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For a comprehensive review of the most interesting recent articles published in the biological sciences, visit Faculty of 1000 Biology, an online literature awareness tool published by BioMed Central. Faculty of 1000 Biology systematically highlights exciting recent publications on the basis of recommendations of a faculty of well over 1,000 of the world's leading researchers. |
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Jonathan A. Eisen
The Institute for Genomic Research, United States of America
MICROBIOLOGY
 New Finding
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This paper is the first detailed study of a large family of ankyrin domain-encoding genes in Wolbachia, which have been hypothesized to play a role in the interactions of Wolbachia species with their invertebrate hosts. The authors use both comparative sequence analysis and comparative gene expression studies to characterize the ankyrin domain-encoding genes in multiple Wolbachia strains. Comparison of the sequence and expression results with the phenotypes caused by the Wolbachia used indicate that some of these genes are good candidates for being responsible not only for interactions with host species, but also for some of the differences in phenotypes caused by different Wolbachia strains.
Evaluated 19 Sep 2005 |
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Michael Wagner
Universität Wien, Austria
MICROBIOLOGY
 Hypothesis
 Tech Advance
 Controversial
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This article shows that horizontal gene transfer (HGT) rates of core orthologous genes are relatively low among prokaryotes, suggesting that the impact of HGT for phylogeny might have been overestimated in the past. In total 40 microbial genomes and 297 orthologous gene clusters were analyzed by statistically comparing topologies from individual gene trees and whole-genome trees. Among the analyzed gene sets, the average rate of HGT in the studied genomes was estimated to be 2%. Organisms whose genomes showed particularly high or low rates of HGT were found to be relatively evenly distributed in the tree of life.
Evaluated 20 Sep 2005 |
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Stephen Scherer
University of Toronto, Canada
GENOMICS & GENETICS
 Confirmation
New Finding
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The aim of this study was to investigate the prevalence of submicroscopic deletions and duplications in mental retardation (MR) patients using whole genome coverage array comparative genomic hybridization (CGH). This is one of the first studies of structural rearrangements in a patient cohort that acknowledges and contends with the fact that the majority of variants detected in this type of study will represent large-scale copy number polymorphisms. By screening a cohort of 100 MR patients and their parents, this study yields novel insight into genomic aberrations underlying MR and extends the current knowledge of large-scale polymorphisms in the human genome. Using array CGH, the authors show that they can explain ~10% of MR cases which did not show any rearrangements by karyotyping or by screening of subtelomeric regions. The results also indicate that the clinically relevant deletions and duplications are larger on average than the copy number polymorphisms detected.
Evaluated 19 Sep 2005 |
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 Recommended
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F1000 Factor 3.0 |
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Origin and evolution of new exons in rodents.
Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L, Zhang J, McDermott J, Samudrala R, Wang J, Yang H, Yu J, Kristiansen K, Wong GK, Wang J
Genome Res 2005 Sep 15(9):1258-64 [abstract on PubMed] [request from library] 
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Selected by | Austin Hughes
Evaluated 22 Sep 2005
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Austin Hughes
University of South Carolina, United States of America
IMMUNOLOGY
New Finding
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This study is the first to provide a genome-wide answer to the question of where new exons come from. By comparing mouse and rat genomes to that of human, the authors found 2695 newly evolved exons in mouse and rat and estimated the rate of new exon formation at about three per thousand genes per million years. This paper is among the first to give us a handle on where new exons come from and thus potentially where entirely novel genes come from. There are important fundamental questions that molecular evolution has largely side-stepped so far, concentrating instead on the relatively well-understood process of gene duplication.
Evaluated 22 Sep 2005 |
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Recommended
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F1000 Factor 3.0 |
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A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK, Wang J, Deng XW, Wang J
Genome Res 2005 Sep 15(9):1274-83 [abstract on PubMed] [request from library]
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Selected by | Daniel Chamovitz
Evaluated 20 Sep 2005
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Daniel Chamovitz
Tel Aviv University, Israel
PLANT BIOLOGY
Confirmation
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I found this article interesting both because of the sheer scale of the genomic microarray analysis and for its illustration of the use of genomic microarrays for confirming putative gene models. These consortia used an oligo array representing >40,000 rice gene models, with about half having no experimental support. Among the various findings they show that the vast majority of predicted genes are indeed expressed.
Evaluated 20 Sep 2005 |
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