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Genomics & Proteomics
International Team Develops Cowpea Genetic Map PDF Print E-mail
Friday, 09 October 2009 05:16
In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, international researchers reported that they have developed a high-density consensus linkage map for the legume Vigna unguiculata, commonly known as cowpea. A team of researchers from the US, Nigeria, and Senegal integrated sequence data on nearly 200,000 expressed sequence tags, identifying thousands of possible genetic markers. After weeding through these, they developed an array that evaluated about 1,500 of the markers. By genotyping almost 1,000 plants from six cowpea lines, the team came up with a genetic map that they then compared with genetic resources for a few other legume and non-legume plants.
International Team Uses Pathway Expression Profiles to Classify Gastric Cancers PDF Print E-mail
Friday, 09 October 2009 04:57
In a paper appearing online today in PLoS Genetics, an international research team described their pathway-based gene expression approach for classifying gastric cancers. Researchers from Singapore, the UK, Korea, and Australia used gene expression profiling and computational approaches to map signaling pathways in hundreds of stomach cancer tumors. Their study highlighted three main pathways that contribute to cancer function in the majority of stomach tumors tested. By looking at which of these pathways were activated in combination, the team was also able to classify the tumors and identify ties to patient outcomes.
European Team Unravels Genetic Basis of Mosquito Resistance to Malaria PDF Print E-mail
Monday, 05 October 2009 04:45
Genetic variants in a lone gene appear to mediate the Anopheles gambiae mosquito's resistance to at least one malarial parasite species, according to a paper appearing online today in Science. A team of German and French researchers assessed malaria sensitive, resistant, and intermediate A. gambiae mosquitoes using several techniques, including a genome-wide association study for resistance, targeted re-sequencing and an approach called reciprocal allele-specific RNA interference, or rasRNAi. In the process, they found variants in one gene — called antiparasitic thioester-containing protein 1, or TEP1 — that apparently governs malaria resistance.
Obama, Collins Laud $5B in NIH Stimulus Funds, Much for Genomics PDF Print E-mail
Monday, 05 October 2009 04:22
The National Institutes of Health has awarded more than 12,000 grants totaling around $5 billion so far under the economic recovery and stimulus package, the White House said today. President Barack Obama commuted to Bethesda this morning to announce the funding as a milestone, to unveil a $175 million grant for cancer genomics, and to tour the NIH campus.
California Team Applies Alignment-Free Approach to Mammalian Phylogeny PDF Print E-mail
Wednesday, 30 September 2009 08:43
The entire mammalian genome, not just coding sequences, contains informative phylogenetic information, according to a study appearing online last night in the Proceedings of the National Academy of Sciences. Researchers from the University of California at Berkeley and the Lawrence Berkeley National Lab used a non-alignment approach called the feature frequency profile (FFP) to compare the non-genic, intronic, exonic, and whole-genome regions of 10 mammalian genomes. Their analysis suggests clues about past evolutionary events are scattered throughout mammalian genomes, with both coding and non-coding regions containing phylogenetic clues.
Helicos Publishes Proof-Of-Principle RNA Sequencing Study PDF Print E-mail
Tuesday, 29 September 2009 10:02

Researchers from Helicos BioSciences today published a proof-of-principle study illustrating the feasibility of doing direct RNA sequencing using its single molecule sequencing technology. The team used a prototype Helicos instrument to directly sequence RNA from Baker's yeast, Saccharomyces cerevisiae without first converting it to complementary DNA. In the process, they also uncovered heterogeneity at the 3' ends of many S. cerevisiae transcripts, as well as evidence that at least some small nucleolar and ribosomal RNAs are polyadenylated in yeast.

Illumina Delays Launch of 'Harmonia' Sequencing Module for iScan System PDF Print E-mail
Tuesday, 29 September 2009 09:06

An Illumina official said today that the company has pushed back the expected launch of the "Harmonia" sequencing module for its iScan array system to the second quarter of 2010. The module, originally scheduled for launch this year, combines the sequencing chemistry of the company’s Genome Analyzer with the iScan Reader of its iScan array system.

MSU scientist helps map potato genome; move will improve crop yield PDF Print E-mail
Friday, 25 September 2009 11:19

EAST LANSING, Mich. - It's been cultivated for at least 7,000 years and spread from South America to grow on every continent except Antarctica. Now the humble potato has had its genome sequenced.

'Junk' DNA May Prove Invaluable In Quest For Gene Therapies PDF Print E-mail
Wednesday, 23 September 2009 03:38

Scientists have identified how a protein enables sections of so-called junk DNA to be cut and pasted within genetic code – a finding which could speed development of gene therapies. The study by researchers at the University of Edinburgh sheds light on the process, known as DNA transposition, in which shifted genes have a significant effect on the behaviour of neighbouring genes. In the human genome, rearrangement of antibody genes can enable the immune system to target infection more effectively.

NCI Team Develops Mouse Stem Cell Assay for Classifying BRCA1 Mutations PDF Print E-mail
Wednesday, 23 September 2009 03:06
Researchers from the National Cancer Institute have developed a mouse embryonic stem cell-based assay to distinguish deleterious from neutral mutations in the human BRCA1 gene. The team used the assay to test more than a dozen mutations in the human breast cancer risk gene BRCA1. In each case, the assay appeared to accurately predict which mutations are deleterious in humans and which are neutral.
NIH-Led Study Confirms Ability to Identify Individuals from GWAS Data PDF Print E-mail
Friday, 09 October 2009 05:02
A new study confirms that it is possible to identify individual study participants from genome-wide association data. In a paper appearing in the advance, online edition of Nature Genetics yesterday, researchers from the National Institutes of Health and elsewhere described their likelihood-based statistical framework approach for using genotype frequencies and individual genotype information to detect individuals in GWAS. In so doing, the team verified their suspicion that GWAS participants — or close relatives — can be identified from aggregate GWAS data.
New type of genetic change identified in inherited cancer PDF Print E-mail
Monday, 05 October 2009 05:44

DURHAM, N.C. Duke University Medical Center and National Cancer Institute scientists have discovered that a novel genetic alteration a second copy of an entire gene is a cause of familial chordoma, an uncommon form of cancer arising in bones and frequently affecting the nervous system. Inherited differences in gene copy number, known as copy number variation (CNV), have been implicated in some hereditary diseases but none of the previously discovered familial cancer genes has had CNV as the genetic change.

Cancer Genome Atlas Gets $275M Funding from Stimulus, NCI and NHGRI PDF Print E-mail
Monday, 05 October 2009 04:37
The Cancer Genome Atlas project will receive a total of $275 million over the next two years to fund genomic mapping of more than 20 types of cancer. The $175 million in ARRA funding announced Wednesday by President Barack Obama will be buttressed by an additional $100 million from the National Cancer Institute and the National Human Genome Research Institute.
Japanese Researchers Apply Comparative Genomics to Enterohemorrhagic E. Coli PDF Print E-mail
Wednesday, 30 September 2009 20:21

A comparative genomics study is providing new insights into the processes that lead to enterohemorrhagic forms of Escherichia coli. Japanese researchers sequenced the genomes of three enterohemorrhagic E. coli, or EHEC, strains and compared these newly sequenced genomes with the genomes of two EHEC O157:H7 strains and 21 strains of Shigella or non-EHEC E. coli.

International Team Applies Comparative Genomics to Hospital Acquired Infection-Causing Bacteria PDF Print E-mail
Wednesday, 30 September 2009 07:34
An international research team used comparative genomics to look for the genetic causes of increased virulence in a strain of Clostridium difficile involved in hospital-acquired infections. In a paper appearing online today in Genome Biology, a team of British, French, and American researchers compared three C. difficile strains: a non-epidemic strain with the so-called 012 ribotype, a non-virulent strain with the 027 ribotype, and a hyper-virulent 027 strain. In so doing, the team identified genetic markers that they say may be useful for understanding the nature of increased C. difficile virulence.
Researchers Find Genetic Clues to India's Population History PDF Print E-mail
Tuesday, 29 September 2009 09:37

Populations found in India today are largely descended from two distinct ancestral groups, according to paper appearing online this afternoon inNature. Researchers from Harvard University, the Broad Institute, and the Centre for Cellular and Molecular Biology in Hyderabad, India, assessed more than half a million SNPs in the genomes of 132 individuals from dozens of Indian populations. Their results indicate that the populations present in India today are anciently mixed — but highly diverged — groups descended from so-called Ancestral North and Ancestral South Indians.

Scandinavians are descended from Stone Age immigrants PDF Print E-mail
Friday, 25 September 2009 11:23

Today's Scandinavians are not descended from the people who came to Scandinavia at the conclusion of the last ice age but, apparently, from a population that arrived later, concurrently with the introduction of agriculture. This is one conclusion of a new study straddling the borderline between genetics and archaeology, which involved Swedish researchers and which has now been published in the journal Current Biology.

Ancestral Populations Of India And Relationships To Modern Groups Revealed PDF Print E-mail
Friday, 25 September 2009 10:57

In a study published in the September 24th issue of Nature, an international team describes how they harnessed modern genomic technology to explore the ancient history of India, the world's second most populous nation. The new research reveals that nearly all Indians carry genomic contributions from two distinct ancestral populations. Following this ancient mixture, many groups experienced periods of genetic isolation from each other for thousands of years. The study, which has medical implications for people of Indian descent, was led by scientists at the Centre for Cellular and Molecular Biology (CCMB) in Hyderabad, India together with US researchers at Harvard Medical School, the Harvard School of Public Health and the Broad Institute of Harvard and MIT.

Gene Variant Linked To Glaucoma Identified PDF Print E-mail
Wednesday, 23 September 2009 03:20

An international team, led by researchers from the University of California, San Diego School of Medicine and the National Eye Institute, has discovered gene variants for glaucoma in a black population. The finding could lead to future treatments or a cure for this disease, which leads to blindness in two million Americans each year.

Researchers Working To Develop, Market Embryonic Test For Bovine Genetics PDF Print E-mail
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Tuesday, 22 September 2009 01:44

Looking at the genetic makeup of cattle to determine their value is nothing new. An examination of a small sample of hair or blood can reveal if a calf has any genetic diseases that will lower the market price. Now, a team of clinicians and diagnosticians and genetic researchers at Iowa State University's College of Veterinary Medicine are looking to test those calves earlier ... before they are born ... even before their mother is pregnant.

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