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Crystal Resolution in Raman Spetctoscopy for Pharmaceutical Analysis

Curator: Larry H. Bernstein, MD, FCAP

 

Investigating Crystallinity Using Low Frequency Raman Spectroscopy: Applications in Pharmaceutical Analysis

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Figure 1: Illustration of an exemplar low-frequency Raman setup with a 785-nm laser.

The second system is based on a pre-built SureBlock XLF-CLM THz-Raman system from Ondax Inc. The laser (830 nm, 200 mW), cleanup filters, and laser line filters are all self-contained inside of the instrument but operate on the same principles as the 785-nm system. The sample is arranged in a 180° backscattering geometry relative to a 10× microscope lens. This system is then coupled via a fiber-optic cable to a Princeton Instruments SP2150i spectrograph and PIXIS 100 CCD camera. The 0.15-m spectrograph is used in conjunction with either a 1200- or 1800-groove/mm blazed diffraction grating to adjust the resolution and spectral range.

Crystalline Versus Amorphous Samples

The Raman spectrum of crystalline and amorphous solids differ greatly in the low-frequency region (see Figure 2) because of the highly ordered and highly disordered molecular environments of the respective solids. However, the mid-frequency region can also be noticeably altered by the changing environment (Figure 3).

 

 

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Figure 3: Raman spectra of griseofulvin

Ensuring Accuracy

A potential issue is optical artifacts, and these may be identified by the analysis of both Stokes and anti-Stokes spectra. One advantage of the experimental setups described is that signal from the sample may be measured within minutes and it is nondestructive, thus allowing Raman spectra to be collected from a single sample using both techniques at virtually the same time. This approach permits the examination of low-frequency Raman data with 785-nm and 830-nm excitation and allows comparison with Fourier transform (FT)-Raman spectra, in which it is possible to collect meaningful data down to a Raman shift of 50 cm-1. The benefits are demonstrated in Figure 4. In this data, each technique produces consistent bands with similar Raman shifts and relative intensities. While Raman data were not collected below 50 cm-1 using the 1064-nm system, the bands at 69 and 96 cm-1 are consistent with the 785- and 830-nm data. Furthermore, the latter two methods show consistency with bands appearing around 32 and 46 cm-1 for both techniques.

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Figure 4: Comparison of the low-frequency region of three Raman spectroscopic techniques.

Case Studies

So far there have been few studies to utilize low-frequency Raman spectroscopy in the analysis of pharmaceutical crystallinity. Despite this, the literature does contain articles that demonstrate the promising applicability of the technique.

Mah and colleagues (38) studied the level of crystallinity of griseofulvin using low-frequency Raman spectroscopy with PLS analysis. In this study a batch of amorphous griseofulvin (which was checked using X-ray powder diffractometry) was prepared by melting the griseofulvin and rapidly cooling it again using liquid nitrogen. Condensed water was removed by placing the sample over phosphorus pentoxide and the glassy sample was then ground using mortar and pestle. Calibrated samples of 2%, 4%, 6%, 8%, and 10% crystallinity were then created though geometric mixing of the amorphous and crystalline samples; following this mixing, the samples were then pressed into tablets. Many tablets were then stored in differing temperatures (30 °C, 35 °C, and 40 °C) at 0% humidity. Low-frequency 785-nm, mid-frequency 785-nm, and FT-Raman spectroscopies were performed simultaneously on each sample. After PLS analysis, limits of detection (LOD) and limits of quantification (LOQ) were calculated. The results of this research showed that each of these three techniques were capable of quantifying crystallinity. It also showed that FT-Raman and low-frequency Raman techniques were able to both detect and quantify crystallinity earlier than the mid-frequency 785 nm Raman technique. The respective LOD and LOQ values for FT-Raman, low-frequency Raman, and mid-frequency Raman are as follows: LOD values: 0.6%, 1.1%, and 1.5%; LOQ values: 1.8%, 3.4%, and 4.6%. The root mean squared errors of prediction (RMSEP) were also calculated and, like the LOD and LOQ values, indicated that the FT-Raman data had the lowest error, followed by the low-frequency Raman, and mid-frequency Raman had the largest errors of the three techniques. The recrystallization tests that were performed indicated that higher temperatures showed a distinct increase in the rate of recrystallization and that each technique provided similar results (within experimental error). It is also important to note that each technique gave similar spectra (where applicable), which provides supporting evidence that the data is meaningful. Overall, the conclusions of this research were that low-frequency predictions of crystallinity are at least as accurate as the predictions made using mid-frequency Raman techniques. It is arguable that low-frequency Raman is better because of the presence of stronger spectral features and because they are intrinsically linked with crystallinity.

Hédoux and colleagues (36) investigated the crystallinity of indomethacin using low-frequency Raman spectroscopy and compared the results with high frequency data. The ranges of interest were indicated to be 5–250 cm-1and 1500–1750 cm-1 regions. Samples of indomethacin were milled using a cryogenic mill to avoid mechanical heating of the sample, with full amorphous samples being obtained after 25 min of milling. Methods used in this study include Raman spectroscopy, isothermal differential scanning calorimetry (DSC), and X-ray diffractometry as well as the milling technique. The primary objective of this research was to use all of these techniques to monitor the crystallization of amorphous indomethacin to the more stable γ-state while the sample was at room temperature–well below the glass transition temperature,Tg = 43 °C. The results of this research did in fact show that low-frequency Raman spectroscopy is a very sensitive technique for identifying very small amounts of crystallinity within mostly amorphous samples. The data was supported by the well-established methods for monitoring crystallinity: XRD and DSC. This paper particularly noted the benefit of low acquisition times associated with low-frequency Raman spectroscopy compared with the other techniques used.

Low-frequency Raman spectroscopy was also used to monitor two polymorphic forms of caffeine after grinding and pressurization of the samples (39). Pressurization was performed hydrostatically using a gasketed membrane diamond anvil cell (MDAC), while ball milling was used as the method of grinding the sample. Analysis methods used were low-frequency Raman and X-ray diffraction. Low-frequency Raman spectra revealed that, upon slight pressurization, caffeine form I transforms into a metastable state slightly different from that of form II and that a disordered (amorphous) state is achieved in both forms when pressurized above 2 GPa. In contrast, it is concluded that grinding results in the transformation of each form into the other with precise grinding times, thus also generating an intermediate form, which was found to only be observable using low-frequency Raman spectroscopy. The caffeine data, as well as the low-frequency data obtained for indomethacin were further discussed by Hédoux and colleagues (40).

Larkin and colleagues (41) used low-frequency Raman in conjunction with other techniques to characterize several different APIs and their various forms. The other techniques include FT-Raman spectroscopy, X-ray powder diffraction (XRPD), and single-crystal X-ray diffractometry. The APIs studied include carbamazepine, apixaban diacid co-crystals, theophylline, and caffeine and were prepared in various ways that are not detailed here. During this research, low-frequency Raman spectroscopy played an important role in understanding the structures while in their various forms. However, more importantly, low-frequency Raman spectroscopy produced information-rich regions below 200 cm-1 for each of the crystalline samples and noticeably broad features when the APIs were in solution.

Wang and colleagues (42) investigated the applicability of low-frequency Raman spectroscopy in the analysis of respirable dosage forms of various pharmaceuticals. The analyzed pharmaceuticals were involved in the treatment of asthma or chronic obstructive pulmonary disease (COPD) and include salmeterol xinafoate, formoterol fumarate, glycopyrronium bromide, fluticasone propionate, mometasone furoate, and salbutamol sulfate. Various formulations of amino acid excipients were also analyzed in this study. Results indicated that the use of low-frequency Raman analysis was beneficial because of the large features found in the region and allowed for reliable identification of each of the dosage forms. Not only this, it also allowed unambiguous identification of two similar bronchodilators, albuterol (Ventolin) and salbutamol (Airomir).

Heyler and colleagues (43) collected both the low-frequency and fingerprint region of Raman spectra from several polymorphs of carbamazepine, an anticonvulsant and mood stabilizer. This study found that the different polymorphs of this API could be distinguished effectively using these two regions. Similarly, Al-Dulaimi and colleagues (44) demonstrated that polymorphic forms of paracetamol, flufenamic acid, and imipramine hydrochloride could be screened using low-frequency Raman and only milligram quantities of each drug. In this study, paracetamol and flufenamic acid were used as the model compounds for comparison with a previously unstudied system (imipramine hydrochloride). Features within the low-frequency Raman regions of spectra were shown to be significantly different between forms of each drug. Therefore this study also indicated that the polymorphs were highly distinguishable using the technique. Hence, like all other previously mentioned case studies, these investigations further demonstrate the utility of low-frequency Raman spectroscopy as a fast and effective method for screening pharmaceuticals for crystallinity.

Conclusions

Low-frequency Raman spectroscopy is a new technique in the field of pharmaceuticals, as well as in general studies of crystallinity. This is despite indications in previous studies showing an innate ability of the technique for identifying crystalline materials and in some cases, quantifying crystallinity. Arguably one of the most beneficial aspects of this technique is the relatively small amount of time necessary to prepare and analyze samples when compared with XRD or DSC. This should ensure the growing use of low-frequency Raman spectroscopy in, not only pharmaceutical crystallinity studies, but also crystallinity studies of other substances as well.

References

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The drawing in Figure 1 is that of a six-membered ring or hexagon. A carbon atom is located at each vertex of the hexagon and a hydrogen atom is attached to each carbon, although it is not written in. The circle inside the ring represents that the electrons are delocalized which is illustrated in Figure 2.

http://images.alfresco.advanstar.com/alfresco_images/pharma/2016/02/12/645ee751-2432-4444-8af1-ded62697ee27/IR-Spectral-figure02_web.jpg

Figure 2: Top: The P orbitals on each of the six carbon atoms in benzene that contribute an electron to the ring. Bottom: the collection of delocalized P orbital electrons forming a cloud of electron density above and below the benzene ring.

Each of the carbon atoms in a benzene ring contains two P orbitals containing a lone electron, and one of these orbitals is perpendicular to the benzene ring as seen in the top of Figure 2. There is enough orbital overlap that these electrons, rather than being confined between two carbon atoms as might be expected, instead delocalize and form clouds of electron density above and below the plane of the ring. This type of bonding is called aromatic bonding(2), and a ring that has aromatic bonding is called an aromatic ring. It is aromatic bonding that gives aromatic rings their unique structures, chemistry, and IR spectra. Benzene is simply a commonly found aromatic ring. Other types of aromatic molecules include polycyclic aromatic hydrocarbons (PAHs), such as naphthalene, that contain two or more benzene rings that are fused (which means adjacent rings share two carbon atoms), and heterocyclic aromatic rings which are aromatic rings that contain a noncarbon atom such as nitrogen. Pyridine is an example of one of these. The interpretation of the IR spectra of these latter aromatic molecules will be discussed in future articles.

The IR Spectrum of Benzene

The IR spectrum of benzene is shown in Figure 3.

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09:00

Super-Resolution Fluorescence Microscopy: Where To Go Now?
Bernd Rieger, Quantitative Imaging Group Leader, Delft University of Technology

09:30

Keynote Presentation

From Molecules To Whole Organs
Francesco Pavone, Principal Investigator, LENS, University of Florence

Some examples of correlative microscopies, combining linear and non linear techniques will be described. Particular attention will be devoted Alzheimer disease or to neural plasticity after damage as neurobiological application.

10:15

Super-Resolution Imaging by dSTORM
Markus Sauer, Professor, Julius-Maximilians-Universität Würzburg

10:45

Coffee and Networking in Exhibition Hall

11:15

Correlated Fluorescence And X-Ray Tomography: Finding Molecules In Cellular CT Scans
Carolyn Larabell, Professor, University of California San Francisco

11:45

Integrating Advanced Fluorescence Microscopy Techniques Reveals Nanoscale Architecture And Mesoscale Dynamics Of Cytoskeletal Structures Promoting Cell Migration And Invasion
Alessandra Cambi, Assistant Professor, University of Nijmegen

This lecture will describe our efforts to exploit and integrate a variety of advanced microscopy techniques to unravel the nanoscale structural and dynamic complexity of individual podosomes as well as formation, architecture and function of mesoscale podosome clusters.

12:15

Multi-Photon-Like Fluorescence Microscopy Using Two-Step Imaging Probes
George Patterson, Investigator, National Institutes of Health

12:45

Lunch & Networking in Exhibition Hall

14:15

Technology Spotlight

14:30

3D Single Particle Tracking: Following Mitochondria in Zebrafish Embryos
Don Lamb, Professor, Ludwig-Maximilians-University

15:00

Visualizing Mechano-Biology: Quantitative Bioimaging Tools To Study The Impact Of Mechanical Stress On Cell Adhesion And Signalling
Bernhard Wehrle-Haller, Group Leader, University of Geneva

15:30

Superresolution Imaging Of Clathrin-Mediated Endocytosis In Yeast
Jonas Ries, Group Leader, EMBL Heidelberg

We use single-molecule localization microscopy to investigate the dynamic structural organization of the east endocytic machinery. We discovered a striking ring-shaped pre-patterning of the actin nucleation zone, which is key for an efficient force generation and membrane invagination.

16:00

Coffee and Networking in Exhibition Hall

16:30

Optical Imaging of Molecular Mechanisms of Disease
Clemens Kaminski, Professor, University of Cambridge

17:00

3-D Optical Tomography For Ex Vivo And In Vivo Imaging
James McGinty, Professor, Imperial College London

17:30

End Of Day One

Wednesday, 15 June 2016

09:00

Imaging Gene Regulation in Living Cells at the Single Molecule Level
James Zhe Liu, Group Leader, Janelia Research Campus, Howard Hughes Medical Institute

09:30

Keynote Presentation

Super-Resolution Microscopy With DNA Molecules
Ralf Jungmann, Group Leader, Max Planck Institute of Biochemistry

10:15

A Revolutionary Miniaturised Instrument For Single-Molecule Localization Microscopy And FRET
Achillefs Kapanidis, Professor, University of Oxford

10:45

Coffee and Networking in Exhibition Hall

11:15

Democratising Live-Cell High-Speed Super-Resolution Microscopy
Ricardo Henriques, Group Leader, University College London

11:45

Democratising Live-Cell High-Speed Super-Resolution Microscopy

12:15

Information In Localisation Microscopy
Susan Cox, Professor, Kings College London

12:45

Lunch & Networking in Exhibition Hall

14:15

Technology Spotlight

14:30

High-Content Imaging Approaches For Drug Discovery For Neglected Tropical Diseases
Manu De Rycker, Team Leader, University of Dundee

The development of new drugs for intracellular parasitic diseases is hampered by difficulties in developing relevant high-throughput cell-based assays. Here we present how we have used image-based high-content screening approaches to address some of these issues.

15:00

High Resolution In Vivo Histology: Clinical in vivo Subcellular Imaging using Femtoseceond Laser Multiphoton/CARS Tomography
Karsten König, Professor, Saarland University

We report on a certified, medical, transportable multipurpose nonlinear microscopic imagingsystem based on a femtosecond excitation source and a photonic crystal fiber with multiple miniaturized time-correlated single-photon counting detectors.

15:30

Coffee and Networking in Exhibition Hall

16:00

Lateral Organization Of Plasma Membrane Constituents At The Nanoscale
Gerhard Schutz, Professor, Vienna University of Technology

It is of interest how proteins are spatially distributed over the membrane, and whether they conjoin and move as part of multi-molecular complexes. In my lecture, I will discuss methods for approaching the two questions, and provide biological examples.

16:30

Correlative Light And Electron Microscopy In Structural Cell Biology
Wanda Kukulski, Group Leader, University of Cambridge

17:00

Close of Conference

 

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Human Factor Engineering: New Regulations Impact Drug Delivery, Device Design And Human Interaction

Curator: Stephen J. Williams, Ph.D.

Institute of Medicine report brought medical errors to the forefront of healthcare and the American public (Kohn, Corrigan, & Donaldson, 1999) and  estimated that between

44,000 and 98,000 Americans die each year as a result of medical errors

An obstetric nurse connects a bag of pain medication intended for an epidural catheter to the mother’s intravenous (IV) line, resulting in a fatal cardiac arrest. Newborns in a neonatal intensive care unit are given full-dose heparin instead of low-dose flushes, leading to threedeaths from intracranial bleeding. An elderly man experiences cardiac arrest while hospitalized, but when the code blue team arrives, they are unable to administer a potentially life-saving shock because the defibrillator pads and the defibrillator itself cannot be physically connected.

Human factors engineering is the discipline that attempts to identify and address these issues. It is the discipline that takes into account human strengths and limitations in the design of interactive systems that involve people, tools and technology, and work environments to ensure safety, effectiveness, and ease of use.

 

FDA says drug delivery devices need human factors validation testing

Several drug delivery devices are on a draft list of med tech that will be subject to a final guidance calling for the application of human factors and usability engineering to medical devices. The guidance calls called for validation testing of devices, to be collected through interviews, observation, knowledge testing, and in some cases, usability testing of a device under actual conditions of use. The drug delivery devices on the list include anesthesia machines, autoinjectors, dialysis systems, infusion pumps (including implanted ones), hemodialysis systems, insulin pumps and negative pressure wound therapy devices intended for home use. Studieshave consistently shown that patients struggle to properly use drug delivery devices such as autoinjectors, which are becoming increasingly prevalent due to the rise of self-administered injectable biologics. The trend toward home healthcare is another driver of usability issues on the patient side, while professionals sometimes struggle with unclear interfaces or instructions for use.

 

Humanfactors engineering, also called ergonomics, or human engineering, science dealing with the application of information on physical and psychological characteristics to the design of devices and systems for human use. ( for more detail see source@ Britannica.com)

The term human-factors engineering is used to designate equally a body of knowledge, a process, and a profession. As a body of knowledge, human-factors engineering is a collection of data and principles about human characteristics, capabilities, and limitations in relation to machines, jobs, and environments. As a process, it refers to the design of machines, machine systems, work methods, and environments to take into account the safety, comfort, and productiveness of human users and operators. As a profession, human-factors engineering includes a range of scientists and engineers from several disciplines that are concerned with individuals and small groups at work.

The terms human-factors engineering and human engineering are used interchangeably on the North American continent. In Europe, Japan, and most of the rest of the world the prevalent term is ergonomics, a word made up of the Greek words, ergon, meaning “work,” and nomos, meaning “law.” Despite minor differences in emphasis, the terms human-factors engineering and ergonomics may be considered synonymous. Human factors and human engineering were used in the 1920s and ’30s to refer to problems of human relations in industry, an older connotation that has gradually dropped out of use. Some small specialized groups prefer such labels as bioastronautics, biodynamics, bioengineering, and manned-systems technology; these represent special emphases whose differences are much smaller than the similarities in their aims and goals.

The data and principles of human-factors engineering are concerned with human performance, behaviour, and training in man-machine systems; the design and development of man-machine systems; and systems-related biological or medical research. Because of its broad scope, human-factors engineering draws upon parts of such social or physiological sciences as anatomy, anthropometry, applied physiology, environmental medicine, psychology, sociology, and toxicology, as well as parts of engineering, industrial design, and operations research.

source@ Britannica.com

The human-factors approach to design

Two general premises characterize the approach of the human-factors engineer in practical design work. The first is that the engineer must solve the problems of integrating humans into machine systems by rigorous scientific methods and not rely on logic, intuition, or common sense. In the past the typical engineer tended either to ignore the complex and unpredictable nature of human behaviour or to deal with it summarily with educated guesses. Human-factors engineers have tried to show that with appropriate techniques it is possible to identify man-machine mismatches and that it is usually possible to find workable solutions to these mismatches through the use of methods developed in the behavioral sciences.

The second important premise of the human-factors approach is that, typically, design decisions cannot be made without a great deal of trial and error. There are only a few thousand human-factors engineers out of the thousands of thousands of engineers in the world who are designing novel machines, machine systems, and environments much faster than behavioral scientists can accumulate data on how humans will respond to them. More problems, therefore, are created than there are ready answers for them, and the human-factors specialist is almost invariably forced to resort to trying things out with various degrees of rigour to find solutions. Thus, while human-factors engineering aims at substituting scientific method for guesswork, its specific techniques are usually empirical rather than theoretical.

HFgeneralpic

 

 

 

 

 

 

 

 

 

 

 

The Man-Machine Model: Human-factors engineers regard humans as an element in systems

The simple man-machine model provides a convenient way for organizing some of the major concerns of human engineering: the selection and design of machine displays and controls; the layout and design of workplaces; design for maintainability; and the work environment.

Components of the Man-Machine Model

  1. human operator first has to sense what is referred to as a machine display, a signal that tells him something about the condition or the functioning of the machine
  2. Having sensed the display, the operator interprets it, perhaps performs some computation, and reaches a decision. In so doing, the worker may use a number of human abilities, Psychologists commonly refer to these activities as higher mental functions; human-factors engineers generally refer to them as information processing.
  3. Having reached a decision, the human operator normally takes some action. This action is usually exercised on some kind of a control—a pushbutton, lever, crank, pedal, switch, or handle.
  4. action upon one or more of these controls exerts an influence on the machine and on its output, which in turn changes the display, so that the cycle is continuously repeated

 

Driving an automobile is a familiar example of a simple man-machine system. In driving, the operator receives inputs from outside the vehicle (sounds and visual cues from traffic, obstructions, and signals) and from displays inside the vehicle (such as the speedometer, fuel indicator, and temperature gauge). The driver continually evaluates this information, decides on courses of action, and translates those decisions into actions upon the vehicle’s controls—principally the accelerator, steering wheel, and brake. Finally, the driver is influenced by such environmental factors as noise, fumes, and temperature.

 

hfactorconsideroutcomes

How BD Uses Human Factors to Design Drug-Delivery Systems

Posted in Design Services by Jamie Hartford on August 30, 2013

 Human factors testing has been vital to the success of the company’s BD Physioject Disposable Autoinjector.

Improving the administration and compliance of drug delivery is a common lifecycle strategy employed to enhance short- and long-term product adoption in the biotechnology and pharmaceutical industries. With increased competition in the industry and heightened regulatory requirements for end-user safety, significant advances in product improvements have been achieved in the injectable market, for both healthcare professionals and patients. Injection devices that facilitate preparation, ease administration, and ensure safety are increasingly prevalent in the marketplace.

Traditionally, human factors engineering addresses individualized aspects of development for each self-injection device, including the following:

  • Task analysis and design.
  • Device evaluation and usability.
  • Patient acceptance, compliance, and concurrence.
  • Anticipated training and education requirements.
  • System resilience and failure.

To achieve this, human factors scientists and engineers study the disease, patient, and desired outcome across multiple domains, including cognitive and organizational psychology, industrial and systems engineering, human performance, and economic theory—including formative usability testing that starts with the exploratory stage of the device and continues through all stages of conceptual design. Validation testing performed with real users is conducted as the final stage of the process.

To design the BD Physioject Disposable Autoinjector System , BD conducted multiple human factors studies and clinical studies to assess all aspects of performance safety, efficiency, patient acceptance, and ease of use, including pain perception compared with prefilled syringes.5 The studies provided essential insights regarding the overall user-product interface and highlighted that patients had a strong and positive response to both the product design and the user experience.

As a result of human factors testing, the BD Physioject Disposable Autoinjector System provides multiple features designed to aide in patient safety and ease of use, allowing the patient to control the start of the injection once the autoinjector is placed on the skin and the cap is removed. Specific design features included in the BD Physioject Disposable Autoinjector System include the following:

  • Ergonomic design that is easy to handle and use, especially in patients with limited dexterity.
  • A 360° view of the drug and injection process, allowing the patient to confirm full dose delivery.
  • A simple, one-touch injection button for activation.
  • A hidden needle before and during injection to reduce needle-stick anxiety.
  • A protected needle before and after injection to reduce the risk of needle stick injury.

 

YouTube VIDEO: Integrating Human Factors Engineering (HFE) into Drug Delivery

 

Notes:

 

 

The following is a slideshare presentation on Parental Drug Delivery Issues in the Future

 The Dangers of Medical Devices

The FDA receives on average 100,000 medical device incident reports per year, and more than a third involve user error.

In an FDA recall study, 44% of medical device recalls are due to design problems, and user error is often linked to the poor design of a product.

Drug developers need to take safe drug dosage into consideration, and this consideration requires the application of thorough processes for Risk Management and Human Factors Engineering (HFE).

Although unintended, medical devices can sometimes harm patients or the people administering the healthcare. The potential harm arises from two main sources:

  1. failure of the device and
  2. actions of the user or user-related errors. A number of factors can lead to these user-induced errors, including medical devices are often used under stressful conditions and users may think differently than the device designer.

Human Factors: Identifying the Root Causes of Use Errors

Instead of blaming test participants for use errors, look more carefully at your device’s design.

Great posting on reasons typical design flaws creep up in medical devices and where a company should integrate fixes in product design.
Posted in Design Services by Jamie Hartford on July 8, 2013

 

 

YouTube VIDEO: Integrating Human Factors Engineering into Medical Devices

 

 

Notes:

 

 Regulatory Considerations

  • Unlike other medication dosage forms, combination products require user interaction
  •  Combination products are unique in that their safety profile and product efficacy depends on user interaction
Human Factors Review: FDA Outlines Highest Priority Devices

Posted 02 February 2016By Zachary Brennan on http://www.raps.org/Regulatory-Focus/News/2016/02/02/24233/Human-Factors-Review-FDA-Outlines-Highest-Priority-Devices/ 

The US Food and Drug Administration (FDA) on Tuesday released new draft guidance to inform medical device manufacturers which device types should have human factors data included in premarket submissions, as well final guidance from 2011 on applying human factors and usability engineering to medical devices.

FDA said it believes these device types have “clear potential for serious harm resulting from use error and that review of human factors data in premarket submissions will help FDA evaluate the safety and effectiveness and substantial equivalence of these devices.”

Manufacturers should provide FDA with a report that summarizes the human factors or usability engineering processes they have followed, including any preliminary analyses and evaluations and human factors validation testing, results and conclusions, FDA says.

The list was based on knowledge obtained through Medical Device Reporting (MDRs) and recall data, and includes:

  • Ablation generators (associated with ablation systems, e.g., LPB, OAD, OAE, OCM, OCL)
  • Anesthesia machines (e.g., BSZ)
  • Artificial pancreas systems (e.g., OZO, OZP, OZQ)
  • Auto injectors (when CDRH is lead Center; e.g., KZE, KZH, NSC )
  • Automated external defibrillators
  • Duodenoscopes (on the reprocessing; e.g., FDT) with elevator channels
  • Gastroenterology-urology endoscopic ultrasound systems (on the reprocessing; e.g., ODG) with elevator channels
  • Hemodialysis and peritoneal dialysis systems (e.g., FKP, FKT, FKX, KDI, KPF ODX, ONW)
  • Implanted infusion pumps (e.g., LKK, MDY)
  • Infusion pumps (e.g., FRN, LZH, MEA, MRZ )
  • Insulin delivery systems (e.g., LZG, OPP)
  • Negative-pressure wound therapy (e.g., OKO, OMP) intended for home use
  • Robotic catheter manipulation systems (e.g., DXX)
  • Robotic surgery devices (e.g., NAY)
  • Ventilators (e.g., CBK, NOU, ONZ)
  • Ventricular assist devices (e.g., DSQ, PCK)

Final Guidance

In addition to the draft list, FDA finalized guidance from 2011 on applying human factors and usability engineering to medical devices.

The agency said it received over 600 comments on the draft guidance, which deals mostly with design and user interface, “which were generally supportive of the draft guidance document, but requested clarification in a number of areas. The most frequent types of comments requested revisions to the language or structure of the document, or clarification on risk mitigation and human factors testing methods, user populations for testing, training of test participants, determining the appropriate sample size in human factors testing, reporting of testing results in premarket submissions, and collecting human factors data as part of a clinical study.”

In response to these comments, FDA said it revised the guidance, which supersedes guidance from 2000 entitled “Medical Device Use-Safety: Incorporating Human Factors Engineering into Risk Management,” to clarify “the points identified and restructured the information for better readability and comprehension.”

Details

The goal of the guidance, according to FDA, is to ensure that the device user interface has been designed such that use errors that occur during use of the device that could cause harm or degrade medical treatment are either eliminated or reduced to the extent possible.

FDA said the most effective strategies to employ during device design to reduce or eliminate use-related hazards involve modifications to the device user interface, which should be logical and intuitive.

In its conclusion, FDA also outlined the ways that device manufacturers were able to save money through the use of human factors engineering (HFE) and usability engineering (UE).

– See more at: http://www.raps.org/Regulatory-Focus/News/2016/02/02/24233/Human-Factors-Review-FDA-Outlines-Highest-Priority-Devices/#sthash.cDTr9INl.dpuf

 

Please see an FDA PowerPoint on Human Factors Regulatory Issues for Combination Drug/Device Products here: MFStory_RAPS 2011 – HF of ComboProds_v4

 

 

 

 

Read Full Post »


BioMEMS The Market aspects of Oligonucleotide-Chips, Products and Applications, Competition, January 21, 2016

Curator: Gérard LOISEAU, ESQ

 

BioMEMS

The Market aspects of Oligonucleotide-Chips, Products, Applications, Competition 

January 21, 2016

2015-2020

The oligonucleotide synthesis market is expected to reach USD 1.918.6Billion at a CAGR of 10.1% by 2020 from USD 1.078.1Billion in 2015.

SOURCE

MARKETSANDMARKETS marketsandmarkets.com/

 

PLAYERS

  • Agilent Technologies Inc.
  • BioAutomation Corp.
  • Biosearch Technologies
  • Gen9 Inc.
  • GenScript Inc.
  • Illumina Inc.
  • Integrated DNA Technologies
  • New England Biolabs Inc.
  • Nitto Denko Avecia Inc.
  • OriGene Technologies Inc.
  • Sigma-Aldrich Corporation
  • Thermo Fisher Scientific Inc.
  • TriLink Biotechnologies

 

Agilent Technologies
 CA NYSE :A


http://www.agilent.com/

  • Agilent was created as a spin off from Hewlett-Packard Company in 1999.
  • Agilent Technologies Inc. is engaged in the life sciences, diagnostics and applied chemical markets. The Company provides application focused solutions that include instruments, software, services and consumables for the entire laboratory workflow. The Company has three business segments:

the life sciences and applied markets business,

the diagnostics and genomics business, and

the Agilent Cross Lab business

  • The Company’s life sciences and applied markets business segment brings together the Company’s analytical laboratory instrumentation and informatics.
  • The Company’s diagnostics and genomics business segment consists of three businesses: the Dako business, the genomics business and the nucleic acid solutions business.
  • The Company’s Agilent Cross Lab business segment combines its analytical laboratory services and consumables business

SOURCE

http://reuters.com/

PRODUCTS AND SERVICES

https://www.agilent.com/en-us/default#collapse-0

  • October 09, 2015 03:21 PM Eastern Daylight Time
  • CARPINTERIA, Calif.–(BUSINESS WIRE)–Dako, an Agilent Technologies company and a worldwide provider of cancer diagnostics, today announced the U.S. Food and Drug Administration has approved a new test that can identify PD-L1 expression levels on the surface of non-small cell lung cancer tumor cells and provide information on the survival benefit with OPDIVO® (nivolumab) for patients with non-squamous NSCLC.

SOURCE

BUSINESS WIRE busibesswire.com/

 

BioAutomation Corp.

 TX


 

http://bioautomation.com/

          PRODUCTS AND SERVICES

  • DNA and RNA synthesis reagents for the MerMades

 

Note: The MerMade 192E Oligonucleotide synthesizer is designed to synthesize DNA, RNA & LNA oligonucleotides in a column format

          PARTNERSHIPS

  • HONGENE BIOTECH : BIOAUTOMATION is the exclusive distributor for the Americas
  • EMD MILLIPORE
  • BIOSEARCH TECHNOLOGIES

 

DISTRIBUTORS

  • LINK TECHNOLOGIES : UK
  • AME BIOSCIENCE : UK
  • BOSUNG SCIENCE : KOREA
  • DNA CHEM : CHINA
  • WAKO : JAPAN
  • ACE PROBE : INDIA

SOURCE

bioautomation.com/

 

Biosearch Technologies
 CA


http://biosearchtech.com/

          PRODUCTS

  • qPCR & SNP Genotyping
  • Custom Oligonucleotides
  • – highly sophisticated oligonucleotides
  • – simple PCR primers
  • Oligos in Plates
  • RNA FISH
  • Synthesis Reagents
  • Immunochemicals
  • Primers
  • Probes
  • Large-Scale Synthesis Oligos
  • Intermediate-Scale Synthesis Oligos

          SERVICES

  • GMP & Commercial Services
  • OEM & Kit Manufacturing
  • qPCR Design Collaborations

          DISTRIBUTORS

Argentina | Australia | Austria | Brazil | Canada |Chile | China | Colombia | Czech Republic | Denmark | Ecuador | Finland | Germany |Hong Kong | Israel | Italy | Japan | Korea | Malaysia | Mexico | New Zealand | Norway | Paraguay | Peru| Philippines | Poland | Romania | Singapore | South Africa | Spain | Sweden |Switzerland | Taiwan ROC | Thailand | Turkey | United Kingdom | Uruguay | Vietnam

SOURCE

biosearchtech.com/

 

Gen9 Inc.
 MA 


http://www.gen9bio.com/

          PRODUCTS

Gen9 is building on advances in synthetic biology to power a scalable fabrication capability that will significantly increase the world’s capacity to produce DNA content. The privately held company’s next-generation gene synthesis technology allows for the high-throughput, automated production of DNA constructs at lower cost and higher accuracy than previous methods on the market. Founded by world leaders in synthetic biology, Gen9 aims to ensure the constructive application of synthetic biology in industries ranging from enzyme and chemical production to pharmaceuticals and biofuels.

          SERVICES

  • Synthetic Biology
  • Gene Synthesis Services
  • Variant Libraries
  • Gene Sequence Design Services

         INVESTORS

  • Agilent Technologies : Private Equity
  • CAMBRIDGE, Mass. and SANTA CLARA, Calif. — April 24, 2013 —Gen9 Receives $21 Million Strategic Investment from Agilent Technologies

SOURCE

gen9bio.com/

 

GenScript Inc.
 NJ 


http://www.genscript.com/

  • GenScript is the largest gene synthesis provider in the USA
  • GenScript Corporation, a biology contract research organization, provides biological research and drug discovery services to pharmaceutical companies, biotech firms, and research institutions in the United States, Europe, and Japan. It offers bio-reagent, custom molecular biology, custom peptide, protein production, custom antibody production, drug candidates testing, assay development and screening, lead optimization, antibody drug development, gene synthesis, and assay-ready cell line production services.
  • The company also offers molecular biology, peptide, protein, immunoassay, chemicals, and cell biology products. It offers its products through distributors in Tokyo, Japan; and Seoul, Korea. GenScript Corporation has a strategic partnership with Immunologix, Inc. The company was founded in 2002 and is based in Piscataway, New Jersey. It has subsidiaries in France, Japan, and China.

 

Note: As of October 24, 2011, Immunologix, Inc. was acquired by Intrexon Corporation. Immunologix, Inc. develops and produces antibody-based therapeutics for various biological targets. It produces human monoclonal antibodies against viral, bacterial, and tumor antigens, as well as human auto antigens.

Intrexon Corporation, founded in 1998, is a leader in synthetic biology focused on collaborating with companies in Health, Food, Energy, Environment and Consumer sectors to create biologically based products that improve quality of life and the health of the planet.

 

 

             PRODUCTS AND SERVICES

  • Gene synthesis
  • Antibody services
  • Protein Services
  • Peptide services

 

               INVESTORS


Note: The Balloch Group (‘TBG’) was established in 2001 by Howard Balloch (Canada‘s ambassador to China from 1996 to 2001). TBG has since grown from a market-entry consultancy working with North American clients in China to a leading advisory and merchant banking firm serving both domestic Chinese companies and multinational corporations. TBG was ranked as the number one boutique investment bank in China by ChinaVenture in 2008.

Kleiner, Perkins, Caufield and Byers

 

Illumina
Inc. CA


http://illumina.com/

 

Monica Heger : SAN FRANCISCO (GenomeWeb) – Illumina today announced two new next-generation sequencing platforms, a targeted sequencing system called MiniSeq and a semiconductor sequencer that is still under development.

Illumina disclosed the initiatives during a presentation at the JP Morgan Healthcare conference held here today. During the presentation, Illumina CEO Jay Flatley also announced a new genotyping array called Infinium XT; a partnership with Bio-Rad to develop a single-cell sequencing workflow; preliminary estimates of its fourth-quarter 2015 revenues; and an update on existing products. The presentation followed the company’s announcement on Sunday that it has launched a new company called Grail to develop a next-generation sequencing test for early cancer detection from patient blood samples.

The MiniSeq system, which is based on Illumina’s current sequencing technology, will begin shipping early this quarter and has a list price of $49,500. It can perform a variety of targeted DNA and RNA applications, from single-gene to pathway sequencing, and promises “all-in” prices, including library prep and sequencing, of $200 to $300 per sample, Flatley said during the JP Morgan presentation.

SOURCES

https://www.genomeweb.com/sequencing-technology/illumina-unveils-mini-targeted-sequencer-semiconductor-sequencing-project-jp

http://investor.biospace.com/biospace/quote?Symbol=ILMN

 

              PRODUCTS AND SERVICES

  •               Mid to large scale manufacturing assets
  •               Analytical Labs
  •               Pre-clinical
  •               Clinical
  •               Launched products

 

              COMPETITORS

https://finance.yahoo.com/q/co?s=ILMN+Competitors Tue, Feb 2, 2016, 2:16pm EST – US Markets

ILMN PVT1 AFFX LMNX Industry
Market Cap: 22.75B N/A 1.13B 835.66M 134.14M
Employees: 3,700 10,000 1,200 745 45.00
Qtrly Rev Growth (yoy): 0.14 N/A -0.01 0.07 0.18
Revenue (ttm): 2.14B 3.80B1 357.74M 235.37M 8.47M
Gross Margin (ttm): 0.73 N/A 0.63 0.71 0.58
EBITDA (ttm): 770.84M N/A 46.64M 52.99M -12.31M
Operating Margin (ttm): 0.30 N/A 0.08 0.17 -1.62
Net Income (ttm): 510.36M 430.90M1 11.22M 39.29M N/A
EPS (ttm): 3.42 N/A 0.13 0.93 -0.34
P/E (ttm): 45.43 N/A 104.40 20.91 25.33
PEG (5 yr expected): 2.68 N/A 4.66 0.55 N/A
P/S (ttm): 10.87 N/A 3.13 3.45 13.65

 

Pvt1 = Life Technologies Corporation (privately held)

AFFX = Affymetrix Inc.

LMNX = Luminex Corporation

 

 

Integrated DNA Technologies (IDT)
IOWA + CA

http://www.com/

 

Integrated DNA Technologies, Inc. (IDT), the global leader in nucleic acid synthesis, serving all areas of life sciences research and development, offers products for a broad range of genomics applications. IDT’s primary business is the production of custom, synthetic nucleic acids for molecular biology applications, including qPCR, sequencing, synthetic biology, and functional genomics. The company manufactures and ships an average of 44,000 custom nucleic acids per day to more than 82,000 customers worldwide. For more information, visit idtdna.com.

 

               PRODUCTS AND SERVICES

               https://eu.idtdna.com/site

  • DNA & RNA Synthesis
  • Custom DNA Oligos 96- & 384-Well Plates Ultramer Oligos Custom RNA Oligos SameDay Oligos HotPlates ReadyMade Primers Oligo Modifications Freedom
  • Dyes GMP for Molecular Diagnostics Large Scale Oligo Synthesis

 

Note : Skokie, IL – December 1, 2015. Integrated DNA Technologies Inc. (“IDT”), the global leader in custom nucleic acid synthesis, has entered into a definitive agreement to acquire the oligonucleotide synthesis business of AITbiotech Pte. Ltd. in Singapore (“AITbiotech”). With this acquisition, IDT expands its customer base across Southeast Asia making it possible for these additional customers to now have access to its broad range of products for genomic applications. AITbiotech will continue operations in its other core business areas.

 

New England Biolabs Inc.
 MA 


http://www.neb.com/

 

                PRODUCTS AND SERVICES

  •                 Restriction Endonucleases
  •                 PCR, Polymerases & Amplification Technologies
  •                 DNA Modifying Enzymes
  •                 Library Preparation for Next Generation Sequencing
  •                 Nucleic Acid Purification
  •                 Markers & Ladders
  •                 RNA Reagents
  •                 Gene Expression
  •                 Cellular Analysis

SOURCE

neb.com/

 

Nitto Denko Avecia Inc.
 MA


http://avecia.com/

 

With over 20 years of experience in oligonucleotide development and production, and over 1000 sequences manufactured, Avecia has played an integral role in the advancing oligo therapeutic market. Our mission is to continue to build value for our customers, as they progress through drug development into commercialization. And as a member of the Nitto Denko Corporation (nitto.com), Avecia is committed to the future of the oligonucleotide market. We are driven by innovative ideas and flexible solutions, designed to provide our customers with the best in service, quality, and technology.

 

SOURCE

http://avecia.com/

 

Note : 1918 Nitto Electric Industrial Co., Ltd. forms in Ohsaki, Tokyo, to produce electrical insulating materials in Japan.

2011 Acquires Avecia Biotechnology Inc. in the U.S.A.

 

 

OriGene Technologies Inc.
 CA

http://www.com/

 

OriGene Technologies, Inc. develops, manufactures, and sells genome wide research and diagnostic products for pharmaceutical, biotechnology, and academic research applications. The company offers cDNA clones, including TrueORF cDNA, viral ORF, destination vectors, TrueClones (human), TrueClones (mouse), organelle marker plasmids, MicroRNA tools, mutant and variant clones, plasmid purification kits, transfection reagents, and gene synthesis service; and HuSH shRNA, siRNA, miRNA, qPCR reagents, plasmid purification products, transfection reagents, PolyA+ and total RNA products, first-strand cDNA synthesis, and CRISPR/Cas9 genome products. It also provides proteins and lysates, such as purified human proteins, over-expression cell lysates, mass spectrometry standard proteins, and protein purification reagents; UltraMAB IHC antibodies, TrueMAB primary antibodies, anti-tag and fluorescent proteins, ELISA antibodies, luminex antibodies, secondary antibodies, and controls and others; and anatomic pathology products, including IHC antibodies, detection systems, and IHC accessories

The company offers luminex and ELISA antibody pairs, autoantibody profiling arrays, ELISA kits, cell assay kits, assay reagents, custom development, and fluorogenic cell assays; TissueFocus search tools; tissue sections; tissue microarrays, cancer protein lysate arrays, TissueScan cDNA arrays, tissue blocks, and quality control products, as well as tissue RNA, DNA, and protein lysates; and lab essentials. Its research areas include cancer biomarker research, RNAi, pathology IHC, stem cell research, ion channels, and protein kinase products. The company provides gene synthesis and molecular biology services, genome editing, custom cloning, custom shRNA, purified protein, monoclonal antibody development, and assay development. It sells its products through distributors worldwide, as well as online. OriGene Technologies, Inc. was incorporated in 1995 and is based in Rockville, Maryland.

SOURCE

http://BLOOMBERG.com

               PRODUCTS AND SERVICES

  •                cDNA Clones
Human, mouse, rat
Expression validated
  •                RNAi
shRNA, siRNA
microRNA & 3’UTR clones
  •                Gene Synthesis
Codon optimization
Variant libraries
  •                Real-time PCR
Primer pairs, panels
SYBR green reagents
  •                Lab Essentials
DNA/RNA purification kits
Transfection reagents
  •                Anatomic Pathology
UltraMAB antibodies
Specificity validated
  •                Recombinant Proteins
10,000 human proteins
from mammalian system
  •                Antibodies
TrueMAB primary antibodies
Anti-tag antibodies
  •                Assays and Kits
ELISA & Luminex antibodies
Autoantibody Profiling Array
  •                Cancer & Normal Tissues
Pathologist verified
gDNA, RNA, sections, arrays

SOURCE

origene.com/

 

Sigma-Aldrich Corporation 
MI 


http://www.sigmaaldrich.com/

Louis, MO – November 18, 2015 Merck KGaA, Darmstadt, Germany, Completes Sigma-Aldrich Acquisition

Merck KGaA today announced the completion of its $17 billion acquisition of Sigma-Aldrich, creating one of the leaders in the $130 billion global industry to help solve the toughest problems in life science.

Press Release: 18-Nov-2015

Letter to our Life Science Customers from Dr. Udit Batra

The life science business of Merck KGaA, Darmstadt, Germany brings together the world-class products and services, innovative capabilities and exceptional talent of EMD Millipore and Sigma-Aldrich to create a global leader in the life science industry.

Everything we do starts with our shared purpose – to solve the toughest problems in life science by collaborating with the global scientific community. 

This combination is built on complementary strengths, which will enable us to serve you even better as one organization than either company could alone.

This means providing a broader portfolio with a catalog of more than 300,000 products, including many of the most respected brands in the industry, greater geographic reach, and an unmatched combination of industry-leading capabilities.

                PRODUCTS AND SERVICES

                http://www.sigmaaldrich.com/configurator/servlet/DesignCenter?btnOpen_0.x=1

                http://www.sigmaaldrich.com/content/dam/sigma-aldrich/common/quality-products.jpg

 

Thermo Fisher Scientific Inc.
 MA 
NYSE :TMO


http://thermofisher.com/

Thermo Fisher Scientific Inc. is a provider of analytical instruments, equipment, reagents and consumables, software and services for research, manufacturing, analysis, discovery and diagnostics. The company operates through four segments: Life Sciences Solutions, provides reagents, instruments and consumables used in biological and medical research, discovery and production of new drugs and vaccines as well as diagnosis of disease; Analytical Instruments, provides instruments, consumables, software and services that are used in the laboratory; Specialty Diagnostics, offers diagnostic test kits, reagents, culture media, instruments and associated products, and Laboratory Products and Services, offers self-manufactured and sourced products for the laboratory.

SOURCE

http://REUTERS.com

 

                PRODUCTS AND SERVICES

  •                 Oligos Value – Standard – Plate
  •                 Primers
  •                 Probes
  •                 Nucleotides

 

                BRANDS

  1.                THERMO SCIENTIFIC
  2.                 APPLIED BIOSYSTEMS
  3.                 INVITROGEN
  4.                 FISHER SCIENTIFIC
  5.                 UNITY LAB SERVICES

 

                 PARTNERSHIPS

AFFYMETRIX : NASDAQ : AFFX : affymetrix.com/

WALTHAM, Mass. & SANTA CLARA, Calif.–(BUSINESS WIRE)–Jan. 8, 2016– Thermo Fisher Scientific Inc. (NYSE:TMO), the world leader in serving science, and Affymetrix Inc. (NASDAQ:AFFX), a leading provider of cellular and genetic analysis products, today announced that their boards of directors have unanimously approved Thermo Fisher’s acquisition of Affymetrix for $14.00 per share in cash. The transaction represents a purchase price of approximately $1.3 billion.

SOURCE

http://BUSINESSWIRE.com

 

TriLink Biotechnologies
 CA 


http://www.com/

 

              PRODUCTS

              Oligonucleotides

  •               DNA Oligos
  •               RNA Oligos
  •               Modified Oligos
  •               Specialty Oligos

              Nucleotides

  •               NTPs (Nucleoside Triphosphates)
  •               Biphosphates
  •               Monophosphates

 

              SERVICES

  •              Custom Chemistry
  •              Reagents
  •              Aptamers

 

             PARTNERSHIPS

  • LIFE TECHNOLOGIES,
  • TERMO FISHER SCIENTIFIC since July 2015 thermofisher.com/
  • GENMARK genmarkdx.com/

SOURCE

http://trilinkbiotech.com/

 

Other related articles published in this Open Access Online Scientific Journal include the following:

Gene Editing: The Role of Oligonucleotide Chips

https://pharmaceuticalintelligence.com/2016/01/07/gene-editing-the-role-of-oligonucleotide-chips/

Gene Editing for Exon 51: Why CRISPR Snipping might be better than Exon Skipping for DMD

https://pharmaceuticalintelligence.com/2016/01/23/gene-editing-for-exon-51-why-crispr-snipping-might-be-better-than-exon-skipping-for-dmd/

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Read Full Post »


newly developed oxazolidinone antibiotics

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

New Antibacterial oxazolidinones in pipeline by Wockhardt

by DR ANTHONY MELVIN CRASTO Ph.D

 

WCK ?

(5S)-N-{3-[3,5-difluoro-4-(4-hydroxy-4-methoxymethyl-piperidin-1-yl)-phenyl]-2-oxo-oxazolidin-5-ylmethyl}-acetamide

MF C19 H25 F2 N3 O5, MW 413.42

Acetamide, N-​[[(5S)​-​3-​[3,​5-​difluoro-​4-​[4-​hydroxy-​4-​(methoxymethyl)​-​1-​piperidinyl]​phenyl]​-​2-​oxo-​5-​oxazolidinyl]​methyl]​-

CAS 957796-51-9

Antibacterial oxazolidinones

THIS MAY BE WCK 4086?????

PATENT

WO 2015173664, US8217058, WO 2012059823, 

 

Oxazolidinone represent a novel chemical class of synthetic antimicrobial agents.Linezolid represents the first member of this class to be used clinically. Oxazolidinones display activity against important Gram-positive human and veterinary pathogens including Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycin Resistant Enterococci (VRE) and β-lactam Resistant Streptococcus pneumoniae (PRSP). The oxazolidinones also show activity against Gram-negative aerobic bacteria, Gram-positive and Gram-negative anaerobes. (Diekema D J et al., Lancet 2001 ; 358: 1975-82).

Various oxazolidinones and their methods of preparation are disclosed in the literature. International Publication No. WO 1995/25106 discloses substituted piperidino phenyloxazolidinones and International Publication No. WO 1996/13502 discloses phenyloxazolidinones having a multisubstituted azetidinyl or pyrrolidinyl moiety. US Patent Publication No. 2004/0063954, International Publication Nos. WO 2004/007489 and WO 2004/007488 disclose piperidinyl phenyl oxazolidinones for antimicrobial use.

Pyrrolidinyl/piperidinyl phenyl oxazohdinone antibacterial agents are also described in Kim H Y et al., Bioorg. & Med. Chem. Lett., (2003), 13:2227-2230. International Publication No. WO 1996/35691 discloses spirocyclic and bicyclic diazinyl and carbazinyl oxazolidinone derivatives. Diazepeno phenyloxazolidinone derivatives are disclosed in the International Publication No. WO 1999/24428. International Publication No. WO 2002/06278 discloses substituted aminopiperidino phenyloxazolidinone derivatives.

Various other methods of preparation of oxazolidinones are reported in US Patent No. 7087784, US Patent No. 6740754, US Patent No. 4948801 , US Patent No. 3654298, US Patent No. 5837870, Canadian Patent No. 681830, J. Med. Chem., 32, 1673 (1989), Tetrahedron, 45, 1323 (1989), J. Med. Chem., 33, 2569 (1990), Tetrahedron Letters, 37, 7937-40 (1996) and Organic Process Research and Development, 11 , 739-741(2007).

Indian Patent Application No. 2534/MUM/2007 discloses a process for the preparation of substituted piperidino phenyloxazolidinones. International Publication No. WO2012/059823 further discloses the process for the preparation of phosphoric acid mono-(L-{4-[(5)-5-(acetylaminomethyl)-2-oxo-oxazolidin-3-yl]-2,6-difluorophenyl}4-methoxymethyl piperidine-4-yl)ester.

US Patent No. 8217058 discloses (5S)-N-{3-[3,5-difluoro-4-(4-hydroxy-4-methoxymethyl-piperidin-l-yl)-phenyl]-2-oxo-oxazolidin-5-ylmethyl}-acetamide as an antibacterial agent and its process for preparation.

PATENT

WO2015173664

https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2015173664&recNum=1&maxRec=&office=&prevFilter=&sortOption=&queryString=&tab=PCTDescription

 

 

PATENT

http://www.google.st/patents/WO2007132314A2?cl=en

 

Figure imgf000004_0001

Wockhardt Ltd,

Figure imgf000006_0001
Figure imgf000006_0002

(3) (4)

 

PATENT

WO 2012059823

http://www.google.co.in/patents/WO2012059823A1?cl=en

Phosphoric acid mono-(l-{4-[(S)-5-(acetylamino- methyl)-2-oxo-oxazolidin-3-yl]-2,6-difluorophenyl}-4-methoxymethyl-piperidin-4-yl) ester of Formula (A),
Figure imgf000022_0001
the process comprising the steps of:
a) Converting intermediate of Formula (1) into intermediate of Formula (3)
Figure imgf000022_0002
b) Converting intermediate of Formula (3) into intermediate of Formula (5)
Figure imgf000022_0003

c) Converting intermediate of Formula (5) into intermediate of structure (6)

Figure imgf000022_0004
(5) <6> d) Converting intermediate of Formula (6) into intermediate of Formula (10)
Figure imgf000023_0001
e) Converting intermediate of Formula (10) into intermediate of Formula (11),
Figure imgf000023_0002

f) Converting intermediate of Formula (11) into compound of Formula (A) or Pharmaceutically acceptable salts thereof

Figure imgf000023_0003

 

 

Figure imgf000006_0001
Figure imgf000006_0002
Figure imgf000006_0003

 

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Hand Held DNA Sequencer

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Point-of-Care DNA Sequencer Inching Closer to Widespread Use as Beta-Testers Praise Oxford Technologies’ Pocketsize, Portable Nanopore Device

November 4, 2015

MinION could help achieve NIH’s goal of $1,000 human genome sequencing and in remote clinics and outbreak zones shift testing away from medical laboratories

Point-of-care DNA sequencing  technology is edging ever closer to widespread commercial use as the Oxford Nanopore MinION sequencer  draws praise and registers successes in pre-release testing.

A pocketsize gene-sequencing machine such as the MinION could transform the marketplace by shifting DNA testing to remote clinics and outbreak zones while eliminating the need to return samples to clinical laboratories for analysis. Such devices also are expected to increase the need for trained genetic pathologists andmedical technologists.

After Much Anticipation, MinION Delivers on Promises

The MinION, produced by United Kingdom-based Oxford Nanopore Technologies, is a miniaturized instrument about the size of a USB memory stick that plugs directly into a PC or laptop computer’s USB port. Unlike bench-top sequencers, the MinION uses nanopore “strand sequencing” technology to deliver ultra-long-read-length single-molecule sequence data.

“The USB-powered sequencer contains thousands of wells, each containing nanopores—narrow protein channels that are only wide enough for a single strand of DNA. When DNA enters the channels, each base gives off a unique electronic signature that can be detected by the system, providing a readout of the DNA sequence,” reported

After several years of unfulfilled promises, Oxford began delivering the MinION in the spring of 2014 to researchers participating in its early access program called MAP . For a $1,000 access fee, participants receive a starter kit and may purchase consumable supplies. The current price for additional flow cells ranges from $900 for one to $500 per piece when purchased in 48-unit quantities.

 

Nick Loman, an Independent Research Fellow in the Institute for Microbiology and Infection at the University of Birmingham, UK, had questioned if MinION’s promise would ever be realized. But the USB-size sequencer won him over after he used it to detect Salmonella within 15 minutes in samples sent from a local hospital.

 

Loman received the MinION in May 2014 as part of the MAP program and quickly tested its usefulness. After using the device to sequence a strain of Pseudomonas aeruginosa, a common hospital-acquired infection (HAI), he next helped solve the riddle of an outbreak of Salmonella infection in a Birmingham hospital that had affected 30 patients and staff.

“The hospital wanted to understand quickly what was happening,” Loman stated. “But routine genome sequencing is quite slow. It usually takes weeks or even months to get information back.”

Using MinION, Loman detected Salmonella in some of the samples sent from the hospital in less than 15 minutes. Ultimately, the main source of the outbreak was traced to a German egg supplier.

“The MinION just blew me away,” Loman stated in Wired. “The idea that you could do sequencing on a sort of USB stick that you can chuck around does stretch credulity.”

Portable Sequencing Opens Up Intriguing Possibilities for Pathologists

In May 2015, Oxford released a second version of the device, the MinION MkI. According to the company website, the updated MinION is a “full production device featuring improvements of performance and ease of use,” such as improved temperature control and updated mechanism to engage the device with the consumable flow cells.

“The bench-top sequencers opened up the market to a certain degree,” Loman says. “You started seeing [them] in intensive research groups and in the clinic. But what if anyone could have this hanging off their key ring and go do sequencing? That’s an insane idea, and we don’t really know what it’s going to mean in terms of the potential applications. We’re very much at the start of thinking about what we might be able to do, if anyone can just sequence anything, anywhere they are.”

 

Joshua Quick, a PhD candidate at the University of Birmingham, UK believes Oxford Nanopore Technologies’ portable and inexpensive device will change the gene sequencing landscape.

 

Accuracy One Trade-off for Portability

Beta-testers have shown that the miniature device can read out relatively long stretches of genetic sequence with increasing accuracy, but according to the report in the journal Nature , the MinION MkI will need to correct several shortcomings found in the original sequencer:

• It is not practical to sequence large genomes with the device, with some experts estimating it would take a year for the original version to sequence the equivalent of a human genome.

• The machine has a high error rate compared with those of existing full-sized sequencers, misidentifying DNA sequence 5%–30% of the time.

• It also has difficulties reading sections of genome that contain long stretches of a single DNA base.

Yet researchers who have used the device remain enthusiastic about the future of this fourth-generation sequencing technique, which may have the potential to achieve the $1,000-per-human-genome goal set by the National Institutes of Health  (NIH).

“This is the democratization of sequencing,” Joshua Quick, a PhD candidate at the University of Birmingham, told Nature. “You don’t have to rely on expensive infrastructure and costly equipment.”

News accounts did not provide information about Oxford Nanopore’s plans to obtain an EU mark for its MinION device. That will be the next step to demonstrating that the device is ready for widespread clinical use. At the same time, clinical laboratory managers and pathologist should take note of the capabilities of the MinION MkI as described above. Researchers are already finding it useful to identify infectious diseases in clinical setting where other diagnostic methods have not yet identified the agent causing the infection.

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pathway and network analysis of complex ‘omics data

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

While blood tests can be used to detect some cancers, the FDA said a San Diego company has no proof its blood test works in patients who have not already been diagnosed with some form of the disease.

WASHINGTON, Sept. 25 (UPI) — A San Diego company selling an early cancer detection test was notified by the U.S. Food and Drug Administration it can find no evidence the test actually works, and is concerned it could prove to be harmful for some people.

Pathway Genomics debuted its CancerIntercept test in early September with claims it can detect cancer cell DNA in the blood, picking up mutations linked to as many as 10 different cancers. The goal is to catch cancer early in people who are “otherwise healthy” and not showing symptoms of the disease.

“Based on our review of your promotional materials and the research publication cited above, we believe you are offering a high risk test that has not received adequate clinical validation and may harm the public health,” said FDA Deputy Director James L. Woods in a letter to the company.

CancerIntercept is billed by the company as a blood test looking for DNA fragments in the bloodstream and testing them for 96 genomic markers it says are found in several specific tumor types.

The direct-to-consumer test can be purchased through the Pathway Genomics website, with programs ranging from a one-time test to a quarterly “subscription” for people who want regular testing.

The company states, in several sections of its website, “the presence of one or more of these genomic markers in a patient’s bloodstream may indicate that the patient has a previously undetected cancer. However, the test is not diagnostic, and thus, follow-up screening and clinical testing would be required to confirm the presence or absence of a specific cancer in the patient.”

The FDA is concerned that people may seek treatment for tumors that do not require medical attention, or spend money and possibly seek out treatment they do not need at all — in either case, unnecessary treatment for cancer is potentially harmful to people, the agency said.

CancerIntercept has not been approved by the FDA for use as a medical device, nor has it been subjected to peer review as most tests of its type would be. The company published a white paper on its website which outlines how the test works, supporting its efficacy with references to several clinical trials on detection of mutated DNA in the bloodstream.

Glenn Braunstein, Chief Medical Officer at Pathway Genomics, told The VergePathway had validated its tests with “hundreds” of patients, though those patients had well-defined, often advanced cancers.

In the letter from the FDA, Woods requests the company provide a timeline for meeting with the agency to review plans for future longitudinal studies on the product and specific details on studies that have been conducted before it was made available to consumers.

http://www.upi.com/Health_News/2015/09/25/FDA-Start-ups-cancer-blood-test-may-be-harmful/4191443181676/

The clinical laboratory is an essential player in the treatment of cancer providing a diagnostic, potentially a prognostic, and follow-up treatment armamentarium.  The laboratory diagnostics industry has grown over the last half century into  a highly accurate, well regulated industry with highly automated and point of care technologies.  Prior to introduction, the tests that are put on the market have to be validated prior to introduction.

How are they validated?

The most common approach is for the test to be used concomitantly with treatment in a clinical trial. Measurements may be made prior to surgical biopsy and treatment, and at a month or 6 months to a year later.  The pharmaceutical and diagnostics industries are independent, even though a large company may have both pharmaceutical and diagnostic divisions.  Consequently, the integration of diagnostics and therapeutics occurs on the front lines of patient care.

How this discrepancy between the FDA and the manufacturer could occur is not clear because prior to introduction, the test would have to be rigorously reviewed by the American Association for Clinical Chemistry, the largest and most competent organization to cover the scientific work, having industry-based committees.  The only problem is that the companies may have products that are patented and have competing claims or interests. This is perhaps most likely to be problematic in the competitive environment of  genomics testing.

The company here reported on is Pathway Genomics, that offers Ingenuity for pathway and variant analysis.  There is no concern about the analysis methods, that are well studied.  The concern is the validation of such method for screening of patients without prior diagnosis.

Model, analyze, and understand the complex biological and chemical systems at the core of life science research with IPA

QIAGEN’S Ingenuity Pathway Analysis (IPA) has been broadly adopted by the life science research community and is cited in thousands of peer-reviewed journal articles.

https://youtu.be/_HDkjuxYRcY

https://youtu.be/_HDkjuxYRcY?t=25

For the analysis and interpretation of ’omics data
Market Leading Pathway Analysis
Unlock the insights buried in experimental data by quickly identifying relationships, mechanisms, functions, and pathways of relevance.
Predictive Causal Analytics
Powerful causal analytics at your fingertips help you to build a more complete regulatory picture and a better understanding of the biology underlying a given gene expression study.
NGS/RNA-Seq Data Analysis
Get a better understanding of the isoform-specific biology resulting from RNA-Seq experiments.
Identify causal variants from human sequencing data
Ingenuity IPA Interpret Biological Meaning Graphic

http://www.ingenuity.com/wp-content/uploads/2014/01/variant-analyisis-interpretation.png

Rapidly Identify and Prioritize Variants

Ingenuity Variant Analysis combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and your own knowledge of disease biology. With Variant Analysis, you can interrogate your variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow-up.

Variant Analysis used in NCI-60 Interpretation of Genomic Variants

The NCI-60 Data Set offers tremendous promise in the development and prescription of cancer drugs

97% of surveyed researchers are satisfied with the ease of use of Ingenuity Variant Analysis and we are honored that they chose to share the data through our Publish tool.

See the research verified by TechValidate

“Being a bioinformatician, I appreciated the speed and the complexity of analysis. Without Variant Analysis, I couldn’t have completed the analysis of 700 exomes in such a short time …. I found Variant Analysis very intuitive and easy to use.”

Francesco Lescai, Senior Research Associate in Genome Analysis, University College of London.

This appears to be the new rocky road to verification for validity in diagnostic and treatment application.

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Advances in Gene Editing Technology: New Gene Therapy Options in Personalized Medicine

Curators: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN

Recent Advances in Gene Editing Technology Adds New Therapeutic Potential for the Genomic Era

Author and Curator: Stephen J Williams, PhD

The fundamental shift presently occurring within the medical field as well as our understanding of underlying biology has been brought on by revolutionary advances in the disciplines referred to as ‘OMICS’ (genomics, metabolomics, transcriptomics, proteomics). This paradigm shift has brought a new, more “personalized” mindset in investigating, treating, detecting, and policy-decision making disease as well as the physician-patient relationship. This Volume One of Genomics explains this paradigm shift as our classical understanding of the gene has evolved with rapid development of molecular technologies and high-end computational methods to a vision beyond the classic model. This new model involves big data to focus of the “code of OMIC signature”, moving from our investigational focus of “one gene at a time” to analysis of the changes in the networks of protein and gene expression occurring during disease progression.

Moving toward this promise of genome-based therapeutics has required the concomitant development of methodologies unavailable to the researcher and drug developer for most of the 20th century. These new technologies have allowed for the sequencing of the whole genome (advanced and inexpensive pyrosequencing), analyze the proteome for changes in post-translational modifications (new mass spectroscopy techniques combined with automated high-throughput gel electrophoresis on robotic platforms), ability to track all the changes happening to a patient’s metabolic profile (LC-MS in combination with an array of biocurated database functions), and develop new therapeutics based on discrete disease-specific changes in protein, enzyme, and DNA/RNA (mutational analysis, and advanced molecular techniques to allow for manipulation of DNA/RNA such as gene editing and therapeutic vectors) all advancements being dependent on the massive advancements in computing power and software development.

Although this final chapter on a specific technology (Cas9-mediated gene editing) might seem out of place to the reader for the subject of this Genomics volume, as discussed above, the development of these omics-related technologies have spurred the advent of personalized therapies. For example, in the 1990’s (as highlighted in the earlier chapters of this book) Dr. Craig Venter founded Celera Genomics with the goals of 1) sequencing the human genome in a cost effective manner (using new DNA sequencing technology and workflow he and colleagues had developed, and 2) use the information from whole genome sequencing to develop a new line of genomic-based therapeutics. Other companies such as Human Genome Sciences, Myriad Genetics, Seattle Genetics and recently new ventures from 23andMe and Google Ventures were also founded based on the promise that high-end sequencing information could directly lead to this new era of genome-based therapeutics. And although many in the medical field have felt that the primary goal of these companies, in particular using genomic analysis to enhance drug development has been a bit disappointing, AS IN ALL SCIENTIFIC AND MEDICAL DISCOVERY, which involves both SERENDIPITY and INDIRECT HAPPENSTANCE, three important breakthroughs, directly related to the development of a post-genomics era personalized medicine approach, resulted from the aforementioned efforts. These were:

  • The detection of disease-specific mutations in exomes resulting in “druggable” protein targets and ability to define the respective drug-responsive patient cohorts

Chronic myelogenous (or myeloid or myelocytic) leukemia (CML) was one of the first cancers attributed to a specific chromosomal aberration, namely the translocation event resulting in a fusion protein between part of the BCR (“breakpoint cluster region”) gene from chromosome 22 with the ABL gene on chromosome 9. Early drug development efforts were directed against the tyrosine kinase activity of the aberrant BCR/ABL protein. The first of this new class of drugs was imatinib mesylate (Gleevec™) showed early success but was later noticed that a subset of patients had significantly greater response rates. This led to more detailed investigation of Gleevec’s mechanism of action and was determined that Gleevec’s therapeutic action depended on the drug’s ability to bind to an ATP binding pocket within the BCR/ABL. Patients with a specific mutation in this ATP pocket (C944T and T1052C) were found resistant to Gleevec. This finding, that pateint’s DNA could be sequenced to stratify them in responder versus nonresponder groups became a cornerstone for tyrosine kinase inhibitor (TKI) development for various cancers. One example is the development of crizotanib, a TKI directed against a mutant version of the anaplastic lymphoma kinase (ALK) enzyme, namely in patients carrying the ALK-EML4 fusion gene. As with Gleevec, certain mutations in the ATP binding pocket confer resistance to the inhibitory effects of crizotanib. Therefore, the Whole Exome Sequencing (WES) has shown its utility not only in drug development against cancer-specific mutant targets but stratifies patient cohorts into eligible versus non-eligible for a specific personalized therapy.

  • Ability to define at-risk populations based on genomic data and development of corresponding genetic risk assessment for disease

Tremendous advances have been made in the area of risk-assessment for a plethora of diseases, including various malignancies, heart disease, and metabolic diseases. These risk factors have been identified given our advances in whole genome sequencing and proteomic and metabolomics. And, although the aforementioned companies had not developed therapeutic agents using these technologies, their major contribution has been the development of the diagnostic tests which identify at-risk patients and susceptible populations for a given disease. For example, the development of tests for carriers of the BRCA1/BRAC2 breast/ovarian cancer susceptibility mutation or APC (for colon cancer) has led to the appearance of Family Risk Assessment Programs and radically changed the discourse between patient and physician. And although determining risk factors to a disease such as cardiac disease in a large population can be fraught with complexities, the advanced research tools together with gene-directed technologies discussed in this Volume and current chapter may give better clarity in this regard. In essence, the technology had been developed well before its use in the clinic had been identified.

  • Supplying and verifying linkages of specific genetic alterations to heritable diseases and offering a framework for future advances in gene-replacement and mutation-correction therapy

Our abilities to phenotypically correct inheritable diseases thru a gene-therapy (either by gene replacement or correction of mutated genes) have been hampered by three main areas. First identifying the specific mutations for a given inheritable disease used to be an arduous time-consuming process (linkage analysis), especially in small affected populations. However as whole exome sequencing rapidly evolved this had no longer become a rate-limiting step toward the development of a gene-directed therapy. Second and more troubling was determining a process which could deliver therapeutic genes in a safe, reliable and persistent manner. The first attempts at gene-therapy, relying on DNA virus and retroviral based delivery met with disaster and set back the field of gene therapy for decades (this story is too long for an introduction but for reference see the link.)   Recently there have been improvements in therapeutic gene-therapy delivery systems such as the use of conditionally replicative adenovirus (cRADs) and novel serotype AAV (Recombinant adeno-associated virus, a nonpathogenic single stranded DNA human parvovirus) which have greatly improved safety and therapeutic profiles). The third issue, directly related to this chapter on Cas9-mediatied DNA editing) is the ability to integrate therapeutic DNA into the genome in a safe manner or correct mutations in their proper place. It is well established that the random integration of pieces of DNA has spurious effects on gene expression or contribute to transformation by an insertional mutagenesis mechanism.

This chapter will discuss how CRISPR/Cas9-mediated gene editing is being used in ex vivo strategies, namely to insert T-cell specific genes, in definable and safe loci, for the development of the new CAR-T cancer immuno-based therapies.   In addition CRISPR/Cas9-mediated gene editing has much hope and promise for correcting specific mutations related to inheritable diseases, although investigations are at an infantile yet rapidly expanding area. As discussed above, new technologies have preceded their clinical use, mostly in a serendipitous and advantageous manner. Therefore it is a natural progression, using the concepts and curations in previous chapters, to investigate how a new technology, such as CRISPR/Cas9 medicated gene editing will fit into the ‘OMICS era of medicine.

Introduction   

Larry H Bernstein, MD, FCAP

This document is a review and of the brilliant accomplishment of the Doudna Laboratory at University of California, Berkeley. It also traces the developments leading up to this groundbreaking work. The principle investigator is a young woman of significant accomplishments with the astounding publication of 4 papers at this time in 2015 and 20 in 2014. She
is a member of the National Academy of Sciences, and recipient of the Breakthrough Prize and the Lurie Prize in Biomedical Sciences, R. B. Woodward Visiting Professor, Harvard University (2000-2001). She achieved the Henry Ford II Professor of Molecular Biophysics and Biochemistry, Center for Structural Biology, Department of Molecular Biophysics and Biochemistry, Yale University (1994-2002) nine years after completion of her B.A. at Pomona College, and her Ph.D. under Jack Stozak at Harvard in 1989, became a Searle Scholar in 1996, and a Howard Hughes Investigator in 1997.

Her work has encompassed the editing of genes using the CRISPR-Cas9 system, and her team replaced a gene in a human cell which was convincing replicated in the Broad Laboratory at Harvard. The laboratory is currently working on the just reported immunological implications for CRISPR-Cas9 with respect to editing prokaryotic CRISPR-Cas genomic loci that encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. This is because acquired and heritable immunity against bacteriophage and plasmids begins with integration of ∼30 base pair foreign DNA sequences into the host genome.

Of special note are the following applications:

21.4.2 CRISPR: Applications for Autoimmune Diseases @UCSF

Reporter: Aviva Lev-Ari, PhD, RN

21.4.3 In vivo validated mRNAs

http://www.appliedstemcell.com/products/knock-in-cell-lines/in-vivo-crispr/

Doudna’s Interview from the National Academy of Science in 2004

Doudna discusses her current work with signal recognition particles, a type of RNA that is found in virtually all cell types and is responsible for directing specific proteins to specific membranes. She also discusses how advances in genomic sequencing may help catalog the complete range of functional RNA molecules. (9 minutes)

SOURCE

http://www.nasonline.org/news-and-multimedia/podcasts/interviews/jennifer-doudna.html

The Doudna lab pursues mechanistic understanding of fundamental biological processes involving RNA molecules. Research in the lab is currently focused on three major areas:

  1. bacterial immunity via the CRISPR system,
  2. RNA interference in eukaryotes, and
  3. translational control logic.

http://rna.berkeley.edu/crispr.html

http://rna.berkeley.edu/rnai.html

Different subunits are colored with invader RNAs in the background. Art by Gerard W.M. Staals

http://rna.berkeley.edu/translation.html

Alu-element regulated miRNA interactions

The Voice of Aviva Lev-Ari, PhD, RN

 

Big Pharma, CRISPR and Cancer

In January, the pharmaceutical giant Novartis announced that it would be using Doudna’s CRISPR technology for its research into cancer treatments. It plans to edit the genes of immune cells so that they will attack tumors.

https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/#ixzz3UaJdJh5t

Evolution of the Discovery

http://www.businessinsider.com/the-biggest-biotech-discovery-of-the-century-is-about-to-change-medicine-forever-2015-2?IR=T

  • In January 2013, the scientists went one step further: They cut out a particular piece of DNA in human cells and replaced it with another one.
  • In the same month, separate teams of scientists at Harvard University and the Broad Institute reported similar success with the gene-editing tool.

https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/#ixzz3UaOF9xi4

  • At Editas, a company based in Cambridge, Massachusetts, scientists have been investigating the Cas9 enzyme made by another species of bacteria, Staphylococcus aureus and Streptococcus pyogenes

https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/#ixzz3UaMPy9Yw

International regulatory landscape and integration of corrective genome editing into in vitro fertilization, Motoko Araki and Tetsuya Ishii*

http://www.rbej.com/content/12/1/108

The Human Germ Line

Don’t edit the human germ line

Nature, 12 March 2015

Heritable human genetic modifications pose serious risks, and the therapeutic benefits are tenuous, warn Edward Lanphier, Fyodor Urnov and colleagues.

The CRISPR technique has dramatically expanded research on genome editing. But we cannot imagine a situation in which its use in human embryos would offer a therapeutic benefit over existing and developing methods. It would be difficult to control exactly how many cells are modified. Increasing the dose of nuclease used would increase the likelihood that the mutated gene will be corrected, but also raise the risk of cuts being made elsewhere in the genome.

http://www.nature.com/news/don-t-edit-the-human-germ-line-1.17111

Engineering the Perfect Baby

By Antonio Regalado on March 5, 2015
http://www.technologyreview.com/featuredstory/535661/engineering-the-perfect-baby/

Industry Body Calls for Gene-Editing Moratorium

Doudna’s Interview from the National Academy of Science in 2004

Track 6: Future Directions (follow link to track 6; requires RealPlayer)
Doudna discusses her current work with signal recognition particles, a type of RNA that is found in virtually all cell types and is responsible for directing specific proteins to specific membranes. She also discusses how advances in genomic sequencing may help catalog the complete range of functional RNA molecules. (9 minutes)

SOURCE

http://www.nasonline.org/news-and-multimedia/podcasts/interviews/jennifer-doudna.html

VIEW VIDEOS on Gene Editing

https://www.physicsforums.com/threads/breakthrough-prize-genome-editing-with-crispr-cas9.798959/

https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/

RNA-guided, site-specific DNA cleavage tool, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), and the CRISPR-associated (Cas)9 system has been developed from the Streptococcus pyogenes type II CRISPR adaptive immune system.

The Structural Biology of CRISPR-Cas Systems

Curr Opin Struct Biol. 2015 Feb 24;30C:100-111

Authors: Jiang F, Doudna JA

Abstract
Prokaryotic CRISPR-Cas genomic loci encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. Acquired and heritable immunity against bacteriophage and plasmids begins with integration of ∼30 base pair foreign DNA sequences into the host genome. CRISPR-derived transcripts assemble with CRISPR-associated (Cas) proteins to target complementary nucleic acids for degradation. Here we review recent advances in the structural biology of these targeting complexes, with a focus on structural studies of the multisubunit Type I CRISPR RNA-guided surveillance and the Cas9 DNA endonuclease found in Type II CRISPR-Cas systems. These complexes have distinct structures that are each capable of site-specific double-stranded DNA binding and local helix unwinding.

PMID: 25723899 [PubMed – as supplied by publisher]

SOURCE

feed://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=1T1hTO9Bp3LXOpYicP1VJ2xtLRuwKXiCBHyYsbxh719dOd_gXi

About CRISPR

“This technology will revolutionize biology in the same way PCR did,” Rudolf Jaenisch introducing Jennifer Doudna, 6/13/2014 @KI Symposium @MIT.

Top CRISPR Related Publications

http://blog.appliedstemcell.com/top-crispr-related-publications/

What is CRISPR? Why are Cas9-CRISPR services so popular?

http://blog.appliedstemcell.com/what-is-crispr-why-are-cas9-crispr-services-so-popular/ 

Custom Rat Model Generation Service Using CRISPR/Cas9

http://www.appliedstemcell.com/services/animal-models/

Annual Margaret Pittman Lecture, honors the NIH’s first female lab chief, March 11, 2015, 3:00:00 PM by Jennifer Doudna, Ph.D., University of California, Berkeley

Jennifer A. Doudna

Jennifer Doudna

Dr. Jennifer Doudna is a member of the departments of Molecular and Cell Biology and Chemistry atUC Berkeley, the Howard Hughes Medical Institute, and Lawrence Berkeley National Lab, along with the National Academy of Sciences, and the American Academy of Arts and Sciences.

http://rna.berkeley.edu/people.html

AWARDS for the Discovery

http://www.google.com/search?hl=en&q=Jennifer+Doudna+Awards&gbv=2&sa=X&oi=image_result_group&ei=VDIHVdrFOe7dsATYtoCoCQ&ved=0CD8QsAQ&tbm=isch

Jennifer Doudna, cosmology teams named 2015 Breakthrough Prize winners

Jennifer Doudna, The winner of the 2014 Lurie Prize in the Biomedical Sciences

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

Doudna was a Searle Scholar and received a 1996 Beckman Young Investigators Award, the 1999 NAS Award for Initiatives in Research and the 2000 Alan T. Waterman Award. She was elected to the National Academy of Sciences in 2002 and to the Institute of Medicine in 2010. In 2014, Doudna was awarded the Lurie Prize in Biomedical Sciences from the Foundation for the National Institutes of Health as well as the Dr. Paul Janssen Award for Biomedical Researchand Breakthrough Prize in Life Sciences, both shared with Emanuelle Charpentier.

SOURCE

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

 

21.1 Introducing CRISPR/Cas9 Gene Editing Technology – Works by Jennifer A. Doudna

21.1.1 Ribozymes and RNA Machines – Work of Jennifer A. Doudna Reporter: Aviva Lev-Ari Ph.D. RN

21.1.2 Evaluate your Cas9 gene editing vectors: CRISPR/Cas Mediated Genome Engineering – Is your CRISPR gRNA optimized for your cell lines? Reporter: Aviva Lev-Ari Ph.D. RN

21.1.3 2:15 – 2:45, 6/13/2014, Jennifer Doudna “The biology of CRISPRs: from genome defense to genetic engineering”

Reporter: Aviva Lev-Ari Ph.D. RN

21.1.4  Prediction of the Winner RNA Technology, the FRONTIER of SCIENCE on RNA Biology, Cancer and Therapeutics  & The Start Up Landscape in BostonGene Editing – New Technology The Missing link for Gene Therapy?

Curator: Aviva Lev-Ari, PhD, RN

21.2 CRISPR in Other Labs

21.2.1 CRISPR @MIT – Genome Surgery

Curator: Aviva Lev-Ari, PhD, RN

21.2.2 The CRISPR-Cas9 System: A Powerful Tool for Genome Engineering and Regulation

Yongmin Yan and Department of Gastroenterology, Hepatology & Nutrition, University of Texas M.D. Anderson Cancer, Houston, USADaoyan Wei*

21.2.3 New Frontiers in Gene Editing: Transitioning From the Lab to the Clinic, February 19-20, 2015 | The InterContinental San Francisco | San Francisco, CA

Reporter: Aviva Lev-Ari Ph.D. RN

21.2.4 Gene Therapy and the Genetic Study of Disease: @Berkeley and @UCSF – New DNA-editing technology spawns bold UC initiative as Crispr Goes Global

Reporter: Aviva Lev-Ari Ph.D. RN

21.2.5 CRISPR & MAGE @ George Church’s Lab @ Harvard

Genome Engineering: CRISPR & MAGE 
Multiplex Automated Genome Engineering (MAGE), is an intentionally broad term. In practice, it has come to be associated with a very efficient oligonucleotide allele-replacment (lambda red beta), so far restricted mainly to E.coli. CRISPR, in contrast, works in nearly every organism tested.

Relevant companies: EnEvolvEgenesisEditas.

News:
Editas (NextBigFuture, 28-Nov-2013, Brian Wang)
A Call to Fight Malaria One Mosquito at a Time by Altering DNA (NY Times, 17-Jul-2014, Carl Zimmer)

Resources:
* Vectors: Addgene
* Computational: Center for Causal Consequences of Variation (CCV)

Relevant Lab Publications:
2013 Probing the limits of genetic recoding in essential genes. Science.
2013 Genomically Recoded Organisms Impart New Biological Functions. Science.
2013 CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotech.
2009 Programming cells by multiplex genome engineering and accelerated evolution. Nature.

SOURCE

http://arep.med.harvard.edu/gmc/B2.html

21.3 Patents Awarded and Pending for CRISPR

21.3.1 Litigation on the Way: Broad Institute Gets Patent on Revolutionary Gene-Editing Method

Reporter: Aviva Lev-Ari, PhD, RN

21.3.2 The Patents for CRISPR, the DNA editing technology as the Biggest Biotech Discovery of the Century

Reporter: Aviva Lev-Ari, PhD, RN

2.4 CRISPR/Cas9 Applications

21.4.1  Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells using a bacterial CRISPR/Cas 

Kennedy EM1Kornepati AV1Goldstein M2Bogerd HP1Poling BC1Whisnant AW1Kastan MB2Cullen BR3.

21.4.2 CRISPR: Applications for Autoimmune Diseases @UCSF

Reporter: Aviva Lev-Ari, PhD, RN

21.4.3 In vivo validated mRNAs

http://www.appliedstemcell.com/products/knock-in-cell-lines/in-vivo-crispr/

Summary

Larry H Bernstein, MD, FCAP 

CRISPR-Cas is a prokaryotic defense system against invading genetic elements. In a collaboration with John van der Oost’s laboratory, we are studying the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). Recently, we showed that multiple Cas proteins and a crRNA guide assemble to recognize and cleave invader RNAs at multiple sites . Our negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes, suggesting a model for cleavage of the target RNA at periodic intervals (in collaboration with Eva Nogales, UC Berkeley, HHMI).

Double-stranded RNA induces potent and specific gene silencing in a broad range of eukaryotic organisms through a pathway known as RNA interference (RNAi). RNAi begins with the processing of endogenous or introduced precursor RNA into micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) 21-25 nucleotides in length by the enzyme Dicer. We previously determined the crystal structure of an intact Dicer enzyme, revealing how Dicer functions as a molecular ruler to measure and cleave duplex RNAs of a specific length. Current work focuses on the mechanism of a complex of proteins known as the RISC loading complex (RLC) which load miRNA into the endonuclease Argonaute. The RLC contains the enzyme Dicer as well as TRBP, an RNA-binding protein hypothesized to interact with miRNA and Dicer during RISC loading. We seek to determine the molecular underpinnings of these interactions, along with the role of TRBP in RISC loading.

MicroRNAs (miRNAs) regulate endogenous eukaryotic genes by repressing gene expression through direct base-pairing interactions with their target messenger RNAs (mRNAs). To date, the rules used to predict miRNA-mRNA interactions have been based on one-dimensional sequence analysis. A more complete picture of miRNA-mRNA interactions should take into account the ability of RNA to form two- and three-dimensional structures. We are investigating the role of mRNA structure in the efficiency and specificity of targeting by miRNAs. Specifically, we are investigating the structure of Alu elements found within the 3′ untranslated regions (UTRs) of many human mRNAs and whether these structured domains serve as targets of a subset of human miRNAs. We are using in vitro biochemical methods and cell-based assays to probe the relationship between miRNA binding and mRNA structure.

The 5’ UTR of mRNA is also the site of multiple regulatory mechanisms, including upstream open reading frames (uORFs), internal ribosome entry sites (IRESs), protein binding sites, and stable secondary structures. Genes that profoundly influence cellular state often are controlled by multiple of these regulatory mechanisms. We are attempting to further understand regulatory elements in the 5′ UTR of mammalian mRNA using a combination of in vitro, cell-based and high-throughput techniques.

What does this mean for the development of therapeutics in the near future?

New methods for programming cell phenotype have broadly enabled drug screening, disease modeling, and regenerative medicine. Current research explores genome engineering tools, such as CRISPR/Cas9-based gene regulation and epigenome editing, to more precisely reprogram gene networks and control cellular decision making.

Donald Zack, M.D., Ph.D., Associate Professor of Ophthalmology and Neuroscience, Johns Hopkins University School of Medicine, is using CRISPR/Cas9 technology to generate retinal cell type-specific reporter ES and iPS lines and to introduce retinal degeneration-associated mutations. These reporter lines can be used to follow retinal neuronal specification during differentiation, they allow the purification of specific cell types by sorting and immunopanning, and they also are useful for the development of drug screening assays.

Jacquin C. Niles, M.D., Ph.D., Associate Professor of Biological Engineering, Massachusetts Institute of Technology is using CRISPR-Cas9 technology to study functional genetics in the human malaria parasite, Plasmodium falciparum. The team has established strategies for achieving controllable gene expression, and has integrated these into an experimental framework that facilitates efficient interrogation of virtually any target parasite gene using CRISPR/Cas9 editing.

Sidi Chen, Ph.D., Postdoctoral Fellow, Laboratory of Dr. Feng Zhang, Broad Institute and the Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology is observing that cancer genomics has revealed hundreds to thousands of mutations associated with human cancer. To test the roles of these mutations, we applied CRISPR/Cas9-mediated genome editing platform to engineer specific mutations in oncogenes and tumor suppressor genes. This results in tumorigenesis in several internal organs in mice. Our method expedites modeling of multigenic cancer with virtually any combination of mutations.

Samuel Hasson, Ph.D., Principal Investigator, Neuroscience, Pfizer, Inc., observes that while RNAi-based functional genomics is a staple of gene pathway and drug target exploration, there is a need for tools to provide rapid orthogonal validation of gene candidates that emerge from RNAi campaigns. CRISPR, CRISPRi, and CRISPRa are not only developing into primary screening platforms, they are a promising method to compliment RNAi and enhance the quality of functional genomic datasets.

These are some of the developments that will be discussed in detail at an upcoming meeting in Boston, MA in June titled ‘Gene Editing for Drug Discovery’.

 SOURCE

http://rna.berkeley.edu/crispr.html

http://rna.berkeley.edu/rnai.html

http://rna.berkeley.edu/translation.html

 

 

Doudna Lab Publications

http://rna.berkeley.edu/publications.html

The structural biology of CRISPR-Cas systems.

Jiang F, Doudna JA
Curr Opin Struct Biol 2015 Feb 24;30C:100-111

Rational design of a split-Cas9 enzyme complex.

Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA
Proc Natl Acad Sci U S A 2015 Feb 23

Genomic Engineering and the Future of Medicine.

Doudna JA
JAMA 2015 Feb 24;313(8):791-792

Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity.

Nuñez JK, Lee AS, Engelman A, Doudna JA
Nature 2015 Feb 18

Dicer-TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis.

Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA
Mol Cell 2014 Dec 30

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery.

Lin S, Staahl B, Alla RK, Doudna JA
Elife 2014 Dec 15;3

Cutting it close: CRISPR-associated endoribonuclease structure and function.

Hochstrasser ML, Doudna JA
Trends Biochem Sci 2014 Nov 18

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus.

Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J
Mol Cell 2014 Nov 20;56(4):518-530

Genome editing. The new frontier of genome engineering with CRISPR-Cas9. (Free Full Text)

Doudna JA, Charpentier E
Science 2014 Nov 28;346(6213):1258096

Preface.

Doudna JA, Sontheimer EJ
Methods Enzymol 2014;546C:xix-xx

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.

Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS
Nucleic Acids Res 2014 Oct 17

Programmable RNA recognition and cleavage by CRISPR/Cas9.

O’Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA
Nature 2014 Sep 28

RNA-guided assembly of Rev-RRE nuclear export complexes.

Bai Y, Tambe A, Zhou K, Doudna JA
Elife 2014;3:e03656

Evolutionarily Conserved Roles of the Dicer Helicase Domain in Regulating RNAi Processing.

Kidwell MA, Chan JM, Doudna JA
J Biol Chem 2014 Aug 18

Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.

Kranzusch PJ, Lee AS, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA
Cell 2014 Aug 12

Insights into RNA structure and function from genome-wide studies.

Mortimer SA, Kidwell MA, Doudna JA
Nat Rev Genet 2014 May 13

Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.

Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA
Nat Struct Mol Biol 2014 May 4

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.

Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA
Proc Natl Acad Sci U S A 2014 Apr 18

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation.

Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA
Science 2014 Feb 6

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA
Nature 2014 Jan 29

http://rna.berkeley.edu/fun/D-lab%202013/SMALL/crisprconf.jpg

http://www.nasonline.org/news-and-multimedia/podcasts/interviews/jennifer-doudna.html

 

The Doudna lab pursues mechanistic understanding of fundamental biological processes involving RNA molecules. Research in the lab is currently focused on three major areas:

  1. bacterial immunity via the CRISPR system,
  2. RNA interference in eukaryotes, and
  3. translational control logic.

 

http://rna.berkeley.edu/crispr.html

http://rna.berkeley.edu/rnai.html

http://rna.berkeley.edu/translation.html

 Other related curation on Gene Editing published as Chapter 21 in 

Genomics Orientations for Individualized Medicine

https://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/volume-one-genomics-orientations-for-personalized-medicine/

  • Advances in Gene Editing Technology: New Gene Therapy Options in Personalized Medicine

Curators: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN

  • Recent Advances in Gene Editing Technology Adds New Therapeutic Potential for the Genomic Era

Author and Curator: Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/volume-one-genomics-orientations-for-personalized-medicine/

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