http://genomebiology.com/ The latest research articles published by Genome Biology 2009-07-02T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Recent work in Arabis alpina, a perennial relative of Arabidopsis, has uncovered subtle differences in control of a gene that represses flowering which contributes to the polycarpic habit. http://genomebiology.com/2009/10/7/228 Genome Biology 2009, 10:228 2009-07-02T00:00:00Z doi:10.1186/gb-2009-10-7-228 Genome Biology 1465-6906 10 228 2009-07-02T00:00:00Z XML Background: Hundreds of proteins modulate neurotransmitter release and synaptic plasticity during neuronal development and in response to synaptic activity. The expression of genes in the pre- and post-synaptic neurons is under stringent spatio-temporal control, but the mechanism underlying the neuronal expression of these genes remains largely unknown. Results: Using unbiased in vivo and in vitro screens, we characterized the cis elements regulating Rab3A gene, which is expressed abundantly in presynaptic neurons. A set of identified regulatory elements of the Rab3A gene corresponded to the defined Rab3A multi-species conserved elements. In order to identify clusters of enriched transcription factor binding sites, for example, cis-regulatory modules, we analyzed intergenic multi-species conserved elements in the vicinity of nine presynaptic genes, including Rab3A, which are highly and specifically expressed in brain regions. Sixteen transcription factor binding motifs were over-represented in these multi-species conserved elements. Based on a combined occurrence for these enriched motifs, multi-species conserved elements in the vicinity of 107 previously identified presynaptic genes were scored and ranked. We then experimentally validated the scoring strategy by showing that 12 of 16 (75%) high-scoring multi-species conserved elements functioned as neuronal enhancers in a cell-based assay. Conclusion: This work introduces an integrative strategy of comparative genomics, experimental, and computational approaches to reveal aspects of a regulatory network controlling neuronal-specific expression of genes in presynaptic neurons. http://genomebiology.com/2009/10/7/R72 Rui Liu Sridhar Hannenhalli Maja Bucan Genome Biology 2009, 10:R72 2009-07-01T00:00:00Z doi:10.1186/gb-2009-10-7-r72 Genome Biology 1465-6906 10 R72 2009-07-01T00:00:00Z PDF Comparison of a regulatory network that specifies dopaminergic neurons in Caenorhabditis elegans to the development of vertebrate dopamine systems in the mouse reveals a possible partial conservation of such a network. http://genomebiology.com/2009/10/7/229 Genome Biology 2009, 10:229 2009-07-01T00:00:00Z doi:10.1186/gb-2009-10-7-229 Genome Biology 1465-6906 10 229 2009-07-01T00:00:00Z XML The construction of a genetic map of the human infective blood fluke (Schistosoma mansoni), coupled with the availability of the genome sequence, offers new approaches for research on this important parasitic worm. http://genomebiology.com/2009/10/6/225 Genome Biology 2009, 10:225 2009-06-30T00:00:00Z doi:10.1186/gb-2009-10-6-225 Genome Biology 1465-6906 10 225 2009-06-30T00:00:00Z XML Background: Schistosoma mansoni is a blood fluke that infects ~90 million people. The complete life cycle can be maintained in the laboratory making this one of the few experimentally tractable human helminth infections and a rich literature reveals heritable variation in important biomedical traits such as virulence, host-specificity, transmission and drug resistance. However, there is a current lack of tools needed to study molecular, quantitative, and population genetics. Our goal was to construct genetic linkage map for S. mansoni, and thus provide a new resource that will help stimulate research on this neglected pathogen. Results: We genotyped grandparents, parents and 88 progeny to construct a 5.6cM linkage map containing 243 microsatellites positioned on 203 of the largest scaffolds in the genome sequence. The map allows 70% of the estimated 300Mb genome to be ordered on chromosomes, and highlights where scaffolds have been incorrectly assembled. The markers fall into 8 main linkage groups, consistent with 7 pairs of autosomes and one pair of sex chromosomes, and we were able to anchor linkage groups to chromosomes using fluorescent in situ hybridization (FISH). The genome measures 1228.6cM. Marker segregation reveals higher female recombination, confirms ZW inheritance patterns, and identifies recombination hotspots and regions of segregation distortion. Conclusion: The genetic linkage map presented here is the first for S. mansoni and first for a species in the phylum Platyhelminthes. The map provides the critical tool necessary for quantitative genetic analysis, aids genome assembly, and furnishes a framework for comparative flatworm genomics and field-based molecular epidemiological studies. http://genomebiology.com/2009/10/6/R71 Charles Criscione Claudia Valentim Hirohisa Hirai Philip LoVerde Timothy Anderson Genome Biology 2009, 10:R71 2009-06-30T00:00:00Z doi:10.1186/gb-2009-10-6-r71 Genome Biology 1465-6906 10 R71 2009-06-30T00:00:00Z PDF Molecular networks are being used to reconcile genotypes and phenotypes by integrating medical information. In this context, networks will be instrumental for the interpretation of disease at the personalized medicine level. http://genomebiology.com/2009/10/6/221 Genome Biology 2009, 10:221 2009-06-29T00:00:00Z doi:10.1186/gb-2009-10-6-221 Genome Biology 1465-6906 10 221 2009-06-29T00:00:00Z XML Lessons in personal genome analysis, social networking or health information? http://genomebiology.com/2009/10/6/108 Genome Biology 2009, 10:108 2009-06-29T00:00:00Z doi:10.1186/gb-2009-10-6-108 Genome Biology 1465-6906 10 108 2009-06-29T00:00:00Z XML Background: Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis. Results: T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species which could not be attributed to the presence of specific mobile elements. Two virus-related regions tgv1 and tgv2 are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun LC-MS/MS approach allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantitation of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis. Conclusions: This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes. http://genomebiology.com/2009/10/6/R70 Yvan Zivanovic Jean Armengaud Arnaud Lagorce Christophe Leplat Philippe Guerin Murielle Dutertre Veronique Anthouard Patrick Forterre Patrick Wincker Fabrice Confalonieri Genome Biology 2009, 10:R70 2009-06-26T00:00:00Z doi:10.1186/gb-2009-10-6-r70 Genome Biology 1465-6906 10 R70 2009-06-26T00:00:00Z PDF A report of BioSysBio 2009, the IET conference on Synthetic Biology, Systems Biology and Bioinformatics, Cambridge, UK, 23-25 March 2009. http://genomebiology.com/2009/10/6/309 Genome Biology 2009, 10:309 2009-06-26T00:00:00Z doi:10.1186/gb-2009-10-6-309 Genome Biology 1465-6906 10 309 2009-06-26T00:00:00Z XML Background: Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. This new model is based on the annotated B. subtilis 168 genome generated by the SEED, one of the most up-to-date and accurate annotations of B. subtilis 168 available. Results: The iBsu1103 model includes 1,437 reactions associated with 1,103 genes, making it the most complete model of B. subtilis available. The model also includes Gibbs free energy change values for 1,403 (97%) of the model reactions estimated by using the group contribution method. This data was used with an improved reaction reversibility prediction method to identify 653 (45%) irreversible reactions in the model. The model was validated against an experimental dataset consisting of 1,500 distinct conditions and was optimized by using an improved model optimization method to increase model accuracy from 89.7% to 93.1%. Conclusions: Basing the iBsu1103 model on the annotations generated by the SEED significantly improved the model completeness and accuracy compared with the most recent previously published model. The enhanced accuracy of the iBsu1103 model also demonstrates the efficacy of the improved reaction directionality prediction method in accurately identifying irreversible reactions in the B. subtilis metabolism. The proposed improved model optimization methodology was also demonstrated to be effective in minimally adjusting model content to improve model accuracy. http://genomebiology.com/2009/10/6/R69 Christopher Henry Jenifer Zinner Matthew Cohoon Rick Stevens Genome Biology 2009, 10:R69 2009-06-25T00:00:00Z doi:10.1186/gb-2009-10-6-r69 Genome Biology 1465-6906 10 R69 2009-06-25T00:00:00Z PDF