A Bioinformatic Challenge

July 27, 2010  from Genome Daily News

Genomic sequencing is getting really cheap — but is it getting too cheap? Iddo Friedberg at Byte Size Biology thinks it is. “As we sequence more and more genomes, our annotation tools cannot keep up with them,” he says. “It’s like unearthing thousands of books at some vast archaeological dig of an ancient library, but being able to read only a few pages here and there.” Friedberg says we should be answering the questions of what these genes do, instead of continually trying to find more and more. Though some researchers are trying to determine gene function, it’s “but a drop in the ocean” compared to those functions we don’t know, he adds. Bioinformatics is the answer, but therein lies another problem, according to Friedberg. “How do we know how well function prediction algorithms perform? How do we compare their accuracy? Which method performs best, and are different methods better for different types of function predictions?” he asks. So Friedberg, and others, have gotten together to form an initiative comparing the different function of prediction software tools. They call it the CAFA challenge: Critical Assessment of Function Annotation. They will release sequences of about 50,000 proteins with unknown functions, and are challenging various research groups to use their own software to predict function, and submit them by January 2011 to the CAFA website. The group is holding its first meeting in Vienna in July 2011 as a satellite of the ISMB 2011 meeting, Friedberg says, where they will compare results and score the predictions.

The Hastings Center 40th Anniversary Essay Contest

Young Scholars: Make Your Voices Heard!

 To mark the fortieth anniversary of the Hastings Center Report, The Hastings Center is asking the next generation what issues in bioethics should be addressed in the coming years.  We invite any college student, graduate fellow, or untenured professor in bioethics (current or former Center staff excluded) to submit an essay of no more than 1,600 words in response. Essays can be sent to us at editorial@thehastingscenter.org and should arrive by August 15, 2010. Winners will be notified in mid-September, and our favorite essays will be published in the November-December 2010 issue.   


Diabetes Related Protein Implicated in Many Disorders

(July 21, 2010) — Studying a protein already known to play an important role in type 2 diabetes and cancer, genomics researchers have discovered that it may have an even broader role in disease, particularly in other metabolic disorders and heart disease. In finding unsuspected links to other disease-related genes, the scientists may have identified future targets for drug treatments.   The paper appeared online July 17 in the British journal Diabetologia.

Music Primes the Brain for Learning and Communication

Now a data-driven review by Northwestern University researchers published July 20 in Nature Reviews Neuroscience pulls together converging research from the scientific literature linking musical training to learning that spills over to skills including language, speech, memory, attention and even vocal emotion. The science covered comes from labs all over the world, from scientists of varying scientific philosophies, using a wide range of research methods.

The Nature article reviews literature showing, for example, that musicians are more successful than non-musicians in learning to incorporate sound patterns for a new language into words. Children who are musically trained show stronger neural activation to pitch changes in speech and have a better vocabulary and reading ability than children who did not receive music training.   Musical training be particularly help for children with dyslexia and other learning disabilities. 

“The effect of music training suggests that, akin to physical exercise and its impact on body fitness, music is a resource that tones the brain for auditory fitness and thus requires society to re-examine the role of music in shaping individual development, ” the researchers conclude.

British Research Links Restricted Diets and Conservation of Telomeres

Research conducted by the BBSRC  (Biotechnology and Biological Sciences Researh Council) Centre for Integrated Systems Biology of Ageing and Nutrition (CISBAN)  is being presented at the conference of the British Society for Research on Ageing (BSRA) in Newcastle, U.K.  This research sheds new light on why restricted diets extend life span in certain organisms.  Mice fed a restricted diet had reduced levels of senescent cells in their livers and intestines, where large numbers of these cells are known to accumulate as animals age.  It was found that the cells of mice fed restricted diets better maintained their telomeres, the protective ‘ends’ of chromosomes that help prevent errors, and aging.  Read more at the BBSRC website.

A New Look at Science Education Standards

The crisis in rational decision-making in our nation and in the world has brought the scientific community to the realization that we cannot ignore the current deficiencies in the teaching of science in our public schools, and that something must be done to improve the science literacy of the public.   The National Research Council has developed a new framework for defining what it means to be proficient in science.   A draft of the framework is now available online for public feedback.   YOUR feedback will contribute to the final version of the framework which will be broadly distributed with the intention and the hope that it will influence cirriculums in science education across the country.   Please take the time to review the draft, and comment.

NCI Proteomics Push Continues with $120M Program

NEW YORK (GenomeWeb News) – The National Cancer Institute wants to push forward protein-focused cancer research technologies by investing between $75 million and $120 million in centers that will conduct biomarker discovery, verification, and new cancer proteomics studies.

The Proteome Characterization Centers (PCC) grants program is the second phase in NCI’s Clinical Proteomic Technologies for Cancer (CPTC) initiative, which was started four years ago to develop technologies for identifying and quantifying proteins that could be useful as cancer biomarkers.

Phase one of the CPTC program established five multidisciplinary centers that showed they could be effective in addressing analytical variability problems in proteomics. Now, the second phase will build a network of centers that will target biomarkers and will aim to improve tools for protein detection, identification, and quantification.

The PCCs will use discovery units and verification units to implement the two-step process in the biomarker development pipeline, and the findings from these studies will be made public through a central data center.

“[We] want to develop a much greater understanding of cancer at the molecular level,” Chris Kinsinger of NCI’s Office of Cancer Clinical Proteomics Research told GenomeWeb Daily News this week.

New Theoretical Model for Moving Polymers Through Membranes

Moving Polymers Through Pores

ScienceDaily (July 13, 2010) — The movement of long chain polymers through nanopores is a key part of many biological processes, including the transport of RNA, DNA, and proteins. New research reported in The Journal of Chemical Physics, which is published by the American Institute of Physics, describes an improved theoretical model for this type of motion. 

The new model addresses both cylindrical pores and tapering pores that simulate the α-hemolysin membrane channel. “Current models do not take into account the motion of the polymer inside the pore,” says author Anatoly Kolomeisky of Rice University. “The leading monomer can move back and forth many times before it finally crosses the line to the other side of the membrane. Not accounting for this behavior introduces errors into predictions.”