Wednesday, March 24, 2010

“Transformative Research and the Fruit Fly - Huffingtonpost.com” plus 3 more

“Transformative Research and the Fruit Fly - Huffingtonpost.com” plus 3 more

Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

Transformative Research and the Fruit Fly - Huffingtonpost.com

Posted: 24 Mar 2010 08:30 AM PDT

Two research studies published earlier this month decoded the entire genome of patients to reveal the precise genetic cause of their diseases. The two studies underscore the importance of transformative research and the evolutionary quality of scientific inquiry, the value of cross-disciplinary collaborations, and the lifesaving potential of studies that may sound absurd to outside observers - in this case involving the genetic make-up of the fruit fly.

As The New York Times reported, decoding the genome of patients "may offer a new start in the so far disappointing effort to identify the genetic roots of major killers like heart disease, diabetes and Alzheimer's." The Times continued: "... common diseases, like cancer, are thought to be caused by mutations in several genes, and finding the causes was the principal goal of the $3 billion human genome project. To that end, medical geneticists have invested heavily over the last eight years in an alluring shortcut. But the shortcut was based on a premise that is turning out to be incorrect. Scientists thought the mutations that caused common diseases would themselves be common." But subsequent research "implies that common diseases, surprisingly, are caused by rare, not common, mutations. In the last few months, researchers have (therefore) begun to conclude that a new approach is needed, one based on decoding the entire genome of patients."

The lead researchers in these two studies are Richard A. Gibbs of the Baylor College of Medicine and Leroy Hood and David J. Galas of the Institute for Systems Biology in Seattle.
Dr. Gibbs is Professor of Molecular and Human Genetics, and Director of the Human Genome Sequencing Center at Baylor. The Center is one of three National Institutes of Health-funded genome centers that were involved in the completion of the first Human Genome Sequence in 2004.

According to Baylor, the Center contributed approximately 10 percent of the total project by sequencing Chromosomes 3, 12 and X. It collaborated with researchers at the U.S. Department of Energy's Lawrence Berkeley Laboratory (which was previously led by current U.S. Energy Secretary Steven Chu) and Celera Genomics to sequence the first species of fruit fly, Drosophila melanogaster. The Center also completed the second species of fruit fly (Drosophila pseudoobscura), the honeybee (Apis mellifera), and led an international consortium to sequence the Brown Norway rat.

Not only is the collaboration between the Baylor College of Medicine and the U.S. Department of Energy the kind of boundary-crossing collaboration that often energizes transformative research, but their collaboration was focused on research topics that could easily have been ridiculed by critics of basic science research. Imagine the fodder that federally funded research on the genome sequencing of the fruit fly could provide. And yet it's precisely that research that has led to the increased understanding that may ultimately lead to cures to widespread diseases.

Drs. Hood and Galas are similarly boundary-crossing in their research orientations. Dr. Hood earned a medical degree at Johns Hopkins before earning a PhD in Biochemistry at Caltech. He founded and chaired the cross-disciplinary Department of Molecular Biotechnology at the University of Washington, before co-founding the Institute for Systems Biology to pioneer systems approaches to biology and medicine.

Dr. Galas earned a PhD in Physics from the University of California, served as Director of Health and Environmental Research at the U.S. Department of Energy's Office of Science, served as Chairman and Professor of Molecular Biology at the University of Southern California and as Chancellor at the Keck Graduate Institute of Applied Life Sciences, among other involvements before joining the Institute for Systems Biology.

This kind of commitment to cross-disciplinary inquiry and collaboration, and the transformative research that it enables, is exactly what inspired Research Corporation for Science Advancement, the foundation that I head, to create a major new research initiative called Scialog® - a multi-year grant program designed to accelerate the work of 21st-century science by funding individuals or multi-disciplinary teams of scientists to pursue transformational research, in collaboration and dialog with their fellow grantees. The initial Scialog, which will focus on the conversion of sunlight directly into useable forms of energy, will fund grants of $100,000 for individual researchers and $250,000 for qualifying teams of researchers, for a total of $3.2 million.

Transformative risk-taking research and cross-disciplinary collaboration are crucial to ensuring breakthroughs in scientific understanding, and basic science is often at the heart of ground-breaking work. Whenever anyone makes fun of understanding the fruit fly, remember that they may be investigating a disease that you wish would be defeated.

The author, a geneticist, is president and CEO of Research Corporation for Science Advancement (www.rescorp.org), America's second-oldest foundation, begun in 1912, and the first dedicated wholly to science.

Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

DSD gets Cray supercomputer - Network World Fusion

Posted: 24 Mar 2010 08:45 AM PDT

The agency responsible for combating cyber security threats to Australia, the Defence Signals Directorate (DSD), has taken charge of a Cray Inc supercomputer.

The supercomputer is expected to support DSD intelligence and cyber security missions, including those undertaken by the Cyber Security Operations Centre (CSOC).

Minister for defence personnel, material and science, Greg Combet, described the work as "fundamental to the security of our deployed forces and to wider government in protecting Australia against external threats such as terrorism".

"This new supercomputer represents a cutting edge capability and was delivered in close collaboration with industry," he said in a statement.

"The Government has made a commitment under the Defence White Paper 2009 to significantly upgrade intelligence and cyber security capabilities."

No additional information on the supercomputer was provided.

In other supercomputer news, up to 10,000 scientists will team up with computer experts and a supercomputer at the University of Melbourne to study human diseases.

The research will involve Victorian medical and life science researchers working alongside IBM computer technicians to study areas including neuroscience, clinical genomics, and structural biology.

The Victorian Life Sciences Computational Initiative aims to improve medical diagnostics, drug discovery and design by pairing computer biology experts with researchers from universities, government, or commercial organisations.

IBM's Blue Gene/P, the latest in the vendor's supercomputer series, will be based on the University of Melbourne campus and will support the lion's share of the research work.

Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

Molecular biologist receives Stephen Jay Gould Prize - UW Madison

Posted: 24 Mar 2010 07:19 AM PDT

March 24, 2010

by Terry Devitt

Sean Carroll, a University of Wisconsin-Madison molecular biologist and a Howard Hughes Medical Institute investigator, has been named the recipient of the 2010 Stephen Jay Gould Prize, an award given in recognition of exemplary efforts to advance public understanding of evolutionary science.

A distinguished researcher whose work lies at the intersection of the disciplines of development and evolution, Carroll is also one of science's most colorful and prolific raconteurs. He is the author of six books, including "The Making of the Fittest" and, most recently, "Remarkable Creatures: Epic Adventures in the Search for the Origin of Species," which was a finalist for the 2009 National Book Award in nonfiction.

Carroll has also served as a consulting producer for NOVA and has appeared in numerous programs on PBS, the BBC, National Public Radio, the Discovery Channel and many others.

"These efforts have made him a leading spokesperson in the public sphere for evolutionary biology," according to a statement from the Society for the Study of Evolution, the group that annually confers the award to individuals who advance "public understanding of evolutionary science and its importance in biology, education and everyday life in the spirit of Stephen Jay Gould."

Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

Evolutionary rates at codon sites may be used to align ... - BioMed Central

Posted: 24 Mar 2010 08:02 AM PDT

Abstract (provisional)

Background

Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution.

Results

A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (Functional Inference using the Rates of Evolution), which aligns sequences using the evolutionary rate at codon sites, as measured by the dN/dS ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions). Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data) may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the method of choice in these cases.

Conclusions

FIRE provides proof of concept that it is possible to align sequences and infer domain function by using evolutionary rates rather than residue similarity. This represents a new approach to sequence analysis with a wide range of potential applications in molecular biology.
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