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At least 811 records · Page 45Linked to original sources
PubMed2003

ToxoDB: accessing the Toxoplasma gondii genome.

ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST project (http://genome.wustl.edu/est/index.php?toxoplasma=1), a BAC clone end-sequencing project (http://www.sanger.ac.uk/Projects/T_gondii/) and an 8X random shotgun genomic sequencing project (http://www.tigr.org/tdb/e2k1/tga1/). ToxoDB was designed to provide a central point of access for all available T. gondii data, and a variety of data mining tools useful for the analysis of unfinished, un-annotated draft sequence during the early phases of the genome project. In later stages, as more and different types of data become available (microarray, proteomic, SNP, QTL, etc.) the database will provide an integrated data analysis platform facilitating user-defined queries across the different data types.

Animals↗
PubMed2000

Weaving women's health across clinical clerkships.

Clerkship directors have an opportunity to develop consensus on learning objectives for women's health issues and to develop curricula that cross disciplinary boundaries. A collaborative interdisciplinary approach assures proper sequencing of knowledge and skill acquisition, conserves educational resources, and reflects the values of connectedness and patient-centeredness that are central to women's health. The informal networks and the institutional structures that bring clerkship directors together for discussion of a variety of educational issues promote such collaboration. The authors describe three approaches to designing and implementing women's health curricula and discuss how each might be applied to the topic of domestic violence: adding free-standing courses to existing curricula, often as electives; delegating pieces of the women's health curriculum to existing courses; and creating new interdisciplinary curricula that then are integrated into the general curriculum. Each has advantages and disadvantages. Ideally, models for curriculum design will reflect the collaborative patient-centered models upon which the field of women's health is based. Such models enhance program effectiveness by taking advantage of discipline-based expertise while allowing for the sharing of both educational responsibilities and educational resources.

Clinical Clerkship↗
PubMed2002

The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.

Collections of full-length nonredundant cDNA clones are critical reagents for functional genomics. The first step toward these resources is the generation and single-pass sequencing of cDNA libraries that contain a high proportion of full-length clones. The first release of the Drosophila Gene Collection Release 1 (DGCr1) was produced from six libraries representing various tissues, developmental stages, and the cultured S2 cell line. Nearly 80,000 random 5' expressed sequence tags (5' expressed sequence tags [ESTs]from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to ~40% of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 5' ESTs from two previously existing and three new libraries. One new library is derived from adult testis, a tissue we previously did not exploit for gene discovery; two new cap-trapped normalized libraries are derived from 0-22-h embryos and adult heads. Taking advantage of the annotated D. melanogaster genome sequence, we clustered the ESTs by aligning them to the genome. Clusters that overlap genes not already represented by cDNA clones in the DGCr1 were analyzed further, and putative full-length clones were selected for inclusion in the new DGC. This second release of the DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70% of the predicted genes in Drosophila.

Animals↗
PubMed2005

Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis.

Substantial experimental datasets defining the subcellular location of Arabidopsis (Arabidopsis thaliana) proteins have been reported in the literature in the form of organelle proteomes built from mass spectrometry data (approximately 2,500 proteins). Subcellular location for specific proteins has also been published based on imaging of chimeric fluorescent fusion proteins in intact cells (approximately 900 proteins). Further, the more diverse history of biochemical determination of subcellular location is stored in the entries of the Swiss-Prot database for the products of many Arabidopsis genes (approximately 1,800 proteins). Combined with the range of bioinformatic targeting prediction tools and comparative genomic analysis, these experimental datasets provide a powerful basis for defining the final location of proteins within the wide variety of subcellular structures present inside Arabidopsis cells. We have analyzed these published experimental and prediction data to answer a range of substantial questions facing researchers about the veracity of these approaches to determining protein location and their interrelatedness. We have merged these data to form the subcellular location database for Arabidopsis proteins (SUBA), providing an integrated understanding of protein location, encompassing the plastid, mitochondrion, peroxisome, nucleus, plasma membrane, endoplasmic reticulum, vacuole, Golgi, cytoskeleton structures, and cytosol (www.suba.bcs.uwa.edu.au). This includes data on more than 4,400 nonredundant Arabidopsis protein sequences. We also provide researchers with an online resource that may be used to query protein sets or protein families and determine whether predicted or experimental location data exist; to analyze the nature of contamination between published proteome sets; and/or for building theoretical subcellular proteomes in Arabidopsis using the latest experimental data.

Arabidopsis↗
PubMed2004

Fine mapping of the muscular dystrophy (AM) gene on chicken chromosome 2q.

Our previous studies revealed that the genetic locus for chicken muscular dystrophy of abnormal muscle (AM) mapped to chromosome 2q, and that the region showed conserved synteny with human chromosome 8q11-24.3. In the current study, we mapped the chicken orthologues of genes from human chromosome 8q11-24 in order to identify the responsible gene. Polymorphisms in the chicken orthologues were identified in the parents of the resource family. Twenty-three genes and expressed sequence tags (ESTs) were mapped to chicken chromosome 2 by linkage analysis. The detailed comparative map shows a high conservation of synteny between chicken chromosome 2q and human chromosome 8q. The AM locus was mapped between [inositol(myo)-1(or4)-monophosphatase 1] (IMPA1) gene and [core-binding factor, runt domain, alpha-subunit 2; translocated to 1; cyclin D-related] (CBFA2T1) gene. The genes located between IMPA1 and CBFA2T1 are the most likely candidates for chicken muscular dystrophy.

Animals↗
PubMed2004

Crossing the Red Sea: phylogeography of the hamadryas baboon, Papio hamadryas hamadryas.

The hamadryas baboon (Papio hamadryas hamadryas) is found both in East Africa and western Arabia and is the only free-ranging nonhuman primate in Arabia. It has been hypothesized that hamadryas baboons colonized Arabia in the recent past and were possibly even transported there by humans. We investigated the phylogeography of hamadryas baboons by sequencing a portion of the control region of mtDNA in 107 baboons from four Saudi Arabian populations and combing these data with published data from Eritrean (African) P. h. hamadryas. Analysis grouped sequences into three distinct clades, with clade 1 found only in Arabia, clade 3 found only in Africa, but clade 2 found in both Arabian and African P. h. hamadryas and also in the olive baboon, P. h. anubis. Patterns of variation within Arabia are neither compatible with the recent colonization of Arabia, implying that baboons were not transported there by humans, nor with a northerly route of colonization of Arabia. We propose that hamadryas baboons reached Arabia via land bridges that have formed periodically during glacial maxima at the straits of Bab el Mandab in the southern Red Sea. We suggest that the genetic differentiation of Arabian from African populations suggests that Arabian populations have a higher conservation status than recognized previously.

Animals↗
PubMed2006

The Candida Genome Database: facilitating research on Candida albicans molecular biology.

The Candida Genome Database (CGD; http://www.candidagenome.org) is a resource for information about the Candida albicans genomic sequence and the molecular biology of its encoded gene products. CGD collects and organizes data from the biological literature concerning C. albicans, and provides tools for viewing, searching, analysing, and downloading these data. CGD also serves as an organizing centre for the C. albicans research community, providing a gene-name registry, contact information, and research community news. This article describes the information contained in CGD and how to access it, either from the perspective of a bench scientist interested in the function of one or a few genes, or from the perspective of a biologist or bioinformatician interpreting large-scale functional genomic datasets.

Alleles↗
PubMed1993

The Australian Incident Monitoring Study. Which monitor? An analysis of 2000 incident reports.

The role of monitors in patients undergoing general anaesthesia was studied by analysing the first 2000 incidents reported to the Australian Incident Monitoring Study; 1256 (63%) were considered applicable to this study. In 52% of these a monitor detected the incident first; oximetry (27%) and capnography (24%) detected over half of the monitor detected incidents, the electrocardiograph 19%, blood pressure monitors 12%, a low pressure (circuit) alarm 8%, and the oxygen analyser 4%. Of the other monitors used, 5 first detected 1-2% of incidents, and the remaining 8 less than 0.5% each. The oximeter would have detected over 40% of the monitor detected incidents had its more informative modulated pulse tone always been relied upon instead of the "bleep" of the ECG. A theoretical analysis was then carried out to determine which of an array of 17 monitors would reliably have detected each incident had each monitor been used on its own and had the incident been allowed to evolve. To facilitate "scoring" of monitors, the incidents were categorized empirically into 60 clinical situations; 40% of applicable incidents were accounted for by only 5 clinical situations, 60% by 10 and nearly 80% by 20. 98% were accounted for by the 60 situations. A pulse oximeter, used on its own, would theoretically have detected 82% of applicable incidents (nearly 60% before any potential for organ damage). These figures for capnography are 55% and 43% and for oximetry and capnography combined are 88% and 65%, respectively. With the addition of blood pressure monitoring these become 93% and 65%, and of an oxygen analyser, 95 and 67%. Other monitors, including the ECG, each increase the yield by by less than 0.5%. The international monitoring recommendations and those of the Australian and New Zealand College of Anaesthetists are thoroughly vindicated by the patterns revealed in this study. The priority sequence of monitor acquisition for those with limited resources should be stethoscope, sphygmomanometer, oxygen analyser if nitrous oxide is to be used, pulse oximeter, capnograph, high pressure alarm, and, if patients are to be mechanically ventilated, a low pressure alarm (or spirometer with alarm); an ECG, a defibrillator, a spirometer and a thermometer should be available.

Accidents↗
PubMed2006

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

BACKGROUND: Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and intronic sequences have been shown to affect splicing efficiency by means of silencing and enhancement mechanisms. Thus, nucleotide substitutions in these sequences can induce aberrant splicing. Web-based resources have recently been developed to facilitate the identification of nucleotide changes that could alter splicing. However, computer predictions do not always correlate with in vivo splicing defects. The issue of unclassified variants in cancer predisposing genes is very important both for the correct ascertainment of cancer risk and for the understanding of the basic mechanisms of cancer gene function and regulation. Therefore we aimed to verify how predictions that can be drawn from in silico analysis correlate with results obtained in an in vivo splicing assay. RESULTS: We analysed 99 hMLH1 and hMSH2 missense mutations with six different algorithms. Transfection of three different cell lines with 20 missense mutations, showed that a minority of them lead to defective splicing. Moreover, we observed that some exons and some mutations show cell-specific differences in the frequency of exon inclusion. CONCLUSION: Our results suggest that the available algorithms, while potentially helpful in identifying splicing modulators especially when they are located in weakly defined exons, do not always correspond to an obvious modification of the splicing pattern. Thus caution must be used in assessing the pathogenicity of a missense or silent mutation with prediction programs. The variations observed in the splicing proficiency in three different cell lines suggest that nucleotide changes may dictate alternative splice site selection in a tissue-specific manner contributing to the widely observed phenotypic variability in inherited cancers.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Monkeys and toads define areas of endemism on Sulawesi.

Ecological or geological phenomena can impose limits on geographic diversification that cause biogeographical patterns of distantly related but sympatrically occurring taxa to be similar. Concordant patterns of diversity facilitate conservation management because strategic designation of protected areas can capture complementary rather than redundant components of variation. Here we demonstrate that on the biodiverse Indonesian island of Sulawesi, seemingly idiosyncratic distributions of diversity in endemic monkeys (Macaca species) and toads (Bufo celebensis) are actually virtually identical on a fine geographic scale. It appears that range fragmentation has generated seven multi-taxon areas of genetic endemism, each of which should be targeted for conservation. Joint consideration of molecular phylogeography, morphology, and demography helps resolve apparent contradictions in paraphyletic macaque mitochondrial DNA and in undifferentiated toad morphology, and facilitates an understanding of biogeography and conservation genetics of Sulawesi fauna.

Animals↗
PubMedDate not supplied

[Financial incentives for employees as part of a policy to upgrade care in a public hospital in Volta Redonda, Rio de Janeiro State, Brazil].

The authors present and analyze six years of regular and steady application of an institutional evaluation policy based on financial incentives in a public hospital in Volta Redonda, Rio de Janeiro State, Brazil, as a part of the hospital's administrative modernization policy. This type of policy is considered implicitly capable of developing a sequence of strategic wagers: (1) release of financial resources for payment of bonuses; (2) creation of an operationally feasible and sensitive evaluation instrument; (3) creation of adequate management mechanisms to improve evaluation policy; (4) employee adherence to the hospital upgrading policy based on the bonus system; and (5) maintenance of the effects of evaluation policy over time. The article discusses the "degree of success" of each of these wagers in an attempt to portray possible gains throughout the process, while also identifying inherent difficulties in such a policy.

Brazil↗
PubMed1995

Relationships and social support: views of parents with mental retardation/intellectual disability.

From the professional perspective, parenting by people with mental retardation, or intellectual disability, is regarded with concern. Little attention has been paid to what constitutes social support for these parents. A qualitative design was used to explore views of parents with intellectual disability about their relationships and social support for their parenting. Most emphasis was placed on the support received from and given to their spouses or partners. Support was not always viewed as beneficial; rather, it was sometimes viewed as a restraint as well as a resource for parenting. Parents also exhibited a preferred sequence in seeking help, beginning with their partners, then family members, and, finally, professionals. Implications in light of policy and service provision were discussed.

Adolescent↗
PubMed2001

The Adaptive Evolution Database (TAED).

BACKGROUND: Developing an understanding of the molecular basis for the divergence of species lies at the heart of biology. The Adaptive Evolution Database (TAED) serves as a starting point to link events that occur at the same time in the evolutionary history (tree of life) of species, based upon coding sequence evolution analyzed with the Master Catalog. The Master Catalog is a collection of evolutionary models, including multiple sequence alignments, phylogenetic trees, and reconstructed ancestral sequences, for all independently evolving protein sequence modules encoded by genes in GenBank [1]. RESULTS: We have estimated from these models the ratio of nonsynonymous to synonymous nucleotide substitution (Ka/Ks), for each branch in their respective evolutionary trees of every subtree containing only chordata or only embryophyta proteins. Branches with high Ka/Ks values represent candidate episodes in the history of the family where the protein may have undergone positive selection, a phenomenon in molecular evolution where the mutant form of a gene must have conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. We have found that an unexpectedly large number of families (between 10 and 20% of those families examined) have at least one branch with a notably high Ka/Ks value (putative adaptive evolution). As a resource for biologists wishing to understand the interaction between protein sequences and the Darwinian processes that shape these sequences, we have collected these into The Adaptive Evolution Database (TAED). CONCLUSIONS: Placed in a phylogenetic perspective, candidate genes that are undergoing evolution at the same time in the same lineage can be viewed together. This framework based upon coding sequence evolution can be readily expanded to include other types of evolution. In its present form, TAED provides a resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.

Animals↗
PubMed2005

Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses.

To gain insight into the transcriptome of the well-used plant model system Physcomitrella patens, several EST sequencing projects have been undertaken. We have clustered, assembled, and annotated all publicly available EST and CDS sequences in order to represent the transcriptome of this non-seed plant. Here, we present our fully annotated knowledge resource for the Physcomitrella patens transcriptome, integrating annotation from the production process of the clustered sequences and from a high-quality annotation pipeline developed during this study. Each transcript is represented as an entity containing full annotations and GO term associations. The whole production, filtering, clustering, and annotation process is being modelled and results in seven datasets, representing the annotated Physcomitrella transcriptome from different perspectives. We were able to annotate 63.4 % of the 26 123 virtual transcripts. The transcript archetype, as covered by our clustered data, is compared to a compilation based on all available Physcomitrella full length CDS. The distribution of the gene ontology annotations (GOA) for the virtual transcriptome of Physcomitrella patens demonstrates consistency in the ratios of the core molecular functions among the plant GOA. However, the metabolism subcategory is over-represented in bryophytes as compared to seed plants. This observation can be taken as an indicator for the wealth of alternative metabolic pathways in moss in comparison to spermatophytes. All resources presented in this study have been made available to the scientific community through a suite of user-friendly web interfaces via www.cosmoss.org and form the basis for assembly and annotation of the moss genome, which will be sequenced in 2005.

3' Untranslated Regions↗
PubMed2002

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and a high level of integration with other databases. Together with its automatically annotated supplement TrEMBL, it provides a comprehensive and high-quality view of the current state of knowledge about proteins. Ongoing developments include the further improvement of functional and automatic annotation in the databases including evidence attribution with particular emphasis on the human, archaeal and bacterial proteomes and the provision of additional resources such as the International Protein Index (IPI) and XML format of SWISS-PROT and TrEMBL to the user community.

Amino Acid Sequence↗
PubMed2006

Diversity of phytases in the rumen.

Examples of a new class of phytase related to protein tyrosine phosphatases (PTP) were recently isolated from several anaerobic bacteria from the rumen of cattle. In this study, the diversity of PTP-like phytase gene sequences in the rumen was surveyed by using the polymerase chain reaction (PCR). Two sets of degenerate primers were used to amplify sequences from rumen fluid total community DNA and genomic DNA from nine bacterial isolates. Four novel PTP-like phytase sequences were retrieved from rumen fluid, whereas all nine of the anaerobic bacterial isolates investigated in this work contained PTP-like phytase sequences. One isolate, Selenomonas lacticifex, contained two distinct PTP-like phytase sequences, suggesting that multiple phytate hydrolyzing enzymes are present in this bacterium. The degenerate primer and PCR conditions described here, as well as novel sequences obtained in this study, will provide a valuable resource for future studies on this new class of phytase. The observed diversity of microbial phytases in the rumen may account for the ability of ruminants to derive a significant proportion of their phosphorus requirements from phytate.

6-Phytase↗
PubMed2001

Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers.

The results of the development of oil palm (Elaeis guineensis Jacq.) microsatellite markers are given step by step, from the screening of libraries enriched in (GA)n, (GT)n, and (CCG)n simple-sequence repeats (SSRs) to the final characterisation of 21 SSR loci. Also published are primer sequences, estimates of allele size range, and expected heterozygosity in E. guineensis and in the closely related species E. oleifera, in which an optimal utility of the SSR markers was observed. Multivariate data analyses showed the ability of SSR markers to efficiently reveal the genetic-diversity structure of the genus Elaeis in accordance with known geographical origins and with measured genetic relationships based on previous molecular studies. High levels of allelic variability indicated that E. guineensis SSRs will be a powerful tool for genetic studies of the genus Elaeis, including variety identification and intra- or inter-specific genetic mapping. PCR amplification tests on a subset of 16 other palm species and allele-sequence data showed that E. guineensis SSRs are putative transferable markers across palm taxa. In addition, phenetic information based on SSR flanking region sequences makes E. guineensis SSR markers a potentially useful molecular resource for any researcher studying the phylogeny of palm taxa.

Africa↗