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Recent News and Articles on the Keywords: genome + stronger + effect  Related to the article below (Last Update: 8/5/2008)

Human Genome Sciences reports stronger sales, bigger losses
Bizjournals.com, NC - Aug 1, 2008
Human Genome Sciences Inc. increased its second-quarter revenue by 28 percent from the same period last year, but also widened its loss by nearly 45 percent ...HGSI
Cheating athletes turn to gene doping
Palm Beach Post,  United States -
Science embarked on this road in 1990, when the Human Genome Project was launched to identify the 20000 to 25000 genes in human DNA and determine what, ...
Genome Alberta using 21st Century biology to tackle the Mountain ...
MarketWatch - Aug 1, 2008
Current control efforts receiving wide attention mostly involve prescribed burns but Genome Alberta and its partners are looking much deeper into the ...
New Protein-Analysis Tool Shows Broad Role for miRNAs in Protein ...
RNAi News (subscription), NY - Jul 31, 2008
This is the first time that changes in protein synthesis have been measured in a genome-wide scale in human cells. When you applied the pSILAC approach, ...

San Diego Union Tribune
The race against gene doping
San Diego Union Tribune, United States - Jul 27, 2008
The future: Doping tests that examine an athlete's whole body and genome. Friedmann is a leading authority on gene doping and a pioneer in gene therapy ...
An Interview with Navigenics
Medgadget.com, CA - Jul 28, 2008
The major goal of Navigenics is to use risk information embedded within the genome to drive prevention strategies early in life. The goal of Navigenics is ...
Basics: Sonic Hedgehog
ScienceBlogs - Aug 1, 2008
We often compare the genome to a toolbox ? a collection of tools that play various roles in the construction of an organism. If I had to say what tool Sonic ...
Roche posts very good results: strong market outperformance ...
Business-News, Switzerland - Jul 20, 2008
The rest was mainly due to strong competition in the US diabetes care market and portfolio mix effects. Professional Diagnostics ? 30 quarters of ...
All manner of human creativity on display
ScienceBlogs - Aug 1, 2008
I guess since some big biotech firms sequenced the rice genome in 2002, a lot of patents have been issued, a lot of info passed around, ...
Designer babies and Curing Cancer Mark D. Drapeau
Opinion Editorials, VA - Jul 6, 2008
This kind of gene will accumulate in genomes over generations because natural selection cannot weed it out, since, again, harmful effects occur after the ...
Source: Google News

Genome-wide association studies for common diseases and complex traits -
JN Hirschhorn, MJ Daly - Nature Reviews Genetics, 2005 - nslij-genetics.org
... Most of the genome falls into segments of strong LD,within ... in a region of
linkage,or on the basis of other evidence that they might affect disease risk ...

[PDF] A genome-wide association study identifiesnovel risklocifor type 2 diabetes -
R Sladek, G Rocheleau, J Rung, C Dina, L Shen, D … - Nature, 2007 - nature.com
... Several other SNPs at that locus also attained genome-wide significance after
correcting ... our stage 1 had limited power to detect their modest effect and also ...
-

… by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome … -
MS Moreno, BL Schneider, RR Maile, W Weyler, MH … - Molecular Microbiology, 2001 - Blackwell Synergy
... be subject to marked glucose effects and were ... before the advent of whole-genome
transcriptional analyses. ... 20?) CcpA-mediated repression, stronger plus glucose ...

Genomic Control for Association Studies -
B Devlin, K Roeder - Biometrics, 1999 - Blackwell Synergy
... the realiza- tion that a dense set of SNP throughout the genome could yield ... methods,
which employ family-based sam- pling to obviate the effects of population ...

Adaptive hitchhiking effects on genome variability -
P Andolfatto - Current Opinion in Genetics & Development, 2001 - Elsevier
... of these modes of selection in shaping patterns of genome variability. ... in regions
of lower recombination where hitchhiking effects are stronger [15 and 16 ...

Positive and Negative Selection on the Human Genome -
JC Fay, GJ Wyckoff, CI Wu - Genetics, 2001 - Genetics Soc America
... individual is expected to carry 627 deleterious mutations in his genome. ... frequency
compared to common SNPs (Fig 1). This effect should be stronger for A ...

Genome-Wide Epistatic Interaction Analysis Reveals Complex Genetic Determinants of Circadian … -
K Shimomura, SS Low-Zeddies, DP King, TDL Steeves, … - Genome Research, 2001 - Cold Spring Harbor Lab
... have applied novel whole-genome techniques, complex ... that have significant main effects
on quantitative ... primarily, or solely, from strong epistatic interactions ...

Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis … -
SI Wright, N Agrawal, TE Bureau - Genome Research, 2003 - Cold Spring Harbor Lab
... structure, and may consequently impose stronger deleterious effects on host fitness.
However, a large fraction of TEs in the Arabidopsis genome lack coding ...

Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals -
TR Gregory - Genome, 2000 - article.pubs.nrc-cnrc.gc.ca
... that place severe limits on the expansion of the genome. ... ge- nome size may have been
under strong positive selection for their effects on metabolism ...

Structure of linkage disequilibrium and phenotypic associations in the maize genome -
DL Remington, JM Thornsberry, Y Matsuoka, LM … - Proceedings of the National Academy of Sciences, 2001 - National Acad Sciences
... 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD ... Provided
the effects of population structure are effectively controlled ...

Source: Google Scholar

Adaptation to the environment has a stronger effect on the genome than anticipated

Faster growth, darker leaves, a different way of branching - wild varieties of the plant Arabidopsis thaliana are often substantially different from the laboratory strain of this small mustard plant, a favorite of many plant biologists. Which detailed differences distinguish the genomes of strains from the polar circle or the subtropics, from America, Africa or Asia has been investigated for the first time by research teams from Tübingen, Germany, and California led by Detlef Weigel from the Max Planck Institute for Developmental Biology. The results were surprising: The extent of the genetic differences far exceeds the expectations for such a streamlined genome, as the scientists write in this week’s edition of Science magazine.
To track down the variation in the genome of the different Arabidopsis strains, the researchers compared the genetic material of 19 wild strains with that of the genome of the lab strain, which was sequenced in the year 2000. Using a very elaborate procedure, they examined every one of the roughly 120 million building blocks of the genome. For their molecular sleuthing they used almost one billion specially designed DNA probes. "All together, these probes would have seven times the length of human genome," illustrates Weigel the extent of the project. The data were evaluated with several specially designed statistical methods, including a variant of machine learning.

The result of this painstaking analysis: on average, every 180th DNA building block is variable. And about four percent of the reference genome either looks very different in the wild varieties, or cannot be found at all. Almost every tenth gene was so defective that it could not fulfill its normal function anymore!

Results such as these raise fundamental questions. For one, they qualify the value of the model genomes sequenced so far. "There isn’t such a thing as the genome of a species," says Weigel. He adds "The insight that the DNA sequence of a single individual is by far not sufficient to understand the genetic potential of a species also fuels current efforts in human genetics."

Still, it is surprising that Arabidopsis has such a plastic genome. In contrast to the genome of humans or many crop plants such as corn, that of Arabidopsis is very much streamlined, and its size is less than a twentieth of that of humans or corn—even though it has about the same number of genes. In contrast to these other genomes, there are few repeats or seemingly irrelevant filler sequences. "That even in a minimal genome every tenth gene is dispensable, has been a great surprise," admits Weigel.
Detailed analyses showed that genes for basic cellular functions such as protein production or gene regulation rarely suffer knockout hits. Genes that are important for the interaction with other organisms, on the other hand, such as those responsible for defense against pathogens or infections, are much more variable than the average gene. "The genetic variability appears to reflect adaptation of local circumstances," says Weigel. It is likely that such variable genes allow plants to withstand dry or wet, hot or cold conditions, or make use of short and long growing seasons.

Such genome analyses of unprecedented details will allow a much better understanding of local adaptation, and this was indeed one of the main reasons for conduction the study. "By extending these types of studies to other species we hope to help breeders to produce varieties that are optimally adapted to rapidly changing environmental conditions," explains Weigel. He is already collaborating with the International Rice Research Institute (IRRI) in the Philippines to apply the methods and experience gathered with Arabidopsis to twenty different rice varieties.

How environment and genome interact is also the goal of new, even more powerful methods. While the technology used so far can only identify genes that have changed or are lost relative to the reference genome, direct sequencing of the genome of wild strains will allow the detection of new genes. The plan is to decipher the genomes of at least 1001 Arabidopsis varieties. A new instrument, with which the entire genome of a plant can be read in just a few days, is already available. Still missing are the computational algorithms to interpret the anticipated flood of data.

Researchers from Tübingen who contributed to the study include Richard Clark, Stephan Ossowski and Norman Warthmann from the MPI for Developmental Biology, Georg Zeller and Gunnar Rätsch from the Friedrich Miescher Laboratory of the Max Planck Society, Gabriele Schweikert and Bernhard Schölkopf from the MPI for Biological Cybernetics, and Daniel Huson from the University Tübingen. Researchers from California who contributed to this study include Huaming Chen, Paul Shinn and Joseph Ecker from the Salk Institute, Christopher Toomajian, Tina Hu and Magnus Nordborg from the University of Southern California, and Glenn Fu, David Hinds and Kelly Frazer from Perlegen Sciences, Inc.

[DW/CB]

Original work:

Richard M. Clark, Gabriele Schweikert, Christopher Toomajian, Stephan Ossowski, Georg Zeller, Paul Shinn, Norman Whartmann, Tina T. Hu, Glenn Fu, David A. Hinds, Huaming Chen, Kelly A. Frazer, Daniel H. Huson, Bernhard Schölkopf, Magnus Nordborg, Gunnar Rätsch, Joseph R. Ecker, Detlef Weigel
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana
Science, July 20, 2007
 
 
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