ABSTRACT
BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.
Subject(s)
Biomedical Research , Database Management Systems , Databases, Factual , Internet , Animals , Bacteria , Fungi , Genome , Humans , International Cooperation , User-Computer Interface , VirusesABSTRACT
Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
Subject(s)
Genome, Bacterial , Genomics , Lactic Acid/metabolism , Lactobacillus/genetics , Streptococcaceae/genetics , Animals , Bacterial Proteins/classification , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biological Evolution , Food Microbiology , Gene Transfer, Horizontal , Lactobacillus/classification , Phylogeny , Streptococcaceae/classificationABSTRACT
We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
Subject(s)
Gene Duplication , Genome, Plant , Populus/genetics , Sequence Analysis, DNA , Arabidopsis/genetics , Chromosome Mapping , Computational Biology , Evolution, Molecular , Expressed Sequence Tags , Gene Expression , Genes, Plant , Oligonucleotide Array Sequence Analysis , Phylogeny , Plant Proteins/chemistry , Plant Proteins/genetics , Polymorphism, Single Nucleotide , Populus/growth & development , Populus/metabolism , Protein Structure, Tertiary , RNA, Plant/analysis , RNA, Untranslated/analysisABSTRACT
A method of accurately manipulating the pressure of helium gas in the range P=10(-1) to 10(-20) Torr, T<5 K is presented. The method requires only a very modest apparatus and makes use of thermodynamic measurements on the 4He-Grafoil system. A calibration curve and a pressure scale for the manometer are developed which will allow convenient application in other laboratories. An experiment which utilizes the technique is briefly disscussed.
ABSTRACT
A case of a traumatic bone cyst is reported because of the unusual nature of the chief complaint. The initial symptom of the disease was mandibular nerve neuropathy with numbness of the left side of the lower lip and chin.
