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Distribution by Scientific Domains
Life Sciences42%
Chemistry28%

Selected Abstracts

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes

FEMS MICROBIOLOGY LETTERS, Issue 2 2002
Leda Cummings
Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. [source]

Advances in molecular ecology: tracking trophic links through predator,prey food-webs

FUNCTIONAL ECOLOGY, Issue 5 2005
S. K. SHEPPARD
Summary 1It is not always possible to track trophic interactions between predators and prey by direct observation. This is especially true when observing small or elusive animals with cryptic food-web ecology. Gut and/or faecal analysis can sometimes allow prey remains to be identified visually but is only possible when a component of the diet is resistant to digestion. In some cases there are no solid remains, and when there are it can lead to bias in interpretation of prey choice. 2Numerous invasive and non-invasive methods have been developed to characterize predator,prey interactions but two principal areas dominate ,molecular' research. These are reviewed under the headings of monoclonal antibodies and DNA-based techniques. 3Early ,molecular' studies of predator,prey food webs were dominated by the development of monoclonal antibodies. These methods continue to be used for mass-screening of field-collected arthropods for insect-specific proteins. 4The application of species-specific primer design, polymerase chain reaction (PCR), restriction fragment length polymorphism analysis (RFLP), DNA cloning and sequencing, comparative sequence analysis (e.g. BLAST; basic local alignment search tool), high-resolution gel electrophoresis, Temperature/denaturing gradient gel electrophoresis (TGGE/DGGE) and automated fragment analysis with fluorescent probes is reviewed. The development of molecular techniques for use in predator,prey studies is primarily limited by their cost and the development of new procedures and equipment that complement them. [source]

Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2006
Jens Allmer
Abstract A new high-throughput computational strategy was established that improves genomic data mining from MS experiments. The MS/MS data were analyzed by the SEQUEST search algorithm and a combination of de novo amino acid sequencing in conjunction with an error-tolerant database search tool, operating on a 256 processor computer cluster. The error-tolerant search tool, previously established as GenomicPeptideFinder (GPF), enables detection of intron-split and/or alternatively spliced peptides from MS/MS data when deduced from genomic DNA. Isolated thylakoid membranes from the eukaryotic green alga Chlamydomonas reinhardtii were separated by 1-D SDS gel electrophoresis, protein bands were excised from the gel, digested in-gel with trypsin and analyzed by coupling nano-flow LC with MS/MS. The concerted action of SEQUEST and GPF allowed identification of 2622 distinct peptides. In total 448 peptides were identified by GPF analysis alone, including 98 intron-split peptides, resulting in the identification of novel proteins, improved annotation of gene models, and evidence of alternative splicing. [source]

Searching PubMed for molecular epidemiology studies: The case of chromosome aberrations

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 4 2006
Donatella Ugolini
Abstract The available tools for searching literature in the field of Molecular Epidemiology are largely unsatisfactory. To identify major problems in retrieving information on this discipline, we comment here on the results of a literature search on cytogenetic biomarkers in children exposed to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1, 1980 to November 30, 2004. Only 2 of the 178 articles were indexed by the MeSH term "Epidemiology, molecular" (introduced in 1994) and 30 of 178 by the MeSH term "Biological markers" (introduced in 1989). The case of chromosome aberration (CA) was emblematic of the problem: 44 of 78 articles (56.4%) were not pertinent to the search. The reasons for this poor performance are reported and discussed. Authors and indexers may be able to improve the efficiency of article retrieval in the field of molecular epidemiology by using relevant terms in the title and abstract. This may suggest appropriate MeSH terms to the indexers for the indexing process. As regards the difficulty in identifiyng population studies using CA, the introduction of a specific MeSH term for chromosome aberrations when used as a biomarker would improve the search process. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source]

Euroethics,a database network on biomedical ethics

HEALTH INFORMATION & LIBRARIES JOURNAL, Issue 3 2006
Ylva Gavel
Background:,euroethics is a database covering European literature on ethics in medicine. It is produced within Eurethnet, a European information network on ethics in medicine and biotechnology. Objectives:, The aim of Euroethics is to disseminate information on European bioethical literature that may otherwise be difficult to find. Methods:, A collaboration model for pooling data from different centres was developed. The policy was to accomplish data uniformity, while still allowing for local differences in terms of software, indexing practices and resources. Records contributed to the database follow common standards in terms of data fields and indexing terms. The indexing terms derive from two thesauri, Thesaurus Ethics in the Life Sciences (TELS) and Medical Subject Headings (MeSH). Combining elements from search tools developed previously, the developers sought to find a technical solution optimized for this data model. An approach relying on a thesaurus database that is loaded along with the bibliographic database is described. Results and conclusions:, The present case study offers examples of possible approaches to several tasks often encountered in database development, such as: merging data from diverse sources, getting the most out of indexing terms used in a database, and handling more than one thesaurus in the same system. [source]

Scatter matters: Regularities and implications for the scatter of healthcare information on the Web

JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY, Issue 4 2010
Suresh K. Bhavnani
Abstract Despite the development of huge healthcare Web sites and powerful search engines, many searchers end their searches prematurely with incomplete information. Recent studies suggest that users often retrieve incomplete information because of the complex scatter of relevant facts about a topic across Web pages. However, little is understood about regularities underlying such information scatter. To probe regularities within the scatter of facts across Web pages, this article presents the results of two analyses: (a) a cluster analysis of Web pages that reveals the existence of three page clusters that vary in information density and (b) a content analysis that suggests the role each of the above-mentioned page clusters play in providing comprehensive information. These results provide implications for the design of Web sites, search tools, and training to help users find comprehensive information about a topic and for a hypothesis describing the underlying mechanisms causing the scatter. We conclude by briefly discussing how the analysis of information scatter, at the granularity of facts, complements existing theories of information-seeking behavior. [source]

Identifying residues in natural organic matter through spectral prediction and pattern matching of 2D NMR datasets

MAGNETIC RESONANCE IN CHEMISTRY, Issue 1 2004
Andre J. Simpson
Abstract This paper describes procedures for the generation of 2D NMR databases containing spectra predicted from chemical structures. These databases allow flexible searching via chemical structure, substructure or similarity of structure as well as spectral features. In this paper we use the biopolymer lignin as an example. Lignin is an important and relatively recalcitrant structural biopolymer present in the majority of plant biomass. We demonstrate how an accurate 2D NMR database of ,600 2D spectra of lignin fragments can be easily constructed, in ,2 days, and then subsequently show how some of these fragments can be identified in soil extracts through the use of various search tools and pattern recognition techniques. We demonstrate that once identified in one sample, similar residues are easily determined in other soil extracts. In theory, such an approach can be used for the analysis of any organic mixtures. Copyright © 2003 John Wiley & Sons, Ltd. [source]