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Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.
Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, Conway de Macario E, Dodsworth JA, Gillett W, Graham DE, Hackett M, Haydock AK, Kang A, Land ML, Levy R, Lie TJ, Major TA, Moore BC, Porat I, Palmeiri A, Rouse G, Saenphimmachak C, Söll D, Van Dien S, Wang T, Whitman WB, Xia Q, Zhang Y, Larimer FW, Olson MV, Leigh JA
J Bacteriol 2004 Oct 186(20):6956-69 [abstract on PubMed][request from library] 
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Selected by | Shiladitya DasSarma
Evaluated 18 Nov 2004
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Shiladitya DasSarma
University of Maryland Biotechnology Institute, United States
MICROBIOLOGY
 New Finding
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This paper reports the complete 1,661,137 bp sequence of one of the few genetically manipulable "model" Archaea. Methanococcus maripaludis is the first genetically tractable hydrogenotrophic methanogenic species to be sequenced and should provide an excellent system for detailed genetic analysis of the metabolism and molecular biology of this class of Archaea. A comprehensive bioinformatic analysis of the genome sequence is presented.
Evaluated 18 Nov 2004 |
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Nicolas Galtier
Université Montpellier 2, France
GENOMICS & GENETICS
 Controversial
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This paper strongly contributes to the hot debate about recombination in mitochondria through an impressive survey of within-species mitochondrial sequence variation in animals. Animal mitochondrial genomes are usually considered as maternally inherited, and therefore non-recombining. A series of reports by Eyre-Walker and colleagues in 1999 {1,2} challenged this paradigm and generated a controversy. In this paper, Piganeau and colleagues examine sequence polymorphism in 279 animal species and reject clonality for a substantial number of species, including a primate (Macaca nemestrina). What remains to be elucidated is whether these recombination events have actually occurred in vivo or reflect experimental artifacts. {1} Eyre-Walker et al. Proc R Soc Lond B Biol Sci 1999, 266:477-83 [PMID:10189711]. {2} Awadalla et al. Science 1999, 286:2524-25 [PMID:10617471].
Evaluated 23 Nov 2004 |
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Cheng-Ming Chiang
Case Western Reserve University, United States
CELL BIOLOGY
New Finding
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This paper describes the identification of a common set of genes regulated by the retinoblastoma (RB) tumor suppressor family protein p130 and the transcription factor E2F4 under three different growth arrest conditions, including serum withdrawal, contact inhibition and p16 cell cycle inhibitor-induced cellular arrest. By further characterizing the p130-E2F4 target genes by computational analysis of their promoter-proximal regions and by chromatin immunoprecipitation (ChIP), small interference RNA (siRNA), reverse transcription-PCR (RT-PCR), and genome-wide analysis of transcription factor occupancy using ChIP-on-chip, the authors uncover a novel role for nuclear respiratory factor-1 (NRF-1) in both growth arrest and mitochondrial function. These studies elegantly illustrate the involvement of specific RB-E2F family members in modulating cell cycle progression and distinct biological processes.
Evaluated 22 Nov 2004 |
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Marjori Matzke
Austrian Academy Of Sciences, Austria
PLANT BIOLOGY
New Finding
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While microRNAs have previously been shown to effect gene silencing by targeting complementary mRNAs for either cleavage or translational repression, this study shows for the first time that certain microRNAs can induce silencing by directing DNA methylation. Two exons downstream of the microRNA complementary site in PHABULOSA and PHAVOLUTA target genes, which are involved in leaf development, are highly methylated in wild type cells, but not in mutant cells in which the microRNA complementary site is disrupted. Because the microRNA binding site is interrupted by an intron, direct interactions between the microRNA and DNA template are unlikely. Instead, a model is presented in which the miRNAs base pair to complementary regions of nascent, newly processed mRNA that remains close to the target DNA, resulting in recruitment of a chromatin modifying complex that catalyzes methylation.
Evaluated 22 Nov 2004 |
Miltos Tsiantis
University of Oxford, United Kingdom
PLANT BIOLOGY
New Finding
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This study offers a novel angle on how microRNAs regulate expression of adaxial fate promoting Arabidopsis class III HD-ZIP transcripts. The authors provide evidence that miRNAs mediate chromatin modification of HD-ZIPIII loci via interacting with newly processed HD-ZIPIII transcripts. According to this model, miRNA mediated repression is not a direct result of miRNA cleavage of target transcripts. Rather, cleaved transcripts may serve as signals that direct chromatin modifications including DNA methylation and hence gene repression.
Evaluated 11 Nov 2004 |
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David Catcheside
Flinders University, Australia
MICROBIOLOGY
 Confirmation
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This paper shows there are similarities but also differences in the gamut of genes in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe that are required to make the double strand breaks in DNA that initiate genetic recombination. This adds to the previously known similarities and differences shown to exist in the gene sets involved in the DNA break repair processes that lead to sequence exchange between homologous chromosomes. Whilst processes broadly similar in principle are involved in strand breakage, heteroduplex DNA formation and strand repair, the details of recombination, which are not yet well understood, are clearly not identical in all organisms. This suggests a proper understanding of recombination requires investigation of the process in a range of species.
Evaluated 18 Nov 2004 |
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