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Twitter is Becoming a Powerful Tool in Science and Medicine

 Curator: Stephen J. Williams, Ph.D.

Article ID #159: Twitter is Becoming a Powerful Tool in Science and Medicine. Published on 11/6/2014

WordCloud Image Produced by Adam Tubman

Updated 4/2016

Life-cycle of Science 2

A recent Science article (Who are the science stars of Twitter?; Sept. 19, 2014) reported the top 50 scientists followed on Twitter. However, the article tended to focus on the use of Twitter as a means to develop popularity, a sort of “Science Kardashian” as they coined it. So the writers at Science developed a “Kardashian Index (K-Index) to determine scientists following and popularity on Twitter.

Now as much buzz Kim Kardashian or a Perez Hilton get on social media, their purpose is solely for entertainment and publicity purposes, the Science sort of fell flat in that it focused mainly on the use of Twitter as a metric for either promotional or public outreach purposes. A notable scientist was mentioned in the article, using Twitter feed to gauge the receptiveness of his presentation. In addition, relying on Twitter for effective public discourse of science is problematic as:

  • Twitter feeds are rapidly updated and older feeds quickly get buried within the “Twittersphere” = LIMITED EXPOSURE TIMEFRAME
  • Short feeds may not provide the access to appropriate and understandable scientific information (The Science Communication Trap) which is explained in The Art of Communicating Science: traps, tips and tasks for the modern-day scientist. “The challenge of clearly communicating the intended scientific message to the public is not insurmountable but requires an understanding of what works and what does not work.” – from Heidi Roop, G.-Martinez-Mendez and K. Mills

However, as highlighted below, Twitter, and other social media platforms are being used in creative ways to enhance the research, medical, and bio investment collaborative, beyond a simple news-feed.  And the power of Twitter can be attributed to two simple features

  1. Ability to organize – through use of the hashtag (#) and handle (@), Twitter assists in the very important task of organizing, indexing, and ANNOTATING content and conversations. A very great article on Why the Hashtag in Probably the Most Powerful Tool on Twitter by Vanessa Doctor explains how hashtags and # search may be as popular as standard web-based browser search. Thorough annotation is crucial for any curation process, which are usually in the form of database tags or keywords. The use of # and @ allows curators to quickly find, index and relate disparate databases to link annotated information together. The discipline of scientific curation requires annotation to assist in the digital preservation, organization, indexing, and access of data and scientific & medical literature. For a description of scientific curation methodologies please see the following links:

Please read the following articles on CURATION

The Methodology of Curation for Scientific Research Findings

Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison

Science and Curation: The New Practice of Web 2.0

  1. Information Analytics –

Multiple analytic software packages have been made available to analyze information surrounding Twitter feeds, including Twitter feeds from #chat channels one can set up to cover a meeting, product launch etc.. Some of these tools include:

Twitter Analytics – measures metrics surrounding Tweets including retweets, impressions, engagement, follow rate, …

Twitter Analytics – Hashtags.org – determine most impactful # for your Tweets For example, meeting coverage of bioinvestment conferences or startup presentations using #startup generates automatic retweeting by Startup tweetbot @StartupTweetSF.

 

  1. Tweet Sentiment Analytics

Examples of Twitter Use

A. Scientific Meeting Coverage

In a paper entitled Twitter Use at a Family Medicine Conference: Analyzing #STFM13 authors Ranit Mishori, MD, Frendan Levy, MD, and Benjamin Donvan analyzed the public tweets from the 2013 Society of Teachers of Family Medicine (STFM) conference bearing the meeting-specific hashtag #STFM13. Thirteen percent of conference attendees (181 users) used the #STFM13 to share their thoughts on the meeting (1,818 total tweets) showing a desire for social media interaction at conferences but suggesting growth potential in this area. As we have also seen, the heaviest volume of conference-tweets originated from a small number of Twitter users however most tweets were related to session content.

However, as the authors note, although it is easy to measure common metrics such as number of tweets and retweets, determining quality of engagement from tweets would be important for gauging the value of Twitter-based social-media coverage of medical conferences.

Thea authors compared their results with similar analytics generated by the HealthCare Hashtag Project, a project and database of medically-related hashtag use, coordinated and maintained by the company Symplur.  Symplur’s database includes medical and scientific conference Twitter coverage but also Twitter usuage related to patient care. In this case the database was used to compare meeting tweets and hashtag use with the 2012 STFM conference.

These are some of the published journal articles that have employed Symplur (www.symplur.com) data in their research of Twitter usage in medical conferences.

B. Twitter Usage for Patient Care and Engagement

Although the desire of patients to use and interact with their physicians over social media is increasing, along with increasing health-related social media platforms and applications, there are certain obstacles to patient-health provider social media interaction, including lack of regulatory framework as well as database and security issues. Some of the successes and issues of social media and healthcare are discussed in the post Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.

However there is also a concern if social media truly engages the patient and improves patient education. In a study of Twitter communications by breast cancer patients Tweeting about breast cancer, authors noticed Tweeting was a singular event. The majority of tweets did not promote any specific preventive behavior. The authors concluded “Twitter is being used mostly as a one-way communication tool.” (Using Twitter for breast cancer prevention: an analysis of breast cancer awareness month. Thackeray R1, Burton SH, Giraud-Carrier C, Rollins S, Draper CR. BMC Cancer. 2013;13:508).

In addition a new poll by Harris Interactive and HealthDay shows one third of patients want some mobile interaction with their physicians.

Some papers cited in Symplur’s HealthCare Hashtag Project database on patient use of Twitter include:

C. Twitter Use in Pharmacovigilance to Monitor Adverse Events

Pharmacovigilance is the systematic detection, reporting, collecting, and monitoring of adverse events pre- and post-market of a therapeutic intervention (drug, device, modality e.g.). In a Cutting Edge Information Study, 56% of pharma companies databases are an adverse event channel and more companies are turning to social media to track adverse events (in Pharmacovigilance Teams Turn to Technology for Adverse Event Reporting Needs). In addition there have been many reports (see Digital Drug Safety Surveillance: Monitoring Pharmaceutical Products in Twitter) that show patients are frequently tweeting about their adverse events.

There have been concerns with using Twitter and social media to monitor for adverse events. For example FDA funded a study where a team of researchers from Harvard Medical School and other academic centers examined more than 60,000 tweets, of which 4,401 were manually categorized as resembling adverse events and compared with the FDA pharmacovigilance databases. Problems associated with such social media strategy were inability to obtain extra, needed information from patients and difficulty in separating the relevant Tweets from irrelevant chatter.  The UK has launched a similar program called WEB-RADR to determine if monitoring #drug_reaction could be useful for monitoring adverse events. Many researchers have found the adverse-event related tweets “noisy” due to varied language but had noticed many people do understand some principles of causation including when adverse event subsides after discontinuing the drug.

However Dr. Clark Freifeld, Ph.D., from Boston University and founder of the startup Epidemico, feels his company has the algorithms that can separate out the true adverse events from the junk. According to their web site, their algorithm has high accuracy when compared to the FDA database. Dr. Freifeld admits that Twitter use for pharmacovigilance purposes is probably a starting point for further follow-up, as each patient needs to fill out the four-page forms required for data entry into the FDA database.

D. Use of Twitter in Big Data Analytics

Published on Aug 28, 2012

http://blogs.ischool.berkeley.edu/i29…

Course: Information 290. Analyzing Big Data with Twitter
School of Information
UC Berkeley

Lecture 1: August 23, 2012

Course description:
How to store, process, analyze and make sense of Big Data is of increasing interest and importance to technology companies, a wide range of industries, and academic institutions. In this course, UC Berkeley professors and Twitter engineers will lecture on the most cutting-edge algorithms and software tools for data analytics as applied to Twitter microblog data. Topics will include applied natural language processing algorithms such as sentiment analysis, large scale anomaly detection, real-time search, information diffusion and outbreak detection, trend detection in social streams, recommendation algorithms, and advanced frameworks for distributed computing. Social science perspectives on analyzing social media will also be covered.

This is a hands-on project course in which students are expected to form teams to complete intensive programming and analytics projects using the real-world example of Twitter data and code bases. Engineers from Twitter will help advise student projects, and students will have the option of presenting their final project presentations to an audience of engineers at the headquarters of Twitter in San Francisco (in addition to on campus). Project topics include building on existing infrastructure tools, building Twitter apps, and analyzing Twitter data. Access to data will be provided.

Other posts on this site on USE OF SOCIAL MEDIA AND TWITTER IN HEALTHCARE and Conference Coverage include:

Methodology for Conference Coverage using Social Media: 2014 MassBio Annual Meeting 4/3 – 4/4 2014, Royal Sonesta Hotel, Cambridge, MA

Strategy for Event Joint Promotion: 14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

REAL TIME Cancer Conference Coverage: A Novel Methodology for Authentic Reporting on Presentations and Discussions launched via Twitter.com @ The 2nd ANNUAL Sachs Cancer Bio Partnering & Investment Forum in Drug Development, 19th March 2014 • New York Academy of Sciences • USA

PCCI’s 7th Annual Roundtable “Crowdfunding for Life Sciences: A Bridge Over Troubled Waters?” May 12 2014 Embassy Suites Hotel, Chesterbrook PA 6:00-9:30 PM

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

Tweeting on 14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

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

Statistical Analysis of Tweet Feeds from the 14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

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

What VCs Think about Your Pitch? Panel Summary of 1st Pitch Life Science Philly

How Social Media, Mobile Are Playing a Bigger Part in Healthcare

Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.

Medical Applications and FDA regulation of Sensor-enabled Mobile Devices: Apple and the Digital Health Devices Market

E-Medical Records Get A Mobile, Open-Sourced Overhaul By White House Health Design Challenge Winners

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Heroes in Medical Research: The Postdoctoral Fellow

Writer: Stephen J. Williams, Ph.D

Thank your Postdoc

The National Postdoctoral Association (NPA) had its Fifth Annual Celebration Of National Postdoc Appreciation Week (NPAW) in September and I wanted to focus a posting on curating stories from postdoctoral fellows as well as private investigators (PIs) and mentors on the impacts that postdoctoral fellows had in research and to recognize the critical and tremendous contributions which postdocs make to science.

During our postdoctoral years, we develop deep friendships which last a lifetime, a close bonding to our kindred scientists different in nature than our bonding with our mentors.  Nothing can replace a great mentor but our fellow postdocs make a huge difference in our complete scientific training.

                                   It’s always the little things that stand out in our fondest memories

Unfortunately I have a plethora of fond, little memories; too many for this posting but just want to ad in a few things:

  • Thank you!    –  To all those postdocs who worked tirelessly to make a memorable PostDoc Day!
  • Thank you!  –  To all my postdoc colleagues who stayed late n the lab with me giving each other moral and scientific support
  • Thank you!  – All my postdoc friends who would give up their time to show me how to make and use a text box correctly in Word
  • Thank you!  =-  for your friendship and understanding in those rough times we had experienced

To enliven the discussion, I ask that postdocs, past, present, and future, as well as PI’s and postdoc mentors comment on their postdoc experience. I also would like PI’s to share the stories how their postdocs made an impact to their labs.

A few interesting links and articles from the web on the importance and struggles of postdocs are included below:

Keith Micoli, from New York University Langone Medical Center states in an Elsevier article on The Academic Executive Brief

“

Consequently, it’s very difficult to come up with accurate numbers. Current estimates on number of postdocs come between 40,000 and 90,000 — a range that is unacceptable. A solid bet is that there are 60,000 postdocs and that more than half, if not two thirds or higher, are international.

– from US research enterprise powered by international postdocs by Keith Micoli at NYU

“

Survey Methodology

Since Science started conducting annual surveys seven years ago, alternating between polling postdocs and postdoc advisors, the attributes that survey respondents select as being most important to a successful postdoc have not varied much.This year’s survey was launched on March 15, 2011, with e-mail invitations sent out to about 40,000 current and former postdoc advisors worldwide. Of the 798 completed surveys that were collected, 71 percent came from Europe (39 percent) and North America (32 percent). The remaining respondents were located in Asia/Australia/Pacific Rim (20 percent) or other areas of the world (9 percent). Most were males (72 percent) 40 years of age and older (76 percent) and worked in academic institutions (70 percent) and government organizations (13 percent). The primary area represented was the life sciences (57 percent).

However only a handful of institutions were featured.

An open letter to AAAS journal “Science”: Postdocs need to address the “The Future of Research”

https://thewinnower.com/papers/an-open-letter-to-aaas-journal-science-postdocs-need-to-address-the-the-future-of-research?jm.npa=

This letter, posted on the Winnower.com, was a response to Callier’s article “Ailing academia needs culture change”1 and discussed how postdoctoral fellows have to lead in effecting change if the US research enterprise is to flourish in the future. In addition, the authors have been organizing Boston area postdoctoral associations and are sponsoring a symposium to be held at Boston University October 2-3 2014, focusing on the challenges facing graduate students and postdoctoral fellows: the “Future of Research” symposium (futureofresearch.org, @FORsymp).

  1. V. Callier, N. L. Vanderford. “Ailing academia needs culture change.” Science, 2014: 345; 6199: 885. DOI: 10.1126/science.345.6199.885-b

On the surface, many acknowledge the importance of postdoctoral fellows to the US research effort,

HOWEVER, the QUESTION remains DO POSTDOCS FEEL APPRECIATED FOR THEIR EFFORTS?

Please read Jacquelyn Gil, Ph.D.’s GREAT blog post

Have you hugged your postdoc today?

in The Contemplative Mammoth about her surviving postdoctoral life.

For some postdoc humor go to

http://phdcomics.com/comics.php where Jorge Cham, Ph.D. has been satiring the Ph.D. life since he was a graduate student in the late 90’s.

and see if you could be a star in their movie about Ph.D.’s: The PhD Movie and the sequel.

Don’t Underestimate Your Postdoc

Dr. Thomas C. Sudhof, MD is an example of a postdoctoral fellow making great contributions to a lab. A summary of his work is seen below and obtained from the site thebestschools.org on the “50 Most Influential Scientists”.

http://www.thebestschools.org/features/50-influential-scientists-world-today/#S%C3%BCdhof

Thomas C. Südhof

Thomas C. Südhof is a biochemist and professor in the School of Medicine in the Department of Molecular and Cellular Physiology at Stanford University. He is best known for his work in the area of synaptic transmission, which is the process by which signaling chemicals known as neurotransmitters are released by one neuron and bind to and activate the receptors of another neuron.

Südhof won the 1985 Nobel Prize in Physiology or Medicine, along with Randy Schekman and James Rothman.

Südhof, a native of Germany, obtained his MD from the University of Göttingen and conducted his postdoctoral training in the department of molecular genetics at the University of Texas’s Health Science Center. During his postdoctoral training, he worked on describing the role of the LDL receptor in cholesterol metabolism, for which Michael S. Brown and Joseph L. Goldstein were awarded the Nobel Prize in Physiology or Medicine in 1985.

 

Another example from the site includes Dr. Craig Mello (Craig C. Mello’s Home Page.) who, along with Dr., Andrew Fire discovered RNAi when both at Carnegie Institute. Both received a Nobel for their work.

So again would love to hear and curate personal stories highlighting how postdocs make a great contribution to US science.

More articles in this “Heroes in Medical Research” series and posts on Scientific Careers from this site include:

Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science

Heroes in Medical Research: Developing Models for Cancer Research

Heroes in Medical Research: Dr. Carmine Paul Bianchi Pharmacologist, Leader, and Mentor

Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

Science Budget FY’14: Stakeholders’ Reactions on Selective Budget Drops and Priorities Shift

Careers for Researchers Beyond Academia

BEYOND THE “MALE MODEL”: AN ALTERNATIVE FEMALE MODEL OF SCIENCE, TECHNOLOGY AND INNOVATION

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Imaging-guided cancer treatment

Imaging-guided cancer treatment

Writer & reporter: Dror Nir, PhD

It is estimated that the medical imaging market will exceed $30 billion in 2014 (FierceMedicalImaging). To put this amount in perspective; the global pharmaceutical market size for the same year is expected to be ~$1 trillion (IMS) while the global health care spending as a percentage of Gross Domestic Product (GDP) will average 10.5% globally in 2014 (Deloitte); it will reach ~$3 trillion in the USA.

Recent technology-advances, mainly miniaturization and improvement in electronic-processing components is driving increased introduction of innovative medical-imaging devices into critical nodes of major-diseases’ management pathways. Consequently, in contrast to it’s very small contribution to global health costs, medical imaging bears outstanding potential to reduce the future growth in spending on major segments in this market mainly: Drugs development and regulation (e.g. companion diagnostics and imaging surrogate markers); Disease management (e.g. non-invasive diagnosis, guided treatment and non-invasive follow-ups); and Monitoring aging-population (e.g. Imaging-based domestic sensors).

In; The Role of Medical Imaging in Personalized Medicine I discussed in length the role medical imaging assumes in drugs development.  Integrating imaging into drug development processes, specifically at the early stages of drug discovery, as well as for monitoring drug delivery and the response of targeted processes to the therapy is a growing trend. A nice (and short) review highlighting the processes, opportunities, and challenges of medical imaging in new drug development is: Medical imaging in new drug clinical development.

The following is dedicated to the role of imaging in guiding treatment.

Precise treatment is a major pillar of modern medicine. An important aspect to enable accurate administration of treatment is complementing the accurate identification of the organ location that needs to be treated with a system and methods that ensure application of treatment only, or mainly to, that location. Imaging is off-course, a major component in such composite systems. Amongst the available solution, functional-imaging modalities are gaining traction. Specifically, molecular imaging (e.g. PET, MRS) allows the visual representation, characterization, and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In oncology, it can be used to depict the abnormal molecules as well as the aberrant interactions of altered molecules on which cancers depend. Being able to detect such fundamental finger-prints of cancer is key to improved matching between drugs-based treatment and disease. Moreover, imaging-based quantified monitoring of changes in tumor metabolism and its microenvironment could provide real-time non-invasive tool to predict the evolution and progression of primary tumors, as well as the development of tumor metastases.

A recent review-paper: Image-guided interventional therapy for cancer with radiotherapeutic nanoparticles nicely illustrates the role of imaging in treatment guidance through a comprehensive discussion of; Image-guided radiotherapeutic using intravenous nanoparticles for the delivery of localized radiation to solid cancer tumors.

 Graphical abstract

 Abstract

One of the major limitations of current cancer therapy is the inability to deliver tumoricidal agents throughout the entire tumor mass using traditional intravenous administration. Nanoparticles carrying beta-emitting therapeutic radionuclides [DN: radioactive isotops that emits electrons as part of the decay process a list of β-emitting radionuclides used in radiotherapeutic nanoparticle preparation is given in table1 of this paper.) that are delivered using advanced image-guidance have significant potential to improve solid tumor therapy. The use of image-guidance in combination with nanoparticle carriers can improve the delivery of localized radiation to tumors. Nanoparticles labeled with certain beta-emitting radionuclides are intrinsically theranostic agents that can provide information regarding distribution and regional dosimetry within the tumor and the body. Image-guided thermal therapy results in increased uptake of intravenous nanoparticles within tumors, improving therapy. In addition, nanoparticles are ideal carriers for direct intratumoral infusion of beta-emitting radionuclides by convection enhanced delivery, permitting the delivery of localized therapeutic radiation without the requirement of the radionuclide exiting from the nanoparticle. With this approach, very high doses of radiation can be delivered to solid tumors while sparing normal organs. Recent technological developments in image-guidance, convection enhanced delivery and newly developed nanoparticles carrying beta-emitting radionuclides will be reviewed. Examples will be shown describing how this new approach has promise for the treatment of brain, head and neck, and other types of solid tumors.

The challenges this review discusses

  • intravenously administered drugs are inhibited in their intratumoral penetration by high interstitial pressures which prevent diffusion of drugs from the blood circulation into the tumor tissue [1–5].
  • relatively rapid clearance of intravenously administered drugs from the blood circulation by kidneys and liver.
  • drugs that do reach the solid tumor by diffusion are inhomogeneously distributed at the micro-scale – This cannot be overcome by simply administering larger systemic doses as toxicity to normal organs is generally the dose limiting factor.
  • even nanoparticulate drugs have poor penetration from the vascular compartment into the tumor and the nanoparticles that do penetrate are most often heterogeneously distributed

How imaging could mitigate the above mentioned challenges

  • The inclusion of an imaging probe during drug development can aid in determining the clearance kinetics and tissue distribution of the drug non-invasively. Such probe can also be used to determine the likelihood of the drug reaching the tumor and to what extent.

Note: Drugs that have increased accumulation within the targeted site are likely to be more effective as compared with others. In that respect, Nanoparticle-based drugs have an additional advantage over free drugs with their potential to be multifunctional carriers capable of carrying both therapeutic and diagnostic imaging probes (theranostic) in the same nanocarrier. These multifunctional nanoparticles can serve as theranostic agents and facilitate personalized treatment planning.

  • Imaging can also be used for localization of the tumor to improve the placement of a catheter or external device within tumors to cause cell death through thermal ablation or oxidative stress secondary to reactive oxygen species.

See the example of Vintfolide in The Role of Medical Imaging in Personalized Medicine

vinta

Note: Image guided thermal ablation methods include radiofrequency (RF) ablation, microwave ablation or high intensity focused ultrasound (HIFU). Photodynamic therapy methods using external light devices to activate photosensitizing agents can also be used to treat superficial tumors or deeper tumors when used with endoscopic catheters.

  • Quality control during and post treatment

For example: The use of high intensity focused ultrasound (HIFU) combined with nanoparticle therapeutics: HIFU is applied to improve drug delivery and to trigger drug release from nanoparticles. Gas-bubbles are playing the role of the drug’s nano-carrier. These are used both to increase the drug transport into the cell and as ultrasound-imaging contrast material. The ultrasound is also used for processes of drug-release and ablation.

 HIFU

Additional example; Multifunctional nanoparticles for tracking CED (convection enhanced delivery)  distribution within tumors: Nanoparticle that could serve as a carrier not only for the therapeutic radionuclides but simultaneously also for a therapeutic drug and 4 different types of imaging contrast agents including an MRI contrast agent, PET and SPECT nuclear diagnostic imaging agents and optical contrast agents as shown below. The ability to perform multiple types of imaging on the same nanoparticles will allow studies investigating the distribution and retention of nanoparticles initially in vivo using non-invasive imaging and later at the histological level using optical imaging.

 multi

Conclusions

Image-guided radiotherapeutic nanoparticles have significant potential for solid tumor cancer therapy. The current success of this therapy in animals is most likely due to the improved accumulation, retention and dispersion of nanoparticles within solid tumor following image-guided therapies as well as the micro-field of the β-particle which reduces the requirement of perfectly homogeneous tumor coverage. It is also possible that the intratumoral distribution of nanoparticles may benefit from their uptake by intratumoral macrophages although more research is required to determine the importance of this aspect of intratumoral radionuclide nanoparticle therapy. This new approach to cancer therapy is a fertile ground for many new technological developments as well as for new understandings in the basic biology of cancer therapy. The clinical success of this approach will depend on progress in many areas of interdisciplinary research including imaging technology, nanoparticle technology, computer and robot assisted image-guided application of therapies, radiation physics and oncology. Close collaboration of a wide variety of scientists and physicians including chemists, nanotechnologists, drug delivery experts, radiation physicists, robotics and software experts, toxicologists, surgeons, imaging physicians, and oncologists will best facilitate the implementation of this novel approach to the treatment of cancer in the clinical environment. Image-guided nanoparticle therapies including those with β-emission radionuclide nanoparticles have excellent promise to significantly impact clinical cancer therapy and advance the field of drug delivery.

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NIH Considers Guidelines for CAR-T therapy: Report from Recombinant DNA Advisory Committee

Reporter: Stephen J. Williams, Ph.D.

UPDATED 5/27/2024

The practice of pharmacovigilence, both premarketing and postmarketing, has very well defined best practices concerning most small molecule drugs and even medical devices.  However, for many cell based therapies and many gene based therapies, often still administered within the university, academic setting, pharmacovigilence reporting and adherence may be a not as efficient and thorough as conducted by large big pharmaceutical firms.  Big pharma will devote massive resources for the conduct of pharmacovigilence data collecting and analysis.  For many cell based therapies, like CAR-T therapies and some gene therapies are almost conducted as clinical trials within university medical centers, which may not have the resources for a large pharmacovigilence program.

In a report by IQVIA, oncologists were asked about their concerns with cell based therapies.  A recurring concern involved the lack of information on the adverse events related to these therapies, especially after an oncologist’s patient would return from administration of their CAR-T therapy and then both patient and oncologist felt ‘on their own’.

Most recently the FDA has issued black box warning on many CAR-T therapies for their risk in inducing secondary malignancies (see What does this mean for Immunotherapy? FDA put a temporary hold on Juno’s JCAR015, Three Death of Cerebral Edema in CAR-T Clinical Trial and Kite Pharma announced Phase II portion of its CAR-T ZUMA-1 trial).

Source: https://www.fiercepharma.com/ai-and-machine-learning/oncologists-have-shopping-car-t-full-complaints-safety-questions-cell?utm_medium=email&utm_source=nl&utm_campaign=LS-NL-FiercePharma+Tracker&oly_enc_id=2360C5096034F3G

Note: the IQVIA will be submitted as an abstract at the current ASCO meeting

UPDATED 5/10/2022

In the mid to late 1970’s a public debate (and related hysteria) had emerged surrounding two emerging advances in recombinant DNA technology;

  1. the development of vectors useful for cloning pieces of DNA (the first vector named pBR322) and
  2. the discovery of bacterial strains useful in propagating such vectors

As discussed by D. S, Fredrickson of NIH’s Dept. of Education and Welfare in his historical review” A HISTORY OF THE RECOMBINANT DNA GUIDELINES IN THE UNITED STATES” this international concern of the biological safety issues of this new molecular biology tool led the National Institute of Health to coordinate a committee (the NIH Recombinant DNA Advisory Committee) to develop guidelines for the ethical use, safe development, and safe handling of such vectors and host bacterium. The first conversations started in 1974 and, by 1978, initial guidelines had been developed. In fact, as Dr. Fredrickson notes, public relief was voiced even by religious organizations (who had the greatest ethical concerns)

On December 16, 1978, a telegram purporting to be from the Vatican was hand delivered to the office of Joseph A. Califano, Jr., Secretary of Health, Education,

and Welfare. “Habemus regimen recombinatum,” it proclaimed, in celebration of the

end of a long struggle to revise the NIH Guidelines for Research Involving

Recombinant DNA Molecules

The overall Committee resulted in guidelines (2013 version) which assured the worldwide community that

  • organisms used in such procedures would have limited pathogenicity in humans
  • vectors would be developed in a manner which would eliminate their ability to replicate in humans and have defined antibiotic sensitivity

So great was the success and acceptance of this committee and guidelines, the NIH felt the Recombinant DNA Advisory Committee should meet regularly to discuss and develop ethical guidelines and clinical regulations concerning DNA-based therapeutics and technologies.

A PowerPoint Slideshow: Introduction to NIH OBA and the History of Recombinant DNA Oversight can be viewed at the following link:

http://www.powershow.com/view1/e1703-ZDc1Z/Introduction_to_NIH_OBA_and_the_History_of_Recombinant_DNA_Oversight_powerpoint_ppt_presentation

Please see the following link for a video discussion between Dr. Paul Berg, who pioneered DNA recombinant technology, and Dr. James Watson (Commemorating 50 Years of DNA Science):

http://media.hhmi.org/interviews/berg_watson.html

The Recombinant DNA Advisory Committee has met numerous times to discuss new DNA-based technologies and their biosafety and clinical implication including:

A recent Symposium was held in the summer of 2010 to discuss ethical and safety concerns and discuss potential clinical guidelines for use of an emerging immunotherapy technology, the Chimeric Antigen Receptor T-Cells (CART), which at that time had just been started to be used in clinical trials.

Considerations for the Clinical Application of Chimeric Antigen Receptor T Cells: Observations from a Recombinant DNA Advisory Committee Symposium Held June 15, 2010[1]

Contributors to the Symposium discussing opinions regarding CAR-T protocol design included some of the prominent members in the field including:

Drs. Hildegund C.J. Ertl, John Zaia, Steven A. Rosenberg, Carl H. June, Gianpietro Dotti, Jeffrey Kahn, Laurence J. N. Cooper, Jacqueline Corrigan-Curay, And Scott E. Strome.

The discussions from the Symposium, reported in Cancer Research[1]. were presented in three parts:

  1. Summary of the Evolution of the CAR therapy
  2. Points for Future Consideration including adverse event reporting
  3. Considerations for Design and Implementation of Trials including mitigating toxicities and risks

1. Evolution of Chimeric Antigen Receptors

Early evidence had suggested that adoptive transfer of tumor-infiltrating lymphocytes, after depletion of circulating lymphocytes, could result in a clinical response in some tumor patients however developments showed autologous T-cells (obtained from same patient) could be engineered to express tumor-associated antigens (TAA) and replace the TILS in the clinical setting.

However there were some problems noticed.

  • Problem: HLA restriction of T-cells. Solution: genetically engineer T-cells to redirect T-cell specificity to surface TAAs
  • Problem: 1st generation vectors designed to engineer T-cells to recognize surface epitopes but engineered cells had limited survival in patients.   Solution: development of 2nd generation vectors with co-stimulatory molecules such as CD28, CD19 to improve survival and proliferation in patients

A summary table of limitations of the two types of genetically-modified T-cell therapies were given and given (in modified form) below

                                                                                                Type of Gene-modified T-Cell

Limitations aβ TCR CAR
Affected by loss or decrease of HLA on tumor cells yes no
Affected by altered tumor cell antigen processing? yes no
Need to have defined tumor target antigen? no yes
Vector recombination with endogenous TCR yes no

A brief history of construction of 2nd and 3rd generation CAR-T cells given by cancer.gov:

http://www.cancer.gov/cancertopics/research-updates/2013/CAR-T-Cells

cartdiagrampic

Differences between  second- and third-generation chimeric antigen receptor T cells. (Adapted by permission from the American Association for Cancer Research: Lee, DW et al. The Future Is Now: Chimeric Antigen Receptors as New Targeted Therapies for Childhood Cancer. Clin Cancer Res; 2012;18(10); 2780–90. doi:10.1158/1078-0432.CCR-11-1920)

Constructing a CAR T Cell (from cancer.gov)

The first efforts to engineer T cells to be used as a cancer treatment began in the early 1990s. Since then, researchers have learned how to produce T cells that express chimeric antigen receptors (CARs) that recognize specific targets on cancer cells.

The T cells are genetically modified to produce these receptors. To do this, researchers use viral vectors that are stripped of their ability to cause illness but that retain the capacity to integrate into cells’ DNA to deliver the genetic material needed to produce the T-cell receptors.

The second- and third-generation CARs typically consist of a piece of monoclonal antibody, called a single-chain variable fragment (scFv), that resides on the outside of the T-cell membrane and is linked to stimulatory molecules (Co-stim 1 and Co-stim 2) inside the T cell. The scFv portion guides the cell to its target antigen. Once the T cell binds to its target antigen, the stimulatory molecules provide the necessary signals for the T cell to become fully active. In this fully active state, the T cells can more effectively proliferate and attack cancer cells.

2. Adverse Event Reporting and Protocol Considerations

The symposium had been organized mainly in response to two reported deaths of patients enrolled in a CART trial, so that clinical investigators could discuss and formulate best practices for the proper conduct and analysis of such trials. One issue raised was lack of pharmacovigilence procedures (adverse event reporting). Although no pharmacovigilence procedures (either intra or inter-institutional) were devised from meeting proceedings, it was stressed that each institution should address this issue as well as better clinical outcome reporting.

Case Report of a Serious Adverse Event Following the Administration of T Cells Transduced With a Chimeric Antigen Receptor Recognizing ERBB2[2] had reported the death of a patient on trial.

In A phase I clinical trial of adoptive transfer of folate receptor-alpha redirected autologous T cells for recurrent ovarian cancer[3] authors: Lana E Kandalaft*, Daniel J Powell and George Coukos from University of Pennsylvania recorded adverse events in pilot studies using a CART modified to recognize the folate receptor, so it appears any adverse event reporting system is at the discretion of the primary investigator.

Other protocol considerations suggested by the symposium attendants included:

  • Plan for translational clinical lab for routine blood analysis
  • Subject screening for pulmonary and cardiac events
  • Determine possibility of insertional mutagenesis
  • Informed consent
  • Analysis of non T and T-cell subsets, e.g. natural killer cells and CD*8 cells

3. Consideration for Design of Trials and Mitigating Toxicities

  • Early Toxic effects– Cytokine Release Syndrome– The effectiveness of CART therapy has been manifested by release of high levels of cytokines resulting in fever and inflammatory sequelae. One such cytokine, interleukin 6, has been attributed to this side effect and investigators have successfully used an IL6 receptor antagonist, tocilizumab (Acterma™), to alleviate symptoms of cytokine release syndrome (see review Adoptive T-cell therapy: adverse events and safety switches by Siok-Keen Tey).

 

Below is a video form Dr. Renier Brentjens, M.D., Ph.D. for Memorial Sloan Kettering concerning the finding he made that the adverse event from cytokine release syndrome may be a function of the tumor cell load, and if they treat the patient with CAR-T right after salvage chemotherapy the adverse events are alleviated..

Please see video below:

http link: https://www.youtube.com/watch?v=4Gg6elUMIVE

  • Early Toxic effects – Over-activation of CAR T-cells; mitigation by dose escalation strategy (as authors in reference [3] proposed). Most trials give billions of genetically modified cells to a patient.
  • Late Toxic Effects – long-term depletion of B-cells . For example CART directing against CD19 or CD20 on B cells may deplete the normal population of CD19 or CD20 B-cells over time; possibly managed by IgG supplementation

Below is a curation of various examples of the need for developing a Pharmacovigilence Framework for Engineered T-Cell Therapies

As shown above the first reported side effects from engineered T-cell or CAR-T therapies stemmed from the first human trial occuring at University of Pennsylvania, the developers of the first CAR-T therapy.  The clinical investigators however anticipated the issue of a potential cytokine storm and had developed ideas in the pre-trial phase of how to ameliorate such toxicity using anti-cytokine antibodies.  However, until the trial was underway they were unsure of which cytokines would be prominent in causing a cytokine storm effect from the CAR-T therapy.  Fortunately, the investigators were able to save patient 1 (described here in other posts) using anti-IL1 and 10 antibodies.  

 

Over the years, however, multiple trials had to be discontinued as shown below in the following posts:

What does this mean for Immunotherapy? FDA put a temporary hold on Juno’s JCAR015, Three Death of Celebral Edema in CAR-T Clinical Trial and Kite Pharma announced Phase II portion of its CAR-T ZUMA-1 trial

The NIH has put a crimp in the clinical trial work of Steven Rosenberg, Kite Pharma’s star collaborator at the National Cancer Institute. The feds slammed the brakes on the production of experimental drugs at two of its facilities–including cell therapies that Rosenberg works with–after an internal inspection found they weren’t in compliance with safety and quality regulations.

In this instance Kite was being cited for manufacturing issues, apparantly fungal contamination in their cell therapy manufacturing facility.  However shortly after other CAR-T developers were having tragic deaths in their initial phase 1 safety studies.

Juno Halts Cancer Trial Using Gene-Altered Cells After 3 Deaths

 

Juno halts its immunotherapy trial for cancer after three patient deaths

By DAMIAN GARDE @damiangarde and MEGHANA KESHAVAN @megkesh

JULY 7, 2016

In Juno patient deaths, echoes seen of earlier failed company

By SHARON BEGLEY @sxbegle

JULY 8, 2016

https://www.statnews.com/2016/07/08/juno-echoes-of-dendreon/

After a deadly clinical trial, will immune therapies for cancer be a bust?

By DAMIAN GARDE @damiangarde

JULY 8, 2016

This led to warnings by FDA and alteration of their trials as well as the use of their CART as a monotherapy

Hours after Juno CAR-T study deaths announced, Kite enrolls CAR-T PhII

Well That Was Quick! FDA Lets Juno Restart Trial With a New Combination Chemotherapuetic

 at Seattle Times

FDA lets Juno restart cancer-treatment trial

Certainly with so many issues there would seem to be more rigorous work to either establish a pharmacovigilence framework or to develop alternative engineered T cells with a safer profile

However here we went again

New paper sheds fresh light on Tmunity’s high-profile CAR-T deaths
Jason Mast
Editor
The industry-wide effort to push CAR-T therapies — wildly effective in several blood cancers — into solid tumors took a hit last year when Tmunity, a biotech founded by CAR-T pioneer Carl June and backed by several blue-chip VCs, announced it shut down its lead program for prostate cancer after two patients died.

On a personal note this trial was announced in a Bio International meeting here in Philadelphia a few years ago in 2019

see Live Conference Coverage on this site

eProceedings for BIO 2019 International Convention, June 3-6, 2019 Philadelphia Convention Center; Philadelphia PA, Real Time Coverage by Stephen J. Williams, PhD @StephenJWillia2

and the indication was for prostate cancer, in particular hormone resistant castration resistant.  Another one was planned for pancreatic cancer from the same group and the early indications were favorable.

From Onclive

Source: https://www.onclive.com/view/car-t-cell-therapy-trial-in-solid-tumors-halted-following-2-patient-deaths 

Tmunity Therapeutics, a clinical-stage biotherapeutics company, has halted the development of its lead CAR T-cell product following the deaths of 2 patients who were enrolled to a trial investigating its use in solid tumors.1

The patients reportedly died from immune effector cell-associated neurotoxicity syndrome (ICANS), which is a known adverse effect associated with CAR T-cell therapies.

“What we are discovering is that the cytokine profiles we see in solid tumors are completely different from hematologic cancers,” Oz Azam, co-founder of Tmunity said in an interview with Endpoints News. “We observed ICANS. And we had 2 patient deaths as a result of that. We navigated the first event and obviously saw the second event, and as a result of that we have shut down the version one of that program and pivoted quickly to our second generation.”

Previously, with first-generation CAR T-cell therapies in patients with blood cancers, investigators were presented with the challenge of overcoming cytokine release syndrome. Now ICANS, or macrophage activation, is proving to have deadly effects in the realm of solid tumors. Carl June, the other co-founder of Tmunity, noted that investigators will now need to dedicate their efforts to engineering around this, as had been done with tocilizumab (Actemra) in 2012.

The company is dedicated to the development of novel approaches that produce best-in-class control over T-cell activation and direction in the body.2 The product examined in the trial was developed to utilize engineered patient cells to target prostate-specific membrane antigen; it was also designed to use a dominant TGFβ receptor to block an important checkpoint involved in cancer.

Twenty-four patients were recruited for the dose-escalating study and the company plans to release data from high-dose cohorts later in 2021.

“We are going to present all of this in a peer-reviewed publication because we want to share this with the field,” Azam said. “Because everything we’ve encountered, no matter what…people are going to encounter this when they get into the clinic, and I don’t think they’ve really understood yet because so many are preclinical companies that are not in the clinic with solid tumors. And the rubber meets the road when you get in the clinic, because the ultimate in vivo model is the human model.”

Azam added that the company plans to develop a new investigational new drug for version 2, which they hope will result in a safer product.

References

  1. Carroll J. Exclusive: Carl June’s Tmunity encounters a lethal roadblock as 2 patient deaths derail lead trial, raise red flag forcing rethink of CAR-T for solid tumors. Endpoints News. June 2, 2021. Accessed June 3, 2021. https://bit.ly/3wPYWm0
  2. Research and Development. Tmunity Therapeutics website. Accessed June 3, 2021. https://bit.ly/3fOH3OR

Forward to 2022

Reprogramming a new type of T cell to go after cancers with less side effects, longer impact

A Sloan Kettering Institute research team thinks new, killer, innate-like T cells could make promising candidates to treat cancers that so far haven’t responded to immunotherapy treatments. (koto_feja)

Immunotherapy is one of the more appealing and effective kinds of cancer treatment when it works, but the relatively new approach is still fairly limited in the kinds of cancer it can be used for. Researchers at the Sloan Kettering Institute have discovered a new kind of immune cell and how it could be used to expand the reach of immunotherapy treatments to a much wider pool of patients.

The cells in question are called killer innate-like T cells, a threatening name for a potentially lifesaving innovation. Unlike normal killer T cells, killer innate-like T cells stay active much longer and can burrow further into potentially cancerous tissue to attack tumors. The research team first reported these cells in 2016, but it’s only recently that they were able to properly understand and identify them.

“We think these killer innate-like T cells could be targeted or genetically engineered for cancer therapy,” said the study’s lead author, Ming Li, Ph.D., in a press release. “They may be better at reaching and killing solid tumors than conventional T cells.”

Below is the referenced paper from Pubmed:

Evaluation of the safety and efficacy of humanized anti-CD19 chimeric antigen receptor T-cell therapy in older patients with relapsed/refractory diffuse large B-cell lymphoma based on the comprehensive geriatric assessment system

Affiliations 

Abstract

Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy has led to unprecedented results to date in relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL), yet its clinical application in elderly patients with R/R DLBCL remains somewhat limited. In this study, a total of 31 R/R DLBCL patients older than 65 years of age were enrolled and received humanized anti-CD19 CAR T-cell therapy. Patients were stratified into a fit, unfit, or frail group according to the comprehensive geriatric assessment (CGA). The fit group had a higher objective response (OR) rate (ORR) and complete response (CR) rate than that of the unfit/frail group, but there was no difference in the part response (PR) rate between the groups. The unfit/frail group was more likely to experience AEs than the fit group. The peak proportion of anti-CD19 CAR T-cells in the fit group was significantly higher than that of the unfit/frail group. The CGA can be used to effectively predict the treatment response, adverse events, and long-term survival.

Introduction

Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma (NHL), accounting for 30–40% of cases, with the median age of onset being older than 65 years [1]. Although the five-year survival rate for patients with DLBCL has risen to more than 60% with the application of standardized treatments and hematopoietic stem cell transplantation, nearly half of patients progress to relapsed/refractory (R/R) DLBCL. Patients with R/R DLBCL, especially elderly individuals, have a poor prognosis [2,3], so new treatments are needed to prolong survival and improve the prognosis of this population.

As a revolutionary immunotherapy therapy, anti-CD19 chimeric antigen receptor (CAR) T-cell therapy has achieved unprecedented results in hematological tumors [4]. As CD19 is expressed on the surface of most B-cell malignant tumors but not on pluripotent bone marrow stem cells, CD19 has been used as a target for B-cell malignancies, including B-cell acute lymphoblastic leukemia, NHL, multiple myeloma, and chronic lymphocytic leukemia [5]. Despite the wide application and high efficacy of anti-CD19 CAR T-cell therapy, reports of adverse events (AEs) such as cytokine release syndrome (CRS) and immune effector cell-associated neurotoxic syndrome (ICANS) have influenced its use [6]. Especially in elderly patients, AEs associated with anti-CD19 CAR T-cell therapy might be more obvious.

Although anti-CD19 CAR T-cell therapy has been reported in the treatment of NHL, including R/R DLBCL, few studies to date have assessed the safety of anti-CD19 CAR T-cell therapy in elderly R/R DLBCL patients, and its clinical application in the elderly R/R DLBCL population is limited. In ZUMA-1 [7] to R/R DLBCL patients who received CAR T-cell therapy, the CR rate in patients ≥65 years was higher than that of in patients <65 years (75% vs. 53%). Lin et al. [8] reported 49 R/R DLBCL patients (24 patients >65 years, 25 patients <65 years) who received CAR T-cell therapy with a median follow-up of 179 days. The CR rate at 100 days was 51%, while the 6-month progression-free survival (PFS) and overall survival (OS) were 48% and 71%, respectively. Neither of the two studies carried out a comprehensive geriatric assessment (CGA) of fit, unfit, and frail groups of R/R DLBCL patients over 65 years of age and further analyzed the differences in efficacy and side effects in the three groups. The CGA is an effective system designed to evaluate the prognosis and improve the survival of elderly patients with cancer. The CGA system includes age, activities of daily living (ADL), instrumental ADL (IADL), and the Cumulative Illness Rating Score for Geriatrics (CIRS-G) [9].

In this study, elderly R/R DLBCL patients were grouped according to their CGA results (fit vs. unfit/frail) before receiving humanized anti-CD19 CAR T-cell therapy. We then analyzed the efficacy and AEs of anti-CD19 CAR T-cell therapy and compared findings between these groups.

 

Well it appears that the discriminator was only fitness going into the trial  a bit odd that the whole field appears to be lacking in development of Safety Biomarkers.

 

 

However Genentech (subsidiary of Roche) may now be using some data to develop therapies which may combat resistance to CART therapies which may provide at least, for now, a toxicokinetic approach to reducing AEs by lowering the amount of CARTs needed to be administered.

 

Source: https://www.fiercebiotech.com/research/genentech-uncovers-how-cancer-cells-resist-t-cell-attack-potential-boon-immunotherapy

Roche’s Genentech is exploring inhibiting ESCRT as an anticancer strategy, said Ira Mellman, Ph.D., Genentech’s vice president of cancer immunology. (Roche)

Cancer cells deploy various tactics to avoid being targeted and killed by the immune system. A research team led by Roche’s Genentech has now identified one such method that cancer cells use to resist T-cell assault by repairing damage.

To destroy their targets, cancer-killing T cells known as cytotoxic T lymphocytes (CTLs) secrete the toxin perforin to form little pores in the target cells’ surface. Another type of toxin called granzymes are delivered directly into the cells through those portals to induce cell death.

By using high-res imaging in live cells, the Genentech-led team found that the membrane damage caused by perforin could trigger a repair response. The tumor cells could recruit endosomal sorting complexes required for transport (ESCRT) proteins to remove the lesions, thereby preventing granzymes from entering, the team showed in a new study published in Science.

The following is the Science paper

Membrane repair in target cell defenses

Killer T cells destroy virus-infected and cancer cells by secreting two protein toxins that act as a powerful one-two punch. Pore-forming toxins, perforins, form holes in the plasma membrane of the target cell. Cytotoxic proteins released by T cells then pass through these portals, inducing target cell death. Ritter et al. combined high-resolution imaging data with functional analysis to demonstrate that tumor-derived cells fight back (see the Perspective by Andrews). Protein complexes of the ESCRT family were able to repair perforin holes in target cells, thereby delaying or preventing T cell–induced killing. ESCRT-mediated membrane repair may thus provide a mechanism of resistance to immune attack. —SMH

Abstract

Cytotoxic T lymphocytes (CTLs) and natural killer cells kill virus-infected and tumor cells through the polarized release of perforin and granzymes. Perforin is a pore-forming toxin that creates a lesion in the plasma membrane of the target cell through which granzymes enter the cytosol and initiate apoptosis. Endosomal sorting complexes required for transport (ESCRT) proteins are involved in the repair of small membrane wounds. We found that ESCRT proteins were precisely recruited in target cells to sites of CTL engagement immediately after perforin release. Inhibition of ESCRT machinery in cancer-derived cells enhanced their susceptibility to CTL-mediated killing. Thus, repair of perforin pores by ESCRT machinery limits granzyme entry into the cytosol, potentially enabling target cells to resist cytolytic attack.
Cytotoxic lymphocytes, including cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells, are responsible for identifying and destroying virus-infected or tumorigenic cells. To kill their targets, CTLs and NK cells secrete a pore-forming toxin called perforin through which apoptosis-inducing serine proteases (granzymes) are delivered directly into the cytosol. Successful killing of target cells often requires multiple hits from single or multiple T cells (1). This has led to the idea that cytotoxicity is additive, often requiring multiple rounds of sublethal lytic granule secretion events before a sufficient threshold of cytosolic granzyme activity is reached to initiate apoptosis in the target (2).
Loss of plasma membrane integrity induced by cytolytic proteins or mechanical damage leads to a membrane repair response. Damage results in an influx of extracellular Ca2+, which has been proposed to lead to the removal of the membrane lesion by endocytosis, resealing of the lesions by lysosomal secretion, or budding into extracellular vesicles (3). Perforin pore formation was initially reported to enhance endocytosis of perforin (4), but subsequent work has challenged this claim (5). Endosomal sorting complexes required for transport (ESCRT) proteins can repair small wounds and pores in the plasma membrane caused by bacterial pore-forming toxins, mechanical wounding, and laser ablation (6, 7). ESCRT proteins are transiently recruited to sites of membrane damage in a Ca2+-dependent fashion, where they assemble budding structures that shed to eliminate the wound and restore plasma membrane integrity. ESCRT-dependent membrane repair has been implicated in the resealing of endogenous pore-mediated plasma membrane damage during necroptosis (8) and pyroptosis (9).

Localization of target-derived ESCRT proteins to the cytolytic synapse

To investigate whether ESCRT-mediated membrane repair might be involved in the removal of perforin pores during T cell killing, we first determined whether ESCRT proteins in cancer-derived cells were recruited to sites of CTL engagement after perforin secretion. We used CTLs from OT-I mice that express a high-affinity T cell receptor (TCR) that recognizes the ovalbumin peptide SIINFEKL (OVA257-264) bound to the major histocompatibility complex (MHC) allele H-2Kb (10). We performed live-cell microscopy of OT-I CTLs engaging SIINFEKL-pulsed target cells that express enhanced green fluorescent protein (EGFP)–tagged versions of Tsg101 or Chmp4b, two ESCRT proteins implicated in membrane repair (6). To correlate recruitment of ESCRT proteins with perforin exposure in time, we monitored CTL-target interaction in media with a high concentration of propidium iodide (PI), a cell-impermeable fluorogenic dye that can rapidly diffuse through perforin pores to bind and illuminate nucleic acids in the cytosol and nucleus of the target (5). EGFP-tagged ESCRT proteins were consistently recruited to the site of CTL engagement within 30 to 60 s after PI influx (Fig. 1, A and B). EGFP-Tsg101 and EGFP-Chmp4b in target cells accumulated at the cytolytic synapse after PI influx in 25 of 27 (92.6%) and 31 of 33 (93.9%) of conjugates monitored, respectively, compared with a cytosolic EGFP control, which was not recruited (Fig. 1C and movies S1 to S3). Notably, ESCRT-laden material, presumably membrane fragments, frequently detached from the target cell and adhered to the surface of the CTL (Fig. 1, D and E, and movie S2). We observed this phenomenon in ~60% of conjugates imaged in which targets expressed EGFP-Tsg101 or EGFP-Chmp4b (17 of 27 and 20 of 33 conjugates, respectively; Fig. 1D). Shedding of ESCRT-positive membrane from the cell after repair occurs after laser-induced plasma membrane wounding (6, 7). Plasma membrane fragments shed from the target cell into the synaptic cleft likely contain ligands for CTL-resident receptors. Target cell death would separate the CTL and target, revealing target-derived material on the CTL surface.
FIG. 1. Fluorescently tagged ESCRT proteins in targets localize to site of CTL killing after perforin secretion.
(A) Live-cell spinning disk confocal imaging of a fluorescently labeled OT-I CTL (magenta) engaging an MC38 cancer cell expressing EGFP-Tsg101 (green) in media containing 100 μM PI (red). Yellow arrowheads highlight ESCRT recruitment. T-0:00 is the first frame of PI influx into the target cell (time in minutes:seconds). Scale bar, 10 μm. (B) Graph of EGFP-Tsg101 and PI fluorescence intensity at the IS within the target over time, from example in (A). AU, arbitrary units. (C and D) Quantification of CTL-target conjugates exhibiting accumulation of EGFP at the synapse after PI influx (C) or detectable EGFP-labeled material associated with CTL after target interaction (D) (EGFP condition: N = 22 conjugates in seven independent experiments; EGFP-Tsg101 condition: N = 27 conjugates in nine independent experiments; EGFP-Chmp4b condition: N = 33 conjugates in 24 independent experiments). (E) Live-cell spinning disk confocal imaging of OT-I CTL (magenta) killing MC38 expressing EGFP-Chmp4b (green), demonstrating the presence of target-derived EGFP-Chmp4b material (yellow arrowheads) associated with CTL membrane after a productive target encounter. T-0:00 is the first frame of PI influx into the target cell. Scale bar, 10 μm.
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3D cryo-SIM and FIB-SEM imaging of CTLs caught in the act of killing target cells

Although live-cell imaging indicated that ESCRT complexes were rapidly recruited at sites of T cell–target cell contact, light microscopy alone is of insufficient resolution to establish that this event occurred at the immunological synapse (IS). We thus sought to capture a comprehensive view of the IS in the moments immediately after secretion of lytic granules. We used cryo–fluorescence imaging followed by correlative focused ion beam–scanning electron microscopy (FIB-SEM), which can achieve isotropic three-dimensional (3D) imaging of whole cells at 8-nm resolution or better (11–13). To capture the immediate response of target cells after perforin exposure, we developed a strategy whereby cryo-fixed CTL-target conjugates were selected shortly after perforation, indicated by the presence of a PI gradient in the target (fig. S1A). In live-cell imaging experiments, PI fluorescence across the nucleus of SIINFEKL-pulsed ID8 target cells began as a gradient and became homogeneous 158 ± 64 s, on average, after initial PI influx (N = 31 conjugates; fig. S1, B and C, and movie S4). Thus, fixed CTL-target conjugates that exhibited a gradient of PI across the nucleus would have been captured within ~3 min of perforin exposure.
Coverslips of CTL-target conjugates underwent high-pressure freezing and were subsequently imaged with wide-field cryogenic fluorescence microscopy followed by 3D cryo–structured illumination microscopy (3D cryo-SIM) performed in a customized optical cryostat (14). We selected candidate conjugates for FIB-SEM imaging on the basis of whether a gradient of PI fluorescence was observed across the nucleus of the target emanating from an attached CTL (movie S5). FIB-SEM imaging of the CTL-target conjugate at 8-nm isotropic voxels resulted in a stack of >10,000 individual electron microscopy (EM) images. The image stack was then annotated using a human-assisted machine learning–computer vision platform to segment the plasma membranes of each cell along with cell nuclei and various organelles (https://ariadne.ai/).
We captured four isotropic 3D 8-nm-resolution EM datasets of CTLs killing cancer cells moments after the secretion of lytic granule contents (Fig. 2A and movie S6). Semiautomated segmentation of the cell membranes, nuclei, lytic granules, Golgi apparatus, mitochondria, and centrosomes of the T cells allow for easier visualization and analysis of the 3D EM data. All FIB-SEM datasets and segmentations can be explored online at https://openorganelle.janelia.org (see links in the supplementary materials). Reconstructed views of the segmented data clearly demonstrate the polarization of the centrosome, Golgi apparatus, and lytic granules to the IS—all of which are hallmarks of CTL killing [Fig. 2A, i to iii, and movie S6, time stamp (TS) 1:33] (15, 16). On the target cell side, we noted cytoplasmic alterations consistent with cell damage including enhanced electron density of mitochondria adjacent to the IS (fig. S2A). Close visual scanning of the postsynaptic target cell membrane in the raw EM data failed to reveal obvious perforin pores, which have diameters (16 to 22 nm) close to the limit of resolution for this technique (17).
FIG. 2. Eight-nm-resolution 3D FIB-SEM imaging of whole CTL-target conjugate.
(A) 3D rendering of segmented plasma membrane predictions derived from isotropic 8-nm-resolution FIB-SEM imaging of a high-pressure frozen OT-I CTL (red) captured moments after secretion of lytic granules toward a peptide-pulsed ID8 ovarian cancer cell (blue). (i) Side-on sliced view corresponding to the gray horizontal line within the inset box in (A). Seen here are 3D renderings of the segmented plasma membrane of the cancer cell (blue) as well as the CTL plasma membrane (red), centrosome (gold), Golgi apparatus (cyan), lytic granules (purple), mitochondria (green), and nucleus (gray). (ii and iii) A zoomed-in view from the dashed white box in (i) shows the details of the IS (ii) and a single corresponding FIB-SEM slice docked onto the segmented data (iii). (B) Single top-down FIB-SEM slice showing overlaid target cell (blue) and CTL (red) segmentation. (i) Zoomed-in view from dashed white box in (B) details the intercellular material (IM) (gray) between the CTL and target at the IS. (C) Zoomed-in image of a 3D rendering of the surface of the target cell plasma membrane (white) opposite the intercellular material (IM) at the IS. Yellow arrowheads mark plasma membrane buds protruding into the synaptic cleft. (i and ii) Accompanying images demonstrate the orientation of the view in (C) with the rendering of the CTL (red) present (i) and removed (ii), and the dashed yellow box in (ii) indicates the area of detail shown in (C).
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The segmentation of the two cells illustrates the detailed topography of the plasma membrane of the CTL and target at the IS (fig. S2B). The raw EM and segmentation data reveal a dense accumulation of particles, vesicles, and multilamellar membranous materials, which crowd the synaptic cleft between the CTL and the target (Fig. 2B and movie S6, TS 0:40 to 0:50). The source of this intercellular material (IM) was likely in part the lytic granules because close inspection revealed similar particles and dense vesicles located within as-yet-unreleased granules (fig. S2C). To determine whether some of the membranous material within the intercellular space might also have been derived from the target cell, we examined the surface topology of the postsynaptic target cell. We noted multiple tubular and bud-like protrusions of the target cell membrane that extended into the synaptic space; thus, at least some of the membrane structures observed were still in continuity with the target cell (Fig. 2C and movie S6, TS 0:58 to 1:11). ESCRT proteins have been shown to generate budding structures in the context of plasma membrane repair (6), which led us to next assess where target-derived ESCRT proteins are distributed in the context of the postsecretion IS.
To map the localization of target-derived ESCRT proteins onto a high-resolution landscape of the IS, we captured three FIB-SEM datasets that have associated 3D cryo-SIM fluorescence data for mEmerald-Chmp4b localization (Fig. 3A, fig. S3, and movie S7). This correlative light and electron microscopy (CLEM) revealed that mEmerald-Chmp4b expressed in the target cell was specifically recruited to the target plasma membrane opposite the secreted IM (Fig. 3, B and C). The topography of the plasma membrane at the site of ESCRT recruitment was markedly convoluted, exhibiting many bud-like projections (movie S7, TS 0:37 to 0:40). mEmerald-Chmp4b fluorescence also overlapped with some vesicular structures in the intercellular synaptic space (Fig. 3C). Together, the live-cell imaging and the 3D cryo-SIM and FIB-SEM CLEM demonstrate the localization of ESCRT proteins at the synapse that was the definitive site of CTL killing and was thus spatially and temporally correlated to perforin secretion. These data implicate the ESCRT complex in the repair of perforin pores.
FIG. 3. Correlative 3D cryo-SIM and FIB-SEM reveal localization of target-derived ESCRT within the cytolytic IS.
(A) Three example datasets showing correlative 3D cryo-SIM and FIB-SEM imaging of OT-I CTLs (red) captured moments after secretion of lytic granules toward peptide-pulsed ID8 cancer cells (blue) expressing mEmerald-Chmp4b (green fluorescence). (B and C) Single FIB-SEM slices corresponding to the orange boxes in (A), overlaid with CTL and cancer cell segmentation (B) or correlative cryo-SIM fluorescence of mEmerald-Chmp4b derived from the target cell (C).
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Function of ESCRT proteins in repair of perforin pores

We next investigated whether ESCRT inhibition could enhance the susceptibility of target cells to CTL-mediated killing. Prolonged inactivation of the ESCRT pathway is itself cytotoxic (9). We thus developed strategies to ablate ESCRT function that would allow us a window of time to assess CTL killing (fig. S4). We used two approaches to block ESCRT function: CRISPR knockout of the Chmp4b gene or overexpression of VPS4aE228Q (E228Q, Glu228 → Gln), a dominant-negative kinase allele that impairs ESCRT function (fig. S4, A to C) (10). We took care to complete our assessment of target killing well in advance of spontaneous target cell death (fig. S4D).
We tested the capacity of OT-I CTLs to kill targets presenting one of four previously characterized peptides that demonstrate a range of potencies at stimulating the OT-I TCR: SIINFEKL (N4), the cognate peptide, and three separate variants (in order of highest to lowest affinity), SIITFEKL (T4), SIIQFEHL (Q4H7), and SIIGFEKL (G4) (18, 19). Target cells were pulsed with peptide, washed, transferred to 96-well plates, and allowed to adhere before the addition of OT-I CTLs. Killing was assessed by monitoring the uptake of a fluorogenic caspase 3/7 indicator (Fig. 4, A to D, and fig. S5A). Killing was significantly more efficient in ESCRT-inhibited target cells for both CRISPR depletion of Chmp4b (Fig. 4, A to C) and expression of the dominant-negative VPS4aE228Q (Fig. 4D). The difference in killing between the ESCRT-inhibited and control cells was greater when the lower-potency T4, Q4H7, and G4 peptides were used. Nevertheless, ESCRT inhibition moderately improved killing efficiency even in the case of the high-potency SIINFEKL peptide. ESCRT inhibition had no effect on MHC class I expression on the surface of target cells (fig. S5B). Thus, ESCRT inhibition could sensitize target cells to perforin- and granzyme-mediated killing, especially at physiologically relevant TCR-peptide MHC affinities.
FIG. 4. ESCRT inhibition enhances susceptibility of cancer cells to CTL killing and recombinant lytic proteins.
(A) Representative time-lapse data of killing of peptide-pulsed Chmp4b knockout (KO) or control B16-F10 cells by OT-I CTLs. Affinity of the pulsed peptide to OT-I TCR decreases from left to right. Error bars indicate SDs. (B) Images extracted from T4 medium-affinity peptide condition show software-detected caspase 3/7+ events in control and Chmp4b KO conditions. (C and D) Data representing the 4-hour time point of assays measuring OT-I T cells killing either Chmp4b KO (C) or VPS4 dominant-negative (D) target cells with matched controls. Error bars indicate SDs of data. Data are representative of at least three independent experimental replicates. pMHC, peptide-MHC; HA, hemagglutinin. (E and F) Determination of sublytic dose of Prf. B16-F10 cells expressing VPS4a (WT or E228Q) were exposed to increasing concentrations of Prf. Cell viability was determined by morphological gating (E). FSC, forward scatter; SSC, side scatter. (G and H) B16-F10 cells expressing VPS4a (WT or E228Q) were exposed to a sublytic dose of Prf in combination with increasing concentrations of recombinant GZMB (rGZMB). Cell death was determined by Annexin V–allophycocyanin (APC) staining (G). Controls include a condition with no perforin and 5000 ng/ml rGZMB and sublytic perforin with no rGZMB. Graphs in (F) and (H) represent the means of three experiments, and error bars indicate SDs. Statistical significance was determined by multiple unpaired t tests with alpha = 0.05. ns, not significant; *P < 0.05; **P < 0.01; ***P < 0.001.
OPEN IN VIEWER
We next directly tested the effects of ESCRT inhibition when target cells were exposed to both recombinant perforin (Prf) and granzyme B (GZMB), the most potently proapoptotic granzyme in humans and mice (20). Prf alone at high concentrations can lyse cells (4), so we first determined a sublytic Prf concentration that would temporarily permeabilize the plasma membrane but permit the cells to recover. B16-F10 cells expressing either VPS4aWT (WT, wild-type) or VPS4aE228Q were exposed to a range of Prf concentrations in the presence of PI, and cell viability and PI uptake were assessed using flow cytometry. Cells that expressed dominant-negative VPS4aE228Q were more sensitive to Prf alone than ESCRT-competent cells (Fig. 4, E and F). At 160 ng/ml Prf, there was no significant difference in cell viability for either condition. Cells in the live gate that were PI+ had been permeabilized by Prf but recovered. Although the percentage of PI+ live cells was similar under both sets of conditions, the mean fluorescence intensity of PI was higher in live ESCRT-inhibited cells (fig. S6). A delay in plasma membrane resealing could account for this difference.
We reasoned that delaying perforin pore repair might also enhance GZMB uptake into the target. ESCRT-inhibited cells were more sensitive to combined perforin-GZMB when cell death was measured by Annexin V staining (Fig. 4, G and H). Similar results were observed when these experiments were repeated with a murine lymphoma cancer cell line (fig. S7). The observation that ESCRT-inhibited target cells are more sensitive to both CTL-secreted and Prf-GZMB supports the hypothesis that the ESCRT pathway contributes to membrane repair after Prf exposure.
Escaping cell death is one of the hallmarks of cancer. Our findings suggest that ESCRT-mediated membrane repair of perforin pores may restrict accessibility of the target cytosol to CTL-secreted granzyme, thus promoting survival of cancer-derived cells under cytolytic attack. Although other factors may contribute to setting the threshold for target susceptibility to killing, the role of active repair of perforin pores must now be considered as a clear contributing factor.

Acknowledgments

We thank members of the Mellman laboratory for advice, discussion, and reagents; B. Haley for assistance with plasmid construct design; the Genentech FACS Core Facility for technical assistance; S. Van Engelenburg of Denver University for invaluable discussions and guidance; A. Wanner, S. Spaar, and the Ariande AI AG (https://ariadne.ai/) for assistance with FIB-SEM segmentation, CLEM coregistration, data presentation, and rendering; D. Bennett of the Janelia Research Campus for assisting with data upload to https://openorganelle.janelia.org; and the Genentech Postdoctoral Program for support.
Funding: A.T.R. and I.M. are funded by Genentech/Roche. C.S.X., G.S., A.W., D.A., N.I., and H.F.H. are funded by the Howard Hughes Medical Institute (HHMI).

Please look for a Followup Post concerning “Developing a Pharmacovigilence Framework for Engineered T-Cell Therapies”

 

References

  1. Ertl HC, Zaia J, Rosenberg SA, June CH, Dotti G, Kahn J, Cooper LJ, Corrigan-Curay J, Strome SE: Considerations for the clinical application of chimeric antigen receptor T cells: observations from a recombinant DNA Advisory Committee Symposium held June 15, 2010. Cancer research 2011, 71(9):3175-3181.
  2. Morgan RA, Yang JC, Kitano M, Dudley ME, Laurencot CM, Rosenberg SA: Case report of a serious adverse event following the administration of T cells transduced with a chimeric antigen receptor recognizing ERBB2. Molecular therapy : the journal of the American Society of Gene Therapy 2010, 18(4):843-851.
  3. Kandalaft LE, Powell DJ, Jr., Coukos G: A phase I clinical trial of adoptive transfer of folate receptor-alpha redirected autologous T cells for recurrent ovarian cancer. Journal of translational medicine 2012, 10:157.

Other posts on this site on Immunotherapy and Cancer include

Report on Cancer Immunotherapy Market & Clinical Pipeline Insight

New Immunotherapy Could Fight a Range of Cancers

Combined anti-CTLA4 and anti-PD1 immunotherapy shows promising results against advanced melanoma

Molecular Profiling in Cancer Immunotherapy: Debraj GuhaThakurta, PhD

Pancreatic Cancer: Genetics, Genomics and Immunotherapy

$20 million Novartis deal with ‘University of Pennsylvania’ to develop Ultra-Personalized Cancer Immunotherapy

Upcoming Meetings on Cancer Immunogenetics

Tang Prize for 2014: Immunity and Cancer

ipilimumab, a Drug that blocks CTLA-4 Freeing T cells to Attack Tumors @DM Anderson Cancer Center

Juno’s approach eradicated cancer cells in 10 of 12 leukemia patients, indicating potential to transform the standard of care in oncology

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What VCs Think about Your Pitch? Panel Summary of 1st Pitch Life Science Philly

Reporter: Stephen J. Williams, PhD

 

The following is a summary of the panel discussions for the  1st Pitch Life Science- Philadelphia: “Eavesdropping on Investors’ Closed Door Discussions” held on September 16, 2014 in Philadelphia.  For synopsis of the meeting see

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

The meeting, as described by meeting organizer and Steering Committee member of Mid Atlantic Bio Angels Lorraine Marchand, as a “benevolent sharktank”, where presenters get open and honest feedback from experienced venture capitalists on how to improve their pitch and business.  The meeting here in Philadelphia was well attended with” over 70 attendants compareable to the 130 we get in New york”, according to MABA Founder Yaniv Sneor.

 

A few key points were discussed to improve the presenters future pitches to VC.

  1. Define your technology/product, its purpose, how it fills an unmet need, and how you are unique.
  2. Timelines and Milestones VERY IMPORTANT to have specific dates on when and what you will accomplish.
  3. If your EXIT Strategy involves OUT-LICENSING, it is important to keep this in mind when framing your patent
  4. VC’s want to see a STRONG MANAGEMENT TEAM, preferably a CEO from big pharma if you need to deal with them later
  5. if PITCH sounds too much like a science project VC’s would NOT be interested.  Show also the BUSINESS not just science
  6. know the REGULATORY RISK – talk with the FDA
  7. if market is small, son’t fret, show PROOF OF CONCEPT then show how relates to other markets
  8. show your TANGIBLE ASSETS in your pitch – if you use a new equipment show it,

Other posts related to this meeting are included below

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

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

LytPhage Presents at 1st Pitch Life Sciences-Philadelphia

RAbD Biotech Presents at 1st Pitch Life Sciences-Philadelphia

Also FOLLOW on TWITTER at

@pharma_BI      https://twitter.com/Pharma_BI

@BioAngelsGroup     https://twitter.com/BioAngelsGroup

 

 

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Upcoming Meetings on Cancer Immunogenetics

 

Curator: Stephen J. Williams, Ph.D.

Below is a curation of upcoming 2014-15 Cancer Immunogenetics symposia. Some listed have CME credits.

August 2014

Target Discovery for T Cell Therapy Symposium
Next Step to Advance Immunotherapies
August 14, 2014 | Part of ImVacS – The Immunotherapies and Vaccine Summit
Learn more | View Agenda PDF | Register by July 18 & SAVE up to $200

 

Q&A with Dr. Adrian Bot of Kite Pharma

 

SITC 2014 Meetings

The Society for Immunotherapy of Cancer (SITC) is a 501 (c)(3) non-profit society of medical professionals. Recent advances in immunology and biology have opened up new horizons in the field of cancer therapy, with an upsurge in the integration of new biologic agents into clinical practice. With several high-caliber scientific meetings with a focus on clinical and translational aspects of biologic approaches to cancer treatment and numerous networking opportunities unique to this organization, the Society for Immunotherapy of Cancer (SITC) has developed into the premier destination for interaction and innovation in the cancer biologics community.

Upcoming SITC Meetings and Activities

sitc banner

Advances in Cancer Immunotherapy™ (ACI™) Regional CME-Certified Programs

  • La Jolla, CA – Friday, August 22, 2014
  • Portland, OR – Friday, October 3, 2014
    Charlotte, NC – Friday, October 3, 2014
  • Tampa, FL – Friday, December 5, 2014

 ACI

September 2014

 

 aacrmeetinghemoto2014

  Hematologic Malignancies: Translating Discoveries to Novel Therapies
    September 20-23, 2014 • Sheraton Philadelphia Downtown • Philadelphia, PA

The AACR is proud to announce our conference focused on the blood-based cancers and associated disorders categorized as hematologic malignancies. Sessions will include presentations on leukemia, lymphoma, myeloma, myelodysplastic syndrome, and myeloproliferative neoplasms.

 

Advances in Melanoma: From Biology to Therapy

Loews Philadelphia • Philadelphia, PA • September 20-23, 2014

With so many recent advances in treating metastatic melanoma, including approaches like immunotherapies, targeted therapies, and combination therapies, melanoma research is at a critical point where it is extremely important for the field to have a continuous exchange of information. Despite the success of various “targeted” inhibitors, therapeutic responses in melanoma patients are often short-lived due to rapidly acquired drug resistance. Therefore, it is essential that melanoma researchers translate the novel understanding of melanoma biology to decipher the mechanisms of innate and acquired drug resistance for the development of improved therapeutic options. To bridge the gap between scientists and clinician-scientists’ professional practice, this conference will provide a platform for discussion and potential collaborations for the discovery of new therapeutic targets.

 

 proimmunegif

The 4th Mastering Immunogenicity Summit

September 15-16, 2014

British Consulate-General, Boston MA, USA

Join leaders in the immunogenicity field for a two day conference to learn what constitutes a successful strategy for managing immunogenicity risk, and explore the business case for introducing immunogenicity assessment into your program.

  • Learn about the latest strategies and exciting new technologies
  • Discuss current and developing challenges and exchange new ideas
  • Improve the outcome of your R&D programs

Our 4th Mastering Immunogenicity Conference will continue to have a strong focus on immunogenicity sciences, particularly on what basic research needs to be carried out to improve our understanding of immune regulation to biotherapeutics. We will review progress made in correlating data from pre-clinical predictive tools to clinical outcomes, as well as continuing our discussions surrounding the benefits that Quality by Design has on reduced immunogenicity, considering subsequent patient benefits as well as competitive advantage. Presentations by experts will provide an overview of the wide range of technologies currently used for immunogenicity risk management and how they can be incorporated for a ‘quality by design’ approach.

 

Immunogenomics 2014

September 29 – October 1, 2014

HudsonAlpha Biotechnology Campus
Huntsville, Alabama, USA

The HudsonAlpha-Science Conference on Immunogenomics will bring together preeminent leaders and thinkers at the intersection of genomics and immunology.

October 2014

canerrersinstlogo

Cancer Immunotherapy: Out of the Gate

October 06, 2014 Grand Hyatt New York Hotel at Grand Central, New York, NY

The Cancer Research Institute (CRI) will host its 22nd Annual International Cancer Immunotherapy Symposium October 6-8, 2014 at The Grand Hyatt in New York City. Attracting clinicians, laboratory scientists, postdoctoral fellows, and graduate students, the symposium will feature plenary presentations from leaders in immunology and cancer immunotherapy, a poster session, and numerous networking opportunities.

This year’s CRI symposium, entitled Cancer Immunotherapy: Out of the Gate, will harness the excitement and enthusiasm generated by recent clinical successes to explore new and emerging areas of basic, translational, and clinical research. Topics such as the use of genomic methods to catalogue cancer heterogeneity, mechanistic studies of checkpoint blockage antibodies, new views on immunosurveillance and immunoregulation, and emerging therapies that are altering the landscape of cancer treatment will be discussed.

– See more at: http://www.cancerresearch.org/grants-programs/conferences-meetings/annual-international-cancer-immunotherapy-symposia/2014-symposium#sthash.PnY56e5E.dpuf

Cytokines 2014

October 26–29, Melbourne, Australia

EMBO Conference: Innate Lymphoid Cells
September 29–October 1, Paris, France

Recommended reading

Laurie Dempsey

 

November 2014

SITC 2014 – November 6-9, 2014

  • Gaylord National Hotel & Convention Center, National Harbor, MD
  • SITC 29th Annual Meeting
  • SITC Workshop on Combination Immunotherapy: Where Do We Go From Here?
  • SITC Primer on Tumor Immunology and Cancer Immunotherapy™
  • SITC Hot Topic Symposium – including two topics explored concurrently:
    • Accelerating Tumor Immunity with Agonist Antibodies
    • Engineered T Cell Toxicities
  • Professional Development Session: A Roadmap for Thriving in Your Career

The Fourth International Conference on Regulatory T cells and TH Subsets and Clinical Application in Human Diseases
November 1–4, Shanghai, China

Recommended reading
Olive Leavy

 

eortspainmeeting

 

 

Keystone Symposium: Cell Death Signaling in Cancer and the Immune System
October 28-November 2, Sao Paolo, Brazil

Recommended reading

December 2014

Tumor Immunology and Immunotherapy: A New Chapter
Co-Chairpersons: Robert H. Vonderheide, Nina Bhardwaj, Stanley Riddell, and Cynthia L. Sears
December 1-4, 2014 • Orlando, FL

2015 Conferences

Keystone Symposia on Molecular and Cellular Biology

Tumor Immunology: Multidisciplinary Science Driving Combination Therapy 

February 8—13, 2015

Fairmont Banff Springs, Banff, Alberta, Canada

 

· March 2015

  1. 8–13, Montreal, Quebec, Canada
  2. 22–27, Banff, Alberta, Canada
  3. 29–3 April, Snowbird, Utah, USA

9th World Immune Regulation Meeting

Keystone Symposium: The Golden Anniversary of B Cell Discovery
Recommended reading

Keystone Symposium: T Cells: Regulation and Effector Function
Recommended reading

 

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Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science

Curator: Stephen J. Williams, Ph.D.

Article ID #147: Heroes in Medical Research: Green Fluorescent Protein and the Rough Road in Science. Published on 7/27/2014

WordCloud Image Produced by Adam Tubman

In this series, “Heroes in Medical Research”, I like to discuss the people who made some important contributions to science and medicine which underlie the great transformative changes but don’t usually get the notoriety given to Nobel Laureates or who seem to fly under the radar of popular news. Their work may be the development of research tools which allowed a great discovery leading to a line of transformative research, a moment of serendipity leading to discovery of a cure, or just contributions to the development of a new field or the mentoring of a new generation of scientists and clinicians. One such discovery, which has probably been pivotal in many of our research, is the discovery of the green fluorescent protein (GFP), commonly used as an invaluable tool to monitor protein for cellular expression and localization studies. Although the development of research tools, whether imaging tools, vectors, animal models, cell lines, and such are not heralded, they always assist in the pivotal discoveries of our time. The following is a heartwarming story by Discover Magazine’s Yudhijit Bhattacharjee behind Dr. Douglas Prasher’s discovery of the green fluorescent protein, his successful efforts to sequence the gene and subsequent struggles in science and finally scientific recognition for his work. In addition the story describes Dr. Prather’s perseverance, a trait necessary for every scientist.

http://discovermagazine.com/2011/apr/30-how-bad-luck-networking-cost-prasher-nobel

 

The following is a wonderful entry into Wikipedia about Dr. Prasher at:

http://en.wikipedia.org/wiki/Douglas_Prasher

including a listing of his publications including the seminal Science and PNAS publications1,2.

 

prasher

 

 

(Photo: Dr. Prasher in the lab at UCSD. Photo credit UCSD and John Galstaldo)

 

 

 

In summary, Dr. Prather had been working at Wood’s Hole in Massachusetts trying to discover, isolate, then clone the protein which allowed a species of jellyfish living in the cold waters of the North Pacific, Aequorea victoria, to emit a green glow. Eventually he cloned the GFP gene, but gave up on work to express the gene in mammalian cells. Before leaving Wood’s Hole he gave the gene to Dr. Roger Tsien, who with Dr. Martin Chalfie and Osamu Shimomura showed the utility of GFP as an intracellular tracer to visualize, in real time, the expression and localization of GFP-tagged proteins (all three shared the 2008 Nobel Prize for this work). Dr. Tsien however realized the importance of Douglas’s cloning work as pivotal for their research, contacted Douglas (who now due to the bad economy was working at a Toyota dealership in Alabama) and invited him to the Nobel Prize Award Ceremony in Sweden as his guest. Although Dr. Prasher had “left academic science” he never really stopped his quest for a scientific career, using his spare time to review manuscripts.

Other researchers have invited their colleagues who made important contributions to the ultimate Nobel work. One such guest was one of my colleagues Dr. Leonard Cohen, who worked with Dr. Irwin Rose and Avram Hershko at the Institute for Cancer Research in Philadelphia a cell-free system from clams to discover the mechanism how cyclin B is degraded during the exit from the cell cycle (from A. Hershko’s Nobel speech). Dr. Hershko had acknowledged a slew of colleagues and highlighted their contributions to the ultimate work. It shows how even small discoveries can contribute to the sphere of scientific knowledge and breakthrough.

Luckily, in the end, perseverance has paid off as Dr. Prasher is now using his talents in Roger Tsien‘s group at the University of California in San Diego.

References:

1. Chalfie, M., Tu, Y., Euskirchen, G., Ward, W.W., Prasher, D.C., Green fluorescent protein as a marker for gene expression. Science, 263(5148), 802-805 (1994).

 

2. Heim, R., Prasher, D.C., Tsien, R.Y., Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA, 91(26), 12501-12504 (1994).

More posts on this site on Heroes in Medical Research series include:

Heroes in Medical Research: Developing Models for Cancer Research

Heroes in Medical Research: Dr. Carmine Paul Bianchi Pharmacologist, Leader, and Mentor

Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

 

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Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson

Life-cycle of Science 2

 

 

 

 

 

 

 

 

 

 

 

Curators and Writer: Stephen J. Williams, Ph.D. with input from Curators Larry H. Bernstein, MD, FCAP, Dr. Justin D. Pearlman, MD, PhD, FACC and Dr. Aviva Lev-Ari, PhD, RN

(this discussion is in a three part series including:

Using Scientific Content Curation as a Method for Validation and Biocuration

Using Scientific Content Curation as a Method for Open Innovation)

 

Every month I get my Wired Magazine (yes in hard print, I still like to turn pages manually plus I don’t mind if I get grease or wing sauce on my magazine rather than on my e-reader) but I always love reading articles written by Clive Thompson. He has a certain flair for understanding the techno world we live in and the human/technology interaction, writing about interesting ways in which we almost inadvertently integrate new technologies into our day-to-day living, generating new entrepreneurship, new value.   He also writes extensively about tech and entrepreneurship.

October 2013 Wired article by Clive Thompson, entitled “How Successful Networks Nurture Good Ideas: Thinking Out Loud”, describes how the voluminous writings, postings, tweets, and sharing on social media is fostering connections between people and ideas which, previously, had not existed. The article was generated from Clive Thompson’s book Smarter Than you Think: How Technology is Changing Our Minds for the Better.Tom Peters also commented about the article in his blog (see here).

Clive gives a wonderful example of Ory Okolloh, a young Kenyan-born law student who, after becoming frustrated with the lack of coverage of problems back home, started a blog about Kenyan politics. Her blog not only got interest from movie producers who were documenting female bloggers but also gained the interest of fellow Kenyans who, during the upheaval after the 2007 Kenyan elections, helped Ory to develop a Google map for reporting of violence (http://www.ushahidi.com/, which eventually became a global organization using open-source technology to affect crises-management. There are a multitude of examples how networks and the conversations within these circles are fostering new ideas. As Clive states in the article:

 

Our ideas are PRODUCTS OF OUR ENVIRONMENT.

They are influenced by the conversations around us.

However the article got me thinking of how Science 2.0 and the internet is changing how scientists contribute, share, and make connections to produce new and transformative ideas.

But HOW MUCH Knowledge is OUT THERE?

 

Clive’s article listed some amazing facts about the mountains of posts, tweets, words etc. out on the internet EVERY DAY, all of which exemplifies the problem:

  • 154.6 billion EMAILS per DAY
  • 400 million TWEETS per DAY
  • 1 million BLOG POSTS (including this one) per DAY
  • 2 million COMMENTS on WordPress per DAY
  • 16 million WORDS on Facebook per DAY
  • TOTAL 52 TRILLION WORDS per DAY

As he estimates this would be 520 million books per DAY (book with average 100,000 words).

A LOT of INFO. But as he suggests it is not the volume but how we create and share this information which is critical as the science fiction writer Theodore Sturgeon noted “Ninety percent of everything is crap” AKA Sturgeon’s Law.

 

Internet live stats show how congested the internet is each day (http://www.internetlivestats.com/). Needless to say Clive’s numbers are a bit off. As of the writing of this article:

 

  • 2.9 billion internet users
  • 981 million websites (only 25,000 hacked today)
  • 128 billion emails
  • 385 million Tweets
  • > 2.7 million BLOG posts today (including this one)

 

The Good, The Bad, and the Ugly of the Scientific Internet (The Wild West?)

 

So how many science blogs are out there? Well back in 2008 “grrlscientist” asked this question and turned up a total of 19,881 blogs however most were “pseudoscience” blogs, not written by Ph.D or MD level scientists. A deeper search on Technorati using the search term “scientist PhD” turned up about 2,000 written by trained scientists.

So granted, there is a lot of

goodbadugly

 

              ….. when it comes to scientific information on the internet!

 

 

 

 

 

I had recently re-posted, on this site, a great example of how bad science and medicine can get propagated throughout the internet:

http://pharmaceuticalintelligence.com/2014/06/17/the-gonzalez-protocol-worse-than-useless-for-pancreatic-cancer/

 

and in a Nature Report:Stem cells: Taking a stand against pseudoscience

http://www.nature.com/news/stem-cells-taking-a-stand-against-pseudoscience-1.15408

Drs.Elena Cattaneo and Gilberto Corbellini document their long, hard fight against false and invalidated medical claims made by some “clinicians” about the utility and medical benefits of certain stem-cell therapies, sacrificing their time to debunk medical pseudoscience.

 

Using Curation and Science 2.0 to build Trusted, Expert Networks of Scientists and Clinicians

 

Establishing networks of trusted colleagues has been a cornerstone of the scientific discourse for centuries. For example, in the mid-1640s, the Royal Society began as:

 

“a meeting of natural philosophers to discuss promoting knowledge of the

natural world through observation and experiment”, i.e. science.

The Society met weekly to witness experiments and discuss what we

would now call scientific topics. The first Curator of Experiments

was Robert Hooke.”

 

– from The History of the Royal Society

 

Royal Society CoatofArms

 

 

 

 

 

 

The Royal Society of London for Improving Natural Knowledge.

(photo credit: Royal Society)

(Although one wonders why they met “in-cognito”)

Indeed as discussed in “Science 2.0/Brainstorming” by the originators of OpenWetWare, an open-source science-notebook software designed to foster open-innovation, the new search and aggregation tools are making it easier to find, contribute, and share information to interested individuals. This paradigm is the basis for the shift from Science 1.0 to Science 2.0. Science 2.0 is attempting to remedy current drawbacks which are hindering rapid and open scientific collaboration and discourse including:

  • Slow time frame of current publishing methods: reviews can take years to fashion leading to outdated material
  • Level of information dissemination is currently one dimensional: peer-review, highly polished work, conferences
  • Current publishing does not encourage open feedback and review
  • Published articles edited for print do not take advantage of new web-based features including tagging, search-engine features, interactive multimedia, no hyperlinks
  • Published data and methodology incomplete
  • Published data not available in formats which can be readably accessible across platforms: gene lists are now mandated to be supplied as files however other data does not have to be supplied in file format

(put in here a brief blurb of summary of problems and why curation could help)

 

Curation in the Sciences: View from Scientific Content Curators Larry H. Bernstein, MD, FCAP, Dr. Justin D. Pearlman, MD, PhD, FACC and Dr. Aviva Lev-Ari, PhD, RN

Curation is an active filtering of the web’s  and peer reviewed literature found by such means – immense amount of relevant and irrelevant content. As a result content may be disruptive. However, in doing good curation, one does more than simply assign value by presentation of creative work in any category. Great curators comment and share experience across content, authors and themes. Great curators may see patterns others don’t, or may challenge or debate complex and apparently conflicting points of view.  Answers to specifically focused questions comes from the hard work of many in laboratory settings creatively establishing answers to definitive questions, each a part of the larger knowledge-base of reference. There are those rare “Einstein’s” who imagine a whole universe, unlike the three blind men of the Sufi tale.  One held the tail, the other the trunk, the other the ear, and they all said this is an elephant!
In my reading, I learn that the optimal ratio of curation to creation may be as high as 90% curation to 10% creation. Creating content is expensive. Curation, by comparison, is much less expensive.

– Larry H. Bernstein, MD, FCAP

Curation is Uniquely Distinguished by the Historical Exploratory Ties that Bind –Larry H. Bernstein, MD, FCAP

The explosion of information by numerous media, hardcopy and electronic, written and video, has created difficulties tracking topics and tying together relevant but separated discoveries, ideas, and potential applications. Some methods to help assimilate diverse sources of knowledge include a content expert preparing a textbook summary, a panel of experts leading a discussion or think tank, and conventions moderating presentations by researchers. Each of those methods has value and an audience, but they also have limitations, particularly with respect to timeliness and pushing the edge. In the electronic data age, there is a need for further innovation, to make synthesis, stimulating associations, synergy and contrasts available to audiences in a more timely and less formal manner. Hence the birth of curation. Key components of curation include expert identification of data, ideas and innovations of interest, expert interpretation of the original research results, integration with context, digesting, highlighting, correlating and presenting in novel light.

– Justin D Pearlman, MD, PhD, FACC from The Voice of Content Consultant on The  Methodology of Curation in Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

 

In Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison, Drs. Larry Bernstein and Aviva Lev-Ari likens the medical and scientific curation process to curation of musical works into a thematic program:

 

Work of Original Music Curation and Performance:

 

Music Review and Critique as a Curation

Work of Original Expression what is the methodology of Curation in the context of Medical Research Findings Exposition of Synthesis and Interpretation of the significance of the results to Clinical Care

… leading to new, curated, and collaborative works by networks of experts to generate (in this case) ebooks on most significant trends and interpretations of scientific knowledge as relates to medical practice.

 

In Summary: How Scientific Content Curation Can Help

 

Given the aforementioned problems of:

        I.            the complex and rapid deluge of scientific information

      II.            the need for a collaborative, open environment to produce transformative innovation

    III.            need for alternative ways to disseminate scientific findings

CURATION MAY OFFER SOLUTIONS

        I.            Curation exists beyond the review: curation decreases time for assessment of current trends adding multiple insights, analyses WITH an underlying METHODOLOGY (discussed below) while NOT acting as mere reiteration, regurgitation

 

      II.            Curation providing insights from WHOLE scientific community on multiple WEB 2.0 platforms

 

    III.            Curation makes use of new computational and Web-based tools to provide interoperability of data, reporting of findings (shown in Examples below)

 

Therefore a discussion is given on methodologies, definitions of best practices, and tools developed to assist the content curation community in this endeavor.

Methodology in Scientific Content Curation as Envisioned by Aviva lev-Ari, PhD, RN

 

At Leaders in Pharmaceutical Business Intelligence, site owner and chief editor Aviva lev-Ari, PhD, RN has been developing a strategy “for the facilitation of Global access to Biomedical knowledge rather than the access to sheer search results on Scientific subject matters in the Life Sciences and Medicine”. According to Aviva, “for the methodology to attain this complex goal it is to be dealing with popularization of ORIGINAL Scientific Research via Content Curation of Scientific Research Results by Experts, Authors, Writers using the critical thinking process of expert interpretation of the original research results.” The following post:

Cardiovascular Original Research: Cases in Methodology Design for Content Curation and Co-Curation

 

http://pharmaceuticalintelligence.com/2013/07/29/cardiovascular-original-research-cases-in-methodology-design-for-content-curation-and-co-curation/

demonstrate two examples how content co-curation attempts to achieve this aim and develop networks of scientist and clinician curators to aid in the active discussion of scientific and medical findings, and use scientific content curation as a means for critique offering a “new architecture for knowledge”. Indeed, popular search engines such as Google, Yahoo, or even scientific search engines such as NCBI’s PubMed and the OVID search engine rely on keywords and Boolean algorithms …

which has created a need for more context-driven scientific search and discourse.

In Science and Curation: the New Practice of Web 2.0, Célya Gruson-Daniel (@HackYourPhd) states:

To address this need, human intermediaries, empowered by the participatory wave of web 2.0, naturally started narrowing down the information and providing an angle of analysis and some context. They are bloggers, regular Internet users or community managers – a new type of profession dedicated to the web 2.0. A new use of the web has emerged, through which the information, once produced, is collectively spread and filtered by Internet users who create hierarchies of information.

.. where Célya considers curation an essential practice to manage open science and this new style of research.

As mentioned above in her article, Dr. Lev-Ari represents two examples of how content curation expanded thought, discussion, and eventually new ideas.

  1. Curator edifies content through analytic process = NEW form of writing and organizations leading to new interconnections of ideas = NEW INSIGHTS

i)        Evidence: curation methodology leading to new insights for biomarkers

 

  1. Same as #1 but multiple players (experts) each bringing unique insights, perspectives, skills yielding new research = NEW LINE of CRITICAL THINKING

ii)      Evidence: co-curation methodology among cardiovascular experts leading to cardiovascular series ebooks

Life-cycle of Science 2

The Life Cycle of Science 2.0. Due to Web 2.0, new paradigms of scientific collaboration are rapidly emerging.  Originally, scientific discovery were performed by individual laboratories or “scientific silos” where the main method of communication was peer-reviewed publication, meeting presentation, and ultimately news outlets and multimedia. In this digital era, data was organized for literature search and biocurated databases. In an era of social media, Web 2.0, a group of scientifically and medically trained “curators” organize the piles of data of digitally generated data and fit data into an organizational structure which can be shared, communicated, and analyzed in a holistic approach, launching new ideas due to changes in organization structure of data and data analytics.

 

The result, in this case, is a collaborative written work above the scope of the review. Currently review articles are written by experts in the field and summarize the state of a research are. However, using collaborative, trusted networks of experts, the result is a real-time synopsis and analysis of the field with the goal in mind to

INCREASE THE SCIENTIFIC CURRENCY.

For detailed description of methodology please see Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

 

In her paper, Curating e-Science Data, Maureen Pennock, from The British Library, emphasized the importance of using a diligent, validated, and reproducible, and cost-effective methodology for curation by e-science communities over the ‘Grid’:

“The digital data deluge will have profound repercussions for the infrastructure of research and beyond. Data from a wide variety of new and existing sources will need to be annotated with metadata, then archived and curated so that both the data and the programmes used to transform the data can be reproduced for use in the future. The data represent a new foundation for new research, science, knowledge and discovery”

— JISC Senior Management Briefing Paper, The Data Deluge (2004)

 

As she states proper data and content curation is important for:

  • Post-analysis
  • Data and research result reuse for new research
  • Validation
  • Preservation of data in newer formats to prolong life-cycle of research results

However she laments the lack of

  • Funding for such efforts
  • Training
  • Organizational support
  • Monitoring
  • Established procedures

 

Tatiana Aders wrote a nice article based on an interview with Microsoft’s Robert Scoble, where he emphasized the need for curation in a world where “Twitter is the replacement of the Associated Press Wire Machine” and new technologic platforms are knocking out old platforms at a rapid pace. In addition he notes that curation is also a social art form where primary concerns are to understand an audience and a niche.

Indeed, part of the reason the need for curation is unmet, as writes Mark Carrigan, is the lack of appreciation by academics of the utility of tools such as Pinterest, Storify, and Pearl Trees to effectively communicate and build collaborative networks.

And teacher Nancy White, in her article Understanding Content Curation on her blog Innovations in Education, shows examples of how curation in an educational tool for students and teachers by demonstrating students need to CONTEXTUALIZE what the collect to add enhanced value, using higher mental processes such as:

  • Knowledge
  • Comprehension
  • Application
  • Analysis
  • Synthesis
  • Evaluation

curating-tableA GREAT table about the differences between Collecting and Curating by Nancy White at http://d20innovation.d20blogs.org/2012/07/07/understanding-content-curation/

 

 

 

 

 

 

 

 

 

 

 

University of Massachusetts Medical School has aggregated some useful curation tools at http://esciencelibrary.umassmed.edu/data_curation

Although many tools are related to biocuration and building databases but the common idea is curating data with indexing, analyses, and contextual value to provide for an audience to generate NETWORKS OF NEW IDEAS.

See here for a curation of how networks fosters knowledge, by Erika Harrison on ScoopIt

(http://www.scoop.it/t/mobilizing-knowledge-through-complex-networks)

 

“Nowadays, any organization should employ network scientists/analysts who are able to map and analyze complex systems that are of importance to the organization (e.g. the organization itself, its activities, a country’s economic activities, transportation networks, research networks).”

– Andrea Carafa insight from World Economic Forum New Champions 2012 “Power of Networks”

 

Creating Content Curation Communities: Breaking Down the Silos!

 

An article by Dr. Dana Rotman “Facilitating Scientific Collaborations Through Content Curation Communities” highlights how scientific information resources, traditionally created and maintained by paid professionals, are being crowdsourced to professionals and nonprofessionals in which she termed “content curation communities”, consisting of professionals and nonprofessional volunteers who create, curate, and maintain the various scientific database tools we use such as Encyclopedia of Life, ChemSpider (for Slideshare see here), biowikipedia etc. Although very useful and openly available, these projects create their own challenges such as

  • information integration (various types of data and formats)
  • social integration (marginalized by scientific communities, no funding, no recognition)

The authors set forth some ways to overcome these challenges of the content curation community including:

  1. standardization in practices
  2. visualization to document contributions
  3. emphasizing role of information professionals in content curation communities
  4. maintaining quality control to increase respectability
  5. recognizing participation to professional communities
  6. proposing funding/national meeting – Data Intensive Collaboration in Science and Engineering Workshop

A few great presentations and papers from the 2012 DICOSE meeting are found below

Judith M. Brown, Robert Biddle, Stevenson Gossage, Jeff Wilson & Steven Greenspan. Collaboratively Analyzing Large Data Sets using Multitouch Surfaces. (PDF) NotesForBrown

 

Bill Howe, Cecilia Aragon, David Beck, Jeffrey P. Gardner, Ed Lazowska, Tanya McEwen. Supporting Data-Intensive Collaboration via Campus eScience Centers. (PDF) NotesForHowe

 

Kerk F. Kee & Larry D. Browning. Challenges of Scientist-Developers and Adopters of Existing Cyberinfrastructure Tools for Data-Intensive Collaboration, Computational Simulation, and Interdisciplinary Projects in Early e-Science in the U.S.. (PDF) NotesForKee

 

Ben Li. The mirages of big data. (PDF) NotesForLiReflectionsByBen

 

Betsy Rolland & Charlotte P. Lee. Post-Doctoral Researchers’ Use of Preexisting Data in Cancer Epidemiology Research. (PDF) NoteForRolland

 

Dana Rotman, Jennifer Preece, Derek Hansen & Kezia Procita. Facilitating scientific collaboration through content curation communities. (PDF) NotesForRotman

 

Nicholas M. Weber & Karen S. Baker. System Slack in Cyberinfrastructure Development: Mind the Gaps. (PDF) NotesForWeber

Indeed, the movement of Science 2.0 from Science 1.0 had originated because these “silos” had frustrated many scientists, resulting in changes in the area of publishing (Open Access) but also communication of protocols (online protocol sites and notebooks like OpenWetWare and BioProtocols Online) and data and material registries (CGAP and tumor banks). Some examples are given below.

Open Science Case Studies in Curation

1. Open Science Project from Digital Curation Center

This project looked at what motivates researchers to work in an open manner with regard to their data, results and protocols, and whether advantages are delivered by working in this way.

The case studies consider the benefits and barriers to using ‘open science’ methods, and were carried out between November 2009 and April 2010 and published in the report Open to All? Case studies of openness in research. The Appendices to the main report (pdf) include a literature review, a framework for characterizing openness, a list of examples, and the interview schedule and topics. Some of the case study participants kindly agreed to us publishing the transcripts. This zip archive contains transcripts of interviews with researchers in astronomy, bioinformatics, chemistry, and language technology.

 

see: Pennock, M. (2006). “Curating e-Science Data”. DCC Briefing Papers: Introduction to Curation. Edinburgh: Digital Curation Centre. Handle: 1842/3330. Available online: http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation– See more at: http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation/curating-e-science-data#sthash.RdkPNi9F.dpuf

 

2.      cBIO -cBio’s biological data curation group developed and operates using a methodology called CIMS, the Curation Information Management System. CIMS is a comprehensive curation and quality control process that efficiently extracts information from publications.

 

3. NIH Topic Maps – This website provides a database and web-based interface for searching and discovering the types of research awarded by the NIH. The database uses automated, computer generated categories from a statistical analysis known as topic modeling.

 

4. SciKnowMine (USC)- We propose to create a framework to support biocuration called SciKnowMine (after ‘Scientific Knowledge Mine’), cyberinfrastructure that supports biocuration through the automated mining of text, images, and other amenable media at the scale of the entire literature.

 

  1. OpenWetWare– OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. Learn more about us.   If you would like edit access, would be interested in helping out, or want your lab website hosted on OpenWetWare, pleasejoin us. OpenWetWare is managed by the BioBricks Foundation. They also have a wiki about Science 2.0.

6. LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory. Authors in PLOS One article, from University of Southampton, report the development of an open, scientific lab notebook using a blogging strategy to share information.

7. OpenScience Project– The OpenScience project is dedicated to writing and releasing free and Open Source scientific software. We are a group of scientists, mathematicians and engineers who want to encourage a collaborative environment in which science can be pursued by anyone who is inspired to discover something new about the natural world.

8. Open Science Grid is a multi-disciplinary partnership to federate local, regional, community and national cyberinfrastructures to meet the needs of research and academic communities at all scales.

 

9. Some ongoing biomedical knowledge (curation) projects at ISI

IICurate
This project is concerned with developing a curation and documentation system for information integration in collaboration with the II Group at ISI as part of the BIRN.

BioScholar
It’s primary purpose is to provide software for experimental biomedical scientists that would permit a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. This project is funded by NIGMS from 2008-2012 ( RO1-GM083871).

10. Tools useful for scientific content curation

 

Research Analytic and Curation Tools from University of Queensland

 

Thomson Reuters information curation services for pharma industry

 

Microblogs as a way to communicate information about HPV infection among clinicians and patients; use of Chinese microblog SinaWeibo as a communication tool

 

VIVO for scientific communities– In order to connect this information about research activities across institutions and make it available to others, taking into account smaller players in the research landscape and addressing their need for specific information (for example, by proving non-conventional research objects), the open source software VIVO that provides research information as linked open data (LOD) is used in many countries.  So-called VIVO harvesters collect research information that is freely available on the web, and convert the data collected in conformity with LOD standards. The VIVO ontology builds on prevalent LOD namespaces and, depending on the needs of the specialist community concerned, can be expanded.

 

 

11. Examples of scientific curation in different areas of Science/Pharma/Biotech/Education

 

From Science 2.0 to Pharma 3.0 Q&A with Hervé Basset

http://digimind.com/blog/experts/pharma-3-0/

Hervé Basset, specialist librarian in the pharmaceutical industry and owner of the blog “Science Intelligence“, to talk about the inspiration behind his recent book  entitled “From Science 2.0 to Pharma 3.0″, published by Chandos Publishing and available on Amazon and how health care companies need a social media strategy to communicate and convince the health-care consumer, not just the practicioner.

 

Thomson Reuters and NuMedii Launch Ground-Breaking Initiative to Identify Drugs for Repurposing. Companies leverage content, Big Data analytics and expertise to improve success of drug discovery

 

Content Curation as a Context for Teaching and Learning in Science

 

#OZeLIVE Feb2014

http://www.youtube.com/watch?v=Ty-ugUA4az0

Creative Commons license

 

DigCCur: A graduate level program initiated by University of North Carolina to instruct the future digital curators in science and other subjects

 

Syracuse University offering a program in eScience and digital curation

 

Curation Tips from TED talks and tech experts

Steven Rosenbaum from Curation Nation

http://www.youtube.com/watch?v=HpncJd1v1k4

 

Pawan Deshpande form Curata on how content curation communities evolve and what makes a good content curation:

http://www.youtube.com/watch?v=QENhIU9YZyA

 

How the Internet of Things is Promoting the Curation Effort

Update by Stephen J. Williams, PhD 3/01/19

Up till now, curation efforts like wikis (Wikipedia, Wikimedicine, Wormbase, GenBank, etc.) have been supported by a largely voluntary army of citizens, scientists, and data enthusiasts.  I am sure all have seen the requests for donations to help keep Wikipedia and its other related projects up and running.  One of the obscure sister projects of Wikipedia, Wikidata, wants to curate and represent all information in such a way in which both machines, computers, and humans can converse in.  About an army of 4 million have Wiki entries and maintain these databases.

Enter the Age of the Personal Digital Assistants (Hellooo Alexa!)

In a March 2019 WIRED article “Encyclopedia Automata: Where Alexa Gets Its Information”  senior WIRED writer Tom Simonite reports on the need for new types of data structure as well as how curated databases are so important for the new fields of AI as well as enabling personal digital assistants like Alexa or Google Assistant decipher meaning of the user.

As Mr. Simonite noted, many of our libraries of knowledge are encoded in an “ancient technology largely opaque to machines-prose.”   Search engines like Google do not have a problem with a question asked in prose as they just have to find relevant links to pages. Yet this is a problem for Google Assistant, for instance, as machines can’t quickly extract meaning from the internet’s mess of “predicates, complements, sentences, and paragraphs. It requires a guide.”

Enter Wikidata.  According to founder Denny Vrandecic,

Language depends on knowing a lot of common sense, which computers don’t have access to

A wikidata entry (of which there are about 60 million) codes every concept and item with a numeric code, the QID code number. These codes are integrated with tags (like tags you use on Twitter as handles or tags in WordPress used for Search Engine Optimization) so computers can identify patterns of recognition between these codes.

Now human entry into these databases are critical as we add new facts and in particular meaning to each of these items.  Else, machines have problems deciphering our meaning like Apple’s Siri, where they had complained of dumb algorithms to interpret requests.

The knowledge of future machines could be shaped by you and me, not just tech companies and PhDs.

But this effort needs money

Wikimedia’s executive director, Katherine Maher, had prodded and cajoled these megacorporations for tapping the free resources of Wiki’s.  In response, Amazon and Facebook had donated millions for the Wikimedia projects.  Google recently gave 3.1 million USD$ in donations.

 

Future postings on the relevance and application of scientific curation will include:

Using Scientific Content Curation as a Method for Validation and Biocuration

 

Using Scientific Content Curation as a Method for Open Innovation

 

Other posts on this site related to Content Curation and Methodology include:

The growing importance of content curation

Data Curation is for Big Data what Data Integration is for Small Data

6 Steps to More Effective Content Curation

Stem Cells and Cardiac Repair: Content Curation & Scientific Reporting

Cancer Research: Curations and Reporting

Cardiovascular Diseases and Pharmacological Therapy: Curations

Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

Exploring the Impact of Content Curation on Business Goals in 2013

Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison

conceived: NEW Definition for Co-Curation in Medical Research

The Young Surgeon and The Retired Pathologist: On Science, Medicine and HealthCare Policy – The Best Writers Among the WRITERS

Reconstructed Science Communication for Open Access Online Scientific Curation

 

 

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Physicians’ View of Supreme Court on an Issue of Public Health

Curator: Larry H. Bernstein, MD, FCAP

  • Where has the reason gone?

http://pharmaceuticalintelligence.com/2014/07/07/where-has-reason-gone-2/

  • Justice Ginsberg written dissent – Third Part

http://pharmaceuticalintelligence.com/2014/07/08/justice-ginsberg-written-dissent/

  • The physicians’ view of Supreme Court on an issue of public health

http://pharmaceuticalintelligence.com/2014/07/08/the-physicians-view-of-supreme-court-on-an-issue-of-public-health/

  •  Reason in Hobby Lobby

http://pharmaceuticalintelligence.com/2014/07/08/reason-in-hobby-lobby/

 

Physicians’ View of Supreme Court on an Issue of Public Health

The physicians are under considerable stress.  They have a minimum of 8 years of post graduate university education to practice as a generalist or  in a medical, pediatric, gynecological or surgical related specialty.  A significant loss is incurred in the cost of loans for education to many. A significant sacrifice is made in time for family.  A primary obligation is incurred toward the wellbeing of the patient, and the community that has to be respected and protected by civil law.

 

Supreme Court Issues Hobby Lobby Decision

By Joyce Frieden, News Editor, MedPage Today  Published: Jun 30, 2014

The Supreme Court has struck down the Affordable Care Act requirement that employers must include no-cost contraceptive coverage in employee health insurance plans. The 5-4 decision decision issued today in the Hobby Lobby case (Burwell v. Hobby Lobby Stores, Inc.) follows conflicting appellate court rulings in cases involving businesses that objected to the ACA’s birth control requirement on religious grounds. The businesses said the ACA stepped on their religious freedoms.

The 2010 health law mandates that all health plans provide preventive services — including birth control — free of cost-sharing. But some corporations — most notably arts-and-crafts giant Hobby Lobby and its sister company Mardel, a Christian bookstore chain — sued the Department of Health and Human Services to be exempted from having to comply with the mandate. In its 5-4 decision, written by Justice Samuel Alito, the Court ruled that the mandate violates the Religious Freedom Restoration Act of 1993, “which prohibits the ‘Government [from] substantially burden[ing] a person’s exercise of religion’” unless it shows that doing so is “in furtherance of a compelling governmental interest” and “is the least restrictive means” of doing do. The decision summary also notes that the Department of Health and Human Serivces (HHS) “argues that the companies cannot sue because they are for-profit corporations, and that the owners cannot sue because the regulations apply only to the companies, but that would leave merchants with a difficult choice:

  • give up the right to seek judicial protection of their religious liberty or forgo the benefits of operating as corporations.

RFRA’s text shows that Congress designed the statute to provide very broad protection for religious liberty and did not intend to put merchants to such a choice.” Donna Harrison, MD, executive director of the American Association of Pro-Life Obstetricians & Gynecologists (AAPLOG), noted that Hobby Lobby was in particular objecting to very specific contraceptives — the emergency contraceptive Ella and intrauterine devices, which she noted are capable of killing embryos, either by preventing their implantation or killing them after they have been implanted.

Art Caplan, PhD, director of the medical ethics division at the NYU Langone Medical Center in New York City, oberved “decision could have a very negative impact” on women’s ability to obtain contraception,  and “it could affect many women even if only a small percentage of companies followed suit.” “The other problem,” he told MedPage Today in a video interview, “is that if your employer says ‘I’m not covering contraception,’ you may decide to go with methods that don’t involve pharmaceutical control, or you may rely on something like emergency contraception” — decisions that could lead to more abortions, which would be

  • an ironic outcome since many employers’ objections to contraception revolve around their objections to abortion.

Harrison, of AAPLOG, noted that the decision should be reassuring to physicians who object to prescribing particular forms of contraception that they see as abortifacients, since insurers may have been considering excluding such doctors from their provider networks if the mandate had been upheld. “This will help incentivize insurers to not exclude ‘conscientious doctors’ from their networks,” she said.

More Physician Groups Weigh In

Many of the other physician groups issuing statements today expressed disappointment in the ruling.

“Allowing for-profit employers to exclude coverage for contraception is itself deeply concerning because of the demonstrated adverse impact it will have on women’s health,” David Fleming, MD, president of the American College of Physicians, said in a statement. “And, “the ruling clearly does not preclude for-profit employers from challenging such mandates (vaccinations), or the courts from granting further coverage exemptions.”

Rebecca Sokol, MD, president of the American Society for Reproductive Medicine in Washington, said in a statement that her organization “profoundly disagrees” with the decision. “Allowing an employer to impose their beliefs about reproduction on their staff is simply wrong, particularly when those beliefs are

  • so clearly misinformed on the scientific and medical facts,” Sokol said.

“In no other field of medicine do we allow employers to substitute their judgment for that of patients and physicians; it should not be allowed just because the subject matter is reproduction.”

Between Women and Their Physicians

Lin-Fan Wang, MD, reproductive health advocacy fellow at Physicians for Reproductive Health in New York City, said in a video interview that

  • “decisions about contraception should really be made between a woman and her doctor, and not by her employer.”

Wang recounted the story of one of her own patients, a woman who had recently had a baby and then went back to work, and was having trouble remembering to take her birth control pills. “She chose one of the intrauterine devices … because it was one of the most effective forms of contraception and she didn’t have to think about it every day,” she said. “Luckily her insurance plan covered the cost of this very expensive form of contraception, but

  • under the ruling today, patients like [her] might not be able to choose that method

and she may end up having to choose a method that is hard for her to take or she’s not happy with.” Reproductive rights groups also expressed their concerns. Bebe Anderson, JD, director of the U.S. Legal Program at the Center for Reproductive Rights in New York City, called the decision “an affront to women of this country.”

“As Justice [Ruth Bader] Ginsburg recognized in her dissent, this decision makes it very difficult for women to get some of the best long-acting reversible forms of contraception,” Anderson told MedPage Today in a video interview. “For example, IUDs are as expensive as 1 month’s pay for someone working at minimum wage.”

Cecile Richards, president of the Planned Parenthood Action Fund, called the ruling “stunning.” On a call with reporters she said it was no coincidence that the majority opinion was decided by five male justices. “It is endlessly frustrating for women that decisions about their healthcare are being made by people who never need to use birth control, and it is no coincidence that all three women on the court signed today’s dissent,” Richards said. On the same call, Marcia Greenberger, co-president of the National Women’s Law Center, said the decision was “a bitter pill for women to swallow …These [plaintiffs] and other closely held companies

  • will now have license to harm their female employees in the name of the company’s religion, and
  • ignore the moral and practical considerations of women themselves.”

Other Implications

Several commenters noted that, although the majority opinion specifically states that this ruling does not apply to religious objections to other healthcare benefits such as vaccinations and blood transfusions, this opens up the way for plaintiffs to sue about those as well. “Regardless of what they said, they’ve opened Pandora’s box and set a precedent,” said Ilyse Hogue, president of NARAL Pro-Choice America. The Tenth Circuit Court of Appeals in Denver ruled in June 2013 that

  • Hobby Lobby should be given the opportunity to show its religious beliefs would be violated by either complying with the law or being forced to pay large fines.

Hobby Lobby faced penalties amounting to $1.3 million a day starting in the summer of 2013 if it didn’t provide FDA-approved contraceptive methods in its self-insured health plans, which cover 13,000 employees. But a court issued an injunction in July that prevented the penalty from taking effect.

A rule from HHS finalized last summer exempted churches and other nonprofit religious organizations that object to contraceptive coverage. But private businesses such as Hobby Lobby weren’t exempt. UPDATE: This article, originally published on June 30 at 10:18 EDT, was updated with new material at 19:12 EDT.  

When Religious Freedom Clashes with Access to Care

Glenn Cohen, J.D., Holly Fernandez Lynch, J.D., M.Bioethics, and Gregory D. Curfman, M.D.

July 2, 2014 DOI: 10.1056/NEJMp1407965

At the tail end of this year’s Supreme Court term, religious freedom came into sharp conflict with the government’s interest in providing affordable access to health care. In a consolidated opinion inBurwell v. Hobby Lobby Stores and Conestoga Wood Specialties Corp. v. Burwell (collectively known as Hobby Lobby) delivered on June 30, the Court sided with religious freedom, highlighting the limitations of our employment-based health insurance system.

Hobby Lobby centered on the contraceptives-coverage mandate, which derived from the Affordable Care Act (ACA) mandate that many employers offer insurance coverage of certain “essential” health benefits, including coverage of “preventive” services without patient copayments or deductibles. The ACA authorized the Department of Health and Human Services (HHS) to define the scope of those preventive services, a task it delegated to the Institute of Medicine, whose list included all 20 contraceptive agents approved by the Food and Drug Administration. HHS articulated various justifications for the resulting mandate, including the fact that many Americans have difficulty affording contraceptives despite their widespread use and

  • the goal of avoiding a disproportionate financial burden on women.

Under the regulation, churches are exempt from covering contraception for their employees, and nonprofit religious organizations may apply for an “accommodation,” which shifts to their insurance companies (or other third parties) the responsibility for providing free access. However,

  • HHS made no exception for for-profit, secular businesses with religious owners.

Hobby Lobby, a craft-store chain with more than 13,000 employees, is a closely held, for-profit corporation owned by a Protestant family that operates the business in accordance with its Christian principles — for example, donating a portion of proceeds to Christian missions and remaining closed on Sundays. The family does not object to providing coverage for some contraceptives, but

  • it challenged the mandate because it includes contraceptive methods that the family believes cause abortion by preventing implantation of a fertilized egg.

The challenge in Hobby Lobby was not about the Constitution or its First Amendment. Rather, it hinged on the Religious Freedom Restoration Act of 1993 (RFRA), which was Congress’s response to a Supreme Court decision holding that

  1. even if a law in fact burdened religion, it could stand as long as it was not intended to burden religion (was “neutral”),
  2. applied without regard to religious beliefs or practices (was “generally applicable”), and
  3. was rationally related to a legitimate government interest — a low bar.

RFRA applies when a federal law is deemed to “substantially” burden a person’s exercise of religion, even if it is neutral and generally applicable. Such laws may be enforced against religious objectors only when they further a compelling government interest using the least restrictive means available. This is the most demanding standard of judicial review, and few laws meet its requirements. In a 5-to-4 decision the Court found that the contraceptives-coverage mandate did not.

In its RFRA analysis, the Court had to address several key questions:

  1. Are closely held, for-profit corporations “persons” for the purposes of RFRA protection?
  2. Can corporations exercise religion?
  3. Does the contraceptives-coverage mandate substantially burden religion?
  4. Does the mandate advance a compelling government interest? And
  5. are there less restrictive alternatives that would achieve the same result?

In a ruling in which Justice Samuel Alito wrote for the majority (joined by Chief Justice John Roberts and Justices Antonin Scalia, Anthony Kennedy, and Clarence Thomas), the mandate came up short. The majority concluded that RFRA was intended to protect even for-profit corporations and that

  • corporations may exercise religion,
  • rejecting as unreasonable any definition of “person” that would include some but not all corporations.

The majority also concluded that the mandate did place a substantial burden on the companies’ religious beliefs, given the dramatic financial consequences of noncompliance (for example, Hobby Lobby would have faced a fine of $475 million per year) and

  • the fact that the government had extended other exemptions and accommodations in recognition of that burden.

The majority assumed that the government has a compelling interest in promoting free access to contraceptive agents, but it held that

  • the government had failed to advance that interest in the least restrictive way, given
  • the possibility of extending its existing exemptions and accommodations to for-profit corporations

Thus, the Court held that as applied to closely held, for-profit corporations with religious objections, the mandate violates RFRA. It was careful, however, to restrict the decision to the case before it, refraining from opining on the implications for other types of employers or objections to other health care services, which it cautioned must be addressed on a case-by-case basis. Nonetheless, the case may have broad practical impact, since

  • approximately 90% of all U.S. companies are closely held, and
  • “closely held” is not synonymous with “small.”

Justice Ruth Bader Ginsburg issued a sharp dissent, in which she was joined by Justice Sonia Sotomayor and in large part by Justices Elena Kagan and Stephen Breyer. Delivering her opinion from the bench, Justice Ginsburg underscored the burden that the majority decision would allow to be placed on women in favor of religious objectors:

“Today’s potentially sweeping decision . . . discounts the disadvantages religion-based opt outs impose on others, in particular, employees who do not share their employer’s religious beliefs.”

Hobby Lobby‘s outcome is of concern to U.S. health care professionals because

  • our health insurance system is still largely dependent on employers.
  • Employers and employees may have fundamentally different perspectives on which medical interventions are acceptable,
  • particularly when the employer’s fundamental mission is not to advance specific religious beliefs and
    • its employees are therefore unlikely to be drawn exclusively from its own religious group.

The Court’s decision allows the beliefs of employers of various sizes and corporate forms to trump the beliefs and needs of their employees, potentially influencing the types of care that will be affordable and accessible to individuals and permitting employers to intrude on clinician–patient relationships.

The case also has important implications for efforts to achieve compromise between religious freedom and health care access. The Obama administration’s attempts to compromise on the contraceptives-coverage mandate ultimately backfired, since its efforts were used to demonstrate that

  • applying the mandate even to secular employers was not necessarily the only way to achieve the government’s interests.

In the future, regulators may be less willing to seek compromise lest their efforts be similarly used against them — and it is bad news for all of us if health policy can be made only through polarization and rancor rather than compromise. On the other hand, in other contraceptives-mandate cases working their way through the courts, nonprofit religious employers argue that the government’s accommodations do not go far enough in protecting their religious freedom, essentially requiring them to deputize a third party to commit what they think is a sin on their behalf.

Finally, in the wake of Hobby Lobby, we may anticipate challenges to other medical services that some religions find objectionable, such as vaccinations, infertility treatments, blood transfusions, certain psychiatric treatments, and even hospice care. Hobby Lobby‘s implications may also extend into civil rights law, with employers asking to “opt out” of laws intended to protect people from employment and housing discrimination based on religion, race, sex, national origin, or pregnancy status. Although the majority deemed these slippery-slope concerns unrealistic, the dissent expressed serious concerns.

Though the decision applies only to closely held, for-profit corporations, it sets a precedent for religious exemptions that could have sweeping implications — and reflects the Supreme Court’s great potential impact on U.S. health care. Yet the Court was applying Congress’s statute, and

  • Congress could, if it chose, scale back the protection offered to religious objectors — a good reason to share public reactions to the decision with our elected representatives.

BUFFER ZONES, BUBBLE ZONES, AND ABORTION CLINICS — ANOTHER WOMEN’S HEALTH CASE

In 2000, concerned about clashes between antiabortion protesters and women seeking abortions, the Massachusetts legislature established an 18-ft radius around the entrances and driveways of facilities providing abortions and specified that within that area, no person could, without consent, approach within 6 ft of another person (a so-called “bubble zone”) for the purpose of protesting, leafleting, counseling, or education. In 2007, the legislature concluded that law was not effective enough and increased its stringency, imposing a 35-ft fixed buffer zone with few exceptions. The law was challenged on free-speech grounds in a case called McCullen v. Coakley, and on June 26, 2014, the U.S. Supreme Court unanimously struck it down as unconstitutional.

The lead opinion by Chief Justice John Roberts, joined by four other justices, noted that sidewalks and public ways hold a “special position in terms of First Amendment protection because of their historic role as sites for discussion and debate.” Although it was abortion that had motivated the statute, the Court held that the law was content- and viewpoint-neutral: it did not focus on what was said but on where it was said, and it burdened all speech, not merely disfavored speech.

On this point, the four remaining justices disagreed. Nevertheless, the Court held that the statute failed the second part of the relevant constitutional test because it was not “narrowly tailored to serve a significant governmental interest.” In particular, though the Court recognized that the buffer zones furthered the state’s interests in “ensuring public safety” on streets and sidewalks and in “preserving access to adjacent healthcare facilities,” it determined that

  • the law problematically criminalized not only protests,
  • but also sidewalk counseling, which could not be done at a distance of 35 ft.
  • It also found that the buffer zones burdened “substantially more speech than necessary to achieve” the state’s interest

and suggested a plethora of less intrusive means the state could have used instead, some of which are used in other states.

Although the decision deals another blow to abortion rights, that blow is not as substantial as some had feared: the finding that the law was content- and viewpoint-neutral allows for the possibility that Massachusetts and other states could pass similar but narrower laws. Moreover, the Court left open the future of the floating “bubble zone” around women approaching clinics for abortions — the strategy that Massachusetts had used from 2000 to 2007 and one that the Court upheld in a Colorado case in 2000. Several justices, however, indicated a willingness to revisit that decision in future litigation.

See §§2000bb–1(a), (b) (requiring the Government to “demonstrat[e] that application of [a substantial] burden to the person . . . is the least restrictive means of furthering [a] compelling governmental interest” (emphasis added)).

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Prologue to Cancer – e-book Volume One – Where are we in this journey?

Prologue to Cancer – e-book Volume One – Where are we in this journey?

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

Article ID #128: Prologue to Cancer – e-book Volume One – Where are we in this journey? Published on 4/13/2014

WordCloud Image Produced by Adam Tubman

Consulting Reviewer and Contributor:  Jose Eduardo de Salles Roselino, MD

 

LH Bernstein

LH Bernstein

Jose Eduardo de Salles Roselino

LES Roselino

 

 

This is a preface to the fourth in the ebook series of Leaders in Pharmaceutical Intelligence, a collaboration of experienced doctorate medical and pharmaceutical professionals.  The topic is of great current interest, and it entails a significant part of current medical expenditure by a group of neoplastic diseases that may develop at different periods in life, and have come to supercede infections or even eventuate in infectious disease as an end of life event.  The articles presented are a collection of the most up-to-date accounts of the state of a now rapidly emerging field of medical research that has benefitted enormously by progress in immunodiagnostics,  radiodiagnostics, imaging, predictive analytics, genomic and proteomic discovery subsequent to the completion of the Human Genome Project, advances in analytic methods in qPCR, gene sequencing, genome mapping, signaling pathways, exome identification, identification of therapeutic targets in inhibitors, activators, initiators in the progression of cell metabolism, carcinogenesis, cell movement, and metastatic potential.  This story is very complicated because we are engaged in trying to evoke from what we would like to be similar clinical events, dissimilar events in their expression and classification, whether they are within the same or different anatomic class.  Thus, we are faced with constructing an objective evidence-based understanding requiring integration of several disciplinary approaches to see a clear picture.  The failure to do so creates a high risk of failure in biopharmaceutical development.

The chapters that follow cover novel and important research and development in cancer related research, development, diagnostics and treatment, and in balance, present a substantial part of the tumor landscape, with some exceptions.  Will there ever be a unifying concept, as might be hoped for? I certainly can’t see any such prediction on the horizon.  Part of the problem is that disease classification is a human construct to guide us, and so are treatments that have existed and are reexamined for over 2,000 years.  In that time, we have changed, our afflictions have been modified, and our environment has changed with respect to the microorganisms within and around us, viruses, the soil, and radiation exposure, and the impacts of war and starvation, and access to food.  The outline has been given.  Organic and inorganic chemistry combined with physics has given us a new enterprise in biosynthetics that is and will change our world.  But let us keep in mind that this is a human construct, just as drug target development is such a construct, workable with limitations.

What Molecular Biology Gained from Physics

We need greater clarity and completeness in defining the carcinogenetic process.  It is the beginning, but not the end.  But we must first examine the evolution of the scientific structure that leads to our present understanding. This was preceded by the studies of anatomy, physiology, and embryology that had to occur as a first step, which was followed by the researches into bacteriology, fungi, sea urchins and the evolutionary creatures that could be studied having more primary development in scale.  They are still major objects of study, with the expectation that we can derive lessons about comparative mechanisms that have been passed on through the ages and have common features with man.  This became the serious intent of molecular biology, the discipline that turned to find an explanation for genetics, and to carry out controlled experiments modelled on the discipline that already had enormous success in physics, mathematics, and chemistry. In 1900, when Max Planck hypothesized that the frequency of light emitted by the black body depended on the frequency of the oscillator that emitted it, it had important ramifications for chemistry and biology (See Appendix II and Footnote 1, Planck equation, energy and oscillation).  The leading idea is to search below the large-scale observations of classical biology.

The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, provides a starting point, but the construct is undergoing revision in light of emerging novel roles for RNA and signaling pathways.   The term, coined by Warren Weaver (director of Natural Sciences for the Rockefeller Foundation), who observed an emergence of significant change given recent advances in fields such as X-ray crystallography. Molecular biology also plays important role in understanding formations, actions, regulations of various parts of cellswhich can be used efficiently for targeting new drugs, diagnosis of disease, physiology of the Cell. The Nobel Prize in Physiology or Medicine in 1969 was shared by Max Delbrück, Alfred D. Hershey, Salvador E. Luria, whose work with viral replication gave impetus to the field.  Delbruck was a physicist who trained in Copenhagen under Bohr, and specifically committed himself to a rigor in biology, as was in physics.

Dorothy Hodgkin protein crystallography

Dorothy Hodgkin protein crystallography

Rosalind Franlin crystallographer double helix

Rosalind Franlin
crystallographer
double helix

 Max Delbruck         molecular biology

Max Delbruck        
molecular biology

Max Planck

Max Planck Quantum Physics

 

 

 

We then stepped back from classical (descriptive) physiology, with the endless complexity, to molecular biology.  This led us to the genetic code, with a double helix model.  It has recently been found insufficiently explanatory, with the recent construction of triplex and quadruplex models. They have a potential to account for unaccounted for building blocks, such as inosine, and we don’t know whether more than one model holds validity under different conditions .  The other major field of development has been simply unaccounted for in the study of proteomics, especially in protein-protein interactions, and in the energetics of protein conformation, first called to our attention by the work of Jacob, Monod, and Changeux (See Footnote 2).  Proteins are not just rigid structures stamped out by the monotonously simple DNA to RNA to protein concept.  Nothing is ever quite so simple. Just as there are epigenetic events, there are posttranslational events, and yet more.

JPChangeux-150x170

JP Changeux

 

 

 

 

 

 

 

 

The Emergence of Molecular Biology

I now return the discussion to the topic of medicine, the emergence of molecular biology and the need for convergence with biochemistry in the mid-20th century. Jose Eduardo de Salles Roselino recalls “I was previously allowed to make of the conformational energy as made by R Marcus in his Nobel lecture revised (J. of Electroanalytical  Chemistry 438:(1997) p251-259. (See Footnote 1) His description of the energetic coordinates of a landscape of a chemical reaction is only a two-dimensional cut of what in fact is a volcano crater (in three dimensions) (each one varies but the sum of the two is constant. Solvational+vibrational=100% in ordinate) nuclear coordinates in abcissa. In case we could represent it by research methods that allow us to discriminate in one by one degree of different pairs of energy, we would most likely have 360 other similar representations of the same phenomenon. The real representation would take into account all those 360 representations together. In case our methodology was not that fine, for instance it discriminates only differences of minimal 10 degrees in 360 possible, will have 36 partial representations of something that to be perfectly represented will require all 36 being taken together. Can you reconcile it with ATGC?  Yet, when complete genome sequences were presented they were described as though we will know everything about this living being. The most important problems in biology will be viewed by limited vision always and the awareness of this limited is something we should acknowledge and teach it. Therefore, our knowledge is made up of partial representations. If we had the entire genome data for the most intricate biological problems, they are still not amenable to this level of reductionism. But going from general views of signals andsymptoms we could get to the most detailed molecular view and in this case genome provides an anchor.”

“Warburg Effect” describes the preference of glycolysis and lactic acid fermentation rather than oxidative phosphorylation for energy production in cancer cells. Mitochondrial metabolism is an important and necessary component in the functioning and maintenance of the cell, and accumulating evidence suggests that dysfunction of mitochondrial metabolism plays a role in cancer. Progress has demonstrated the mechanisms of the mitochondrial metabolism-to-glycolysis switch in cancer development and how to target this metabolic switch.

 

 

Glycolysis

glycolysis

 

Otto Heinrich Warburg (1883- )

Otto Warburg

435px-Louis_Pasteur,_foto_av_Félix_Nadar_Crisco_edit

Louis Pasteur

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The expression “Pasteur effect” was coined by Warburg when inspired by Pasteur’s findings in yeast cells, when he investigated this metabolic observation (Pasteur effect) in cancer cells. In yeast cells, Pasteur had found that the velocity of sugar used was greatly reduced in presence of oxygen. Not to be confused, in the “Crabtree effect”, the velocity of sugar metabolism was greatly increased, a reversal, when yeast cells were transferred from the aerobic to an anaerobic condition. Thus, the velocity of sugar metabolism of yeast cells was shown to be under metabolic regulatory control in response to change in environmental oxygen conditions in growth. Warburg had to verify whether cancer cells and tissue related normal mammalian cells also have a similar control mechanism. He found that this control was also found in normal cells studied, but was absent in cancer cells. Strikingly, cancer cells continue to have higher anaerobic gycolysis despite the presence of oxygen in their culture media (See Footnote 3).

Taking this a step further, food is digested and supplied to cells In vertebrates mainly in the form of glucose, which is metabolized producing Adenosine Triphosphate (ATP) by two pathways. Glycolysis, occurs via anaerobic metabolism in the cytoplasm, and is of major significance for making ATP quickly, but in a minuscule amount (2 molecules).  In the presence of oxygen, the breakdown process continues in the mitochondria via the Krebs’s cycle coupled with oxidative phosphorylation, which is more efficient for ATP production (36 molecules). Cancer cells seem to depend on glycolysis. In the 1920s, Otto Warburg first proposed that cancer cells show increased levels of glucose consumption and lactate fermentation even in the presence of ample oxygen (known as “Warburg Effect”). Based on this theory, oxidative phosphorylation switches to glycolysis which promotes the proliferation of cancer cells. Many studies have demonstrated glycolysis as the main metabolic pathway in cancer cells.

Albert Szent Gyogy (Warburg’s student) and Otto Meyerhof both studied striated skeletal muscle metabolism invertebrates, and they found those changes observed in yeast by Pasteur. The description of the anaerobic pathway was largely credited to Emden and Meyerhof. Whenever there is increase in muscle work, energy need is above what can be provided by blood supply, the cell metabolism changes from aerobic (where  Acetyl CoA  provides the chemical energy for aerobic production of ATP) to anaerobic metabolism of glucose. In this condition, glucose is obtained directly from its muscle glycogen stores (not from hepatic glycogenolysis).  This is the sole source of chemical energy that is independent of oxygen supplied to the cell. It is a physiological change on muscle metabolism that favors autonomy. It does not depend upon the blood oxygen for aerobic metabolim or blood sources of carbon metabolites borne out from adipose tissue (free fatty acids) or muscle proteins (branched chain amino acids), or vascular delivery of glucose. On that condition, the muscle can perform contraction by its internal source of ATP and uses conversion of pyruvate to lactate in order to regenerate much-needed NAD (by hydride transfer from pyruvate) as a replacement for this mitochondrial function. This regulatory change, keeps glycolysis going at fast rate in order to meet ATP needs of the cell under low yield condition (only two or three ATP for each glucose converted into two lactate molecules). Therefore, it cannot last for long periods of time. This regulatory metabolic change is made in seconds, minutes and therefore happens with the proteins that are already presented in the cell. It does not requires the effect of transcription factors and/or changes in gene expression (See Footnote 1, 2).

In other types mammalian cells, like those from the lens of the eye (86% gycolysis + pentose shunt),  and red blood cells (RBC)[both lacking mitochondria], and also in the deep medullary layer of the kidneys, for lack of mitochondria in the first two cases and normally reduced blood perfusion in the third – A condition required for the counter current mechanism and our ability to concentrate urine also have, permanent higher anaerobic metabolism. In the case of RBC, it includes the ability to produce in a shunt of glycolytic pathway 2,3 diphospho- glycerate that is required to place the hemogloblin macromolecule in an unstable equilibrium between its two forms (R and T – Here presented as simplified accordingly to the model of Monod, Wyman and Changeux. The final model would be even much complex (see for instance, H-W and K review Nature 2007 vol 450: p 964-972 )

Any tissue under a condition of ischemia that is required for some medical procedures (open heart surgery, organ transplants, etc) displays this fast regulatory mechanism (See Footnote 1, 2). A display of these regulatory metabolic changes can be seen in: Cardioplegia: the protection of the myocardium during open heart surgery: a review. D. J. Hearse J. Physiol., Paris, 1980, 76, 751-756 (Fig 1).  The following points are made:

1-       It is a fast regulatory response. Therefore, no genetic mechanism can be taken into account.

2-       It moves from a reversible to an irreversible condition, while the cells are still alive. Death can be seen at the bottom end of the arrow. Therefore, it cannot be reconciled with some of the molecular biology assumptions:

A-       The gene and genes reside inside the heart muscle cells but, in order to preserve intact, the source of coded genetic information that the cell reads and transcribes, DNA must be kept to a minimal of chemical reactivity.

B-       In case sequence determines conformation, activity and function , elevated potassium blood levels could not cause cardiac arrest.

In comparison with those conditions here presented, cancer cells keep the two metabolic options for glucose metabolism at the same time. These cells can use glucose that our body provides to them or adopt temporarily, an independent metabolic form without the usual normal requirement of oxygen (one or another form for ATP generation).  ATP generation is here, an over-simplification of the metabolic status since the carbon flow for building blocks must also be considered and in this case oxidative metabolism of glucose in cancer cells may be viewed as a rich source of organic molecules or building blocks that dividing cells always need.

JES Roselino has conjectured that “most of the Krebs cycle reaction works as ideal reversible thermodynamic systems that can supply any organic molecule that by its absence could prevent cell duplication.” In the vision of Warburg, cancer cells have a defect in Pasteur-effect metabolic control. In case it was functioning normally, it will indicate which metabolic form of glucose metabolism is adequate for each condition. What more? Cancer cells lack differentiated cell function. Any role for transcription factors must be considered as the role of factors that led to the stable phenotypic change of cancer cells. The failure of Pasteur effect must be searched for among the fast regulatory mechanisms that aren’t dependent on gene expression (See Footnote 3).

Extending the thoughts of JES Roselino (Hepatology 1992;16: 1055-1060), reduced blood flow caused by increased hydrostatic pressure in extrahepatic cholestasis decreases mitochondrial function (quoted in Hepatology) and as part of Pasteur effect normal response, increased glycolysis in partial and/or functional anaerobiosis and therefore blocks the gluconeogenic activity of hepatocytes that requires inhibited glycolysis. In this case, a clear energetic link can be perceived between the reduced energetic supply and the ability to perform differentiated hepatic function (gluconeogenesis). In cancer cells, the action of transcription factors that can be viewed as different ensembles of kaleidoscopic pieces (with changing activities as cell conditions change) are clearly linked to the new stable phenotype. In relation to extrahepatic cholestasis mentioned above it must be reckoned that in case a persistent chronic condition is studied a secondary cirrhosis is installed as an example of persistent stable condition, difficult to be reversed and without the requirement for a genetic mutation. (See Footnote 4).

 The Rejection of Complexity

Most of our reasoning about genes was derived from scientific work in microorganisms. These works have provided great advances in biochemistry.

250px-DNA_labeled DNA diagram showing base pairing

double helix

 

hgp_hubris_220x288_72 genome cartoon

Dna triplex pic

Triple helix

 

formation of a triplex DNA structure

formation of triple helix

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1-      The “Gelehrter idea”: No matter what you are doing you will always be better off, in case you have a gene (In chapter 7 Principles of Medical Genetics Gelehrter and Collins Williams & Wilkins 1990).

2-      The idea that everything could be found following one gene one enzyme relationship that works fine for our understanding of the metabolism, in all biological problems.

3-      The idea that everything that explains biochemistry in microorganisms explains also for every living being (J Nirenberg).

4-      The idea that biochemistry may not require that time should be also taken into account. Time must be considered only for genetic and biological evolution studies (S Luria. In Life- The unfinished experiment 1977 C Scribner´s sons NY).

5-      Finally, the idea that everything in biology, could be found in the genome. Since all information in biology goes from DNA through RNA to proteins. Alternatively, are in the DNA, in case the strict line that includes RNA is not included.

This last point can be accepted in case it is considered that ALL GENETIC information is in our DNA. Genetics as part of life and not as its total expression.

For example, when our body is informed that the ambient temperature is too low or alternatively is too high, our body is receiving an information that arrives from our environment. This external information will affect our proteins and eventually, in case of longer periods in a new condition will cause adaptive response that may include conformational changes in transcription factors (proteins) that will also, produce new readings on the DNA. However, it is an information that moves from outside, to proteins and not from DNA to proteins. The last pathway, when transcription factors change its conformation and change DNA reading will follow the dogmatic view as an adaptive response (See Footnotes 1-3).

However, in case, time is taken into account, the first reactions against cold or warmer temperatures will be the ones that happen through change in protein conformation, activities and function before any change in gene expression can be noticed at protein level. These fast changes, in seconds, minutes cannot be explained by changes in gene expression and are strongly linked to what is needed for the maintenance of life.

“It is possible”, says Roselino, “desirable, to explain all these fast biochemical responses to changes in a living being condition as the sound foundation of medical practices without a single mention to DNA. In case a failure in any mechanism necessary to life is found to be genetic in its origin, the genome in context with with this huge set of transcription factors must be taken into account. This is the biochemical line of reasoning that I have learned with Houssay and Leloir. It would be an honor to see it restored in modern terms.”

More on the Mechanism of Metabolic Control

It was important that genomics would play such a large role in medical research for the last 70 years. There is also good reason to rethink the objections of the Nobelists James Watson and Randy Schekman in the past year, whatever discomfort it brings.  Molecular biology has become a tautology, and as a result deranged scientific rigor inside biology.

Crick & Watson with their DNA model, 1953

Eatson and Crick

Randy-Schekman Berkeley

Randy-Schekman Berkeley

 

 

According to JES Roselino, “consider that glycolysis is oscillatory thanks to the kinetic behavior of Phosphofructokinase. Further, by its effect upon Pyruvate kinase through Fructose 1,6 diphosphate oscillatory levels, the inhibition of gluconeogenesis is also oscillatory. When the carbon flow through glycolysis is led to a maximal level gluconeogenesis will be almost completely blocked. The reversal of the Pyruvate kinase step in liver requires two enzymes (Pyruvate carboxylase (maintenance of oxaloacetic levels) + phosphoenolpyruvate carboxykinase (E.C. 4.1.1.32)) and energy requiring reactions that most likely could not as an ensemble, have a fast enough response against pyruvate kinase short period of inhibition during high frequency oscillatory periods of glycolytic flow. Only when glycolysis oscillates at low frequency the opposite reaction could enable gluconeogenic carbon flow.”

In case it can be shown in a rather convincing way, the same reasoning could be applied to understand how simple replicative signals inducing Go to G1 transition in cells, could easily overcome more complex signals required for cell differentiation and differentiated function.

Perhaps the problem of overextension of the equivalence of the DNA and what happens to the organism is also related to the initial reliance on a single cell model to relieve the complexity (which isn’t fully the case).

For instance, consider this fragment:
“Until only recently it was assumed that all proteins take on a clearly defined three-dimensional structure – i.e. they fold in order to be able to assume these functions.”
Cold Spring Harbour Symp. Quant. Biol. 1973  p 187-193 J.C Seidel and J Gergely – Investigation of conformational changes in Spin-Labeled Myosin Model for muscle contraction:
Huxley, A. F. 1971 Proc. Roy. Soc (London) (B) 178:1
Huxley, A.F and R. M. Simmons,1971. Nature 233:633
J.C Haselgrove X ray Evidence for a conformational Change in the Actin-containing filaments…Cold Spring Harbour Symp Quant Biol.1972 v 37: p 341-352

Only a very small sample indicating otherwise. Proteins were held as interacting macromolecules, changing their conformation in regulatory response to changes in the microenvironment (See Footnote 2). DNA was the opposite, non-interacting macromolecules to be as stable as a library must be.

The dogma held that the property of proteins could be read in DNA alone. Consequenly, the few examples quoted above, must be ignored and all people must believe that DNA alone, without environmental factors roles, controls protein amino acid sequence (OK), conformation (not true), activity (not true) and function (not true).

It appeared naively to be correct from the dogma to conclude from interpreting your genome: You have a 50% increased risk of developing the following disease (deterministic statement).  The correct form must be: You belong to a population that has a 50% increase in the risk of….followed by –  what you must do to avoid increase in your personal risk and the care you should take in case you want to have longer healthy life.  Thus, genetics and non-genetic diseases were treated as the same and medical foundations were reinforced by magical considerations (dogmas) in a very profitable way for those involved besides the patient.

 Footnotes:

  1. There is a link of electricity with ions in biology and the oscillatory behavior of some electrical discharges.  In addition, the oscillatory form of electrical discharged may have allowed Planck to relate high energy content with higher frequencies and conversely, low energy content in low frequency oscillatory events.  One may think of high density as an indication of great amount of matter inside a volume in space.  This helps the understanding of Planck’s idea as a high-density-energy in time for a high frequency phenomenon.
  1. Take into account a protein that may have its conformation restricted by an S-S bridge. This protein also, may move to another more flexible conformation in case it is in HS HS condition when the S-S bridge is broken. Consider also that, it takes some time for a protein to move from one conformation for instance, the restricted conformation (S-S) to other conformations. Also, it takes a few seconds or minutes to return to the S-S conformation (This is the Daniel Koshland´s concept of induced fit and relaxation time used by him in order to explain allosteric behavior of monomeric proteins- Monod, Wyman and Changeux requires tetramer or at least, dimer proteins).
  1. In case you have glycolysis oscillating in a frequency much higher than the relaxation time you could lead to the prevalence of high NADH effect leading to high HS /HS condition and at low glycolytic frequency, you could have predominance of S-S condition affecting protein conformation. In case you have predominance of NAD effect upon protein S-S you would get the opposite results.  The enormous effort to display the effect of citrate and over Phosphofructokinase conformation was made by others. Take into account that ATP action as an inhibitor in this case, is a rather unusual one. It is a substrate of the reaction, and together with its action as activator  F1,6 P (or its equivalent F2,6 P) is also unusual. However, it explains oscillatory behaviour of glycolysis. (Goldhammer , A.R, and Paradies: PFK structure and function, Curr. Top Cell Reg 1979; 15:109-141).
  1. The results presented in our Hepatology work must be viewed in the following way: In case the hepatic (oxygenated) blood flow is preserved, the bile secretory cells of liver receive well-oxygenated blood flow (the arterial branches bath secretory cells while the branches originated from portal vein irrigate the hepatocytes.  During extra hepatic cholestasis the low pressure, portal blood flow is reduced and the hepatocytes do not receive enough oxygen required to produce ATP that gluconeogenesis demands. Hepatic artery do not replace this flow since, its branches only join portal blood fluxes after the previous artery pressure  is reduced to a low pressure venous blood – at the point where the formation of hepatic vein is. Otherwise, the flow in the portal vein would be reversed or, from liver to the intestine. It is of no help to take into account possible valves for this reasoning since minimal arterial pressure is well above maximal venous pressure and this difference would keep this valve in permanent close condition. In low portal blood flow condition, the hepatocyte increases pyruvate kinase activity and with increased pyruvate kinase activity Gluconeogenesis is forbidden (See Walsh & Cooper revision quoted in the Hepatology as ref 23). For the hemodynamic considerations, role of artery and veins in hepatic portal system see references 44 and 45 Rappaport and Schneiderman and Rappapaport.

 

 Appendix I.

metabolic pathways

metabolic pathways

Signals Upstream and Targets Downstream of Lin28 in the Lin28 Pathway

Signals Upstream and Targets Downstream of Lin28 in the Lin28 Pathway

 

 

 

 

 

 

 

 

1.  Functional Proteomics Adds to Our Understanding

Ben Schuler’s research group from the Institute of Biochemistry of the University of Zurich has now established that an increase in temperature leads to folded proteins collapsing and becoming smaller. Other environmental factors can trigger the same effect. The crowded environments inside cells lead to the proteins shrinking. As these proteins interact with other molecules in the body and bring other proteins together, understanding of these processes is essential “as they play a major role in many processes in our body, for instance in the onset of cancer”, comments study coordinator Ben Schuler.

Measurements using the “molecular ruler”

“The fact that unfolded proteins shrink at higher temperatures is an indication that cell water does indeed play an important role as to the spatial organisation eventually adopted by the molecules”, comments Schuler with regard to the impact of temperature on protein structure. For their studies the biophysicists use what is known as single-molecule spectroscopy. Small colour probes in the protein enable the observation of changes with an accuracy of more than one millionth of a millimetre. With this “molecular yardstick” it is possible to measure how molecular forces impact protein structure.

With computer simulations the researchers have mimicked the behaviour of disordered proteins. They want to use them in future for more accurate predictions of their properties and functions.

Correcting test tube results

That’s why it’s important, according to Schuler, to monitor the proteins not only in the test tube but also in the organism. “This takes into account the fact that it is very crowded on the molecular level in our body as enormous numbers of biomolecules are crammed into a very small space in our cells”, says Schuler. The biochemists have mimicked this “molecular crowding” and observed that in this environment disordered proteins shrink, too.

Given these results many experiments may have to be revisited as the spatial organisation of the molecules in the organism could differ considerably from that in the test tube according to the biochemist from the University of Zurich. “We have, therefore, developed a theoretical analytical method to predict the effects of molecular crowding.” In a next step the researchers plan to apply these findings to measurements taken directly in living cells.

Explore further: Designer proteins provide new information about the body’s signal processesMore information: Andrea Soranno, Iwo Koenig, Madeleine B. Borgia, Hagen Hofmann, Franziska Zosel, Daniel Nettels, and Benjamin Schuler. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. PNAS, March 2014. DOI: 10.1073/pnas.1322611111

 

Effects of Hypoxia on Metabolic Flux

  1. Glucose-6-phosphate dehydrogenase regulation in the hepatopancreas of the anoxia-tolerantmarinemollusc, Littorina littorea

JL Lama , RAV Bell and KB Storey

Glucose-6-phosphate dehydrogenase (G6PDH) gates flux through the pentose phosphate pathway and is key to cellular antioxidant defense due to its role in producing NADPH. Good antioxidant defenses are crucial for anoxia-tolerant organisms that experience wide variations in oxygen availability. The marine mollusc, Littorina littorea, is an intertidal snail that experiences daily bouts of anoxia/hypoxia with the tide cycle and shows multiple metabolic and enzymatic adaptations that support anaerobiosis. This study investigated the kinetic, physical and regulatory properties of G6PDH from hepatopancreas of L. littorea to determine if the enzyme is differentially regulated in response to anoxia, thereby providing altered pentose phosphate pathway functionality under oxygen stress conditions.

Several kinetic properties of G6PDH differed significantly between aerobic and 24 h anoxic conditions; compared with the aerobic state, anoxic G6PDH (assayed at pH 8) showed a 38% decrease in K G6P and enhanced inhibition by urea, whereas in pH 6 assays Km NADP and maximal activity changed significantly.

All these data indicated that the aerobic and anoxic forms of G6PDH were the high and low phosphate forms, respectively, and that phosphorylation state was modulated in response to selected endogenous protein kinases (PKA or PKG) and protein phosphatases (PP1 or PP2C). Anoxia-induced changes in the phosphorylation state of G6PDH may facilitate sustained or increased production of NADPH to enhance antioxidant defense during long term anaerobiosis and/or during the transition back to aerobic conditions when the reintroduction of oxygen causes a rapid increase in oxidative stress.

Lama et al.  Peer J 2013.   http://dx.doi.org/10.7717/peerj.21

 

  1. Structural Basis for Isoform-Selective Inhibition in Nitric Oxide Synthase

    TL. Poulos and H Li

In the cardiovascular system, the important signaling molecule nitric oxide synthase (NOS) converts L-arginine into L-citrulline and releases nitric oxide (NO). NO produced by endothelial NOS (eNOS) relaxes smooth muscle which controls vascular tone and blood pressure. Neuronal NOS (nNOS) produces NO in the brain, where it influences a variety of neural functions such as neural transmitter release. NO can also support the immune system, serving as a cytotoxic agent during infections. Even with all of these important functions, NO is a free radical and, when overproduced, it can cause tissue damage. This mechanism can operate in many neurodegenerative diseases, and as a result the development of drugs targeting nNOS is a desirable therapeutic goal.

However, the active sites of all three human isoforms are very similar, and designing inhibitors specific for nNOS is a challenging problem. It is critically important, for example, not to inhibit eNOS owing to its central role in controlling blood pressure. In this Account, we summarize our efforts in collaboration with Rick Silverman at Northwestern University to develop drug candidates that specifically target NOS using crystallography, computational chemistry, and organic synthesis. As a result, we have developed aminopyridine compounds that are 3800-fold more selective for nNOS than eNOS, some of which show excellent neuroprotective effects in animal models. Our group has solved approximately 130 NOS-inhibitor crystal structures which have provided the structural basis for our design efforts. Initial crystal structures of nNOS and eNOS bound to selective dipeptide inhibitors showed that a single amino acid difference (Asp in nNOS and Asn in eNOS) results in much tighter binding to nNOS. The NOS active site is open and rigid, which produces few large structural changes when inhibitors bind. However, we have found that relatively small changes in the active site and inhibitor chirality can account for large differences in isoform-selectivity. For example, we expected that the aminopyridine group on our inhibitors would form a hydrogen bond with a conserved Glu inside the NOS active site. Instead, in one group of inhibitors, the aminopyridine group extends outside of the active site where it interacts with a heme propionate. For this orientation to occur, a conserved Tyr side chain must swing out of the way. This unanticipated observation taught us about the importance of inhibitor chirality and active site dynamics. We also successfully used computational methods to gain insights into the contribution of the state of protonation of the inhibitors to their selectivity. Employing the lessons learned from the aminopyridine inhibitors, the Silverman lab designed and synthesized symmetric double-headed inhibitors with an aminopyridine at each end, taking advantage of their ability to make contacts both inside and outside of the active site. Crystal structures provided yet another unexpected surprise. Two of the double-headed inhibitor molecules bound to each enzyme subunit, and one molecule participated in the generation of a novel Zn site that required some side chains to adopt alternate conformations. Therefore, in addition to achieving our specific goal, the development of nNOS selective compounds, we have learned how subtle differences in and structure can control proteinligand interactions and often in unexpected ways.

 

300px-Nitric_Oxide_Synthase

Nitric oxide synthase

arginine-NO-citulline cycle

arginine-NO-citulline cycle

active site of eNOS (PDB_1P6L) and nNOS (PDB_1P6H).

active site of eNOS (PDB_1P6L) and nNOS (PDB_1P6H).

 

 

NO - muscle, vasculature, mitochondria

NO – muscle, vasculature, mitochondria

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure:  (A) Structure of one of the early dipeptide lead compounds, 1, that exhibits excellentisoform selectivity. (B, C) show the crystal structures of the dipeptide inhibitor 1 in the active site of eNOS (PDB: 1P6L) and nNOS (PDB: 1P6H). In nNOS, the inhibitor “curls” which enables the inhibitor R-amino group to interact with both Glu592 and Asp597. In eNOS, Asn368 is the homologue to nNOS Asp597.

Accounts in Chem Res 2013; 46(2): 390-98.

  1. Jamming a Protein Signal

Interfering with a single cancer-promoting protein and its receptor can open this resistance mechanism by initiating autophagy of the affected cells,  according to researchers at The University of Texas MD Anderson Cancer Center  in the journal Cell Reports.  According to Dr. Anil Sood and Yunfei Wen, lead and first authors, blocking  prolactin, a potent growth factor for ovarian cancer, sets off downstream events that result in cell by autophagy, the process  recycles damaged organelles and proteins for new use by the cell through the phagolysozome. This in turn, provides a clinical rationale for blocking prolactin and its receptor to initiate sustained autophagy as an alternative strategy for treating cancers.

Steep reductions in tumor weight

Prolactin (PRL) is a hormone previously implicated in ovarian, endometrial and other cancer development andprogression. When PRL binds to its cell membrane receptor, PRLR, activation of cancer-promoting cell signaling pathways follows.  A variant of normal prolactin called G129R blocks the reaction between prolactin and its receptor. Sood and colleagues treated mice that had two different lines of human ovarian cancer, both expressing the prolactin receptor, with G129R. Tumor weights fell by 50 percent for mice with either type of ovarian cancer after 28 days of treatment with G129R, and adding the taxane-based chemotherapy agent paclitaxel cut tumor weight by 90 percent. They surmise that higher doses of G129R may result in even greater therapeutic benefit.

 

3D experiments show death by autophagy

 

[video width=”1280″ height=”720″ mp4=”http://pharmaceuticalintelligence.com/wp-content/uploads/2014/04/1741-7007-11-65-s1-macromolecular-juggling-by-ubiquitylation-enzymes1.mp4″][/video]

 

Next the team used the prolactin-mimicking peptide to treat cultures of cancer spheroids which sharply reduced their numbers, and blocked the activation of JAK2 and STAT signaling pathways.

Protein analysis of the treated spheroids showed increased presence of autophagy factors and genomic analysis revealed increased expression of a number of genes involved in autophagy progression and cell death.  Then a series of experiments using fluorescence and electron microscopy showed that the cytosol of treated cells had large numbers of cavities caused by autophagy.

The team also connected the G129R-induced autophagy to the activity of PEA-15, a known cancer inhibitor. Analysis of tumor samples from 32 ovarian cancer patients showed that tumors express higher levels of the prolactin receptor and lower levels of phosphorylated PEA-15 than normal ovarian tissue. However, patients with low levels of the prolactin receptor and higher PEA-15 had longer overall survival than those with high PRLR and low PEA-15.

Source: MD Anderson Cancer Center

 

  1. Chemists’ Work with Small Peptide Chains of Enzymes

Korendovych and his team designed seven simple peptides, each containing seven amino acids. They then allowed the molecules of each peptide to self-assemble, or spontaneously clump together, to form amyloids. (Zinc, a metal with catalytic properties, was introduced to speed up the reaction.) What they found was that four of the seven peptides catalyzed the hydrolysis of molecules known as esters, compounds that react with water to produce water and acids—a feat not uncommon among certain enzymes.

“It was the first time that a peptide this small self-assembled to produce an enzyme-like catalyst,” says Korendovych. “Each enzyme has to be an exact fit for its respective substrate,” he says, referring to the molecule with which an enzyme reacts. “Even after millions of years, nature is still testing all the possible combinations of enzymes to determine which ones can catalyze metabolic reactions. Our results make an argument for the design of self-assembling nanostructured catalysts.”

Source: Syracuse University

Here are three articles emphasizing the value of combinatorial analysis, which can be formed from genomic, clinical, and proteomic data sets.

 

  1. Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks

    F Islam , M Hoque , RS Banik , S Roy , SS Sumi, et al.

As most biological networks show modular properties, the analysis of differential modularity between normal and cancer protein interaction networks can be a good way to understand cancer more significantly. Two aspects of biological network modularity e.g. detection of molecular complexes (potential modules or clusters) and identification of crucial nodes forming the overlapping modules have been considered in this regard.

The computational analysis of previously published protein interaction networks (PINs) has been conducted to identify the molecular complexes and crucial nodes of the networks. Protein molecules involved in ten major cancer signal transduction pathways were used to construct the networks based on expression data of five tissues e.g. bone, breast, colon, kidney and liver in both normal and cancer conditions.

Cancer PINs show higher level of clustering (formation of molecular complexes) than the normal ones. In contrast, lower level modular overlapping is found in cancer PINs than the normal ones. Thus a proposition can be made regarding the formation of some giant nodes in the cancer networks with very high degree and resulting in reduced overlapping among the network modules though the predicted molecular complex numbers are higher in cancer conditions.

Islam et al. Journal of Clinical Bioinformatics 2013, 3:19-32

  1. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

    Wanting Liu , Yonghong Peng and Desmond J. Tobin
    PeerJ 1:e49;        http://dx.doi.org/10.7717/peerj.49

Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, andWNT4).We have begun to experimentally validate a subset of these genes involved inMAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be overexpressed inmetastatic and primarymelanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin.

 

catalytic amyloid forming particle

catalytic amyloid forming particle

 

 

 

 

 

 

 

        8.    PanelomiX: A threshold-based algorithm to create panels of biomarkers

X Robin , N Turck , A Hainard , N Tiberti, et al.
               Translational Proteomics 2013.    http://dx.doi.org/10.1016/j.trprot.2013.04.003

The PanelomiX toolbox combines biomarkers and evaluates the performance of panels to classify patients better than singlemarkers or other classifiers. The ICBTalgorithm proved to be an efficient classifier, the results of which can easily be interpreted.

Here are two current examples of the immense role played by signaling pathways in carcinogenic mechanisms and in treatment targeting, which is also confounded by acquired resistance.

 

  1. Triple-Negative Breast Cancer

  1. epidermal growth factor receptor (EGFR or ErbB1) and
  2. high activity of the phosphatidylinositol 3-kinase (PI3K)–Akt pathway

are both targeted in triple-negative breast cancer (TNBC).

  • activation of another EGFR family member [human epidermal growth factor receptor 3 (HER3) (or ErbB3)] may limit the antitumor effects of these drugs.

This study found that TNBC cell lines cultured with the EGFR or HER3 ligand EGF or heregulin, respectively, and treated with either an Akt inhibitor (GDC-0068) or a PI3K inhibitor (GDC-0941) had increased abundance and phosphorylation of HER3.

The phosphorylation of HER3 and EGFR in response to these treatments

  1. was reduced by the addition of a dual EGFR and HER3 inhibitor (MEHD7945A).
  2. MEHD7945A also decreased the phosphorylation (and activation) of EGFR and HER3 and
  3. the phosphorylation of downstream targets that occurred in response to the combination of EGFR ligands and PI3K-Akt pathway inhibitors.

In culture, inhibition of the PI3K-Akt pathway combined with either MEHD7945A or knockdown of HER3

  1. decreased cell proliferation compared with inhibition of the PI3K-Akt pathway alone.
  2. Combining either GDC-0068 or GDC-0941 with MEHD7945A inhibited the growth of xenografts derived from TNBC cell lines or from TNBC patient tumors, and
  3. this combination treatment was also more effective than combining either GDC-0068 or GDC-0941 with cetuximab, an EGFR-targeted antibody.
  4. After therapy with EGFR-targeted antibodies, some patients had residual tumors with increased HER3 abundance and EGFR/HER3 dimerization (an activating interaction).

Thus, we propose that concomitant blockade of EGFR, HER3, and the PI3K-Akt pathway in TNBC should be investigated in the clinical setting.

Reference: Antagonism of EGFR and HER3 Enhances the Response to Inhibitors of the PI3K-Akt Pathway in Triple-Negative Breast Cancer. JJ Tao, P Castel, N Radosevic-Robin, M Elkabets, et al.  Sci. Signal., 25 March 2014;
7(318), p. ra29   http://dx.doi.org/10.1126/scisignal.2005125

 

                  10.   Metastasis in RAS Mutant or Inhibitor-Resistant Melanoma Cells

The protein kinase BRAF is mutated in about 40% of melanomas, and BRAF inhibitors improve progression-free and overall survival in these patients. However, after a relatively short period of disease control, most patients develop resistance because of reactivation of the RAF–ERK (extracellular signal–regulated kinase) pathway, mediated in many cases by mutations in RAS. We found that BRAF inhibition induces invasion and metastasis in RAS mutant melanoma cells through a mechanism mediated by the reactivation of the MEK (mitogen-activated protein kinase kinase)–ERK pathway.

Reference: BRAF Inhibitors Induce Metastasis in RAS Mutant or Inhibitor-Resistant Melanoma Cells by Reactivating MEK and ERK Signaling. B Sanchez-Laorden, A Viros, MR Girotti, M Pedersen, G Saturno, et al., Sci. Signal., 25 March 2014;  7(318), p. ra30  http://dx.doi.org/10.1126/scisignal.2004815

Appendix II.

The world of physics in the twentieth century saw the end of determinism established by Newton. This is characterized by discrete laws that describe natural observations. These are in gravity and in eletricity. In an early phase of investigation, an era of galvanic or voltaic electricity represented a revolutionary break from the historical focus on frictional electricity. Alessandro Voltadiscovered that chemical reactions could be used to create positively charged anodes and negatively charged cathodes.  In 1790, Prof. Luigi Alyisio Galvani of Bologna, while conducting experiments on “animal electricity“, noticed the twitching of a frog’s legs in the presence of an electric machine. He observed that a frog’s muscle, suspended on an iron balustrade by a copper hook passing through its dorsal column, underwent lively convulsions without any extraneous cause, the electric machine being at this time absent.  Volta communicated a description of his pile to the Royal Society of London and shortly thereafter Nicholson and Cavendish (1780) produced the decomposition of water by means of the electric current, using Volta’s pile as the source of electromotive force.

Siméon Denis Poisson attacked the difficult problem of induced magnetization, and his results provided  a first approximation. His innovation required the application of mathematics to physics.  His memoirs on the theory of electricity and magnetism created a new branch of mathematical physics.  The discovery of electromagnetic induction was made almost simultaneously and independently by Michael Faraday and Joseph Henry. Michael Faraday, the successor of Humphry Davy, began his epoch-making research relating to electric and electromagnetic induction in 1831. In his investigations of the peculiar manner in which iron filings arrange themselves on a cardboard or glass in proximity to the poles of a magnet, Faraday conceived the idea of magnetic “lines of force” extending from pole to pole of the magnet and along which the filings tend to place themselves. On the discovery being made that magnetic effects accompany the passage of an electric current in a wire, it was also assumed that similar magnetic lines of force whirled around the wire. He also posited that iron, nickel, cobalt, manganese, chromium, etc., are paramagnetic (attracted by magnetism), whilst other substances, such as bismuth, phosphorus, antimony, zinc, etc., are repelled by magnetism or are diamagnetic.

Around the mid-19th century, Fleeming Jenkin‘s work on ‘ Electricity and Magnetism ‘ and Clerk Maxwell’s ‘ Treatise on Electricity and Magnetism ‘ were published. About 1850 Kirchhoff published his laws relating to branched or divided circuits. He also showed mathematically that according to the then prevailing electrodynamic theory, electricity would be propagated along a perfectly conducting wire with the velocity of light. Herman Helmholtz investigated the effects of induction on the strength of a current and deduced mathematical equations, which experiment confirmed. In 1853 Sir William Thomson (later Lord Kelvin) predicted as a result of mathematical calculations the oscillatory nature of the electric discharge of a condenser circuit.  Joseph Henry, in 1842 discerned  the oscillatory nature of the Leyden jardischarge.

In 1864 James Clerk Maxwell announced his electromagnetic theory of light, which was perhaps the greatest single step in the world’s knowledge of electricity. Maxwell had studied and commented on the field of electricity and magnetism as early as 1855/6 when On Faraday’s lines of force was read to the Cambridge Philosophical Society. The paper presented a simplified model of Faraday’s work, and how the two phenomena were related. He reduced all of the current knowledge into a linked set of differential equations with 20 equations in 20 variables. This work was later published as On Physical Lines of Force in1861. In order to determine the force which is acting on any part of the machine we must find its momentum, and then calculate the rate at which this momentum is being changed. This rate of change will give us the force. The method of calculation which it is necessary to employ was first given by Lagrange, and afterwards developed, with some modifications, by Hamilton’s equations. Now Maxwell logically showed how these methods of calculation could be applied to the electro-magnetic field. The energy of a dynamical systemis partly kinetic, partly potential. Maxwell supposes that the magnetic energy of the field is kinetic energy, the electric energy potential.  Around 1862, while lecturing at King’s College, Maxwell calculated that the speed of propagation of an electromagnetic field is approximately that of the speed of light.   Maxwell’s electromagnetic theory of light obviously involved the existence of electric waves in free space, and his followers set themselves the task of experimentally demonstrating the truth of the theory. By 1871, he presented the Remarks on the mathematical classification of physical quantities.

A Wave-Particle Dilemma at the Century End

In 1896 J.J. Thomson performed experiments indicating that cathode rays really were particles, found an accurate value for their charge-to-mass ratio e/m, and found that e/m was independent of cathode material. He made good estimates of both the charge e and the mass m, finding that cathode ray particles, which he called “corpuscles”, had perhaps one thousandth of the mass of the least massive ion known (hydrogen). He further showed that the negatively charged particles produced by radioactive materials, by heated materials, and by illuminated materials, were universal.  In the late 19th century, the Michelson–Morley experiment was performed by Albert Michelson and Edward Morley at what is now Case Western Reserve University. It is generally considered to be the evidence against the theory of a luminiferous aether. The experiment has also been referred to as “the kicking-off point for the theoretical aspects of the Second Scientific Revolution.” Primarily for this work, Albert Michelson was awarded theNobel Prize in 1907.

Wave–particle duality is a theory that proposes that all matter exhibits the properties of not only particles, which have mass, but also waves, which transfer energy. A central concept of quantum mechanics, this duality addresses the inability of classical concepts like “particle” and “wave” to fully describe the behavior of quantum-scale objects. Standard interpretations of quantum mechanics explain this paradox as a fundamental property of the universe, while alternative interpretations explain the duality as an emergent, second-order consequence of various limitations of the observer. This treatment focuses on explaining the behavior from the perspective of the widely used Copenhagen interpretation, in which wave–particle duality serves as one aspect of the concept of complementarity, that one can view phenomena in one way or in another, but not both simultaneously.  Through the work of Max Planck, Albert Einstein, Louis de Broglie, Arthur Compton, Niels Bohr, and many others, current scientific theory holds that all particles also have a wave nature (and vice versa).

Beginning in 1670 and progressing over three decades, Isaac Newton argued that the perfectly straight lines of reflection demonstrated light’s particle nature, but Newton’s contemporaries Robert Hooke and Christiaan Huygens—and later Augustin-Jean Fresnel—mathematically refined the wave viewpoint, showing that if light traveled at different speeds in different, refraction could be easily explained. The resulting Huygens–Fresnel principle was supported by Thomas Young‘s discovery of double-slit interference, the beginning of the end for the particle light camp.  The final blow against corpuscular theory came when James Clerk Maxwell discovered that he could combine four simple equations, along with a slight modification to describe self-propagating waves of oscillating electric and magnetic fields. When the propagation speed of these electromagnetic waves was calculated, the speed of light fell out. While the 19th century had seen the success of the wave theory at describing light, it had also witnessed the rise of the atomic theory at describing matter.

Matter and Light

In 1789, Antoine Lavoisier secured chemistry by introducing rigor and precision into his laboratory techniques. By discovering diatomic gases, Avogadro completed the basic atomic theory, allowing the correct molecular formulae of most known compounds—as well as the correct weights of atoms—to be deduced and categorized in a consistent manner. The final stroke in classical atomic theory came when Dimitri Mendeleev saw an order in recurring chemical properties, and created a table presenting the elements in unprecedented order and symmetry.   Chemistry was now an atomic science.

Black-body radiation, the emission of electromagnetic energy due to an object’s heat, could not be explained from classical arguments alone. The equipartition theorem of classical mechanics, the basis of all classical thermodynamic theories, stated that an object’s energy is partitioned equally among the object’s vibrational modes. This worked well when describing thermal objects, whose vibrational modes were defined as the speeds of their constituent atoms, and the speed distribution derived from egalitarian partitioning of these vibrational modes closely matched experimental results. Speeds much higher than the average speed were suppressed by the fact that kinetic energy is quadratic—doubling the speed requires four times the energy—thus the number of atoms occupying high energy modes (high speeds) quickly drops off. Since light was known to be waves of electromagnetism, physicists hoped to describe this emission via classical laws. This became known as the black body problem. The Rayleigh–Jeans law which, while correctly predicting the intensity of long wavelength emissions, predicted infinite total energy as the intensity diverges to infinity for short wavelengths.

The solution arrived in 1900 when Max Planck hypothesized that the frequency of light emitted by the black body depended on the frequency of the oscillator that emitted it, and the energy of these oscillators increased linearly with frequency (according to his constant h, where E = hν). By demanding that high-frequency light must be emitted by an oscillator of equal frequency, and further requiring that this oscillator occupy higher energy than one of a lesser frequency, Planck avoided any catastrophe; giving an equal partition to high-frequency oscillators produced successively fewer oscillators and less emitted light. And as in the Maxwell–Boltzmann distribution, the low-frequency, low-energy oscillators were suppressed by the onslaught of thermal jiggling from higher energy oscillators, which necessarily increased their energy and frequency. Planck had intentionally created an atomic theory of the black body, but had unintentionally generated an atomic theory of light, where the black body never generates quanta of light at a given frequency with energy less than hν.

In 1905 Albert Einstein took Planck’s black body model in itself and saw a wonderful solution to another outstanding problem of the day: the photoelectric effect, the phenomenon where electrons are emitted from atoms when they absorb energy from light.   Only by increasing the frequency of the light, and thus increasing the energy of the photons, can one eject electrons with higher energy. Thus, using Planck’s constant h to determine the energy of the photons based upon their frequency, the energy of ejected electrons should also increase linearly with frequency; the gradient of the line being Planck’s constant. These results were not confirmed until 1915, when Robert Andrews Millikan, produced experimental results in perfect accord with Einstein’s predictions. While  the energy of ejected electrons reflected Planck’s constant, the existence of photons was not explicitly proven until the discovery of the photon antibunching effect  When Einstein received his Nobel Prizein 1921, it was  for the photoelectric effect, the suggestion of quantized light. Einstein’s “light quanta” represented the quintessential example of wave–particle duality. Electromagnetic radiation propagates following  linear wave equations, but can only be emitted or absorbed as discrete elements, thus acting as a wave and a particle simultaneously.

Radioactivity Changes the Scientific Landscape

The turn of the century also features radioactivity, which later came to the forefront of the activities of World War II, the Manhattan Project, the discovery of the chain reaction, and later – Hiroshima and Nagasaki.

Marie Curie

Marie Curie

 

 

 

Marie Skłodowska-Curie was a Polish and naturalized-French physicist and chemist who conducted pioneering research on radioactivity. She was the first woman to win a Nobel Prize, the only woman to win in two fields, and the only person to win in multiple sciences. She was also the first woman to become a professor at the University of Paris, and in 1995 became the first woman to be entombed on her own merits in the Panthéon in Paris. She shared the 1903 Nobel Prize in Physics with her husband Pierre Curie and with physicist Henri Becquerel. She won the 1911 Nobel Prize in Chemistry.  Her achievements included a theory of radioactivity (a term that she coined, techniques for isolating radioactive isotopes, and the discovery of polonium and radium. She named the first chemical element that she discovered – polonium, which she first isolated in 1898 – after her native country. Under her direction, the world’s first studies were conducted into the treatment of neoplasms using radioactive isotopes. She founded the Curie Institutes in Paris and in Warsaw, which remain major centres of medical research today. During World War I, she established the first military field radiological centres.  Curie died in 1934 due to aplastic anemia brought on by exposure to radiation – mainly, it seems, during her World War I service in mobile X-ray units created by her.

 

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