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Genome Biology 2005, 6(9):345
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F1000 Factor 3.0


Behavior and the limits of genomic plasticity: power and replicability in microarray analysis of honeybee brains.
Cash AC, Whitfield CW, Ismail N, Robinson GE
Genes Brain Behav 2005 Jun 4(4):267-71 [
abstract on PubMed][request from library]
Selected by | Martin Giurfa
Evaluated 8 Aug 2005

Faculty Comments
Faculty Member Comments
Martin Giurfa
Centre National de la Recherche Scientifique (CNRS), France
NEUROSCIENCE


New Findinge
Tech Advance
The authors demonstrate the existence of gene expression differences in the brain of honeybees depending on their task specialization. Tasks that occupy longer periods (> 1 week) such as nursing and foraging are consistently associated with different brain gene expression. Transient tasks that are performed during 1 or 2 days such as guarding or undertaking do not show such differences. These results support the notion that genomic plasticity underlies changes in behavioral tasks in a social system based on the division of labor.

Evaluated 8 Aug 2005

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Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families.
Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ
Syst Biol 2005 Jun 54(3):441-54 [
abstract on PubMed] [request from library]
Selected by | Elizabeth Kellogg
Evaluated 29 Jul 2005

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Faculty Member Comments
Elizabeth Kellogg
University of Missouri-St. Louis, United States of America
DEVELOPMENTAL BIOLOGY


New Finding
Another family, another genome duplication; this paper documents a duplication event that preceded the divergence of Glycine (soybean) and Medicago, placing the duplication near the origin of the papilionoid legumes. The authors use a powerful combination of phylogenetic analysis and estimates of synonymous mutation rates to show that even the "diploid" Medicago truncatula is an ancient polyploid. It is possible to distinguish the recent genome duplication that led to tetraploid Glycine from the more ancient event that characterizes at least one major clade of legumes.

Evaluated 29 Jul 2005

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Analysis of microbial gene transcripts in environmental samples.
Poretsky RS, Bano N, Buchan A, Lecleir G, Kleikemper J, Pickering M, Pate WM, Moran MA, Hollibaugh JT
Appl Environ Microbiol 2005 Jul 71(7):4121-6 [
abstract on PubMed] [request from library]
Selected by | Russell Hill
Evaluated 26 Jul 2005

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Faculty Member Comments
Russell Hill
University of Maryland Biotechnology Institute, United States of America
MICROBIOLOGY


New Finding
Tech Advance
This is the first study to analyze gene expression in marine and freshwater bacterioplankton communities by the direct retrieval of mRNA transcripts. This environmental transcriptomics approach has the advantage of revealing all genes that are expressed whether they are present in databases or not, unlike most PCR-based approaches in which primers are designed to retrieve only known sequences. Many transcripts from microbial communities from a tidal salt water marsh creek and Mono Lake could be linked to environmentally important processes. This approach has great potential for linking genetic potential indicated by environmental genomics with biogeochemical activity in natural microbial communities.

Evaluated 26 Jul 2005

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RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble.
Ding Y, Chan CY, Lawrence CE
RNA 2005 Aug 11(8):1157-66 [
abstract on PubMed] [request from library]
Selected by | Douglas Turner
Evaluated 4 Aug 2005

Faculty Comments
Faculty Member Comments
Douglas Turner
University of Rochester, United States of America
STRUCTURAL BIOLOGY


Tech Advance
This article provides a way to deal with the large number of possible RNA secondary structures that are generated by algorithms that use thermodynamics to predict structure. The authors use a statistical sampling method to show that the large number of structures generated usually belong to a small number of centroids, i.e. similar structures. They also provide a program that will present the most representative structure of a centroid.

Evaluated 4 Aug 2005

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Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues.
Ge X, Yamamoto S, Tsutsumi S, Midorikawa Y, Ihara S, Wang SM, Aburatani H
Genomics 2005 Aug 86(2):127-141 [
abstract on PubMed] [request from library]
Selected by | Charles Auffray
Evaluated 27 Jul 2005

Faculty Comments
Faculty Member Comments
Charles Auffray
Centre National de la Recherche Scientifique (CNRS), France
PHYSIOLOGY


Tech Advance
This paper highlights the value of using gene expression profiles registered in normal tissues as signatures for the interpretation of cancer type and status. The authors have collected expression profiles using pooled normal human tissue samples and published datasets, to identify tissue-specific sets of genes. They demonstrate that the tissue-specific signatures can be used to identify precisely the tissue origin of cancer samples including metastases established in other tissues.

Evaluated 27 Jul 2005













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