Biology Net: Bioinformatics

Biology News Net - Bioinformatics

• Genome signatures enable tracking of algal complexity
  

  On the long and difficult road toward a carbon-neutral source of transportation fuels, the U.S. Department of Energy (DOE) is pursuing a diversified approach. This effort involves exploring a range of potential new fuel sources in nature: from plants that may serve as cellulosic feedstocks—fast-growing trees and perennial grasses on land—to oil-producing organisms in aquatic and other environments, such as algae and bacteria.

  
  
  
• Large-scale genomic analysis of prostate cancer unveiled
  

  A unique collaboration among physician-scientists at Memorial Sloan-Kettering Cancer Center (MSKCC) has yielded the most comprehensive genomic analysis of prostate cancer to date. "Genomic studies in other cancer types have resulted in new drug targets and strategies to classify patients into clinically meaningful subgroups that improve treatment decisions," said senior study author Charles Sawyers, Chair of the Human Oncology and Pathogenesis Program at MSKCC and a HHMI investigator. "This first -ever database of its type brings us one step closer to achieving that goal in prostate cancer."

  
  
  
• Sequencing of the human body louse genome
  

  The results of the sequencing and analysis of the human body louse genome, which were published on June 21 in the Proceedings of the National Academy of Sciences (PNAS), offer new insights into the intriguing biology of this disease-vector insect. The project involved more than 70 international scientists led by Professor Evgeny Zdobnov at the University of Geneva Medical School and the SIB Swiss Institute of Bioinformatics, with Professor Barry Pittendrigh at the University of Illinois and Professor Ewen Kirkness at the J. Craig Venter Institute.

  
  
  
• Data mining algorithm explains complex temporal interactions among genes
  

  Researchers at Virginia Tech, New York University (NYU), and the University of Milan, Italy, have created a data mining algorithm they call GOALIE that can automatically reveal how biological processes are coordinated in time.

  
  
  
• 1000 Genomes Project releases pilot data
  

  The completion of three pilot projects designed to determine how best to build an extremely detailed map of human genetic variation begins a new chapter in the international project called 1,000 Genomes (http://www.1000genomes.org/page.php?page=home), said the director of the Baylor College of Medicine Human Genome Sequencing Center (http://www.hgsc.bcm.tmc.edu/), which is a major contributor to the effort.

  
  
  
• Sequencing a single genome yields cause of inherited bone disorder
  

  Combining new, whole-genome sequencing technology with classic genetic approaches to understanding inherited diseases, Duke University Medical Center geneticists and colleagues at Johns Hopkins have discovered two gene mutations that cause metachondromatosis, a rare, heritable disorder that leads to bony growths, typically on hands and feet.

  
  
  
• New world Helicobacter pylori genome sequenced, dynamics of inflammation-related genes revealed
  

  An international team of researchers led by scientists at the Virginia Bioinformatics Institute (VBI) at Virginia Tech have sequenced the genome of an Amerindian strain of the gastric bug Helicobacter pylori, confirming the out-of-Africa migration of this bacterial stowaway to the New World. Experiments in animals have highlighted how specific genes in the bacterial strain may be crucial to the onset of inflammation and disease.

  
  
  
• Scientists discover ancient viral invasion that shaped human genome
  

  Scientists at the Genome Institute of Singapore (GIS), a biomedical research institute of the Agency for Science, Technology and Research (A*STAR), and their colleagues from the National University of Singapore, Nanyang Technological University, Duke-NUS Graduate Medical School and Princeton University have recently discovered that viruses that 'invaded' the human genome millions of years ago have changed the way genes get turned on and off in human embryonic stem (ES) cells.

  
  
  
• Genome of bacteria responsible for tuberculosis of olive tree sequenced
  

  Researchers at the Public University of Navarra, the Polytechnic University of Madrid (CBGP), the University of Malaga, the University of Wisconsin and the Valencian Institute of Agricultural Research have managed to sequence the genome of the bacteria responsible for tuberculosis in the olive tree. The study, included in the June issue of Environmental Microbiology, represents the first sequencing of the genome of a pathogenic bacteria undertaken in Spain, being the first genome known worldwide of a pathogenic Pseudomonas in woody plants.

  
  
  
• Low-cost, ultra-fast DNA sequencing brings diagnostic use closer
  

  Sequencing DNA could get a lot faster and cheaper – and thus closer to routine use in clinical diagnostics – thanks to a new method developed by a research team based at Boston University. The team has demonstrated the first use of solid state nanopores — tiny holes in silicon chips that detect DNA molecules as they pass through the pore — to read the identity of the four nucleotides that encode each DNA molecule. In addition, the researchers have shown the viability of a novel, more efficient method to detect single DNA molecules in nanopores.