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Volume 6 Issue 8
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Comment |
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The life aquatic
Gregory A Petsko Genome Biology 2005, 6:116 (28 July 2005)
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Editor’s summary
If we want to know for sure whether there was, or still is, life on Mars, we have to send people there.
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Datasets for evolutionary comparative genomics
David A Liberles Genome Biology 2005, 6:117 (28 July 2005)
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Editor’s summary
A rationale for deciding about whole-genome sequencing projects is discussed, along with other important strategies for understanding the phenotypic divergence of species. |
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Review |
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The SET-domain protein superfamily: protein lysine methyltransferases
Shane C Dillon, Xing Zhang, Raymond C Trievel, Xiaodong Cheng Genome Biology 2005, 6:227 (2 August 2005)
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Editor’s summary
The SET-domain protein methyltransferase superfamily includes all but one of the proteins known to methylate histones on lysine. Histone methylation is important in the regulation of chromatin and gene expression. |
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Cytological profiling: providing more haystacks for chemists' needles
Janet Lorang, Randall W King Genome Biology 2005, 6:228 (29 July 2005)
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Editor’s summary
A recent study describes how unbiased screening of cellular morphology, followed by affinity purification to identify targets of compounds with interesting effects, can lead to the identification of novel inhibitors. |
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Metagenomics for studying unculturable microorganisms: cutting the Gordian knot
Patrick D Schloss, Jo Handelsman Genome Biology 2005, 6:229 (1 August 2005)
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Editor’s summary
Recent advances in shotgun sequencing and computational methods for genome assembly have advanced the field of metagenomics, the culture-independent cloning and analysis of microbial DNA extracted directly from an environmental sample, to provide glimpses into the life of uncultured microorganisms. |
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Report |
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Articles selected by Faculty of 1000: angiosperm relationships; chemorecpetor diversity; antibiotic-resistance genes; horizontal transfer in yeasts; centriole proteome
Genome Biology 2005, 6:339 (14 July 2005)
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Editor’s summary
A selection of evaluations from Faculty of 1000 covering angiosperm relationships; chemorecpetor diversity; antibiotic-resistance genes; horizontal transfer in yeasts; centriole proteome. |
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Articles selected by Faculty of 1000: detecting metalloproteins; microRNA expression profiles; Thermotoga genome plasticity; circadian clock systems biology; new non-coding RNA genes
Genome Biology 2005, 6:340 (26 July 2005)
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Editor’s summary
A selection of evaluations from Faculty of 1000 covering detecting metalloproteins; microRNA expression profiles; Thermotoga genome plasticity; circadian clock systems biology; new non-coding RNA genes. |
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Physiology engages with functional genomics - at last
Julian AT Dow, Jennifer M Lee Genome Biology 2005, 6:335 (20 July 2004)
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Editor’s summary
A report on the XXXV International Congress of Physiological Sciences, held together with Experimental Biology 2005, San Diego, USA, 31 March - 6 April 2005. |
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Fungal biology reaps the benefit of genomics
Ralph Dean, Thomas Mitchell, Nicole Donofrio, Jun-Seop Jeong, Amy Powell Genome Biology 2005, 6:336 (28 July 2005)
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Editor’s summary
A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. |
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Human genome research enters a new phase
Harukazu Suzuki, Yoshihide Hayashizaki Genome Biology 2005, 6:337 (29 July 2005)
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Editor’s summary
A report on HGM2005, the tenth annual Human Genome Meeting, Kyoto, Japan, 18-21 April 2005. |
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Systems biology: where it's at in 2005
Ben Lehner, Julia Tischler, Andrew G Fraser Genome Biology 2005, 6:338 (1 August 2005)
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Editor’s summary
A report on the joint Keystone Symposia on Systems and Biology and Proteomics and Bioinformatics, Keystone, USA, 8-13 April 2005. |
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Molecular insight into the genesis of ranked caste populations of western India based upon polymorphisms across non-recombinant and recombinant regions in genome
Sonali Gaikwad, V K Kashyap Genome Biology 2005, 6:P10 (19 July 2005)
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Editor’s summary
To trace admixture and genesis of caste populations of western India, polymorphisms were examined across non-recombining 20 Y-SNPs, 20 Y-STRs, 18 mtDNA diagnostic sites, HVS-1 plus HVS-2 regions; and recombining 15 highly polymorphic autosomal STRs in four predominant caste populations- upper-ranking Desasth-brahmin and Chitpavan-brahmin; a middle-ranking Kshtriya Maratha; and a lower-rank peasant Dhangar.
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Research |
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Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
Alexander S Brodsky, Clifford A Meyer, Ian A Swinburne, Giles Hall, Benjamin J Keenan, Xiaole S Liu, Edward A Fox, Pamela A Silver Genome Biology 2005, 6:R64 (15 July 2005)
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Editor’s summary
Determination of the distribution of RNA Polymerase II within regions of the human genome identifies novel sites of transcription and suggests that a major factor of transcription elongation control in mammals is the coordination of transcription and pre-mRNA processing to define exons. |
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The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles
Rickard Sandberg, Ingemar Ernberg Genome Biology 2005, 6:R65 (27 July 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
A meta analysis comparing 60 tumor cell lines, 135 normal tissue samples and 176 tumor tissue samples in humans shows significant differential expression between cell lines and tissues of around 30% of the 7,000 genes analyzed. |
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Evolution of selenium utilization traits
Héctor Romero, Yan Zhang, Vadim N Gladyshev, Gustavo Salinas Genome Biology 2005, 6:R66 (27 July 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
Completely sequenced genomes were analyzed for occurrence of SelA, B, C, D and ybbB genes. SelB and SelC were found to be signatures for the Sec decoding trait, while SelD defines the overall selenium utilization. |
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Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
Penelope R Haddrill, Brian Charlesworth, Daniel L Halligan, Peter Andolfatto Genome Biology 2005, 6:R67 (27 July 2005)
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Editor’s summary
An analysis of inter-specific divergence in 225 intron fragments in Drosophila melanogaster and D. simulans reveals a strongly negative correlation between intron length and divergence and intron divergence and GC content. This suggests that most intronic DNA is evolving under considerable constraint. |
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The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles
Andrew Wilkins, Karol Szafranski, Derek J Fraser, Deenadayalan Bakthavatsalam, Rolf Müller, Paul R Fisher, Gernot Glöckner, Ludwig Eichinger, Angelika A Noegel, Robert H Insall Genome Biology 2005, 6:R68 (28 July 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
A survey of the Dictyostelium genome reveals at least 25 RasGEFs, all of which appear to be expressed at some point in development. Disruption of several of these novel RasGEFs reveals that many have clear phenotypes, suggesting that the unexpectedly large number of RasGEF genes reflects an evolutionary expansion of the range of Ras signaling. |
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Tandem repeat copy-number variation in protein-coding regions of human genes
Colm T O'Dushlaine, Richard J Edwards, Stephen D Park, Denis C Shields Genome Biology 2005, 6:R69 (28 July 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
Tandem repeat polymorphisms in human proteins were characterized using the UniGene dataset. This analysis suggests that 1 in 20 proteins are likely to contain tandem repeat copy-number polymorphisms within coding regions; these were prevalent among protein-binding proteins. |
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Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria
Keith A Corbino, Jeffrey E Barrick, Jinsoo Lim, Rüdiger Welz, Brian J Tucker, Izabela Puskarz, Maumita Mandal, Noam D Rudnick, Ronald R Breaker Genome Biology 2005, 6:R70 (1 August 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
Comparative sequence analysis and structural probing identified five RNA elements in the intergenic region of Agrobacterium tumefaciens and other α-proteobacteria. One of these RNA elements is probably a SAM-II, the only riboswitch class identified so far that is not found in Gram-positive bacteria. |
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MicroRNA profiling of the murine hematopoietic system
Silvia Monticelli, K Mark Ansel, Changchun Xiao, Nicholas D Socci, Anna M Krichevsky, To-Ha Thai, Nikolaus Rajewsky, Debora S Marks, Chris Sander, Klaus Rajewsky, Anjana Rao, Kenneth S Kosik Genome Biology 2005, 6:R71 (1 August 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
The first report of systematic miRNA profiling in cells of the hematopoietic system suggests that, in addition to regulating commitment to particular cellular lineages, miRNAs might have a general role in cell differentiation and cell identity. |
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Genome-wide promoter extraction and analysis in human, mouse, and rat
Zhenyu Xuan, Fang Zhao, Jinhua Wang, Gengxin Chen, Michael Q Zhang Genome Biology 2005, 6:R72 (1 August 2005)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Editor’s summary
An investigation of how to improve mammalian promoter prediction by incorporating both transcript and conservation information leads to the creation of CSHLmpd, a mammalian promoter database. |
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Correspondence |
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Correction: Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Waraporn Tongprasit, Songgang Li, Jun Wang, Xiping Wang, Xing Deng Genome Biology 2005, 6:403 (21 July 2005)
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