
state and local departments of health to track, prevent and arrest
epidemics as they emerged. During 1918, PHS officers found themselves
battling not only influenza but also polio, typhus, typhoid, smallpox
and a range of other diseases. In 1918, the PHS operated research
laboratories stretching from Hamilton, Montana to Washington DC.
Scientific researchers at these laboratories ultimately discovered
both the causes and cures of diseases ranging from Rocky Mountain
Spotted Fever to pellagra.

Sewers and Sanitation:

In the nineteenth century, most physicians and public health experts
believed that disease was caused not by microorganisms but rather by dirt itself.

Sanitarians, as these people were called, argued that cleaning dirt-
infested cities and building better sewage systems would both prevent
and end many epidemics. At their urging, cities and towns across the United
States built better sewage systems and provided citizens with access to
clean water. By 1918, these improved water and sewage systems had greatly
contributed to a decline in gastrointestinal infections and a significant
reduction in mortality rates among infants, children and young adults.

But because diseases are caused by microorganisms, not dirt, these
tactics were not completely effective in ending all epidemics.

Sanitation: Controlling problems at source

Box 1: Sharing toilets in Uganda

A recent survey by the Ministry of Health in Uganda suggested that there is only one toilet for every 700 Ugandan pupils, compared to one for every 328 pupils in 1995. Out of 8000 schools surveyed, only 33% of the 8000 schools sampled have separate latrines for girls. The deterioration in sanitary conditions was attributed to increased enrolment in schools. UNICEF surveyed 90 primary schools in crisis-affected districts of north and west Uganda: only 2% had adequate latrine facilities (IRIN, 1999).

Box 2: Sanitation and diarrhoeal disease

Gwatkin and Guillot (1999) have claimed that diarrhoea accounts for 11% of all deaths in the poorest 20% of all countries. This toll could be reduced by key measures: better sanitation to reduce the cause of water linked diarrhoea; and more widespread use of oral rehydration therapy (ORT) to treat its effects. Improving water supplies, sanitation facilities and hygiene practices reduces diarrhoea incidence by 26%. Even more impressive, deaths due to diarrhoea are reduced by 65% with these same improvements (Esrey et al., 1991). Of the 2.2 million people that die from diarrhoea each year, many of those deaths are caused by one bacteria – Shigella. Simple hand washing with soap and water reduces Shigella and other diarrhoea transmission by 35% (Kotloff et al., 1999; Khan, 1982). ORT is effective in reducing deaths due to diarrhoea but does not prevent it.

http://www.who.int/water_sanitation_health/sanitproblems/en/index1.html

Garbage-A-polluted-creek

Garbage-A-polluted-creek

Influenza Strikes

Throughout history, influenza viruses have mutated and caused
pandemics or global epidemics. In 1890, an especially virulent influenza
pandemic struck, killing many Americans. Those who survived that
pandemic and lived to experience the 1918 pandemic tended to be
less susceptible to the disease.

From Kansas to Europe and back again, wave after wave, the
unfolding of the pandemic, mobilizing to fight influenza, the
pandemic hits, protecting yourself, communication, fading of
the pandemic.

Influenza ward

Influenza ward

When it came to treating influenza patients, doctors, nurses and
druggists were at a loss. [Credit: Office of the Public Health Service Historian]

The influenza pandemic of 1918-1919 killed more people than the
Great War, known today as World War I (WWI), at somewhere
between 20 and 40 million people. It has been cited as the most
devastating epidemic in recorded world history. More people died of
influenza in a single year than in four-years of the Black Death Bubonic
Plague from 1347 to 1351. Known as “Spanish Flu” or “La Grippe”
the influenza of 1918-1919 was a global disaster.

Grim Reaper

Grim Reaper

The Grim Reaper by Louis Raemaekers

In the fall of 1918 the Great War in Europe was winding down and
peace was on the horizon. The Americans had joined in the fight,
bringing the Allies closer to victory against the Germans. Deep within
the trenches these men lived through some of the most brutal conditions
of life, which it seemed could not be any worse. Then, in pockets
across the globe, something erupted that seemed as benign as the
common cold. The influenza of that season, however, was far more
than a cold. In the two years that this scourge ravaged the earth,
a fifth of the world’s population was infected. The flu was most deadly
for people ages 20 to 40. This pattern of morbidity was unusual for
influenza which is usually a killer of the elderly and young children.
It infected 28% of all Americans (Tice). An estimated 675,000
Americans died of influenza during the pandemic, ten times as
many as in the world war. Of the U.S. soldiers who died in Europe,
half of them fell to the influenza virus and not to the enemy (Deseret
News). An estimated 43,000 servicemen mobilized for WWI died
of influenza (Crosby). 1918 would go down as unforgettable year
of suffering and death and yet of peace. As noted in the Journal
of the American Medical Association final edition of 1918:   “The 1918
has gone: a year momentous as the termination of the most cruel war
in the annals of the human race; a year which marked, the end at
least for a time, of man’s destruction of man; unfortunately a year in
which developed a most fatal infectious disease causing the death
of hundreds of thousands of human beings. Medical science for
four and one-half years devoted itself to putting men on the firing
line and keeping them there. Now it must turn with its whole might to
combating the greatest enemy of all–infectious disease,” (12/28/1918).

From Kansas to Europe and Back Again:

scourge ravaged the earth

scourge ravaged the earth

Where did the 1918 influenza come from? And why was it so lethal?

In 1918, the Public Health Service had just begun to require state
and local health departments to provide them with reports about
diseases in their communities. The problem? Influenza wasn’t
a reportable disease.

But in early March of 1918, officials in Haskell County in Kansas
sent a worrisome report to the Public Health Service.Although
these officials knew that influenza was not a reportable disease,
they wanted the federal government to know that “18 cases
of influenza of a severe type” had been reported there.

By May, reports of severe influenza trickled in from Europe. Young
soldiers, men in the prime of life, were becoming ill in large
numbers. Most of these men recovered quickly but some developed
a secondary pneumonia of “a most virulent and deadly type.”

Within two months, influenza had spread from the military to the
civilian population in Europe. From there, the disease spread outward—to Asia, Africa, South America and, back again, to North America.

Wave After Wave:

In late August, the influenza virus probably mutated again and
epidemics now erupted in three port cities: Freetown, Sierra
Leone; Brest, France, and Boston, Massachusetts. In Boston,
dockworkers at Commonwealth Pier reported sick in massive
numbers during the last week in August. Suffering from fevers
as high as 105 degrees, these workers had severe muscle and
joint pains. For most of these men, recovery quickly followed. But
5 to 10% of these patients developed severe and massive
pneumonia. Death often followed.

Public health experts had little time to register their shock at the
severity of this outbreak. Within days, the disease had spread
outward to the city of Boston itself. By mid-September, the epidemic
had spread even further with states as far away as California, North
Dakota, Florida and Texas reporting severe epidemics.

The Unfolding of the Pandemic:

The pandemic of 1918-1919 occurred in three waves. The first
wave had occurred when mild influenza erupted in the late
spring and summer of 1918. The second wave occurred with an
outbreak of severe influenza in the fall of 1918 and the final wave
occurred in the spring of 1919.

In its wake, the pandemic would leave about twenty million dead
across the world. In America alone, about 675,000 people in
a population of 105 million would die from the disease.

Find out what happened in your state during the Pandemic

Mobilizing to Fight Influenza:

Although taken unaware by the pandemic, federal, state and local
authorities quickly mobilized to fight the disease.

On September 27th, influenza became a reportable disease. However,
influenza had become so widespread by that time that most states
were unable to keep accurate records. Many simply failed to
report to the Public Health Service during the pandemic, leaving
epidemiologists to guess at the impact the disease may have
had in different areas.

World War I had left many communities with a shortage of trained
medical personnel. As influenza spread, local officials urgently
requested the Public Health Service to send nurses and doctors.
With less than 700 officers on duty, the Public Health Service was
unable to meet most of these requests. On the rare occasions when
the PHS was able to send physicians and nurses, they often became
ill en route. Those who did reach their destination safely often found
themselves both unprepared and unable to provide real assistance.

In October, Congress appropriated a million dollars for the Public
Health Service. The money enabled the PHS to recruit and pay
for additional doctors and nurses. The existing shortage of doctors
and nurses, caused by the war, made it difficult for the PHS to locate and hire qualified practitioners. The virulence of the disease also meant that many nurses and doctors contracted influenza
within days of being hired.

Confronted with a shortage of hospital beds, many local officials
ordered that community centers and local schools be transformed
into emergency hospitals. In some areas, the lack of doctors meant
that nursing and medical students were drafted to staff these
makeshift hospitals.

The Pandemic Hits:

Entire families became ill. In Philadelphia, a city especially hard hit,
so many children were orphaned that the Bureau of Child Hygiene
found itself overwhelmed and unable to care for them.

As the disease spread, schools and businesses emptied. Telegraph
and telephone services collapsed as operators took to their
beds. Garbage went uncollected as garbage men reported sick.
The mail piled up as postal carriers failed to come to work.

State and local departments of health also suffered from high
absentee rates. No one was left to record the pandemic’s spread
and the Public Health Service’s requests for information went
unanswered.

As the bodies accumulated, funeral parlors ran out of caskets
and bodies went uncollected in morgues.

Protecting Yourself From Influenza:

In the absence of a sure cure, fighting influenza seemed an
impossible task.

In many communities, quarantines were imposed to prevent
the spread of the disease.Schools, theaters, saloons, pool
halls and even churches were all closed. As the bodies
mounted, even funerals were held out doors to protect mourners
against the spread of the disease.

Emergency Hospital for Influenza Patients

An Emergency Hospital for Influenza Patients

The effect of the influenza epidemic was so severe that the
average life span in the US was depressed by 10 years.
The influenza virus had a profound virulence, with a mortality
rate at 2.5% compared to the previous influenza epidemics, which
were less than 0.1%. The death rate for 15 to 34-year-olds of
influenza and pneumonia were 20 times higher in 1918 than in
previous years (Taubenberger). People were struck
with illness on the street and died rapid deaths.

One anecdote shared of 1918 was of four women playing bridge
together late into the night. Overnight, three of the women died
from influenza (Hoagg). Others told stories of people on their way
to work suddenly developing the flu and dying within hours
(Henig). One physician writes that patients with seemingly
ordinary influenza would rapidly “develop the most viscous
type of pneumonia that has ever been seen” and later when
cyanosis appeared in the patients, “it is simply a struggle for air
until they suffocate,” (Grist, 1979). Another physician recalls
that the influenza patients “died struggling to clear their airways
of a blood-tinged froth that sometimes gushed from their nose
and mouth,” (Starr, 1976). The physicians of the time were
helpless against this powerful agent of influenza. In 1918 children
would skip rope to the rhyme (Crawford):

I had a little bird,

Its name was Enza.

I opened the window,

And in-flu-enza.

schools inspected -

schools inspected –

The influenza pandemic circled the globe. Most of humanity felt the
effects of this strain of the influenza virus. It spread following
the path of its human carriers, along trade routes and shipping lines.
Outbreaks swept through North America, Europe, Asia, Africa, Brazil
and the South Pacific (Taubenberger). In India the mortality rate was
extremely high at around 50 deaths from influenza per 1,000
people (Brown). The Great War, with its mass movements of men
in armies and aboard ships, probably aided in its rapid diffusion
and attack. The origins of the deadly flu disease were unknown but
widely speculated upon. Some of the allies thought of the epidemic as a
biological warfare tool of the Germans. Many thought it was a result of
the trench warfare, the use of mustard gases and the generated “smoke
and fumes” of the war. A national campaign began using the ready
rhetoric of war to fight the new enemy of microscopic proportions. A
study attempted to reason why the disease had been so devastating
in certain localized regions, looking at the climate, the weather and
the racial composition of cities. They found humidity to be linked with
more severe epidemics as it “fosters the dissemination of the bacteria,”
(Committee on Atmosphere and Man, 1923). Meanwhile the new
sciences of the infectious agents and immunology were
racing to come up with a vaccine or therapy to stop the epidemics.

The experiences of people in military camps encountering the
influenza pandemic: An excerpt for the memoirs of a survivor at
Camp Funston of the pandemic Survivor A letter to a fellow physician
describing conditions during the influenza epidemic at Camp Devens.

A collection of letters of a soldier stationed in Camp Funston Soldier

The origins of this influenza variant is not precisely known. It is thought
to have originated in China in a rare genetic shift of the influenza virus.
The recombination of its surface proteins created a virus novel to
almost everyone and a loss of herd immunity. Recently the virus
has been reconstructed from the tissue of a dead soldier and is
now being genetically characterized.

The name of Spanish Flu came from the early affliction and large
mortalities in Spain (BMJ,10/19/1918) where it allegedly killed 8
million in May (BMJ, 7/13/1918). However, a first wave of influenza
appeared early in the spring of 1918 in Kansas and in military
camps throughout the US. Few noticed the epidemic in the midst of
the war. Wilson had just given his 14 point address. There was
virtually no response or acknowledgment to the epidemics in March
and April in the military camps. It was unfortunate that no steps were
taken to prepare for the usual recrudescence of the virulent influenza
strain in the winter. The lack of action was later criticized when the
epidemic could not be ignored in the winter of 1918 (BMJ, 1918).
These first epidemics at training camps were a sign of what was
coming in greater magnitude in the fall and winter of 1918 to the
entire world.

The war brought the virus back into the US for the second wave
of the epidemic. It first arrived in Boston in September of 1918
through the port busy with war shipments of machinery and supplies.
The war also enabled the virus to spread and diffuse. Men across
the nation were mobilizing to join the military and the cause. As they
came together, they brought the virus with them and to those they
contacted. The virus  killed almost 200,00 in October of 1918
alone. In November 11 of 1918 the end of the war enabled a resurgence.
As people celebrated Armistice Day with parades and large parties, a
complete disaster from the public health standpoint, a rebirth of
the epidemic occurred in some cities. The flu that winter was beyond
imagination as millions were infected and thousands died. Just as
the war had effected the course of influenza, influenza affected
the war. Entire fleets were ill with the disease and men on the front
were too sick to fight. The flu was devastating to both sides, killing
more men than their own weapons could.

With the military patients coming home from the war with battle wounds
and mustard gas burns, hospital facilities and staff were taxed
to the limit. This created a shortage of physicians, especially in the
civilian sector as many had been lost for service with the military.
Since the medical practitioners were away with the troops, only
the medical students were left to care for the sick. Third and forth
year classes were closed and the students assigned jobs as
interns or nurses (Starr,1976). One article noted that “depletion has
been carried to such an extent that the practitioners are brought
very near the breaking point,” (BMJ, 11/2/1918). The shortage was
further confounded by the added loss of physicians to the epidemic.
In the U.S., the Red Cross had to recruit more volunteers to contribute
to the new cause at home of fighting the influenza epidemic. To respond
with the fullest utilization of nurses, volunteers and medical supplies, the
Red Cross created a National Committee on Influenza. It was involved
in both military and civilian sectors to mobilize all forces to fight Spanish
influenza (Crosby, 1989). In some areas of the US, the nursing shortage
was so acute that the Red Cross had to ask local businesses to
allow workers to have the day off if they volunteer in the hospitals
at night (Deseret News). Emergency hospitals were created to
take in the patients from the US and those arriving sick from overseas.

chelsea marine hospital in 1918

chelsea marine hospital in 1918

red_cross_public_health_nurse

red_cross_public_health_nurse

The pandemic affected everyone. With one-quarter of the US and
one-fifth of the world infected with the influenza, it was  impossible
to escape from the illness. Even President Woodrow Wilson suffered
from the flu in early 1919 while negotiating the crucial treaty of
Versailles to end the World War (Tice). Those who were
lucky enough to avoid infection had to deal with the public health
ordinances to restrain the spread of the disease.

The public health departments distributed gauze masks to be worn
in public. Stores could not hold sales, funerals were limited
to 15 minutes. Some towns required a signed certificate to
enter and railroads would not accept passengers without
them. Those who ignored the flu ordinances had to pay steep
fines enforced by extra officers (Deseret News). Bodies pilled up
as the massive deaths of the epidemic ensued. Besides the
lack of health care workers and medical supplies, there was a shortage
of coffins, morticians and gravediggers (Knox). The conditions in 1918
were not so far removed from the Black Death in the era of the
bubonic plague of the Middle Ages.

iowa_flu

iowa_flu

In 1918-19 this deadly influenza pandemic erupted during the final
stages of World War I. Nations were already attempting to deal with
the  effects and costs of the war. Propaganda campaigns and war
restrictions and rations had been implemented by governments.
Nationalism pervaded as people accepted government authority.
This allowed the public health departments to easily step in and
implement their restrictive measures. The war also gave science
greater importance as governments relied on scientists, now armed
with the new germ theory and the development of antiseptic surgery,
to design vaccines and reduce mortalities of disease and battle
wounds. Their new technologies could preserve the men on
the front and ultimately save the world. These conditions
created by World War I, together with the current social attitudes
and ideas, led to the relatively calm response of the public and
application of scientific ideas. People allowed for strict measures
and loss of freedom during the war as they submitted to the
needs of the nation ahead of their personal needs. They had
accepted the limitations placed with rationing and drafting.
The responses of the public health officials reflected the new
allegiance to science and the wartime society. The medical
and scientific communities had developed new theories and
applied them to prevention, diagnostics and treatment of the
influenza patients.

The Medical and Scientific Conceptions of Influenza

Scientific ideas about influenza, the disease and its origins,
shaped the public health and medical responses. In 1918
infectious diseases were beginning to be unraveled. Pasteur
and Koch had solidified the germ theory of disease through
clear experiments clever science. The bacillus responsible
for many infections such as tuberculosis and anthrax  had
been visualized, isolated and identified. Koch’s postulates
had been developed to clearly link a disease to a specific
microbial agent.

Robert Koch

Robert Koch

The petri dish was widely used to grow sterile cultures of bacteria
and investigate bacterial flora. Vaccines had been created for
bacterial infections and even the unseen rabies virus by
serial passage techniques. The immune system was explained by
Paul Erhlich and his side-chain theory. Tests of antibodies such as
Wasserman and coagulation experiments were becoming commonplace.
Science and medicine were on their way to their complete entanglement
and fusion as scientific principles and methodologies made their way
into clinical practice, diagnostics and therapy.

The Clinical Descriptions of Influenza

Patients with the influenza disease of the epidemic were generally
characterized by common complaints associated with the flu. They had
body aches, muscle and joint pain, headache, a sore throat and a
unproductive cough with occasional harsh breathing (JAMA, 1/25/1919).

The most common sign of infection was the fever, which ranged from
100 to 104 F and lasted for a few days. The onset of the epidemic influenza
was peculiarly sudden, as people were struck down with dizziness, weakness
and pain while on duty or in the street (BMJ, 7/13/1918). After  the
disease was established the mucous membranes became reddened
with sneezing. In some cases there was a hemorrhage of the
mucous membranes of the nose and bloody noses were commonly
seen. Vomiting occurred on occasion, and also sometimes diarrhea
but more commonly there was constipation (JAMA, 10/3/1918).

The danger of an influenza infection was its tendency to progress into
the often fatal secondary bacterial infection of pneumonia. In the
patients that did not rapidly recover after three or four days of fever, there
is an “irregular pyrexia” due to bronchitis or broncopneumonia (BMJ,
7/13/1918). The pneumonia would often appear after a period of
normal temperature with a sharp spike and expectorant of bright
red blood. The lobes of the lung became speckled with “pneumonic
consolidations.” The fatal cases developed toxemia and vasomotor
depression (JAMA, 10/3/1918). It was this tendency for secondary
complications that made this influenza infection so deadly.

pneumonia

pneumonia

hospital ward in 1918

hospital ward in 1918

A military hospital ward in 1918

In the medical literature characterizing the influenza disease, new
diagnostic techniques are frequently used to describe the clinical
appearance. The most basic clinical guideline was the temperature,
a record of which was kept in a table over time. Also closely
monitored was the pulse rate. One clinical account said that
“the pulse was remarkably slow,” (JAMA, 4/12/1919) while others
noted that the pulse rate did not increase as expected. With the
pulse, the respiration rate was measured and reported to provide
clues of the clinical progression.
Patients were also occasionally “roentgenographed” or chest x-rayed,
(JAMA, 1/25/1919). The discussion of clinical influenza also often
included analysis of the blood. The number of white blood cells were
counted for many patients. Leukopenia was commonly associated
with influenza. The albumin was also measured, since it was noted that
transient albuminuria was frequent in influenza patients. This was
done by urine analysis. The Wassermann reaction was another
added new test of the blood for antibodies (JAMA, 10/3/1918).
These new measurements enabled to physicians to have an
image of action and knowledge using scientific instruments. They
could record precisely the progress of the influenza infection and perhaps
were able to forecast its outcome.

The most novel of these tests were the blood and sputum cultures.
Building on the germ theory of disease, the physicians and their
associated research scientists attempted to find the culprit for this
deadly infection. Physicians would commonly order both blood and sputum
cultures of their influenza and pneumonia patients mostly for research
and investigative purposes. At the military training camp
Camp Lewis during a influenza epidemic, “in all cases of pneumonia.
a sputum study, white blood and differential count, blood culture
and urine examinations were made as routine,” (JAMA, 1/25/1919).

The bacterial flora of the nasopharynx of some patients was also cultured
since droplet infection was where the disease disseminated. The
collected swabs and specimens were inoculated onto blood agar of
petri dishes. The grown up bacterial colonies were closely studied to
find the causal organism. Commonly found were pneumococcus,
streptococcus, staphylococcus and Bacillus influenzae (JAMA, 4/12/1919).

pneumonia

pneumonia

These new laboratory tests used in the clinical setting brought in a solid
scientific, biological link to the practice of medicine. Medicine had
become fully scientific and technologic in its understanding and
characterization of the influenza epidemic.

Treatment and Therapy

The therapeutic remedies for influenza patients varied from the
newly developed drugs to oils and herbs. The therapy was much less
scientific than the diagnostics, as the drugs had no clear explanatory
theory of action. The treatment was largely symptomatic, aiming to
reduce fever or pain. Aspirin, or acetylsalicylic acid was a common remedy.
For secondary pneumonia doses of epinephrin were given. To
combat the cyanosis physicians gave oxygen by mask or some
injected it under the skin (JAMA, 10/3/1918). Others used salicin which
reduced pain, discomfort and fever and claimed to reduce the infectivity
of the patient. Another popular remedy was cinnamon in powder or oil form
with milk to reduce temperature (BMJ, 10/19/1918). Finally, salt of quinine
was suggested as a treatment. Most physicians agreed that the patient should
be  kept in bed (BMJ, 7/13/1918). With that was the advice of plenty of
fluids and nourishment. The application of cold to the head, with
warm packs or warm drinks was also advised. Warm baths were used
as a hydrotherapeutic method in hospitals but were discarded for
lack of success (JAMA, 10/3/1918). These treatments, like the
suggested prophylactic measures of the public health officials, seemed to
originate in the common social practices and not in the growing field of
scientific medicine. It seems that as science was entering the medical
field, it served only for explanatory, diagnostic and preventative
measures such as vaccines and technical tests. This science had
little use once a person was ill.

However, a few proposed treatment did incorporate scientific ideas
of germ theory and the immune system. O’Malley and Hartman
suggested to treat influenza patients with the serum of convalescent
patients. They utilize the theorized antibodies to boost the immune
system of sick patients. Other treatments were “digitalis,” the
administration of isotonic glucose and sodium bicarbonate intravenously
which was done in military camps (JAMA, 1/4/1919). Ross and
Hund too utilized ideas about the immune system and properties of the
blood to neutralize toxins and circulate white blood cells. They believed
that the best treatment for influenza should aim to: “…neutralize or render
the intoxicant inert…and prevent the blood destruction with its destructive
leukopenia and lessened coagulability,” (JAMA, 3/1/1919). They tried
to create a therapeutic immune serum to fight infection. These therapies
built on current scientific ideas and represented the highest
biomedical, technological treatment like the antitoxin to diphtheria.

influenza

influenza

In July, an American soldier said that while influenza caused a heavy
fever, it “usually only confines the patient to bed for a few days.” The
mutation of the virus changed all that. [Credit: National Library of Medicine]

recovering_from_influenza

recovering_from_influenza

An old cliché maintained that influenza was a wonderful disease as
it killed no one but provided doctors with lots of patients. The 1918
pandemic turned this saying on its head. [Credit: The Etiology of
Influenza in 1918]

During the 1890 influenza epidemic, Pfeiffer found what he
determined to be the microbial agent to cause influenza.
In the sputum and respiratory tract of influenza patients in 1892,
he isolated the bacteria Bacillus influenzae , which was
accepted as the true “virus” though it was not found in localized
outbreaks (BMJ, 11/2/1918). However, in studies of the 1907-8
epidemic in the US, Lord had found the bacillus in only 3 of 20 cases.
He also found the bacillus in 30% of cultures of sputum from TB patients.
Rosenthal further refuted the finding when he found the bacillus in 1 of 6
healthy people in 1900 (JAMA, 1/18/1919). The bacillus was also
found to be present in all cases of whooping cough and many cases
of measles, chronic bronchitis and scarlet fever (JAMA, 10/5/1918).
The influenza pandemic provided scientists the opportunity to confirm
or refute this contested microbe as the cause of influenza. The sputum
studies from the Camp Lewis epidemic found only a few influenza cases
harvesting the influenza bacilli and mostly type IV pneumococcus . They
concluded that “the recent epidemic at Camp Lewis was an acute
respiratory infection and not an epidemic due to Bacillus influenzae ,”
(JAMA, 1/25/1919). This finding along with others suggested to most
scientists that the Pfeiffer’s Bacillus was not the cause of influenza.

In the 1918-19 influenza pandemic, there was a great drive to find the
etiological agent responsible for the deadly scourge. Scientists in their
labs were working hard, using the cultures obtained from physician clinics,
to isolate the etiological agent for influenza. As a report early in the
epidemic said, “the ‘influence’ of influenza is still veiled in mystery, ”
(JAMA, 10/5/1918). The nominated bacillus influenzae bacteria
seemed to be incorrect and scientists scrambled to isolate the true cause.
In the journals, many authors speculated on the type of agent- was
it a new microbe, was it a bacteria, was it a virus? One journal offered
that “the severity of the present pandemic, the suddenness of onset…
led to the suggestion that the disease cannot be influenza but some other
and more lethal infection,” (BMJ, 11/2/1918). However, most accepted that
the epidemic disease was influenza based on the familiar symptoms
and known pattern of disease. The respiratory disease of influenza was
understood to give warning in the late spring of its potential effects
upon its recrudescence once the weather turned cold in the winter
(BMJ, 10/19/1918).One article with foresight stated that ” there can
be no question that the virus of influenza is a living organism…

flu virus EM

flu virus EM

it is possibly beyond the range of microscopic vision,” (BMJ, 11/16/1918). Another
article confirmed the idea of an “undiscovered virus” and noted that pneumococci
and streptococci were responsible for “the gravity of the secondary pulmonary
complications,” (BMJ, 11/2/1918). The article went on to offer the idea of a
symbiosis of virus and secondary bacterial infection combining to make it
such a severe disease.

The investigators as they attempted to find the responsible agent for the influenza
pandemic were developing ideas of infectious microbes and the concept of the
virus. The idea of the virus as an infectious agent had been around for years.
The articles of the period refer to the “virus” in their discussion but do not
consistently use it to be an infectious microbe, distinctive from bacteria. The
term virus has the same usage and application as bacillus. In 1918, a virus
was defined scientifically to be a submicroscopic infectious entity which could
be filtered but not grown in vitro . In the 1880s Pasteur developed an attenuated
vaccine for the rabies virus by serial passage way ahead of his time. Ivanoski’s
work on the tobacco mosaic virus in 1890s lead to the discovery of the virus.
He found an infectious agent that acted as a micro-organism as it multiplied
yet which passed through the sterilizing filter as a nonmicrobe. By the 1910s
several viruses, defined as filterable infectious microbes, had been identified
as causing infectious disease (Hughes). However, the scientists were still
conceptually behind in defining a virus; they distinguished it only by size
from a bacteria and not as an obligate parasite with a distinct life cycle
dependent on infecting a host cell.

The influenza epidemic afforded the opportunity to research the etiological
agent and develop the idea of the virus. Experiments by Nicolle and Le Bailly in
Paris were the earliest suggestions that influenza was caused by a “filter-passing
virus,” (BMJ, 11/2/1918). They filtered out the bacteria from bronchial expectoration
of an influenza patient and injected the filtrate into the eyes and nose of two monkeys.
The monkeys developed a fever and a marked depression. The filtration was later
administered to a volunteer subcutaneously who developed typical signs of influenza.
They reasoned that the inoculated person developed influenza from the filtrate since
no one else in their quarters developed influenza (JAMA, 12/28/1918). These scientists
followed Koch’s postulates as they isolated the causal agent from patients with the
illness and used it to reproduce the same illness in animals. Through these studies,
the scientists proved that influenza was due to a submicroscopic infectious agent
and not a bacteria, refuting the claims of Pfeiffer and advancing virology. They were
on their way to discerning the virus and characterizing the orthomyxo viruses that
lead to the disease of influenza.

These scientific experiments which unravel the cause of influenza, had immediate
preventative applications. They would assist in the effort to create a effective
vaccine to prevent influenza. This was the ultimate goal of most studies, since
vaccines were thought to be the best preventative solution in the early 20th century.
Several experiments attempted to produce vaccines, each with a different
understanding of the etiology of fatal influenza infection. A Dr. Rosenow invented
a vaccine to target the multiple bacterial agents involved from the serum of patients.
He aimed to raise the immunity to against the bacteria, the “common causes of death,
“and not the cause of the initial symptoms by inoculating with the proportions found
in the lungs and sputum (JAMA, 1/4/1919). The vaccines made for the British forces
took a similar approach and were “mixed vaccines” of pneumococcus and
lethal streptococcus. The vaccine development therefore focused on the culture
results of what could be isolated from the sickest patients and lagged behind the
scientific progress.

Fading of the Pandemic:

In November, two months after the pandemic had erupted, the Public Health Service
began reporting that influenza cases were declining.

Communities slowly lifted their quarantines. Masks were discarded. Schools were
re-opened and citizens flocked to celebrate the end of World War I.

Communities and the disease continued to be a threat throughout the spring of 1919.

By the time the pandemic had ended, in the summer of 1919, nearly 675,000
Americans were dead from influenza. Hundred of thousands more were orphaned
and widowed.

The Legacy of the Pandemic

No one knows exactly how many people died during the 1918-1919 influenza
pandemic. During the 1920s, researchers estimated that 21.5 million people died
as a result of the 1918-1919 pandemic. More recent estimates have estimated
global mortality from the 1918-1919 pandemic at anywhere between 30 and 50
million. An estimated 675,000 Americans were among the dead.

Twentieth-Century Influenza Pandemics or Global Epidemics:

The pandemic which occurred in 1918-1919 was not the only influenza pandemic
of the twentieth century. Influenza returned in a pandemic form in 1957-1958
and, again, in 1968-1969. These two later pandemics were much less severe than the 1918-1919 pandemic.
Estimated deaths within the United States for these two later pandemics were 70,000 excess deaths (1957-1958) and 33,000 excess deaths (1968-1967).

Research, forgetting the pandemic of 1918-1919, scientific milestones, 20th century influenza or global pandemics.
The Influenza Pandemic occurred in three waves in the United States throughout
1918 and 1919.

More Americans died from influenza than died in World War I. [Credit: National Library of Medicine]

All of these deaths caused a severe disruption in the economy. Claims against life
insurance policies skyrocketed, with one insurance company reporting a 745 percent
rise in the number of claims made. Small businesses, many of which had been unable to operate during the pandemic, went bankrupt.

Joseph goldberger

Joseph goldberger

Joseph Goldberger, one of the leading researchers in the PHS, studied influenza
during the pandemic. But Goldberger had multiple interests and influenza research
became less important to him in the years following 1918. [Credit: Office of the Public
Health Service Historian]

In the summer and fall of 1919, Americans called for the government to research
both the causes and impact of the pandemic. In response, both the federal government
and private companies, such as Metropolitan Life Insurance, dedicated money
specifically for flu research.

In an attempt to determine the effect influenza had different communities, the Public
Health Service conducted several small epidemiological studies. These studies,
however, were conducted after the pandemic and most PHS officers
admitted that the data which was collected was probably inaccurate.

PHS scientists continued to search for the causative agent of influenza in their
laboratories as did their fellow scientists in and outside the United States.

But while there was a burst of enthusiasm for funding flu research in
1918- 1919, the funds allocated for this research were actually fairly meager.
As time passed, Americans became less interested in the pandemic and its
causes. And even when funding for medical research dramatically increased
after World War II, funding for research on the 1918-1919 pandemic remained
limited.

Forgetting the 1918-1919 Pandemic:

In the years following 1919, Americans seemed eager to forget the pandemic.
Given the devastating impact of the pandemic, the reasons for this forgetfulness
are puzzling.

It is possible, however, that the pandemic’s close association with World War I
may have caused this amnesia. While more people died from the pandemic than
from World War I, the war had lasted longer than the pandemic and caused
greater and more immediate changes in American society.

Influenza also hit communities quickly. Often it disappeared within a few weeks of
its arrival. As one historian put it, “the disease moved too fast, arrived, flourished
and was gone before…many people had time to fully realize just how great
was the danger.” Small wonder, then, that many Americans forgot about the
pandemic in the years which followed.

Scientific Milestones in Understanding and Preventing Influenza:

In the early stages of the pandemic, many scientists believed that the agent
responsible for influenza was Pfeiffer’s bacillus. Autopsies and research conducted
during the pandemic ultimately led many scientists to discard this theory.

In late October of 1918, some researchers began to argue that influenza was
caused by a virus. Although scientists had understood that viruses could cause
diseases for more than two decades, virology was still very much in its infancy at
this time.

It was not until 1933 that the influenza A virus, which causes almost every type
of endemic and pandemic influenza, was isolated. Seven years later, in 1940,
the influenza B virus was isolated. The influenza C virus was finally isolated in 1950.

Influenza vaccine was first introduced as a licensed product in the United States in
1944. Because of the rapid rate of mutation of the influenza virus, the
effectiveness of a given vaccine usually lasts for only a year or two.

By the 1950s, vaccine makers were able to prepare and routinely release vaccines
which could be used in the prevention or control of future pandemics. During the
1960s, increased understanding of the virus enabled scientists to develop both
more potent and purer vaccines.

Mass production of influenza vaccines continued, however, to require several
months lead time.

Twentieth-Century Influenza Pandemics or Global Epidemics:

The pandemic which occurred in 1918-1919 was not the only influenza pandemic
of the twentieth century. Influenza returned in a pandemic form in 1957-1958
and, again, in 1968-1969.

These two later pandemics were much less severe than the 1918-1919 pandemic.
Estimated deaths within the United States for these two later pandemics
were 70,000 excess deaths (1957-1958) and 33,000 excess deaths (1968-1967).

Tuberculosis

Mycobacterium tuberculosis was first discovered in 1882 by Robert Koch and is one of almost 200 mycobacterial species which have been detected by molecular techniques. The genus Actinobacteria (given its own family, the Mycobacteriaceae) includes pathogens known to cause serious diseases in mammals, including tuberculosis (MTBC) and leprosy (M. leprae). Mycobacteria are grouped neither as Gram-positive nor Gram-negative bacteria. MTBC consists of M. tuberculosis, M. bovis, M. bovis BCG (bacillus Calmette-Guérin), M. africanum M. caprae, M. microti, M. canettii and M. pinnipedii, all of which share genetic homology, with no significant variation between sequences (∼0.01 to 0.03%), although differences in phenotypes are present. Cells in the genus have a typical rod, or slightly curved-shape, with dimensions of 0.2 to 0.6 μm by 1 to 10 μm.

Mycobacterium tuberculosis has a waxy mycolic acid lipid complex coating on its cell surface. The cells are impervious to Gram staining, so a common staining procedure used is Ziehl-Neelsen (ZN) staining. The outer compartment of the cell wall contains lipid-linked polysaccharides, is water-soluble, and interacts with the immune system. The inner wall is impermeable. Mycobacteria have some unique qualities that are divergent from members of the Gram-positive group, such as the presence of mycolic acids in the cell wall.

MTBC and M. leprae replication occurs in the tissues of warm-blooded human hosts. This air-borne pathogen is transmitted from an active pulmonary tuberculosis patient by coughing. Droplet nuclei, approximately 1 to 5 μm in size “meander” in the air and are transmitted to susceptible individuals by inhalation. Mycobacteria are incapable of replicating in or on inanimate objects. The risk of infection is dependent to the load of the bacillus that has been inhaled, level of infectiousness, contact perimeter and the immune competency of potential hosts. Due to the size of the droplets inhaled into the lungs, the infection penetrates the defense systems of the bronchi and enters the terminal alveoli. Invading bacteria are then engulfed by alveolar macrophage and dendritic cells.

The cell-mediated immune response alleviates the multiplication of M. tuberculosis and halts infection. Infected individuals with strong immune systems are generally able to combat the infection within 2 to 8 weeks post-infection, when the active cell-mediated immune response stops further multiplication of M. tuberculosis. Tuberculosis infection shows several significant clinical manifestations in pulmonary and extra-pulmonary sites. Prolonged coughing, severe weigh-lost, night sweats, low-grade fever, dyspnoea and chest pain are clinical symptoms indicated from pulmonary infections.

Fort Bayard, N.M., T.B. service assignment

Fort Gayard, NM

Fort Gayard, NM

Fort Bayard, NM Post Hospital circa 1890

U.S. Army, General Hospital, Fort Bayard, New Mexico, General View,

U.S. Army, General Hospital, Fort Bayard, New Mexico, General View,

Tuberculosis, (Pvt.) Richard Johnson said, was “regarded as a much dreaded disease that was easily contracted by association.” In fact, so many hospital corpsmen requested transfers out that the Surgeon General established a policy that no such requests would be considered until after two years of service. Consequently, Johnson noted, “During my time there we had a high percentage of desertions.” For example, all four of the men who arrived with Johnson, within a year—“two of them,” he dryly observed, “owing me money.”

Four years later another young man arrived at Fort Bayard. He, too, remarked on the long journey by rail through the “desert waste of New Mexico,” and then the wagon ride over “dry desolate foothills,” to the post. But his reaction was different from Johnson’s. Capt. Earl Bruns moved from being a patient to a physician at the hospital. For Bruns Fort Bayard was “a veritable oasis in the desert, studded with shade trees, green lawns, shrubbery, and flowers.” He credited the hospital commander, Colonel (Col.) George E. Bushnell, writing that, “[i]n this one spot one man had made the desert bloom like a rose.”

Johnson’s and Bruns’ different views from 1904 and 1908, respectively, may reflect the fact that Johnson was healthy and assigned grudgingly to work at the tuberculosis hospital, whereas Bruns had few other options and came in hopes of regaining his health—or it may reflect the improvements Bushnell made during his first years in command. But every week for the more than twenty years that Fort Bayard was an Army tuberculosis hospital, workers and patients arrived with dread and foreboding, or joy and relief—or a mix of them all.

The approach Fort Bayard and George Bushnell took to tuberculosis was similar to how physicians manage the disease today in that it involved isolating the patient, treating the disease, and educating the patient and his family on how to maintain their health. The hospital offered patients sanctuary from the demands, fears, and prejudices regarding tuberculosis in the outside world. Fort Bayard treated tuberculosis patients with prolonged bed rest, fresh air, and a healthy diet, but undertaking this “rest treatment”—confining oneself to bed for months—proved difficult if not impossible for many patients. Fort Bayard involved patients’ adaptation to new lifestyles as people with tuberculosis. Finally, Fort Bayard managed patients’ transition back to the outside world.

One of the most striking aspects of Fort Bayard was that many of the medical staff had tuberculosis themselves, including George Bushnell. Tuberculosis weakened Bushnell’s lungs and shaped his life in numerous ways. He tired easily, had to carefully monitor his health, and as Earl Bruns observed, “was never a well man.” Bushnell had active tuberculosis five times in his life: the fourth time in 1919 with a breakdown from the strain of wartime work; and the fifth and the final illness in 1924 that lead to his death at age 70. In 1911 he advised his superiors that, “I did not consider myself strong enough to carry on the work of commanding this Hospital and keeping myself in condition for active duty.” The War Department generally required officers in poor physical condition to retire, but the Surgeon General secured a waiver for Bushnell, because “the interests of the service would suffer by his retirement.” After a leave of absence in 1909–10, Bushnell’s annual reports on the competency of his officers included his own name on the list of those competent for hospital duty, but “unfit for active field service.”

“What would our sanatorium movement and our anti-tuberculosis crusade amount to,” wrote tuberculosis expert Adolphus Knopf, “were it not for the labors of tuberculous physicians, or one-time tuberculous physicians, who, because of their infirmity, had become interested in tuberculosis?” Well-known leaders in the antituberculosis movement such as Edward Trudeau and Lawrence Flick established their sanatoriums after they recovered from tuberculosis in order to offer others the treatment. Twenty-one of the first thirty recipients of the Trudeau Medal, established in 1926 for outstanding work in tuberculosis, had the disease. James Waring, a tuberculosis physician who arrived at a Colorado Springs sanatorium on a stretcher in 1908, later wrote, “It has been my good fortune to serve three separate and extended ‘hitches’ as a ‘bed patient,’ the time so spent numbering in all about nine years.” He, like many physicians, saw his personal experience as an asset in his practice. The three key figures in the Army tuberculosis program during World War I were Bushnell, Bruns, and Gerald Webb of Colorado Springs who started a tuberculosis sanatorium after his wife died of the disease.

Bushnell turned tuberculosis into an asset for the Army Medical Department, making Fort Bayard a center of national expertise on the disease. His personal experience with chronic pulmonary tuberculosis gave him good rapport and credibility with many of his patients. Medical officer Earl Bruns wrote that, “[H]e went among the patients and talked to them individually” and thereby provided “a living example of a cure due to rational treatment.” Bruns described how Bushnell spent his days attending to patients, carrying out administrative duties, and devoted hours to supervising the work in the gardens and grounds of Fort Bayard.

(Who’s Who in America, 1924-25. E. H. Bruns in American Review of Tuberculosis, June 1925. 0. B. Webb in Outdoor Life, Sept. 1924. Lancet. Lond., 1924. Jour. Am. Med. Ass’n., 1924, p. 374.)

General George M. Sternberg

In addition to being an Army surgeon, Sternberg was also a noted bacteriologist who, in 1880, had translated Antoine Magnin’s The Bacteria, which presented the latest research in germ theory. Sternberg’s work contributed to preparing American understanding of Robert Koch’s pronouncement in 1882 of the existence of the tubercle bacillus (Ott 1996:55). Over the next two decades Koch’s analysis gained converts, leading to the universally accepted belief that tuberculosis represented a bacterium infection that could be diagnosed and then monitored by microscopic inspection of patient’s sputum.

Sternberg was no doubt aware of the efforts of Edward Livingston Trudeau. Beginning in the 1870s, when he undertook his own recovery from consumption by withdrawing to the Adirondack Mountains, Trudeau had become an advocate of extended bed rest in remote, healthful environments. Quickly accepting Koch’s research, Trudeau argued that those afflicted by the tubercle bacillus could best be healed when removed from cities and placed under the care of physicians who carefully monitored their weight and sputum and who prescribed constant bed rest with exposure to fresh air. Preferring the term “sanatorium,” derived from the Latin word “to heal,” to “sanitarium,” derived from the Latin term for health, Trudeau founded his Adirondack Cottage Sanatorium at Saranac, New York, in 1885. This spawned the opening of hundreds of similar institutions throughout the country (Caldwell 1988:70).

In 1899, Fort Bayard remained within the Army under the auspices of the Army Medical Department. The Army’s decision to retain the fort, even after it had outlived its military usefulness, grew from the strong interest that General George M. Sternberg, Surgeon General of the Army, had in pulmonary tuberculosis and its treatment.
Sternberg was also aware of the relatively good health that the Army’s soldiers had enjoyed serving in the higher elevations of the American West. Members of Zebulon Pike’s expedition of 1810 and of Fremont’s exploratory parties of the 1840s had witness their health improve while in the Rocky Mountains.

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Upon assuming command in 1904, Bushnell, who had studied botany for years, immediately began to plant flowers, shrubs, and trees. When President Theodore Roosevelt created the Gila Forest Reserve in 1905, Bushnell ensured that Fort Bayard, which adjoined the Reserve, was part of a government reforestation project. The first year alone the Forest Service gave the hospital 250 seedlings of Himalayan cedar and yellow pine. Bushnell also got approval to fence in land for pasturing dairy cattle and arranged to recultivate long-neglected garden plots. The first year he predicted that the garden would generate “about 1300 dollars worth of produce.” After the quartermaster located an underground water source, Bushnell redoubled his cultivation efforts, planting trees, flowers, and grass to mitigate the wind and dust, and “to beautify the Post.” In later years Bushnell successfully grew beans from ancient cave dwellers (Anasazi beans), and made a less successful effort to grow Giant Sequoia from California.28 By 1910 Fort Bayard had four acres of vegetable gardens, a greenhouse, an orchard of 200 fruit trees, and alfalfa fields and hay fields for the dairy herd of 115 Holsteins, which the Silver City Enterprise proclaimed “one of the finest in the west.” The hospital also raised all of the beef consumed at the hospital (thereby avoiding Daniel Appel’s purchasing problems) and consumed pork at small expense by feeding the pigs the waste food. The hospital laboratory raised its own Belgian hares and guinea pigs for experiments.

Bushnell oversaw years of construction at Fort Bayard. In the wake of Florence Nightingale’s writings, nineteenth-century sanitation practices stressed cleanliness and ventilation, giving rise to pavilion style hospitals, narrow one- or two-story buildings lined with windows to provide patients with ample ventilation. In March 1904, Bushnell sent the Surgeon General plans for an “open court building” in modified pavilion style (Figure 2-1).

Plan for tuberculosis patient ward, as designed by George E. Bushnell, providing fresh air porches for each patient, United States Army Tuberculosis Hospital in New Mexico, .

Plan for tuberculosis patient ward, as designed by George E. Bushnell, providing fresh air porches for each patient, United States Army Tuberculosis Hospital in New Mexico, .

The building consisted of a quadrangle of long, narrow dressing rooms around an open court with porches along both the exterior and interior of the building. The rooms could be used for sleeping in inclement weather and the porches allowed patients to seek sun or shade as they wished. Wide doors enabled the easy movement of beds between the rooms and the porches. “The object of this style of building is to facilitate sleeping out of doors, which is now considered so important in modern sanatoria for the treatment of tuberculosis,” Bushnell explained.

The United States escaped the cauldron of WWI until April 1917. But after years of trying to maintain neutrality, President Woodrow Wilson’s administration mobilized the nation to fight in the most deadly enterprise the world had ever seen. Modern industrialized warfare would kill millions of soldiers, sailors, and civilians and unleash disease and famine across the globe. Typhus flourished in Eastern Europe and a lethal strain of influenza exploded out of the Western Front in 1918, producing one of the worst pandemics in history. Although eclipsed by such fierce epidemics, tuberculosis also fed on the war.

He was ordered to the office of The Surgeon General on June 2, 1917, and placed in charge of the Division of Internal Medicine and on June 13 there appeared S. G. O. Circular No. 20, Examinations for pulmonary tuberculosis in the military service, establishing a standard method of examination of the lungs for tuberculosis. Through his efforts a reexamination of all personnel already in the service was made by tuberculosis examiners and about 24,000 were rejected on that score. He had charge of the location, construction, and administration of all army tuberculosis hospitals, of which eight were built with a capacity of 8,000 patients.

With his relief from service in 1919 he took up his residence on a small farm at Bedford, Mass., where he prepared his Study of the Epidemiology of Tuberculosis (1920) and later Diseases of the Chest (1925) in collaboration with Dr. Joseph H. Pratt of Boston. As chief delegate of the National Tuberculosis Association he attended the first meeting of the International Union Against Tuberculosis in London in 1921. During the winter of 1922-23 he delivered a series of lectures on military medicine at Harvard University. In the summer of 1923 he moved to California and took up his residence at Pasadena.

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In eighteen months the Selective Service registered twenty-five million men for the draft, examined ten million for military service, and enlisted more than four million soldiers, sailors, and Marines. To the dismay of many people, medical screening boards across the nation soon discovered that American men were not as strong and healthy as they had assumed. Of those eligible for military service, 30 percent were physically unfit; a number of them deemed ineligible to serve had tuberculosis. Therefore, in 1917 Surgeon General William Gorgas called George Bushnell to Washington, DC, to establish the Office of Tuberculosis in the Division of Internal Medicine, leaving Bushnell’s protégé, Earl Bruns, in charge of Fort Bayard. Given the Medical Department’s mission to maintain a strong and healthy fighting force, Bushnell’s new job was to minimize the incidence of tuberculosis among active-duty soldiers and avoid the high cost of disability pensions for men who incurred the disease during military service. It was a tall order.

Wartime tuberculosis had already received attention in 1916, when reports circulated that the French army had sent home 86,000 men with the disease, raising the specter that life in the trenches would generate hundreds of thousands of cases. One investigator found that tuberculosis rates in the British army were double those in peacetime, reversing the prewar downward trend. The head of the New York City Public Health Department, Hermann Biggs, declared that “tuberculosis
offers a problem of stupendous magnitude in France.” Subsequent studies revealed that only 20 percent or less of the French soldiers sent home with tuberculosis actually had the disease; others were either misdiagnosed or had had tuberculosis prior to entering the military and therefore had not contracted it in the trenches. The reports nevertheless galvanized public health officials to address the tuberculosis problem. The Rockefeller Foundation, for example, in cooperation with the American Red Cross, established a Commission for the Prevention of Tuberculosis in France to help the French and protect any Americans from contracting tuberculosis “over there.”

Bushnell established four “tuberculosis screens” by (1) examining all volunteers and draftees before enlistment, (2) checking recruits again in the training camps, (3) examining soldiers already in the Army for tuberculosis, and (4) screening military personnel at discharge to ensure they returned to civil life in sound condition. To implement these activities, Bushnell developed a protocol under which physicians could quickly examine men for tuberculosis as part of the larger physical examination process. He standardized the procedures for examinations throughout the Army, and crafted a narrow definition of what constituted a tuberculosis diagnosis to enable the Army to enlist as many young men as possible. Despite these efforts, soldiers developed active cases of tuberculosis throughout the war. Bushnell’s office also created eight more tuberculosis hospitals in the United States and designated three hospitals with the American Expeditionary Forces (AEF) in France to care for soldiers who developed active tuberculosis in the camps and trenches. Short of resources and knowledge, however, the Army Medical Department at times struggled just to provide beds for tuberculosis patients, let alone deliver the individual care Bushnell and his staff had provided at Fort Bayard before the war.

Overburdened medical personnel worked long hours, in often poor conditions. Thousands of tuberculosis patients resented the diagnosis and protested the conditions in which at times they were virtually warehoused. The draft, which brought millions of young men into government control and responsibility, also exposed the Army Medical Department to public scrutiny. Congress launched an investigation in 1919. World War I, which so dramatically changed the world, profoundly altered the Army’s tuberculosis program as well. It also challenged George Bushnell’s expertise. The Army’s tuberculosis expert had founded his policies on assumptions that, although widely held at the time, proved to be inaccurate and costly in lives and treasure. Wartime tuberculosis, therefore, shows the power of disease to overwhelm both knowledge and institutions.

Bushnell and his contemporaries were familiar with the concept of immunity and the power of vaccination, and the Army Medical Department vaccinated soldiers for smallpox and typhoid. Extending this concept of immunity to tuberculosis, medical officers differentiated between primary infection in childhood and secondary infection later in life. Observing that tuberculosis was often fatal for infants and young children, they reasoned that for survivors, an early infection of tuberculosis bacilli immunized a person against the disease later in life.
A “primary infection,” wrote Bushnell, gave a person some immunity, which “while not sufficient in many cases to prevent extension of disease [within the body]…is sufficient to counteract new infections from without.”8 In an article on “The Tuberculous Soldier,” the revered physician William Osler agreed. For years autopsies had uncovered healed tuberculosis lesions in people who had died in accidents or of other diseases. Although it was not known how many men between the ages of eighteen and forty harbored the tubercle bacillus, Osler wrote, “We do know that it is exceptional not to find a few [lesions] in the bodies of men between these ages dead of other diseases.” Thus, he argued, “In a majority of cases the germ enlists with the soldier. A few, very few, catch the disease in infected billets or barracks.”9 Bushnell reasoned if adults developed tuberculosis, “they do it on account of failure of their resistance.”

At one point Bushnell told the chief surgeon of the AEF, “Personally I have no fear of the contagion of tuberculosis between adults and see no reason why patients of this kind should not be treated in the ordinary hospital.” He asserted that the “really cruel persecution of the consumptive…through the fear that he will infect others, is based on what I must characterize as highly exaggerated notions of the danger of such infection.” This, too, was the prevailing view. Boston bacteriologist Edward O. Otis, who served as a medical officer during the war, wrote that “Undue fear of the communicability of pulmonary tuberculosis from one adult to another is unwarranted in the present state of our knowledge.”
Bushnell reasoned that if men infected with tuberculosis could indeed easily spread it to others, there would be much more tuberculosis in the Army than there was. British physician Leslie Murry, reasoned that although the crowded and damp conditions of trench warfare would have unfavorable effects on soldiers’ health, living outside with plenty of fresh air and good food and hygienic practices would improve their resistance to tuberculosis. Public health specialist George Thomas Palmer countered that although reactivation may not be higher in the military than in civil life, the United States had enough men without tuberculosis to bar anyone suspected of it from the military and thereby avoid an “added financial burden to the nation.” The challenge was to keep tuberculosis out of the Army and tuberculars off the disability rolls, but not to exclude so many men as to impair the nation’s ability to amass an army.

Bushnell’s views of tuberculosis immunity, contagion, interaction with military life, and the risk of overdiagnosis shaped the Army Medical Department programs for screening recruits. He knew he could not guarantee that all tuberculosis could be eliminated from the Army, but asserted that, “a sufficiently rigid selection of promising material in itself practically excludes tuberculosis.” In addition to enlisting the strongest men, Bushnell believed that a massive screening program would pay for itself by eliminating those who would later cost the government in medical services and disability benefits.

But the nation at war did not have the time or resources for the meticulous one-hour examination practiced at Fort Bayard, so Bushnell developed a protocol for civilian and military physicians to examine volunteers, draftees, trainees, and soldiers for tuberculosis in a matter of minutes. Circular No. 20 detailed how physicians should examine recruits, and became the single most important Army tuberculosis document during the war. The circular explained that the apices, or the tops of lungs, were the most common location for tuberculosis lesions, and that “the only trustworthy sign of activity in apical tuberculosis is the presence of persistent moist rales.” Circular No. 20 directed that “the presence of tubercle bacilli in the sputum is a cause for rejection,” and that “no examination for tuberculosis is complete without auscultation following a cough.” It recommended that a sputum sample “be coughed up in [the examiner’s] presence,” to ensure that it was actually from the examinee.

The last one-third of the document detailed X-ray examinations, summarizing eight different kinds of conditions that may appear and that would be grounds for rejection, and which conditions would not. By 1915, a Fort Bayard medical officer stated that X-ray technology “has become one of the most valued procedures in the diagnosis of pulmonary tuberculosis.” Medical officers F. E. Diemer and R. D. MacRae at Camp Lewis, Washington, argued in the pages of the JAMA that X-rays should be the primary diagnostic tool, not an “adjunct.” World War I ultimately, however, did encourage X-ray technology by revealing its power to thousands of physicians, stimulating the search for technical advances, and demonstrating the importance of specialization in reading X-rays. By the end of the war, the Army Medical Department had shipped to France hundreds of X-ray machines for use in Army hospitals and at the bedside, and developed various modes of X-ray equipment, including X-ray ambulances

Calculating that it would require 600 examiners for the screening process, the Medical Department turned to training general practitioners from civil life who knew little about tuberculosis. Bushnell’s office established a six-week tuberculosis course to prepare physicians. The first course at the Army Medical School in Washington, DC, was so popular that instructors offered it at several other training camps in the country. General Hospital No. 16, operating in conjunction with Yale Medical School, also offered a course on hospital administration to train medical officers to run tuberculosis hospitals.

Public health officials and the National Tuberculosis Association asked to be informed of any tuberculous individuals being sent to their communities, including the name and address of the “party assuming responsibility for such continued treatment and care.” The journal American Medicine published an article by British tuberculosis specialist Halliday Sutherland, who expressed concern that if men declined treatment and returned home they could spread tuberculosis to their families. He suggested that the U.S. Army retain men diagnosed with tuberculosis so that the government could provide treatment and discipline them if they resisted. Members of Congress opposed simply discharging men with tuberculosis. Representative Carl Hayden of Arizona argued that such men had given up their civilian lives upon induction into the Army, only to discover “that they were afflicted with a dread disease which prevents them from earning a livelihood.” He suggested that “some provision should be made for the care of such men until they are able to provide for themselves.”

While Bushnell’s policies succeeded in suppressing tuberculosis rates in the Army, the narrow definition of a tuberculosis diagnosis explicitly allowed men with healed lesions in their lungs to serve, and the rapid screening system caused some examiners to miss cases of active disease. Bushnell recognized that “a standard, though imperfect, is believed to be an indispensable adjunct in Army tuberculosis work not only to support the examiner but also to secure the necessary uniformity of practice in the matter of discharge for tuberculosis.” Nationwide, local draft boards and training camps rejected more than 88,000 men for tuberculosis, about 2.3 percent of the 3.8 million men examined. Postwar assessments calculated that of the more than two million soldiers who went to France to serve in the AEF, only 8,717 were evacuated with a diagnosis of tuberculosis, an incidence of only 0.4 percent.

In early 1918 a strep infection in the training camps in the United States caused medical officers to send hundreds of trainees to Army hospitals misdiagnosed with tuberculosis, crowding hospitals and generating paperwork and confusion. For a time, therefore, the Office of The Surgeon General ordered that no one should be discharged for tuberculosis from the training camps unless he had bacilli in his sputum—meaning the very severe cases. More than 50 percent of the patients being sent back to the United States from France with a diagnosis of tuberculosis did not actually have the disease. Bushnell viewed such overdiagnoses as “evil,” because it took men out of the AEF and overburdened tuberculosis hospitals and naval transports, which had to segregate suspected tuberculosis cases in isolation rooms or on open decks.

Faced with what he called “leaking” of soldiers from the AEF due to erroneous tuberculosis diagnoses, Bushnell turned to a specialist for assistance, Gerald B. Webb (Figure 4-3), from Colorado Springs.61 An Englishman by birth, Webb had married an American, and when she developed tuberculosis the couple traveled to Colorado Springs, Colorado, for treatment. His wife struggled with the disease for ten years until her death in 1903, and afterward Webb stayed on in Colorado Springs, remarrying and building a medical practice specializing in tuberculosis. In addition to his medical practice, Webb pioneered research into the body’s immune function, searched for a tuberculosis vaccine, and was a founder of the American Association of Immunologists (1913). Still somewhat bored in Colorado Springs, Webb volunteered for the Medical Corps soon after the United States declared war and helped organize and run tuberculosis screening boards at Camp Russell, Wyoming, and Camp Bowie, Texas. Bushnell
appointed him senior tuberculosis consultant for the AEF. After meeting with Bushnell in Washington and attending the Army War Course for senior officers at Columbia University, Webb sailed to France in March 1918.

Gerald B. Webb, World War I, Gerald B. Webb Papers.

Gerald B. Webb, World War I,

Gerald B. Webb, World War I,

Photograph courtesy of Special Collections, Tutt Library, Colorado College, Colorado Springs, Colorado.

Immunity in tuberculosis: Further experiments Unknown Binding – 1914

Webb instituted a screening process similar to that in the United States, distributing Circular No. 20, and preparing an illustrated version for medical officers in the field. He established a policy directing that only patients with sputum positive for tuberculosis should be sent back to the United States. Others would be tagged “tuberculosis observation” and sent to one of three hospitals designated as tuberculosis observation centers. There, specialists—Bushnell’s “good tuberculosis men”—would distinguish tuberculosis signs from other lung problems such as bronchitis and pneumonia, determining that he was free of disease, and send only patients who were indeed positive for tuberculosis back to the homeland.

Webb traveled to field and base hospitals throughout France. He would typically spend three days at a hospital, examining patients, leading conferences, giving lectures, and, according to his biographer, Helen Clapesattle, “preaching his gospel of fresh air and absolute rest.” He recruited a radiologist to teach the proper reading of X-ray plates, and advocated the early detection of tuberculosis, explaining, “Just as the wounded do better if they are got to the surgeons quickly, so the tuberculosis-wounded are more likely to recover if they are spotted and sent to the doctors early.”

In the 1930s, as Webb had concluded in 1919, scientists came to recognize that early tuberculosis infections did not provide protection and that adults could be reinfected with tuberculosis and develop active disease. In the meantime, with his AEF work done, in January 1919 Webb returned to his family and medical practice in Colorado Springs. The National Tuberculosis Association recognized Webb’s war work by electing him president in 1920, and Webb set the Association on a course of tuberculosis research on the immunity question and the standardization of X-ray diagnostics. He did not return to military service, but was a mentor for young physicians Esmond Long and James Waring, who would be leaders in the Army Medical Department’s tuberculosis program during the next war.

May 1941, as the United States stood on the brink of another world war, Benjamin Goldberg, president of the American College of Chest Physicians, recited some stunning figures at the association’s annual meeting in Cleveland, Ohio. He calculated that from 1919 to 1940 the Veterans Administration had admitted 293,761 tuberculosis patients to its hospitals. These patients had received government care and benefits for a total of 1,085,245 patient-years, at a cost of $1,185,914,489.56. Goldberg’s remarks reveal that although tuberculosis rates in the United States were declining 3 to 4 percent annually during the interwar years, the government’s burden to care for tuberculosis patients remained heavy. The Army was only three-quarters the size it was before World War I (131,000 versus 175,000 strength) and experienced no major epidemics, so that suicide and automobile accidents became the leading causes of death in the peacetime Army. Although hospital admissions of active duty personnel for tuberculosis declined during the decade, tuberculosis admissions at Fitzsimons Hospital in Denver remained constant due to a steady stream of patients who were veterans of the war. Tuberculosis, in fact, became a leading cause of disability discharges from the Army and, with nervous and mental disorders, generated the greatest amount of veterans’ benefits between the wars,

The story of tuberculosis in the Army after World War I, then, is one of increasing demand and decreasing resources, a dynamic that left Fitzsimons financially strapped even before the country entered the Great Depression. An examination of Fitzsimons’ postwar environment—the modern hospital and technology, the ever-changing landscape of veterans’ benefits, and new, invasive treatments for tuberculosis—illuminates these stresses.

President Franklin Delano Roosevelt proclaimed a “limited national emergency” on 8 September 1939, a week after Germany invaded Poland. But due to underfunding during the interwar period, one observer wrote that, “to prepare for war the Medical Department had to start almost from scratch.”1 Given the lean years of the 1920s and 1930s and the Army Medical Department’s policy of discharging officers with tuberculosis from duty, Surgeon General James C. Magee had to turn to the civilian sector for a tuberculosis expert. He recruited Esmond R. Long, M.D., Ph.D., director of the Henry Phipps Institute for the Study, Prevention and Treatment of Tuberculosis in Philadelphia. He could not have made a better choice. Long was also professor of pathology at the University of Pennsylvania, director of medical research for the National Tuberculosis Association, and the youngest person to be awarded the Trudeau Medal at age forty-two years (in 1932) for his tuberculosis research.2 He would now become the Army’s point man on the disease and stand at the front lines of the Medical Department’s struggle with tuberculosis beginning before Pearl Harbor to well after V-J (Victory-Japan) Day.

His mission to reduce the effect of tuberculosis on the Army differed from that of Colonel (Col.) George Bushnell in the previous war because disease was less of a threat. In fact, World War II would be the first war in which more American personnel died of battle wounds than of disease. Of 405,399 recorded fatalities, battle deaths outnumbered those from disease and nonbattle injuries more than two to one: 291,557 to 113,842.3 Malaria, sexually transmitted diseases, and respiratory infections did sicken millions of soldiers, sailors, Marines, and airmen, but most survived. Thanks in part to sulfa drugs and, beginning in 1943, penicillin to treat bacterial infections, the Army Medical Department had only 14,904 deaths of 14,998,369 disease admissions worldwide, a 0.1 percent death rate.4 Tuberculosis declined, too, representing only 1 percent of Army hospital admissions for diseases—1.2 per 1,000 cases per year—a rate much lower than the 12 per 1,000 cases per year during World War I. The Medical Department concluded that “tuberculosis was not a major cause of non-effectiveness during the war.”

But Sir Arthur S. McNalty, chief medical officer of the British Ministry of Health (1935–40), called tuberculosis “one of the camp followers of war.” War abetted tuberculosis, he explained, because of the “lowering of bodily resistance and increased physical or mental strain or both.”6 It also found fertile ground in crowded barracks and camps, and ran rampant in the World War II prison camps and Nazi concentration camps. And just one active case of tuberculosis per thousand in the Army meant thousands of tuberculosis sufferers among the 11 million Americans in uniform, each of whom consumed Medical Department resources: the average hospital stay per case during the war was 113 days.7

But if tuberculosis was a camp follower, Esmond Long (Figure 8-1) was a tuberculosis follower.8 He tracked it down, studied it, and tried to prevent its spread at every stage of American involvement in the war. With war looming in 1940, the National Research Council asked Long to chair the Division of Medical Sciences, Subcommittee for Tuberculosis, to advise the government on preventing and controlling tuberculosis in both civilian and military populations during war mobilization. Once the United States entered the war, Long received a commission as a colonel in the Medical Corps and moved his family from Philadelphia to Washington, DC. Working out of the Office of The Surgeon General, Long set up a screening process with the Selective Service to keep tuberculosis out of the Army and then traveled to more than ninety induction camps to ensure adherence to the procedures. He also oversaw the expansion of tuberculosis treatment facilities in the United States, inspected Fitzsimons and other Army tuberculosis hospitals, advised medical officers on treating patients, kept abreast of research developments in the labs, monitored outbreaks of tuberculosis in the theaters of war, and wrote articles for medical and lay periodicals to publicize the Army’s antituberculosis program.

In 1945 Long traveled to the European theater to inspect hospitals caring for tubercular refugees and liberated prisoners of war (POWs). There he saw the horrors of the concentration camps at Buchenwald and Dachau where Army medical personnel cared for thousands of former prisoners sick and dying of typhus, starvation, and tuberculosis. After the war Long organized the tuberculosis control program for the Allied occupation of Germany, and returned annually in the 1950s to assess its progress. He split his time between the Army Medical Department and the Veterans Administration (VA) to supervise the transition of the federal tuberculosis treatment program from the War Department to the VA. He also helped organize and evaluate the antibiotic trials, which ultimately led to an effective cure for tuberculosis. After returning to civilian life Long continued to study tuberculosis in the Army, and he wrote the key tuberculosis chapters for the Army Medical Department’s official history of the war.

With Long as a guide, this chapter shows how war once again served as handmaiden to disease around the globe. This time the Army Medical Department assumed not only national but international responsibilities for the control of tuberculosis in military and civilian populations, among friend and foe. Long and the Army Medical Department did succeed in demoting tuberculosis from the leading cause of disability discharge for American World War I personnel (13.5 percent of discharges), to thirteenth position during the years 1942–45 (1.9 percent of all discharges), behind conditions such as psychoneuroses, ulcers, respiratory diseases, arthritis, and other diseases.9 But this achievement required continued vigilance, an Army-wide surveillance program, and dedicated personnel and resources. The first step was to keep tuberculosis out of the Army.

After war broke out in Europe, Congress passed the National Defense Act of 1940, which established the first peacetime military draft in U.S. history, increasing Army strength eightfold from 210,000 in September 1939 to almost 1.7 million (1,686,403) by December 1941. This resulted in a 75 percent rise in the number of patients in military hospitals, straining the Medical Department, which had only seven general hospitals and 119 station hospitals in 1939.

Esmond R. Long, who directed the Army tuberculosis program during World War II.

Esmond R. Long, who directed the Army tuberculosis program during World War II.

Figure.. Esmond R. Long, who directed the Army tuberculosis program during World War II. Photograph courtesy of the National Library of Medicine, Image #B017302.

“Good Tuberculosis Men”

Soon appropriating freely, pledging “all of the resources of the country“ to meet the crisis, the War Department was constantly readjusting to meet the escalating emergency.

The National Research Council Committee on Medicine, Subcommittee on Tuberculosis, chaired by Long, met for the first time on 24 July 1940 and prioritized its responsibilities: first, develop recommendations on how to screen draft registrants for tuberculosis; second, screen civilians in federal service and wartime industries; third, figure out how to care for people rejected by the draft for the disease; and finally, help civilian and military agencies prepare for tuberculosis in war refugee populations. In its first nine-hour meeting, the subcommittee decided on centralized tuberculosis screening centers at 200 recruiting stations and generated a list of tuberculosis specialists nationwide to evaluate recruits and interpret X-rays at those centers. Subcommittee members stressed the importance of maintaining good records for processing any subsequent benefits claims and, most importantly, called for X-ray screening of all inductees—not just those who looked like they might have tuberculosis.

The War Department leadership initially rejected such comprehensive screening of inductees as expensive and time-consuming. The fact that tuberculosis death rates in the country had fallen two-thirds from 140 per 100,000 people in 1917 to 45 per 100,000 people in 1941, and in the Army from 4.6 per 1,000 in 1922 to 1.4 per 1,000 in 1940, may have led to complacency. But Long, his colleagues, and the national tuberculosis community, mindful of the cost to the nation in sickness, death, and disability benefits in the previous war, persisted. The American College of Chest Surgeons asked in July 1940, “Shall We Spread or Eliminate Tuberculosis in the Army?” and their president, Benjamin Goldberg, reported that the VA had spent almost $1.2 billion on tuberculosis patients through 1940. One medical officer calculated that 31 percent of all veterans who died as a result of World War I service and whose dependents received benefits, had died of tuberculosis. Even the lay press chimed in with a TIME magazine article, “TB Warning,” that stressed the importance of chest X-rays.16 Advocates pointed out that X-ray technology was more available and less expensive than in the previous war, and radiologists were more plentiful and skillful. They were also confident that new technology, such as the development of a lens that allowed the direct and rapid photography of a fluoroscopic image and new 4 x 5 inch films, which made storage and transport easier than that of the 11 x 14 inch films, rendered screening more practical than in 1917–18.

The Army Medical Department agreed with the National Research Council subcommittee. Since 1934 it had required X-rays for all Army personnel assigned overseas, but it had not yet convinced the War Department on universal screening. In June 1941, Brigadier General (Brig. Gen.) Charles Hillman, Chief, Office of The Surgeon General Professional Service Division, told the National Tuberculosis chairman, C. M. Hendricks, that “the desirability of routine X-rays had long been recognized by the Surgeon General’s Office,” but “considerations other than medical entered the picture and the character of induction

Camp Follower: Tuberculosis in World War II 277

Examinations had to be adapted to the limitations of time, place, and available equipment.” When Fitzsimons informed Hillman later that new recruits were arriving at the hospital with tuberculosis, he responded almost plaintively. “I am working with the Adjutant General to devise some method by which every volunteer for enlistment in the Regular Army will have a chest X-ray and serological test before acceptance.” He asked for all available evidence of sick recruits, explaining that “data on Regular Army men of short service now in Fitzsimons with tuberculosis will help me get the thing across.” As the data and advice accumulated, in January 1942, the Adjutant General required that all voluntary applicants and reenlisting men be given chest X-rays. Finally, on 15 March 1942, mobilization regulations made chest X-rays mandatory in all induction physicals.

With universal screening in place, Long, as chief of the tuberculosis branch in the Office of The Surgeon General, oversaw the screening process and faced a task similar to that of George Bushnell in 1917–18, finding that fine line between excluding as much tuberculosis as possible from the Army without rejecting too few or too many men. Conscious of his predecessor’s miscalculations, Long was careful not to criticize Bushnell’s tuberculosis program, at one point noting that World War I medical officers were “not to be reproached for not having knowledge that came into existence only later, any more than the chief of the Army air service in 1917 is to be reproached because more efficient airplanes are available now than then.”

The wartime emergency produced a public health campaign regarding tuberculosis and other disease threats. A War Department pamphlet, What Every Citizen Should Know about Wartime Medicine, presented the issue as one of maintaining troop health and limiting public costs. “The strenuous activity of soldiering is likely to cause extension of an incipient (early) tuberculous invasion of the lungs, or to precipitate the breakdown and reactivation of arrested cases,” it explained. Such illness could result in disability “and the necessity of providing long care of these patients in military hospitals where they must remain isolated from nontuberculous patients.” The Public Health Service also created a tuberculosis office to handle the expected increase in tuberculosis, and, as the National Research Council Subcommittee recommended, gave war industry workers chest examinations.

As military and civilian screening boards found thousands of people with active tuberculosis and sent many of them to tuberculosis sanatoriums and hospitals, they generated what a public health nurse referred to as “potentially the greatest case finding program that workers in tuberculosis control have ever known.” At the same time, however, war mobilization drew civilian medical personnel into the military, reducing staffing in home front institutions. Army medical personnel ultimately numbered more than 688,000, including 48,000 physicians in the Medical Corps, 14,000 dentists in the Dental Corps, and 56,000 nurses in the Army Nurse Corps—a large portion of the nation’s medical professionals.27 To maintain his nursing staff, VA Director Frank Hynes even asked the Army Nurse Corps in May 1942 not to hire VA nurses away from his hospitals.

Army tuberculosis rates during World War II, while lower than during World War I, did show a similar “U” curve with high rates at the beginning of the war as the Selective Service built up the military forces and cases that had eluded screening became active during training or combat (Figure 8-2). Tuberculosis rates fell as radiologists became more proficient at identifying tuberculosis infections, and then another sharp, higher increase in cases at the end of the war as discharge examinations found people who had developed active tuberculosis during their service. Postwar studies also revealed a seemingly paradoxical phenomenon that during the war military personnel serving overseas had lower tuberculosis rates than those serving in the United States, yet higher rates when they returned home.

chart-comparing-incidence-rates-of-tb-in-wwi-wwii

chart-comparing-incidence-rates-of-tb-in-wwi-wwii

Chart comparing the incidence curves of tuberculosis in the Army during World War I and World War II. From Esmond R. Long, “Tuberculosis,” in John Boyd Coates, Robert S. Anderson, and W. Paul Havens, eds., Internal Medicine in World War II, Medical Department, U.S. Army in World War II, vol. 2, Infectious Diseases (Washington, DC: Office of The Surgeon General, Department of the Army, 1961), chart 17, p. 335. Available at http://history.amedd.army.mil/booksdocs/wwii/infectiousdisvolii/chapter11chart17.pdf.

The Medical Department of the United States Army in the World War. Communicable and Other Diseases. Washington: U. S. Government Printing Office, 1928, vol. IX, pp. 171-202.
Letter, The Adjutant General, to Commanding Generals of all Corps Areas and Departments, 25 Oct. 1940, subject: Chest X-rays on Induction Examinations.
M. R. No. 1-9, Standards of Physical Examination During Mobilization, 31 Aug. 1940 and 15 Mar. 1942
Long, E. R.: Exclusion of Tuberculosis. Physical Standards for Induction and Appointment.[Official record.]

Long, E. R., and Stearns, W. II.: Physical Examination at Induction; Standards With Respect to Tuberculosis Induction and Their Application as Illustrated by a Review of 53,400 X-ray Films of Men in the Army of the United States. Radiology 41: 144-150, August 1943.
Long, Esmond R., and Jablon, Seymour: Tuberculosis in the Army of the United States in World War II. An Epidemiological Study with an Evaluation of X-ray Screening. Washington: U. S. Government Printing Office, 1955.

It is estimated that, before roentgen examination became mandatory (MR No. 1-9, 15 March 1942), one. million men had been accepted without this form of examination. Where roentgen examination was practiced, it resulted in a rejection rate of about 1 percent for tuberculosis. Applying this figure, it can be estimated that some 10,000 men were accepted who would have been rejected if they had been subjected to chest roentgen-ray study. Various studies have shown that approximately one-half of these would have been cases of active

http://history.amedd.army.mil/booksdocs/wwii/PM4/CH14.Tuberculosis.htm

Troops who developed tuberculosis were not discovered until their separation examinations, conducted when they were once again in the United States.

In the end, the screening process rejected 171,300 men for tuberculosis as the primary cause (thousands more had tuberculosis in addition to the disqualifying condition), and Long calculated that this saved the government millions of dollars in hospitalization costs. After the war, however, Long identified two factors that allowed tuberculous men into the Army: the failure to screen all inductees until March 1942, and the 4 x 5 inch stereoscopic (fluorographic) films, which were used in the interest of speed but which Long believed caused examiners to miss about 10 percent of minimal tuberculosis lesions in recruits. To better understand the latter problem he had two radiologists read the same X-rays and found substantial disagreement between their findings. Long therefore concluded that “if the induction films had each been read by two different radiologists, undoubtedly many more of the men who had tuberculosis at entry could have been excluded from service.” The Army ultimately discharged 15,387 enlisted men for tuberculosis during the war, which earned it thirteenth position as a cause of disability discharge.

American military forces fought in nine theaters of war—five in the Pacific and Asia, the other four in North Africa, the Mediterranean, Europe, and the Middle East. The Allies gave priority to defeating Germany and Italy in Europe beginning with operations in North Africa and the Mediterranean. After fighting in Tunisia in 1942–43, the Allies invaded Sicily on 10 July 1943, and moved up the Italian peninsula. By April 1944—in preparation for the D-Day invasion on 6 June 1944—the United States had more than 3 million soldiers in Europe, supported by 258,000 medical personnel managing a total of 318 hospitals with 252,050 beds. The war against Japan got off to a slower start as U.S. military forces developed the means to execute an island war across vast expanses of ocean. After fighting began in the Southwest Pacific, military forces grew from 62,500 troops in March 1942 to 670,000 in the summer of 1944 with 60,140 medical personnel. Even though military personnel developed tuberculosis in all of the nine theaters, the numbers were not high and tuberculosis was not a major military problem. In the Southwest Pacific theater, for example, only sixty-four of more than 40,000 hospital admissions were for the disease.

Tuberculosis was of the greatest consequence in the North Africa and Mediterranean theaters, in part due to poor screening early in the war, but also because, according to historian Charles Wiltse, it was the theater “in which the lessons of ground combat were learned by the Medical Department as much as by the line troops.” In general, medical personnel learned the importance of treating battle casualties as promptly as possible and keeping hospitals and clearing stations mobile and far forward to shorten evacuation and turnaround times. With regard to tuberculosis, the Medical Department had to relearn the World War I lesson of the importance of having skilled practitioners—or “good tuberculosis men”—in theater. They also ascertained which treatments were appropriate close to the battle lines and which were not, and when and how best to evacuate tubercular patients to the United States.

When soldiers with tuberculosis began to appear at Army medical stations in North Africa in late 1942, Major General (Maj. Gen.) Paul R. Hawley, chief of medical services for the European theater of operations, called for a tuberculosis specialist. On Long’s recommendation, Hawley appointed Col. Theodore Badger (Figure 8-3) as a senior consultant in tuberculosis on 2 January 1943. A professor of medicine at the Harvard School of Medicine, Badger had served in the Navy during World War I, and then attended Yale and Harvard where he earned his medical degree. Chief of medical service of the 5th General Hospital (GH), organized out of Harvard, Badger would play a role similar to that played by Gerald Webb during World War I—medical specialist, teacher, and troubleshooter.

Assessing the tuberculosis situation in the Mediterranean theater, Badger identified five hazards: (1) the development of active disease in American troops who had not been X-rayed upon induction; (2) association with British troops and civilians who had not been screened for tuberculosis; (3) drinking of nonpasteurized and possibly infected milk that could transmit tuberculosis; (4) battlefield conditions that could activate soldiers’ latent infections; and (5) the undetermined effects of other respiratory infections.41 Badger soon got the Army to use pasteurized milk and to establish X-ray centers with the proper equipment and trained staff, but he was not able to examine the thousands of American soldiers in the war zone. To gauge the extent of the tuberculosis problem he therefore arranged for a mobile X-ray unit to conduct spot surveys of troops in the field. Three examinations of some 3,000 troops each found only about 1 percent with signs of tuberculosis. To avoid losing manpower, Badger reported in mid-1943 that “up to the present time no individual has been removed from duty because of X-ray findings, and follow-up study has, so far, not indicated the necessity for it.” Badger planned to recheck those with suspicious films every few months to see if the signs had advanced. Badger recommended that patients with pleural effusion, the accumulation of fluid between the layers of the membranes that line the lungs and chest cavity that often indicates tuberculosis, be evacuated back to the United States. He also ended the practice of transporting some tuberculosis patients sitting up

. As the first true air war, World War II saw the introduction of air evacuation when Army aeromedical squadrons deployed in early 1943. After successful trials in the Pacific and North Africa, air evacuation increased so that during the Battle of the Bulge (1944–45), some patients arrived in U.S. hospitals within three days of being wounded. Some medical officers were concerned about the effects of transporting tuberculosis patients by air where they would be exposed to high speeds, jolting, and reduced air pressure. Tuberculosis specialists in New Mexico and Colorado therefore studied 143 white, male military patients, twenty-two-years old to twenty-eight-years old, with active tuberculosis flown to Army hospitals in nonpressurized air ambulances for any signs of trouble. Fearing the worst, they instead found that “severe discomfort, pulmonary hemorrhage, and spontaneous pneumothorax did not occur in the series either during or following the flight,” and concluded that air transport up to 10,000 feet was safe and preferable to time-consuming travel by water. By the end of the war the consensus was that rapid air evacuation to the United States also reduced the need to give a tuberculosis patient a pneumothorax in the field.

From the roof of Fitzsimons’ new building in April 1943, Rocky Mountain News reporter John Stephenson could see the Rocky Mountain Arsenal, the Denver Ordnance Plant, and Lowry Field, “places where the Army studies how to kill people.” But, he wrote, “The Army is merciful. It lets the right-hand of justice know what the left hand of mercy is doing at Fitzsimons General Hospital.” The largest Army hospital in the world, Fitzsimons had 322 buildings on 600 acres, paved streets with traffic lights, a post office, barbershop, pharmacy school, dental school, print shop, bakery, fire department, and chapel. It was, wrote Stephenson, “a city of 10,000.”61 No longer a liability, Fitzsimons was the pride of the Army Medical Department. One Army inspector reported that “it is apparent that no expense has been spared in this extraordinary building or in the general equipment and maintenance of the whole hospital plant.”62 As Congressman Lawrence Lewis had hoped, Fitzsimons’ mission now extended beyond caring for tuberculosis patients to meeting the general medical and surgical needs of the wider military community in the Denver region.

During the war the hospital maintained about 3,500 beds, reaching its highest daily patient population after the war—3,719 on 3 February 1946. The annual occupancy rate, calculated in patient days, increased from 603,683 in 1942 to a high of 1,097,760 for 1945, about 85 percent capacity.

With the reduction of tuberculosis in the Army over the years, the percentage of tuberculosis patients among all those at Fitzsimons had declined from 80 percent to 90 percent in the 1920s to 40 percent to 50 percent in the late 1930s. As the Army grew it now rose again. During the war Fitzsimons admitted more than 8,100 patients with tuberculosis. In fact, in 1943, only eighteen patients had battle injuries; the rest were in the hospital for illness and noncombat injuries. Unlike during the previous war, however, this Medical Department had a network of more than fifty veterans’ hospitals to which it could transfer patients too disabled by tuberculosis or other disease or injury to return to duty. Now, instead of allowing patients to stay in the service and receive the benefit of hospitalization with the hopes that they would recover and return to duty, the Medical Department discharged patients to VA hospitals as soon as they were determined to be unfit for military service, thereby reserving capacity for active-duty personnel. Maj. D. P. Greenlee had returned from a training course in penicillin therapy at Bushnell General Hospital in Utah to supervise the administration of the new drug on a variety of infections. He soon reported a cure rate of 93 percent. There were fewer victories in tuberculosis treatment.

During the war about one-quarter of all tuberculosis patients were treated with pneumothorax. During the war Fitzsimons surgeon Col. John B. Grow and other surgeons tried lung resection to treat tuberculosis, with few patient deaths. In 1946, however, when Grow’s staff contacted thirty patients who had had such surgery, they found that half of them were doing well, but three others had died, seven were seriously ill, and the rest were still under treatment. “It was felt that pulmonary resection in the presence of positive sputum was extremely hazardous and the indications were consequently narrowed down.”

Outside the operating rooms, the “City of 10,000” had a rich social life with people arriving at the post from all corners of the country. With Congressman Lewis’s acquisition of the School for Medical Technicians, Fitzsimons assumed the role of medical trainer, offering six- to twelve-week courses in technical training for dental, laboratory, X-ray, surgical, clinical, and pharmacy assistants. By 1946 the School had graduated more than 28,000 such technicians to serve around the world. The Women’s Army Corps arrived at Fitzsimons in February 1944 when 165 women attended the medical technicians school as part of the first coeducational class.74 Members of the Women’s Army Corps, rehabilitation aides, Education Department staff, dietitians, as well as nurses increased the female presence at Fitzsimons, as did activities of welfare organizations such as the Gold Star Mothers, the Red Cross, and the Junior League. Fitzsimons’ patients and staff also enjoyed visits from celebrities, including Jack Benny, Miss America, Gary Cooper, Dorothy Lamour, and other entertainers such as the big band leader Fred Waring and his Pennsylvanians, the Denver Symphony Orchestra, and an African American Methodist Church children’s choir from Denver. Like communities across the country, the hospital participated in war bond campaigns and had a huge war garden that produced thousands of ears of sweet corn and bushels of other vegetables.

Despite national mobilization and generous congressional funding, the Army could not escape the strain on its hospitals. By July 1944, Fitzsimons had reached capacity so the Medical Department designated two more hospitals as specialty centers for tuberculosis. Earl Bruns’ widow Caroline, who lived in Denver at the time, was no doubt pleased when the department named Bruns General Hospital in Santa Fe, New Mexico, in honor of her husband. Bruns along with Moore General Hospital in Swannanoa, North Carolina, cared for enlisted patients with minimal or suspected tuberculosis.

As Allied troops liberated France in 1944 and crossed into Germany they encountered thousands of refugees or “displaced persons”—escaped prisoners from Nazi concentration camps, exhausted and terrified Jews, slave laborers, political prisoners, Allied POWs, and other victims. The Nazi camps that held these people served as incubators for diseases such as tuberculosis and typhus, and the frightened, sick, and starved refugees inundated Army hospitals in late 1944 and early 1945. Theodore Badger reported one of the first waves that arrived on 18 December 1944 when 304 men, most of them Russians, came to the 50th GH in Commercy, France. They had been in the Nazi labor camps for the mines and heavy industries, where thousands died and survivors were malnourished and sick. All of the 304 had tuberculosis, 90 percent with moderate or advanced disease. Four were dead on arrival, eight more died in the first week, and one-third of the patients would die by May.96 Alarmed, Gen. Hawley, Chief Surgeon of the European Theater of Operations, ordered that all displaced civilians and recovered military personnel be examined for signs of tuberculosis “to establish the gravity of the situation.” The situation was dire. At one time the 46th GH had more than 1,000 tuberculosis patients, all recovered Allied POWs, causing Esmond Long to remark that the hospital “had the largest number of tuberculosis patients of any Army hospital in the world.”

The 46th GH from Portland, Oregon, which had cared for tuberculosis patients in the Mediterranean theater, also stood on the front lines of the tuberculosis problem in Europe. Serving at Besancon, France, the hospital would receive the Meritorious Service Unit Plaque and Col. J. G. Strohm, the commanding officer, the Bronze Star Medal for service during the liberation of France. During the spring of 1945, the 46th GH admitted 2,472 Russians, forty-one Poles, and 128 Yugoslav POWs and former slave laborers freed by American forces. The influx began on 12 March and within four days the 46th GH had admitted 1,200 such patients.

“The hospital staff was agast [sic] at the terrible physical condition of these people,” reported the hospital commander.99 When Badger visited the 46th GH in March 1945 he said the patients “constitute one of the most seriously affected groups with tuberculosis and malnutrition that I have ever seen,” explaining that most of them suffered “acute fulminating, rapidly fatal disease, mixed with chronic, slowly progressive, fibrotic tuberculosis. ”Medical personnel (Figure 8-4) cared for these patients as best they could, comforting many of them as they died. They began the rest treatment with some men but, as Badger reported, convincing Allied POWs to submit to absolute bed rest after months of confinement was “practically impossible.” Badger was able to report that after a month “those men who did not die of acute tuberculosis showed marked improvement.”

46th General Hospital nurses who cared for former prisoners of war.

46th General Hospital nurses who cared for former prisoners of war.

Figure 8-4. 46th General Hospital nurses who cared for former prisoners of war. Photograph courtesy of Oregon Health Sciences University, Historical Collections and Archives, Portland, Oregon.

26th Gen Hospital WWII, North Africa

26th Gen Hospital WWII, North Africa

In late 1944 Hawley requested 100,000 additional hospital beds for the displaced persons and POWs he expected to encounter after the German surrender, but Gen. George Marshall and Secretary of War Henry L. Stimson denied the request, believing they could not spare resources of that magnitude. The European Theater, they decided, must use German medical personnel and hospitals to care for the prisoners. Only after the war did American hospital units transfer their equipment and supplies to German civilians and Allies for their use.

The liberation of Europe also freed American POWs, who, not surprisingly, had higher rates of tuberculosis than other American military personnel. Captured British medical officer Capt. A. L. Cochrane cared for some of them in the prison where he was confined and noted sardonically that imprisonment was “an excellent place to study tuberculosis; [and] to learn the vast importance of food in human health and happiness.” German prison guards gave POWs only 1,000 to 1,500 calories per day, so Red Cross food parcels, which provided an additional 1,500 daily calories per person, were critical to preventing malnutrition and physical breakdown. Cochrane observed that the American and British POWs received the most parcels and had the lowest tuberculosis rates in the camp, while the Russians received nothing at all and had the highest rates. During the eighteen months that French POWs received the Red Cross parcels, he noted, just two men of 1,200 developed tuberculosis but when parcels for the French ceased to arrive in 1945, their tuberculosis rate rose to equal that of the Russians. The situation, he concluded, showed the “vast importance of nutrition in the incidence of tuberculosis.” Not all Americans got their parcels, though. William H. Balzer, with an American artillery unit, was captured in February 1943, and remembered how German guards stole the Americans’ packages.
Balzer survived imprisonment but never recovered from the ordeal. Severely disabled (70 percent), he died in 1960 on his forty-sixth birthday.

Exact tuberculosis rates among American POWs are not known because the rush of events surrounding the liberation of prisoners from German and Japanese control prevented a systematic X-ray survey. Rates did appear to be higher, though, for prisoners of the Japanese than for prisoners of the Germans. Long reported that about 0.6 percent of recovered troops from European POW camps had tuberculosis, whereas data from the Pacific theater suggested that 1 percent of recovered prisoners had tuberculosis. Moreover, an analysis of the chest X-rays done at West Coast debarkation hospitals revealed that 101 (or 2.7 percent) of 3,742 former POWs of the Japanese showed evidence of active tuberculosis. John R. Bumgarner was a tuberculosis ward officer at Sternberg General Hospital in Manila, the Philippines, before the war. A POW for forty-two months after the Japanese invasion, he described his experience in Parade of the Dead. Bumgarner did what he could to care for many of the 13,000 prisoners in the camp, but knew that “my patients were poorly diagnosed and poorly treated.” The narrow cots were so close together, he wrote, “the crowding and the breathing of air loaded with this bacilliary miasma from coughing ensured that those mistakenly segregated would be infected.”

Bumgarner was able to stay relatively healthy throughout his imprisonment. His luck ended, however, because “on my way home across the Pacific I had the first symptoms of tuberculosis.” Severe chest pain and subsequent X-rays at Letterman Hospital in San Francisco revealed active disease. “I had gone through more than four years of hell—now this!” Discharged on disability for tuberculosis in September 1946 he began to work at the Medical College of Virginia but soon had a lung hemorrhage. This time it took eight years of rest, with surgery and new antibiotic treatment for him to recover. By 1956, however, Bumgarner had married his sweetheart, Evelyn, and begun a medical career in cardiology that lasted for thirty years.

Tuberculosis continued to take its toll on POWs for years after the war. The VA followed POWs as a special group because, explained Long, of “the hardships that many of these men endured, and the notorious tendency for tuberculosis to make its appearance years after the acquisition of infection.” A follow-up study published in 1954 reported that for American POWs during the six years after liberation tuberculosis was the second highest cause of death, after accidents.

If the challenges Army medical personnel faced in caring for sick and starving POWs and refugees were unprecedented, the scale of disease and suffering they encountered in the Nazi concentration camps was almost unimaginable. Allied troops had heard about secret and deadly camps but were not prepared for what they found. As the Allies converged on Berlin from the East and the West, the Nazis evacuated thousands of prisoners—most of them Jews seized from across Europe, as well as POWs—to interior camps to hide their crimes and prevent the inmates from falling into Allied hands. These evacuations became death marches as SS (abbreviation of Schutzstaffel, which stood for “defense squadron”) guards beat and murdered people, and failed to feed them for days on end. Survivors were crowded into camps such as Buchenwald and Dachau making them even more chaotic and deadly. Americans, therefore, liberated camps that were riven with disease, especially typhus, tuberculosis, and malnutrition.

The Allies liberated Buchenwald on 11 April 1945. The following day the world learned that Franklin Roosevelt had died. Americans then liberated Dachau on 29 April, the day Italian partisans executed Mussolini in Milan, and the next day Hitler killed himself in his bunker. Dachau (Figure 8-5) had been the first of hundreds of concentration camps in the German Reich to which the Nazis sent political enemies, the disabled, people accused of socially deviant behavior, and, increasingly after the Kristallnacht pogroms of 1938, Jewish men, women, and children. In January1945 Dachau held 67,000 prisoners, but with troops of the Seventh U.S. Army approaching the SS began evacuating and killing prisoners. Capt. Marcus J. Smith, a medical officer in his thirties, arrived at Dachau on 30 April 1945, the day after liberation, part of a small team trained to treat persons displaced by the war. Horror greeted him outside the camp in a train of forty boxcars loaded with more than two thousand corpses. Smith called the frost that had formed on the bodies in the intense cold, “Nature’s shroud.” Inside Dachau he encountered more grotesque piles of naked, skeletal bodies of prisoners and scattered, mutilated bodies of German guards.

Dachau survivors gather by the moat to greet American liberators, 29 April 1945

Dachau survivors gather by the moat to greet American liberators, 29 April 1945

Figure 8-5. Dachau survivors gather by the moat to greet American liberators, 29 April 1945. Photograph courtesy of the United States Holocaust Memorial Museum, Washington, DC.
Smith found more than 30,000 prisoners, mostly Jews of forty nationalities, and all men except for about 300 women the SS had kept in a brothel. They were in desperate condition. Typhus and dysentery raged, at least half of the prisoners were starving, and hundreds had advanced tuberculosis. “The well, the sick, the dying, and the dead lie next to each other in these poorly ventilated, unheated, dark, stinking buildings,” Smith told his wife. The men were “malnourished and emaciated, their diseases in all stages of development: early, late, and terminal.” He wondered, “What am I going to write in my notebook?” and then started a list of needed supplies: clothes, shoes, socks, towels, bedding, beds, soap, toilet paper, more latrines, and new quarters. He almost despaired. “What are we going to do with the starving patients? How will we care for them without sterile bandages, gloves, bedpans, urinals, thermometers, and all the basic material? How do we manage without an organization? No interns, no nursing staff, no ambulances, no bathtubs, no laboratories, no charts, and no orderlies, no administrator, and no doctors.… I feel helpless and empty. I cannot think of anything like this in modern medical history.”

American efforts did prevent a deadly typhus epidemic from sweeping postwar Europe and helped contain tuberculosis rates in Germany, but the Nazis had created a human catastrophe so immense that even the most dedicated efforts would at times fall short.

Faced with horror on such a scale, Smith and other Army Medical Department personnel assigned to the concentration camps threw themselves into the work of cleansing, comforting, treating, and nurturing their patients. American commanders called in at least six Army evacuation hospitals (EH) to care for the sick and dying in the liberated camps. EH No. 116 and EH No. 127 began arriving at Dachau on 2 May with some forty medical officers, forty nurses, and 220 enlisted men. Consulting with Smith and his team, the units set up in the former SS guard barracks. They tore out partitions to create larger wards, scrubbed the walls and floors with Cresol solution, sprayed them with dichloro-diphenyl-trichloroethane (DDT), and then set up cots to create two hospitals of 1,200 beds each. Medical staff also discovered physician-prisoners who had cared for the sick and injured as well as they could, and could now advise and assist, and in some cases translate for the medical staff. In two days the hospitals were ready to admit patients by triage, segregating them by disease and prognosis. Laurence Ball, the EH No. 116 commander, noted that more than 900 patients had “two or more diseases, such as malnutrition, typhus, diarrhea, and tuberculosis.” Staff bathed and deloused them, gave them clean pajamas, and put them to bed.

Death by overeating was but one of the dangers that the prisoners faced. During May 1945, American hospitals at Dachau had more than 4,000 typhus patients and lost 2,226 to typhus and other diseases. Typhus, a rickettsial disease transmitted by body lice, had a mortality rate as high as 40 percent. With no medical cure, treatment consisted of supportive care—keeping patients clean and nourished—to mitigate effects of prolonged fever, such as the breakdown of tissue into gangrene. The Americans knew that typhus had taken three million lives in Eastern Europe after World War I, but now they had a means of prevention and better weapons—a typhus vaccine and DDT. On 2 May, the day the evacuation hospitals arrived, the commander of the Seventh Army imposed quarantines for typhus and tuberculosis, and summoned the U.S. Typhus Commission, which had controlled a typhus outbreak in Naples, Italy. A typhus team arrived the next day and began to immunize American personnel and dust them with DDT. On 7 May staff began to vaccinate inmates but kept typhus patients isolated for at least twenty-one days from the onset of illness to prevent transmission to others. This meant that the Americans did not immediately enter the inner camp barracks—the worst, most typhus-infested part of the camp—nor did they quickly relieve crowding there for fear of spreading typhus-bearing lice. It took over a week for personnel to prepare more spacious and clean quarters.

Smith wrote his lists, reported to his wife, and kept track of the daily death toll, finding comfort as the number of people who died daily fell from 200 during the first week to twenty by the end of May. Another medical officer performed autopsies. He chose ten of the dead bodies, five from the death train and five from the camp yard, to see what had caused their deaths. All had typhus and extreme malnutrition, eight had advanced tuberculosis, and some bodies had signs of fractures and head injuries.

Survivors in Dachau, 1 May 1945

Survivors in Dachau, 1 May 1945

By the end of May, conditions at Dachau had improved. Typhus was abating and American officials began to release groups of inmates by nationality. Beyond Dachau, the U.S. Typhus Commission tracked down new cases of typhus in civilian and military populations, deloused one million people, sprayed fifteen tons of DDT, and created a cordon sanitaire on the Rhine requiring all who crossed from Germany to be vaccinated and dusted to prevent the spread of disease. Thus the Army averted a broader typhus epidemic.138 The tuberculosis situation was more complicated and presented the Americans with a conundrum. What to do with thousands of people suffering from a long-term, infectious, and deadly disease?

As with the American POWs, tuberculosis continued to follow Dachau survivors into their new lives. Thousands of Jewish survivors emigrated to what would become the state of Israel. Fifteen years after liberation, the Israeli Minister of Health reported that although concentration camp survivors comprised only 25 percent of the population, they accounted for 65 percent of the tuberculosis cases in the country. Tuberculosis continued to thrive in Europe as well.

Historian Albert Cowdrey has credited the American actions with preventing a number of postwar scourges: “No one can prove that a great typhus epidemic, mass deaths of prisoners of war, or widespread outbreaks of disease among the German population would have taken place without the efforts of Army doctors of the field forces and the military government.” But, he continued, “conditions were ripe for such tragedies to occur, and Army medics brought both professional knowledge and military discipline to forestalling what might have been the last calamities of the war in Europe.” Thus, as usual, in public health the good news is no news at all.

Thousands of men survived the Vietnam War because of the quality of their hospital care. US hospitals in Vietnam were the best that could be deployed, incorporating several improvements from previous field hospitals. Army doctors were better trained, and they had good facilities at the semi-permanent base camps. As a result, more advanced surgical procedures were possible: more laparotomies, thoracotomies, vascular repairs (including even aortic and carotid repairs), advanced neurosurgery for head wounds, and other medical procedures. Blood transfusions were performed, with massive quantities of blood available for seriously wounded patients; some patients received as many as 50 units of blood. Advances in equipment resulted in the development of intensive care units with mechanical ventilators. There were far more medications available for particular diseases than in earlier conflicts.

With about 30 physicians assigned, the 12th could keep four or five operating tables going all day, and two or three all night. A common practice was delayed primary closure for wounds with a high likelihood of infection. Instead of stitching the wound closed immediately, dirt and contaminants were flushed out, bleeding was controlled, dead flesh was removed (debrided), the wound was packed with sterile gauze, and antibiotics were administered. For a few days the patient healed, while nurses changed the bandages and made sure the wound did
not get worse. Then doctors removed any remaining contaminants or dead flesh and stitched up the wound. This procedure reduced the incidence of infection compared to immediate wound closure at a risk of a larger scar.

In any given year in Vietnam, about one soldier in three was hospitalized for disease. The main causes for hospitalization were malaria, psychiatric problems, and ordinary fevers. Although many men fell sick, competent care was available and most recovered quickly and returned to duty.

The war spurred advances in surgery and medical trauma research. New surgical techniques allowed limbs that previously would have been amputated to remain functional. Nurse anesthetist Rosemary Sue Smith recalled the development of new blood-handling procedures:

We started separating blood into its components, because we were getting a lot of aggregates that were causing a lot of disseminated intravascular coagulopathy in patients, and causing a lot of blood clots, and pulmonary thrombosis, and a lot of ARDS, Adult Respiratory Distress Syndrome, which started in Da Nang and was called Da Nang Lung initially. It has developed into today being called Adult Respiratory Distress Syndrome, and they did a lot of research on this, and they were having us separate our blood into its components, into fresh frozen plasma and into platelets, and then we started doing blood tests to see which the patients would need. If their platelets were low, or if their blood clotting factors were low, we would just give them the particular products. We actually started breaking these products down and administering them in the Vietnam War, and it’s carried over into civilian life now. They’re used today in acute trauma to prevent disseminated intravascular coagulopathy and prevent Adult Respiratory Distress Syndrome on massive traumas that have to be naturally resuscitated with blood and blood products.

In the 1960s, intensive care was still quite new and the 12th had only one (later two) intensive care wards fully equipped and staffed. A key piece of equipment was the ventilator, then called “respirator.” Ventilators worked on pure oxygen until 1969, when research revealed physiological problems from prolonged breathing of pure oxygen. Early ventilators required considerable maintenance; valves needed frequent cleaning or the machines broke down.

Antibiotics were important because of the wide variety of bacteria and large number of penetrating wounds; in the face of a possible systemic infection (the development of sepsis), antibiotics were delivered through an IV. Nurse Rosie Parmeter recalled having to prepare antibiotics to be delivered through an IV several times a day for each patient, a necessary but time-consuming task.

About two-thirds of patients cared for by the 12th were US military; the other third were mainly Vietnamese but also included nonmilitary Americans and Free World Military Assistance Forces personnel. Staff regularly dealt with the Vietnamese, both military and civilian, enemy and friendly. There were wards set aside for enemy prisoners (who were stabilized, then transferred to hospitals at POW camps) and civilians. Wounded South Vietnamese Army soldiers were also stabilized and transferred to hospitals run by the Army of the Republic of Vietnam (ARVN). Civilian patients often stayed longer because the war swamped the available hospitals for Vietnamese civilians.

Through the years of the Vietnam War, US forces sustained 313,616 wounded in action; at peak strength, there were 26 American hospitals. The 12th Evacuation Hospital was at Cu Chi for 4 years and treated just over 37,000 patients. Records for the 12th are incomplete, but the average died-of-wounds rate in Vietnam was about 2.8% of patients who reached a hospital alive. Applied to the 12th, that rate amounted to about 1,036 patients, including prisoners and Vietnamese as well as Americans. But over 36,000 people survived and could return home because of the treatment they received at the 12th Evac.

Sources:

Fort Bayard,  by David Kammer, Establishment of Fort Bayard Army Post
http://newmexicohistory.org/places/fort-bayard
George Ensign Bushnell, Colonel, Medical Corps, U. S. Army
THE ARMY MEDICAL BULLETIN, NUMBER 50 (OCTOBER 1939)
http://history.amedd.army.mil/biographies/bushnell
Chapter One, The Early Years: Fort Bayard, New Mexico
http://www.cs.amedd.army.mil/borden/FileDownloadpublic.aspx?docid=332041d7-dbd2-4edf-823f-29a66c0b65ef
Dachau concentration camp (Wikipedia)
http://en.wikipedia.org/wiki/Dachau_concentration_camp
Office of Medical History – United States Army
Esmond R. Long, M. D., TUBERCULOSIS IN WORLD WAR I
Chapter 14 – Tuberculosis
http://history.amedd.army.mil/booksdocs/wwii/PM4/CH14.Tuberculosis.htm

Chapter Four, Tuberculosis in World War I
Chapter Five, “A Gigantic Task”: Treating and Paying for Tuberculosis in the Interwar Period
Chapter Six, “Good Tuberculosis Women”: Tuberculosis Nursing during the Interwar Period
Chapter Seven, Surviving the Great Depression: Fitzsimons and the New Deal
Chapter Eight, Camp Follower: Tuberculosis in World War II
http://www.cs.amedd.army.mil/FileDownload aspx?
Good Tuberculosis Men”: The Army Medical Department’s Struggle with Tuberculosis Carol R. Byerly
http://www.cs.amedd.army.mil/borden/FileDownloadpublic.aspx?docid=986faf8a-b833-46a8-a251-00f72c91da2f

The Global Distribution of Yellow Fever and Dengue
D.J. Rogers1, A.J. Wilson1, S.I. Hay1,2, and A.J. Graham1
Adv Parasitol. 2006 ; 62: 181–220. http://dx.doi.org:/10.1016/S0065-308X(05)62006-4.

http://www.historyofvaccines.org/content/timelines/yellow-fever

History of yellow fever
http://en.wikipedia.org/wiki/History_of_yellow_fever

Additional Reading:

Open Wound: The Tragic Obsession of William Beaumont.
Jason Karlawish

The Great Influenzs. John M. Barry.
Penguin. 2004.
Univ Mich Press. 2011.

Flu. The story of the great influenza pandemic of 1918 and
the search for the virus that caused it.
Gina Kolata.
Touchstone. 1999

Pestilence. A Medieval Tale of Plague.
Jeani Rector
The HorrorZime. 2012

Knife Man: The extraordinary life of John Hunter, Father of Modern Surgery
Wendy Moore.
Broadway Books. 2005

Hospital.
Julie Salamon.
Penguin Press. 2008.

Overdosed America.

John Abramson.
Harper. 2004.

Sick.
Jonathen Cohn.
Harper Collins. 2007.
.

Read Full Post »

Summary and Perspectives: Impairments in Pathological States: Endocrine Disorders, Stress Hypermetabolism and Cancer

Summary and Perspectives: Impairments in Pathological States: Endocrine Disorders, Stress Hypermetabolism and Cancer

Author and Curator: Larry H. Bernstein, MD, FCAP

Article ID #160: Summary and Perspectives: Impairments in Pathological States: Endocrine Disorders, Stress Hypermetabolism and Cancer. Published on 11/9/2014

WordCloud Image Produced by Adam Tubman

This summary is the last of a series on the impact of transcriptomics, proteomics, and metabolomics on disease investigation, and the sorting and integration of genomic signatures and metabolic signatures to explain phenotypic relationships in variability and individuality of response to disease expression and how this leads to  pharmaceutical discovery and personalized medicine.  We have unquestionably better tools at our disposal than has ever existed in the history of mankind, and an enormous knowledge-base that has to be accessed.  I shall conclude here these discussions with the powerful contribution to and current knowledge pertaining to biochemistry, metabolism, protein-interactions, signaling, and the application of the -OMICS to diseases and drug discovery at this time.

The Ever-Transcendent Cell

Deriving physiologic first principles By John S. Torday | The Scientist Nov 1, 2014
http://www.the-scientist.com/?articles.view/articleNo/41282/title/The-Ever-Transcendent-Cell/

Both the developmental and phylogenetic histories of an organism describe the evolution of physiology—the complex of metabolic pathways that govern the function of an organism as a whole. The necessity of establishing and maintaining homeostatic mechanisms began at the cellular level, with the very first cells, and homeostasis provides the underlying selection pressure fueling evolution.

While the events leading to the formation of the first functioning cell are debatable, a critical one was certainly the formation of simple lipid-enclosed vesicles, which provided a protected space for the evolution of metabolic pathways. Protocells evolved from a common ancestor that experienced environmental stresses early in the history of cellular development, such as acidic ocean conditions and low atmospheric oxygen levels, which shaped the evolution of metabolism.

The reduction of evolution to cell biology may answer the perennially unresolved question of why organisms return to their unicellular origins during the life cycle.

As primitive protocells evolved to form prokaryotes and, much later, eukaryotes, changes to the cell membrane occurred that were critical to the maintenance of chemiosmosis, the generation of bioenergy through the partitioning of ions. The incorporation of cholesterol into the plasma membrane surrounding primitive eukaryotic cells marked the beginning of their differentiation from prokaryotes. Cholesterol imparted more fluidity to eukaryotic cell membranes, enhancing functionality by increasing motility and endocytosis. Membrane deformability also allowed for increased gas exchange.

Acidification of the oceans by atmospheric carbon dioxide generated high intracellular calcium ion concentrations in primitive aquatic eukaryotes, which had to be lowered to prevent toxic effects, namely the aggregation of nucleotides, proteins, and lipids. The early cells achieved this by the evolution of calcium channels composed of cholesterol embedded within the cell’s plasma membrane, and of internal membranes, such as that of the endoplasmic reticulum, peroxisomes, and other cytoplasmic organelles, which hosted intracellular chemiosmosis and helped regulate calcium.

As eukaryotes thrived, they experienced increasingly competitive pressure for metabolic efficiency. Engulfed bacteria, assimilated as mitochondria, provided more bioenergy. As the evolution of eukaryotic organisms progressed, metabolic cooperation evolved, perhaps to enable competition with biofilm-forming, quorum-sensing prokaryotes. The subsequent appearance of multicellular eukaryotes expressing cellular growth factors and their respective receptors facilitated cell-cell signaling, forming the basis for an explosion of multicellular eukaryote evolution, culminating in the metazoans.

Casting a cellular perspective on evolution highlights the integration of genotype and phenotype. Starting from the protocell membrane, the functional homolog for all complex metazoan organs, it offers a way of experimentally determining the role of genes that fostered evolution based on the ontogeny and phylogeny of cellular processes that can be traced back, in some cases, to our last universal common ancestor.  ….

As eukaryotes thrived, they experienced increasingly competitive pressure for metabolic efficiency. Engulfed bacteria, assimilated as mitochondria, provided more bioenergy. As the evolution of eukaryotic organisms progressed, metabolic cooperation evolved, perhaps to enable competition with biofilm-forming, quorum-sensing prokaryotes. The subsequent appearance of multicellular eukaryotes expressing cellular growth factors and their respective receptors facilitated cell-cell signaling, forming the basis for an explosion of multicellular eukaryote evolution, culminating in the metazoans.

Casting a cellular perspective on evolution highlights the integration of genotype and phenotype. Starting from the protocell membrane, the functional homolog for all complex metazoan organs, it offers a way of experimentally determining the role of genes that fostered evolution based on the ontogeny and phylogeny of cellular processes that can be traced back, in some cases, to our last universal common ancestor.

Given that the unicellular toolkit is complete with all the traits necessary for forming multicellular organisms (Science, 301:361-63, 2003), it is distinctly possible that metazoans are merely permutations of the unicellular body plan. That scenario would clarify a lot of puzzling biology: molecular commonalities between the skin, lung, gut, and brain that affect physiology and pathophysiology exist because the cell membranes of unicellular organisms perform the equivalents of these tissue functions, and the existence of pleiotropy—one gene affecting many phenotypes—may be a consequence of the common unicellular source for all complex biologic traits.  …

The cell-molecular homeostatic model for evolution and stability addresses how the external environment generates homeostasis developmentally at the cellular level. It also determines homeostatic set points in adaptation to the environment through specific effectors, such as growth factors and their receptors, second messengers, inflammatory mediators, crossover mutations, and gene duplications. This is a highly mechanistic, heritable, plastic process that lends itself to understanding evolution at the cellular, tissue, organ, system, and population levels, mediated by physiologically linked mechanisms throughout, without having to invoke random, chance mechanisms to bridge different scales of evolutionary change. In other words, it is an integrated mechanism that can often be traced all the way back to its unicellular origins.

The switch from swim bladder to lung as vertebrates moved from water to land is proof of principle that stress-induced evolution in metazoans can be understood from changes at the cellular level.

http://www.the-scientist.com/Nov2014/TE_21.jpg

A MECHANISTIC BASIS FOR LUNG DEVELOPMENT: Stress from periodic atmospheric hypoxia (1) during vertebrate adaptation to land enhances positive selection of the stretch-regulated parathyroid hormone-related protein (PTHrP) in the pituitary and adrenal glands. In the pituitary (2), PTHrP signaling upregulates the release of adrenocorticotropic hormone (ACTH) (3), which stimulates the release of glucocorticoids (GC) by the adrenal gland (4). In the adrenal gland, PTHrP signaling also stimulates glucocorticoid production of adrenaline (5), which in turn affects the secretion of lung surfactant, the distension of alveoli, and the perfusion of alveolar capillaries (6). PTHrP signaling integrates the inflation and deflation of the alveoli with surfactant production and capillary perfusion.  THE SCIENTIST STAFF

From a cell-cell signaling perspective, two critical duplications in genes coding for cell-surface receptors occurred during this period of water-to-land transition—in the stretch-regulated parathyroid hormone-related protein (PTHrP) receptor gene and the β adrenergic (βA) receptor gene. These gene duplications can be disassembled by following their effects on vertebrate physiology backwards over phylogeny. PTHrP signaling is necessary for traits specifically relevant to land adaptation: calcification of bone, skin barrier formation, and the inflation and distention of lung alveoli. Microvascular shear stress in PTHrP-expressing organs such as bone, skin, kidney, and lung would have favored duplication of the PTHrP receptor, since sheer stress generates radical oxygen species (ROS) known to have this effect and PTHrP is a potent vasodilator, acting as an epistatic balancing selection for this constraint.

Positive selection for PTHrP signaling also evolved in the pituitary and adrenal cortex (see figure on this page), stimulating the secretion of ACTH and corticoids, respectively, in response to the stress of land adaptation. This cascade amplified adrenaline production by the adrenal medulla, since corticoids passing through it enzymatically stimulate adrenaline synthesis. Positive selection for this functional trait may have resulted from hypoxic stress that arose during global episodes of atmospheric hypoxia over geologic time. Since hypoxia is the most potent physiologic stressor, such transient oxygen deficiencies would have been acutely alleviated by increasing adrenaline levels, which would have stimulated alveolar surfactant production, increasing gas exchange by facilitating the distension of the alveoli. Over time, increased alveolar distension would have generated more alveoli by stimulating PTHrP secretion, impelling evolution of the alveolar bed of the lung.

This scenario similarly explains βA receptor gene duplication, since increased density of the βA receptor within the alveolar walls was necessary for relieving another constraint during the evolution of the lung in adaptation to land: the bottleneck created by the existence of a common mechanism for blood pressure control in both the lung alveoli and the systemic blood pressure. The pulmonary vasculature was constrained by its ability to withstand the swings in pressure caused by the systemic perfusion necessary to sustain all the other vital organs. PTHrP is a potent vasodilator, subserving the blood pressure constraint, but eventually the βA receptors evolved to coordinate blood pressure in both the lung and the periphery.

Gut Microbiome Heritability

Analyzing data from a large twin study, researchers have homed in on how host genetics can shape the gut microbiome.
By Tracy Vence | The Scientist Nov 6, 2014

Previous research suggested host genetic variation can influence microbial phenotype, but an analysis of data from a large twin study published in Cell today (November 6) solidifies the connection between human genotype and the composition of the gut microbiome. Studying more than 1,000 fecal samples from 416 monozygotic and dizygotic twin pairs, Cornell University’s Ruth Ley and her colleagues have homed in on one bacterial taxon, the family Christensenellaceae, as the most highly heritable group of microbes in the human gut. The researchers also found that Christensenellaceae—which was first described just two years ago—is central to a network of co-occurring heritable microbes that is associated with lean body mass index (BMI).  …

Of particular interest was the family Christensenellaceae, which was the most heritable taxon among those identified in the team’s analysis of fecal samples obtained from the TwinsUK study population.

While microbiologists had previously detected 16S rRNA sequences belonging to Christensenellaceae in the human microbiome, the family wasn’t named until 2012. “People hadn’t looked into it, partly because it didn’t have a name . . . it sort of flew under the radar,” said Ley.

Ley and her colleagues discovered that Christensenellaceae appears to be the hub in a network of co-occurring heritable taxa, which—among TwinsUK participants—was associated with low BMI. The researchers also found that Christensenellaceae had been found at greater abundance in low-BMI twins in older studies.

To interrogate the effects of Christensenellaceae on host metabolic phenotype, the Ley’s team introduced lean and obese human fecal samples into germ-free mice. They found animals that received lean fecal samples containing more Christensenellaceae showed reduced weight gain compared with their counterparts. And treatment of mice that had obesity-associated microbiomes with one member of the Christensenellaceae family, Christensenella minuta, led to reduced weight gain.   …

Ley and her colleagues are now focusing on the host alleles underlying the heritability of the gut microbiome. “We’re running a genome-wide association analysis to try to find genes—particular variants of genes—that might associate with higher levels of these highly heritable microbiota.  . . . Hopefully that will point us to possible reasons they’re heritable,” she said. “The genes will guide us toward understanding how these relationships are maintained between host genotype and microbiome composition.”

J.K. Goodrich et al., “Human genetics shape the gut microbiome,” Cell,  http://dx.doi.org:/10.1016/j.cell.2014.09.053, 2014.

Light-Operated Drugs

Scientists create a photosensitive pharmaceutical to target a glutamate receptor.
By Ruth Williams | The Scentist Nov 1, 2014
http://www.the-scientist.com/?articles.view/articleNo/41279/title/Light-Operated-Drugs/

light operated drugs MO1

light operated drugs MO1

http://www.the-scientist.com/Nov2014/MO1.jpg

The desire for temporal and spatial control of medications to minimize side effects and maximize benefits has inspired the development of light-controllable drugs, or optopharmacology. Early versions of such drugs have manipulated ion channels or protein-protein interactions, “but never, to my knowledge, G protein–coupled receptors [GPCRs], which are one of the most important pharmacological targets,” says Pau Gorostiza of the Institute for Bioengineering of Catalonia, in Barcelona.

Gorostiza has taken the first step toward filling that gap, creating a photosensitive inhibitor of the metabotropic glutamate 5 (mGlu5) receptor—a GPCR expressed in neurons and implicated in a number of neurological and psychiatric disorders. The new mGlu5 inhibitor—called alloswitch-1—is based on a known mGlu receptor inhibitor, but the simple addition of a light-responsive appendage, as had been done for other photosensitive drugs, wasn’t an option. The binding site on mGlu5 is “extremely tight,” explains Gorostiza, and would not accommodate a differently shaped molecule. Instead, alloswitch-1 has an intrinsic light-responsive element.

In a human cell line, the drug was active under dim light conditions, switched off by exposure to violet light, and switched back on by green light. When Gorostiza’s team administered alloswitch-1 to tadpoles, switching between violet and green light made the animals stop and start swimming, respectively.

The fact that alloswitch-1 is constitutively active and switched off by light is not ideal, says Gorostiza. “If you are thinking of therapy, then in principle you would prefer the opposite,” an “on” switch. Indeed, tweaks are required before alloswitch-1 could be a useful drug or research tool, says Stefan Herlitze, who studies ion channels at Ruhr-Universität Bochum in Germany. But, he adds, “as a proof of principle it is great.” (Nat Chem Biol, http://dx.doi.org:/10.1038/nchembio.1612, 2014)

Enhanced Enhancers

The recent discovery of super-enhancers may offer new drug targets for a range of diseases.
By Eric Olson | The Scientist Nov 1, 2014
http://www.the-scientist.com/?articles.view/articleNo/41281/title/Enhanced-Enhancers/

To understand disease processes, scientists often focus on unraveling how gene expression in disease-associated cells is altered. Increases or decreases in transcription—as dictated by a regulatory stretch of DNA called an enhancer, which serves as a binding site for transcription factors and associated proteins—can produce an aberrant composition of proteins, metabolites, and signaling molecules that drives pathologic states. Identifying the root causes of these changes may lead to new therapeutic approaches for many different diseases.

Although few therapies for human diseases aim to alter gene expression, the outstanding examples—including antiestrogens for hormone-positive breast cancer, antiandrogens for prostate cancer, and PPAR-γ agonists for type 2 diabetes—demonstrate the benefits that can be achieved through targeting gene-control mechanisms.  Now, thanks to recent papers from laboratories at MIT, Harvard, and the National Institutes of Health, researchers have a new, much bigger transcriptional target: large DNA regions known as super-enhancers or stretch-enhancers. Already, work on super-enhancers is providing insights into how gene-expression programs are established and maintained, and how they may go awry in disease.  Such research promises to open new avenues for discovering medicines for diseases where novel approaches are sorely needed.

Super-enhancers cover stretches of DNA that are 10- to 100-fold longer and about 10-fold less abundant in the genome than typical enhancer regions (Cell, 153:307-19, 2013). They also appear to bind a large percentage of the transcriptional machinery compared to typical enhancers, allowing them to better establish and enforce cell-type specific transcriptional programs (Cell, 153:320-34, 2013).

Super-enhancers are closely associated with genes that dictate cell identity, including those for cell-type–specific master regulatory transcription factors. This observation led to the intriguing hypothesis that cells with a pathologic identity, such as cancer cells, have an altered gene expression program driven by the loss, gain, or altered function of super-enhancers.

Sure enough, by mapping the genome-wide location of super-enhancers in several cancer cell lines and from patients’ tumor cells, we and others have demonstrated that genes located near super-enhancers are involved in processes that underlie tumorigenesis, such as cell proliferation, signaling, and apoptosis.

Super-enhancers cover stretches of DNA that are 10- to 100-fold longer and about 10-fold less abundant in the genome than typical enhancer regions.

Genome-wide association studies (GWAS) have found that disease- and trait-associated genetic variants often occur in greater numbers in super-enhancers (compared to typical enhancers) in cell types involved in the disease or trait of interest (Cell, 155:934-47, 2013). For example, an enrichment of fasting glucose–associated single nucleotide polymorphisms (SNPs) was found in the stretch-enhancers of pancreatic islet cells (PNAS, 110:17921-26, 2013). Given that some 90 percent of reported disease-associated SNPs are located in noncoding regions, super-enhancer maps may be extremely valuable in assigning functional significance to GWAS variants and identifying target pathways.

Because only 1 to 2 percent of active genes are physically linked to a super-enhancer, mapping the locations of super-enhancers can be used to pinpoint the small number of genes that may drive the biology of that cell. Differential super-enhancer maps that compare normal cells to diseased cells can be used to unravel the gene-control circuitry and identify new molecular targets, in much the same way that somatic mutations in tumor cells can point to oncogenic drivers in cancer. This approach is especially attractive in diseases for which an incomplete understanding of the pathogenic mechanisms has been a barrier to discovering effective new therapies.

Another therapeutic approach could be to disrupt the formation or function of super-enhancers by interfering with their associated protein components. This strategy could make it possible to downregulate multiple disease-associated genes through a single molecular intervention. A group of Boston-area researchers recently published support for this concept when they described inhibited expression of cancer-specific genes, leading to a decrease in cancer cell growth, by using a small molecule inhibitor to knock down a super-enhancer component called BRD4 (Cancer Cell, 24:777-90, 2013).  More recently, another group showed that expression of the RUNX1 transcription factor, involved in a form of T-cell leukemia, can be diminished by treating cells with an inhibitor of a transcriptional kinase that is present at the RUNX1 super-enhancer (Nature, 511:616-20, 2014).

Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization 
Andrea Sánchez-Vallet, et al.   eLife 2013;2:e00790 http://elifesciences.org/content/2/e00790#sthash.LnqVMJ9p.dpuf

LysM effector

LysM effector

http://img.scoop.it/ZniCRKQSvJOG18fHbb4p0Tl72eJkfbmt4t8yenImKBVvK0kTmF0xjctABnaLJIm9

While host immune receptors

  • detect pathogen-associated molecular patterns to activate immunity,
  • pathogens attempt to deregulate host immunity through secreted effectors.

Fungi employ LysM effectors to prevent

  • recognition of cell wall-derived chitin by host immune receptors

Structural analysis of the LysM effector Ecp6 of

  • the fungal tomato pathogen Cladosporium fulvum reveals
  • a novel mechanism for chitin binding,
  • mediated by intrachain LysM dimerization,

leading to a chitin-binding groove that is deeply buried in the effector protein.

This composite binding site involves

  • two of the three LysMs of Ecp6 and
  • mediates chitin binding with ultra-high (pM) affinity.

The remaining singular LysM domain of Ecp6 binds chitin with

  • low micromolar affinity but can nevertheless still perturb chitin-triggered immunity.

Conceivably, the perturbation by this LysM domain is not established through chitin sequestration but possibly through interference with the host immune receptor complex.

Mutated Genes in Schizophrenia Map to Brain Networks
From www.nih.gov –  Sep 3, 2013

Previous studies have shown that many people with schizophrenia have de novo, or new, genetic mutations. These misspellings in a gene’s DNA sequence

  • occur spontaneously and so aren’t shared by their close relatives.

Dr. Mary-Claire King of the University of Washington in Seattle and colleagues set out to

  • identify spontaneous genetic mutations in people with schizophrenia and
  • to assess where and when in the brain these misspelled genes are turned on, or expressed.

The study was funded in part by NIH’s National Institute of Mental Health (NIMH). The results were published in the August 1, 2013, issue of Cell.

The researchers sequenced the exomes (protein-coding DNA regions) of 399 people—105 with schizophrenia plus their unaffected parents and siblings. Gene variations
that were found in a person with schizophrenia but not in either parent were considered spontaneous.

The likelihood of having a spontaneous mutation was associated with

  • the age of the father in both affected and unaffected siblings.

Significantly more mutations were found in people

  • whose fathers were 33-45 years at the time of conception compared to 19-28 years.

Among people with schizophrenia, the scientists identified

  • 54 genes with spontaneous mutations
  • predicted to cause damage to the function of the protein they encode.

The researchers used newly available database resources that show

  • where in the brain and when during development genes are expressed.

The genes form an interconnected expression network with many more connections than

  • that of the genes with spontaneous damaging mutations in unaffected siblings.

The spontaneously mutated genes in people with schizophrenia

  • were expressed in the prefrontal cortex, a region in the front of the brain.

The genes are known to be involved in important pathways in brain development. Fifty of these genes were active

  • mainly during the period of fetal development.

“Processes critical for the brain’s development can be revealed by the mutations that disrupt them,” King says. “Mutations can lead to loss of integrity of a whole pathway,
not just of a single gene.”

These findings support the concept that schizophrenia may result, in part, from

  • disruptions in development in the prefrontal cortex during fetal development.

James E. Darnell’s “Reflections”

A brief history of the discovery of RNA and its role in transcription — peppered with career advice
By Joseph P. Tiano

James Darnell begins his Journal of Biological Chemistry “Reflections” article by saying, “graduate students these days

  • have to swim in a sea virtually turgid with the daily avalanche of new information and
  • may be momentarily too overwhelmed to listen to the aging.

I firmly believe how we learned what we know can provide useful guidance for how and what a newcomer will learn.” Considering his remarkable discoveries in

  • RNA processing and eukaryotic transcriptional regulation

spanning 60 years of research, Darnell’s advice should be cherished. In his second year at medical school at Washington University School of Medicine in St. Louis, while
studying streptococcal disease in Robert J. Glaser’s laboratory, Darnell realized he “loved doing the experiments” and had his first “career advancement event.”
He and technician Barbara Pesch discovered that in vivo penicillin treatment killed streptococci only in the exponential growth phase and not in the stationary phase. These
results were published in the Journal of Clinical Investigation and earned Darnell an interview with Harry Eagle at the National Institutes of Health.

Darnell arrived at the NIH in 1956, shortly after Eagle  shifted his research interest to developing his minimal essential cell culture medium, still used. Eagle, then studying cell metabolism, suggested that Darnell take up a side project on poliovirus replication in mammalian cells in collaboration with Robert I. DeMars. DeMars’ Ph.D.
adviser was also James  Watson’s mentor, so Darnell met Watson, who invited him to give a talk at Harvard University, which led to an assistant professor position
at the MIT under Salvador Luria. A take-home message is to embrace side projects, because you never know where they may lead: this project helped to shape
his career.

Darnell arrived in Boston in 1961. Following the discovery of DNA’s structure in 1953, the world of molecular biology was turning to RNA in an effort to understand how
proteins are made. Darnell’s background in virology (it was discovered in 1960 that viruses used RNA to replicate) was ideal for the aim of his first independent lab:
exploring mRNA in animal cells grown in culture. While at MIT, he developed a new technique for purifying RNA along with making other observations

  • suggesting that nonribosomal cytoplasmic RNA may be involved in protein synthesis.

When Darnell moved to Albert Einstein College of Medicine for full professorship in 1964,  it was hypothesized that heterogenous nuclear RNA was a precursor to mRNA.
At Einstein, Darnell discovered RNA processing of pre-tRNAs and demonstrated for the first time

  • that a specific nuclear RNA could represent a possible specific mRNA precursor.

In 1967 Darnell took a position at Columbia University, and it was there that he discovered (simultaneously with two other labs) that

  • mRNA contained a polyadenosine tail.

The three groups all published their results together in the Proceedings of the National Academy of Sciences in 1971. Shortly afterward, Darnell made his final career move
four short miles down the street to Rockefeller University in 1974.

Over the next 35-plus years at Rockefeller, Darnell never strayed from his original research question: How do mammalian cells make and control the making of different
mRNAs? His work was instrumental in the collaborative discovery of

  • splicing in the late 1970s and
  • in identifying and cloning many transcriptional activators.

Perhaps his greatest contribution during this time, with the help of Ernest Knight, was

  • the discovery and cloning of the signal transducers and activators of transcription (STAT) proteins.

And with George Stark, Andy Wilks and John Krowlewski, he described

  • cytokine signaling via the JAK-STAT pathway.

Darnell closes his “Reflections” with perhaps his best advice: Do not get too wrapped up in your own work, because “we are all needed and we are all in this together.”

Darnell Reflections - James_Darnell

Darnell Reflections – James_Darnell

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Recent findings on presenilins and signal peptide peptidase

By Dinu-Valantin Bălănescu

γ-secretase and SPP

γ-secretase and SPP

Fig. 1 from the minireview shows a schematic depiction of γ-secretase and SPP

http://www.asbmb.org/assets/0/366/418/428/85528/85529/85530/c2de032a-daad-41e5-ba19-87a17bd26362.png

GxGD proteases are a family of intramembranous enzymes capable of hydrolyzing

  • the transmembrane domain of some integral membrane proteins.

The GxGD family is one of the three families of

  • intramembrane-cleaving proteases discovered so far (along with the rhomboid and site-2 protease) and
  • includes the γ-secretase and the signal peptide peptidase.

Although only recently discovered, a number of functions in human pathology and in numerous other biological processes

  • have been attributed to γ-secretase and SPP.

Taisuke Tomita and Takeshi Iwatsubo of the University of Tokyo highlighted the latest findings on the structure and function of γ-secretase and SPP
in a recent minireview in The Journal of Biological Chemistry.

  • γ-secretase is involved in cleaving the amyloid-β precursor protein, thus producing amyloid-β peptide,

the main component of senile plaques in Alzheimer’s disease patients’ brains. The complete structure of mammalian γ-secretase is not yet known; however,
Tomita and Iwatsubo note that biochemical analyses have revealed it to be a multisubunit protein complex.

  • Its catalytic subunit is presenilin, an aspartyl protease.

In vitro and in vivo functional and chemical biology analyses have revealed that

  • presenilin is a modulator and mandatory component of the γ-secretase–mediated cleavage of APP.

Genetic studies have identified three other components required for γ-secretase activity:

  1. nicastrin,
  2. anterior pharynx defective 1 and
  3. presenilin enhancer 2.

By coexpression of presenilin with the other three components, the authors managed to

  • reconstitute γ-secretase activity.

Tomita and Iwatsubo determined using the substituted cysteine accessibility method and by topological analyses, that

  • the catalytic aspartates are located at the center of the nine transmembrane domains of presenilin,
  • by revealing the exact location of the enzyme’s catalytic site.

The minireview also describes in detail the formerly enigmatic mechanism of γ-secretase mediated cleavage.

SPP, an enzyme that cleaves remnant signal peptides in the membrane

  • during the biogenesis of membrane proteins and
  • signal peptides from major histocompatibility complex type I,
  • also is involved in the maturation of proteins of the hepatitis C virus and GB virus B.

Bioinformatics methods have revealed in fruit flies and mammals four SPP-like proteins,

  • two of which are involved in immunological processes.

By using γ-secretase inhibitors and modulators, it has been confirmed

  • that SPP shares a similar GxGD active site and proteolytic activity with γ-secretase.

Upon purification of the human SPP protein with the baculovirus/Sf9 cell system,

  • single-particle analysis revealed further structural and functional details.

HLA targeting efficiency correlates with human T-cell response magnitude and with mortality from influenza A infection

From www.pnas.org –  Sep 3, 2013 4:24 PM

Experimental and computational evidence suggests that

  • HLAs preferentially bind conserved regions of viral proteins, a concept we term “targeting efficiency,” and that
  • this preference may provide improved clearance of infection in several viral systems.

To test this hypothesis, T-cell responses to A/H1N1 (2009) were measured from peripheral blood mononuclear cells obtained from a household cohort study
performed during the 2009–2010 influenza season. We found that HLA targeting efficiency scores significantly correlated with

  • IFN-γ enzyme-linked immunosorbent spot responses (P = 0.042, multiple regression).

A further population-based analysis found that the carriage frequencies of the alleles with the lowest targeting efficiencies, A*24,

  • were associated with pH1N1 mortality (r = 0.37, P = 0.031) and
  • are common in certain indigenous populations in which increased pH1N1 morbidity has been reported.

HLA efficiency scores and HLA use are associated with CD8 T-cell magnitude in humans after influenza infection.
The computational tools used in this study may be useful predictors of potential morbidity and

  • identify immunologic differences of new variant influenza strains
  • more accurately than evolutionary sequence comparisons.

Population-based studies of the relative frequency of these alleles in severe vs. mild influenza cases

  • might advance clinical practices for severe H1N1 infections among genetically susceptible populations.

Metabolomics in drug target discovery

J D Rabinowitz et al.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ.
Cold Spring Harbor Symposia on Quantitative Biology 11/2011; 76:235-46.
http://dx.doi.org:/10.1101/sqb.2011.76.010694 

Most diseases result in metabolic changes. In many cases, these changes play a causative role in disease progression. By identifying pathological metabolic changes,

  • metabolomics can point to potential new sites for therapeutic intervention.

Particularly promising enzymatic targets are those that

  • carry increased flux in the disease state.

Definitive assessment of flux requires the use of isotope tracers. Here we present techniques for

  • finding new drug targets using metabolomics and isotope tracers.

The utility of these methods is exemplified in the study of three different viral pathogens. For influenza A and herpes simplex virus,

  • metabolomic analysis of infected versus mock-infected cells revealed
  • dramatic concentration changes around the current antiviral target enzymes.

Similar analysis of human-cytomegalovirus-infected cells, however, found the greatest changes

  • in a region of metabolism unrelated to the current antiviral target.

Instead, it pointed to the tricarboxylic acid (TCA) cycle and

  • its efflux to feed fatty acid biosynthesis as a potential preferred target.

Isotope tracer studies revealed that cytomegalovirus greatly increases flux through

  • the key fatty acid metabolic enzyme acetyl-coenzyme A carboxylase.
  • Inhibition of this enzyme blocks human cytomegalovirus replication.

Examples where metabolomics has contributed to identification of anticancer drug targets are also discussed. Eventual proof of the value of

  • metabolomics as a drug target discovery strategy will be
  • successful clinical development of therapeutics hitting these new targets.

 Related References

Use of metabolic pathway flux information in targeted cancer drug design. Drug Discovery Today: Therapeutic Strategies 1:435-443, 2004.

Detection of resistance to imatinib by metabolic profiling: clinical and drug development implications. Am J Pharmacogenomics. 2005;5(5):293-302. Review. PMID: 16196499

Medicinal chemistry, metabolic profiling and drug target discovery: a role for metabolic profiling in reverse pharmacology and chemical genetics.
Mini Rev Med Chem.  2005 Jan;5(1):13-20. Review. PMID: 15638788 [PubMed – indexed for MEDLINE] Related citations

Development of Tracer-Based Metabolomics and its Implications for the Pharmaceutical Industry. Int J Pharm Med 2007; 21 (3): 217-224.

Use of metabolic pathway flux information in anticancer drug design. Ernst Schering Found Symp Proc. 2007;(4):189-203. Review. PMID: 18811058

Pharmacological targeting of glucagon and glucagon-like peptide 1 receptors has different effects on energy state and glucose homeostasis in diet-induced obese mice. J Pharmacol Exp Ther. 2011 Jul;338(1):70-81. http://dx.doi.org:/10.1124/jpet.111.179986. PMID: 21471191

Single valproic acid treatment inhibits glycogen and RNA ribose turnover while disrupting glucose-derived cholesterol synthesis in liver as revealed by the
[U-C(6)]-d-glucose tracer in mice. Metabolomics. 2009 Sep;5(3):336-345. PMID: 19718458

Metabolic Pathways as Targets for Drug Screening, Metabolomics, Dr Ute Roessner (Ed.), ISBN: 978-953-51-0046-1, InTech, Available from: http://www.intechopen.com/books/metabolomics/metabolic-pathways-as-targets-for-drug-screening

Iron regulates glucose homeostasis in liver and muscle via AMP-activated protein kinase in mice. FASEB J. 2013 Jul;27(7):2845-54.
http://dx.doi.org:/10.1096/fj.12-216929. PMID: 23515442

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

Drug Discov. Today 19 (2014), 171–182     http://dx.doi.org:/10.1016/j.drudis.2013.07.014

Highlights

  • We now have metabolic network models; the metabolome is represented by their nodes.
  • Metabolite levels are sensitive to changes in enzyme activities.
  • Drugs hitchhike on metabolite transporters to get into and out of cells.
  • The consensus network Recon2 represents the present state of the art, and has predictive power.
  • Constraint-based modelling relates network structure to metabolic fluxes.

Metabolism represents the ‘sharp end’ of systems biology, because changes in metabolite concentrations are

  • necessarily amplified relative to changes in the transcriptome, proteome and enzyme activities, which can be modulated by drugs.

To understand such behaviour, we therefore need (and increasingly have) reliable consensus (community) models of

  • the human metabolic network that include the important transporters.

Small molecule ‘drug’ transporters are in fact metabolite transporters, because

  • drugs bear structural similarities to metabolites known from the network reconstructions and
  • from measurements of the metabolome.

Recon2 represents the present state-of-the-art human metabolic network reconstruction; it can predict inter alia:

(i) the effects of inborn errors of metabolism;

(ii) which metabolites are exometabolites, and

(iii) how metabolism varies between tissues and cellular compartments.

However, even these qualitative network models are not yet complete. As our understanding improves

  • so do we recognise more clearly the need for a systems (poly)pharmacology.

Introduction – a systems biology approach to drug discovery

It is clearly not news that the productivity of the pharmaceutical industry has declined significantly during recent years

  • following an ‘inverse Moore’s Law’, Eroom’s Law, or
  • that many commentators, consider that the main cause of this is
  • because of an excessive focus on individual molecular target discovery rather than a more sensible strategy
  • based on a systems-level approach (Fig. 1).
drug discovery science

drug discovery science

Figure 1.

The change in drug discovery strategy from ‘classical’ function-first approaches (in which the assay of drug function was at the tissue or organism level),
with mechanistic studies potentially coming later, to more-recent target-based approaches where initial assays usually involve assessing the interactions
of drugs with specified (and often cloned, recombinant) proteins in vitro. In the latter cases, effects in vivo are assessed later, with concomitantly high levels of attrition.

Arguably the two chief hallmarks of the systems biology approach are:

(i) that we seek to make mathematical models of our systems iteratively or in parallel with well-designed ‘wet’ experiments, and
(ii) that we do not necessarily start with a hypothesis but measure as many things as possible (the ’omes) and

  • let the data tell us the hypothesis that best fits and describes them.

Although metabolism was once seen as something of a Cinderella subject,

  • there are fundamental reasons to do with the organisation of biochemical networks as
  • to why the metabol(om)ic level – now in fact seen as the ‘apogee’ of the ’omics trilogy –
  •  is indeed likely to be far more discriminating than are
  • changes in the transcriptome or proteome.

The next two subsections deal with these points and Fig. 2 summarises the paper in the form of a Mind Map.

metabolomics and systems pharmacology

metabolomics and systems pharmacology

http://ars.els-cdn.com/content/image/1-s2.0-S1359644613002481-gr2.jpg

Metabolic Disease Drug Discovery— “Hitting the Target” Is Easier Said Than Done

David E. Moller, et al.   http://dx.doi.org:/10.1016/j.cmet.2011.10.012

Despite the advent of new drug classes, the global epidemic of cardiometabolic disease has not abated. Continuing

  • unmet medical needs remain a major driver for new research.

Drug discovery approaches in this field have mirrored industry trends, leading to a recent

  • increase in the number of molecules entering development.

However, worrisome trends and newer hurdles are also apparent. The history of two newer drug classes—

  1. glucagon-like peptide-1 receptor agonists and
  2. dipeptidyl peptidase-4 inhibitors—

illustrates both progress and challenges. Future success requires that researchers learn from these experiences and

  • continue to explore and apply new technology platforms and research paradigms.

The global epidemic of obesity and diabetes continues to progress relentlessly. The International Diabetes Federation predicts an even greater diabetes burden (>430 million people afflicted) by 2030, which will disproportionately affect developing nations (International Diabetes Federation, 2011). Yet

  • existing drug classes for diabetes, obesity, and comorbid cardiovascular (CV) conditions have substantial limitations.

Currently available prescription drugs for treatment of hyperglycemia in patients with type 2 diabetes (Table 1) have notable shortcomings. In general,

Therefore, clinicians must often use combination therapy, adding additional agents over time. Ultimately many patients will need to use insulin—a therapeutic class first introduced in 1922. Most existing agents also have

  • issues around safety and tolerability as well as dosing convenience (which can impact patient compliance).

Pharmacometabolomics, also known as pharmacometabonomics, is a field which stems from metabolomics,

  • the quantification and analysis of metabolites produced by the body.

It refers to the direct measurement of metabolites in an individual’s bodily fluids, in order to

  • predict or evaluate the metabolism of pharmaceutical compounds, and
  • to better understand the pharmacokinetic profile of a drug.

Alternatively, pharmacometabolomics can be applied to measure metabolite levels

  • following the administration of a pharmaceutical compound, in order to
  • monitor the effects of the compound on certain metabolic pathways(pharmacodynamics).

This provides detailed mapping of drug effects on metabolism and

  • the pathways that are implicated in mechanism of variation of response to treatment.

In addition, the metabolic profile of an individual at baseline (metabotype) provides information about

  • how individuals respond to treatment and highlights heterogeneity within a disease state.

All three approaches require the quantification of metabolites found

relationship between -OMICS

relationship between -OMICS

http://upload.wikimedia.org/wikipedia/commons/thumb/e/eb/OMICS.png/350px-OMICS.png

Pharmacometabolomics is thought to provide information that

Looking at the characteristics of an individual down through these different levels of detail, there is an

  • increasingly more accurate prediction of a person’s ability to respond to a pharmaceutical compound.
  1. the genome, made up of 25 000 genes, can indicate possible errors in drug metabolism;
  2. the transcriptome, made up of 85,000 transcripts, can provide information about which genes important in metabolism are being actively transcribed;
  3. and the proteome, >10,000,000 members, depicts which proteins are active in the body to carry out these functions.

Pharmacometabolomics complements the omics with

  • direct measurement of the products of all of these reactions, but with perhaps a relatively
  • smaller number of members: that was initially projected to be approximately 2200 metabolites,

but could be a larger number when gut derived metabolites and xenobiotics are added to the list. Overall, the goal of pharmacometabolomics is

  • to more closely predict or assess the response of an individual to a pharmaceutical compound,
  • permitting continued treatment with the right drug or dosage
  • depending on the variations in their metabolism and ability to respond to treatment.

Pharmacometabolomic analyses, through the use of a metabolomics approach,

  • can provide a comprehensive and detailed metabolic profile or “metabolic fingerprint” for an individual patient.

Such metabolic profiles can provide a complete overview of individual metabolite or pathway alterations,

This approach can then be applied to the prediction of response to a pharmaceutical compound

  • by patients with a particular metabolic profile.

Pharmacometabolomic analyses of drug response are

Pharmacogenetics focuses on the identification of genetic variations (e.g. single-nucleotide polymorphisms)

  • within patients that may contribute to altered drug responses and overall outcome of a certain treatment.

The results of pharmacometabolomics analyses can act to “inform” or “direct”

  • pharmacogenetic analyses by correlating aberrant metabolite concentrations or metabolic pathways to potential alterations at the genetic level.

This concept has been established with two seminal publications from studies of antidepressants serotonin reuptake inhibitors

  • where metabolic signatures were able to define a pathway implicated in response to the antidepressant and
  • that lead to identification of genetic variants within a key gene
  • within the highlighted pathway as being implicated in variation in response.

These genetic variants were not identified through genetic analysis alone and hence

  • illustrated how metabolomics can guide and inform genetic data.

en.wikipedia.org/wiki/Pharmacometabolomics

Benznidazole Biotransformation and Multiple Targets in Trypanosoma cruzi Revealed by Metabolomics

Andrea Trochine, Darren J. Creek, Paula Faral-Tello, Michael P. Barrett, Carlos Robello
Published: May 22, 2014   http://dx.doi.org:/10.1371/journal.pntd.0002844

The first line treatment for Chagas disease, a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi,

  • involves administration of benznidazole (Bzn).

Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active. We used a

  • non-targeted MS-based metabolomics approach to study the metabolic response of T. cruzi to Bzn.

Parasites treated with Bzn were minimally altered compared to untreated trypanosomes, although the redox active thiols

  1. trypanothione,
  2. homotrypanothione and
  3. cysteine

were significantly diminished in abundance post-treatment. In addition, multiple Bzn-derived metabolites were detected after treatment.

These metabolites included reduction products, fragments and covalent adducts of reduced Bzn

  • linked to each of the major low molecular weight thiols:
  1. trypanothione,
  2. glutathione,
  3. g-glutamylcysteine,
  4. glutathionylspermidine,
  5. cysteine and
  6. ovothiol A.

Bzn products known to be generated in vitro by the unusual trypanosomal nitroreductase, TcNTRI,

  • were found within the parasites,
  • but low molecular weight adducts of glyoxal, a proposed toxic end-product of NTRI Bzn metabolism, were not detected.

Our data is indicative of a major role of the

  • thiol binding capacity of Bzn reduction products
  • in the mechanism of Bzn toxicity against T. cruzi.

 

 

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LIVE – Now –>> CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121

Reporter: Aviva Lev-Ari, PhD, RN

Article ID #157: Article ID #159: CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121. Published on 10/26/2014

WordCloud Image Produced by Adam Tubman

REAL TIME Conference Coverage by Dr. Aviva Lev-Ari, PhD, RN

For more Biotech Conferences Covered in Real Time by Dr. Aviva Lev-Ari, PhD, RN for Leaders in Pharmaceutical Business Intelligence using Social Media and Open Access Online Scientific Journal http://pharmaceuticalintelligence.com

click on

http://pharmaceuticalintelligence.com/press-coverage/

For articles on CRISPR-Cas9 in Open Access Online Scientific Journal http://pharmaceuticalintelligence.com

click on

http://pharmaceuticalintelligence.com/?s=CRISPR-Cas9

 

LIVE CONTENT from 

Gabbay Award Lecture in Biotechnology and Medicine @Brandeis

is been added 0n 10/27 @3;30PM

InVivo Target Search Mechanism – Fast Cas9 Diffusion in Live Cells

First Speaker

Emmanuelle Charpentier (Dept. of Molecular Biology. Umea University; Dept. of Regulation in Infection Biology, Helmholtz Centre for Infection Research)

CRISPR-Cas9: How a Bacterial Immune System Revolutionizes Life Sciences and Medicine

application in dairy industry basilicum, bacteria

Second Speaker

Jennifer Doudna (Dept. of Biochemistry, Biophysics and Structural Biology, UC Berkeley)CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering

Bacterial/archaeal chromosome

a single gene CAs9m- enzyme single-guide RNAs (sgRNAs)

crRNA

A Programmable Dual-RNA- Genome editing begins with dsDNA cleavange

ZFHs, TALENs, HEs, Cas9:sgRNA

protein DNA recognition

Genome targeting technologies: ZFN & TALEN

/Cas9/targeting RNA bound by a nuclease

2012-RNA-guided DNA endonuclease

1/2013 Church, Zhang

Re-Writing the Genome:

DNA structu

restriction enzymes

PCR

Specific genome editing in cell and in organizmism

robust transcriptional control with ccatalyrtic

In the Lab @Berkeley

Hoe Cas9 find DNA targets with high specificity

Mechanism of DNA interrogation

  • high affinity product binding, no substrate turnover
  • binding first occur at PAM motifs
  • PAM binding triggers Cas9 catalytic activity

CRISPR: Clusters of Regulary

three steps to acquire immunity in bacteria

1. adaptation

2. crRNA biogenesis

3. Interference

CRISPR in Structural Biology

  • RNA-induced conversion of Cas9 into an active confrontation – crystal structure morphology

Models for DNA interrogation by Cas9:RNA

Programmed RNA cleavage using Cas9:gRNA in O’Connell at al. (2014) Nature

 

  • Therapeutic Applications

1. Delivery of antibiotic small molecule

2. Animal models live cell (catalitic inactive version vs active version)

 

Third Speaker

Feng Zhang (McGovern Inst. for Brain Research, MIT)
Development and Applications of CRISPR-Cas9 for Genome Editing

Brain Research – Applications for CRISPER

  • Genetics & epigenetics
  • signals – optogenetics Neuromodulation
  • optogenetics — fibers — cells

The CRISPR/Cas bacterial

Crispr RNA maturation

E.coli – immunity for using Crispr

Streptococcus thermophilus – CRISPr editing applied

Development of a Technology Platform

  • expand modes of Genomic Pertubation

develop efficient co-transduction of primary neurons

multiplex knockout un the denate

  • demonstrate uses in biological therapeutic context

CRISPR — Reagents development, protocol developed, discussion forums

targeting of MeCP2 gyrus leads to robust protein depletion and behavior change

toxicity potential researched

Cre-dedendent CAs9 MOUSE FOR CANCER MODELING – mouth lung

  • develop an open source for the community

Genome-scale CRISPR knockout (GeCKO) Screen – generate library pool of cell – mutation identification – melanoma treated by BRAF inhibitor – targets for menanoma resistence

Comparison of shRNA vs GeCKO – CRISPR more robust and statisticaly significant, However, GeCKO provides higher sensitivity than shRNA

  •  foundational technology development

Crystal structure of Cas9 in complex wiht guided RNA and target DNA

Cre-dependent Cas9 Mouse

 

For Twitter.com

#Cas9
#CRISPR
#molecularbiology
#biotechnology
#GeneEditing
#genetic#engineering (sometimes these two # are put together like this)
#Boston

@BrandeisU
@MIT
@UCBerkeley
@CRISPRpapers
@UmeaUniversity
@mcgovernmit (this is for Feng Zhang)
@pharma_BI

 

CRISPR Service / Cas9

Commercialization by

 http://www.appliedstemcell.com/services/cell-line-models/cell-line-modification/

The CRISPR/Cas9 system uses the Cas9 nuclease to facilitate RNA-guided site-specific DNA cleavage. The system consists of two components:

(1) Mammalian codon-optimized version of the Cas9 protein carrying a nuclear localization signal to ensure nuclear compartmentalization in mammalian cells

(2) Guide RNAs (gRNAs) to direct Cas9 protein to sequence-specifically cleave the targeted DNA

The advantage of CRISPR/Cas9 over ZFNs or TALENs is its scalability and multiplexibility in that multiple sites within the mammalian genome can be simultaneously modified, providing a robust, high-throughput approach for gene editing in mammalian cells.

CRISPR Service (Point mutation, Deletion, Small DNA insertion)

crispr

We are experts in CRISPR Service! Applied StemCell is in Nature Biotechnology as one of the select companies for CRISPR-Cas9 tools! Monya Baker, “Gene Editing at CRISPR Speed,” Nature Biotechnology, 32: 309-312, April 2014.

Since Applied Stem Cell started out as a company focused on induced pluripotent stem cells (iPSCs), we have excellent capabilities of correcting mutations in disease-model iPSCs using CRISPR/ Cas9.

 

 

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Introduction to Metabolomics

Introduction to Metabolomics

Author: Larry H. Bernstein, MD, FCAP

 

This is the first volume of the Series D: e-Books on BioMedicine – Metabolomics, Immunology, Infectious Diseases.  It is written for comprehension at the third year medical student level, or as a reference for licensing board exams, but it is also written for the education of a first time bachalaureate degree reader in the biological sciences.  Hopefully, it can be read with great interest by the undergraduate student who is undecided in the choice of a career.

In the Preface, I failed to disclose that the term Metabolomics applies to plants, animals, bacteria, and both prokaryotes and eukaryotes.  The metabolome for each organism is unique, but from an evolutionary perspective has metabolic pathways in common, and expressed in concert with the environment that these living creatures exist. The metabolome of each has adaptive accommodation with suppression and activation of pathways that are functional and necessary in balance, for its existence.  Was it William Faulkner who said in his Nobel Prize acceptance that mankind shall not merely exist, but survive? That seems to be the overlying theme for all of life. If life cannot persist, a surviving “remnant” might continue. The history of life may well be etched into the genetic code, some of which is not expressed.

This work is apportioned into chapters in a sequence that is first directed at the major sources for the energy and the structure of life, in the carbohydrates, lipids, and fats, which are sourced from both plants and animals, and depending on their balance, results in an equilibrium, and a disequilibrium we refer to as disease.  There is also a need to consider the nonorganic essentials which are derived from the soil, from water, and from the energy of the sun and the air we breathe, or in the case of water-bound metabolomes, dissolved gases.

In addition to the basic essential nutrients and their metabolic utilization, they are under cellular metabolic regulation that is tied to signaling pathways.  In addition, the genetic expression of the organism is under regulatory control by the interaction of RNAs that interact with the chromatin genetic framework, with exosomes, and with protein modulators.This is referred to as epigenetics, but there are also drivers of metabolism that are shaped by the interactions between enzymes and substartes, and are related to the tertiary structure of a protein.  The framework for diseases in a separate chapter.  Pharmaceutical interventions that are designed to modulate specific metabolic targets are addressed as the pathways are unfolded. Neutraceuticals and plant based nutrition are covered in Chapter 8.

Chapter 1: Metabolic Pathways

Chapter 2. Lipid Metabolism

Chapter 3. Cell Signaling

Chapter 4. Protein Synthesis and Degradation

Chapter 5: Sub-cellular Structure

Chapter 6: Proteomics

Chapter 7: Metabolomics

Chapter 8. Impairments in Pathological States: Endocrine Disorders; Stress Hypermetabolism and Cancer

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Metabolomics Summary and Perspective

Metabolomics Summary and Perspective

Author and Curator: Larry H Bernstein, MD, FCAP 

 

This is the final article in a robust series on metabolism, metabolomics, and  the “-OMICS-“ biological synthesis that is creating a more holistic and interoperable view of natural sciences, including the biological disciplines, climate science, physics, chemistry, toxicology, pharmacology, and pathophysiology with as yet unforeseen consequences.

There have been impressive advances already in the research into developmental biology, plant sciences, microbiology, mycology, and human diseases, most notably, cancer, metabolic , and infectious, as well as neurodegenerative diseases.

Acknowledgements:

I write this article in honor of my first mentor, Harry Maisel, Professor and Emeritus Chairman of Anatomy, Wayne State University, Detroit, MI and to my stimulating mentors, students, fellows, and associates over many years:

Masahiro Chiga, MD, PhD, Averill A Liebow, MD, Nathan O Kaplan, PhD, Johannes Everse, PhD, Norio Shioura, PhD, Abraham Braude, MD, Percy J Russell, PhD, Debby Peters, Walter D Foster, PhD, Herschel Sidransky, MD, Sherman Bloom, MD, Matthew Grisham, PhD, Christos Tsokos, PhD,  IJ Good, PhD, Distinguished Professor, Raool Banagale, MD, Gustavo Reynoso, MD,Gustave Davis, MD, Marguerite M Pinto, MD, Walter Pleban, MD, Marion Feietelson-Winkler, RD, PhD,  John Adan,MD, Joseph Babb, MD, Stuart Zarich, MD,  Inder Mayall, MD, A Qamar, MD, Yves Ingenbleek, MD, PhD, Emeritus Professor, Bette Seamonds, PhD, Larry Kaplan, PhD, Pauline Y Lau, PhD, Gil David, PhD, Ronald Coifman, PhD, Emeritus Professor, Linda Brugler, RD, MBA, James Rucinski, MD, Gitta Pancer, Ester Engelman, Farhana Hoque, Mohammed Alam, Michael Zions, William Fleischman, MD, Salman Haq, MD, Jerard Kneifati-Hayek, Madeleine Schleffer, John F Heitner, MD, Arun Devakonda,MD, Liziamma George,MD, Suhail Raoof, MD, Charles Oribabor,MD, Anthony Tortolani, MD, Prof and Chairman, JRDS Rosalino, PhD, Aviva Lev Ari, PhD, RN, Rosser Rudolph, MD, PhD, Eugene Rypka, PhD, Jay Magidson, PhD, Izaak Mayzlin, PhD, Maurice Bernstein, PhD, Richard Bing, Eli Kaplan, PhD, Maurice Bernstein, PhD.

This article has EIGHT parts, as follows:

Part 1

Metabolomics Continues Auspicious Climb

Part 2

Biologists Find ‘Missing Link’ in the Production of Protein Factories in Cells

Part 3

Neuroscience

Part 4

Cancer Research

Part 5

Metabolic Syndrome

Part 6

Biomarkers

Part 7

Epigenetics and Drug Metabolism

Part 8

Pictorial

genome cartoon

genome cartoon

 iron metabolism

iron metabolism

personalized reference range within population range

personalized reference range within population range

Part 1.  MetabolomicsSurge

metagraph  _OMICS

metagraph _OMICS

Metabolomics Continues Auspicious Climb

Jeffery Herman, Ph.D.
GEN May 1, 2012 (Vol. 32, No. 9)

Aberrant biochemical and metabolite signaling plays an important role in

  • the development and progression of diseased tissue.

This concept has been studied by the science community for decades. However, with relatively

  1. recent advances in analytical technology and bioinformatics as well as
  2. the development of the Human Metabolome Database (HMDB),

metabolomics has become an invaluable field of research.

At the “International Conference and Exhibition on Metabolomics & Systems Biology” held recently in San Francisco, researchers and industry leaders discussed how

  • the underlying cellular biochemical/metabolite fingerprint in response to
  1. a specific disease state,
  2. toxin exposure, or
  3. pharmaceutical compound
  • is useful in clinical diagnosis and biomarker discovery and
  • in understanding disease development and progression.

Developed by BASF, MetaMap® Tox is

  • a database that helps identify in vivo systemic effects of a tested compound, including
  1. targeted organs,
  2. mechanism of action, and
  3. adverse events.

Based on 28-day systemic rat toxicity studies, MetaMap Tox is composed of

  • differential plasma metabolite profiles of rats
  • after exposure to a large variety of chemical toxins and pharmaceutical compounds.

“Using the reference data,

  • we have developed more than 110 patterns of metabolite changes, which are
  • specific and predictive for certain toxicological modes of action,”

said Hennicke Kamp, Ph.D., group leader, department of experimental toxicology and ecology at BASF.

With MetaMap Tox, a potential drug candidate

  • can be compared to a similar reference compound
  • using statistical correlation algorithms,
  • which allow for the creation of a toxicity and mechanism of action profile.

“MetaMap Tox, in the context of early pre-clinical safety enablement in pharmaceutical development,” continued Dr. Kamp,

  • has been independently validated “
  • by an industry consortium (Drug Safety Executive Council) of 12 leading biopharmaceutical companies.”

Dr. Kamp added that this technology may prove invaluable

  • allowing for quick and accurate decisions and
  • for high-throughput drug candidate screening, in evaluation
  1. on the safety and efficacy of compounds
  2. during early and preclinical toxicological studies,
  3. by comparing a lead compound to a variety of molecular derivatives, and
  • the rapid identification of the most optimal molecular structure
  • with the best efficacy and safety profiles might be streamlined.
Dynamic Construct of the –Omics

Dynamic Construct of the –Omics

Targeted Tandem Mass Spectrometry

Biocrates Life Sciences focuses on targeted metabolomics, an important approach for

  • the accurate quantification of known metabolites within a biological sample.

Originally used for the clinical screening of inherent metabolic disorders from dried blood-spots of newborn children, Biocrates has developed

  • a tandem mass spectrometry (MS/MS) platform, which allows for
  1. the identification,
  2. quantification, and
  3. mapping of more than 800 metabolites to specific cellular pathways.

It is based on flow injection analysis and high-performance liquid chromatography MS/MS.

Clarification of Pathway-Specific Inhibition by Fourier Transform Ion Cyclotron Resonance.Mass Spectrometry-Based Metabolic Phenotyping Studies F5.large

common drug targets

common drug targets

The MetaDisIDQ® Kit is a

  • “multiparamatic” diagnostic assay designed for the “comprehensive assessment of a person’s metabolic state” and
  • the early determination of pathophysiological events with regards to a specific disease.

MetaDisIDQ is designed to quantify

  • a diverse range of 181 metabolites involved in major metabolic pathways
  • from a small amount of human serum (10 µL) using isotopically labeled internal standards,

This kit has been demonstrated to detect changes in metabolites that are commonly associated with the development of

  • metabolic syndrome, type 2 diabetes, and diabetic nephropathy,

Dr. Dallman reports that data generated with the MetaDisIDQ kit correlates strongly with

  • routine chemical analyses of common metabolites including glucose and creatinine

Biocrates has also developed the MS/MS-based AbsoluteIDQ® kits, which are

  • an “easy-to-use” biomarker analysis tool for laboratory research.

The kit functions on MS machines from a variety of vendors, and allows for the quantification of 150-180 metabolites.

The SteroIDQ® kit is a high-throughput standardized MS/MS diagnostic assay,

  • validated in human serum, for the rapid and accurate clinical determination of 16 known steroids.

Initially focusing on the analysis of steroid ranges for use in hormone replacement therapy, the SteroIDQ Kit is expected to have a wide clinical application.

Hormone-Resistant Breast Cancer

Scientists at Georgetown University have shown that

  • breast cancer cells can functionally coordinate cell-survival and cell-proliferation mechanisms,
  • while maintaining a certain degree of cellular metabolism.

To grow, cells need energy, and energy is a product of cellular metabolism. For nearly a century, it was thought that

  1. the uncoupling of glycolysis from the mitochondria,
  2. leading to the inefficient but rapid metabolism of glucose and
  3. the formation of lactic acid (the Warburg effect), was

the major and only metabolism driving force for unchecked proliferation and tumorigenesis of cancer cells.

Other aspects of metabolism were often overlooked.

“.. we understand now that

  • cellular metabolism is a lot more than just metabolizing glucose,”

said Robert Clarke, Ph.D., professor of oncology and physiology and biophysics at Georgetown University. Dr. Clarke, in collaboration with the Waters Center for Innovation at Georgetown University (led by Albert J. Fornace, Jr., M.D.), obtained

  • the metabolomic profile of hormone-sensitive and -resistant breast cancer cells through the use of UPLC-MS.

They demonstrated that breast cancer cells, through a rather complex and not yet completely understood process,

  1. can functionally coordinate cell-survival and cell-proliferation mechanisms,
  2. while maintaining a certain degree of cellular metabolism.

This is at least partly accomplished through the upregulation of important pro-survival mechanisms; including

  • the unfolded protein response;
  • a regulator of endoplasmic reticulum stress and
  • initiator of autophagy.

Normally, during a stressful situation, a cell may

  • enter a state of quiescence and undergo autophagy,
  • a process by which a cell can recycle organelles
  • in order to maintain enough energy to survive during a stressful situation or,

if the stress is too great,

  • undergo apoptosis.

By integrating cell-survival mechanisms and cellular metabolism

  • advanced ER+ hormone-resistant breast cancer cells
  • can maintain a low level of autophagy
  • to adapt and resist hormone/chemotherapy treatment.

This adaptation allows cells

  • to reallocate important metabolites recovered from organelle degradation and
  • provide enough energy to also promote proliferation.

With further research, we can gain a better understanding of the underlying causes of hormone-resistant breast cancer, with

  • the overall goal of developing effective diagnostic, prognostic, and therapeutic tools.

NMR

Over the last two decades, NMR has established itself as a major tool for metabolomics analysis. It is especially adept at testing biological fluids. [Bruker BioSpin]

Historically, nuclear magnetic resonance spectroscopy (NMR) has been used for structural elucidation of pure molecular compounds. However, in the last two decades, NMR has established itself as a major tool for metabolomics analysis. Since

  • the integral of an NMR signal is directly proportional to
  • the molar concentration throughout the dynamic range of a sample,

“the simultaneous quantification of compounds is possible

  • without the need for specific reference standards or calibration curves,” according to Lea Heintz of Bruker BioSpin.

NMR is adept at testing biological fluids because of

  1.  high reproducibility,
  2. standardized protocols,
  3. low sample manipulation, and
  4. the production of a large subset of data,

Bruker BioSpin is presently involved in a project for the screening of inborn errors of metabolism in newborn children from Turkey, based on their urine NMR profiles. More than 20 clinics are participating to the project that is coordinated by INFAI, a specialist in the transfer of advanced analytical technology into medical diagnostics. The construction of statistical models are being developed

  • for the detection of deviations from normality, as well as
  • automatic quantification methods for indicative metabolites

Bruker BioSpin recently installed high-resolution magic angle spinning NMR (HRMAS-NMR) systems that can rapidly analyze tissue biopsies. The main objective for HRMAS-NMR is to establish a rapid and effective clinical method to assess tumor grade and other important aspects of cancer during surgery.

Combined NMR and Mass Spec

There is increasing interest in combining NMR and MS, two of the main analytical assays in metabolomic research, as a means

  • to improve data sensitivity and to
  • fully elucidate the complex metabolome within a given biological sample.
  •  to realize a potential for cancer biomarker discovery in the realms of diagnosis, prognosis, and treatment.

.

Using combined NMR and MS to measure the levels of nearly 250 separate metabolites in the patient’s blood, Dr. Weljie and other researchers at the University of Calgary were able to rapidly determine the malignancy of a  pancreatic lesion (in 10–15% of the cases, it is difficult to discern between benign and malignant), while avoiding unnecessary surgery in patients with benign lesions.

When performing NMR and MS on a single biological fluid, ultimately “we are,” noted Dr. Weljie,

  1. “splitting up information content, processing, and introducing a lot of background noise and error and
  2. then trying to reintegrate the data…
    It’s like taking a complex item, with multiple pieces, out of an IKEA box and trying to repackage it perfectly into another box.”

By improving the workflow between the initial splitting of the sample, they improved endpoint data integration, proving that

  • a streamlined approach to combined NMR/MS can be achieved,
  • leading to a very strong, robust and precise metabolomics toolset.

Metabolomics Research Picks Up Speed

Field Advances in Quest to Improve Disease Diagnosis and Predict Drug Response

John Morrow Jr., Ph.D.
GEN May 1, 2011 (Vol. 31, No. 9)

As an important discipline within systems biology, metabolomics is being explored by a number of laboratories for

  • its potential in pharmaceutical development.

Studying metabolites can offer insights into the relationships between genotype and phenotype, as well as between genotype and environment. In addition, there is plenty to work with—there are estimated to be some 2,900 detectable metabolites in the human body, of which

  1. 309 have been identified in cerebrospinal fluid,
  2. 1,122 in serum,
  3. 458 in urine, and
  4. roughly 300 in other compartments.

Guowang Xu, Ph.D., a researcher at the Dalian Institute of Chemical Physics.  is investigating the causes of death in China,

  • and how they have been changing over the years as the country has become a more industrialized nation.
  •  the increase in the incidence of metabolic disorders such as diabetes has grown to affect 9.7% of the Chinese population.

Dr. Xu,  collaborating with Rainer Lehman, Ph.D., of the University of Tübingen, Germany, compared urinary metabolites in samples from healthy individuals with samples taken from prediabetic, insulin-resistant subjects. Using mass spectrometry coupled with electrospray ionization in the positive mode, they observed striking dissimilarities in levels of various metabolites in the two groups.

“When we performed a comprehensive two-dimensional gas chromatography, time-of-flight mass spectrometry analysis of our samples, we observed several metabolites, including

  • 2-hydroxybutyric acid in plasma,
  •  as potential diabetes biomarkers,” Dr. Xu explains.

In other, unrelated studies, Dr. Xu and the German researchers used a metabolomics approach to investigate the changes in plasma metabolite profiles immediately after exercise and following a 3-hour and 24-hour period of recovery. They found that

  • medium-chain acylcarnitines were the most distinctive exercise biomarkers, and
  • they are released as intermediates of partial beta oxidation in human myotubes and mouse muscle tissue.

Dr. Xu says. “The traditional approach of assessment based on a singular biomarker is being superseded by the introduction of multiple marker profiles.”

Typical of the studies under way by Dr. Kaddurah-Daouk and her colleaguesat Duke University

  • is a recently published investigation highlighting the role of an SNP variant in
  • the glycine dehydrogenase gene on individual response to antidepressants.
  •  patients who do not respond to the selective serotonin uptake inhibitors citalopram and escitalopram
  • carried a particular single nucleotide polymorphism in the GD gene.

“These results allow us to pinpoint a possible

  • role for glycine in selective serotonin reuptake inhibitor response and
  • illustrate the use of pharmacometabolomics to inform pharmacogenomics.

These discoveries give us the tools for prognostics and diagnostics so that

  • we can predict what conditions will respond to treatment.

“This approach to defining health or disease in terms of metabolic states opens a whole new paradigm.

By screening hundreds of thousands of molecules, we can understand

  • the relationship between human genetic variability and the metabolome.”

Dr. Kaddurah-Daouk talks about statins as a current

  • model of metabolomics investigations.

It is now known that the statins  have widespread effects, altering a range of metabolites. To sort out these changes and develop recommendations for which individuals should be receiving statins will require substantial investments of energy and resources into defining the complex web of biochemical changes that these drugs initiate.
Furthermore, Dr. Kaddurah-Daouk asserts that,

  • “genetics only encodes part of the phenotypic response.

One needs to take into account the

  • net environment contribution in order to determine
  • how both factors guide the changes in our metabolic state that determine the phenotype.”

Interactive Metabolomics

Researchers at the University of Nottingham use diffusion-edited nuclear magnetic resonance spectroscopy to assess the effects of a biological matrix on metabolites. Diffusion-edited NMR experiments provide a way to

  • separate the different compounds in a mixture
  • based on the differing translational diffusion coefficients (which reflect the size and shape of the molecule).

The measurements are carried out by observing

  • the attenuation of the NMR signals during a pulsed field gradient experiment.

Clare Daykin, Ph.D., is a lecturer at the University of Nottingham, U.K. Her field of investigation encompasses “interactive metabolomics,”which she defines as

“the study of the interactions between low molecular weight biochemicals and macromolecules in biological samples ..

  • without preselection of the components of interest.

“Blood plasma is a heterogeneous mixture of molecules that

  1. undergo a variety of interactions including metal complexation,
  2. chemical exchange processes,
  3. micellar compartmentation,
  4. enzyme-mediated biotransformations, and
  5. small molecule–macromolecular binding.”

Many low molecular weight compounds can exist

  • freely in solution,
  • bound to proteins, or
  • within organized aggregates such as lipoprotein complexes.

Therefore, quantitative comparison of plasma composition from

  • diseased individuals compared to matched controls provides an incomplete insight to plasma metabolism.

“It is not simply the concentrations of metabolites that must be investigated,

  • but their interactions with the proteins and lipoproteins within this complex web.

Rather than targeting specific metabolites of interest, Dr. Daykin’s metabolite–protein binding studies aim to study

  • the interactions of all detectable metabolites within the macromolecular sample.

Such activities can be studied through the use of diffusion-edited nuclear magnetic resonance (NMR) spectroscopy, in which one can assess

  • the effects of the biological matrix on the metabolites.

“This can lead to a more relevant and exact interpretation

  • for systems where metabolite–macromolecule interactions occur.”

Diffusion-edited NMR experiments provide a way to separate the different compounds in a mixture based on

  • the differing translational diffusion coefficients (which reflect the size and shape of the molecule).

The measurements are carried out by observing

  • the attenuation of the NMR signals during a pulsed field gradient experiment.

Pushing the Limits

It is widely recognized that many drug candidates fail during development due to ancillary toxicity. Uwe Sauer, Ph.D., professor, and Nicola Zamboni, Ph.D., researcher, both at the Eidgenössische Technische Hochschule, Zürich (ETH Zürich), are applying

  • high-throughput intracellular metabolomics to understand
  • the basis of these unfortunate events and
  • head them off early in the course of drug discovery.

“Since metabolism is at the core of drug toxicity, we developed a platform for

  • measurement of 50–100 targeted metabolites by
  • a high-throughput system consisting of flow injection
  • coupled to tandem mass spectrometry.”

Using this approach, Dr. Sauer’s team focused on

  • the central metabolism of the yeast Saccharomyces cerevisiae, reasoning that
  • this core network would be most susceptible to potential drug toxicity.

Screening approximately 41 drugs that were administered at seven concentrations over three orders of magnitude, they observed changes in metabolome patterns at much lower drug concentrations without attendant physiological toxicity.

The group carried out statistical modeling of about

  • 60 metabolite profiles for each drug they evaluated.

This data allowed the construction of a “profile effect map” in which

  • the influence of each drug on metabolite levels can be followed, including off-target effects, which
  • provide an indirect measure of the possible side effects of the various drugs.

Dr. Sauer says.“We have found that this approach is

  • at least 100 times as fast as other omics screening platforms,”

“Some drugs, including many anticancer agents,

  • disrupt metabolism long before affecting growth.”
killing cancer cells

killing cancer cells

Furthermore, they used the principle of 13C-based flux analysis, in which

  • metabolites labeled with 13C are used to follow the utilization of metabolic pathways in the cell.

These 13C-determined intracellular responses of metabolic fluxes to drug treatment demonstrate

  • the functional performance of the network to be rather robust,
conformational changes leading to substrate efflux.

conformational changes leading to substrate efflux.

leading Dr. Sauer to the conclusion that

  • the phenotypic vigor he observes to drug challenges
  • is achieved by a flexible make up of the metabolome.

Dr. Sauer is confident that it will be possible to expand the scope of these investigations to hundreds of thousands of samples per study. This will allow answers to the questions of

  • how cells establish a stable functioning network in the face of inevitable concentration fluctuations.

Is Now the Hour?

There is great enthusiasm and agitation within the biotech community for

  • metabolomics approaches as a means of reversing the dismal record of drug discovery

that has accumulated in the last decade.

While the concept clearly makes sense and is being widely applied today, there are many reasons why drugs fail in development, and metabolomics will not be a panacea for resolving all of these questions. It is too early at this point to recognize a trend or a track record, and it will take some time to see how this approach can aid in drug discovery and shorten the timeline for the introduction of new pharmaceutical agents.

Degree of binding correlated with function

Degree of binding correlated with function

Diagram_of_a_two-photon_excitation_microscope_

Diagram_of_a_two-photon_excitation_microscope_

Part 2.  Biologists Find ‘Missing Link’ in the Production of Protein Factories in Cells

Biologists at UC San Diego have found

  • the “missing link” in the chemical system that
  • enables animal cells to produce ribosomes

—the thousands of protein “factories” contained within each cell that

  • manufacture all of the proteins needed to build tissue and sustain life.
‘Missing Link’

‘Missing Link’

Their discovery, detailed in the June 23 issue of the journal Genes & Development, will not only force

  • a revision of basic textbooks on molecular biology, but also
  • provide scientists with a better understanding of
  • how to limit uncontrolled cell growth, such as cancer,
  • that might be regulated by controlling the output of ribosomes.

Ribosomes are responsible for the production of the wide variety of proteins that include

  1. enzymes;
  2. structural molecules, such as hair,
  3. skin and bones;
  4. hormones like insulin; and
  5. components of our immune system such as antibodies.

Regarded as life’s most important molecular machine, ribosomes have been intensively studied by scientists (the 2009 Nobel Prize in Chemistry, for example, was awarded for studies of its structure and function). But until now researchers had not uncovered all of the details of how the proteins that are used to construct ribosomes are themselves produced.

In multicellular animals such as humans,

  • ribosomes are made up of about 80 different proteins
    (humans have 79 while some other animals have a slightly different number) as well as
  • four different kinds of RNA molecules.

In 1969, scientists discovered that

  • the synthesis of the ribosomal RNAs is carried out by specialized systems using two key enzymes:
  • RNA polymerase I and RNA polymerase III.

But until now, scientists were unsure if a complementary system was also responsible for

  • the production of the 80 proteins that make up the ribosome.

That’s essentially what the UC San Diego researchers headed by Jim Kadonaga, a professor of biology, set out to examine. What they found was the missing link—the specialized

  • system that allows ribosomal proteins themselves to be synthesized by the cell.

Kadonaga says that he and coworkers found that ribosomal proteins are synthesized via

  • a novel regulatory system with the enzyme RNA polymerase II and
  • a factor termed TRF2,”

“For the production of most proteins,

  1. RNA polymerase II functions with
  2. a factor termed TBP,
  3. but for the synthesis of ribosomal proteins, it uses TRF2.”
  •  this specialized TRF2-based system for ribosome biogenesis
  • provides a new avenue for the study of ribosomes and
  • its control of cell growth, and

“it should lead to a better understanding and potential treatment of diseases such as cancer.”

Coordination of the transcriptome and metabolome

Coordination of the transcriptome and metabolome

the potential advantages conferred by distal-site protein synthesis

the potential advantages conferred by distal-site protein synthesis

Other authors of the paper were UC San Diego biologists Yuan-Liang Wang, Sascha Duttke and George Kassavetis, and Kai Chen, Jeff Johnston, and Julia Zeitlinger of the Stowers Institute for Medical Research in Kansas City, Missouri. Their research was supported by two grants from the National Institutes of Health (1DP2OD004561-01 and R01 GM041249).

Turning Off a Powerful Cancer Protein

Scientists have discovered how to shut down a master regulatory transcription factor that is

  • key to the survival of a majority of aggressive lymphomas,
  • which arise from the B cells of the immune system.

The protein, Bcl6, has long been considered too complex to target with a drug since it is also crucial

  • to the healthy functioning of many immune cells in the body, not just B cells gone bad.

The researchers at Weill Cornell Medical College report that it is possible

  • to shut down Bcl6 in diffuse large B-cell lymphoma (DLBCL)
  • while not affecting its vital function in T cells and macrophages
  • that are needed to support a healthy immune system.

If Bcl6 is completely inhibited, patients might suffer from systemic inflammation and atherosclerosis. The team conducted this new study to help clarify possible risks, as well as to understand

  • how Bcl6 controls the various aspects of the immune system.

The findings in this study were inspired from

  • preclinical testing of two Bcl6-targeting agents that Dr. Melnick and his Weill Cornell colleagues have developed
  • to treat DLBCLs.

These experimental drugs are

  • RI-BPI, a peptide mimic, and
  • the small molecule agent 79-6.

“This means the drugs we have developed against Bcl6 are more likely to be

  • significantly less toxic and safer for patients with this cancer than we realized,”

says Ari Melnick, M.D., professor of hematology/oncology and a hematologist-oncologist at NewYork-Presbyterian Hospital/Weill Cornell Medical Center.

Dr. Melnick says the discovery that

  • a master regulatory transcription factor can be targeted
  • offers implications beyond just treating DLBCL.

Recent studies from Dr. Melnick and others have revealed that

  • Bcl6 plays a key role in the most aggressive forms of acute leukemia, as well as certain solid tumors.

Bcl6 can control the type of immune cell that develops in the bone marrow—playing many roles

  • in the development of B cells, T cells, macrophages, and other cells—including a primary and essential role in
  • enabling B-cells to generate specific antibodies against pathogens.

According to Dr. Melnick, “When cells lose control of Bcl6,

  • lymphomas develop in the immune system.

Lymphomas are ‘addicted’ to Bcl6, and therefore

  • Bcl6 inhibitors powerfully and quickly destroy lymphoma cells,” .

The big surprise in the current study is that rather than functioning as a single molecular machine,

  • Bcl6 functions like a Swiss Army knife,
  • using different tools to control different cell types.

This multifunction paradigm could represent a general model for the functioning of other master regulatory transcription factors.

“In this analogy, the Swiss Army knife, or transcription factor, keeps most of its tools folded,

  • opening only the one it needs in any given cell type,”

He makes the following analogy:

  • “For B cells, it might open and use the knife tool;
  • for T cells, the cork screw;
  • for macrophages, the scissors.”

“this means that you only need to prevent the master regulator from using certain tools to treat cancer. You don’t need to eliminate the whole knife,” . “In fact, we show that taking out the whole knife is harmful since

  • the transcription factor has many other vital functions that other cells in the body need.”

Prior to these study results, it was not known that a master regulator could separate its functions so precisely. Researchers hope this will be a major benefit to the treatment of DLBCL and perhaps other disorders that are influenced by Bcl6 and other master regulatory transcription factors.

The study is published in the journal Nature Immunology, in a paper titled “Lineage-specific functions of Bcl-6 in immunity and inflammation are mediated by distinct biochemical mechanisms”.

Part 3. Neuroscience

Vesicles influence function of nerve cells 
Oct, 06 2014        source: http://feeds.sciencedaily.com

Neurons (blue) which have absorbed exosomes (green) have increased levels of the enzyme catalase (red), which helps protect them against peroxides.

Neurons (blue) which have absorbed exosomes (green) have increased levels of the enzyme catalase (red), which helps protect them against peroxides.

Neurons (blue) which have absorbed exosomes (green) have increased levels of the enzyme catalase (red), which helps protect them against peroxides.

Tiny vesicles containing protective substances

  • which they transmit to nerve cells apparently
  • play an important role in the functioning of neurons.

As cell biologists at Johannes Gutenberg University Mainz (JGU) have discovered,

  • nerve cells can enlist the aid of mini-vesicles of neighboring glial cells
  • to defend themselves against stress and other potentially detrimental factors.

These vesicles, called exosomes, appear to stimulate the neurons on various levels:

  • they influence electrical stimulus conduction,
  • biochemical signal transfer, and
  • gene regulation.

Exosomes are thus multifunctional signal emitters

  • that can have a significant effect in the brain.
Exosome

Exosome

The researchers in Mainz already observed in a previous study that

  • oligodendrocytes release exosomes on exposure to neuronal stimuli.
  • these are absorbed by the neurons and improve neuronal stress tolerance.

Oligodendrocytes, a type of glial cell, form an

  • insulating myelin sheath around the axons of neurons.

The exosomes transport protective proteins such as

  • heat shock proteins,
  • glycolytic enzymes, and
  • enzymes that reduce oxidative stress from one cell type to another,
  • but also transmit genetic information in the form of ribonucleic acids.

“As we have now discovered in cell cultures, exosomes seem to have a whole range of functions,” explained Dr. Eva-Maria Krmer-Albers. By means of their transmission activity, the small bubbles that are the vesicles

  • not only promote electrical activity in the nerve cells, but also
  • influence them on the biochemical and gene regulatory level.

“The extent of activities of the exosomes is impressive,” added Krmer-Albers. The researchers hope that the understanding of these processes will contribute to the development of new strategies for the treatment of neuronal diseases. Their next aim is to uncover how vesicles actually function in the brains of living organisms.

http://labroots.com/user/news/article/id/217438/title/vesicles-influence-function-of-nerve-cells

The above story is based on materials provided by Universitt Mainz.

Universitt Mainz. “Vesicles influence function of nerve cells.” ScienceDaily. ScienceDaily, 6 October 2014. www.sciencedaily.com/releases/2014/10/141006174214.htm

Neuroscientists use snail research to help explain “chemo brain”

10/08/2014
It is estimated that as many as half of patients taking cancer drugs experience a decrease in mental sharpness. While there have been many theories, what causes “chemo brain” has eluded scientists.

In an effort to solve this mystery, neuroscientists at The University of Texas Health Science Center at Houston (UTHealth) conducted an experiment in an animal memory model and their results point to a possible explanation. Findings appeared in The Journal of Neuroscience.

In the study involving a sea snail that shares many of the same memory mechanisms as humans and a drug used to treat a variety of cancers, the scientists identified

  • memory mechanisms blocked by the drug.

Then, they were able to counteract or

  • unblock the mechanisms by administering another agent.

“Our research has implications in the care of people given to cognitive deficits following drug treatment for cancer,” said John H. “Jack” Byrne, Ph.D., senior author, holder of the June and Virgil Waggoner Chair and Chairman of the Department of Neurobiology and Anatomy at the UTHealth Medical School. “There is no satisfactory treatment at this time.”

Byrne’s laboratory is known for its use of a large snail called Aplysia californica to further the understanding of the biochemical signaling among nerve cells (neurons).  The snails have large neurons that relay information much like those in humans.

When Byrne’s team compared cell cultures taken from normal snails to

  • those administered a dose of a cancer drug called doxorubicin,

the investigators pinpointed a neuronal pathway

  • that was no longer passing along information properly.

With the aid of an experimental drug,

  • the scientists were able to reopen the pathway.

Unfortunately, this drug would not be appropriate for humans, Byrne said. “We want to identify other drugs that can rescue these memory mechanisms,” he added.

According the American Cancer Society, some of the distressing mental changes cancer patients experience may last a short time or go on for years.

Byrne’s UT Health research team includes co-lead authors Rong-Yu Liu, Ph.D., and Yili Zhang, Ph.D., as well as Brittany Coughlin and Leonard J. Cleary, Ph.D. All are affiliated with the W.M. Keck Center for the Neurobiology of Learning and Memory.

Byrne and Cleary also are on the faculty of The University of Texas Graduate School of Biomedical Sciences at Houston. Coughlin is a student at the school, which is jointly operated by UT Health and The University of Texas MD Anderson Cancer Center.

The study titled “Doxorubicin Attenuates Serotonin-Induced Long-Term Synaptic Facilitation by Phosphorylation of p38 Mitogen-Activated Protein Kinase” received support from National Institutes of Health grant (NS019895) and the Zilkha Family Discovery Fellowship.

Doxorubicin Attenuates Serotonin-Induced Long-Term Synaptic Facilitation by Phosphorylation of p38 Mitogen-Activated Protein Kinase

Source: Univ. of Texas Health Science Center at Houston

http://www.rdmag.com/news/2014/10/neuroscientists-use-snail-research-help-explain-E2_9_Cchemo-brain

Doxorubicin Attenuates Serotonin-Induced Long-Term Synaptic Facilitation by Phosphorylation of p38 Mitogen-Activated Protein Kinase

Rong-Yu Liu*,  Yili Zhang*,  Brittany L. Coughlin,  Leonard J. Cleary, and  John H. Byrne   +Show Affiliations
The Journal of Neuroscience, 1 Oct 2014, 34(40): 13289-13300;
http://dx.doi.org:/10.1523/JNEUROSCI.0538-14.2014

Doxorubicin (DOX) is an anthracycline used widely for cancer chemotherapy. Its primary mode of action appears to be

  • topoisomerase II inhibition, DNA cleavage, and free radical generation.

However, in non-neuronal cells, DOX also inhibits the expression of

  • dual-specificity phosphatases (also referred to as MAPK phosphatases) and thereby
  1. inhibits the dephosphorylation of extracellular signal-regulated kinase (ERK) and
  2. p38 mitogen-activated protein kinase (p38 MAPK),
  3. two MAPK isoforms important for long-term memory (LTM) formation.

Activation of these kinases by DOX in neurons, if present,

  • could have secondary effects on cognitive functions, such as learning and memory.

The present study used cultures of rat cortical neurons and sensory neurons (SNs) of Aplysia

  • to examine the effects of DOX on levels of phosphorylated ERK (pERK) and
  • phosphorylated p38 (p-p38) MAPK.

In addition, Aplysia neurons were used to examine the effects of DOX on

  • long-term enhanced excitability, long-term synaptic facilitation (LTF), and
  • long-term synaptic depression (LTD).

DOX treatment led to elevated levels of

  • pERK and p-p38 MAPK in SNs and cortical neurons.

In addition, it increased phosphorylation of

  • the downstream transcriptional repressor cAMP response element-binding protein 2 in SNs.

DOX treatment blocked serotonin-induced LTF and enhanced LTD induced by the neuropeptide Phe-Met-Arg-Phe-NH2. The block of LTF appeared to be attributable to

  • overriding inhibitory effects of p-p38 MAPK, because
  • LTF was rescued in the presence of an inhibitor of p38 MAPK
    (SB203580 [4-(4-fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)-1H-imidazole]) .

These results suggest that acute application of DOX might impair the formation of LTM via the p38 MAPK pathway.
Terms: Aplysia chemotherapy ERK  p38 MAPK serotonin synaptic plasticity

Technology that controls brain cells with radio waves earns early BRAIN grant

10/08/2014

bright spots = cells with increased calcium after treatment with radio waves,  allows neurons to fire

bright spots = cells with increased calcium after treatment with radio waves, allows neurons to fire

BRAIN control: The new technology uses radio waves to activate or silence cells remotely. The bright spots above represent cells with increased calcium after treatment with radio waves, a change that would allow neurons to fire.

A proposal to develop a new way to

  • remotely control brain cells

from Sarah Stanley, a research associate in Rockefeller University’s Laboratory of Molecular Genetics, headed by Jeffrey M. Friedman, is

  • among the first to receive funding from U.S. President Barack Obama’s BRAIN initiative.

The project will make use of a technique called

  • radiogenetics that combines the use of radio waves or magnetic fields with
  • nanoparticles to turn neurons on or off.

The National Institutes of Health is one of four federal agencies involved in the BRAIN (Brain Research through Advancing Innovative Neurotechnologies) initiative. Following in the ambitious footsteps of the Human Genome Project, the BRAIN initiative seeks

  • to create a dynamic map of the brain in action,

a goal that requires the development of new technologies. The BRAIN initiative working group, which outlined the broad scope of the ambitious project, was co-chaired by Rockefeller’s Cori Bargmann, head of the Laboratory of Neural Circuits and Behavior.

Stanley’s grant, for $1.26 million over three years, is one of 58 projects to get BRAIN grants, the NIH announced. The NIH’s plan for its part of this national project, which has been pitched as “America’s next moonshot,” calls for $4.5 billion in federal funds over 12 years.

The technology Stanley is developing would

  • enable researchers to manipulate the activity of neurons, as well as other cell types,
  • in freely moving animals in order to better understand what these cells do.

Other techniques for controlling selected groups of neurons exist, but her new nanoparticle-based technique has a

  • unique combination of features that may enable new types of experimentation.
  • it would allow researchers to rapidly activate or silence neurons within a small area of the brain or
  • dispersed across a larger region, including those in difficult-to-access locations.

Stanley also plans to explore the potential this method has for use treating patients.

“Francis Collins, director of the NIH, has discussed

  • the need for studying the circuitry of the brain,
  • which is formed by interconnected neurons.

Our remote-control technology may provide a tool with which researchers can ask new questions about the roles of complex circuits in regulating behavior,” Stanley says.
Rockefeller University’s Laboratory of Molecular Genetics
Source: Rockefeller Univ.

Part 4.  Cancer

Two Proteins Found to Block Cancer Metastasis

Why do some cancers spread while others don’t? Scientists have now demonstrated that

  • metastatic incompetent cancers actually “poison the soil”
  • by generating a micro-environment that blocks cancer cells
  • from settling and growing in distant organs.

The “seed and the soil” hypothesis proposed by Stephen Paget in 1889 is now widely accepted to explain how

  • cancer cells (seeds) are able to generate fertile soil (the micro-environment)
  • in distant organs that promotes cancer’s spread.

However, this concept had not explained why some tumors do not spread or metastasize.

The researchers, from Weill Cornell Medical College, found that

  • two key proteins involved in this process work by
  • dramatically suppressing cancer’s spread.

The study offers hope that a drug based on these

  • potentially therapeutic proteins, prosaposin and Thrombospondin 1 (Tsp-1),

might help keep human cancer at bay and from metastasizing.

Scientists don’t understand why some tumors wouldn’t “want” to spread. It goes against their “job description,” says the study’s senior investigator, Vivek Mittal, Ph.D., an associate professor of cell and developmental biology in cardiothoracic surgery and director of the Neuberger Berman Foundation Lung Cancer Laboratory at Weill Cornell Medical College. He theorizes that metastasis occurs when

  • the barriers that the body throws up to protect itself against cancer fail.

But there are some tumors in which some of the barriers may still be intact. “So that suggests

  • those primary tumors will continue to grow, but that
  • an innate protective barrier still exists that prevents them from spreading and invading other organs,”

The researchers found that, like typical tumors,

  • metastasis-incompetent tumors also send out signaling molecules
  • that establish what is known as the “premetastatic niche” in distant organs.

These niches composed of bone marrow cells and various growth factors have been described previously by others including Dr. Mittal as the fertile “soil” that the disseminated cancer cell “seeds” grow in.

Weill Cornell’s Raúl Catena, Ph.D., a postdoctoral fellow in Dr. Mittal’s laboratory, found an important difference between the tumor types. Metastatic-incompetent tumors

  • systemically increased expression of Tsp-1, a molecule known to fight cancer growth.
  • increased Tsp-1 production was found specifically in the bone marrow myeloid cells
  • that comprise the metastatic niche.

These results were striking, because for the first time Dr. Mittal says

  • the bone marrow-derived myeloid cells were implicated as
  • the main producers of Tsp-1,.

In addition, Weill Cornell and Harvard researchers found that

  • prosaposin secreted predominantly by the metastatic-incompetent tumors
  • increased expression of Tsp-1 in the premetastatic lungs.

Thus, Dr. Mittal posits that prosaposin works in combination with Tsp-1

  • to convert pro-metastatic bone marrow myeloid cells in the niche
  • into cells that are not hospitable to cancer cells that spread from a primary tumor.
  • “The very same myeloid cells in the niche that we know can promote metastasis
  • can also be induced under the command of the metastatic incompetent primary tumor to inhibit metastasis,”

The research team found that

  • the Tsp-1–inducing activity of prosaposin
  • was contained in only a 5-amino acid peptide region of the protein, and
  • this peptide alone induced Tsp-1 in the bone marrow cells and
  • effectively suppressed metastatic spread in the lungs
  • in mouse models of breast and prostate cancer.

This 5-amino acid peptide with Tsp-1–inducing activity

  • has the potential to be used as a therapeutic agent against metastatic cancer,

The scientists have begun to test prosaposin in other tumor types or metastatic sites.

Dr. Mittal says that “The clinical implications of the study are:

  • “Not only is it theoretically possible to design a prosaposin-based drug or drugs
  • that induce Tsp-1 to block cancer spread, but
  • you could potentially create noninvasive prognostic tests
  • to predict whether a cancer will metastasize.”

The study was reported in the April 30 issue of Cancer Discovery, in a paper titled “Bone Marrow-Derived Gr1+ Cells Can Generate a Metastasis-Resistant Microenvironment Via Induced Secretion of Thrombospondin-1”.

Disabling Enzyme Cripples Tumors, Cancer Cells

First Step of Metastasis

First Step of Metastasis

Published: Sep 05, 2013  http://www.technologynetworks.com/Metabolomics/news.aspx?id=157138

Knocking out a single enzyme dramatically cripples the ability of aggressive cancer cells to spread and grow tumors.

The paper, published in the journal Proceedings of the National Academy of Sciences, sheds new light on the importance of lipids, a group of molecules that includes fatty acids and cholesterol, in the development of cancer.

Researchers have long known that cancer cells metabolize lipids differently than normal cells. Levels of ether lipids – a class of lipids that are harder to break down – are particularly elevated in highly malignant tumors.

“Cancer cells make and use a lot of fat and lipids, and that makes sense because cancer cells divide and proliferate at an accelerated rate, and to do that,

  • they need lipids, which make up the membranes of the cell,”

said study principal investigator Daniel Nomura, assistant professor in UC Berkeley’s Department of Nutritional Sciences and Toxicology. “Lipids have a variety of uses for cellular structure, but what we’re showing with our study is that

  • lipids can send signals that fuel cancer growth.”

In the study, Nomura and his team tested the effects of reducing ether lipids on human skin cancer cells and primary breast tumors. They targeted an enzyme,

  • alkylglycerone phosphate synthase, or AGPS,
  • known to be critical to the formation of ether lipids.

The researchers confirmed that

  1. AGPS expression increased when normal cells turned cancerous.
  2. inactivating AGPS substantially reduced the aggressiveness of the cancer cells.

“The cancer cells were less able to move and invade,” said Nomura.

The researchers also compared the impact of

  • disabling the AGPS enzyme in mice that had been injected with cancer cells.

Nomura. observes -“Among the mice that had the AGPS enzyme inactivated,

  • the tumors were nonexistent,”

“The mice that did not have this enzyme

  • disabled rapidly developed tumors.”

The researchers determined that

  • inhibiting AGPS expression depleted the cancer cells of ether lipids.
  • AGPS altered levels of other types of lipids important to the ability of the cancer cells to survive and spread, including
    • prostaglandins and acyl phospholipids.

“What makes AGPS stand out as a treatment target is that the enzyme seems to simultaneously

  • regulate multiple aspects of lipid metabolism
  • important for tumor growth and malignancy.”

Future steps include the

  • development of AGPS inhibitors for use in cancer therapy,

“This study sheds considerable light on the important role that AGPS plays in ether lipid metabolism in cancer cells, and it suggests that

  • inhibitors of this enzyme could impair tumor formation,”

said Benjamin Cravatt, Professor and Chair of Chemical Physiology at The Scripps Research Institute, who is not part of the UC.

Agilent Technologies Thought Leader Award Supports Translational Research Program
Published: Mon, March 04, 2013

The award will support Dr DePinho’s research into

  • metabolic reprogramming in the earliest stages of cancer.

Agilent Technologies Inc. announces that Dr. Ronald A. DePinho, a world-renowned oncologist and researcher, has received an Agilent Thought Leader Award.

DePinho is president of the University of Texas MD Anderson Cancer Center. DePinho and his team hope to discover and characterize

  • alterations in metabolic flux during tumor initiation and maintenance, and to identify biomarkers for early detection of pancreatic cancer together with
  • novel therapeutic targets.

Researchers on his team will work with scientists from the university’s newly formed Institute of Applied Cancer Sciences.

The Agilent Thought Leader Award provides funds to support personnel as well as a state-of-the-art Agilent 6550 iFunnel Q-TOF LC/MS system.

“I am extremely pleased to receive this award for metabolomics research, as the survival rates for pancreatic cancer have not significantly improved over the past 20 years,” DePinho said. “This technology will allow us to

  • rapidly identify new targets that drive the formation, progression and maintenance of pancreatic cancer.

Discoveries from this research will also lead to

  • the development of effective early detection biomarkers and novel therapeutic interventions.”

“We are proud to support Dr. DePinho’s exciting translational research program, which will make use of

  • metabolomics and integrated biology workflows and solutions in biomarker discovery,”

said Patrick Kaltenbach, Agilent vice president, general manager of the Liquid Phase Division, and the executive sponsor of this award.

The Agilent Thought Leader Program promotes fundamental scientific advances by support of influential thought leaders in the life sciences and chemical analysis fields.

The covalent modifier Nedd8 is critical for the activation of Smurf1 ubiquitin ligase in tumorigenesis

Ping Xie, Minghua Zhang, Shan He, Kefeng Lu, Yuhan Chen, Guichun Xing, et al.
Nature Communications
  2014; 5(3733).  http://dx.doi.org:/10.1038/ncomms4733

Neddylation, the covalent attachment of ubiquitin-like protein Nedd8, of the Cullin-RING E3 ligase family

  • regulates their ubiquitylation activity.

However, regulation of HECT ligases by neddylation has not been reported to date. Here we show that

  • the C2-WW-HECT ligase Smurf1 is activated by neddylation.

Smurf1 physically interacts with

  1. Nedd8 and Ubc12,
  2. forms a Nedd8-thioester intermediate, and then
  3. catalyses its own neddylation on multiple lysine residues.

Intriguingly, this autoneddylation needs

  • an active site at C426 in the HECT N-lobe.

Neddylation of Smurf1 potently enhances

  • ubiquitin E2 recruitment and
  • augments the ubiquitin ligase activity of Smurf1.

The regulatory role of neddylation

  • is conserved in human Smurf1 and yeast Rsp5.

Furthermore, in human colorectal cancers,

  • the elevated expression of Smurf1, Nedd8, NAE1 and Ubc12
  • correlates with cancer progression and poor prognosis.

These findings provide evidence that

  • neddylation is important in HECT ubiquitin ligase activation and
  • shed new light on the tumour-promoting role of Smurf1.
 Swinging domains in HECT E3

Swinging domains in HECT E3

Subject terms: Biological sciences Cancer Cell biology

Figure 1: Smurf1 expression is elevated in colorectal cancer tissues.

Smurf1 expression is elevated in colorectal cancer tissues.

Smurf1 expression is elevated in colorectal cancer tissues.

(a) Smurf1 expression scores are shown as box plots, with the horizontal lines representing the median; the bottom and top of the boxes representing the 25th and 75th percentiles, respectively; and the vertical bars representing the ra

Figure 2: Positive correlation of Smurf1 expression with Nedd8 and its interacting enzymes in colorectal cancer.

Positive correlation of Smurf1 expression with Nedd8 and its interacting enzymes in colorectal cancer

Positive correlation of Smurf1 expression with Nedd8 and its interacting enzymes in colorectal cancer

(a) Representative images from immunohistochemical staining of Smurf1, Ubc12, NAE1 and Nedd8 in the same colorectal cancer tumour. Scale bars, 100 μm. (bd) The expression scores of Nedd8 (b, n=283 ), NAE1 (c, n=281) and Ubc12 (d, n=19…

Figure 3: Smurf1 interacts with Ubc12.

Smurf1 interacts with Ubc12

Smurf1 interacts with Ubc12

(a) GST pull-down assay of Smurf1 with Ubc12. Both input and pull-down samples were subjected to immunoblotting with anti-His and anti-GST antibodies. Smurf1 interacted with Ubc12 and UbcH5c, but not with Ubc9. (b) Mapping the regions…

Figure 4: Nedd8 is attached to Smurf1through C426-catalysed autoneddylation.

Nedd8 is attached to Smurf1through C426-catalysed autoneddylation

Nedd8 is attached to Smurf1through C426-catalysed autoneddylation

(a) Covalent neddylation of Smurf1 in vitro.Purified His-Smurf1-WT or C699A proteins were incubated with Nedd8 and Nedd8-E1/E2. Reactions were performed as described in the Methods section. Samples were analysed by western blotting wi…

Figure 5: Neddylation of Smurf1 activates its ubiquitin ligase activity.

Neddylation of Smurf1 activates its ubiquitin ligase activity.

Neddylation of Smurf1 activates its ubiquitin ligase activity.

(a) In vivo Smurf1 ubiquitylation assay. Nedd8 was co-expressed with Smurf1 WT or C699A in HCT116 cells (left panels). Twenty-four hours post transfection, cells were treated with MG132 (20 μM, 8 h). HCT116 cells were transfected with…

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The deubiquitylase USP33 discriminates between RALB functions in autophagy and innate immune response

M Simicek, S Lievens, M Laga, D Guzenko, VN. Aushev, et al.
Nature Cell Biology 2013; 15, 1220–1230    http://dx.doi.org:/10.1038/ncb2847

The RAS-like GTPase RALB mediates cellular responses to nutrient availability or viral infection by respectively

  • engaging two components of the exocyst complex, EXO84 and SEC5.
  1. RALB employs SEC5 to trigger innate immunity signalling, whereas
  2. RALB–EXO84 interaction induces autophagocytosis.

How this differential interaction is achieved molecularly by the RAL GTPase remains unknown.

We found that whereas GTP binding

  • turns on RALB activity,

ubiquitylation of RALB at Lys 47

  • tunes its activity towards a particular effector.

Specifically, ubiquitylation at Lys 47

  • sterically inhibits RALB binding to EXO84, while
  • facilitating its interaction with SEC5.

Double-stranded RNA promotes

  • RALB ubiquitylation and
  • SEC5–TBK1 complex formation.

In contrast, nutrient starvation

  • induces RALB deubiquitylation
  • by accumulation and relocalization of the deubiquitylase USP33
  • to RALB-positive vesicles.

Deubiquitylated RALB

  • promotes the assembly of the RALB–EXO84–beclin-1 complexes
  • driving autophagosome formation. Thus,
  • ubiquitylation within the effector-binding domain
  • provides the switch for the dual functions of RALB in
    • autophagy and innate immune responses.

Part 5. Metabolic Syndrome

Single Enzyme is Necessary for Development of Diabetes

Published: Aug 20, 2014 http://www.technologynetworks.com/Metabolomics/news.aspx?ID=169416

12-LO enzyme promotes the obesity-induced oxidative stress in the pancreatic cells.

An enzyme called 12-LO promotes the obesity-induced oxidative stress in the pancreatic cells that leads

  • to pre-diabetes, and diabetes.

12-LO’s enzymatic action is the last step in

  • the production of certain small molecules that harm the cell,

according to a team from Indiana University School of Medicine, Indianapolis.

The findings will enable the development of drugs that can interfere with this enzyme, preventing or even reversing diabetes. The research is published ahead of print in the journal Molecular and Cellular Biology.

In earlier studies, these researchers and their collaborators at Eastern Virginia Medical School showed that

  • 12-LO (which stands for 12-lipoxygenase) is present in these cells
  • only in people who become overweight.

The harmful small molecules resulting from 12-LO’s enzymatic action are known as HETEs, short for hydroxyeicosatetraenoic acid.

  1. HETEs harm the mitochondria, which then
  2. fail to produce sufficient energy to enable
  3. the pancreatic cells to manufacture the necessary quantities of insulin.

For the study, the investigators genetically engineered mice that

  • lacked the gene for 12-LO exclusively in their pancreas cells.

Mice were either fed a low-fat or high-fat diet.

Both the control mice and the knockout mice on the high fat diet

  • developed obesity and insulin resistance.

The investigators also examined the pancreatic beta cells of both knockout and control mice, using both microscopic studies and molecular analysis. Those from the knockout mice were intact and healthy, while

  • those from the control mice showed oxidative damage,
  • demonstrating that 12-LO and the resulting HETEs
  • caused the beta cell failure.

Mirmira notes that fatty diet used in the study was the Western Diet, which comprises mostly saturated-“bad”-fats. Based partly on a recent study of related metabolic pathways, he says that

  • the unsaturated and mono-unsaturated fats-which comprise most fats in the healthy,
  • relatively high fat Mediterranean diet-are unlikely to have the same effects.

“Our research is the first to show that 12-LO in the beta cell

  • is the culprit in the development of pre-diabetes, following high fat diets,” says Mirmira.

“Our work also lends important credence to the notion that

  • the beta cell is the primary defective cell in virtually all forms of diabetes and pre-diabetes.”

A New Player in Lipid Metabolism Discovered

Published: Aug18, 2014  http://www.technologynetworks.com/Metabolomics/news.aspx?ID=169356

Specially engineered mice gained no weight, and normal counterparts became obese

  • on the same high-fat, obesity-inducing Western diet.

Specially engineered mice that lacked a particular gene did not gain weight

  • when fed a typical high-fat, obesity-inducing Western diet.

Yet, these mice ate the same amount as their normal counterparts that became obese.

The mice were engineered with fat cells that lacked a gene called SEL1L,

  • known to be involved in the clearance of mis-folded proteins
  • in the cell’s protein making machinery called the endoplasmic reticulum (ER).

When mis-folded proteins are not cleared but accumulate,

  • they destroy the cell and contribute to such diseases as
  1. mad cow disease,
  2. Type 1 diabetes and
  3. cystic fibrosis.

“The million-dollar question is why don’t these mice gain weight? Is this related to its inability to clear mis-folded proteins in the ER?” said Ling Qi, associate professor of molecular and biochemical nutrition and senior author of the study published online July 24 in Cell Metabolism. Haibo Sha, a research associate in Qi’s lab, is the paper’s lead author.

Interestingly, the experimental mice developed a host of other problems, including

  • postprandial hypertriglyceridemia,
  • and fatty livers.

“Although we are yet to find out whether these conditions contribute to the lean phenotype, we found that

  • there was a lipid partitioning defect in the mice lacking SEL1L in fat cells,
  • where fat cells cannot store fat [lipids], and consequently
  • fat goes to the liver.

During the investigation of possible underlying mechanisms, we discovered

  • a novel function for SEL1L as a regulator of lipid metabolism,” said Qi.

Sha said “We were very excited to find that

  • SEL1L is required for the intracellular trafficking of
  • lipoprotein lipase (LPL), acting as a chaperone,” .

and added that “Using several tissue-specific knockout mouse models,

  • we showed that this is a general phenomenon,”

Without LPL, lipids remain in the circulation;

  • fat and muscle cells cannot absorb fat molecules for storage and energy combustion,

People with LPL mutations develop

  • postprandial hypertriglyceridemia similar to
  • conditions found in fat cell-specific SEL1L-deficient mice, said Qi.

Future work will investigate the

  • role of SEL1L in human patients carrying LPL mutations and
  • determine why fat cell-specific SEL1L-deficient mice remain lean under Western diets, said Sha.

Co-authors include researchers from Cedars-Sinai Medical Center in Los Angeles; Wageningen University in the Netherlands; Georgia State University; University of California, Los Angeles; and the Medical College of Soochow University in China.

The study was funded by the U.S. National Institutes of Health, the Netherlands Organization for Health Research and Development National Institutes of Health, the Cedars-Sinai Medical Center, Chinese National Science Foundation, the American Diabetes Association, Cornell’s Center for Vertebrate Genomics and the Howard Hughes Medical Institute.

Part 6. Biomarkers

Biomarkers Take Center Stage

Josh P. Roberts
GEN May 1, 2013 (Vol. 33, No. 9)  http://www.genengnews.com/

While work with biomarkers continues to grow, scientists are also grappling with research-related bottlenecks, such as

  1. affinity reagent development,
  2. platform reproducibility, and
  3. sensitivity.

Biomarkers by definition indicate some state or process that generally occurs

  • at a spatial or temporal distance from the marker itself, and

it would not be an exaggeration to say that biomedicine has become infatuated with them:

  1. where to find them,
  2. when they may appear,
  3. what form they may take, and
  4. how they can be used to diagnose a condition or
  5. predict whether a therapy may be successful.

Biomarkers are on the agenda of many if not most industry gatherings, and in cases such as Oxford Global’s recent “Biomarker Congress” and the GTC “Biomarker Summit”, they hold the naming rights. There, some basic principles were built upon, amended, and sometimes challenged.

In oncology, for example, biomarker discovery is often predicated on the premise that

  • proteins shed from a tumor will traverse to and persist in, and be detectable in, the circulation.

By quantifying these proteins—singularly or as part of a larger “signature”—the hope is

  1. to garner information about the molecular characteristics of the cancer
  2. that will help with cancer detection and
  3. personalization of the treatment strategy.

Yet this approach has not yet turned into the panacea that was hoped for. Bottlenecks exist in

  • affinity reagent development,
  • platform reproducibility, and
  • sensitivity.

There is also a dearth of understanding of some of the

  • fundamental principles of biomarker biology that we need to know the answers to,

said Parag Mallick, Ph.D., whose lab at Stanford University is “working on trying to understand where biomarkers come from.”

There are dogmas saying that

  • circulating biomarkers come solely from secreted proteins.

But Dr. Mallick’s studies indicate that fully

  • 50% of circulating proteins may come from intracellular sources or
  • proteins that are annotated as such.

“We don’t understand the processes governing

  • which tumor-derived proteins end up in the blood.”

Other questions include “how does the size of a tumor affect how much of a given protein will be in the blood?”—perhaps

  • the tumor is necrotic at the center, or
  • it’s hypervascular or hypovascular.

He points out “The problem is that these are highly nonlinear processes at work, and

  • there is a large number of factors that might affect the answer to that question,” .

Their research focuses on using

  1. mass spectrometry and
  2. computational analysis
  • to characterize the biophysical properties of the circulating proteome, and
  • relate these to measurements made of the tumor itself.

Furthermore, he said – “We’ve observed that the proteins that are likely to

  • first show up and persist in the circulation, ..
  • are more stable than proteins that don’t,”
  • “we can quantify how significant the effect is.”

The goal is ultimately to be able to

  1. build rigorous, formal mathematical models that will allow something measured in the blood
  2. to be tied back to the molecular biology taking place in the tumor.

And conversely, to use those models

  • to predict from a tumor what will be found in the circulation.

“Ultimately, the models will allow you to connect the dots between

  • what you measure in the blood and the biology of the tumor.”

Bound for Affinity Arrays

Affinity reagents are the main tools for large-scale protein biomarker discovery. And while this has tended to mean antibodies (or their derivatives), other affinity reagents are demanding a place in the toolbox.

Affimers, a type of affinity reagent being developed by Avacta, consist of

  1. a biologically inert, biophysically stable protein scaffold
  2. containing three variable regions into which
  3. distinct peptides are inserted.

The resulting three-dimensional surface formed by these peptides

  • interacts and binds to proteins and other molecules in solution,
  • much like the antigen-binding site of antibodies.

Unlike antibodies, Affimers are relatively small (13 KDa),

  • non-post-translationally modified proteins
  • that can readily be expressed in bacterial culture.

They may be made to bind surfaces through unique residues

  • engineered onto the opposite face of the Affimer,
  • allowing the binding site to be exposed to the target in solution.

“We don’t seem to see in what we’ve done so far

  • any real loss of activity or functionality of Affimers when bound to surfaces—

they’re very robust,” said CEO Alastair Smith, Ph.D.

Avacta is taking advantage of this stability and its large libraries of Affimers to develop

  • very large affinity microarrays for
  • drug and biomarker discovery.

To date they have printed arrays with around 20–25,000 features, and Dr. Smith is “sure that we can get toward about 50,000 on a slide,” he said. “There’s no real impediment to us doing that other than us expressing the proteins and getting on with it.”

Customers will be provided with these large, complex “naïve” discovery arrays, readable with standard equipment. The plan is for the company to then “support our customers by providing smaller arrays with

  • the Affimers that are binding targets of interest to them,” Dr. Smith foretold.

And since the intellectual property rights are unencumbered,

  • Affimers in those arrays can be licensed to the end users
  • to develop diagnostics that can be validated as time goes on.

Around 20,000-Affimer discovery arrays were recently tested by collaborator Professor Ann Morgan of the University of Leeds with pools of unfractionated serum from patients with symptoms of inflammatory disease. The arrays

  • “rediscovered” elevated C-reactive protein (CRP, the clinical gold standard marker)
  • as well as uncovered an additional 22 candidate biomarkers.
  • other candidates combined with CRP, appear able to distinguish between different diseases such as
  1. rheumatoid arthritis,
  2. psoriatic arthritis,
  3. SLE, or
  4. giant cell arteritis.

Epigenetic Biomarkers

Methylation of adenine

Sometimes biomarkers are used not to find disease but

  • to distinguish healthy human cell types, with
  •  examples being found in flow cytometry and immunohistochemistry.

These widespread applications, however, are difficult to standardize, being

  • subject to arbitrary or subjective gating protocols and other imprecise criteria.

Epiontis instead uses an epigenetic approach. “What we need is a unique marker that is

  • demethylated only in one cell type and
  • methylated in all the other cell types,”

Each cell of the right cell type will have

  • two demethylated copies of a certain gene locus,
  • allowing them to be enumerated by quantitative PCR.

The biggest challenge is finding that unique epigenetic marker. To do so they look through the literature for proteins and genes described as playing a role in the cell type’s biology, and then

  • look at the methylation patterns to see if one can be used as a marker,

They also “use customized Affymetrix chips to look at the

  • differential epigenetic status of different cell types on a genomewide scale.”

explained CBO and founder Ulrich Hoffmueller, Ph.D.

The company currently has a panel of 12 assays for 12 immune cell types. Among these is an assay for

  • regulatory T (Treg) cells that queries the Foxp3 gene—which is uniquely demethylated in Treg
  • even though it is transiently expressed in activated T cells of other subtypes.

Also assayed are Th17 cells, difficult to detect by flow cytometry because

  • “the cells have to be stimulated in vitro,” he pointed out.

Developing New Assays for Cancer Biomarkers

Researchers at Myriad RBM and the Cancer Prevention Research Institute of Texas are collaborating to develop

  • new assays for cancer biomarkers on the Myriad RBM Multi-Analyte Profile (MAP) platform.

The release of OncologyMAP 2.0 expanded Myriad RBM’s biomarker menu to over 250 analytes, which can be measured from a small single sample, according to the company. Using this menu, L. Stephen et al., published a poster, “Analysis of Protein Biomarkers in Prostate and Colorectal Tumor Lysates,” which showed the results of

  • a survey of proteins relevant to colorectal (CRC) and prostate (PC) tumors
  • to identify potential proteins of interest for cancer research.

The study looked at CRC and PC tumor lysates and found that 102 of the 115 proteins showed levels above the lower limit of quantification.

  • Four markers were significantly higher in PC and 10 were greater in CRC.

For most of the analytes, duplicate sections of the tumor were similar, although some analytes did show differences. In four of the CRC analytes, tumor number four showed differences for CEA and tumor number 2 for uPA.

Thirty analytes were shown to be

  • different in CRC tumor compared to its adjacent tissue.
  • Ten of the analytes were higher in adjacent tissue compared to CRC.
  • Eighteen of the markers examined demonstrated  —-

significant correlations of CRC tumor concentration to serum levels.

“This suggests.. that the Oncology MAP 2.0 platform “provides a good method for studying changes in tumor levels because many proteins can be assessed with a very small sample.”

Clinical Test Development with MALDI-ToF

While there have been many attempts to translate results from early discovery work on the serum proteome into clinical practice, few of these efforts have progressed past the discovery phase.

Matrix-assisted laser desorption/ionization-time of flight (MALDI-ToF) mass spectrometry on unfractionated serum/plasma samples offers many practical advantages over alternative techniques, and does not require

  • a shift from discovery to development and commercialization platforms.

Biodesix claims it has been able to develop the technology into

  • a reproducible, high-throughput tool to
  • routinely measure protein abundance from serum/plasma samples.

“.. we improved data-analysis algorithms to

  • reproducibly obtain quantitative measurements of relative protein abundance from MALDI-ToF mass spectra.

Heinrich Röder, CTO points out that the MALDI-ToF measurements

  • are combined with clinical outcome data using
  • modern learning theory techniques
  • to define specific disease states
  • based on a patient’s serum protein content,”

The clinical utility of the identification of these disease states can be investigated through a retrospective analysis of differing sample sets. For example, Biodesix clinically validated its first commercialized serum proteomic test, VeriStrat®, in 85 different retrospective sample sets.

Röder adds that “It is becoming increasingly clear that

  • the patients whose serum is characterized as VeriStrat Poor show
  • consistently poor outcomes irrespective of
  1. tumor type,
  2. histology, or
  3. molecular tumor characteristics,”

MALDI-ToF mass spectrometry, in its standard implementation,

  • allows for the observation of around 100 mostly high-abundant serum proteins.

Further, “while this does not limit the usefulness of tests developed from differential expression of these proteins,

  • the discovery potential would be greatly enhanced
  • if we could probe deeper into the proteome
  • while not giving up the advantages of the MALDI-ToF approach,”

Biodesix reports that its new MALDI approach, Deep MALDI™, can perform

  • simultaneous quantitative measurement of more than 1,000 serum protein features (or peaks) from 10 µL of serum in a high-throughput manner.
  • it increases the observable signal noise ratio from a few hundred to over 50,000,
  • resulting in the observation of many lower-abundance serum proteins.

Breast cancer, a disease now considered to be a collection of many complexes of symptoms and signatures—the dominant ones are labeled Luminal A, Luminal B, Her2, and Basal— which suggests different prognose, and

  • these labels are considered too simplistic for understanding and managing a woman’s cancer.

Studies published in the past year have looked at

  1. somatic mutations,
  2. gene copy number aberrations,
  3. gene expression abnormalities,
  4. protein and miRNA expression, and
  5. DNA methylation,

coming up with a list of significantly mutated genes—hot spots—in different categories of breast cancers. Targeting these will inevitably be the focus of much coming research.

“We’ve been taking these large trials and profiling these on a variety of array or sequence platforms. We think we’ll get

  1. prognostic drivers
  2. predictive markers for taxanes and
  3. monoclonal antibodies and
  4. tamoxifen and aromatase inhibitors,”
    explained Brian Leyland-Jones, Ph.D., director of Edith Sanford Breast Cancer Research. “We will end up with 20–40 different diseases, maybe more.”

Edith Sanford Breast Cancer Research is undertaking a pilot study in collaboration with The Scripps Research Institute, using a variety of tests on 25 patients to see how the information they provide complements each other, the overall flow, and the time required to get and compile results.

Laser-captured tumor samples will be subjected to low passage whole-genome, exome, and RNA sequencing (with targeted resequencing done in parallel), and reverse-phase protein and phosphorylation arrays, with circulating nucleic acids and circulating tumor cells being queried as well. “After that we hope to do a 100- or 150-patient trial when we have some idea of the best techniques,” he said.

Dr. Leyland-Jones predicted that ultimately most tumors will be found

  • to have multiple drivers,
  • with most patients receiving a combination of two, three, or perhaps four different targeted therapies.

Reduce to Practice

According to Randox, the evidence Investigator is a sophisticated semi-automated biochip sys­tem designed for research, clinical, forensic, and veterinary applications.

Once biomarkers that may have an impact on therapy are discovered, it is not always routine to get them into clinical practice. Leaving regulatory and financial, intellectual property and cultural issues aside, developing a diagnostic based on a biomarker often requires expertise or patience that its discoverer may not possess.

Andrew Gribben is a clinical assay and development scientist at Randox Laboratories, based in Northern Ireland, U.K. The company utilizes academic and industrial collaborators together with in-house discovery platforms to identify biomarkers that are

  • augmented or diminished in a particular pathology
  • relative to appropriate control populations.

Biomarkers can be developed to be run individually or

  • combined into panels of immunoassays on its multiplex biochip array technology.

Specificity can also be gained—or lost—by the affinity of reagents in an assay. The diagnostic potential of Heart-type fatty acid binding protein (H-FABP) abundantly expressed in human myocardial cells was recognized by Jan Glatz of Maastricht University, The Netherlands, back in 1988. Levels rise quickly within 30 minutes after a myocardial infarction, peaking at 6–8 hours and return to normal within 24–30 hours. Yet at the time it was not known that H-FABP was a member of a multiprotein family, with which the polyclonal antibodies being used in development of an assay were cross-reacting, Gribben related.

Randox developed monoclonal antibodies specific to H-FABP, funded trials investigating its use alone, and multiplexed with cardiac biomarker assays, and, more than 30 years after the biomarker was identified, in 2011, released a validated assay for H-FABP as a biomarker for early detection of acute myocardial infarction.

Ultrasensitive Immunoassays for Biomarker Development

Research has shown that detection and monitoring of biomarker concentrations can provide

  • insights into disease risk and progression.

Cytokines have become attractive biomarkers and candidates

  • for targeted therapies for a number of autoimmune diseases, including rheumatoid arthritis (RA), Crohn’s disease, and psoriasis, among others.

However, due to the low-abundance of circulating cytokines, such as IL-17A, obtaining robust measurements in clinical samples has been difficult.

Singulex reports that its digital single-molecule counting technology provides

  • increased precision and detection sensitivity over traditional ELISA techniques,
  • helping to shed light on biomarker verification and validation programs.

The company’s Erenna® immunoassay system, which includes optimized immunoassays, offers LLoQ to femtogram levels per mL resolution—even in healthy populations, at an improvement of 1-3 fold over standard ELISAs or any conventional technology and with a dynamic range of up to 4-logs, according to a Singulex official, who adds that

  • this sensitivity improvement helps minimize undetectable samples that
  • could otherwise delay or derail clinical studies.

The official also explains that the Singulex solution includes an array of products and services that are being applied to a number of programs and have enabled the development of clinically relevant biomarkers, allowing translation from discovery to the clinic.

In a poster entitled “Advanced Single Molecule Detection: Accelerating Biomarker Development Utilizing Cytokines through Ultrasensitive Immunoassays,” a case study was presented of work performed by Jeff Greenberg of NYU to show how the use of the Erenna system can provide insights toward

  • improving the clinical utility of biomarkers and
  • accelerating the development of novel therapies for treating inflammatory diseases.

A panel of inflammatory biomarkers was examined in DMARD (disease modifying antirheumatic drugs)-naïve RA (rheumatoid arthritis) vs. knee OA (osteoarthritis) patient cohorts. Markers that exhibited significant differences in plasma concentrations between the two cohorts included

  • CRP, IL-6R alpha, IL-6, IL-1 RA, VEGF, TNF-RII, and IL-17A, IL-17F, and IL-17A/F.

Among the three tested isoforms of IL-17,

  • the magnitude of elevation for IL-17F in RA patients was the highest.

“Singulex provides high-resolution monitoring of baseline IL-17A concentrations that are present at low levels,” concluded the researchers. “The technology also enabled quantification of other IL-17 isoforms in RA patients, which have not been well characterized before.”

The Singulex Erenna System has also been applied to cardiovascular disease research, for which its

  • cardiac troponin I (cTnI) digital assay can be used to measure circulating
  • levels of cTnI undetectable by other commercial assays.

Recently presented data from Brigham and Women’s Hospital and the TIMI-22 study showed that

  • using the Singulex test to serially monitor cTnI helps
  • stratify risk in post-acute coronary syndrome patients and
  • can identify patients with elevated cTnI
  • who have the most to gain from intensive vs. moderate-dose statin therapy,

according to the scientists involved in the research.

The study poster, “Prognostic Performance of Serial High Sensitivity Cardiac Troponin Determination in Stable Ischemic Heart Disease: Analysis From PROVE IT-TIMI 22,” was presented at the 2013 American College of Cardiology (ACC) Annual Scientific Session & Expo by R. O’Malley et al.

Biomarkers Changing Clinical Medicine

Better Diagnosis, Prognosis, and Drug Targeting Are among Potential Benefits

  1. John Morrow Jr., Ph.D.

Researchers at EMD Chemicals are developing biomarker immunoassays

  • to monitor drug-induced toxicity including kidney damage.

The pace of biomarker development is accelerating as investigators report new studies on cancer, diabetes, Alzheimer disease, and other conditions in which the evaluation and isolation of workable markers is prominently featured.

Wei Zheng, Ph.D., leader of the R&D immunoassay group at EMD Chemicals, is overseeing a program to develop biomarker immunoassays to

  • monitor drug-induced toxicity, including kidney damage.

“One of the principle reasons for drugs failing during development is because of organ toxicity,” says Dr. Zheng.
“proteins liberated into the serum and urine can serve as biomarkers of adverse response to drugs, as well as disease states.”

Through collaborative programs with Rules-Based Medicine (RBM), the EMD group has released panels for the profiling of human renal impairment and renal toxicity. These urinary biomarker based products fit the FDA and EMEA guidelines for assessment of drug-induced kidney damage in rats.

The group recently performed a screen for potential protein biomarkers in relation to

  • kidney toxicity/damage on a set of urine and plasma samples
  • from patients with documented renal damage.

Additionally, Dr. Zheng is directing efforts to move forward with the multiplexed analysis of

  • organ and cellular toxicity.

Diseases thought to involve compromised oxidative phosphorylation include

  • diabetes, Parkinson and Alzheimer diseases, cancer, and the aging process itself.

Good biomarkers allow Dr. Zheng to follow the mantra, “fail early, fail fast.” With robust, multiplexible biomarkers, EMD can detect bad drugs early and kill them before they move into costly large animal studies and clinical trials. “Recognizing the severe liability that toxicity presents, we can modify the structure of the candidate molecule and then rapidly reassess its performance.”

Scientists at Oncogene Science a division of Siemens Healthcare Diagnostics, are also focused on biomarkers. “We are working on a number of antibody-based tests for various cancers, including a test for the Ca-9 CAIX protein, also referred to as carbonic anhydrase,” Walter Carney, Ph.D., head of the division, states.

CAIX is a transmembrane protein that is

  • overexpressed in a number of cancers, and, like Herceptin and the Her-2 gene,
  • can serve as an effective and specific marker for both diagnostic and therapeutic purposes.
  • It is liberated into the circulation in proportion to the tumor burden.

Dr. Carney and his colleagues are evaluating patients after tumor removal for the presence of the Ca-9 CAIX protein. If

  • the levels of the protein in serum increase over time,
  • this suggests that not all the tumor cells were removed and the tumor has metastasized.

Dr. Carney and his team have developed both an immuno-histochemistry and an ELISA test that could be used as companion diagnostics in clinical trials of CAIX-targeted drugs.

The ELISA for the Ca-9 CAIX protein will be used in conjunction with Wilex’ Rencarex®, which is currently in a

  • Phase III trial as an adjuvant therapy for non-metastatic clear cell renal cancer.

Additionally, Oncogene Science has in its portfolio an FDA-approved test for the Her-2 marker. Originally approved for Her-2/Neu-positive breast cancer, its indications have been expanded over time, and was approved

  • for the treatment of gastric cancer last year.

It is normally present on breast cancer epithelia but

  • overexpressed in some breast cancer tumors.

“Our products are designed to be used in conjunction with targeted therapies,” says Dr. Carney. “We are working with companies that are developing technology around proteins that are

  • overexpressed in cancerous tissues and can be both diagnostic and therapeutic targets.”

The long-term goal of these studies is to develop individualized therapies, tailored for the patient. Since the therapies are expensive, accurate diagnostics are critical to avoid wasting resources on patients who clearly will not respond (or could be harmed) by the particular drug.

“At this time the rate of response to antibody-based therapies may be very poor, as

  • they are often employed late in the course of the disease, and patients are in such a debilitated state
  • that they lack the capacity to react positively to the treatment,” Dr. Carney explains.

Nanoscale Real-Time Proteomics

Stanford University School of Medicine researchers, working with Cell BioSciences, have developed a

  • nanofluidic proteomic immunoassay that measures protein charge,
  • similar to immunoblots, mass spectrometry, or flow cytometry.
  • unlike these platforms, this approach can measure the amount of individual isoforms,
  • specifically, phosphorylated molecules.

“We have developed a nanoscale device for protein measurement, which I believe could be useful for clinical analysis,” says Dean W. Felsher, M.D., Ph.D., associate professor at Stanford University School of Medicine.

Critical oncogenic transformations involving

  • the activation of the signal-related kinases ERK-1 and ERK-2 can now be followed with ease.

“The fact that we measure nanoquantities with accuracy means that

  • we can interrogate proteomic profiles in clinical patients,

by drawing tiny needle aspirates from tumors over the course of time,” he explains.

“This allows us to observe the evolution of tumor cells and

  • their response to therapy
  • from a baseline of the normal tissue as a standard of comparison.”

According to Dr. Felsher, 20 cells is a large enough sample to obtain a detailed description. The technology is easy to automate, which allows

  • the inclusion of hundreds of assays.

Contrasting this technology platform with proteomic analysis using microarrays, Dr. Felsher notes that the latter is not yet workable for revealing reliable markers.

Dr. Felsher and his group published a description of this technology in Nature Medicine. “We demonstrated that we could take a set of human lymphomas and distinguish them from both normal tissue and other tumor types. We can

  • quantify changes in total protein, protein activation, and relative abundance of specific phospho-isoforms
  • from leukemia and lymphoma patients receiving targeted therapy.

Even with very small numbers of cells, we are able to show that the results are consistent, and

  • our sample is a random profile of the tumor.”

Splice Variant Peptides

“Aberrations in alternative splicing may generate

  • much of the variation we see in cancer cells,”

says Gilbert Omenn, Ph.D., director of the center for computational medicine and bioinformatics at the University of Michigan School of Medicine. Dr. Omenn and his colleague, Rajasree Menon, are

  • using this variability as a key to new biomarker identification.

It is becoming evident that splice variants play a significant role in the properties of cancer cells, including

  • initiation, progression, cell motility, invasiveness, and metastasis.

Alternative splicing occurs through multiple mechanisms

  • when the exons or coding regions of the DNA transcribe mRNA,
  • generating initiation sites and connecting exons in protein products.

Their translation into protein can result in numerous protein isoforms, and

  • these isoforms may reflect a diseased or cancerous state.

Regulatory elements within the DNA are responsible for selecting different alternatives; thus

  • the splice variants are tempting targets for exploitation as biomarkers.
Analyses of the splice-site mutation

Analyses of the splice-site mutation

Despite the many questions raised by these observations, splice variation in tumor material has not been widely studied. Cancer cells are known for their tremendous variability, which allows them to

  • grow rapidly, metastasize, and develop resistance to anticancer drugs.

Dr. Omenn and his collaborators used

  • mass spec data to interrogate a custom-built database of all potential mRNA sequences
  • to find alternative splice variants.

When they compared normal and malignant mammary gland tissue from a mouse model of Her2/Neu human breast cancers, they identified a vast number (608) of splice variant proteins, of which

  • peptides from 216 were found only in the tumor sample.

“These novel and known alternative splice isoforms

  • are detectable both in tumor specimens and in plasma and
  • represent potential biomarker candidates,” Dr. Omenn adds.

Dr. Omenn’s observations and those of his colleague Lewis Cantley, Ph.D., have also

  • shed light on the origins of the classic Warburg effect,
  • the shift to anaerobic glycolysis in tumor cells.

The novel splice variant M2, of muscle pyruvate kinase,

  • is observed in embryonic and tumor tissue.

It is associated with this shift, the result of

  • the expression of a peptide splice variant sequence.

It is remarkable how many different areas of the life sciences are tied into the phenomenon of splice variation. The changes in the genetic material can be much greater than point mutations, which have been traditionally considered to be the prime source of genetic variability.

“We now have powerful methods available to uncover a whole new category of variation,” Dr. Omenn says. “High-throughput RNA sequencing and proteomics will be complementary in discovery studies of splice variants.”

Splice variation may play an important role in rapid evolutionary changes, of the sort discussed by Susumu Ohno and Stephen J. Gould decades ago. They, and other evolutionary biologists, argued that

  • gene duplication, combined with rapid variability, could fuel major evolutionary jumps.

At the time, the molecular mechanisms of variation were poorly understood, but today

  • the tools are available to rigorously evaluate the role of
  • splice variation and other contributors to evolutionary change.

“Biomarkers derived from studies of splice variants, could, in the future, be exploited

  • both for diagnosis and prognosis and
  • for drug targeting of biological networks,
  • in situations such as the Her-2/Neu breast cancers,” Dr. Omenn says.

Aminopeptidase Activities

“By correlating the proteolytic patterns with disease groups and controls, we have shown that

  • exopeptidase activities contribute to the generation of not only cancer-specific
  • but also cancer type specific serum peptides.

according to Paul Tempst, Ph.D., professor and director of the Protein Center at the Memorial Sloan-Kettering Cancer Center.

So there is a direct link between peptide marker profiles of disease and differential protease activity.” For this reason Dr. Tempst argues that “the patterns we describe may have value as surrogate markers for detection and classification of cancer.”

To investigate this avenue, Dr. Tempst and his colleagues have followed

  • the relationship between exopeptidase activities and metastatic disease.

“We monitored controlled, de novo peptide breakdown in large numbers of biological samples using mass spectrometry, with relative quantitation of the metabolites,” Dr. Tempst explains. This entailed the use of magnetic, reverse-phase beads for analyte capture and a MALDI-TOF MS read-out.

“In biomarker discovery programs, functional proteomics is usually not pursued,” says Dr. Tempst. “For putative biomarkers, one may observe no difference in quantitative levels of proteins, while at the same time, there may be substantial differences in enzymatic activity.”

In a preliminary prostate cancer study, the team found a significant difference

  • in activity levels of exopeptidases in serum from patients with metastatic prostate cancer
  • as compared to primary tumor-bearing individuals and normal healthy controls.

However, there were no differences in amounts of the target protein, and this potential biomarker would have been missed if quantitative levels of protein had been the only criterion of selection.

It is frequently stated that “practical fusion energy is 30 years in the future and always will be.” The same might be said of functional, practical biomarkers that can pass muster with the FDA. But splice variation represents a new handle on this vexing problem. It appears that we are seeing the emergence of a new approach that may finally yield definitive diagnostic tests, detectable in serum and urine samples.

Part 7. Epigenetics and Drug Metabolism

DNA Methylation Rules: Studying Epigenetics with New Tools

The tools to unravel the epigenetic control mechanisms that influence how cells control access of transcriptional proteins to DNA are just beginning to emerge.

Patricia Fitzpatrick Dimond, Ph.D.

http://www.genengnews.com/media/images/AnalysisAndInsight/Feb7_2013_24454248_GreenPurpleDNA_EpigeneticsToolsII3576166141.jpg

New tools may help move the field of epigenetic analysis forward and potentially unveil novel biomarkers for cellular development, differentiation, and disease.

DNA sequencing has had the power of technology behind it as novel platforms to produce more sequencing faster and at lower cost have been introduced. But the tools to unravel the epigenetic control mechanisms that influence how cells control access of transcriptional proteins to DNA are just beginning to emerge.

Among these mechanisms, DNA methylation, or the enzymatically mediated addition of a methyl group to cytosine or adenine dinucleotides,

  • serves as an inherited epigenetic modification that
  • stably modifies gene expression in dividing cells.

The unique methylomes are largely maintained in differentiated cell types, making them critical to understanding the differentiation potential of the cell.

In the DNA methylation process, cytosine residues in the genome are enzymatically modified to 5-methylcytosine,

  • which participates in transcriptional repression of genes during development and disease progression.

5-methylcytosine can be further enzymatically modified to 5-hydroxymethylcytosine by the TET family of methylcytosine dioxygenases. DNA methylation affects gene transcription by physically

  • interfering with the binding of proteins involved in gene transcription.

Methylated DNA may be bound by methyl-CpG-binding domain proteins (MBDs) that can

  • then recruit additional proteins. Some of these include histone deacetylases and other chromatin remodeling proteins that modify histones, thereby
  • forming compact, inactive chromatin, or heterochromatin.

While DNA methylation doesn’t change the genetic code,

  • it influences chromosomal stability and gene expression.

Epigenetics and Cancer Biomarkers

multistage chemical carcinogenesis

multistage chemical carcinogenesis

And because of the increasing recognition that DNA methylation changes are involved in human cancers, scientists have suggested that these epigenetic markers may provide biological markers for cancer cells, and eventually point toward new diagnostic and therapeutic targets. Cancer cell genomes display genome-wide abnormalities in DNA methylation patterns,

  • some of which are oncogenic and contribute to genome instability.

In particular, de novo methylation of tumor suppressor gene promoters

  • occurs frequently in cancers, thereby silencing them and promoting transformation.

Cytosine hydroxymethylation (5-hydroxymethylcytosine, or 5hmC), the aforementioned DNA modification resulting from the enzymatic conversion of 5mC into 5-hydroxymethylcytosine by the TET family of oxygenases, has been identified

  • as another key epigenetic modification marking genes important for
  • pluripotency in embryonic stem cells (ES), as well as in cancer cells.

The base 5-hydroxymethylcytosine was recently identified as an oxidation product of 5-methylcytosine in mammalian DNA. In 2011, using sensitive and quantitative methods to assess levels of 5-hydroxymethyl-2′-deoxycytidine (5hmdC) and 5-methyl-2′-deoxycytidine (5mdC) in genomic DNA, scientists at the Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California investigated

  • whether levels of 5hmC can distinguish normal tissue from tumor tissue.

They showed that in squamous cell lung cancers, levels of 5hmdC showed

  • up to five-fold reduction compared with normal lung tissue.

In brain tumors,5hmdC showed an even more drastic reduction

  • with levels up to more than 30-fold lower than in normal brain,
  • but 5hmdC levels were independent of mutations in isocitrate dehydrogenase-1, the enzyme that converts 5hmC to 5hmdC.

Immunohistochemical analysis indicated that 5hmC is “remarkably depleted” in many types of human cancer.

  • there was an inverse relationship between 5hmC levels and cell proliferation with lack of 5hmC in proliferating cells.

Their data suggest that 5hmdC is strongly depleted in human malignant tumors,

  • a finding that adds another layer of complexity to the aberrant epigenome found in cancer tissue.

In addition, a lack of 5hmC may become a useful biomarker for cancer diagnosis.

Enzymatic Mapping

But according to New England Biolabs’ Sriharsa Pradhan, Ph.D., methods for distinguishing 5mC from 5hmC and analyzing and quantitating the cell’s entire “methylome” and “hydroxymethylome” remain less than optimal.

The protocol for bisulphite conversion to detect methylation remains the “gold standard” for DNA methylation analysis. This method is generally followed by PCR analysis for single nucleotide resolution to determine methylation across the DNA molecule. According to Dr. Pradhan, “.. bisulphite conversion does not distinguish 5mC and 5hmC,”

Recently we found an enzyme, a unique DNA modification-dependent restriction endonuclease, AbaSI, which can

  • decode the hydryoxmethylome of the mammalian genome.

You easily can find out where the hydroxymethyl regions are.”

AbaSI, recognizes 5-glucosylatedmethylcytosine (5gmC) with high specificity when compared to 5mC and 5hmC, and

  • cleaves at narrow range of distances away from the recognized modified cytosine.

By mapping the cleaved ends, the exact 5hmC location can, the investigators reported, be determined.

Dr. Pradhan and his colleagues at NEB; the Department of Biochemistry, Emory University School of Medicine, Atlanta; and the New England Biolabs Shanghai R&D Center described use of this technique in a paper published in Cell Reports this month, in which they described high-resolution enzymatic mapping of genomic hydroxymethylcytosine in mouse ES cells.

In the current report, the authors used the enzyme technology for the genome-wide high-resolution hydroxymethylome, describing simple library construction even with a low amount of input DNA (50 ng) and the ability to readily detect 5hmC sites with low occupancy.

As a result of their studies, they propose that

factors affecting the local 5mC accessibility to TET enzymes play important roles in the 5hmC deposition

  • including include chromatin compaction, nucleosome positioning, or TF binding.
  •  the regularly oscillating 5hmC profile around the CTCF-binding sites, suggests 5hmC ‘‘writers’’ may be sensitive to the nucleosomal environment.
  • some transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus.

“We were able to do complete mapping in mouse embryonic cells and are pleased about what this enzyme can do and how it works,” Dr. Pradhan said.

And the availability of novel tools that make analysis of the methylome and hypomethylome more accessible will move the field of epigenetic analysis forward and potentially novel biomarkers for cellular development, differentiation, and disease.

Patricia Fitzpatrick Dimond, Ph.D. (pdimond@genengnews.com), is technical editor at Genetic Engineering & Biotechnology News.

Epigenetic Regulation of ADME-Related Genes: Focus on Drug Metabolism and Transport

Published: Sep 23, 2013

Epigenetic regulation of gene expression refers to heritable factors that are functionally relevant genomic modifications but that do not involve changes in DNA sequence.

Examples of such modifications include

  • DNA methylation, histone modifications, noncoding RNAs, and chromatin architecture.

Epigenetic modifications are crucial for

packaging and interpreting the genome, and they have fundamental functions in regulating gene expression and activity under the influence of physiologic and environmental factors.

In this issue of Drug Metabolism and Disposition, a series of articles is presented to demonstrate the role of epigenetic factors in regulating

  • the expression of genes involved in drug absorption, distribution, metabolism, and excretion in organ development, tissue-specific gene expression, sexual dimorphism, and in the adaptive response to xenobiotic exposure, both therapeutic and toxic.

The articles also demonstrate that, in addition to genetic polymorphisms, epigenetics may also contribute to wide inter-individual variations in drug metabolism and transport. Identification of functionally relevant epigenetic biomarkers in human specimens has the potential to improve prediction of drug responses based on patient’s epigenetic profiles.

http://www.technologynetworks.com/Metabolomics/news.aspx?ID=157804

This study is published online in Drug Metabolism and Disposition

Part 8.  Pictorial Maps

 Prediction of intracellular metabolic states from extracellular metabolomic data

MK Aurich, G Paglia, Ottar Rolfsson, S Hrafnsdottir, M Magnusdottir, MM Stefaniak, BØ Palsson, RMT Fleming &

Ines Thiele

Metabolomics Aug 14, 2014;

http://dx.doi.org:/10.1007/s11306-014-0721-3

http://link.springer.com/article/10.1007/s11306-014-0721-3/fulltext.html#Sec1

http://link.springer.com/static-content/images/404/art%253A10.1007%252Fs11306-014-0721-3/MediaObjects/11306_2014_721_Fig1_HTML.gif

Metabolic models can provide a mechanistic framework

  • to analyze information-rich omics data sets, and are
  • increasingly being used to investigate metabolic alternations in human diseases.

An expression of the altered metabolic pathway utilization is the selection of metabolites consumed and released by cells. However, methods for the

  • inference of intracellular metabolic states from extracellular measurements in the context of metabolic models remain underdeveloped compared to methods for other omics data.

Herein, we describe a workflow for such an integrative analysis

  • emphasizing on extracellular metabolomics data.

We demonstrate,

  • using the lymphoblastic leukemia cell lines Molt-4 and CCRF-CEM,

how our methods can reveal differences in cell metabolism. Our models explain metabolite uptake and secretion by predicting

  • a more glycolytic phenotype for the CCRF-CEM model and
  • a more oxidative phenotype for the Molt-4 model,
  • which was supported by our experimental data.

Gene expression analysis revealed altered expression of gene products at

  • key regulatory steps in those central metabolic pathways, and

literature query emphasized the role of these genes in cancer metabolism.

Moreover, in silico gene knock-outs identified unique

  •  control points for each cell line model, e.g., phosphoglycerate dehydrogenase for the Molt-4 model.

Thus, our workflow is well suited to the characterization of cellular metabolic traits based on

  • -extracellular metabolomic data, and it allows the integration of multiple omics data sets
  • into a cohesive picture based on a defined model context.

Keywords Constraint-based modeling _ Metabolomics _ Multi-omics _ Metabolic network _ Transcriptomics

1 Introduction

Modern high-throughput techniques have increased the pace of biological data generation. Also referred to as the ‘‘omics avalanche’’, this wealth of data provides great opportunities for metabolic discovery. Omics data sets

  • contain a snapshot of almost the entire repertoire of mRNA, protein, or metabolites at a given time point or

under a particular set of experimental conditions. Because of the high complexity of the data sets,

  • computational modeling is essential for their integrative analysis.

Currently, such data analysis is a bottleneck in the research process and methods are needed to facilitate the use of these data sets, e.g., through meta-analysis of data available in public databases [e.g., the human protein atlas (Uhlen et al. 2010) or the gene expression omnibus (Barrett et al.  2011)], and to increase the accessibility of valuable information for the biomedical research community.

Constraint-based modeling and analysis (COBRA) is

  • a computational approach that has been successfully used to
  • investigate and engineer microbial metabolism through the prediction of steady-states (Durot et al.2009).

The basis of COBRA is network reconstruction: networks are assembled in a bottom-up fashion based on

  • genomic data and extensive
  • organism-specific information from the literature.

Metabolic reconstructions capture information on the

  • known biochemical transformations taking place in a target organism
  • to generate a biochemical, genetic and genomic knowledge base (Reed et al. 2006).

Once assembled, a

  • metabolic reconstruction can be converted into a mathematical model (Thiele and Palsson 2010), and
  • model properties can be interrogated using a great variety of methods (Schellenberger et al. 2011).

The ability of COBRA models

  • to represent genotype–phenotype and environment–phenotype relationships arises
  • through the imposition of constraints, which
  • limit the system to a subset of possible network states (Lewis et al. 2012).

Currently, COBRA models exist for more than 100 organisms, including humans (Duarte et al. 2007; Thiele et al. 2013).

Since the first human metabolic reconstruction was described [Recon 1 (Duarte et al. 2007)],

  • biomedical applications of COBRA have increased (Bordbar and Palsson 2012).

One way to contextualize networks is to

  • define their system boundaries according to the metabolic states of the system, e.g., disease or dietary regimes.

The consequences of the applied constraints can

  • then be assessed for the entire network (Sahoo and Thiele 2013).

Additionally, omics data sets have frequently been used

  • to generate cell-type or condition-specific metabolic models.

Models exist for specific cell types, such as

  1. enterocytes (Sahoo and Thiele2013),
  2. macrophages (Bordbar et al. 2010),
  3. adipocytes (Mardinoglu et al. 2013),
  4. even multi-cell assemblies that represent the interactions of brain cells (Lewis et al. 2010).

All of these cell type specific models, except the enterocyte reconstruction

  • were generated based on omics data sets.

Cell-type-specific models have been used to study

  • diverse human disease conditions.

For example, an adipocyte model was generated using

  • transcriptomic, proteomic, and metabolomics data.

This model was subsequently used to investigate metabolic alternations in adipocytes

  • that would allow for the stratification of obese patients (Mardinoglu et al. 2013).

The biomedical applications of COBRA have been

  1. cancer metabolism (Jerby and Ruppin, 2012).
  2. predicting drug targets (Folger et al. 2011; Jerby et al. 2012).

A cancer model was generated using

  • multiple gene expression data sets and subsequently used
  • to predict synthetic lethal gene pairs as potential drug targets
  • selective for the cancer model, but non-toxic to the global model (Recon 1),

a consequence of the reduced redundancy in the cancer specific model (Folger et al. 2011).

In a follow up study, lethal synergy between FH and enzymes of the heme metabolic pathway

  • were experimentally validated and resolved the mechanism by which FH deficient cells,
    e.g., in renal-cell cancer cells survive a non-functional TCA cycle (Frezza et al. 2011).

Contextualized models, which contain only the subset of reactions active in a particular tissue (or cell-) type,

  • can be generated in different ways (Becker and Palsson, 2008; Jerby et al. 2010).

However, the existing algorithms mainly consider

  • gene expression and proteomic data
  • to define the reaction sets that comprise the contextualized metabolic models.

These subset of reactions are usually defined

  • based on the expression or absence of expression of the genes or proteins (present and absent calls),
  • or inferred from expression values or differential gene expression.

Comprehensive reviews of the methods are available (Blazier and Papin, 2012; Hyduke et al. 2013). Only the compilation of a large set of omics data sets

  • can result in a tissue (or cell-type) specific metabolic model, whereas

the representation of one particular experimental condition is achieved

  • through the integration of omics data set generated from one experiment only (condition-specific cell line model).

Recently, metabolomic data sets have become more comprehensive and

  • using these data sets allow direct determination of the metabolic network components (the metabolites).

Additionally, metabolomics has proven to be stable, relatively inexpensive, and highly reproducible (Antonucci et al. 2012). These factors make metabolomic data sets particularly valuable for

  • interrogation of metabolic phenotypes.

Thus, the integration of these data sets is now an active field of research (Li et al. 2013; Mo et al. 2009; Paglia et al. 2012b; Schmidt et al. 2013).

Generally, metabolomic data can be incorporated into metabolic networks as

  • qualitative, quantitative, and thermodynamic constraints (Fleming et al. 2009; Mo et al. 2009).

Mo et al. used metabolites detected in the

  • spent medium of yeast cells to determine intracellular flux states through a sampling analysis (Mo et al. 2009),
  • which allowed unbiased interrogation of the possible network states (Schellenberger and Palsson 2009) and
  • prediction of internal pathway use.
Modes of transcriptional regulation during the YMC

Modes of transcriptional regulation during the YMC

Such analyses have also been used to reveal the effects of

  1. enzymopathies on red blood cells (Price et al. 2004),
  2. to study effects of diet on diabetes (Thiele et al. 2005) and
  3. to define macrophage metabolic states (Bordbar et al. 2010).

This type of analysis is available as a function in the COBRA toolbox (Schellenberger et al. 2011).

In this study, we established a workflow

  • for the generation and analysis of condition-specific metabolic cell line models
  • that can facilitate the interpretation of metabolomic data.

Our modeling yields meaningful predictions regarding

  • metabolic differences between two lymphoblastic leukemia cell lines (Fig. 1A).

Fig. 1

metabol leukem cell lines11306_2014_721_Fig1_HTML

metabol leukem cell lines11306_2014_721_Fig1_HTML

A Combined experimental and computational pipeline to study human metabolism.

  1. Experimental work and omics data analysis steps precede computational modeling.
  2. Model predictions are validated based on targeted experimental data.
  3. Metabolomic and transcriptomic data are used for model refinement and submodel extraction.
  4. Functional analysis methods are used to characterize the metabolism of the cell-line models and compare it to additional experimental data.
  5. The validated models are subsequently used for the prediction of drug targets.

B Uptake and secretion pattern of model metabolites. All metabolite uptakes and secretions that were mapped during model generation are shown.

  • Metabolite uptakes are depicted on the left, and
  • secreted metabolites are shown on the right.
  1. A number of metabolite exchanges mapped to the model were unique to one cell line.
  2. Differences between cell lines were used to set quantitative constraints for the sampling analysis.

C Statistics about the cell line-specific network generation.

D Quantitative constraints.

For the sampling analysis, an additional set of constraints was imposed on the cell line specific models,

  • emphasizing the differences in metabolite uptake and secretion between cell lines.

Higher uptake of a metabolite was allowed

  • in the model of the cell line that consumed more of the metabolite in vitro, whereas
  • the supply was restricted for the model with lower in vitro uptake.

This was done by establishing the same ratio between the models bounds as detected in vitro.

X denotes the factor (slope ratio) that distinguishes the bounds, and

  • which was individual for each metabolite.

(a) The uptake of a metabolite could be x times higher in CCRF-CEM cells,

(b) the metabolite uptake could be x times higher in Molt-4,

(c) metabolite secretion could be x times higher in CCRF-CEM, or

(d) metabolite secretion could be x times higher in Molt-4 cells.LOD limit of detection.

The consequence of the adjustment was, in case of uptake, that one model was constrained to a lower metabolite uptake (A, B), and the difference depended on the ratio detected in vitro. In case of secretion, one model

  • had to secrete more of the metabolite, and again
  • the difference depended on the experimental difference detected between the cell lines

2 Results

We set up a pipeline that could be used to infer intracellular metabolic states

  • from semi-quantitative data regarding metabolites exchanged between cells and their environment.

Our pipeline combined the following four steps:

  1. data acquisition,
  2. data analysis,
  3. metabolic modeling and
  4. experimental validation of the model predictions (Fig. 1A).

We demonstrated the pipeline and the predictive potential to predict metabolic alternations in diseases such as cancer based on

^two lymphoblastic leukemia cell lines.

The resulting Molt-4 and CCRF-CEM condition-specific cell line models could explain

^  metabolite uptake and secretion
^  by predicting the distinct utilization of central metabolic pathways by the two cell lines.
^  the CCRF-CEM model resembled more a glycolytic, commonly referred to as ‘Warburg’ phenotype,
^  our model predicted a more respiratory phenotype for the Molt-4 model.

We found these predictions to be in agreement with measured gene expression differences

  • at key regulatory steps in the central metabolic pathways, and they were also
  • consistent with additional experimental data regarding the energy and redox states of the cells.

After a brief discussion of the data generation and analysis steps, the results derived from model generation and analysis will be described in detail.

2.1 Pipeline for generation of condition-specific metabolic cell line models

integration of exometabolomic (EM) data

integration of exometabolomic (EM) data

2.1.1 Generation of experimental data

We monitored the growth and viability of lymphoblastic leukemia cell lines in serum-free medium (File S2, Fig. S1). Multiple omics data sets were derived from these cells.Extracellular metabolomics (exo-metabolomic) data,

integration of exometabolomic (EM) data

integration of exometabolomic (EM) data

^  comprising measurements of the metabolites in the spent medium of the cell cultures (Paglia et al. 2012a),
^ were collected along with transcriptomic data, and these data sets were used to construct the models.

2.1.4 Condition-specific models for CCRF-CEM and Molt-4 cells

To determine whether we had obtained two distinct models, we evaluated the reactions, metabolites, and genes of the two models. Both the Molt-4 and CCRF-CEM models contained approximately half of the reactions and metabolites present in the global model (Fig. 1C). They were very similar to each other in terms of their reactions, metabolites, and genes (File S1, Table S5A–C).

(1) The Molt-4 model contained seven reactions that were not present in the CCRF-CEM model (Co-A biosynthesis pathway and exchange reactions).
(2) The CCRF-CEM contained 31 unique reactions (arginine and proline metabolism, vitamin B6 metabolism, fatty acid activation, transport, and exchange reactions).
(3) There were 2 and 15 unique metabolites in the Molt-4 and CCRF-CEM models, respectively (File S1, Table S5B).
(4) Approximately three quarters of the global model genes remained in the condition-specific cell line models (Fig. 1C).
(5) The Molt-4 model contained 15 unique genes, and the CCRF-CEM model had 4 unique genes (File S1, Table S5C).
(6) Both models lacked NADH dehydrogenase (complex I of the electron transport chain—ETC), which was determined by the absence of expression of a mandatory subunit (NDUFB3, Entrez gene ID 4709).

Rather, the ETC was fueled by FADH2 originating from succinate dehydrogenase and from fatty acid oxidation, which through flavoprotein electron transfer

FADH2

FADH2

  • could contribute to the same ubiquinone pool as complex I and complex II (succinate dehydrogenase).

Despite their different in vitro growth rates (which differed by 11 %, see File S2, Fig. S1) and
^^^ differences in exo-metabolomic data (Fig. 1B) and transcriptomic data,
^^^ the internal networks were largely conserved in the two condition-specific cell line models.

2.1.5 Condition-specific cell line models predict distinct metabolic strategies

Despite the overall similarity of the metabolic models, differences in their cellular uptake and secretion patterns suggested distinct metabolic states in the two cell lines (Fig. 1B and see “Materials and methods” section for more detail). To interrogate the metabolic differences, we sampled the solution space of each model using an Artificial Centering Hit-and-Run (ACHR) sampler (Thiele et al. 2005). For this analysis, additional constraints were applied, emphasizing the quantitative differences in commonly uptaken and secreted metabolites. The maximum possible uptake and maximum possible secretion flux rates were reduced
^^^ according to the measured relative differences between the cell lines (Fig. 1D, see “Materials and methods” section).

We plotted the number of sample points containing a particular flux rate for each reaction. The resulting binned histograms can be understood as representing the probability that a particular reaction can have a certain flux value.

A comparison of the sample points obtained for the Molt-4 and CCRF-CEM models revealed

  • a considerable shift in the distributions, suggesting a higher utilization of glycolysis by the CCRF-CEM model
    (File S2, Fig. S2).

This result was further supported by differences in medians calculated from sampling points (File S1, Table S6).
The shift persisted throughout all reactions of the pathway and was induced by the higher glucose uptake (34 %) from the extracellular medium in CCRF-CEM cells.

The sampling median for glucose uptake was 34 % higher in the CCRF-CEM model than in Molt-4 model (File S2, Fig. S2).

The usage of the TCA cycle was also distinct in the two condition-specific cell-line models (Fig. 2). Interestingly,
the models used succinate dehydrogenase differently (Figs. 2, 3).

TCA_reactions

TCA_reactions

The Molt-4 model utilized an associated reaction to generate FADH2, whereas

  • in the CCRF-CEM model, the histogram was shifted in the opposite direction,
  • toward the generation of succinate.

Additionally, there was a higher efflux of citrate toward amino acid and lipid metabolism in the CCRF-CEM model (Fig. 2). There was higher flux through anaplerotic and cataplerotic reactions in the CCRF-CEM model than in the Molt-4 model (Fig. 2); these reactions include

(1) the efflux of citrate through ATP-citrate lyase,
(2) uptake of glutamine,
(3) generation of glutamate from glutamine,
(4) transamination of pyruvate and glutamate to alanine and to 2-oxoglutarate,
(5) secretion of nitrogen, and
(6) secretion of alanine.

energetics-of-cellular-respiration

energetics-of-cellular-respiration

The Molt-4 model showed higher utilization of oxidative phosphorylation (Fig. 3), again supported by
elevated median flux through ATP synthase (36 %) and other enzymes, which contributed to higher oxidative metabolism. The sampling analysis therefore revealed different usage of central metabolic pathways by the condition-specific models.

Fig. 2

Differences in the use of  the TCA cycle by the CCRF-CEM model (red) and the Molt-4 model (blue).

Differences in the use of the TCA cycle by the CCRF-CEM model (red) and the Molt-4 model (blue).

Differences in the use of the TCA cycle by the CCRF-CEM model (red) and the Molt-4 model (blue).

The table provides the median values of the sampling results. Negative values in histograms and in the table describe reversible reactions with flux in the reverse direction. There are multiple reversible reactions for the transformation of isocitrate and α-ketoglutarate, malate and fumarate, and succinyl-CoA and succinate. These reactions are unbounded, and therefore histograms are not shown. The details of participating cofactors have been removed.

Figure 3.

Molt-4 has higher median flux through ETC reactions II–IV 11306_2014_721_Fig3_HTML

Molt-4 has higher median flux through ETC reactions II–IV 11306_2014_721_Fig3_HTML

Atp ATP, cit citrate, adp ADP, pi phosphate, oaa oxaloacetate, accoa acetyl-CoA, coa coenzyme-A, icit isocitrate, αkg α-ketoglutarate, succ-coa succinyl-CoA, succ succinate, fumfumarate, mal malate, oxa oxaloacetate,
pyr pyruvate, lac lactate, ala alanine, gln glutamine, ETC electron transport chain

Ingenuity network analysis showing up (red) and downregulation (green) of miRNAs involved in PC and their target genes

Ingenuity network analysis showing up (red) and downregulation (green) of miRNAs involved in PC and their target genes

metabolic pathways 1476-4598-10-70-1

metabolic pathways 1476-4598-10-70-1

Metabolic Systems Research Team fig2

Metabolic Systems Research Team fig2

Metabolic control analysis of respiration in human cancer tissue. fphys-04-00151-g001

Metabolic control analysis of respiration in human cancer tissue. fphys-04-00151-g001

Metabolome Informatics Research fig1

Metabolome Informatics Research fig1

Modelling of Central Metabolism network3

Modelling of Central Metabolism network3

N. gaditana metabolic pathway map ncomms1688-f4

N. gaditana metabolic pathway map ncomms1688-f4

protein changes in biological mechanisms

protein changes in biological mechanisms

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Development Of Super-Resolved Fluorescence Microscopy

 

Author and Curator: Larry H. Bernstein, MD, FCAP

CSO, Leaders in Pharmaceutical Business Intelligence

Article ID #153: Development Of Super-Resolved Fluorescence Microscopy. Published on 10/12/2014

WordCloud Image Produced by Adam Tubman

Development Of Super-Resolved Fluorescence Microscopy

 

Part I. Nobel Prize For Chemistry 2014: Eric Betzig, Stefan W. Hell
and William E. Moerner Honored For Development Of Super-
Resolved Fluorescence Microscopy

The 2014 Nobel Prize in Chemistry was awarded on 10/08/2014 to
Eric Betzig, Stefan W. Hell and William E. Moerner for
“the development of super-resolved fluorescence microscopy.”

The invention of the electron microscope by Max Knoll and Ernst Ruska at the
Berlin Technische Hochschule in 1931 finally overcame the barrier to higher
resolution that had been imposed by the limitations of visible light. Since then
resolution has defined the progress of the technology.

The ultimate goal was atomic resolution – the ability to see atoms – but this would
have to be approached incrementally over the course of decades. The earliest microscopes merely proved the concept: electron beams could, indeed, be tamed
to provide visible images of matter. By the late 1930s electron microscopes with theoretical resolutions of 10 nm were being designed and produced, and by 1944
this was further reduced to 2 nm. (The theoretical resolution of a an optical light microscope is 200 nm.)

Increases in the accelerating voltage of the electron beam accounted for much of
the improvement in resolution. But voltage was not everything. Improvements in electron lens technology minimized aberrations and provided a clearer picture,
which also contributed to improved resolution, as did better vacuum systems and brighter electron guns. So increasing the resolution of electron microscopes was a main driving force throughout the instrument’s development.

With nanoscopy, scientists could observe viruses, proteins and molecules there
are smaller than 0.0000002 metres.

Three researchers won the 2014 Nobel Prize in Chemistry on Wednesday,
October 8, for giving microscopes much sharper vision than was thought possible, letting scientists peer into living cells with unprecedented detail to seek the roots
of disease.  It was awarded to U.S. researchers Eric Betzig and William Moerner
and German scientist Stefan Hell. They found ways to use molecules that glow on demand to overcome what was considered a fundamental limitation for optical microscopes.

Hell, 52, of Germany, is the director at the Max Planck Institute for Biophysical Chemistry and the division head at the German Cancer Research Center in
Heidelberg. He was honored for his work on fluorescence microscopy, a kind
of nano-flashlight where scientists use fluorescent molecules to see parts of a
cell. Later in his career, he developed the STED microscope, which collects light
from “a multitude of small volumes to create a whole.”

Moerner, a 61-year-old professor in chemistry and applied physics at Stanford University in California, is the recipient of the 2008 Wolf Prize in Chemistry, the
2009 Irving Langmuir Award and the 2013 Peter Debye Award. In 1989, he
was the first scientist to be able to measure the light absorption of a single molecule.
This inspired many chemists to begin focusing on single molecules, including Betzig.

Betzig, 54, the group leader at Janelia Farm Research campus at the Howard
Hughes Medical Institute in Virginia, developed new optical imaging tools for
biology. His work involved taking images of the same area multiple times, and illuminating just a few molecules each time. These images were then
superimposed to create a dense super image at the nano level,

The limitation of optical microscopy was thought to have been determined in a calculation published in 1873 that defined the limit of how tiny a detail could be revealed by optical microscopes. Based on experimental evidence and basic principles of physics, Ernst Abbe and Lord Rayleigh defined and formulated
this diffraction-limited resolution in the late 19th century (Abbe, 1873; Rayleigh,
1896
).  However, only cellular structure and objects that were at least 200 to
350 nm apart could be resolved by light microscopy because, the optical resolution
of light microscopy was limited to approximately half of the wavelength of the light used.  Later key innovations—including fluorescence and confocal laser scanning microscopy (CLSM)—made optical microscopy one of the most powerful and
versatile diagnostic tools in modern cell biology. Using highly specific fluorescent labeling techniques such as immunocytochemistry, in situ hybridization, or
fluorescent protein tags, the spatial distribution and dynamics of virtually every subcellular structure, protein, or genomic sequence of interest can be analyzed in chemically fixed or living samples (Conchello and Lichtman, 2005; Giepmans et al., 2006).

The result of their advance is “really a window into the cell which we didn’t have before,” said Catherine Lewis, director of the cell biology and biophysics division
of the National Institute of General Medical Sciences in Bethesda, Maryland.

“You can observe the behavior of individual molecules in living cells in real time.
You can see … molecules moving around inside the cell. You can see them interacting with each other.”

The research of the three men has let scientists study diseases such as
Parkinson’s, Alzheimer’s and Huntington’s at a molecular level, the Royal
Swedish Academy of Sciences said.

Part II. Electron microscopy limitations

Manfred Von Ardenne in Berlin produced the earliest scanning-transmission
electron microscope in 1937. At the University of Toronto in Canada, Cecil Hall, James Hillier, and Albert Prebus, working under the direction of Eli Burton,
produced an advanced 1938 Toronto Model electron microscope that would
later become the basis for Radio Corporation of America’s Model B, the first commercial electron microscope in North America. Ruska at Siemens in
Germany produced the first commercial electron microscope in the world in 938.

Starting in 1939, scientists in Japan gathered to decide on the best way to build
an electron microscope. This group evolved into the Japan Electron Optics Laboratory (JEOL) that would eventually produce more models and varieties
of electron microscopes than any other company. Hitachi and Toshiba in Japan
also played a major role in the early development process.

The 1960s through the 1990s produced many innovative instruments and trends.
The introduction of the first commercial scanning electron microscopes (SEMs)
in 1965 opened up a new world of analysis for materials scientists. Ultrahigh
voltage TEM instruments (up to 3 MeV at CEMES-LOE/CNRS in Toulouse,
France, and at Hitachi in Tokyo, Japan), in the 1960s and 1970s gave electrons higher energy to penetrate more deeply into thick samples. The evolution and incorporation of other detectors (electron microprobes, electron energy loss spectroscopy (EELS), etc.) made the SEM into a true analytical electron
microscope (AEM) beginning in the 1970s. The development of brighter
electron sources, such as the lanthanum hexaboride filament (LAB6) and the
field emission gun in the 1960s, and their commercialization in the 1970s
brought researchers a brighter source of electrons and with it better imaging
and resolution. Tilting specimen stages permitting examination of the specimen
from different angles aided significantly in the determination of crystal structure.
In the late 1980s and throughout the 1990s, the environmental electron
microscopes that allow scientists to examine samples under more natural
conditions of temperature and pressure have dramatically expanded the
types of samples that can be examined.

In medicine, the EM made a unique contribution to diagnostic anatomic
pathology in renal biopsy analysis. However, the small sample had to be
embedded, and in the early days one cut the specimen by breaking glass
for the cutting of the specimen. But even though EM ushered in a new era of molecular pathology, the contribution was limited, despite incremental
improvements.

In the past, the use of microscopes was limited by a physical restriction;
scientists could only see items that were larger than roughly half the
wavelength of light (.2 micrometers)
. However, the groundbreaking work
of the Nobel laureates bypassed the maximum resolution of traditional
microscopes and launched optical microscopy into the nanodimension.

Part III. Super resolution fluorescence microscopy

Bo Huang,1,2 Mark Bates,3 and Xiaowei Zhuang1,2,4
Author information ► Copyright and License information ►
Annu Rev Biochem. 2009; 78: 993–1016.
http://dx.doi.org:/10.1146/annurev.biochem.77.061906.092014
PMCID: PMC2835776  NIHMSID: NIHMS179491

Achieving a spatial resolution that is not limited by the diffraction of
light, recent developments of super-resolution fluorescence microscopy
techniques allow the observation of many biological structures not
resolvable in conventional fluorescence microscopy. New advances
in these techniques now give them the ability to image three-dimensional
(3D) structures, measure interactions by multicolor colocalization, and
record dynamic processes in living cells at the nanometer scale. It is
anticipated that super-resolution fluorescence microscopy will become
a widely used tool for cell and tissue imaging to provide previously
unobserved details of biological structures and processes.

Keywords: Sub-diffraction limit, single-molecule, multicolor imaging,
three-dimensional imaging, live cell imaging, single-particle tracking,
photoswitchable probe

Among the various microscopy techniques, fluorescence microscopy is
one of the most widely used because of its two principal advantages:
Specific cellular components may be observed through molecule-specific
labeling, and light microscopy allows the observation of structures inside
a live sample in real time. Compared to other imaging techniques such
as electron microscopy (EM), however, conventional fluorescence
microscopy is limited by relatively low spatial resolution because of the
diffraction of light. This diffraction limit, about 200–300 nm in the lateral
direction and 500–700 nm in the axial direction, is comparable to or larger
than many subcellular structures, leaving them too small to be observed in
detail. In recent years, a number of “super-resolution” fluorescence microscopy techniques have been invented to overcome the diffraction barrier, including techniques that employ nonlinear effects to sharpen the point-spread function
of the microscope, such as stimulated emission depletion (STED) microscopy
(1, 2), related methods using other reversible saturable optically linear
fluorescence transitions (RESOLFTs) (3), and saturated structured-illumination microscopy (SSIM) (4), as well as techniques that are based on the localization
of individual fluorescent molecules, such as stochastic optical reconstruction microscopy (STORM) (5), photoactivated localization microscopy (PALM) (6),
and fluorescence photoactivation localization microscopy (FPALM) (7). These methods have yielded an order of magnitude improvement in spatial resolution
in all three dimensions over conventional light microscopy.

THE RESOLUTION LIMIT IN OPTICAL MICROSCOPY

Microscopes can be used to visualize fine structures in a sample by providing
a magnified image. However, even an arbitrarily high magnification does not
translate into the ability to see infinitely small details. Instead, the resolution
of light microscopy is limited because light is a wave and is subject to diffraction.

The diffraction limit

An optical microscope can be thought of as a lens system that produces a
magnified image of a small object. In this imaging process, light rays from
each point on the object converge to a single point at the image plane. However,
the diffraction of light prevents exact convergence of the rays, causing a sharp
point on the object to blur into a finite-sized spot in the image. The three-
dimensional (3D) intensity distribution of the image of a point object is called
the point spread function (PSF). The size of the PSF determines the resolution
of the microscope: Two points closer than the full width at half-maximum
(FWHM) of the PSF will be difficult to resolve because their images overlap substantially.

The FWHM of the PSF in the lateral directions (the x–y directions perpendicular
to the optical axis) can be approximated as Δxy ≈ 0.61λ / NA, where λ is the wavelength of the light, and NA is the numerical aperture of the objective
defined as NA = n sinα, with n being the refractive index of the medium and
α being the half-cone angle of the focused light produced by the objective.
The axial width of the PSF is about 2–3 times as large as the lateral width
for ordinary high NA objectives. When imaging with visible light (λ ≈ 550 nm),
the commonly used oil immersion objective with NA = 1.40 yields a PSF with
a lateral size of ~200 nm and an axial size of ~500 nm in a refractive index-
matched medium (Figure 1) (8).

Figure 1

The PSF of a common oil immersion objective with NA = 1.40, showing the
focal spot of 550 nm light in a medium with refractive index n = 1.515. The
intensity distribution in the x-z plane of the focus spot is computed numerically.

PFS of oil immersion microscope

PFS of oil immersion microscope

Because the loss of high-frequency spatial information in optical microscopy
results from the diffraction of light when it propagates through a distance larger
than the wavelength of the light (far field), near-field microscopy is one of the
earliest approaches sought to achieve high spatial resolution. By exciting the fluorophores or detecting the signal through the nonpropagating light near the fluorophore, high-resolution information be retained. Near-field scanning optical microscopy (NSOM) acquires an image by scanning a sharp probe tip across
the sample, typically providing a resolution of 20–50 nm (911). Wide-field
imaging has also been recently demonstrated in the near-field regime using
a super lens with negative refractive index (12, 13). However, the short range
of the near-field region (tens of nanometers) compromises the ability of light microscopy to look into a sample, limiting the application of near-field microscopy
to near-surface features only. This limit highlights the need to develop far-field
high-resolution imaging methods.

Among far-field fluorescence microscopy techniques, confocal and multiphoton microscopy are among the most widely used to moderately enhance the spatial resolution (14, 15). By combining a focused laser for excitation and a pinhole for detection, confocal microscopy can, in principle, have a factor of √2 improvement
in the spatial resolution. In multiphoton microscopy, nonlinear absorption processes reduce the effective size of the excitation PSF. However, this gain in the PSF size
is counteracted by the increased wavelength of the excitation light. Thus, instead
of improving the resolution, the main advantage of confocal and multi-photon microscopy over wide-field microscopy is the reduction of out-of-focus fluorescence background, allowing optical sectioning in 3D imaging.

Two techniques, 4Pi and I5M microscopy, approach this ideal situation by using
two opposing objectives for excitation and/or detection (16, 17). By acquiring
multiple images with illumination patterns of different phases and orientations,
a high-resolution image can be reconstructed. Because the illumination pattern
itself is also limited by the diffraction of light, structured illumination microscopy
(SIM) is only capable of doubling the spatial resolution by combining two diffraction-limited sources of information.  The best achievable result using these methods
would be an isotropic PSF with an additional factor of 2 in resolution improvement. This would correspond to ~100-nm image resolution in all three dimensions, as
has been demonstrated by the I5S technique, which combines I5M and SIM (22). Albeit a significant improvement, this resolution is still fundamentally limited by
the diffraction of light.

SUPER RESOLUTION FLUORESCENCE MICROSCOPY BY SPATIALLY PATTERNED EXCITATION

One approach to attain a resolution far beyond the limit of diffraction, i.e., to
realize super-resolution microscopy, is to introduce sub-diffraction-limit features
in the excitation pattern so that small-length-scale information can be read out.
We refer to this approach, including STED, RESOLFT, and SSIM, as super-
resolution microscopy by spatially patterned excitation or the “patterned excitation” approach.

The concept of STED microscopy was first proposed in 1994 (1) and subsequently demonstrated experimentally (2). Simply speaking, it uses a second laser (STED laser) to suppress the fluorescence emission from the fluorophores located off the center of the excitation. This suppression is achieved through stimulated emission: When an excited-state fluorophores encounters a photon that matches the energy difference between the excited and the ground state, it can be brought back to
the ground state through stimulated emission before spontaneous fluorescence emission occurs. This process effectively depletes excited-state fluorophores
capable of fluorescence emission (Figure 2a,b).

Figure 2

The principle of STED microscopy. (a) The process of stimulated emission. A
ground state (S0) fluorophore can absorb a photon from the excitation light and
jump to the excited state (S1).

STED microsopy

STED microsopy

The pattern of the STED laser is typically generated by inserting a phase mask
into the light path to modulate its phase-spatial distribution (Figure 2b). One such phase mask generates a donut-shaped STED pattern in the xy plane (Figure 2c)
and has provided an xy resolution of ~30 nm (24). STED can also be employed
in 4Pi microscopy (STED-4Pi), resulting in an axial resolution of 30–40 nm (25). STED has been applied to biological samples either immuno-stained with
fluorophore labeled antibodies (26) or genetically tagged with fluorescent
proteins (FPs) (27). Dyes with high photostability under STED conditions and
large stimulated emission cross sections in the visible to near infrared (IR) range
are preferred. Atto 532 and Atto 647N are among the most often used dyes for
STED microscopy.

Stimulated emission is not the only mechanism capable of suppressing
undesired fluorescence emission. A more general scheme using saturable
depletion to achieve super resolution has been formalized with the name
RESOLFT microscopy (3). This scheme employs fluorescent probes that
can be reversibly photoswitched between a fluorescent on state and a dark
off state. The off state can be the ground state of a fluorophores as in the
case of STED, the triplet state as in ground-state-depletion microscopy
(28, 29), or the dark state of a reversibly photoswitchable fluorophore (30).  RESOLFT has been demonstrated using a reversibly photoswitchable
fluorescent protein as FP595 which leads to a resolution better than 100 nm
at a depletion laser intensity of 600 W/cm2(30).

The same concept of employing saturable processes can also be applied
to SIM by introducing sub-diffraction-limit spatial features into the excitation
pattern. SSIM has been demonstrated using the saturation of fluorescence
emission, which occurs when a fluorophore is illuminated by a very high
intensity of excitation light (4). Under this strong excitation, it is immediately
pumped to the excited state each time it returns to the ground state. In SSIM,
where the sample is illuminated with a sinusoidal pattern of strong excitation
light, the peaks of the excitation pattern can be clipped by fluorescence
saturation and become flat, whereas fluorescence emission is still absent
from the zero points in the valleys (Figure 3a). These effects add higher order
spatial frequencies to the excitation pattern. Mixing this excitation pattern with
the high-frequency spatial features in the sample can effectively bring the sub-diffraction-limit spatial features into the detection range of the microscopy
(Figure 3b).

Figure 3

The principle of SSIM. (a) The generation of the illumination pattern. A
diffractive grating in the excitation path splits the light into two beams. Their interference after emerging from the objective and reaching the sample creates
a sinusoidal illumination

SSIM

SSIM

Although the image of a single fluorophore, which resembles the PSF, is a
finite-sized spot, the precision of determining the fluorophores position from
its image can be much higher than the diffraction limit, as long as the image
results from multiple photons emitted from the fluorophore. Fitting an image
consisting of N photons can be viewed as N measurements of the fluorophore position, each with an uncertainty determined by the PSF (8), thus leading to
a localization precision approximated by:

Δloc≈ΔN−−√

where Δloc is the localization precision and Δ is the size of the PSF. This
scaling of the localization precision with the photon number allows super-
resolution microscopy with a resolution not limited by the diffraction of light.

High-precision localization of bright light has reached a precision as high
as ~1 Å (33). Taking advantage of single-molecule detection and imaging
(34, 35), nanometer localization precision has been achieved for single
fluorescent molecules (36).

Using fluorescent probes that can switch between a fluorescent and a dark
state, a recent invention overcomes this barrier by separating in the time
domain the otherwise spatially overlapping fluorescent images. In this approach, molecules within a diffraction limited region can be activated at different time
points so that they can be individually imaged, localized, and subsequently deactivated (Figure 4). Massively parallel localization is achieved through
wide-field imaging, so that the coordinates of many fluorophores can be
mapped and a super-resolution images subsequently reconstructed. This
concept has been independently conceived and implemented by three labs,
and it was given the names STORM (5), PALM (6), and FPALM (7), respectively.

Iterating the activation and imaging process allows the locations of many
fluorophores to be mapped and a super-resolution image to be constructed
from these fluorophore locations. In the following, we refer to this approach
as super-resolution microscopy by single-molecule localization.

Figure 4

The principle of stochastic optical reconstruction microscopy (STORM), photoactivated localization microscopy (PALM), and fluorescence photo-
activation localization microscopy (FPALM). Different fluorescent probes
marking the sample structure are activated.

STORM

STORM

After capturing the images with a digital camera, the point-spread functions
of the individual molecules are localized with high precision based on the
photon output before the probes spontaneously photo-bleach or switch to
a dark state. The positions of localized molecular centers are indicated with
black crosses. The process is repeated in Figures (c) through (e) until all of
the fluorescent probes are exhausted due to photo-bleaching or because the background fluorescence becomes too high. The final super-resolution image
(Figure (f)) is constructed by plotting the measured positions of the fluorescent probes.
http://microscopyu.com/tutorials/flash/superresolution/storm/index.html

The resolution of this technique is limited by the number of photons detected
per photoactivation event, which varies from several hundred for FPs (6) to
several thousand for cyanine dyes such as Cy5 (5, 46). These numbers
theoretically allow more than an order of magnitude improvement in spatial
resolution according to the √N scaling rule. In practice, a lateral resolution
of ~20 nm has been established experimentally using the photoswitchable
cyanine dyes (5, 46). Super-resolution images of biological samples have
been reported with directly labeled DNA structures and immunostained DNA-
protein complexes in vitro (5) as well as with FPtagged or immunostained
cellular structures (6, 44, 46).

Table 1   Photoswitchable fluorophores used in super resolution
fluorescence microscopy

Photoswitchable fluorophores

Photoswitchable fluorophores

Recent advances in super-resolution fluorescence microscopy
(including the capability for 3D, multicolor, live-cell imaging) enable
new applications in biological samples. These technical advances
were made possible through the development of both imaging optics
and fluorescent probes.

  • 3D imaging using the single-molecule localization approach
  • 3D imaging using the patterned excitation approach
  • Multicolor imaging
  • Multicolor imaging using the patterned excitation approach
  • Multicolor imaging using the single-molecule localization approach
  • Live cell imaging

Fluorescence imaging of a live cell has two requirements: specific labeling
of the cell and a time resolution that is high enough to record relevant
dynamics in the cell.  Many fluorescent proteins and organic dyes, including
cyanine dyes (46) and caged dyes, have been shown switchable in live cells.

Because STED has a much smaller PSF than scanning confocal microscopy,
STED would inherently take more time to scan though the same size of image
field. By increasing the scanning speed and limiting the field of view to a few µm, Westphal and coworkers have observed Brownian motion of a dense suspension
of nanoparticles with an impressive rate of 80 frames per second (fps) using
STED microscopy (63). More recently, they have demonstrated video-rate
(28 fps) imaging of live hippocampal neurons and observed the movement of individual synaptic vesicles with 60–80-nm resolution (64).

Sub-diffraction-limit imaging of focal adhesion proteins in live cells has recently
been demonstrated (65). Photoswitchable fluorescent protein, EosFP, was used
to label the focal adhesion protein paxillin. A time resolution of ~25–60 seconds
per frame was obtained, and during this time interval, approximately 103
fluorophores were activated and localized per square micrometer, providing
an effective resolution of 60–70 nm by the Nyquist criterion (65). More recently, super-resolution imaging has also been demonstrated in live bacteria with photoswitchable enhanced yellow fluorescent protein (EYFP), allowing the
MreB structure in the cell to be traced (66).

The optical resolution

Optical resolution is the intrinsic ability of a given method to resolve a structure
and can be defined as the ability to distinguish two point sources in proximity.
For the patterned excitation approaches, such as STED, SSIM, and RESOLFT,
the optical resolution is represented by the size of the effective PSF. For the
single-molecule localization approach, such as STORM/PALM/FPALM, the
precision of determining the positions of individual fluorescent probes is the
principal measure of optical resolution.

By using a spatially patterned excitation profile, this approach achieves super resolution by generating an effective excitation volume with dimensions far
below the diffraction limit. Taking STED as an example, the sharpness of the
PSF results from the saturation of depletion of excited-state fluorophores in
the region neighboring the zero point of the STED laser (which coincide with
the focal point of the excitation laser). With an increasing STED laser power,
the saturated region expands toward the zero point, but fluorophores at the
zero point are not affected by the STED laser if the zero point is strictly kept
at zero intensity. Therefore, a theoretically unlimited gain in spatial resolution
may be achieved if the zero point in the depletion pattern is ideal.

The single-molecule localization approach achieves super resolution through
high precision localization of individual fluorophores. The number of photons
collected from a fluorophore is a principal factor limiting the localization
precision and hence the resolution of the final image.

Several photoswitchable fluorophores have been reported to give thousands
of photons detected per activation event [e.g., 6000 from Cy5 (46)].With the
PSF fitting procedure and the mechanical stability of the system optimized,
the background signal suppressed, and the nonuniformity of camera pixels
corrected, optical resolution of just a few nanometers could potentially be
achieved, reaching the molecular scale. As in the case of the patterned
excitation approach, the optical resolution here is also unlimited, in principle,
given a sufficient number of photons detected from the fluorescent probes.

Part III. A guide to super-resolution fluorescence microscopy

L Schermelleh1R Heintzmann2,3,4, and H Leonhardt1
JCB Jul 19, 2010 // 190(2): 165-175
The Rockefeller University Press,
http://dx.doi.org:/10.1083/jcb.201002018

Based on experimental evidence and basic principles of physics, Ernst Abbe
and Lord Rayleigh defined and formulated this diffraction-limited resolution in
the late 19th century (Abbe, 1873Rayleigh, 1896). Later key innovations—including fluorescence and confocal laser scanning microscopy (CLSM)—made optical microscopy one of the most powerful and versatile diagnostic
tools in modern cell biology.

The optical resolution defines the physical limit of the smallest structure it
can resolve. When imaging a biological sample, the effective resolution is
also affected by several sample-specific factors, including the labeling density,
probe size, and how well the ultrastructures are preserved during sample
preparation.

The diffraction (Abbe) limit of detection

Resolution is often defined as the largest distance at which the image of
two point-like objects seems to amalgamate. Thus, most resolution criteria
(Rayleigh limit,Sparrow limit, full width at half maximum of the PSF) directly
relate to properties of the PSF. These are useful resolution criteria for visible
observation of specimen, but there are several shortcomings of such a definition
of resolution: (1) Knowing that the image is an image of two particles, these
can in fact be discriminated with the help of a computer down to arbitrary
smaller distances. Determining the positions of two adjacent particles thus
becomes a question of experimental precision and most notably photon statistics
rather than being described by the Rayleigh limit. (2) These limits do not
necessarily correspond well to what level of detail can be seen in images or
real world objects; e.g., the Rayleigh limit is defined as the distance from the
center to the first minimum of the point spread function, which can be made
arbitrarily small with the help of ordinary linear optics (e.g., Toraldo-filters),
albeit at the expense of the side lobes becoming much higher than the central
maximum. (3)

Abbe’s formulation of a resolution limit avoids all of the above shortcomings
at the expense of a less direct interpretation. The process of imaging can be
described by a convolution operation. With the help of a Fourier transformation,
every object (whether periodic or not) can uniquely be described as a sum of
sinusoidal curves with different spatial frequencies (where higher frequencies
represent fine object details and lower frequencies represent coarse details).
The rather complex process of convolution can be greatly simplified by looking
at the equivalent operation in Fourier space: The Fourier-transformed object
just needs to be multiplied with the
Fourier-transformed PSF to yield the Fourier-transformed ideal image (without
the noise). Because the Fourier-transformed PSF now describes how well each
spatial frequency of the Fourier-transformed object gets transferred to appear in the
image, this Fourier-transformed PSF is called the optical transfer function, OTF
(right panel). Its strength at each spatial frequency (e.g., measured in oscillations
per meter) conveniently describes the contrast that a sinusoidal object would
achieve in an image.

Abbe limit

Abbe limit

Interestingly, the detection OTF of a microscope has a fixed frequency
border (Abbe limit frequency, right panel). The maximum-to-maximum
distance Λmin of the corresponding sine curve is commonly referred to
as Abbe’s limit (left panel). In other words: The Abbe limit is the smallest
periodicity in a structure, which can be discriminated in its image. As a
point object contains all spatial frequencies, this Abbe limit sine curve
needs to also be present in the PSF. A standard wide-field microscope
creates an image of a point object (e.g., an emitting molecule) by capturing
the light from that molecule at various places of the objective lens, and
processing it with further lenses to then interfere at the image plane.
Conveniently due to the reciprocity principle in optics, the Abbe limit Λmin
along an in-plane direction in fluorescence imaging corresponds to the
maximum-to-maximum distance of the intensity structure one would get by
interfering two waves at extreme angles captured by the objective lens:
where λ/n is the wavelength of light in the medium of refractive index n.
The term NA = n sin(α) conveniently combines the half opening angle α
of the objective and the refractive index n of the embedding medium.

Abbe’s famous resolution limit is so attractive because it simply depends
on the maximal relative angle between different waves leaving the
object and being captured by the objective lens to be sent to the image.
It describes the smallest level of detail that can possibly be imaged with
this PSF “brush”. No periodic object detail smaller than this shortest
wavelength can possibly be transferred to the image.

Confocal laser scanning microscopy employs a redesigned optical
path and specialized hardware. A tightly focused spot of laser light is
used to scan the sample and a small aperture (or pinhole) in the
confocal image plane of the light path allows only light originating
from the nominal focus to pass (Cremer and Cremer, 1978Sheppard
and Wilson, 1981
Brakenhoff et al., 1985). The emitted light is
detected by a photomultiplier tube (PMT) or an avalanche photodiode
(APD) and the image is then constructed by mapping the detected
light in dependence of the position of the scanning spot. CLSM can
achieve a better resolution than wide-field fluorescence microscopy
but, to obtain a significant practical advantage, the pinhole needs to
be closed to an extent where most of the light is discarded
(Heintzmann et al., 2003).

Wide-field deconvolution and CLSM have long been the gold standards
in optical bioimaging, but we are now witnessing a revolution in light
microscopy that will fundamentally expand our perception of the cell.
Recently, several new technologies,collectively termed super-resolution
microscopy or nanoscopy, have been developed that break or bypass
the classical diffraction limit and shift the optical resolution down to
macromolecular or even molecular levels (Table I).

Super-resolution light microscopy methods

super resolution microscopy

super resolution microscopy

http://zeiss-campus.magnet.fsu.edu/articles/superresolution/introduction.html

Conceptually, one can discern near-field from far-field methods and
whether the subdiffraction resolution is based on a linear or nonlinear
response of the sample to its locally illuminating (exciting or depleting) irradiance. The required nonlinearity is currently achieved by using reversible saturable optical fluorescence transitions (RESOLFT) between molecular states (Hofmann et al., 2005Hell, 2007).

Besides these saturable optical fluorescence transitions also other
approaches, e.g., Rabi oscillations, could be used to generate the
required nonlinear response.

Note that each of the novel imaging modes has its individual signal-
to-noise consideration depending on various factors.  A full
discussion of this issue is beyond the scope of this review, but as a
general rule, single-point scanning systems, albeit fundamentally limited
in speed by fluorescence saturation effects, can have better signal-
to-noise performance for thicker samples.

With three-dimensional SIM (3D-SIM), an additional twofold increase
in the axial resolution can be achieved by generating an excitation
light modulation along the z-axis using three-beam interference
(Gustafsson et al., 2008Schermelleh et al.,2008) and processing a
z-stack of images accordingly. Thus, with 3D-SIM an approximately eightfold smaller volume can be resolved in comparison to conventional microscopy (Fig. 2). To computationally reconstruct a three-dimensional dataset of a typical mammalian cell of 8-µm height with a
z-spacing of 125 nm, roughly 1,000 raw images (512 × 512 pixels) are
recorded. Because no special photophysics is needed, virtually all modern fluorescent labels can be used provided they are sufficiently photostable
to accommodate the additional exposure cycles.

Resolvable volumes obtained with current commercial super-resolution microscopes.

A schematic 3D representation of focal volumes is shown for the indicated
emission maxima. The approximate lateral (x,y) and axial (z) resolution
and resolvable volumes are listed. Note that STED/CW-STED and 3D-SIM
can reach up to 20 µm into the sample, whereas PALM/STORM is usually
confined to the evanescent wave field near the sample bottom. It should be
noted that deconvolution approaches can further improve STED resolution.
For comparison the “focal volume” for PALM/STORM was estimated based
on the localization precision in combination with the z-range of TIRF.

Resolvable volumes obtained

Resolvable volumes obtained

Super-resolution microscopy of biological samples.

(A) Conventional wide-field image (left) and 3D-SIM image of a mouse
C2C12 prometaphase cell stained with primary antibodies against
lamin B and tubulin, and secondary antibodies conjugated to Alexa 488
(green) and Alexa 594 (red), respectively. Nuclear chromatin was stained
with DAPI (blue). 3D image stacks were acquired with a DeltaVision OMX
prototype system (Applied Precision). The bottom panel shows the
respective orthogonal cross sections. (B) HeLa cell stained with primary
antibodies against the nuclear pore complex protein Nup153 and
secondary antibodies conjugated with ATTO647N. The image was
acquired with a TCS STED confocal microscope (Leica). (C) TdEosFP-
paxillin expressed in a Hep G2 cell to label adhesion complexes at
the lower surface. The image was acquired on an ELYRA P.1
prototype system (Carl Zeiss, Inc.) using TIRF illumination. Single
molecule positional information was projected from 10,000 frames
recorded at 30 frames per second. On the left, signals were summed
up to generate a TIRF image with conventional wide-field lateral
resolution. Bars: 5 µm (insets, 0.5 µm).

biological images

biological images

APPLICATIONS IN BIOLOGICAL SYSTEMS

The cytoskeleton of mammalian cells, especially microtubules
(Figure 5a) (29444652), is the most commonly used benchmark
structure for super-resolution imaging. Other cytoskeletal structures
imaged so far include actin filaments in the lamellipodium (6),
keratin intermediate filaments (59), neurofilaments (2683) and
MreB in Caulobacter (66).

Figure 5

cytoskeleton. f5.

cytoskeleton. f5.

Examples of super-resolution images of biological samples.
(a) Two-color STORM imaging of immunostained microtubule (green)
and clathrin-coated pits (red) (From Reference 46. Reprinted with
permission from AAAS).

Organelles, such as the endoplasmic reticulum (27), lysosome (6),
endocytic and exocytic vesicles (465264), and mitochondria
(65356), have also been imaged. For example, using the single-molecule localization approach, 3D STORM imaging has clearly
resolved the ~150-nm diameter, hemispherical cage shape of clathrin-coated pits (4652), which only appear as diffraction-limited spots
without any feature in conventional fluorescence microscopy (Figure 5a,b).
Two-color 3D STED has resolved the hollow shape of the mitochondrial
outer membrane (marked by the translocase protein Tom20), enclosing
a matrix protein Hsp60 (56), even though the diameter of mitochondria is
only about 300–500 nm (Figure 5c). The outer membrane structure of
mitochondria and their interactions with microtubules have been resolved
by two-color 3D STORM (53). The transport of synaptic vesicles
has been recorded at video rate using 2D STED (Figure 5d ) (64).

Many plasma membrane proteins or membrane associated protein
complexes have also been studied by super-resolution fluorescence
microscopy. For example, synaptotagmin clusters after exocytosis in
primary cultured hippocampal neurons (84), the donut-shaped
clusters of Drosophila protein Bruchpilot at the neuromuscular
synaptic active zone (85), and the size distribution of syntaxin clusters
have all been imaged (8687). Photoactivation has enabled the tracking
of the influenza protein hemagglutinin and the retroviral protein Gag in
live cells, revealing the membrane microdomains (67) and the spatial
heterogeneity of membrane diffusion (68). The morphology and transport
of the focal adhension complex has also been observed using live-cell
PALM (Figure 5e) (65).

Summary points

  1. Super resolution fluorescence microscopy with a spatial resolution not limited by the diffraction of
    light has been implemented using saturated depletion/excitation or single-molecule localization
    of switchable fluorophores.
  2. Three-dimensional imaging with an optical resolution as high as ~20 nm in the lateral direction
    and 40–50 nm in axial dimension has been achieved.
  3. The resolution of these super-resolution fluorescence microscopy techniques can in principle
    reach molecular scale.
  4. In practice, the resolution of the images are not only limited by the intrinsic optical resolution,
    but also by sample specific factors including the labeling density, probe size and sample preservation.
  5. Multicolor super resolution imaging has been implemented, allowing colocalization measurements
    to be performed at nanometer scale resolution and molecular interaction to be more précisely
    identified in cells.
  6. Super-resolution fluorescence imaging allows dynamic processes to be investigated at the tens of
    nanometer resolution in living cells.
  7. Many cellular structures have been imaged at sub-diffraction-limit resolution.

Future issues

  1. Achieving molecular scale resolution (a few nanometers or less).
  2. Fast super resolution imaging of a large view field by multi-point scanning or high-speed single-molecule switching/localization.
  3. Developing new fluorescent probes that are brighter, more photostable and switchable fluorophores
    that have high on-off contrast and fast switching rate.
  4. Developing fluorescent labeling methods that can stain the target with small molecules at high specificity,
    high density and good ultrastructure preservation.
  5. Application of super resolution microscopy to provide novel biological insights

Acronyms

FP

Fluorescent Protein

FPALM

Fluorescence PhotoActivation Localization Microscopy

I5M

Combination of I2M (Illumination Interference Microscopy) and I3M
(Incoherent Imaging Interference Microscopy)

PALM

PhotoActivated Localization Microscopy

PSF

Point Spread Function

RESOLFT

REversible Saturable Optically Linear Fluorescence Transition

SIM

Structured Illumination Microscopy

SSIM

Saturated Structured Illumination Microscopy

STED

STimulated Emission Depletion

STORM

STochastic Optical Reconstruction Microscopy

glossary

Numerical aperture (NA)

The numerical aperture of an objective characterizes the solid angle
of light collected from a point light source at the focus of the objective.

Stimulated emission

The process that an excited state molecule or atom jumps to the
ground state by emitting another photon that is identical to the incoming
photon. It is the basis of laser.

Fluorescence saturation

At high excitation intensity, the fluorescence lifetime instead of the excitation
rate becomes the rate limiting step of fluorescence emission, causing the
fluorescence signal not to increase proportionally with the excitation intensity.

Nyquist criterion

To determine a structure, the sampling interval needs to be no larger than
half of the feature size.

Mitochondria

Organelles in eukaryotic cells for APT generation, consisting of two
membrane (inner and outer) enclosing the inter membrane space and
the matrix inside the inner membrane.

Clathrin-coated pit

Vesicle forming machinery involved in endocytosis and intracellular
vesicle transport, consisting of clathrin coats, adapter proteins, and
other regulatory proteins.

Focal adhesion

The macromolecular complex serving as the mechanical connection
and signaling hub between a cell and the extracellular matrix or other cells.

Selected references with abstract

Near-Field Optics: Microscopy, Spectroscopy, and Surface
Modification Beyond the Diffraction Limit
Eric Betzig,  Jay K. Trautman
AT&T Bell Laboratories, Murray Hill, NJ 07974
Science 10 Jul 1992; 257(5067) pp. 189-195
http://dx.doi.org:/0.1126/science.257.5067.189

 The near-field optical interaction between a sharp probe and a sample
of interest can be exploited to image, spectroscopically probe, or modify
surfaces at a resolution (down to ∼12 nm) inaccessible by traditional far-field
techniques. Many of the attractive features of conventional optics are
retained, including noninvasiveness, reliability, and low cost. In addition, most
optical contrast mechanisms can be extended to the near-field regime,
resulting in a technique of considerable versatility. This versatility
is demonstrated by several examples, such as the imaging of nanometric-scale features in mammalian tissue sections and the creation of ultrasmall,
magneto-optic domains having implications for high density data storage.
Although the technique may find uses in many diverse fields, two of the
most exciting possibilities are localized optical spectroscopy of semiconductors
and the fluorescence imaging of living cells.

Imaging Intracellular Fluorescent Proteins at Nanometer Resolution

 E Betzig1,2,*,†, GH. Patterson3, R Sougrat3, O.W Lindwasser3,
S Olenych4, JS. Bonifacino3, MW. Davidson4, JL Schwartz3, HF. Hess5,*  1 Howard Hughes Medical Institute, Janelia Farm Research Campus,
Ashburn, VA   2 New Millennium Research, LLC, Okemos, MI.   3 Cell Biology and Metabolism Branch, National Institute of Child Health
and Human Development (NICHD), Bethesda, MD.  4 National High
Magnetic Field Laboratory, Florida State University, Tallahassee, FL.
5 NuQuest Research, LLC, La Jolla, CA.
Science 15 Sep 2006; 313(5793): pp. 1642-1645
http://dx.doi.org:/10.1126/science.1127344

We introduce a method for optically imaging intracellular proteins at
nanometer spatial resolution. Numerous sparse subsets of photo-activatable fluorescent protein molecules were activated, localized
(to ∼2 to 25 nanometers), and then bleached. The
aggregate position information from all subsets was then assembled
into a super-resolution image. We used this method—termed photo-
activated localization microscopy to image specific target proteins
in thin sections of lysosomes and mitochondria; in fixed whole cells,
we imaged vinculin at focal adhesions, actin within a lamellipodium,
and the distribution of the retroviral protein Gag at the plasma
membrane.

Toward fluorescence nanoscopy.

Hell SW.   Author information 
Nat Biotechnol. 2003 Nov; 21(11):1347-55.
http://www.ncbi.nlm.nih.gov/pubmed/14595362

For more than a century, the resolution of focusing light microscopy
has been limited by diffraction to 180 nm in the focal plane and to
500 nm along the optic axis. Recently, microscopes have been
reported that provide three- to seven-fold improved axial
resolution in live cells. Moreover, a family of concepts has emerged
that overcomes the diffraction barrier altogether. Its first exponent,
stimulated emission depletion microscopy, has so far displayed a
resolution down to 28 nm. Relying on saturated optical transitions,
these concepts are limited only by the attainable saturation level.
As strong saturation should be feasible at low light intensities,
nanoscale imaging with focused light may be closer than ever.
PMID: 14595362

Far-field optical nanoscopy.

Hell SW.  Author information 
Science. 2007 May 25;316(5828):1153-8.
http://www.ncbi.nlm.nih.gov/pubmed/17525330

In 1873, Ernst Abbe discovered what was to become a well-known
paradigm: the inability of a lens-based optical microscope to
discern details that are closer together than half of the wavelength
for its most popular imaging mode, fluorescence microscopy, the
diffraction barrier is crumbling. Here, I discuss the physical concepts
that have pushed fluorescence microscopy to the nanoscale, once
the prerogative of electron and scanning probe microscopes. Initial
applications indicate that emergent far-field optical nanoscopy will
have a strong impact in the life sciences and in other areas benefiting
from nanoscale visualization.
PMID:  17525330

Imaging intracellular fluorescent proteins at nanometer resolution.

Betzig E1, Patterson GHSougrat RLindwasser OWOlenych S,
Bonifacino JSDavidson MWLippincott-Schwartz JHess HF.
Author information
Science. 2006 Sep 15;313(5793):1642-5. Epub 2006 Aug 10
http://www.ncbi.nlm.nih.gov/pubmed/16902090

We introduce a method for optically imaging intracellular proteins at
nanometer spatial resolution. Numerous sparse subsets of photo-ctivatable fluorescent protein molecules were activated, localized
(to approximately 2 to 25 nanometers), and then bleached. The
aggregate position information from all subsets was then assembled
into a super-resolution image. We used this method–termed photo-activated localization microscopy–to image specific target proteins in
thin sections of lysosomes and mitochondria; in fixed whole cells,
we imaged vinculin at focal adhesions, actin within a lamellipodium,
and the distribution of the retroviral protein Gag at the plasma
membrane.

Comment in

PMID:  16902090  [PubMed – indexed for MEDLINE]

Illuminating single molecules in condensed matter.

Moerner WE1, Orrit M.  Author information 
Science. 1999 Mar 12;283(5408):1670-6.
http://www.ncbi.nlm.nih.gov/pubmed/10073924

Efficient collection and detection of fluorescence coupled with careful
minimization of background from impurities and Raman scattering
now enable routine optical microscopy and study of single molecules
in complex condensed matter environments. This ultimate method
for unraveling ensemble averages leads to the observation of
new effects and to direct measurements of stochastic fluctuations.
Experiments at cryogenic temperatures open new directions in
molecular spectroscopy, quantum optics, and solid-state dynamics.
Room-emperature investigations apply several techniques
(polarization microscopy, single-molecule imaging, emission time
dependence, energy transfer, lifetime studies, and the like) to a
growing array of biophysical problems where new insight may be
gained from direct observations of hidden static and dynamic
inhomogeneity.  PMID: 10073924

Fluorescence microscopy with super-resolved optical sections.

Egner A1, Hell SW.  Author information 
Trends Cell Biol. 2005 Apr;15(4):207-15.
http://www.ncbi.nlm.nih.gov/pubmed/15817377

The fluorescence microscope, especially its confocal variant, has
become a standard tool in cell biology research for delivering
3D-images of intact cells. However, the resolution of any standard
optical microscope is atleast 3 times poorer along the axis of the
lens that in its focal plane. Here, we review principles and applications
of an emerging family of fluorescence microscopes, such as 4Pi
microscopes, which improve axial resolution by a factor of seven by
employing two opposing lenses. Noninvasive axial sections of 80-160 nm
thickness deliver more faithful 3D-images of subcellular features,
providing a new opportunity to significantly enhance our understanding
of cellular structure and function. PMID: 15817377

4Pi-confocal microscopy provides three-dimensional images of the
microtubule network with 100- to 150-nm resolution.

Nagorni M1, Hell SW.  Author information 
J Struct Biol. 1998 Nov;123(3):236-47.

We show the applicability of 4Pi-confocal microscopy to three-dimensional imaging of the microtubule network in a fixed mouse
fibroblast cell.Comparison with two-photon confocal resolution
reveals a fourfold better axial resolution in the 4Pi-confocal case.
By combining 4Pi-confocal microscopy with Richardson-Lucy
image restoration a further resolution increase is achieved.
Featuring a three-dimensional resolution in the range 100-150 nm,
the 4Pi-confocal (restored) images are intrinsically more detailed
than their confocal counterparts. Our images constitute what
to our knowledge are the best-resolved three-dimensional
images of entangled cellular microtubules obtained with light
to date.  PMID: 9878578

Part IV. Super-resolution microscopy

Super-resolution microscopy is a form of light microscopy. Due
to the diffraction of light, the resolution of conventional light
microscopy is limited as stated by Ernst Abbe in 1873.[1]
A good approximation of the resolution attainable is the full
width at half maximum 
 (FWHM) of the point spread function,
and a precise wide-field microscope with high numerical
aperture
 and visible light usually reaches a resolution of ~250 nm.

Super-resolution techniques allow the capture of images with
a higher resolution than the diffraction limit. They fall into
two broad categories,
“true” super-resolution techniques, which capture information
contained in evanescent waves, and “functional” super-
resolution techniques, which use clever experimental
techniques and known limitations on the matter being
imaged to reconstruct a super-resolution image.[2]

True subwavelength imaging techniques include those that
utilize the Pendry Superlens and near field scanning optical
microscopy
, the 4Pi Microscope and structured illumination
microscopy technologies like SIM and SMI. However, the
majority of techniques of importance in biological imaging
fall into the functional category.

Groups of methods for functional super-resolution microscopy:

  1. Deterministic super-resolution: The most commonly used emitters in biological
    microscopy, fluorophores, show a nonlinear response to excitation, and this
    nonlinear response can be exploited to enhance resolution. These
    methods include STEDGSDRESOLFTand SSIM.
  2. Stochastic super-resolution: The chemical complexity of many molecular
    light sources gives them a complex temporal behaviour, which can be used
    to make several close-by fluorophores emit light at separate times and
    thereby become resolvable in time.  These methods include SOFI and all
    single-molecule localization methods (SMLM) such as SPDM,
    SPDMphymodPALM, FPALM, STORM and dSTORM.

Part V. HIV-1

Conformational dynamics of single HIV-1 envelope
trimers on the surface of native virions

James B. Munro1,*,Jason Gorman2Xiaochu Ma1,
Zhou Zhou3James Arthos4,
Dennis R. Burton5,6, et al.
1Department of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, CT. 2Vaccine Research
Center, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, MD .
3Department of Physiology and Biophysics, Weill
Cornell Medical College of Cornell University, New York, NY .
4Laboratory of Immunoregulation, National Institute of Allergy
and Infectious Diseases, National Institutes of Health, Bethesda,
MD . 5Department of Immunology and Microbial Science, and
IAVI Neutralizing Antibody Center, The Scripps Research
Institute, La Jolla, CA . 6Ragon Institute of MGH, MIT, and
Harvard, Cambridge, MA. 7International AIDS Vaccine Initiative
(IAVI), New York, NY . 8Department of
Chemistry, University of Pennsylvania, Philadelphia, PA.

The HIV-1 envelope (Env) mediates viral entry into host cells.
To enable the direct imaging of conformational dynamics
within Env we introduced fluorophores into variable
regions of the gp120 subunit and measured single-molecule
fluorescence resonance energy transfer (smFRET) within
the context of native trimers on the surface of HIV-1 virions.
Our observations revealed unliganded HIV-1 Env to be
intrinsically dynamic, transitioning between three distinct
pre-fusion conformations, whose relative occupancies
were remodeled by receptor CD4 and antibody binding.
The distinct properties of neutralization-sensitive and
neutralization-resistant HIV-1 isolates support a dynamics-based mechanism of immune evasion and ligand recognition.

Read Full Post »

Mechanisms of Drug Resistance

Curator: Larry H. Bernstein, MD, FCAP

Leaders in Pharmaceutical Intelligence, CSO

 

Mechanisms of Drug Resistance

This discussion is a continuing discussion of matters of metabolomics and the
essential role of genomic or epigenetic mechanisms to guide the development of
proteomic driven effectors of resistance to drug therapy.
We start with the elucidation of efflux pumps in bacteria, and we conclude with
consideration of cancer cells.

Part 1. Antimicrobial Resistance

Antimicrobial resistance is the ability of microbes, such as bacteria, viruses,
parasites, or
fungi, to grow in the presence of a chemical (drug) that would normally kill it
or limit its growth.

difference between non-resistant bacteria and drug resistant bacteria

difference between non-resistant bacteria and drug resistant bacteria

http://www.niaid.nih.gov/SiteCollectionImages/topics/antimicrobialresistance/1whatIs
DrugResistance.gif

Non-resistant bacteria multiply, and upon drug treatment, the bacteria die. Drug
resistant bacteria multiply as well, but upon drug treatment, the bacteria continue
to spread.

Many infectious diseases are increasingly difficult to treat because of antimicrobial-resistant organisms, including HIV infection, staphylococcal infection, tuberculosis,
influenza, gonorrhea, candida infection, and malaria.

Between 5 and 10 percent of all hospital patients develop an infection. About 90,000
of these patients die each year as a result of their infection, up from 13,300 patient
deaths in 1992.

According to the Centers for Disease Control and Prevention (April 2011), antibiotic
resistance in the United States costs an estimated $20 billion a year in excess health
care costs. In addition, a cost of $35 million in other societal costs and more than 8
million additional days that people spend in the hospital. This is because people
infected with antimicrobial-resistant organisms are more likely to have longer hospital stays and may require more complicated treatment.

Diagnostic tests designed to determine which microbe is causing infection and to
which antimicrobials the microbe might be resistant take a few days or weeks to give
results because of a requirement for the microbe to grow for it to be identified.

Part 2. Antibiotic Tolerance   
Reported By Jef Akst | June 25, 2014

Optimization of lag time underlies antibiotic tolerance in evolved bacterial
populations

O. Fridma et al.    Nature, 2014 
http://dx.doi.org://10.1038/nature13469

Populations of Escherichia coli grown in the lab develop tolerance when exposed to
repeated treatments with the antibiotic ampicillin. The bacteria evolved to stay in a
dormant “lag” phase for just longer than three-, five-, or eight-hour-long treatment
courses. Antibiotic tolerance, which allows bacteria to survive even high levels of
antibiotics by remaining dormant. Tolerance may lead to an inaccurate assumption
that an unsuccessful antibiotic treatment failed as a result of resistance, in which
the microbe has evolved to grow in the presence of the drug. Resistance is very well
known; but the issue of tolerance is much less known,” according to Tom Coenye of
the Laboratory of Pharmaceutical Microbiology (LPM) at Gent University in Belgium,
who was not involved in the research.  This is a new phenomenon, extended lag,
where mutants have a longer lag time, and that extended lag allows them to survive
an attack by antibiotics.

To gain a better understanding of how bacterial populations might evolve to tolerate
antibiotic exposure, Nathalie Q. Balaban, a microbiologist and physicist at The Hebrew
University of Jerusalem in Israel and her colleagues exposed cultures of E. coli to high
concentrations of ampicillin for three, five, or eight hours, then washed the drug away
and suspended the bacteria in fresh media to be grown overnight. The next day, the
team repeated these treatments. In 10 cycles we could see that tolerance had evolved,
” Balaban said. Indeed, while the ampicillin treatments killed more than 99.9 percent of
the E. coli, by day 10, bacterial survival had increased 100-fold.

Moreover, the bacteria were also tolerant to norfloxacin, an antibiotic with a different mechanism of action than ampicillin but also ineffective during the dormant stage,
further supporting the idea that the E. coli populations had evolved to tolerate certain
durations of antibiotic exposure. “This is characteristic of tolerance,” said Balaban.
“The bacteria that have evolved tolerance under ampicillin are also more tolerant to
this completely different class of antibiotics.” Resistance, on the other hand, is usually
class-specific, she noted.

The researchers identified three genes that seemed to play a functional role in antibiotic
tolerance. While the exact mechanism of how mutations in these genes may have
lengthened the bacteria’s lag time is not yet known, two of the genes are part of pathways
that were previously implicated in bacterial persistence, including an antitoxin in a
common toxin-antitoxin module
 that may help regulate that bacteria’s growth.

Part 3. Multidrug Resistance Perspective

Mechanisms of antibiotic resistance in salmonella: efflux pumps, genetics,
quorum sensing and biofilm formation.

Perspectives in Drug Discovery and Design 02/2011; 8:114-123.
Martins M, McCusker, Amaral, Fanning S

Multidrug resistance (MDR) to antibiotics presents a serious therapeutic problem
in the treatment of bacterial infections. The importance of this mechanism of resistance
in clinical settings is reflected in the increasing number of reports of multidrug resistant
isolates. In Salmonella enterica, the most common etiological agent of food borne
salmonellosis worldwide, MDR is becoming a major concern.

In Salmonella the main mechanisms of antibiotic resistance are mutations in target
genes (such as DNA gyrase and topoisomerase IV) and the over-expression of efflux pumps. However, other mechanisms such as

  1. changes in the cell envelope;
  2. down regulation of membrane porins;
  3. increased lipopolysaccharide (LPS) component of the outer cell membrane;
  4. quorum sensing and
  5. biofilm formation

can also contribute to the resistance seen in this microorganism. To overcome
this problem new therapeutic approaches are urgently needed.

In the case of efflux-mediated multidrug resistant isolates, one of the treatment
options could be

  • the use of efflux pump inhibitors (EPIs)
  • in combination with the antibiotics to which the bacteria is resistant.

By blocking the efflux pumps

  • resistance is partly or wholly reversed,
  • allowing antibiotics showing no activity against the MDR strains
  • to be used to treat these infections.

Compounds that show potential as an EPI are therefore of interest, as well as new
strategies to target the efflux systems. Quorum sensing (QS) and biofilm formation
are systems also known to be involved in antibiotic resistance. Consequently,
compounds that

  • can disrupt or inhibit these bacterial “communication systems” will be of use in
    the treatment of these infections.

Part 5. Effux pumps and S. Aureus

Multidrug Efflux Pumps in Staphylococcus aureus: an Update

SS Costa, M Viveiros, L Amaral and I Couto
1Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e
Medicina Tropical, Universidade Nova de Lisboa (IHMT, UNL), 2Centro de Recursos
Microbiológicos (CREM), UNL, Portugal,3COST ACTION BM0701 (ATENS), Brussels,
Belgium
The Open Microbiology Journal 2013;(Suppl 1-M5): 59-71

The emergence of infections caused by multi- or pan-resistant bacteria in the hospital
or in the community settings is an increasing health concern. Albeit there is no single
resistance mechanism behind multi-resistance, multidrug efflux pumps,

  • proteins that cells use to detoxify from noxious compounds,

seem to play a key role in the emergence of these multidrug resistant (MDR) bacteria.
During the last decades, experimental data has established their contribution to low
level resistance to antimicrobials in bacteria and their

  • potential role in the appearance of MDR phenotypes, by the extrusion of multiple,
    unrelated compounds.

Recent studies suggest that

  • efflux pumps may be used by the cell as a first-line defense mechanism,

avoiding the drug to reach lethal concentrations, until a stable, more efficient alteration
occurs, that allows survival in the presence of that agent.

In this paper we review the current knowledge on

  • MDR efflux pumps and their
  • intricate regulatory network in Staphylococcus aureus,

a major pathogen, responsible from mild to life-threatening infections. Particular emphasis will be given to the potential role that

  • aureus MDR efflux pumps,
  • either chromosomal or plasmid-encoded, have
  • on resistance towards different antimicrobial agents and
  • on the selection of drug – resistant strains.

We will also discuss the many questions that still remain on the role of each specific
efflux pump and the need to establish appropriate methodological approaches to
address all these questions.

        Table 1. Multidrug Efflux Pumps Described for Staphylococcus aureus

Efflux Pump  Family Regulator(s) Substrate Specificity  References 
Chromosomally-encoded Efflux Systems 
NorA MFS MgrA,
NorG(?)
Hydrophilic fluoroquinolones (ciprofloxacin,
norfloxacin) QACs (tetraphenylphosphonium,
benzalkonium chloride) Dyes (e.g. ethidium
bromide, rhodamine)
[16,18,19]
NorB MFS MgrA,
NorG
Fluoroquinolones (e.g. hydrophilic: ciprofloxacin,
norfloxacin and hydrophobic: moxifloxacin,
sparfloxacin) Tetracycline QACs (e.g.
tetraphenylphosphonium, cetrimide) Dyes (e.g. ethidium bromide)
[31]
NorC MFS MgrA(?),
NorG
Fluoroquinolones (e.g. hydrophilic: ciprofloxacin
and hydrophobic: moxifloxacin) Dyes
(e.g. rhodamine)
[35,36]
MepA MATE MepR Fluoroquinolones (e.g. hydrophilic: ciprofloxacin,
norfloxacin and hydrophobic: moxifloxacin,
sparfloxacin) Glycylcyclines (e.g. tigecycline) QACs (e.g. tetraphenylphosphonium, cetrimide, benzalkonium chloride) Dyes
(e.g. ethidium bromide)
[37,38]
MdeA MFS n.i. Hydrophilic fluoroquinolones (e.g. ciprofloxacin,
norfloxacin) Virginiamycin, novobiocin, mupirocin,
fusidic acid QACs (e.g. tetraphenylphosphonium,
benzalkonium chloride, dequalinium) Dyes (e.g. ethidium bromide)
[39,40]
SepA n.d. n.i. QACs (e.g. benzalkonium chloride) Biguanidines
(e.g. chlorhexidine) Dyes (e.g. acriflavine)
[41]
SdrM MFS n.i. Hydrophilic fluoroquinolones (e.g. norfloxacin) Dyes (e.g. ethidium bromide, acriflavine) [42]
LmrS MFS n.i. Oxazolidinone (linezolid) Phenicols
(e.g. choramphenicol, florfenicol) Trimethoprim, erythromycin, kanamycin,
fusidic acid QACs (e.g. tetrapheny-
lphosphonium) Detergents (e.g. sodium
docecyl sulphate) Dyes (e.g. ethidium
bromide)
[43]
Plasmid-encoded Efflux Systems

QacA MFS QacR QACs (e.g. tetraphenylphosphonium,
benzalkonium chloride, dequalinium)
Biguanidines (e.g. chlorhexidine)
Diamidines (e.g. pentamidine) Dyes
(e.g. ethidium bromide,
rhodamine, acriflavine)
[45,49]
QacB MFS QacR QACs (e.g. tetraphenylphosphonium,
benzalkonium chloride)Dyes (e.g. ethidium bromide, rhodamine,
acriflavine)
[53]
Smr SMR n.i. QACs (e.g. benzalkonium chloride,
cetrimide) Dyes (e.g. ethidium bromide)
[58,61]
QacG SMR n.i. QACs (e.g. benzalkonium chloride,
cetyltrymethylammonium) Dyes
(e.g. ethidium bromide)
[67]
QacH SMR n.i. QACs (e.g. benzalkonium chloride,
cetyltrymethylammonium) Dyes
(e.g. ethidium bromide)
[68]
QacJ SMR n.i. QACs (e.g. benzalkonium chloride,
cetyltrymethylammonium) Dyes
(e.g. ethidium bromide)
[69]

a n.d.: The family of transporters to which SepA belongs is not elucidated to date.
b n.i.: The transporter has no regulator identified to date.
QACs: quaternary ammonium compounds

Identification of the plasmid-encoded qacA efflux pump gene
in meticillin-resistant Staphylococcus aureus (MRSA)
strain HPV107, a representative of the MRSA Iberian clone

S.S. Costaa,b, E. Ntokouc, A. Martinsa,d, M. Viveirosa,e, S. Pournarasc,
I. Coutoa,b, L. Amarala,d,e,∗
a Unidade de Micobactérias, Instituto de Higiene e Medicina Tropical,
Universidade Nova de Lisboa (IHMT, UNL), b Centro de Recursos Microbiológicos,
Universidade Nova de Lisboa (CREM, UNL), d Unidade de Parasitologia e
Microbiologia Médica (UPMM), Instituto de Higiene e Medicina Tropical, Universidade
Nova de Lisboa (IHMT, UNL), Lisbon, Portugal; e COST ACTION BM0701 (ATENS)
c Department of Microbiology, Medical School, University of Thessaly, Larissa, Greece;
Int J Antimicrobial Agents  2010; 36: 557–561
http://www.elsevier.com/locate/ijantimicag

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial
bacterium for which prevention and control measures consist mainly of

  • the application of biocides with antiseptic and disinfectant activity.

In this study, we demonstrated the presence of

  • the plasmid-located efflux pump gene qacA in MRSA strain HPV107,

a clinical isolate representative of the MRSA Iberian clone. The existence
of efflux activity in strain HPV107 due to the QacA pump was found and

  • this QacA efflux activity was linked with a phenotype of
  • reduced susceptibility towards several biocide compounds.

No association could be made with antibiotic resistance. This work
emphasises the potential of QacA pump activity in

  • the maintenance and dissemination of important MRSA strains in
    the hospital setting and, increasingly, in the community.

Efflux-mediated response of Staphylococcus aureus exposed to
ethidium bromide

I Couto1,2, S S Costa1, M Viveiros1, M Martins1,3 and L Amaral1,3*
1Unidade de Micobacterias, Instituto de Higiene e Medicina Tropical,
Universidade Nova de Lisboa (UNL), 2Centro de Recursos Microbiolo´gicos (CREM), Faculdade de Cieˆncias e Tecnologia, UNL,3UPMM,
Instituto de Higiene e Medicina Tropical, UNL, Portugal
J Antimicrob Chemother  (2008) 62, 504–513
http://dx.doi.org:/10.1093/jac/dkn217

By adapting an antibiotic-susceptible Staphylococcus aureus strain to
increasing concentrations of ethidium bromide, a known substrate
of efflux pumps (EPs), and

  • by phenotypically and genotypically analysing the resulting progeny,
  • we characterized the molecular mechanisms of S. aureus
    adaptation to ethidium bromide.

ATCC 25923 was grown in increasing concentrations of ethidium bromide.
The MICs of representatives of eight classes of antibiotics, eight biocides
and two dyes against ATCC 25923 and its ethidium bromide-resistant progeny
ATCC 25923EtBr were determined

  • with or without six efflux pump inhibitors (EPIs).

Efflux activity in the presence/absence of EPIs was evaluated by realtime
fluorometry. The presence and expression of eight EP genes were assayed
by PCR and quantitative RT–PCR (qRT–PCR), respectively. Mutations in
grlA, gyrA and norA promoter regions were screened by DNA sequencing.

Compared with its parental strain, ATCC 25923EtBr was

  • 32-fold more resistant to ethidium bromide and
  • also more resistant to biocides and hydrophilic fluoroquinolones.
  • Resistance to these could be reduced by the EPIs chlorpromazine,
    thioridazine and reserpine.

Increased efflux of ethidium bromide by ATCC 25923EtBr could be
inhibited by the same EPIs. qRT–PCR showed that

  • norA was 35-fold over-expressed in ATCC 25923EtBr,

whereas the remaining EP genes showed no significant increase in their

expression. Sequencing of the norA promoter region revealed

  • a 70 bp deletion in ATCC 25923EtBr.

Exposure of S. aureus to quaternary compounds such as ethidium bromide
results in decreased susceptibility of the organism to a wide variety of
compounds, including quinolones and biocides

  • through an efflux-mediated response, which
  • for strain ATCC 25923 is mainly NorA-mediated.

This altered expression may result from alterations in the norA
promoter region
.

Ethnic consumption of plant leaf extracts and appraisal of
their nutraceutical efficacy against multidrug resistant
staphylococcus aureus

Kaushik S1, 2*, Tomar Rs1, Shrivastav V1, Shrivastav A2 And Jain Sk3
Amity Institute of Biotechnology, Amity University Madhya Pradesh,
Gwalior (M.P.);  2: College of Life Sciences, Cancer Hospital and
Research Institute, Gwalior (M.P.); 3: Department of Microbiology,
Vikram University, Ujjain (M.P.), INDIA
IJBPAS, Feb, 2014, 3(2): 204-209

Nutraceuticals are natural bioactive chemical compounds that have
health promoting, disease preventing or medicinal properties.
Emergence of Multi Drug Resistant Staphylococci is increasing at
alarming rates and diseases caused by these strains leave patients
against multiple resistant Staphylococcus aureus.

The test bacteria were isolated and characterized by standard and
NCCLS recommended microbiological techniques. A total of eighteen
plant extracts were analysed for their antimicrobial activity. The
selection of medicinal plants was based on their traditional uses in
India. However most of these plants were not previously screened.
Antibacterial activity of these components was performed by standard
Kirby Bauer Disk Diffusion method approved by NCCLS and the
inhibitory effect was analysed by calculating Zone of inhibition.

Among the eighteen plant extracts analysed we found highest
activity in the effect of chemotherapy and as promising bio control agents

  • Guava,
  • Mango,
  • Jamun and
  • Pomengrate plant extracts,

while most of the other plants were either showing very moderate/
least activity against test bacteria. Our recent experiment indicated
that phytochemicals extracted with methanol can be utilized as
nutraceutical to lower the side.

Part 6. Efflux pumps and gram-negative organisms

Efflux Pumps that Bestow Multi-Drug Resistance of Pathogenic Gram-
negative 
Bacteria 

Amaral L1,2*, Spengler G2, Martins A2,3 and Molnar J2
1Travel Medicine of the Centre for Malaria and Other Tropical Diseases (CMDT),
Institute of Hygiene and Tropical Medicine, Lisbon, Portugal 2Department of
Medical Microbiology and Immunobiology, Faculty of Medicine, University of
Szeged, Szeged, Hungary 3Unit of Parasitology and Medical Microbiology
(UPMM), Institute of Hygiene and Tropical Medicine, Lisbon, Portugal
Amaral et al., Biochem Pharmacol 2013; 2:3
http://dx.doi.org/10.4172/2167-0501.1000119

The efflux pump

The efflux pump

Efflux pumps are integral plasma membrane protein systems that recognize and bind
noxious compounds present in the cytoplasm (toxic products produced by metabolism;
compounds that have penetrated the cell), or periplasm of the bacterial cell and extrude
it into the environment in which the bacterium resides [1].

The efflux pump machinery gives the cell additional protection to the one provided by

  • the constituents of its cell wall (example: lipopolysaccharides), and
  • provides an initial protection to noxious agents present in its
    natural environment that have penetrated into the cell (example: bile
    salts in the colon) [1].

The efflux pump machinery is divided into five superfamily classes;

  • the major facilitator (MF),
  • the ATP-binding cassette (ABC),
  • the resistance-nodulation-division (RND),
  • the small multi-drug resistance (SMR) and
  • the multi-drug and toxic compound extrusion (MATE).

With respect to Gram-negative bacteria, although they all play
important roles in the protection of the bacterium from noxious
agents present in the environment, the

  • main efflux pump of the Gram negative bacterium is a
    member of the RND superfamily, and
  • because multi-drug resistance of clinical isolates have
    been associated with the over-expression of this pump,

it has received a great deal of attention [2].

The first in vitro response of bacteria to a given noxious agent,
such as an antibiotic, is to over-express its main efflux pump [2].
If the bacterium is serially exposed in vitro to increasing
concentrations of that compound, it responds by increasing
the effective number of its main efflux pump, as well as others
that provide redundant protection [2].

However, if that “adapted” bacterium is now maintained at a
constant level of a noxious agent, the level of efflux pump
activity increases up to a maximum, followed by a gradual
return of efflux pump activity to its basal level. Concomitant
to this process, an accumulation of mutations of essential
proteins located in the plasma membrane (example penicillin
binding proteins), mutations 30 S component of the ribosome
and gyrase take place [3]. These events suggest that when
the organism is faced with an environment that contains a
constant toxic level of a compound, and the cost for
maintaining an energy consuming system, such as that
needed for the energy dependent efflux pump, is too
great a price to pay.

Therefore, in order to survive in this unchanging environment,
other mechanisms are activated. For example, activation of a
mutator master gene is thought to be an important step at this
level, which results in the mutation of genes that code for
essential proteins, reversing the over-expression of efflux-
pumps, but still conferring the bacterial resistant to the
environmental pressure via other mechanism(s), yet
to be understood [4,5].

During therapy, the level of resistance increases many fold
higher than that of the initial infecting strain. Hence, clinical
isolates from treated patients often show much higher levels
of antibiotic resistance than that of their wild type counterpart
(sometimes it can even present a 1000 fold increase) [6].
At this stage, resistance is usually related to the presence
of mutations, which reduces the survival of the resistant
bacteria,

  • once it is transferred to a noxious agent-free environment

that contains the competing wild type counterpart [3,4].

Depending upon when during therapy a clinical strain is isolated,
its resistance to two or more antibiotic classes (multi-drug
resistance (MDR)), may be due entirely to over-expressed
efflux pumps; to a mixture of over-expressed efflux pumps
and increasing accumulation of mutations; and only to mutations [3,4].

The degree of resistance can readily be determined with
methods that employ compounds known for their modulation
of efflux pump activity, such as

  • phenothiazines [7] or phenyl-arginine-betanaphthylamide
    (PAβN),
  • the latter which competes with the antibiotic as
    substrate of the efflux pump [8].

If in presence of such compounds,

  • the MDR bacterium is rendered fully susceptible
    to the antibiotic(s) to which it was initially resistant,
  • resistance is most likely due to its overexpressed
    efflux pump systems.
  • Contributions made by accumulated mutations
    render the organism less and less affected by the EPI.

This type of information is of great value to clinicians faced
with long-term therapy of a bacterial infection that
progresses to an MDR phenotype. It should be understood
that although the Gram-negative bacterium has essentially
one main efflux pump, such as

  • the AcrAB (Escherichia coli) or
  • the MexAB (Pseudomonas aeruginosa),

the deletion of the main efflux pump results in the over-
expression of one or more other RND efflux pumps,
such as is the case for deletion of the AcrAB, followed by

  • the over-expression of the AcrEF pump [2].

Redundancy of as many as nine RND efflux pumps [2],
provides additional protection to the organism.

The pumps belonging to the RND family form

  • a tripartite complex together with
  • the periplasmic proteins belonging to the
    membrane fusion-protein (MFP) family and
  • the outer membrane channels.

RND transporters consist of

  • a transporter protein that recognises and
    binds the noxious agent
    in the cytoplasm or periplasm and
  • transports it to the contiguous channel (TolC),
  • ending at the surface of the outer membrane.

The transporter is attached to the plasma membrane
by two or three fusion proteins, which are believed to assist the

  • extrusion of the substrate by peristaltic actions [9].

Although the actual structure of RND efflux pumps
in the cell envelop is not completely understood,

  • the structure of the transporter, TolC and fusion
    proteins are well established for major Gram-negative
    bacteria [10].

The PMF energy dependent efflux pump most likely needs the
passage of hydronium ions through its internal cavity,

  • for the release of the substrate that is
  • in turn ejected into the TolC channel via the
  • peristaltic action of the fusion proteins [11].

A low pH,

  • the concentration of hydronium ions at the surface of the cell
  • results in a pH difference of 2 or 3 pH units compared
    to that of the milieu,

the surface concentration of hydronium ions

  • provides the force for the mobility of hydronium ions
  • through porins leading to the acidification of the periplasm,
  • providing the low pH needed by the transporter
  • for the release of the substrate.

At high pH, these hydronium ions come from

  • hydrolysis of ATP by ATP synthase, and
  • are passed into the transporter, thereby
  • reducing its internal pH, so that
  • the release of the substrates can take place [11,12].

EPIs, such as the phenothiazines chlorpromazine or thioridazine,

  • exert their inhibition at pH above 6, and
  • are thought to affect hydrolysis of ATP
  • denying the efflux pump transporter hydronium ions needed

for release of the bound substrate [11,12].

The search for EPIs that are clinically useful continues, although

with respect to thioridazine, this old neuroleptic has been shown

  • to inhibit efflux pumps of pathogenic mycobacteria [13], and
  • has been successfully used to treat extensively drug resistant
    tuberculosis infections [14].

The regulation of the main efflux pump of Escherichia coli may
take place via   distinct pathways. The induced synthesis of the
transporter component of the AcrAB efflux pump, when the
organism is exposed in vitro to a noxious agent,

  1. involves the activation of the stress gene soxS,
  2. followed by the activation of the local regulator marA,
  3. then by the activation of the transporter gene acrB [8].

In the case of Salmonella spp. two component resistance
mechanisms, such as the PmrA/PmrB system, directly
activate the master efflux pump regulator ram A gene [15].
The activation of the PmrA/PmrB system takes place
readily when Salmonella spp. is phagocytosed due to
the acidic nature of the phagolysosome [15], as follows:

  1. PmrB is a sensor that self-phosphorylates, and
  2. then transfers the phosphate to PmrA.
  3. PmrA activates a nine gene operon, which
  4. codes for Lipid A introduced into the nascent
    lipopolysaccharide layer of the outer membrane.
  5. The increased presence of Lipid A renders the
    phagocytosed bacterium practically immune to
    everything, including the hydrolases of the
    phagolysososome [15].

Although some EPIs are in clinical trials, none have yet to
reach the marketplace,    mainly due to their common
toxicity against healthy mammalian cells, affecting
intrinsic mammalian efflux pumps, as for example
those of the blood brain barrier. Lastly, it should be
noted that compounds that inhibit the efflux pump
of bacteria also have the capacity to promote the
removal of plasmids that carry antibiotic resistant
genes [16,17].

  1. Nikaido H, Pages JM (2012) Broad-specificity efflux
    pumps and their role in multidrug resistance of Gram-
    negative bacteria. FEMSMicrobiol Rev 36: 340-363.
  2. Viveiros M, Jesus A, Brito M, Leandro C, Martins M,
    et al. (2005) Inducement and reversal of tetracycline
    resistance in Escherichia coli K-12 and expression of
    proton gradient-dependent multidrug efflux pump
    genes. Antimicrob Agents Chemother 49: 3578-3582.
  3. Martins A, Couto I, Aagaard L, Martins M, Viveiros M
    (2007) Prolonged exposure of methicillin-resistant
    Staphylococcus aureus (MRSA) COL strain to
    increasing concentrations of oxacillin results in a
    multidrug-resistant phenotype. Int J Antimicrob
    Agent 29: 302-305.
  4. Martins A, Spengler G, Molnar J, Amaral L (2012)
    Sequential responses of bacteria to noxious agents
    (antibiotics) leading to accumulation of mutations
    and permanent resistance. Biochem Pharmacol J
    Open Access 1: 7.

Inhibitors of efflux pumps of Gram-negative
bacteria inhibit Quorum Sensing

Leonard Amaral, Joseph Molnar
1 Grupo de Micobacterias, Unidade de Microbacterilogia,
Centro de Malaria e Doenças Tropicais (CMDT), Instituto de
Higiene e Medicina Tropical, Universidade Nova de Lisboa,
Lisbon, Portugal; 2 Cost Action BM0701 (ATENS) of the
European Commission/European Science Foundation;
3 Department of Medical Microbiology and Immunobiology,
University of Szeged, Szeged, Hungary
Open Journal of Pharmacology, 2012, 2-2

Quorum Sensing (QS) systems of bacteria consist of

  • a producer of the QS signal and the responder.

The generation of a QS signal provides the means by which
a population can behave in a concerted manner such as

  • swarming, swimming and secretion of biofilm, etc.

Because concerted bahaviour bestows protection to the bacterial
species, and hence factors involved in the severity of an infection
such as virulence are products of QS systems, compounds that
inhibit the QS system have significant clinical relevance. Recent
evidence suggests that

  • the secretion of QS signals takes place via
  • the efflux pump system of the producer of the signal.

Interestingly, compounds such as phenothiazines and
trifluoromethyl ketones (TFs)

  • that inhibit proton motive force (PMF) activities such
    as swarming and swimming also
  • inhibit the PMF dependent efflux pump systems of
    bacteria and their QS   systems.

This review discusses the relationship between the efflux
pump, the QS system and the compounds that affect both.
Lastly, suggestions are made regarding classes of compounds
that have been shown

  • to inhibit PMF dependent efflux pumps and the need
  • to evaluate them for QS inhibitory properties.

Keywords: Quorum Sensing, QS signal, acylated hydroxyl
lactone (AHL), efflux pumps, Proton Motive Force (PMF),
inhibitors of efflux pumps, inhibitors of QS systems,
phenothiazines, Trifluormethyl Ketones (TFs), plants
sources for QS inhibitors

Efflux pumps of bacteria provide protection from noxious
agents that are present in the environment in which they
exist. Noxious agents may be naturally occurring compounds
present in environments outside and within the human.

Because over-expressed efflux pumps render antibiotic
therapy problematic, an intense search for agents that
inhibit specific efflux pumps of specific bacteria has
been conducted during the past decade [9].

Communication between bacteria of the same strain
or species and between species contributes to their
survival [11-13]. Communication involves the secretion
of signals that invoke a specific response from the responder
[11-13]. This  communication process is termed Quorum
sensing (QS). When it takes place between strains of the
same species,

  • communication is directed towards the reduction
    of population growth and
  • reducing the possibility of exceeding the nutritional
    support of the environment

Other signals may involve a population response that involves

  • the secretion of bioactive molecules that inhibit the
    replication of a competing population species [14-16]
    or even kill [biocidins) [17-21] or
  • promote a swarming effect that recruits members
    of the same species to migrate  to a specific location [22-24]
    similar to swarming by insects subsequent to signals
    indicating site of food [example bees).
  • biofilm, encase the bacteria at distances from each other
    [25-29] and within the matrix of this biofilm are
    channels used for further communication [30].

Biofilms are produced in the wild, at sites such as surfaces
of rocks which maintain the bacterial population in situ [31]
and are also produced at sites of the human colonized by
infecting bacteria [32, 33].

Agents that inhibit the QS response of the infecting bacterium
are obviously important and hence, the search for such agents
that inhibit the QS system and biofilm formation has been in
effect for the past two decades [11-13].

There is a relationship between efflux pumps (EP), QS and
biofilm (BF) secretion which has come to the forefront only
recently [13]. Control of this relationship is critical for
successful therapy of MDR bacterial infections which have
become rather commonplace. It is the intent of this review
to identify agents which may serve to interfere with the
complex system of EP-QS-BF interaction.

Proton motive force (PMF) dependent transporters obtain
their energy for function from the proton motive force. The
proton motive force is the result of cellular metabolism which
yields protons that are not used for coupling with molecular
oxygen and which are exported to the surface of the cell [43-45]
where they are distributed and bound to components of
the protective lipopolysaccharide layer that covers the cell
and constitutes a part of the outer cell wall of Gram-negative
[46] and the cell wall of Gram positive bacteria [47].

The larger the concentration of protons (hydronium ions)
on the surface of the cell with respect to their lower
concentration on the medial side of the cytoplasmic
membrane creates an electrochemical gradient that
is termed the proton motive force (PMF) [48].

Because hydronium ions cannot penetrate the cell wall
or the membrane, they may re-enter the cell only
through channels such as porins in general [49, 50].
The movement of these hydromium ions from the
surface of the cell to the periplasm or cytoplasm is
predicated upon systems that use the PMF as source
of energy-namely the resistance nodulation division
(RND) family of transporters.

E. coli has a multiplicity of efflux pumps that may
exceed 30 in number [51]. However, the main
efflux pump of this organism is the AcrAB-TolC
efflux pump [52, 53] which when deleted, its
function is replaced by the AcrEF-TolC efflux
pump [51]. Both efflux pumps are members
of the resistance nodulation division family of
transporters [51] and consist of three proteins:

  1. The transporter AcrB coded by the gene acrB and
    is intimately attached to the  plasma membrane;
  2. Two fusion proteins AcrA coded by the gene acrA
    that flank the AcrB transporter and are thought
    to assist the movement of a substrate through
    the AcrB transporter [35]; and,
  3. TolC which is also part of other tri-unit efflux pumps
    of the organism [35], is contiguous with the AcrB
    transporter and provides a conduit for the extrusion
    of the substrate [38].

Although the means for the recognition of the substrate to
be extruded appears to involve a pocket within the transporter,
it appears to be

  • defined by a phenyalanine residue [54].

Nevertheless, studies employing fluorochromes recognised by
the AcrB transporter indicate that the binding and release of
the substrate are pH dependent [55].

  • At low pH the dissociation of the substrate is high and
  • at high pH it is very slow.

In a physiological environment of ca. pH 7, if the dissociation
of the substrate is slow or not at all, then the effectiveness of
the pump to extrude a noxious agent would be nullified.
However, since the pump functions at this pH, conditions that
result in the dissociation of the substrate needed for continuous
pump action must involve a

  • decrease of the pH of the internal cavity of the pump
    to which the substrate is bound.

It has been postulated that the lowering of the pH takes place
by the generation of hydronium ions from metabolism [6] which

  • pass from the cytoplasmic side of the plasma membrane
    through the transporter.

At lower pH, there is no need for the generation of metabolically
derived  hydronium ions since these ions can be

  • diverted by the PMF from the surface of the cell
    to the periplasm via porins.

Whether hydronium ions are to be generated from the
hydrolysis of ATP at high pH or used for the synthesis
of ATP at low pH is a special

  • function of ATP synthase [56-58].

Model of the AcrAB-TolC efflux pump of a Gram-
negative bacterium

AcrAB-TolC efflux pump of a Gram-negative bacterium

AcrAB-TolC efflux pump of a Gram-negative bacterium

Hypothesis. At near neutral pH, Hydronium ions from hydrolysis of ATP
by ATP synthase pass through the AcrB

transporter, reduce the pH to a point that causes the release of the
substrate. When the hydronium ions reach the surface of the cell they
are distributed over that surface and bind to lipopolysaccharides
and basic amino acids. When there is a need for hydronium ions for
activity of the efflux pump and the pH is lower than neutral, and
the hydrolysis of ATP is not favoured, hydronium ions from the
surface of cell via the PMF mobilize through the Aqua porins
and reach the transporter where they are pushed through
the transporter by the peristaltic action caused by the fusion
proteins. Substrates bound to the transporter dissociate
when the pH is reduced by the flow of hydronium ions and
are carried out by the flow of water.

Inhibitors of bacterial efflux pumps
Inhibitors of the QS of bacteria

Because phenothiazines inhibit many energy dependent systems
of bacteria such as motility [89, 90, 95], and these phenothiazines
also inhibit efflux pumps of bacteria [6, 7, 9, 41, 51, 73, 74, 76-83],
there seems to be a correlation between an active efflux pump
system and a functional QS system. That this assumption is correct,
recent evidence has been provided showing that the efflux pumps of
the AHL responding environmental Chromobacterium violaceum
(CV026) bacterium and that of E. coli are inhibited by the phenothiazine
thioridazine (TZ) [12]. Because TZ is known to inhibit genes that
regulate and code for efflux pumps of bacteria [41, 119, 120], it is
possible that the inhibition of the responding CV0126 bacterium to
AHLs [12] involves the inhibition of genes that code and regulate
the efflux pump of the responder which is assumed to recognise the
AHL signal as an noxious agent and hence would extrude it to the
environment [12]. The inhibition of an efflux pump should manifest
itself as an inhibitor of the QS component responsible for biofilm
formation.

Since the discovery of berberine a powerful inhibitor of bacterial
efflux pumps [159], plants have become sources of inhibitors of
efflux pumps [160-164]. Given that efflux pumps and the  QS of
bacteria have an intimate relationship as described in this review,
attention has been focused on plants for potential sources of inhibitors
of efflux pumps and QS systems. Essential oils from Columbian
plants have yielded a large number of compounds that inhibit the
QS system of responding bacteria such as

  1. limonene-carvone , the
  2. citral (geranial-neral) (isolated from Lippia alba),
  3. α-pinene (from Ocotea sp.),
  4. β-pinene (from Swinglea glutinosa),
  5. cineol (from Elettaria cardamomun),
  6. α-zingiberene (from Zingiber officinale) and
  7.  pulegone (from Minthostachys mollis) [165].

Several other essential oils, in particular were shown to present
promising inhibitory properties for the short chain AHL quorum
sensing (QS) system in Escherichia coli containing the biosensor

  •  plasmid pJBA132, in  particular Lippia alba.

Citral was the only  essential oil that presented some activity for
the long chain AHL QS system in Pseudomonas putida containing

  •  the plasmid pRK-C12 [165].

The essence of this review is to correlate the relationship of the
efflux pump system to the QS system of bacteria via the use of
compounds that inhibit both systems. Simply put, inhibitors of
the efflux pump system also, when studied, inhibit the QS system
as well. Because the PMF dependent efflux pump system of Gram-
negatives that is overexpressed is responsible for the multi-drug
phenotype of the bacterium, compounds that affect the PMF of
the bacterium are candidates that will inhibit the activity of the
pump. Consequently, this inhibition will inhibit the secretion of
biofilm, and because biofilm is a deterrent to the action of antibiotics,
compounds that affect the efflux pump system are promising
candidates for clinical evaluation.

Limiting and controlling carbapenem-resistant
Klebsiella pneumonia

L Saidel-Odes, A Borer.
1Infection Control and Hospital Epidemiology Unit, 2Infectious
Diseases Institute, Soroka University Medical Center and the
Faculty of Health Sciences, Ben-Gurion University of the Negev,
Beer-Sheva, Israel
Infection and Drug Resistance 2014:7 9–14

Carbapenem-resistant Klebsiella pneumoniae (CRKP)

  • is resistant to almost all antimicrobial agents,
  • is associated with substantial morbidity and mortality, and
  • poses a serious threat to public health.

The ongoing worldwide spread of this pathogen emphasizes the
need for immediate intervention. This article reviews the global
spread and risk factors for CRKP colonization/infection, and
provides an overview of the strategy to combat CRKP dissemination

Outbreaks of CRKP that have occurred around the world have
been associated with the plasmid-encoded carbapenemase
K. pneumoniae carbapenemase (KPC),

  • a carbapenem-hydrolyzing β-lactamase.19

CRKP isolates are resistant to almost all available antimicrobials
and are susceptible

  • only to polymyxins and tigecycline;
  • a minority to the few remaining aminoglycosides,
    though resistance to these agents is increasingly reported.20,21

Several investigators have evaluated predictors for CRKP colonization.
The following summarizes various studies.

  1. In a multivariate analysis, prior use of macrolides and
    any antibiotic exposure $14 days remained the only
    independent factors associated with CRKP bacteremia
  2. Nosocomial isolation of CRKP was strongly favored by the
    selection pressure of carbapenem. In this study, prior
    treatment with fluoroquinolones was associated with
    decreased risk for the emergence of CRKP.
  3. Previous use of carbapenem and cephalosporin
  4. Nursing home residency before hospital admission, bedridden
    status, and previous antibiotic therapy
  5. exposure to fluoroquinolones
  6. the recipient of antibiotics
  7. intensive care unit (ICU) stay, and
  8. Poor functional status,
  9. Independent predictors of subsequent carbapenem-
    resistant Enterobacteriaceae (CRE) infection were
  • admission to the ICU,
  • having a central venous  catheter,
  • receipt of antibiotics, and
  • diabetes mellitus

Schwaber et al and the Israeli CRE Working Group enforced the
Israel Ministry of Health guidelines mandating physical separation
of hospitalized carriers of CRE and dedicated staffing and appointed
a professional task force charged with containment.19 The monthly
incidence of nosocomial CRE was reduced from 55.5 to 11.7 cases
per 100,000 patient days within 15 months.

Part 7.  Tuberculosis

The Mechanism by which the Phenothiazine Thioridazine
Contributes to Cure Problematic Drug-Resistant Forms
of Pulmonary Tuberculosis: Recent Patents for “New Use”

L Amaral1*, A Martins2,3, G Spengler2, A Hunyadi4 and J Molnar2
Recent Patents on Anti-Infective Drug Discovery 2013; 8(3):000-000

At this moment, over half million patients suffer from multi-drug
resistant tuberculosis (MDR-TB) according to the data from the WHO.
A large majority is terminally ill with essentially incurable pulmonary
tuberculosis. This herein mini-review provides the experimental and
observational evidence that a specific phenothiazine,

  • thioridazine,

will contribute to cure any form of drug-resistant tuberculosis. This
antipsychotic agent is no longer under patent  protection for its
initial use. The reader is informed on the recent developments

  • in patenting this compound for “new use” with a special
  • emphasis on the aspects of drug-resistance.

Given that economic motivation can stimulate the use of this drug
as an antitubercular agent, future prospects are also discussed.

Thioridazine is not the only phenothiazine that has been recommended
for therapy of pulmonary tuberculosis. In general, many phenothiazines
have been implicated for antitubercular activity [62, 80-86]. Among
these are

  • trifluoperazine [87-94],
  • methdilazine [95, 96],
  • promazine [97, 98],
  • promethazine [97, 98],
  • fluphenazin [99],
  • propiomazine [100], and
  • the methylene blue related toluidine blue [101].

There are phenothiazine compounds derived from the parental
methylene blue for therapy of pathologies unrelated to tuberculosis
that also possess

  •  antitubercular [44, 48] and/or antimalarial properties [44].

Moreover, derivatives made from any of the phenothiazines that
have in vitro activity against Mycobacterium tuberculosis are also
active [61, 67, 102, 103], suggesting ample opportunities for
patenting of new analogs developed from known, active phenothiazines
with even less side effects than those of TZ, as recently suggested by
Musuka and co-authors [104]. It is important to mention, that the
commercially available phenothiazines such as for example

  •  trifluoperazine, methdilazine, promazine, promethazine,
    fluphenazin and propiomazine

are beyond patent protection as initially intended. Nevertheless,
these compounds have been patented as adjuvants for the treatment
of MDR cancer (patent expired in 2011 [105]; and, right afterwards,
a new patent has been filed with a priority date of 28th March, 2012,
claiming combination therapy of cancer with a chemotherapeutic
agent and a dopamine receptor antagonist against Cancer stem cells (CSC).

Taking into account that intrinsic MDR is considered as one of the key
properties of CSCs [107], the subject to be covered is indeed related.
According to the MDR, XDR and TDR Mycobacterium tuberculosis,
subjects of this herein paper, the initial step for actually reaching those
in need has been made: a patent has been published in December, 2007,
for the use of TZ and its derivatives for reversing anti-microbial drug
resistance [108]. We must note, however, that, despite the six years
passed since, we were unable to find any related clinical trials, which
would certainly be of outmost importance and urgency in order to
proceed towards an effective therapy of highly resistant mycobacterial
infections.

Mechanism Of Action Of Tz: Why It Cures Multi-Drug,
Extensively Drug Resistant And Probably Totally Drug
Resistant Tuberculosis

Over-expressed efflux pumps of Mycobacterium tuberculosis render
the organism multi-drug resistant [13]. Special attention has been
given to those coded by the

  • mmpL7, p55, efpA, mmr, Rv1258c and Rv2459 genes [109].

The activity of these efflux pumps can be suppressed by

  • concentrations of TZ that have no effect on the viability of
    Mycobacterium tuberculosis
  • rendering the organism susceptible to the antibiotic to
    which it was initially resistant
  • as a consequence of the over-expression of its
    efflux pumps [109].

TZ has also been shown to inhibit the activity of the main

  • efflux pumps of bacteria belonging to other species.

TZ has strong inhibitory activity against the genes that code for
essential proteins of M. tuberculosis [122-124].  Consequently, we
may conclude that the in vitro activity of TZ involves

  • the inhibition of the efflux pumps of M. tuberculosis and that
  • the in vitro exposure of this organism to TZ renders the organism
  • susceptible to antibiotics to which it was initially resistant
  • as a consequence of over-expressed efflux pumps [21].

Phenothiazines such as CPZ, TZ, trifluoperazine, etc., also inhibit

  • the binding of calcium to calcium binding proteins such as

calmodulin in eukaryotes [125], and

  • interfere with other proteins involved in
  • the regulation of cellular activity [126].

They inhibit the transport of calcium and potassium systems

  • in eukaryotic cells [127-129] as well as in
  • mycobacteria [89, 130] and
  • E. coli [113].

In fact, in the latter case, calcium was shown essential to

  • the continuous activity of the thioridiazine sensitive
    efflux system [113].

The killing activity of the human macrophage as well as that
of the neutrophil

  • is dependent upon the retention of calcium and potassium
  • within the phagolysosome of the cell [131].

Considering this, several alternative choices are available for
patenting under “new use”, which would allow a “fresh start”
for the compound to be developed. However, the needed
experimental proof that these phenothiazine agents have
activity at the pulmonary macrophage of the alveolar unit
(the site where the causative organism of pulmonary tuberculosis
resides) is still absent.

Targeting the Human Macrophage with Combinations
of Drugs and Inhibitors of Ca2+ and K+ Transport to
Enhance the Killing of Intracellular Multi-Drug Resistant
M. tuberculosis (MDR-TB) – a Novel, Patentable Approach
to Limit the Emergence of XDR-TB

Marta Martins
UCD Centre for Food Safety, School of Agriculture, Food Science and
Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
& Unit of Mycobacteriology and UPMM; Instituto de Higiene e Medicina
Tropical, Universidade Nova de Lisboa (IHMT/UNL),  Lisbon, Portugal
Recent Patents on Anti-Infective Drug Discovery, 2011, 6, 000-000

The emergence of resistance in Tuberculosis has become a serious
problem for the control of this disease. For that reason, new therapeutic
strategies that can be implemented in the clinical setting are urgently
needed. The design of new compounds active against mycobacteria
must take into account that Tuberculosis is mainly an intracellular
infection of the alveolar macrophage and therefore must maintain
activity within the host cells.

An alternative therapeutic approach will be described in this review,
focusing on the activation of the phagocytic cell and the subsequent
killing of the internalized bacteria. This approach explores the combined
use of antibiotics and phenothiazines, or Ca2+ and K+ flux inhibitors,
in the infected macrophage.

Targeting the infected macrophage and not the internalized bacteria
could overcome the problem of bacterial multi-drug resistance. This
will potentially eliminate the appearance of new multi-drug resistant
tuberculosis (MDR-TB) cases and subsequently prevent the emergence
of extensively-drug resistant tuberculosis (XDR-TB).

Patents resulting from this novel and innovative approach could be
extremely valuable if they can be implemented in the clinical setting.
Other patents will also be discussed such as the treatment of TB
using immunomodulator compounds (for example: betaglycans).

Role of Phenothiazines and Structurally Similar
Compounds of Plant Origin in the Fight against
Infections by Drug Resistant Bacteria


SG. Dastidar 1, JE. Kristiansen 2, J Molnar 3 and L Amaral
Antibiotics 2013; 2: 58-71;
http://dx.doi.org:/10.3390/antibiotics2010058

Phenothiazines have their primary effects on the plasma membranes
of prokaryotes and eukaryotes. Among the components of the
prokaryotic plasma membrane affected are

  • efflux pumps,
  • their energy sources
  • and energy providing enzymes, such as ATPase,
  • and genes that regulate and code for the permeability
    aspect of a bacterium.

The response of multidrug and extensively drug resistant
tuberculosis to phenothiazines shows an alternative therapy for the
treatment of these dreaded diseases, which are claiming more and
more lives every year throughout the world.

Many phenothiazines have shown

  • synergistic activity with several antibiotics thereby
  • lowering the doses of antibiotics administered to patients
    suffering from specific bacterial infections.

Trimeprazine is synergistic with trimethoprim. Flupenthixol (Fp)
has been found to be synergistic with penicillin and chlorpromazine
(CPZ); in addition, some antibiotics are also synergistic. Along with
the antibacterial action described in this review,

  • many phenothiazines possess plasmid curing activities, which
  • render the bacterial carrier of the plasmid sensitive to antibiotics.

Thus, simultaneous applications of a phenothiazine like TZ would not
only act as an additional antibacterial agent but also would help

  • to eliminate drug resistant plasmid from
    the infectious bacterial cells.

Part 8.  Cancer Cytotherapy

Synthesis and Structure-Activity Relationships of Novel
Dioxolanes as MDR Modulators in Cancer

A Martins 1,2,†,*, J Csábi 3,†, A Balázs 4, DKitka 1, L Amaral 5,
J Molnár 1, A Simon 6, G Tóth 6 and A Hunyadi 3,
Molecules 2013, 18, 15255-15275;
http://dx.doi.org:/10.3390/molecules181215255

Ecdysteroids, molting hormones of insects, can exert several mild,
non-hormonal bioactivities in mammals, including humans. In a
previous study, we have found a significant effect of certain derivatives

  • on the ABCB1 transporter mediated multi-drug resistance of a
  • transfected murine leukemia cell line.

In this paper, we present a structure-activity relationship study
focused on

  • the apolar dioxolane derivatives of 20-hydroxyecdysone.

Semi-synthesis and bioactivity of a total of 32 ecdysteroids, including
20 new compounds, is presented, supplemented with their

  • complete 1H- and 13C-NMR signal assignment

As published before [9], the 20,22-diol moiety of 20E is more reactive
than the 2,3-diol, probably due to the free rotation of the 20,22-bond
of 20E that allows the 20,22-dioxolane ring to form with less strain.

This allowed us to selectively obtain the 20,22-mono-dioxolane
derivatives 2–14, or, depending on the amount of reagent and the
reaction time, the 2,3;20,22-bis-homo-dioxolanes 17 and 21–25.

By utilizing the 20,22-monodioxolane ecdysteroids, another aldehyde
or ketone could be coupled to position 2,3, resulting in several bis-hetero-
dioxolane derivatives 26–33. For this, however, gradually decreasing
reactivity with the increase of the size of the reagent was a limiting factor:

  • larger aldehydes or ketones (mainly those containing a
    substituted aromatic ring) could not be coupled at the 2,3-position.
  • The 2,3-monodioxolane derivatives also appeared to be present as
    minor side-products of the reactions, and as a consequence of their
    low amount, only one such compound (compound 15) was isolated and studied.

To selectively obtain this kind of a compound (16) in a more reasonable
yield, another, three-step approach was successfully applied:

  • after protecting the 20,22-diol with phenylboronic acid, the
    2,3-acetonide could be prepared, and
  • removal of the 20,22 protecting group afforded the desired
    2,3-monoacetonide in a one-pot procedure.

In the case of the reactions with aldehydes or asymmetric ketones,
the new C-28 and C-29 central atoms of the dioxolane rings are
stereogenic centers and thus two possible diastereomers can be
formed at both diols. Their configuration was elucidated by two-
dimensional ROESY or selective one-dimensional ROESY experiments,
e.g., in the doubly substituted

  • dioxolane derivative 22 (R1 = R4 = n-Bu, R2 = R3 = H)
  • the unambiguous differentiation of the 1H and 13C signals of
    the two n-butyl groups was achieved in the following way
    (see Figure 2).

Assignment of the H-C(28) atoms (δ = 4.93/105.9 ppm) was supported by

  • the H-2/C-28 and H-3/C-28 HMBC correlations, and
  • that of H-C(29) (δ = 4.91/105.6 ppm) by the H-22/C-29
    cross peak, respectively.

The selective ROESY experiment irradiating at 4.93 ppm showed

  • contacts with the Hα-2 and Hα-3 atoms proving the
    α position of the R2 = H atom.

The ROESY response obtained irradiating H = R3 signal (δ = 4.91)
on H-22 (δ = 3.64 ppm) revealed their

  • cis arrangement and the R configuration around C-29.

The unambiguous assignments of the signals

  • of the two n-butyl groups R1 and R4 were achieved by
  • selective TOCSY experiments (irradiation at
  • δ = 4.93 and 4.91, respectively).

Figure 2

Stereostructure of 22. Red-ROESY proximitries. Blue- 1H. Black-1 001

Stereostructure of 22. Red-ROESY proximitries. Blue- 1H. Black-1 001

Stereostructure of 22. Red arrows indicate the detected ROESY
steric proximities, the blue numbers give the characteristic 1H,
and the black numbers the 13C chemical shifts.

 

Related Material

Identification of Efflux Pump-mediated Multidrug-resistant
Bacteria by the Ethidium Bromide-agar Cartwheel Method

M Martins, M Viveiros, I Couto, SS. Costa, T Pacheco, S Fanning,
Jean-Marie Pagès, and L Amaral
in vivo 2011; 25: 171-178  

Index for efflux activity of the MDR strains. The capacity to efflux EtBr
of each bacterial strain was ranked relative to the reference strain
according to the following formula:

 

Index for efflux activity of the MDR strains

Index for efflux activity of the MDR strains

A Simple Method for Assessment of MDR Bacteria for
Over-Expressed Efflux Pumps

M Martinsa,b*, MP. McCuskera,b, M Viveirosa,c, I Coutoc,d,
S Fanninga,b, Jean-Marie Pagès b,e, L Amaral,b,
The Open Microbiol J 2013; 7: 1-5  1874-2858/13 Bentham

Flowchart followed to test bacterial strains using the EtBr-agar
Cartwheel method.

Flowchart followed to test bacterial strains using the EtBr-agar Cartwheel method.

Flowchart followed to test bacterial strains using the EtBr-agar Cartwheel method.

EtBr-agar cartwheel method applied to different bacterial species

EtBr-agar cartwheel method applied to different bacterial species

EtBr-agar cartwheel method applied to different bacterial species

The effect of selected EPIs on the resistance of the induced and
MDR Gram-positive bacteria.

TET
Enterococcus EFC
ATCC29212
HSEFM-D
1.5
>2.5
w/o
EPI
+
TZ
+
CPZ
+
RES
4
16
4
4
4
4
4
8
(4×) (4×) (2×)
                                MCEtBr NOR  (mg/l) MIC NOR (mg/l)
HSEFM-E >2.5 0.125 0.125 0.125 0.125

EPI: Efflux pump inhibitor; w/o: without; TZ: thioridazine; CPZ:
chlorpromazine; PAN: phenyl arginine β-naphthylamide. Values
in bold-type correspond to a decrease of 4-fold or higher on
the MIC values in comparison to those in the absence of inhibitor.
Values in parenthesis indicate the MIC decrease relative to that
of the original culture. The concentration of each EPI used is
defined in the Materials and Methods section.

Macrocyclic diterpenes resensitizing multidrug
resistant phenotypes 

MA. Reis a, A Paterna a, RJ. Ferreira a, H Lage b,
Maria-José U. Ferreira a,⇑
a Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade
de Farmácia, Universidade de Lisboa, Lisboa, Portugal
b Charité Campus Mitte, Institute of Pathology, Berlin, Germany
Bioorganic & Medicinal Chemistry xxx (2014) xxx–xxx

Herein, collateral sensitivity effect was exploited as a strategy to
select effective compounds to overcome multidrug resistance in
cancer. Thus, eleven macrocyclic diterpenes, namely jolkinol D (1),
isolated from Euphorbia piscatoria, and its derivatives (2–11) were
evaluated for their activity on three different Human cancer entities:

  • gastric (EPG85-257), pancreatic (EPP85-181) and colon (HT-29)

each with a variant selected for resistance to mitoxantrone

  1. EPG85-257RN;
  2. EPP85-181RN;
  3. HT-29RN and
  • one to daunorubicin (EPG85-257RD; EPP85-181RD; HT-29RD).

Jolkinol D (1) and most of its derivatives (2–11) exhibited significant
collateral sensitivity effect towards the cell lines

  • EPG85-257RN (associated with P-glycoprotein overexpression) and
  • HT-29RD (altered topoisomerase II expression).

The benzoyl derivative, jolkinoate L (8) demonstrated ability to

  • target different cellular contexts with
  • concomitant high antiproliferative activity.

These compounds were previously assessed as
P-glycoprotein modulators,

  • at non-cytotoxic doses, on MDR1-mouse lymphoma cells.

A regression analysis between

  1. the antiproliferative activity presented herein and
  2. the previously assessed P-glycoprotein modulatory effect

showed a strong relation between the compounds that presented

  • both high P-glycoprotein modulation and cytotoxicity.

Molecular Docking Characterizes Substrate-Binding Sites
and Efflux Modulation Mechanisms within P
Glycoprotein.

Ferreira,† Maria-José U. Ferreira,† and DJVA dos Santos*,†,‡
†Research Institute for Medicines and Pharmaceutical Sciences
(iMed.UL), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
‡REQUIMTE, Department of Chemistry & Biochemistry, Faculty of
Sciences, University of Porto, Porto, Portugal
J. Chem. Inf. Model. XXXX, XXX, XXX−XXX
http://dx.doi.org:/10.1021/ci400195v

P-Glycoprotein (Pgp) is one of the best characterized ABC
transporters
, often involved

  • in the multidrug-resistance phenotype
  • overexpressed by several cancer cell lines.

Experimental studies contributed to important knowledge concerning
substrate polyspecificity, efflux mechanism, and drug binding sites.
This information is, however, scattered through different perspectives,
not existing a unifying model for the knowledge available for this transporter.
Using a previously refined structure of murine Pgp,

  • three putative drug-binding sites were hereby characterized
  • by means of molecular docking.

The modulator site (M-site) is characterized by

  • cross interactions between both Pgp halves

herein defined for the first time, having an important role in

  • impairing conformational changes leading to substrate efflux.

Two other binding sites, located next to the inner leaflet of the lipid bilayer,

  • were identified as the substrate binding H and R sites
  • by matching docking and experimental results.

A new classification model

  • with the ability to discriminate substrates from modulators

is also proposed, integrating a vast number of theoretical and experimental data.

conformational changes leading to substrate efflux

conformational changes leading to substrate efflux

conformational changes leading to substrate efflux

http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jcisd8/
2013/jcisd8.2013.53.issue-7/ci400195v/production/pdfimages_v02/normal.img-000.jpg

 

 

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LytPhage Presents at 1st Pitch Life Sciences-Philadelphia-September 16, 2014

Reporter: Stephen J. Williams, PhD

 

LytPhage presented at Mid-Atlantic BioAngels 1st Pitch Life Sciences in  Philadelphia Tuesday Sept. 16, 2014.

LytPhage is a new biotech company using novel bioengineering to develop therapeutics to address the worldwide crisis of antibiotic resistant organisms.  They are developing a treatment for vancomycin resistant systemic infections with their platform, which can be adapted for other problematic organisms.  LytPhage is a spin-out form Temple University.

The overall goal is to use genetically modified bacteriophage (bacterial viruses) as an antimicrobial therapy against drug-resistant strains.  Their genetically modifed viruses are only lytic, meaning they result in cell death of the host but do not integrate in the host DNA.  In additon preliminary studies using mainly clinical isolates have shown good efficacy against most drug-resistant strains found in common hospital infections like Clostridium difficile colitis.  The presenters noted that bacteriophage therapy had successfully been used in Europe but no approved therapy in US

For more information about this meeting please see posting on this site

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