Wellcome Supports Effort To Crowdsource Review of Chemical Probes

Nature Chemical Biology has published a Commentary on its website about chemical probes.  These are important tools in biochemical research for their ability to explore the function of proteins in broader contexts.  The commentary notes the increased utility of these probes and how their use has increased over the last few years.

But there are problems.  These chemicals are difficult to produce in high quality, and lower quality probes lead to poor results.  To try and mitigate those problems, the commentary authors have developed a crowdsourced resources for information on high-quality chemical probes and how to use them (H/T ScienceInsider).  Online at http://www.chemicalprobes.org/, the site is supported by The Wellcome Trust, and endorsed by The Broad Institute, The Institute for Cancer Research, and the Structural Genomics Consortium.

The site provides information, and can connect interested parties with the experts behind the website.  This includes suggesting new chemicals for inclusion on the site.  While there is not yet an online submission process, those using the feedback mechanism on the site can make suggestions to the reviewers.

White House Launches Effort To Revise Biotechnology Regulation

While I find the timing suspect, on Thursday John Holdren, Director of the White House Office of Science and Technology Policy (OSTP), announced (along with other senior White House staff) the Administration will be reviewing the Coordinated Framework for the Regulation of Biotechnology, the policy that designates agency responsibilities for overseeing the introduction of biotechnology products into the environment (H/T Grist).  First developed in 1986, the last revision was in 1992.  So, clearly overdue.

Holdren’s announcement accompanied a memorandum to the Environmental Protection Agency, the Department of Agriculture and the Food and Drug Administration.  It (along with Holdren’s blog post) outlines the elements of the review process:

  • Updating the Common Framework (with public input) to clarify the biotechnology product areas (not processes) for which each agency will be responsible.  This will include how to handle situations where more than one agency may be responsible.
  • Developing a long-term strategy (with public input) to ensure that the Federal regulatory process will be better prepared for emerging biotechnologies.  This would include horizon scanning exercises and additional support of so-called ‘regulatory science.’
  • An independent examination of the future landscape of biotechnology.  The National Academies have already been engaged to start this analysis.

This all sounds great, but there are some aspects of this that give me pause.  First, the announcement comes the afternoon before the July Fourth holiday weekend.  It screams news dump – an effort to ensure that very few people become aware of the effort.

Additionally, while the revisions and the strategy will involve public input, Holdren asks for people interested in additional information to register.  If this wasn’t already part of an announcement that seems timed to minimize public reception, I might not think much of it.  But I can see the Administration limiting its subsequent publicity on this project to the people who register.  If they are going to try and hold listening sessions around the country (the first one will take place this fall), I think they should spread their message far and wide.

Finally, I guess I’m still a bit chagrined from other efforts to revise (or develop) regulations related to science and technology research.  The effort to revise the Common Rule related to human subjects research stalled out after a big public comment push in 2011.  And it still seems as though the push on scientific integrity policies has failed mainly from a lack of coordinated follow-through from the OSTP.

I’d love to see this not happen with the revisions to the Coordinated Framework, but I’m not optimistic – especially with roughly 18 months to go with this Administration.

A Step Towards Standardizing DNA Sequencing

Last month The New York Times reported that the National Institute of Standards and Technology (NIST) has developed a reference standard for use in DNA genetic sequencing.  Specifically, NIST has made available genetic material that can be tested to confirm that a lab would find the known mutations in the proper places when sequencing the reference material.  This would help assure the reliability of the testing at that lab.

By providing this testing standard, labs will be able to better demonstrate the reliability of their tests, which should stimulate demand for the tests, and may make insurance companies more likely to pay for them.  This might help address the concerns agencies like the Food and Drug Administration have had about direct-to-consumer genetic testing – at least where reliability is concerned.

While this is the first NIST reference material for genetic sequencing, it has developed reference materials for other DNA tests and procedures.  Those reference materials, developed by NIST’s Applied Genetics Lab, are usually smaller amounts of DNA, often produced via Polymerase Chain Reaction and targeted to tests looking at specific genetic sequences.

Lab Issues Go Beyond The Really Nasty Bugs

Recently federal labs have come under scrutiny for failing to effectively control the quantities of nasty bugs like anthrax they have in stock.  Unfortunately, that is not the extent of the problems facing National Institutes of Health (NIH) facilities.

The NIH has closed its Pharmaceutical Development Section, which produces pharmaceutical drugs for its clinical trials (H/T Nature News).  After investigating a complaint, the Food and Drug Administration (FDA) found the Section failed to comply with standard operating procedures and had serious manufacturing problems.  The problems included finding fungal contamination and insects in manufacturing facilities, and insufficient dress for lab staff.

While the Section is closed, an external expert group will convene to conduct a thorough review.  Participants in clinical trials are being notified about the possible contamination of the drugs being tested, and some are requesting exemptions in order to continue taking the drugs.  The NIH has promised the FDA a corrective action plan by June 19.

Agencies Want Help With Dengue Forecasting

Today the U.S. government announced the beginning of a forecasting project on Dengue Fever.  The Centers for Disease Control (CDC), the National Oceanic and Atmospheric Administration (NOAA), and the Armed Forces Medical Surveillance Center (AFMSC) have made available datasets on Dengue fever from Puerto Rico and Peru.

This data, when coupled with environmental and climate data from the area and associated climate models, should allow scientists the ability to forecast the emergence of Dengue outbreaks.  Interested parties will have four months (until September 2) to use this data to develop their forecasting models.  An evaluation team will decide on the finalists (up to six teams), who will be invited (on their own dime, regrettably) to appear before the Interagency Pandemic Prediction and Forecasting Science and Technology Working Group of the National Science and Technology Council.

This is not a competition in the now-traditional sense of a short term contest with a cash prize.  Project organizers, according to this description, are looking to publish the evaluations, and all those who submit will have their predictions included.  Team leaders will be invited to receive author credit.

For more detailed information on submission procedures and project rules, consult the Dengue Forecasting Project portion of the Epidemic Prediction Initiative (EPI) website.  The EPI is a product of the Department of Health and Human Services Idea Lab, and is currently in beta.

White House Holds Forum On Antibiotic Stewardship

Tuesday the White House hosted a forum on antibiotic stewardship (H/T Reuters).  It’s the latest in a sequence of actions the Administration has held over the last several months on the issue.  Attending the forum were representatives from food producers, hospitals, restaurant chains and medical societies.  Several companies have announced measures to reduce and/or eliminate the use of antibiotics in their products and services (The White House included a list of company actions with its Fact Sheet on the event).

The actions taken by companies are focused on curtailing the use of medically important antibiotics – drugs intended for medical uses (whether for humans or animals) and not growth promotion.  In the case of restaurants and food producers, this usually means restricting or eliminating the use of such drugs.  For medical providers and medical societies, the focus is on not only reducing the overprescription of these drugs, but also on improving related medical tests.  These tests include detecting resistant pathogens and the sensitivity of pathogens to various strains of antibiotics.  Reporting on antibiotic use and the persistence of pathogens will increase as well.

As part of the Administration’s ongoing efforts, President Obama signed a Presidential Memorandum setting preferences for how the kind of meat and poultry the government will purchase.  For Federal cafeterias that preference will be for meat and poultry grown consistent with responsible antibiotic use policies.  Agencies operating cafeterias serving their employees will need to incorporate this preference into their procurement practices by 2020.

So We Can Encode Music Into DNA

Opening next month at the Dilston Grove Gallery at GDP London is Music of the Spheres, an exhibition that uses bioinformatics to record music.  Dr. Nick Goldman of the European Bioinformatics Institute has been working on new technologies for encoding large amounts of information into DNA.  Collaborating with Charlotte Jarvis, the two have worked on installations of bubbles that would contain DNA encoded with music (the DNA is suspended in soap solution).

The music is provided by the Kreutzer Quartet, and the second movement of their new composition has been encoded into DNA for the installation.  Visitors to the installation can be ‘bathed’ in music by moving through the bubbles that contain the music-encoded DNA.  The installation will be accompanied by film as well as music, and was funded in part from a Kickstarter campaign (H/T Fact magazine).

The methods for encoding information will be helpful moving forward as it allows for the possibility of a more persistent data storage medium.  While the bursting bubbles of the exhibition would release a cloud of vapor containing music on DNA, it’s possible that a future data cloud would rely on DNA instead of the kind of server farms we know today.