• It is one of the several genes that appeared in the search in expressed sequence tag (EST) databases of mouse. (wikipedia.org)
  • Regulation of these oocyte-specific genes is thru direct binding of NOBOX to its promoter regions via the specific consensus sequences, the NOBOX DNA binding elements (NBEs). (wikipedia.org)
  • In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. (nih.gov)
  • These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
  • HomB protein contributes to the colonization and persistence of H. pylori , and the presence of homB genes affects the number of bacteria adhering to the host cells. (nature.com)
  • With 35,000 genes and hundreds of thousands of protein states to identify, correlate, and understand, it no longer suffices to rely on studies of one gene, gene product, or process at a time. (genomicglossaries.com)
  • using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. (biomedcentral.com)
  • Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (biomedcentral.com)
  • Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
  • The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
  • The genomes of the pediococcal strains were sequenced and searched for genes encoding aminotransferases to test the hypothesis that AABA could result from the transamination of α-ketobutyrate. (springeropen.com)
  • The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. (biomedcentral.com)
  • Targeted integration by homologous recombination enables in-situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum . (umontreal.ca)
  • Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5′ UTRs. (biomedcentral.com)
  • Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions. (biomedcentral.com)
  • In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. (frontiersin.org)
  • As orthologous genes are commonly mutated in canine models of human blinding disorders, canine ABCA4 appears to be an ideal candidate gene to identify and study sequence changes in dogs affected by various forms of inherited retinal degeneration. (upenn.edu)
  • In-silico prediction and functional analysis of salt stress responsive genes in Rice (Oryza sativa), J Rice Res 4: 164. (cabgrid.res.in)
  • Neoantigens expressed from genes with mutations acquired during carcinogenesis may be tumor-specific and thus can be potential targets for personalized neoantigen-based immunotherapy. (genominfo.org)
  • It is well known that bar-code (tag) microarrays of yeast gene-deletion collections allow the systematic identification of genes required for growth in any condition of interest. (genominfo.org)
  • Quantitative PCR and high-throughput methods, such as expressed sequence tag analysis, have been used for measuring gene expression and identifying subsets of elm genes that are differentially expressed in the presence of O. novo-ulmi . (sisef.it)
  • These analyses have also helped identify genes that were differentially expressed in DED fungi grown under defined experimental conditions. (sisef.it)
  • Genes adjacent to pvtramp were identified in silico to determine the degree of similarity between the protein sequences encoded by equivalent chromosomic fragments in P. falciparum and Plasmodium knowlesi . (biomedcentral.com)
  • For all significantly differentially expressed microRNAs inside of the 2 groups, we now have produced gene sets from their expressed target genes. (pdpksignaling.com)
  • Through the comparison of NB or PCC groups with all the investigated 54 usual tissues and tumor kinds, we've got recognized 36 genes appreciably differentially expressed in in excess of 80% of comparisons. (pdpksignaling.com)
  • B, solute carrier relatives six member 2, solute carrier relatives 18 member one, and transcription factors and homeobox genes involved in neural crest derived cell de velopment, paired like homeobox 2a and 2b, GATA binding protein two and 3, heart and neural crest derivatives expressed two. (pdpksignaling.com)
  • A protein-protein interaction network was constructed based on the Search Tool for the retrieval of Interacting Genes/Proteins. (lncrnablog.com)
  • Transcription factors (TFs) of differentially expressed genes were identified based on TRANSFAC database and then a regulatory network was constructed. (lncrnablog.com)
  • Moreover, 2 TFs including FOS and EGR were identified to be involved in the regulatory network of the differentially expressed genes-TFs in periodontitis. (lncrnablog.com)
  • The presence of a stop codon in exon 13 generates two families of Sec31B gene products (each displaying additional patterns of mRNA splicing): a group of full-length proteins (hereafter referred to as Sec31B-F) and also a group of truncated proteins (hereafter referred to as Sec31B-T), distinguished by their utilization of exon 13. (biologists.com)
  • Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. (biomedcentral.com)
  • In addition, these studies provide useful information about expression abundance at the mRNA and protein levels, allowing further investigations into the molecular mechanisms of translational control in this evolutionarily divergent protist. (biomedcentral.com)
  • Translation efficiency (TE) reflects the rate of protein production per mRNA transcript in a given cellular context [ 6 ]. (biomedcentral.com)
  • On one hand, codon redundancy (i.e. that 61 codons specify 20 amino acids [ 21 ]) potentially allows a wide variety of mRNA sequences carrying different codons to specify the same protein product. (biomedcentral.com)
  • These small non-coding RNAs derived from their precursor sequences, bind to their target mRNAs and negatively mediate the gene expressions in pre-transcriptional or post-transcriptional stages by impeding mRNA translation [ 12 , 13 ]. (springeropen.com)
  • The reverse activity transcribes the ZAR2 mRNA with 966 nt coding sequence which codes for a 321 amino acid protein. (biomedcentral.com)
  • Gene sets established both by in silico examination of mRNA expres sion, GSEA of microRNA and comparative genomic hybridization gene sets have been subjected to IPA and considerable pathways were in contrast to each other. (pdpksignaling.com)
  • This bioinformatic study aims to construct a putative competing endogenous RNA (ceRNA) network by integrating lncRNA, miRNA and mRNA expression, based on high-throughput RNA sequencing and microarray data about periodontitis. (lncrnablog.com)
  • To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. (bvsalud.org)
  • In 2006, the Joint Genome Institute completed low coverage survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi species. (biomedcentral.com)
  • Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
  • The small genomes of the DED fungi also facilitate genomic analyses. (sisef.it)
  • Standard techniques like cell synchronization by serum starvation, flow cytometry, N-terminal or C-terminal FLAG epitope-tagged protein expression, immunofluorescence confocal microscopy, dual luciferase assay for promoter evaluation, and chromatin immunoprecipitation assay were employed during this study. (biomedcentral.com)
  • In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. (bvsalud.org)
  • Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera . (biomedcentral.com)
  • During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. (biomedcentral.com)
  • Participated a training programme on Next Generation Sequencing: Data Analysis & Annotation during 12th - 16th March, 2013 at IISR, Calicut, India. (cabgrid.res.in)
  • Analysis and Functional Annotation of Expressed Sequence Tags of Water Buffalo. (cabgrid.res.in)
  • We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. (biomedcentral.com)
  • We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. (biomedcentral.com)
  • Accurate annotation has traditionally been maintained manually with the experience of individual experts and the experimental characterisation of sequences. (biomedcentral.com)
  • Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
  • To investigate the complexity of alternative splicing in the retina, we sequenced and analyzed a total of 115,706 clones from normalized cDNA libraries from mouse neural retina (66,217) and rat retinal pigmented epithelium (49,489). (bvsalud.org)
  • In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)
  • A model is proposed where the relative levels of active antagonist (RsbV1) and switch-protein anti-sigma factor (RsbW) control the availability of σ 66 and subsequently act as a molecular 'throttle' for Chlamydia growth and development. (plos.org)
  • The development of next-generation sequencing methods and related molecular tools has greatly increased the pace of virus discovery ( 1 , 2 ), and these methods have become widely used for the investigation of novel zoonotic infections. (cdc.gov)
  • When available, the information provided by whole-genome sequencing projects provides an entry into an understanding of genome structure and evolution and gene discovery, and function. (biomedcentral.com)
  • Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. (springeropen.com)
  • Participated a training programme on Statistical Approaches for Genomic Data Analysis , during 7th - 19th January, 2013 at IASRI, New Delhi, India. (cabgrid.res.in)
  • However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. (nih.gov)
  • The importance of this plant species to agriculture has made the development of genomic resources a high priority. (biomedcentral.com)
  • The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. (researchgate.net)
  • As a consequence, the frequent use of codons matching common (i.e. 'preferred codons') or rare aminoacyl-tRNA species can lead to different levels of protein production, as delays or pauses in translation are likely to occur at rare codon sites. (biomedcentral.com)
  • Phylogenetic Analysis and Secondary Structure Prediction for Drought Tolerant Cap Binding Proteins in Plant Species. (cabgrid.res.in)
  • In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. (biomedcentral.com)
  • Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (biomedcentral.com)
  • We used metagenomic sequence libraries for retrospective screening of plasma samples for the recently discovered human hepegivirus 1 (HHpgV-1). (cdc.gov)
  • Following the example of the previous use of metagenomic libraries to detect human pathogens ( 7 - 9 ), we developed a bioinformatics-based method to screen existing libraries for HHpgV-1 and HPgV sequences from previously tested persons in the United Kingdom, enabling viremia frequencies in different risk groups to be estimated. (cdc.gov)
  • Samples used to generate libraries with and without HHpgV-1 sequences were retrieved and used to validate the specificity and sensitivity of a newly developed reverse transcription PCR (RT-PCR)-based method for sample screening. (cdc.gov)
  • Moreover, PRIN2 and CSP41b form a distinct protein complex in vitro that binds DNA. (frontiersin.org)
  • The subunits are held together and connected to the underlying cell surface by non-covalent interactions, and they spontaneously reassemble in vitro by an entropy-driven process, i.e. the subunit proteins are very poorly water-soluble [ 8 ]. (biomedcentral.com)
  • Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
  • In vitro analysis revealed that a putative switch-protein kinase regulator, RsbW, is capable of interacting directly with σ 66 , as well as phosphorylating its own antagonist, RsbV1, rendering it inactive. (plos.org)
  • In vitro, the recombinant tagged viruses exhibited morphologies, plaque, and growth kinetics similar to the parental BTV-16, and expressed both VP2 and HA tag. (morulaivf.com)
  • Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. (biomedcentral.com)
  • The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. (biomedcentral.com)
  • The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). (biomedcentral.com)
  • Expression of the canine gene transcripts and protein was analyzed by Northern and Western blotting and immunocytochemistry. (upenn.edu)
  • Ehwa Womans University, Korea) presented a bioinformatics tool, FusionScan for predicting fusion transcripts from RNA-sequencing (RNA-Seq) data. (genominfo.org)
  • Using NcGRA17-BirA* fusion protein as bait, we have identified some known GRAs and verified localization of 11 novel GRA proteins by gene endogenous tagging or overexpression in the Nc1 strain. (biomedcentral.com)
  • A number of these targets were confirmed by gene overexpression or endogenous tagging in the Nc1 strain, thereby validating our approach. (biomedcentral.com)
  • The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
  • We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean ( Glycine max L. Merr. (biomedcentral.com)
  • EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available. (springeropen.com)
  • We demonstrated adhesive and significant pathogen inhibitory efficacies among the swine intestinal L. amylovorus strains studied, pointing to their potential use as probiotic feed supplements, but no independent role could be demonstrated for the major S-layer proteins in adherence to epithelial cells. (biomedcentral.com)
  • We describe the functional analysis methods for HA, including the expression of recombinant proteins, binding to glycoproteins and epithelial cells, and localization in mouse intestinal tissue. (morulaivf.com)
  • When expressed as a fusion protein with eYFP in cultured cells, Sec31B-F associates with the endoplasmic reticulum and with vesicular-tubular clusters, displays restricted intracellular movement characteristic of COPII vesicle dynamics, co-distributes on organelles with Sec13, Sec31A and Sec23 (markers of the COPII coat), and concentrates with ts045-VSV-G-CFP (VSV-G) when examined early in the secretory pathway or after temperature or nocodazole inhibition. (biologists.com)
  • The gene was cloned and its gene product was produced as a His-tagged fusion protein in Escherichia coli to determine the substrate specificity of this enzyme. (springeropen.com)
  • Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. (biomedcentral.com)
  • When the background expectation is similarity, how does one use low coverage genome sequencing to detect that which makes organisms distinct? (biomedcentral.com)
  • All six members of this family exhibit a high sequence similarity in their C-terminal DNA binding domain and a more diverge regulatory N-terminus [ 1 , 2 ]. (biomedcentral.com)
  • Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. (elifesciences.org)
  • Detection of HHpgV-1 and HPgV was concordant with parallel PCR-based screening using conserved primers matching groups 1 (HPgV) and 2 (HHPgV-1) nonstructural 3 region sequences. (cdc.gov)
  • The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. (biomedcentral.com)
  • In contrast to expectations, none of the major S-layer proteins of the IPEC-1 -adhering strains mediated bacterial adherence. (biomedcentral.com)
  • They are composed of numerous identical (glyco)protein subunits (with a 25-71 kDa size in lactobacilli), which form a regular, symmetric and porous array, completely covering the bacterial cell surface. (biomedcentral.com)
  • Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
  • Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent. (biomedcentral.com)
  • MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. (uni-bielefeld.de)
  • However, the increasing gap between the amount of sequence data available and the time needed for their experimental characterisation demands computational function prediction in complementing manual curation [ 1 - 4 ]. (biomedcentral.com)
  • A collection of different allotypes or allelic protein variants, a new type of protein library. (genomicglossaries.com)
  • The Web site "www.artichokegenome.unito.it" hosts all the available genomic sequences, together with their structural/functional annotations and project information are presented to users via the open-source tool JBrowse, allowing the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for Cynara cardunculus genomics. (researchgate.net)
  • Multiple alternatively spliced transcript variants have been found for this protein. (cancerindex.org)
  • Here, we report computational and comparative analyses of survey sequence data to address the question of diversity. (biomedcentral.com)
  • Our sequence analysis of the complete canine ABCA4 coding region will clearly provide a baseline and tools for future association studies and comparative genomics to further delineate the role of ABCA4 in canine blinding disorders. (upenn.edu)
  • Immunocytochemistry of normal canine retina demonstrated specific localization of protein to the RPE basolateral plasma membranes. (upenn.edu)
  • In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. (nature.com)
  • The purified recombinant protein showed aminotransferase activity at pH 5.5. (springeropen.com)
  • to rescue four recombinant viruses in which HA (influenza hemagglutinin) tags were inserted at different sites of VP2. (morulaivf.com)
  • Subsequently, the selected recombinant tagged viruses were prepared as inactivated vaccines to immunize IFNAR(-/-) mice and sheep, and serological detection results of an anti-HA antibody provided discriminative detection. (morulaivf.com)
  • In summary, we used plasmid-based RGS to rescue BTV recombinant viruses with HA tags inserted into VP2, and detected several sites on VP2 that can accommodate HA tags. (morulaivf.com)
  • Some of the recombinant tagged viruses have potential to be developed into distinctive inactivated vaccines. (morulaivf.com)
  • In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. (nih.gov)
  • This gene encodes a protein with protease activity and is expressed in the placenta. (cancerindex.org)
  • The transcript is predominantly expressed in RPE/choroid and encodes bestrophin, a 580-amino acid protein of 66 kDa. (upenn.edu)
  • A variety of methods has been designed to annotate sequences on a large scale. (biomedcentral.com)
  • Rapid and comprehensive analysis of putative proteinous allergens ( allergenome ) by applying such a proteomic strategy … With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. (genomicglossaries.com)
  • The p53 interacting partner protein NUMB (homology of numb protein) preserves this intrinsic cellular asymmetry by preventing ubiquitin-mediated proteolysis of p53 catalyzed by the MDM2 E3 ubiquitin ligase 11 . (nature.com)
  • To date, most NcGRAs have been discovered individually by bioinformatics searches for proteins exhibiting homology to known Toxoplasma dense granule proteins (TgGRAs). (biomedcentral.com)
  • Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. (nih.gov)
  • We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
  • Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
  • In a series of degradation steps, the proteins are broken down into amino acids. (springeropen.com)
  • Thereby, lactic acid bacteria (LAB) play an important role as they use the free amino acids for energy production, regulation of the internal pH, regeneration of co-substrates, and protein biosynthesis (Ardö 2006 ). (springeropen.com)
  • TC can be estimated through an in silico method using the data from the effect sizes derived from genome-wide association studies and transcription level in RNA-seq to estimate TC. (genominfo.org)
  • This study provides evidence that a switch-protein kinase regulatory network controls availability of σ 66 , the main sigma subunit for transcription in Chlamydia . (plos.org)
  • CCAAT/enhancer-binding protein β (C/EBPβ), is a member of a family of transcription factors consisting of six structurally related basic leucine-zipper DNA-binding proteins. (biomedcentral.com)
  • Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. (nature.com)
  • Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (biomedcentral.com)
  • Music fly us yet look a Victorian download preservation which is topics that exist through process data of the Protein:( 15)where,, and. (lightseed.com)
  • The biotinylated proteins were affinity-purified for mass spectrometric analysis, and the candidate GRA proteins from BioID data set were identified by gene tagging. (biomedcentral.com)
  • They tested whether or not a new MGISEQ-2000 sequencer delivers the high-quality sequence data. (genominfo.org)
  • In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. (mpob.gov.my)
  • Cell-fate-determinant molecule NUMB-interacting protein (TBC1D15) is overexpressed and contributes to p53 degradation in TICs. (nature.com)
  • To modify the PV, the parasite secretes an array of proteins, including dense granule proteins (GRAs). (biomedcentral.com)
  • Inducing an interferon response enables IFN-γ-inducible immunity-related GTPase (IRG protein) to accumulate on the PV and to restrict parasite growth. (life-science-alliance.org)
  • Ongoing genome sequencing and recent developments in cDNA sequencing projects have led to an exponential rise in the amount of sequence information. (biomedcentral.com)
  • Nevertheless, in-silico analysis, we noted modulation of stability and motifs structure of Hemagglutinin (HA) antigen among the co-infecting H9N2 AI and the IBV and isolates from the diseased flocks. (morulaivf.com)
  • An increasing number of GO-mapped sequence databases make it possible to replace traditional database searches with GO-related searches. (biomedcentral.com)
  • The gene encoding PvTRAMP was identified through an extensive search of the databases hosting the genome sequence of P. vivax . (biomedcentral.com)
  • In 2013, the genome sequences of O. ulmi and O. novo-ulmi were publicly released. (sisef.it)