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At least 1,351 records · Page 75Linked to original sources
PubMed2005

Autonomic nervous system activity during actual and mentally simulated preparation for movement.

The aim of this study was to compare actual versus mentally simulated preparation for a complex motor skill. Two behavioral periods are observed during weightlifting: (i) an initial phase in which the subject standing behind the bar is thought to focus his attention on forthcoming execution and (ii) a second phase between hands/bar contact and execution during which the subject is thought to increase activation. Such mental processes accompanying behavioral sequences are correlated with autonomic nervous system activity, phasic responses corresponding to allocation of attentional resources, and tonic variations related to increasing general activation. To study mental processes during preparation for action, 12 subjects performed actual and imagined preparation phases of execution. Six autonomic variables were measured continuously. Skin potential (chi2 = 0.16), skin temperature amplitude (Z = -0.66) and duration (Z = -1.78), skin blood flow amplitude (Z = -0.56) and duration (Z = -1.51), respiratory frequency amplitude (Z = -0.14) and duration (Z = -0.13), and duration of heart rate response (Z = -1.25) were shown to be comparable (p > .05), whatever the modality of preparation. However, during mentally simulated preparation, skin resistance response was shorter than in actual preparation (Z = -2.12, p < .05), thus attesting to a weaker load, whereas lower decrease in heart rate was elicited (Z = -1.96, p < .05). This may be explained by this particular experimental condition because mental preparation would not lead to actual action. Such autonomic variables could be used as feedback to improve performance.

Adolescent↗
PubMed2006

Evaluation of CACNA1H in European patients with childhood absence epilepsy.

CACNA1H was evaluated in a resource of Caucasian European patients with childhood absence epilepsy by linkage analysis and typing of sequence variants previously identified in Chinese patients. Linkage analysis of 44 pedigrees provided no evidence for a locus in the CACNA1H region and none of the Chinese variants were found in 220 unrelated patients.

Asian People↗
PubMed2006

Roles of genetic variations in signalling/immunoregulatory molecules in susceptibility to systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a complex genetic basis that includes many susceptibility genes on multiple chromosomes. As complex human diseases like SLE involve multiple, interacting genetic and environmental determinants, identifying genes for complex traits is challenging and has had limited success so far. However, recent advances in genetic resources and technology have been providing new tools to identify the novel pathways or the sequence variants that contribute to autoimmune diseases. During the past several years, several new candidate genes have been implicated in development of SLE though association studies. In this article we describe an overview of the latest findings in the genetics of SLE, especially focusing on the genetic variations in the signalling or immunoregulatory molecules including CD28 and IRF family members.

Animals↗
PubMed2000

Analysis of the effect of endogenous viral genes in the Smyth line chicken model for autoimmune vitiligo.

The Smyth line (SL) chicken, an animal model for autoimmune human vitiligo, is characterized by a spontaneous posthatch pigment loss, determined to be the result of an autoimmune phenomenon. Because endogenous virus (EV) genes have been reported to be associated with a number of autoimmune diseases of human and animal models, we designed this experiment to investigate the role of EV in the SL vitiligo by using the complete sequence of Rous-associated virus-2 as a probe for EV. An F(2) resource population was developed by the matings of SL and parental control (BL) chickens. Linkage disequilibrium between vitiligo and EV was apparent (16.2-kb SacI fragment, P </= 0.05 and a 19-kb HindIII fragment, P </= 0.03). Methylation analyses revealed that the EV and endogenous avian retroviral (EAV) genes were methylated in both the SL and BL sublines of chickens; therefore, methylation does not appear to be responsible for the differences in the expression of vitiligo between SL and BL sublines. Expression of the EV genes correlated with the disease in vitiliginous SL101 birds and also in 5-Azacytidine-induced vitiliginous BL101 parental control chickens. Only one EV locus was detected in the unrelated Light Brown Leghorn control chickens (1q14) by in situ hybridization, whereas 3 EV loci were identified in SL101 and BL101 chickens (1p25, 2q26, and an unidentifiable microchromosome). Our observations indicate that EV genes may play a role in the induction of autoimmune vitiligo in the SL chicken model.

Animals↗
PubMed2000

In silico studies of energy metabolism of normal and diseased heart.

Biotechnology research is developing into genomic analyses that involve the simultaneous monitoring of thousands of genes. The development of various bioinformatics resources that provide efficient access to information is necessary. We have used single-pass sequencing of randomly selected cDNA clones to generate expressed sequence tags (ESTs). These ESTs data has been widely used to study gene expression in a variety of heart libraries [1, 21]. Data annotation on our recent finding allows us to construct the profiles of genes in the energy metabolizing pathways (glycolysis and glycogen metabolism) that are expressed in heart cDNA libraries. In silico studies of genes of energy metabolism yields data that are consistent with results derived from conventional metabolic experiments. The change in gene profiles describing the metabolism of diseased hearts is also presented here.

Cardiomegaly↗
PubMed1999

Internet resources for the clinical geneticist.

The Internet offers a number of resources to clinical geneticists. This review outlines some of these with special emphasis on sites present at the National Center for Biotechnology Information (NCBI) at the National Library of Medicine at the National Institutes of Health. Special attention is presented on how these various resources make use of PubMed, the premiere source of MEDLINE information on the Internet. Three NCBI resources are presented here. 1) 'Genes and diseases': a general curated series of web pages outlining various references to known genetic diseases with links to relevant on-line resources. 2) The Online Mendelian Inheritance in Man (OMIM) from Victor A. McKusick at Johns Hopkins University presents our current knowledge of all known human genetic diseases. 3) Human genome resources describe our current knowledge on the human genome project (HGP). A list of relevant uniform resource locators (URLs) is also included.

Amino Acid Sequence↗
PubMed1995

A high-density YAC contig map of human chromosome 22.

We have constructed a high-resolution clone map of human chromosome 22 which integrates the available physical and genetic information, establishing a single consensus. The map consists of all classes of DNA landmarks ordered on 705 yeast artificial chromosomes (YACs) at an average landmark density of more than one per 70 kilobases. This map represents the practical limits of currently available YAC resources and provides the basis for determination of the entire gene content and genomic DNA sequence of human chromosome 22.

Chromosome Mapping↗
PubMed2001

Analysis of candidate genes in the CLN6 critical region using in silico cloning.

CLN6, the gene for variant late infantile neuronal ceroid lipofuscinosis, was mapped to a 4 cM region on chromosome 15q22-23. Subsequently the critical region was narrowed to less than 1 cM between microsatellite markers D15S988 and D15S1000 by additional marker typing in an expanded family resource. A physical map was constructed across this region using YAC and PAC clones and sequence was generated from two PAC clones. This sequence was analysed together with overlapping sequence generated by the Human Genome Project to identify genes within the region using an in silico cloning approach. In all, 29 genes have been identified and 18 have been analysed for mutations by direct sequencing. This powerful new approach will lead to the identification of CLN6.

Chromosome Mapping↗
PubMedDate not supplied

Neuroglobin and cytoglobin: genes, proteins and evolution.

Hemoglobin and myoglobin are oxygen transport and storage proteins of most vertebrates. Neuroglobin (Ngb) and cytoglobin (Cygb)--two recent additions to the vertebrate globin superfamily--have still disputed functions. Combining the data from all available resources, we investigate the evolution of these novel globins. Both Ngb and Cygb show little sequence variation in vertebrate evolution, suggesting conserved structures and functions, and an important role in the animal's metabolism. Exon-intron patterns remained unchanged in Ngb and Cygb, with the exception of the addition of a 3' exon to Cygb early in mammalian evolution. In phylogenetic analyses, Ngb forms a common branch with globin X, another recently identified globin with undefined function in lower vertebrates, and with some invertebrate nerve globins. This shows an early divergence of this branch in animal evolution. Cygb is related to myoglobin, and associated with an eye-specific globin from birds. The pattern of globin evolution shows that proteins with clear respiratory roles evolved independently from intracellular globins with uncertain functions. This result suggests either multiple independent functional changes or a yet undefined respiratory role of tissue globins like Ngb and Cygb.

Amino Acid Sequence↗
PubMed2005

WebACT--an online companion for the Artemis Comparison Tool.

UNLABELLED: WebACT is an online resource which enables the rapid provision of simultaneous BLAST comparisons between up to five genomic sequences in a format amenable for visualization with the well-known Artemis Comparison Tool (ACT). Comparisons can be generated on-the-fly using sequences directly retrieved via EMBL database queries, or by entering or uploading user sequences. Furthermore, pre-computed comparisons are available between all publicly available, completed prokaryotic genomes and plasmids currently contained within the Genome Reviews database (372 sequences, representing 175 different species). The system is designed to minimize the volume of downloaded data and maximize performance. Genome sequences, annotation and pre-computed comparisons are stored in a relational database allowing flexible querying based on user-defined sequence regions, from whole genome to a defined region flanking a specified gene. Comparison and sequence files, whether computed online or retrieved from the database of pre-computed genome comparisons, can be viewed online using ACT and are available for download. AVAILABILITY: Freely accessible at http://www.webact.org. SUPPLEMENTARY INFORMATION: User guide and worked examples are available at http://www.webact.org/WebACT/docs.

Computational Biology↗
PubMed2006

cisRED: a database system for genome-scale computational discovery of regulatory elements.

We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred.org). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.

Animals↗
PubMed2005

Detection of viral, bacterial, and parasitological RNA or DNA of nine intestinal pathogens in fecal samples archived as part of the english infectious intestinal disease study: assessment of the stability of target nucleic acid.

Fecal samples were collected from cases and controls as part of the Infectious Intestinal Disease (IID) study in England and were stored as frozen suspensions for 8 to 12 years. The purpose of this study was to apply PCR-based procedures to assess the stability of pathogen-specific nucleic acid sequences present in this archive. Samples from which Cryptosporidium, Giardia, Salmonella, Campylobacter, enteroaggregative Escherichia coli (EAggEC), enterotoxigenic Clostridium perfringens, rotaviruses, noroviruses, or sapoviruses had been previously detected during the IID study using conventional methods were selected from the archive. A generic nucleic acid extraction method to recover RNA or DNA was used. Complementary DNA was generated from RNA by reverse transcription with random priming. Block-based and real-time PCR assays were used to amplify and detect gene fragments from each of these pathogens. The percentage reconfirmation of target was as follows: Giardia duodenalis 68%, Cryptosporidium 96%, Campylobacter 98%, Salmonella 98%, enterotoxigenic C perfringens 34%, EAggEC 93.3%, rotavirus 95%, norovirus 73%, and sapovirus 85%. This study has shown that nucleic acid can be extracted and specific sequences amplified and detected from archived fecal samples. The IID archive therefore represents a valuable resource for further studies, especially the investigation of the samples from which no pathogens had previously been detected.

Cryopreservation↗
PubMed2005

UPF3 suppresses aberrant spliced mRNA in Arabidopsis.

It has been reported that eukaryotic organisms have a nonsense-mediated mRNA decay (NMD) system to exclude aberrant mRNAs that produce truncated proteins. NMD is an RNA surveillance pathway that degrades mRNAs possessing premature translation termination codons (PTCs), thus avoiding production of possibly toxic truncated proteins. Three interacting proteins, UPF1, UPF2 and UPF3, are required for NMD in mammals and yeasts, and their amino acid sequences are well conserved among most eukaryotes, including plants. In this study, 'The Arabidopsis Information Resource' database was searched for mRNAs with premature termination codons. We selected five of these mRNAs and checked for the presence of PTCs in these mRNAs when translated in vivo. As a result we identified aberrant mRNAs produced by alternative splicing for each gene. These genes produced at least one alternative splicing variant including a PTC (PTC+) and another variant without a PTC (PTC-). We analyzed their PTC+/PTC- ratios in wild-type Arabidopsis and upf3 mutant plants and showed that the PTC+/PTC- ratios were higher in atupf3 mutant plants than wild-type plants and that the atupf3 mutant was less able to degrade mRNAs with premature termination codons than wild-type plants. This indicated that the AtUPF3 gene is required by the plant NMD system to obviate aberrantly spliced mRNA.

Alternative Splicing↗
PubMed2003

Database for renal collecting duct regulatory and transporter proteins.

The mammalian kidney collecting duct plays an important role in the fine regulation of Na, K, water, and acid-base balance. Functional genomic and proteomic studies of the kidney offer new opportunities in the understanding of renal physiology and pathophysiology, and the collecting duct is an appropriate target tissue because of the relative simplicity of its cells and the ease of isolating or culturing large numbers of collecting duct cells. Study of the collecting duct includes assessment of gene expression and protein regulation and abundance. For example, DNA and protein microarrays can be used to quantitate gene expression and protein regulation and abundance under varying physiological conditions. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones.

Animals↗
PubMed2006

Meta-All: a system for managing metabolic pathway information.

BACKGROUND: Many attempts are being made to understand biological subjects at a systems level. A major resource for these approaches are biological databases, storing manifold information about DNA, RNA and protein sequences including their functional and structural motifs, molecular markers, mRNA expression levels, metabolite concentrations, protein-protein interactions, phenotypic traits or taxonomic relationships. The use of these databases is often hampered by the fact that they are designed for special application areas and thus lack universality. Databases on metabolic pathways, which provide an increasingly important foundation for many analyses of biochemical processes at a systems level, are no exception from the rule. Data stored in central databases such as KEGG, BRENDA or SABIO-RK is often limited to read-only access. If experimentalists want to store their own data, possibly still under investigation, there are two possibilities. They can either develop their own information system for managing that own data, which is very time-consuming and costly, or they can try to store their data in existing systems, which is often restricted. Hence, an out-of-the-box information system for managing metabolic pathway data is needed. RESULTS: We have designed META-ALL, an information system that allows the management of metabolic pathways, including reaction kinetics, detailed locations, environmental factors and taxonomic information. Data can be stored together with quality tags and in different parallel versions. META-ALL uses Oracle DBMS and Oracle Application Express. We provide the META-ALL information system for download and use. In this paper, we describe the database structure and give information about the tools for submitting and accessing the data. As a first application of META-ALL, we show how the information contained in a detailed kinetic model can be stored and accessed. CONCLUSION: META-ALL is a system for managing information about metabolic pathways. It facilitates the handling of pathway-related data and is designed to help biochemists and molecular biologists in their daily research. It is available on the Web at http://bic-gh.de/meta-all and can be downloaded free of charge and installed locally.

Database Management Systems↗
PubMed2006

PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.

The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from http://phylogenomics.berkeley.edu/phylofacts.

Animals↗
PubMed1997

Identification, isolation, and characterization of a 41-kilodalton protein from rat germ cell-conditioned medium exhibiting concentration-dependent dual biological activities.

In this report, we describe the purification of a novel protease with dual biological actions from germ cell-conditioned medium (GCCM) where germ cells were isolated from adult rat testes using a mechanical procedure. Using multiple HPLC columns and two sequential high performance electrophoresis chromatography steps in association with an [125I]-collagen film assay to detect protease activity, a 41-kDa polypeptide (41-kDa-P) was purified to apparent homogeneity from GCCM. Partial N-terminal amino acid sequence analysis of the purified protein revealed a sequence of NH2-KYEFYEIXLL that, when compared with the existing database at Protein Identification Resource (PIR), GenBank, and BLAST revealed that this is a unique protein. The purified protein, when incubated with [125I]-testin, a Sertoli cell secretory product that is localized at the intertesticular cell junction and is resistant to tryptic digest, was found capable of hydrolyzing testin dose dependently. The proteolysis of [125I]-testin by this 41-kDa protein was inhibited by alpha2-macroglobulin (a Sertoli cell secretory product) also in a dose-dependent manner. A study on the interactions between different classes of protease inhibitors and the purified 41-kDa protein revealed that it is a serine protease. At doses ranging between 0.5 and 50 ng/ml, 41-kDa-P induced a dose-dependent inhibition of Sertoli cell secretory function using testin and clusterin as markers without any apparent proteolytic activity. However, at doses greater than 0.5 microg/ml, 41-kDa-P was found to cleave [125I]-collagen and [125I]-testin at physiological pH, indicating that this 41-kDa protein has dual biological activities whose primary action is concentration dependent. In view of the biological activities of this protease, it is postulated that this protein may be involved in facilitating germ cell migration in the epithelium.

Animals↗
PubMed2001

BAC FISH analysis in Allium cepa.

Onion (Allium cepa L.; 1C=15,000 Mb) is an agriculturally important plant. The genome of onion has been extensively studied at the conventional cytogenetic level, but molecular analyses have lagged behind due to its large genome size. To overcome this bottleneck, a partial bacterial artificial chromosome (BAC) library of onion was constructed. The average insert size of the BAC library was about 100 kb. A total of 48,000 clones, corresponding to 0.32 genome equivalent, were obtained. Fluorescent in situ hybridization (FISH) screening resulted in identification of BAC clones localized on centromeric, telomeric, or several limited interstitial chromosomal regions, although most of the clones hybridized with entire chromosomes. The partial BAC library proved to be a useful resource for molecular cytogenetic studies of onion, and should be useful for further mapping and sequencing studies of important genes of this plant. BAC FISH screening is a powerful method for identification of molecular cytogenetic markers in large-genome plants.

Centromere↗