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PubMed2005

IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes.

IMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation. IMGT/GENE-DB is freely available at http://imgt.cines.fr.

Alleles↗
PubMed2006

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mapping experiments for individual genes, or, starting from release 73, from mass genome annotation projects. Subsets of promoter sequences with customized 5' and 3' extensions can be downloaded from the EPD website. The focus of current development efforts is to reach complete promoter coverage for important model organisms as soon as possible. To speed up this process, a new class of preliminary promoter entries has been introduced as of release 83, which requires less stringent admission criteria. As part of a continuous integration process, new web-based interfaces have been developed, which allow joint analysis of promoter sequences with other bioinformatics resources developed by our group, in particular programs offered by the Signal Search Analysis Server, and gene expression data stored in the CleanEx database. EPD can be accessed at http://www.epd.isb-sib.ch.

Animals↗
PubMed2006

Protein-protein interaction analysis by C-terminally specific fluorescence labeling and fluorescence cross-correlation spectroscopy.

Here, we describe novel puromycin derivatives conjugated with iminobiotin and a fluorescent dye that can be linked covalently to the C-terminus of full-length proteins during cell-free translation. The iminobiotin-labeled proteins can be highly purified by affinity purification with streptavidin beads. We confirmed that the purified fluorescence-labeled proteins are useful for quantitative protein-protein interaction analysis based on fluorescence cross-correlation spectroscopy (FCCS). The apparent dissociation constants of model protein pairs such as proto-oncogenes c-Fos/c-Jun and archetypes of the family of Ca2+-modulated calmodulin/related binding proteins were in accordance with the reported values. Further, detailed analysis of the interactions of the components of polycomb group complex, Bmi1, M33, Ring1A and RYBP, was successfully conducted by means of interaction assay for all combinatorial pairs. The results indicate that FCCS analysis with puromycin-based labeling and purification of proteins is effective and convenient for in vitro protein-protein interaction assay, and the method should contribute to a better understanding of protein functions by using the resource of available nucleotide sequences.

Calmodulin↗
PubMed2005

A resource of 5,814 dissociation transposon-tagged and sequence-indexed lines of Arabidopsis transposed from start loci on chromosome 5.

We report here the generation of an additional collection of Dissociation (Ds) transposon-tagged, sequence-indexed lines of Arabidopsis thaliana. Our RIKEN Ds insertion collection now totals 17,668 lines. Our collection has preferential insertions in chromosomes 1 and 5, because Ds was transposed from start loci on those chromosomes (11,854 and 5,814 lines, respectively). We describe here features of the latter 5,814 lines. The former 11,854 lines have been described previously. We have created a searchable database of the insertion sites and mutated genes (http://rarge.gsc.riken.jp/), and are depositing these lines in the RIKEN BioResource Center (http://www.brc.riken.go.jp/lab/epd/Eng/). Our collection of these mutants will contribute to progress in functional genomics of plants.

Arabidopsis↗
PubMed1988

Non-essential genes in the vaccinia virus HindIII K fragment: a gene related to serine protease inhibitors and a gene related to the 37K vaccinia virus major envelope antigen.

The complete nucleotide sequence of a cloned copy of the HindIII K fragment of the WR strain of vaccinia virus has been determined. Eight open reading frames (ORFs) have been identified, on the basis of size and codon usage. The predicted amino acid sequences of the putative genes have been compared to the Protein Identification Resource and to published vaccinia virus sequences. One gene, predicted to encode a 42.2K protein, is highly related to the family of serine protease inhibitors. It shows approximately 25% identity to human antithrombin III and 19% identity to the cowpox virus 38K protein gene which is also related to serine protease inhibitors. The product of another gene shows a similar high level of identity to the 37K vaccinia virus major envelope antigen. The existence of viable deletion mutants and recombinants containing foreign DNA inserted into both these genes indicates that they are non-essential.

Amino Acid Sequence↗
PubMed2002

Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.

To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains. These sequences were processed to identify 15,311 high-quality ESTs representing 8912 putative transcripts. Putative transcripts were functionally annotated (using the Gene Ontology classification system) based on matching gene sequences in Drosophila melanogaster. The brain ESTs represent a broad range of molecular functions and biological processes, with neurobiological classifications particularly well represented. Roughly half of Drosophila genes currently implicated in synaptic transmission and/or behavior are represented in the Apis EST set. Of Apis sequences with open reading frames of at least 450 bp, 24% are highly diverged with no matches to known protein sequences. Additionally, over 100 Apis transcript sequences conserved with other organisms appear to have been lost from the Drosophila genome. DNA microarrays were fabricated with over 7000 EST cDNA clones putatively representing different transcripts. Using probe derived from single bee brain mRNA, microarrays detected gene expression for 90% of Apis cDNAs two standard deviations greater than exogenous control cDNAs. [The sequence data described in this paper have been submitted to Genbank data library under accession nos. BI502708-BI517278. The sequences are also available at http://titan.biotec.uiuc.edu/bee/honeybee_project.htm.]

Animals↗
PubMed1998

Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome.

Raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. To demonstrate the utility of such a resource, 870 single-stranded M13 clones were sequenced from a shotgun library of the Salmonella typhi Ty2 genome. The sequence reads averaged over 400 bases and sampled the genome with an average spacing of once every 5,000 bases. A total of 339,243 bases of unique sequence was generated (approximately 7% representation). The sample of 870 sequences was compared to the complete Escherichia coli K-12 genome and to the rest of the GenBank database, which can also be considered a collection of sampled sequences. Despite the incomplete S. typhi data set, interesting categories could easily be discerned. Sixteen percent of the sequences determined from S. typhi had close homologs among known Salmonella sequences (P < 1e-40 in BlastX or BlastN), reflecting the proportion of these genomes that have been sequenced previously; 277 sequences (32%) had no apparent orthologs in the complete E. coli K-12 genome (P > 1e-20), of which 155 sequences (18%) had no close similarities to any sequence in the database (P > 1e-5). Eight of the 277 sequences had similarities to genes in other strains of E. coli or plasmids, and six sequences showed evidence of novel phage lysogens or sequence remnants of phage integrations, including a member of the lambda family (P < 1e-15). Twenty-three sample sequences had a significantly closer similarity a sequence in the database from organisms other than the E. coli/Salmonella clade (which includes Shigella and Citrobacter). These sequences are new candidate lateral transfer events to the S. typhi lineage or deletions on the E. coli K-12 lineage. Eleven putative junctions of insertion/deletion events greater than 100 bp were observed in the sample, indicating that well over 150 such events may distinguish S. typhi from E. coli K-12. The need for automatic methods to more effectively exploit sample sequences is discussed.

Bacteriophages↗
PubMed2002

Limbic hyperreactivity in bipolar II disorder.

OBJECTIVE: The authors' goal was to determine whether patients with bipolar II disorder had altered regional brain responses to novel motor sequences. METHOD: Regional cerebral blood flow was measured with positron emission tomography in 13 patients with bipolar II disorder and 14 healthy comparison subjects. Participants performed a serial reaction time task in which they were visually cued to press one of four buttons at a time. The order of button presses was determined by a complex sequence that was changed in the latter half of the study. RESULTS: In the comparison subjects a spatial attention circuit in the superior parietal lobe and supplementary motor area was activated in response to the introduction of the new sequence. Patients did not display this activation pattern; instead, a widespread limbic network was activated in response to the new sequence. CONCLUSIONS: The attentional resources of patients with bipolar II disorder are not reallocated when they are confronted with a nonemotional motor task; rather, their performance is altered through activation of limbic circuitry.

Adult↗
PubMed1998

Complete amino acid sequence of chitinase-a from bulbs of gladiolus (Gladiolus gandavensis).

The complete amino acid sequence of gladiolus bulb chitinase-a (GBC-a) was determined. First the tryptic peptides from GBC-a after it was reduced and S-carboxymethylated were sequenced and then the peptides were further studied by chemical cleavage of the enzyme. GBC-a consisted of 274 amino acid residues and had a molecular mass of 30,714 Da. Two consensus sequences essential for chitinase activity by plant class III chitinases were conserved in GBC-a, although its sequence similarity with plant class III chitinases was less than 20%. Sequence comparison of GBC-a with sequences of other proteins in a protein identification resource (PIR) showed that the GBC-a sequence was 33% similar to that of narbonin, a seed storage 2S globulin from narbon beans.

Amino Acid Sequence↗
PubMed2025

Rapid assessment of clinical severity for salmonellosis cases via protein family domain analysis and machine learning.

Salmonella is a common pathogen, infecting more than a million people yearly. Rapid assessment of clinical case severity is essential for improving patient outcomes and optimizing healthcare resources. Advancements in genome sequencing technologies have enabled the analysis of bacterial genomes from many clinical cases, opening up new opportunities for precise and timely diagnosis. This study proposes a genome-based framework for identifying critical Salmonella cases before the onset of critical symptoms and facilitating early medical intervention. By leveraging protein family (Pfam) domains as the representation for genomic data, the complex genetic profiles of Salmonella cases are simplified into interpretable features. The severity levels of cases were investigated through rigorous data analysis, resulting in a set of 70 Pfam domains that could be potentially used as biomarkers. Machine Learning was employed to assess the predictive power of the curated Pfam biomarkers, achieving high accuracy (~93%) in sorting cases into critical, moderate, and mild categories. The results demonstrate the efficacy of the proposed approach. This framework highlights the potential of using bacterial genomic data in clinical decision-making, opening the window for timely personalized interventions for Salmonella infection management.

Domains of unknown function (DUFs)↗
PubMed2001

Linking teaching approaches and learning styles: how can it help students?

Although limited, one study revealed that the preferred learning style for paramedic students is that of assimilator. Assimilators prefer a more passive/reflective role in the learning situation and tend to favor lectures with an emphasis on concepts, assigned readings, exams and assigned tasks. By increasing complexity and requiring more self-directed activities in your teaching approach, you are encouraging students (particularly the assimilators) to move from a role of dependence on you for facts and direction to a role in which they begin to 1) seek some knowledge on their own; 2) assume responsibility for analyzing potential solutions to problems; and 3) justify decisions. You should be able to document their progress toward independence through clinical and field evaluations by preceptors. Students should reach the point of competently assuming control of patient care for the majority of patients they encounter by the end of their field internship. Instructors should keep in mind that there is currently no consensus on a definition of learning styles, and different indicators identify different factors. Learning style inventory results, regardless of the instrument used, should not be a primary factor in decisions to alter curriculum approaches. However, although there is inconsistency in the data on its reliability and validity, and Kolb's LSI measures only certain factors, the results that are available seem significant enough to at least consider learning styles as one resource for adapting and sequencing our teaching methodologies. A learning-styles inventory administered to students at the beginning of a training program would provide faculty with the knowledge of the preferred learning style of that class. This knowledge could prove extremely helpful, not only in planning classroom activities, but also in developing approaches for remediating students experiencing difficulty in mastering the curriculum content. The more knowledge we have about our students, the greater our likelihood of success in reaching our ultimate goal of providing the best possible learning experience.

Emergency Medical Technicians↗
PubMed2003

ABRF-ESRG'03: analysis of a PVDF-bound known protein with a homogeneous amino-terminus.

The Association of Biomolecular Resource Facilities 2003 Edman Sequencing Research Group (ABRF-ESRG'03) sample is the 15th in a series of studies designed to allow participating members to evaluate their abilities to analyze the N-terminus of a protein or peptide using automated Edman degradation chemistry. It is a follow-up study to the ESRG'02 sample, which was a single protein with a heterogeneous N-terminus. Both the 2002 and 2003 samples were obtained from the same protein complex and were resolved by SDS-PAGE followed by electrophoretic transfer to PVDF membrane. The ABRF-ESRG'03 sample had an apparent molecular weight of 49 kDa and a single N-terminus, with initial yields of approximately 2 pmol. Participants were asked to sequence 25 residues and return their results to the ESRG for analysis along with two completed surveys and an area/pmol table for repetitive and initial yield calculations. Data for 46 responses are presented which include initial yields, repetitive yields, sequencer performance, and ability to identify the protein.

Amino Acid Sequence↗
PubMed2005

[Analysis of gene expression information in the fat and muscle tissues of pig].

An in silico study was developed to detect the gene expression profile of pig fat and muscle tissues by using the porcine EST resources and human gene sequences,and thus provided candidate information for basic genetic analysis in meat quality improvement of pig. In this study,a BLAST search was performed to identify homologies between the cDNA sequences of human genes and the ESTs sequences of pig,and the high homologous records were screened out. Four Java programs were developed to retrieve and collect sequences, and analyze the BLAST alignment results. By statistical analysis, it was found that there were at least 2002 genes expressed in the fat and muscle tissues of pig, and 1087 in the fat tissue, 1205 in the muscle respectively (290 genes co-expressed in the two tissues). The top-ranking records were screened out,and meantime, 114 basic active genes (BAGs) were found to express in the two tissues,80 in the fat tissue and 34 in the muscle tissue respectively. The top 10 records were described in the paper. This study was summarized in relation to current meat quality improvement of pig at molecular level.

Adipose Tissue↗
PubMed2006

Integration of genomic data for pharmacology and toxicology using Internet resources.

Genome based technologies such as sequencing and gene expression profiling using microarrays are creating massive amounts of data. Results from these studies have provided unique insights into targets, biochemical pathways, and biological systems affected by drug or xenobiotic chemical treatments. Moreover, these genomic technologies offer the potential to identify biomarkers for pharmacological development or toxicological prediction. Nonetheless, microarray studies involving a single compound produce useful although limited data. To gain further power from these individual studies, the ability to combine datasets through integration schemes has become imperative. In the current study, we describe and analyze currently available Internet resources designed to address this problem. Many functionalities, such as ability to cross reference orthologous genes across species or to combine same technology platform data, are present in these resources. Nonetheless, these resources are limited in the number of technology platforms they can support. While the ability to integrate all currently existing gene expression datasets remains enigmatic, the current tools provide a partial solution that may still yield unique insights into the affects of exogenous molecules at the level of gene expression.

Databases, Genetic↗
PubMed2002

Carotenoids and egg quality in the lesser blackbacked gull Larus fuscus: a supplemental feeding study of maternal effects.

Egg quality is a phenotype of, and can profoundly influence fitness in, both mother and offspring. However, the physiological mechanisms that underlie this maternal effect are poorly understood. Carotenoids are hypothesized to enhance antioxidant activity and immune function, and are responsible for the pigmentation of egg yolk. The proximate basis and consequences of this maternal investment, however, have not previously been studied in wild birds. In this supplemental feeding study of lesser black-backed gulls, Larus fuscus, carotenoid-fed females are shown to have increased integument pigmentation, higher plasma concentrations of carotenoids and antioxidant activity, and lower plasma concentrations of immunoglobulins (Igs) in comparison with controls. In turn, carotenoid-fed females produced eggs containing high carotenoid but low Ig concentrations (i.e. passive immunity), whereas control females produced eggs containing low carotenoid but high Ig concentrations. Within-clutch patterns of these resources varied over the laying sequence in a similar manner in both carotenoid-fed and control nests. Our results suggest that carotenoids could be one resource responsible for egg quality maternal effects in birds. We discuss the possible implications of carotenoid-mediated effects on phenotype for fitness in mothers and their offspring.

Animal Feed↗
PubMed2001

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Orthologs are genes in different species that originate from a single gene in the last common ancestor of these species. Such genes have often retained identical biological roles in the present-day organisms. It is hence important to identify orthologs for transferring functional information between genes in different organisms with a high degree of reliability. For example, orthologs of human proteins are often functionally characterized in model organisms. Unfortunately, orthology analysis between human and e.g. invertebrates is often complex because of large numbers of paralogs within protein families. Paralogs that predate the species split, which we call out-paralogs, can easily be confused with true orthologs. Paralogs that arose after the species split, which we call in-paralogs, however, are bona fide orthologs by definition. Orthologs and in-paralogs are typically detected with phylogenetic methods, but these are slow and difficult to automate. Automatic clustering methods based on two-way best genome-wide matches on the other hand, have so far not separated in-paralogs from out-paralogs effectively. We present a fully automatic method for finding orthologs and in-paralogs from two species. Ortholog clusters are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for both orthologs and in-paralogs. The program, called INPARANOID, was tested on all completely sequenced eukaryotic genomes. To assess the quality of INPARANOID results, ortholog clusters were generated from a dataset of worm and mammalian transmembrane proteins, and were compared to clusters derived by manual tree-based ortholog detection methods. This study led to the identification with a high degree of confidence of over a dozen novel worm-mammalian ortholog assignments that were previously undetected because of shortcomings of phylogenetic methods.A WWW server that allows searching for orthologs between human and several fully sequenced genomes is installed at http://www.cgb.ki.se/inparanoid/. This is the first comprehensive resource with orthologs of all fully sequenced eukaryotic genomes. Programs and tables of orthology assignments are available from the same location.

Algorithms↗
PubMed2002

Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants.

PURPOSE: To explore the expression profile of the human lens and to provide a resource for microarray studies, expressed sequence tag (EST) analysis has been performed on cDNA libraries from adult lenses. METHODS: A cDNA library was constructed from two adult (40 year old) human lenses. Over two thousand clones were sequenced from the unamplified, un-normalized library. The library was then normalized and a further 2200 sequences were obtained. All the data were analyzed using GRIST (GRouping and Identification of Sequence Tags), a procedure for gene identification and clustering. RESULTS: The lens library (by) contains a low percentage of non-mRNA contaminants and a high fraction (over 75%) of apparently full length cDNA clones. Approximately 2000 reads from the unamplified library yields 810 clusters, potentially representing individual genes expressed in the lens. After normalization, the content of crystallins and other abundant cDNAs is markedly reduced and a similar number of reads from this library (fs) yields 1455 unique groups of which only two thirds correspond to named genes in GenBank. Among the most abundant cDNAs is one for a novel gene related to glutamine synthetase, which was designated "lengsin" (LGS). Analyses of ESTs also reveal examples of alternative transcripts, including a major alternative splice form for the lens specific membrane protein MP19. Variant forms for other transcripts, including those encoding the apoptosis inhibitor Livin and the armadillo repeat protein ARVCF, are also described. CONCLUSIONS: The lens cDNA libraries are a resource for gene discovery, full length cDNAs for functional studies and microarrays. The discovery of an abundant, novel transcript, lengsin, and a major novel splice form of MP19 reflect the utility of unamplified libraries constructed from dissected tissue. Many novel transcripts and splice forms are represented, some of which may be candidates for genetic diseases.

Adult↗
PubMed2002

Activation of antigen-presenting cells by immunostimulatory plant DNA: a natural resource for potential adjuvant.

Genomic DNA sequences (bacteria, insect, nematodes and molluscs) or synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG motifs (CpG-DNA/ODN) are regarded as promising candidates for new medical adjuvants for their ability to stimulate the mammalian immune system and enhance immune responses to specific antigens. Here, we first report the immunostimulatory activity of total genomic DNA from two plants, Brassica chinensis L. and Zea may, the CpG methylation status of which is incomplete compared with E. coli DNA. These plant DNA can activate B cells to proliferate. Plant DNA promotes secretion of IL-12, and increases expression of MHC and costimulatory molecules by bone marrow-derived dendritic cells (BMDC). Plant DNA can also enhance antigen presentation capacity of BMDC and macrophages. When administrated in vivo, plant DNA can inhibit tumor growth in situ or metastasis in tumor-bearing mice. The immunostimulatory activity of plant DNA could be abolished by methylation. Our data showed that plant DNA can activate antigen-presenting cells (APC) including DC, macrophages and B cells, indicating that plant DNA is a new kind of potential adjuvant. Therefore, we conclude that plant DNA is another natural source of CpG-DNA, and that green plants may provide abundant resources for this potential medical adjuvant.

Adjuvants, Immunologic↗