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At least 433 records · Page 24Linked to original sources
PubMed1998

IMGT/LIGM-DB: a systematized approach for ImMunoGeneTics database coherence and data distribution improvement.

IMGT, the international ImMunoGeneTics database (http:(/)/imgt.cnusc.fr:8104), created by Marie-Paule Lefranc, Montpellier, France, is an integrated database specializing in antigen receptors and MHC of all vertebrate species. IMGT includes LIGM-DB, developed for Immunoglobulins and T-cell-receptors. LIGM-DB distributes high quality data with an important increment value added by the LIGM expert annotations. LIGM-DB accurate immunogenetics data is based on the standardization of biological knowledge related to keywords, annotation labels and gene identification. The management of such data resulting from biological research requires an high flexible implementation to quickly reflect up-to-date results, and to integrate new knowledge. We developed a systematized approach and defined LIGM-DB systems which manage and realize the major tasks for the database survey. In this paper, we will focus on the coherence system, which became absolutely crucial to maintain data quality as the database is growing up and as the biological knowledge continues to improve, and on the distribution system which makes LIGM-DB data easy to access, download and reuse. Efforts have been done to improve the data distribution procedures and adapt them to the current bioinformatics needs. Recently, we have developed an API which allows Java programmers to remotely access and integrate LIGM-DB data in other computer environments.

Animals↗
PubMed2005

Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.

A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.

Animals↗
PubMed2005

High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions.

We describe a streamlined and systematic method for cloning green fluorescent protein (GFP)-open reading frame (ORF) fusions and assessing their subcellular localization in Arabidopsis thaliana cells. The sequencing of the Arabidopsis genome has made it feasible to undertake genome-based approaches to determine the function of each protein and define its subcellular localization. This is an essential step towards full functional analysis. The approach described here allows the economical handling of hundreds of expressed plant proteins in a timely fashion. We have integrated recombinational cloning of full-length trimmed ORF clones (available from the SSP consortium) with high-efficiency transient transformation of Arabidopsis cell cultures by a hypervirulent strain of Agrobacterium. To demonstrate its utility, we have used a selection of trimmed ORFs, representing a variety of key cellular processes and have defined the localization patterns of 155 fusion proteins. These patterns have been classified into five main categories, including cytoplasmic, nuclear, nucleolar, organellar and endomembrane compartments. Several genes annotated in GenBank as unknown have been ascribed a protein localization pattern. We also demonstrate the application of flow cytometry to estimate the transformation efficiency and cell cycle phase of the GFP-positive cells. This approach can be extended to functional studies, including the precise cellular localization and the prediction of the role of unknown proteins, the confirmation of bioinformatic predictions and proteomic experiments, such as the determination of protein interactions in vivo, and therefore has numerous applications in the post-genomic analysis of protein function.

Agrobacterium tumefaciens↗
PubMed2004

Annotation and cross-indexing of array elements on multiple platforms.

On the surface, transcript profiling using microarrays seems to offer a way of looking at the global response of the cell to perturbation, with a focus on changes in gene expression. The difficulty, however, is that the response of a particular gene is actually measured on the array by an element that is a short, defined nucleic acid sequence. Sequences that map back to the same genetic locus may actually be given different names and descriptions when they are deposited in public sequence databases; when such sequences are used in microarray construction, elements that monitor the same genetic locus may have different names and descriptions. The algorithm described here uses a hierarchical approach to assign a single best annotation to the elements in a given microarray in such a fashion that elements from one microarray platform may be cross-indexed with those of another. The algorithm relies on the nucleic acid accession number for a given array element, and uses that to retrieve annotation from the most recent versions of LocusLink and UniGene. Both database resources are searched, with a priority being given to annotation derived from the curated LocusLink database. In lieu of annotation found in these databases, the default GenBank annotation is used. As a final outcome, a cross-chip identifier is generated that may be used to cross-index array elements. The program is available as a practical extraction and report language (Perl) script that can run under any Perl interpreter.

Algorithms↗
PubMed2000

Proteomic analysis of the Escherichia coli outer membrane.

Outer membrane proteins (OMPs) of Gram-negative bacteria are key molecules that interface the cell with the environment. Traditional biochemical and genetic approaches have yielded a wealth of knowledge relating to the function of OMPs. Nonetheless, with the completion of the Escherichia coli genome sequencing project there is the opportunity to further expand our understanding of the organization, expression and function of the OMPs in this Gram-negative bacterium. In this report we describe a proteomic approach which provides a platform for parallel analysis of OMPs. We propose a rapid method for isolation of bacterial OMPs using carbonate incubation, purification and protein array by two-dimensional electrophoresis, followed by protein identification using mass spectrometry. Applying this method to examine E. coli K-12 cells grown in minimal media we identified 21 out of 26 (80%) of the predicted integral OMPs that are annotated in SWISS-PROT release 37 and predicted to separate within the range of pH 4-7 and molecular mass 10-80 kDa. Five outer membrane lipoproteins were also identified and only minor contamination by nonmembrane proteins was observed. Importantly, this research readily demonstrates that integral OMPs, commonly missing from 2D gel maps, are amenable to separation by two-dimensional electrophoresis. Two of the identified OMPs (YbiL, YeaF) were previously known only from their ORFs, and their identification confirms the cognate genes are transcribed and translated. Furthermore, we show that like the E. coli iron receptors FhuE and FhuA, the expression of YbiL is markedly increased by iron limitation, suggesting a putative role for this protein in iron transport. In an additional demonstration we show the value of parallel protein analysis to document changes in E. coli OMP expression as influenced by culture temperature.

Bacterial Outer Membrane Proteins↗
PubMed2006

Gene profiling and bioinformatic analysis of Schwann cell embryonic development and myelination.

To elucidate the molecular mechanisms involved in Schwann cell development, we profiled gene expression in the developing and injured rat sciatic nerve. The genes that showed significant changes in expression in developing and dedifferentiated nerve were validated with RT-PCR, in situ hybridisation, Western blot and immunofluorescence. A comprehensive approach to annotating micro-array probes and their associated transcripts was performed using Biopendium, a database of sequence and structural annotation. This approach significantly increased the number of genes for which a functional insight could be found. The analysis implicates agrin and two members of the collapsin response-mediated protein (CRMP) family in the switch from precursors to Schwann cells, and synuclein-1 and alphaB-crystallin in peripheral nerve myelination. We also identified a group of genes typically related to chondrogenesis and cartilage/bone development, including type II collagen, that were expressed in a manner similar to that of myelin-associated genes. The comprehensive function annotation also identified, among the genes regulated during nerve development or after nerve injury, proteins belonging to high-interest families, such as cytokines and kinases, and should therefore provide a uniquely valuable resource for future research.

Agrin↗
PubMed2002

The necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria: amino acid, purine and pyrimidine metabolism in Mollicutes.

Bacteria of the class Mollicutes have no cell wall. One species, Mycoplasma genitalium is the personification of the simplest form of independent cell-free life. Its small genome (580 kbp) is the smallest of any cell. Mollicutes have unique metabolic properties, perhaps because of their limited coding space and high mutability. Based on 16S rRNA analyses the Mollicutes Mycoplasma gallisepticum is thought to be the most mutable bacteria. Enzyme activities found in most Bacteria are absent from Mollicutes. The functions of apparently absent genes and enzymes can apparently be fulfilled by other genes and their expression products that have multiple capabilities. Because of these and other properties predictions of their metabolism based only on, e.g., either annotation, enzymatic assay, proteomic studies or structural analyses is problematic. To obtain a more confident appraisal of the functional capabilities of these simplest cells genomic and enzymatic data were combined to obtain a "metabolic consensus". The consensus is represented by a biochemical circuit for central metabolism involving purine and pyrimidine interconversions and their linkages to amino acid metabolism, glycolysis and the pentose phosphate pathway in three human Mollicutes pathogens: Mycoplasma pneumoniae, Mycoplasma genitalium and Ureaplasma urealyticum.

Amino Acids↗
PubMed2006

The proteome of Mannheimia succiniciproducens, a capnophilic rumen bacterium.

Mannheimia succiniciproducens MBEL55E isolated from bovine rumen is an industrially important bacterium as an efficient succinic acid producer. Recently, its full genome sequence was determined. In the present study, we analyzed the M. succiniciproducens proteome based on the genome information using 2-DE and MS. We established proteome reference map of M. succiniciproducens by analyzing whole cellular proteins, membrane proteins, and secreted proteins. More than 200 proteins were identified and characterized by MS/MS supported by various bioinformatic tools. The presence of proteins previously annotated as hypothetical proteins or proteins having putative functions were also confirmed. Based on the proteome reference map, cells in the different growth phases were analyzed at the proteome level. Comparative proteome profiling revealed valuable information to understand physiological changes during growth, and subsequently suggested target genes to be manipulated for the strain improvement.

Animals↗
PubMed2025

Construction of a Core Germplasm and Identification of Candidate SNPs Associated with Growth Performance of Epinephelus tukula by Whole-Genome Resequencing.

Epinephelus tukula is an economically important aquaculture animal, and a major parent in grouper crossbreeding. To better preserve and exploit E. tukula germplasm resources, a core collection (containing 34 individuals derived from 10 genetic groups) was first constructed based on phenotypic growth traits and whole-genome resequencing (WGS) data. The phenotypic traits of the individuals within the core collection were not significantly different from those in the original collection, suggesting effective representativeness of the core collection. Additionally, we performed genome-wide association study (GWAS) of E. tukula to identify candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits, to facilitate the improvements in the growth performance of this species. Twenty-six significant SNPs were identified, scattered among multiple chromosomes. Five SNPs were confirmed to be correlated with growth in another new group of 101 individuals. Based on the annotation results, these five SNPs were located in CCDC102A, NTRK2, CTSL, OTOF, and nestin, and were involved in cell development, differentiation and proliferation, glycolytic metabolism, neurological development, and myoblast differentiation. Our findings not only provide an effective basis for the conservation and utilization of E. tukula germplasm resources, but also promote the development of marker-assisted selection of E. tukula.

Polymorphism, Single Nucleotide↗
PubMed2006

Identification of FGF-dependent genes in the Drosophila tracheal system.

The embryonic development of the tracheal system of the fruit fly Drosophila provides a paradigm for genetic studies of branching morphogenesis. Efforts of many laboratories have identified Branchless (Bnl, a fibroblast growth factor homologue) and Breathless (Btl, the receptor homologue) as crucial factors at many stages of tracheal system development. The downstream targets of the Bnl/Btl signalling cascade, however, remain mostly unknown. Misexpression of the bnl gene results in specific tracheal phenotypes that lead to larval death. We characterised the transcriptional profiles of targeted over-expression of bnl in the embryonic trachea and of loss-of-function bnl(P1) mutant embryos. Gene expression data was mapped to high-throughput in situ hybridisation based ImaGO-annotation. Thus, we identified and confirmed by quantitative PCR 13 Bnl-dependent genes that are expressed in cells within and outside of the tracheal system.

Amino Acid Sequence↗
PubMed2002

Proteomic map and database of lymphoblastoid proteins.

Advances in genomics have led to the accumulation of an unprecedented amount of data, giving rise to a new field in biochemistry, proteomics. We used a combination of two dimensional gel electrophoresis, analysis and annotation using third-generation software, and mass spectrometry to establish the proteome maps of lymphoblastoid B-cells, a prerequisite for analysis of drug effects and lymphocyte cell diseases. About 1200 protein spots were detected and characterised in terms of their isoelectric point, molecular mass and expression. The present status of proteomic technologies, as well as a description of the usefulness of human hematopoietic cells proteomic database are discussed.

Databases, Protein↗
PubMed2005

Current issues in mouse genome engineering.

The mouse is the foremost vertebrate experimental model because its genome can be precisely and variously engineered. Now that the mouse genome has been sequenced and annotated, the task of mutating each gene is feasible, and an international cooperation is providing mutated embryonic stem cells and mice as readily available resources. Because these resources will change biomedical research, decisions about their nature will have far-reaching effects. It is therefore timely to consider topical issues for mouse genome engineering, such as the background genotype; homologous, site-specific and transpositional recombination; conditional mutagenesis; RNA-mediated interference; and functional genomics with embryonic stem cells.

Animals↗
PubMed2001

An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima.

A gene encoding a putative GTPase containing two tandemly repeated GTP-binding domains from a hyperthermophilic bacterium, Thermotoga maritima, was cloned and expressed in Escherichia coli. The gene (TM1446) termed der is highly conserved in Eubacteria including E. coli. The purified der product (Tm-Der) has GTPase activity but no ATPase activity. GTP, GDP, and dGTP but not GMP, ATP, CTP, and UTP compete for GTP binding to Tm-Der. An optimal condition for the GTPase assay was determined to be pH 7.5 in 400 mm KCl and 5 mm MgCl(2) at 70 degrees C, where K(m), V(max), and k(cat) values were determined to be 110 microm, 3.46 microm/min, and 0.87 min(-1), respectively. A der deletion strain of E. coli was constructed by replacing the der gene (originally annotated yfgK) with a kanamycin resistance gene. The deletion strain was found to form colonies only if the cells harbored a plasmid containing der, indicating that der is essential for E. coli growth.

Amino Acid Sequence↗
PubMed2006

Create and assess protein networks through molecular characteristics of individual proteins.

MOTIVATION: The study of biological systems, pathways and processes relies increasingly on analyses of networks. Most often, such analyses focus on network topology, thereby treating all proteins or genes as identical, featureless nodes. Integrating molecular data and insights about the qualities of individual proteins into the analysis may enhance our ability to decipher biological pathways and processes. RESULTS: Here, we introduce a novel platform for data integration that generates networks on the macro system-level, analyzes the molecular characteristics of each protein on the micro level, and then combines the two levels by using the molecular characteristics to assess networks. It also annotates the function and subcellular localization of each protein and displays the process on an image of a cell, rendering each protein in its respective cellular compartment. By thus visualizing the network in a cellular context we are able to analyze pathways and processes in a novel way. As an example, we use the system to analyze proteins implicated with Alzheimers disease and show how the integrated view corroborates previous observations and how it helps in the formulation of new hypotheses regarding the molecular underpinnings of the disease. AVAILABILITY: http://www.rostlab.org/services/pinat.

Cell Physiological Phenomena↗
PubMed2005

Role for HtrA in stress induction and virulence potential in Listeria monocytogenes.

In silico analysis of the Listeria monocytogenes genome revealed lmo0292, a gene predicted to encode a HtrA-like serine protease. A stable insertion mutant was constructed, revealing a requirement for htrA in the listerial response to heat, acid, and penicillin stress. Transcriptional analysis revealed that htrA is not induced in response to heat shock but is induced in response to low pH and penicillin G stress. Furthermore, htrA expression was shown to be dependent upon the LisRK two-component sensor-kinase, a system known to respond to changes in integrity of the cell envelope. In addition, we demonstrated that a second in-frame start codon, upstream of that previously annotated for L. monocytogenes htrA, incorporating a putative signal sequence appears to influence virulence potential. Finally, a significant virulence defect was observed for the htrA mutant, indicating that this gene is required for full virulence in mice. Our findings suggest that L. monocytogenes lmo0292 encodes an HtrA-like serine protease that is not part of the classical heat shock response but is involved in stress responses and virulence.

Amino Acid Sequence↗
PubMed2013

Structural insights into adeno-associated virus serotype 5.

The adeno-associated viruses (AAVs) display differential cell binding, transduction, and antigenic characteristics specified by their capsid viral protein (VP) composition. Toward structure-function annotation, the crystal structure of AAV5, one of the most sequence diverse AAV serotypes, was determined to 3.45-Å resolution. The AAV5 VP and capsid conserve topological features previously described for other AAVs but uniquely differ in the surface-exposed HI loop between βH and βI of the core β-barrel motif and have pronounced conformational differences in two of the AAV surface variable regions (VRs), VR-IV and VR-VII. The HI loop is structurally conserved in other AAVs despite amino acid differences but is smaller in AAV5 due to an amino acid deletion. This HI loop is adjacent to VR-VII, which is largest in AAV5. The VR-IV, which forms the larger outermost finger-like loop contributing to the protrusions surrounding the icosahedral 3-fold axes of the AAVs, is shorter in AAV5, creating a smoother capsid surface topology. The HI loop plays a role in AAV capsid assembly and genome packaging, and VR-IV and VR-VII are associated with transduction and antigenic differences, respectively, between the AAVs. A comparison of interior capsid surface charge and volume of AAV5 to AAV2 and AAV4 showed a higher propensity of acidic residues but similar volumes, consistent with comparable DNA packaging capacities. This structure provided a three-dimensional (3D) template for functional annotation of the AAV5 capsid with respect to regions that confer assembly efficiency, dictate cellular transduction phenotypes, and control antigenicity.

Capsid Proteins↗
PubMed2005

Peripheral genotype-phenotype correlations in Asian Indians with type 2 diabetes mellitus.

OBJECTIVE: A genome-wide scan of gene expression in leucocytes in Asian Indians with type 2 diabetes was performed and correlated with their known phenotype. METHODS: Microarray gene profiling of 13,474 sequence-verified, non-redundant human cDNAs was done to study leukocyte gene expression in Asian Indians with type 2 diabetes (DM: n=3) and matched controls (n=3). RESULTS: Significant differential expression (fold change <0.3 or >3) was noted for 897 genes in DM vs. controls. The 147 known genes in this category belonged to following broad functional groups (%): enzyme (32), nucleic acid binding (22), ligand binding or carrier (10), signal transducer (9), transporter (7), structural protein (6), cell adhesion (3), tumor suppressor (3), transcription factor binding (2), enzyme inhibitor (2), chaperone (2), cell cycle regulator (1), and defense/immunity protein (1). The 20 genes with at least a 3-fold change, annotated with known phenotypic associations in the current gene databank (phenotype association, fold change) were aspartoacylase (Canavan disease, 9.96), growth hormone receptor (Laron dwarfism, idiopathic short stature, 8.25), lipoprotein lipase (familial chylomicronemia syndrome, lipoprotein lipase deficiency, 8.00), vitamin D (1,25- dihydroxyvitamin D3) receptor (involutional osteoporosis, vitamin D resistant rickets, 7.94), intercellular adhesion molecule 1 human rhinovirus receptor (cerebral malaria susceptibility, 7.16), peroxisomal membrane protein 3 35-kDa (Refsum disease, infantile form, Zellweger syndrome-3, 6.00), Bardet-Biedl syndrome 2 (Bardet-Biedl syndrome, 5.87), ribosomal protein S19 (Diamond Blackfan anemia, 5.85), apolipoprotein C-III (hypertriglyceridemia, 5.44), argininosuccinate lyase (argininosuccinicaciduria, 5.22), myosin VA (Griscelli syndrome-type pigmentary dilution with mental retardation, 4.92), lysozyme (renal amyloidosis, 4.17), SAM domain, SH3 domain and nuclear localisation signals 1 (Cherubism, 4.12 ), von Hippel-Lindau syndrome (hemangioblastoma, cerebellar, somatic, von Hippel-Lindau syndrome, 3.94), early-onset breast cancer 1 (BRCA1, papillary serous carcinoma of the peritoneum, 3.73), UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase (inclusion body myopathy, autosomal recessive, sialuria, 3.53), apolipoprotein A-I (amyloidosis, 3 or more types, hypoalphalipoproteinemia, 3.29), midline 1 Opitz/BBB syndrome (Opitz G syndrome, type I, 3.28), ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide (familial hemiplegic migraine, 3.05). Canavan disease, Zellweger syndrome, infantile Refsum disease, Griscelli syndrome, cherubism, breast cancer, peritoneal papillary serous carcinoma, Opitz G/BBB syndrome, and familial hemiplegic migraine (FHM) are phenotypes not previously reported in association with type 2 DM, but whose underlying genes were up-regulated in this peripheral genome scan of Asian Indians. CONCLUSION: Rare and/or previously unknown phenotypes linked to known genes with significant differential expression in type 2 DM are reported. Further testing of heterogeneity in diabetes phenotype syndromes may reveal common pathogenic mechanisms and potential candidate genes responsible for type 2 DM.

Asian People↗
PubMed2004

Integrative bioinformatics for functional genome annotation: trawling for G protein-coupled receptors.

G protein-coupled receptors (GPCR) are amongst the best studied and most functionally diverse types of cell-surface protein. The importance of GPCRs as mediates or cell function and organismal developmental underlies their involvement in key physiological roles and their prominence as targets for pharmacological therapeutics. In this review, we highlight the requirement for integrated protocols which underline the different perspectives offered by different sequence analysis methods. BLAST and FastA offer broad brush strokes. Motif-based search methods add the fine detail. Structural modelling offers another perspective which allows us to elucidate the physicochemical properties that underlie ligand binding. Together, these different views provide a more informative and a more detailed picture of GPCR structure and function. Many GPCRs remain orphan receptors with no identified ligand, yet as computer-driven functional genomics starts to elaborate their functions, a new understanding of their roles in cell and developmental biology will follow.

Algorithms↗