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Mixing genomics and geography yields insights into life and environment
January 23, 2009In an upcoming issue of Proceedings of the National Academy of Sciences, Yale researchers used newly developed mathematical models to analyze huge amounts of data on physical characteristics such as temperature and salinity in different ocean habitats and metabolic activity in marine micro-organisms.
They were able to see in unprecedented detail how environment influences molecular changes within living organisms. As the technology dubbed "metagenomics" progresses, scientists might be able to detect environmental change or toxic chemicals not simply by using mechanical sensors or monitoring sensor species, but by examining biological changes within tiny organisms, said Mark Gerstein, the Albert L. Williams professor of biomedical informatics and professor of molecular biophysics & biochemistry and computer science.
The research team was headed by computational biology and bioinformatics Ph.D. student Tara A. Gianoulis under the laboratories of Gerstein and Michael Snyder, the Lewis B. Cullman professor of molecular, cellular & developmental biology and professor of molecular biophysics & biochemistry, The team incorporated biochemical and environmental data from the previously published Global Ocean Survey, which catalogued information from 40 different aquatic sites. The GOS data effectively doubled the number of known proteins, and through a statistical analysis of these data, the Yale team was able to infer microbial adaptations to the environment.
"The genomics world has developed amazing technology that has captured a tremendous amount of information about living organisms, giving rise to an era of big data," Gerstein said. "Meanwhile, you have this explosion of geo-spatial information from satellites and global sensors. When key data sets connect these two disparate worlds, you find a subtle richness of connections."
Through a complex statistical analysis, the study showed that organisms switched energy conversion strategies depending on the environment, used components of membranes differently, and provided evidence that factors such as metals may play a large role in how micro-organisms adapt to their environments.
Yale University
Genomics Current Events and Genomics News RSSDelft breakthrough in bioethanol production from agricultural waste
With the introduction of a single bacterial gene into yeast, researchers from Delft University of Technology in the Netherlands achieved three improvements in bioethanol production from agricultural waste material: 'More ethanol, less acetate and elimination of the major by-product glycerol' This week the invention was published in the scientific journal Applied and Environmental Microbiology.
Scientists at UA, collaborating institutions decode maize genome
Scientists from the University of Arizona led by Arizona Genomics Institute director Rod A. Wing and from collaborating institutions have deciphered the complete genetic code of the maize plant for the first time.
Cigarettes Harbor Many Bacteria Harmful to Human Health
Cigarettes are "widely contaminated" with bacteria, including some known to cause disease in people, concludes a new international study conducted by a University of Maryland environmental health researcher and microbial ecologists at the Ecole Centrale de Lyon in France.
Unknowlingly consuming endangered tuna
While most of us would never willingly consume a highly endangered species, doing so might be as easy as plucking sushi from a bento box.
Maize cell wall genes identified, giving boost to biofuel research
Purdue University scientists have helped identify and group the genes thought to be responsible for cell wall development in maize, an effort that expands their ability to discover ways to produce the biomass best suited for biofuels production.
Protein changes in heart strengthen link between Alzheimer's disease and chronic heart failure
A team of U.S., Canadian and Italian scientists led by researchers at Johns Hopkins report evidence from studies in animals and humans supporting a link between Alzheimer's disease and chronic heart failure, two of the 10 leading causes of death in the United States.
Largest gene study of childhood IBD identifies 5 new genes
In the largest, most comprehensive genetic analysis of childhood-onset inflammatory bowel disease (IBD), an international research team has identified five new gene regions, including one involved in a biological pathway that helps drive the painful inflammation of the digestive tract that characterizes the disease.
Pathogen protection and virulence: Dark side of fungal membrane protein revealed
Researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech and Montana State University have discovered a fungal protein that plays a key role in causing disease in plants and animals and which also shields the pathogen from oxidative stress.
Study sheds light on evolution of human complexity
A painstaking analysis of thousands of genes and the proteins they encode shows that human beings are biologically complex, at least in part, because of the way humans evolved to cope with redundancies arising from duplicate genes.
TGen seeks emergency FDA approval of new swine flu test
The Phoenix-based non-profit Translational Genomics Research Institute (TGen) announced today that, along with a business collaborator, it will submit a request to the U.S. Food and Drug Administration for emergency use of a new test to diagnose the 2009 H1N1 swine flu virus.
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Introduction to Genomics by Arthur Lesk (Author) Our genome is the blueprint to our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. But it is more than a static information store: our genome is a dynamic, tightly-regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the process of life? Introduction to Genomics is a fascinating insight into what can be revealed from the study of genomics: how organisms differ or match; how different organisms evolved; how the genome is constructed and how it operates; and what... |
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A Primer of Genome Science, 2nd Edition by Greg Gibson (Author), Spencer V. Muse (Author) A Primer of Genome Science bridges the gap between standard genetics textbooks and highly specialized, technical, and advanced treatments of the subdisciplines. It provides an affordable and up-to-date introduction to the field that is suited to advanced undergraduate or early graduate courses. Bioinformatic principles and experimental strategies are explained side-by-side with the experimental methods, establishing a framework that allows teachers to explore topics and the literature at their own pace. |
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Genomics: Fundamentals and Applications by Supratim Choudhuri (Editor), David B. Carlson (Editor) This unique new text delivers a solid foundation for understanding the role of genomics in human health and in advances that promise to help improve the quality of human life. Unlike other works that focus mainly on toxicogenomic techniques, Genomics presents a thorough overview of the field in four major sections: 1) fundamentals of genes and genome structure, function, expression, variations, and genomic technology platforms; 2) applications of genomics in drug discovery and drug development, safety evaluation, genomic database maintenance, mining, and analysis, food safety monitoring, and translational toxicogenomics; 3) how regulatory agencies such as the FDA and EPA use genomic data in their safety evaluation; and 4) a summary of the current state and the future prospect of the... |
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