• Genomics
  • The quantity and variety of expressed EC genes identified in this study is sufficient to serve as a global transcriptome dataset for longan EC and to provide more molecular resources for longan functional genomics. (biomedcentral.com)
  • Many aspects of structural gene prediction are based on current understanding of underlying biochemical processes in the cell such as gene transcription, translation, protein-protein interactions and regulation processes, which are subject of active research in the various omics fields such as transcriptomics, proteomics, metabolomics, and more generally structural and functional genomics. (wikipedia.org)
  • 1997
  • A C. elegans genomic clone (F52B5.1) was identified when the Ambys-toma kidney NBC (aNBC) was used in a BLAST search against GenBank (Romero et al, Nature 387:409, 1997). (mcmaster.ca)
  • cDNA clones
  • The same thirty randomly selected cDNA clones encoding for proteins with specific functions associated with colonization were identified from each of the subtraction cDNA libraries. (beds.ac.uk)
  • kinase
  • Sequence and model comparison predict 3 potential, N-linked glycosylation sites and several putative, phospho-rylation sites (9 protein kinase C, 9 casein kinase II, and 3 protein kinase A). We subcloned this cDNA into a Xenopus expression vector, transcribed cRNA, and injected the RNA into oocytes for expression. (mcmaster.ca)
  • Right open reading frame protein kinase 2 (RIOK-2) is a member of the atypical kinase family and shown in other organisms to be responsible for ribosomal RNA biogenesis and cell-cycle progression, as well as involves in nematode development. (biomedcentral.com)
  • In silico analyses of the amino acid sequence of Sj -RIOK-2 revealed typical features of this class of kinases including a winged helix (wHTH) domain and a RIO kinase domain. (biomedcentral.com)
  • Detection of mutations in the mitogen-activated protein kinase pathway in human melanoma," Clin. (freepatentsonline.com)
  • Mitogen-activated protein kinase signaling is activated in prostate tumors but not mediated by B-RAF mutations," Eur Urol. (freepatentsonline.com)
  • In addition, myo- blasts were incubated with CHI3L1 protein and activation of MAP kinase signalling as well as proliferation was measured. (uio.no)
  • physiologic
  • These proteins mediate signals to the interior of the cell via activation of heterotrimeric G proteins that in turn activate various effector proteins, ultimately resulting in a physiologic response. (wikipedia.org)
  • RGD is working with groups such as the Programs for Genomic Applications at MCW and the National BioResource Project for the Rat (NBPR-Rat) in Japan to collect and make available comprehensive physiologic data for a variety of rat strains. (wikipedia.org)
  • They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse and human. (wikipedia.org)
  • membrane proteins
  • TRAM2 is a component of the translocon, a gated macromolecular channel that controls the posttranslational processing of nascent secretory and membrane proteins at the endoplasmic reticulum (ER) membrane. (wikipedia.org)
  • genetic
  • Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. (frontiersin.org)
  • Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. (frontiersin.org)
  • Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. (frontiersin.org)
  • Given a protein sequence, a family of possible coding DNA sequences can be derived by reverse translation of the genetic code. (wikipedia.org)
  • RGD began as a collaborative effort between leading research institutions involved in rat genetic and genomic research. (wikipedia.org)
  • Its goal, as stated in RFA: HL-99-013, was the establishment of a Rat Genome Database to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. (wikipedia.org)
  • In recent years, there has been a rapid increase in rat genetic and genomic data. (wikipedia.org)
  • encode
  • In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. (wikipedia.org)
  • The first and second each contain 7 exons and encode the same full-length protein isoform a (786 amino acids, considered the major isoform), the third one contains 6 exons and encodes a shorter isoform b (732 amino acids) and the fourth one contains 5 exons and encodes the shortest isoform c (349 amino acids). (wikipedia.org)
  • However, ETV6 is also an anti-oncogene or tumor suppressor gene in that mutations in it that encode for a truncated and therefore inactive protein are also associated with certain types of cancers. (wikipedia.org)
  • clones
  • Reverse transcriptase-polymerase chain reaction analysis on 10 individual ruptured and 10 individual stable plaques showed a striking consistency of expression for the clones SSH6, present in 8 ruptured and 2 stable plaques, and perilipin, expressed in 8 ruptured plaques and completely absent in stable plaques. (ahajournals.org)
  • Clones showing at least a 2-fold difference in expression were sequenced. (ahajournals.org)
  • We used the predicted protein in another BLAST search against the expressed se-quence tag (EST) database and identified several clones corresponding to the predicted protein. (mcmaster.ca)
  • EST sequences implied that all clones were likely part of the same cDNA, so we chose the largest clone for sequencing (yk41h3 or ceNBC). (mcmaster.ca)
  • The encoded protein is ~40% identical to the vertebrate NBC clones, indicating that along with NBCs and the anion exchangers (AE1-3), ceNBC belongs to the Bicarbonate Transporter Superfamily. (mcmaster.ca)
  • species
  • Reactive oxygen species (ROS), such as superoxide radical, hydroxyl radical and hydrogen peroxide, can damage cellular DNA, lipids and proteins (reviewed by Lesser, 2006 ). (biologists.org)
  • These resources were a key component leading to selection of cattle as a species for complete genome sequencing, which now has opened the door for much more detailed analysis of genome function and evolution among mammals. (usda.gov)
  • Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. (wikipedia.org)
  • In addition, protein or translated sequence queries are more effective for identifying distant matches and for cross-species analysis than DNA sequence queries. (wikipedia.org)
  • human
  • In this study, we used suppression subtractive hybridization to make an inventory of genes that are differentially expressed in whole-mount human stable and ruptured plaques. (ahajournals.org)
  • We identified several genes that were differentially expressed in a larger panel of individual ruptured and stable human atherosclerotic plaques. (ahajournals.org)
  • Despite their pathogenic properties, helminth proteins have potential to be co-opted to treat a number of other human diseases. (wikipedia.org)
  • Given the modulatory properties of helminth proteins, it has been suggested that they may be co-opted to successfully treat other human diseases, particularly those associated with auto-immunity disorders. (wikipedia.org)
  • Insulin-like growth factor binding protein-related protein 1 (IGFBP-rP1) has potential tumour-suppressive activity in human lung cancer," J. Pathol. (freepatentsonline.com)
  • The exercise-regulated myokine chitinase-3-like protein 1 stimulates human myocyte proliferation. (uio.no)
  • Incubation of cultured human myoblasts with CHI3L1 protein leads to a strong activation of p44/42, p38 MAPK and Akt as well as enhanced myoblast proliferation. (uio.no)
  • For example, some human genes may be expressed only during development as an embryo or fetus, which might be difficult to study for ethical reasons. (wikipedia.org)
  • JMJD1B protein, human at the US National Library of Medicine Medical Subject Headings (MeSH) This article incorporates text from the United States National Library of Medicine, which is in the public domain. (wikipedia.org)
  • BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. (wikipedia.org)
  • It was designed primarily to decrease the time needed to align millions of mouse genomic reads and expressed sequence tags against the human genome sequence. (wikipedia.org)
  • Prediction of the coding sequences of unidentified human genes. (wikipedia.org)
  • similarity
  • Given a sequence, local alignment algorithms such as BLAST, FASTA and Smith-Waterman look for regions of similarity between the target sequence and possible candidate matches. (wikipedia.org)
  • A high degree of similarity to a known messenger RNA or protein product is strong evidence that a region of a target genome is a protein-coding gene. (wikipedia.org)
  • It is designed to work best on sequences with great similarity. (wikipedia.org)
  • Using a yeast two-hybrid approach, the CASS4 protein SH3 domain was shown to interact with the FAK C-terminus, despite the lowest overall similarity to other SH3 domains in the CAS group. (wikipedia.org)
  • Although this lack of sequence similarity may mean a reduced functionality of the CASS4 protein, molecular modeling analysis performed by Singh and colleagues using p130CAS/BCAR1 structures as templates suggested an almost identical fold between CASS4 and p130CAS/BCAR1 within their SH3 domains, and substantial similarity within 432-591 residues of CASS4 and 449-610 residues of p130Cas/BCAR1 at the level of secondary and tertiary structures. (wikipedia.org)
  • Differentiation
  • The protein encoded by this gene is involved in osteo- and chondrogenic cellular differentiation (the cells which are responsible for the development of bone and cartilage respectively). (wikipedia.org)
  • ETV6 interacts with other proteins that regulate the differentiation and growth of cells. (wikipedia.org)
  • genomes
  • Comparative analysis performed at the DNA sequence level has demonstrated that colinearity between the grass genomes is retained at the molecular level (microcolinearity) in most cases. (jove.com)
  • binds
  • This protein binds to IL18, prevents the binding of IL18 to its receptor, and thus inhibits IL18-induced IFN-gamma production. (wikipedia.org)
  • The protein binds to hemi-methylated DNA during S-phase and recruits the main DNA methyltransferase gene, DNMT1, to regulate chromatin structure and gene expression. (wikipedia.org)
  • It was concluded that capsulin heterodimerizes with E12 and binds the specific E-box consensus sequence (CANNTG), though not activating transcription through this sequence on its own. (wikipedia.org)
  • and c) the C-terminal DNA-binding domain, ETS, which binds to the consensus DNA sequence, 5-GGAA/T-3 within a 9-to-10 bp sequence, in the target genes it regulates. (wikipedia.org)
  • hybridization
  • Suppression subtractive hybridization (SSH) 13 on whole-mount specimens was used to make an inventory of genes differentially expressed in both lesion types. (ahajournals.org)
  • RNA in situ hybridization using 33P-labeled riboprobes was used to identify the cell types that expressed Pod-1 in the developing kidney and other tissues. (wikipedia.org)
  • Methylation of adenosine does not affect its ability to base-pair with thymidine or uracil, so N6-methyladenosine (m6A) cannot be detected using standard sequencing or hybridization methods. (wikipedia.org)
  • lipids
  • All three of these proteins are able to deliver lipids to acceptor membranes, but this transfer process in Ov-FAR-1 and ABA-1A1 (a type of NPA) requires an aqueous diffusion step. (wikipedia.org)
  • analysis
  • Phylogenetic analysis of cynS sequences retrieved from the Global Ocean Survey database identified >60% as belonging to unicellular marine cyanobacteria, suggesting an important role for cyanase in their nitrogen metabolism. (embl-heidelberg.de)
  • In the past 10 years research in my laboratory has focused on generation of genomic tools to enable analysis of genome function and facilitate detection of naturally occurring variation in livestock affecting a variety of functions with impact on food animal production. (usda.gov)
  • The chromosomal location of Pod-1 in the mouse was then determined using an interspecific backcross panel along with genomic southern blot analysis to identify restriction fragment length polymorphisms (RFLPs) between inbred mouse strains. (wikipedia.org)
  • In epitranscriptomic sequencing, most methods focus on either (1) enrichment and purification of the modified RNA molecules before running on the RNA sequencer, or (2) improving or modifying bioinformatics analysis pipelines to call the modification peaks. (wikipedia.org)
  • assays
  • Antioxidant enzymes, particularly SODs and catalase, have been identified in several cnidarians through catalytic assays, antibody-based detection of proteins and/or cloning of the corresponding genes. (biologists.org)
  • Predicting the function of a gene and confirming that the gene prediction is accurate still demands in vivo experimentation through gene knockout and other assays, although frontiers of bioinformatics research[citation needed] are making it increasingly possible to predict the function of a gene based on its sequence alone. (wikipedia.org)
  • Capsulin was translated in a rabbit reticulocyte lysate in the presence and absence of the widely expressed bHLH protein E12 and performed gel mobility shift assays with several E-box sequences as probes to test the protein's DNA binding activity. (wikipedia.org)
  • Luciferase reporter assays with constructs covering CGI3 sequences in sense and antisense orientation demonstrated that CGI3 harbors a promoter that directs the synthesis of a previously unknown long non-coding RNAs (lncRNAs) in antisense orientation to TCF21. (wikipedia.org)
  • transcription
  • Gene prediction is closely related to the so-called 'target search problem' investigating how DNA-binding proteins (transcription factors) locate specific binding sites within the genome. (wikipedia.org)
  • Transcription factor 21 (TCF21), also known as pod-1, capsulin, or epicardin, is a protein that in humans is encoded by the TCF21 gene on chromosome 1. (wikipedia.org)
  • ETV6 (i.e. translocation-Ets-leukemia virus) protein is a transcription factor that in humans is encoded by the ETV6 (previously known as TEL) gene. (wikipedia.org)
  • strains
  • The cynS gene that encodes cyanase was identified among bacterial, fungal, and plant sequences in public databases, and the gene was particularly prevalent among cyanobacteria, including numerous Prochlorococcus and Synechococcus strains. (embl-heidelberg.de)
  • We demonstrate here that marine cyanobacteria have a functionally active cyanase, the transcriptional regulation of which varies among strains and reflects the genomic context of cynS. (embl-heidelberg.de)
  • For congenic and mutant strains, genomic positions are assigned for the introgressed region (congenic strains) or the location of the mutated sequence (mutant strains). (wikipedia.org)
  • QTLs
  • Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. (frontiersin.org)
  • regulation
  • Pod-1 was the first tissue-restricted bHLH protein to be identified in the developing kidney and tied to regulation of morphogenetic events. (wikipedia.org)
  • Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. (wikipedia.org)
  • Organisms
  • Not only is this expensive, but in complex organisms, only a subset of all genes in the organism's genome are expressed at any given time, meaning that extrinsic evidence for many genes is not readily accessible in any single cell culture. (wikipedia.org)
  • epithelial
  • Results showed that in humans and mice, Pod-1 was most highly expressed in the kidney, lung and heart, with selective expression at sites of epithelial-mesenchymal interaction in the kidney, lung, intestine and pancreas of developing mouse embryos. (wikipedia.org)
  • Additionally
  • Additionally, the database can also be used to develop protein targets for new drugs to treat helminth infections. (wikipedia.org)
  • Additionally, injection of proteins secreted by Fasciola hepatica in nonobese diabetic mice prevented the onset of type I diabetes, with 84% of the mice showing normal glucose levels 26 weeks after injection. (wikipedia.org)
  • reads
  • Since the RNA strands are randomly chopped up, the m6A site should, in principle, lie somewhere in the center of the regions to which sequence reads align. (wikipedia.org)
  • database
  • The success of this approach is limited by the contents and accuracy of the sequence database. (wikipedia.org)
  • BLAT is used to find regions in a target genomic database which are similar to a query sequence under examination. (wikipedia.org)
  • The general algorithmic process followed by BLAT is similar to BLAST's in that it first searches for short segments in the database and query sequences which have a certain number of matching elements. (wikipedia.org)
  • It does this by keeping an indexed list (hash table) of the target database in memory, which significantly reduces the time required for the comparison of the query sequences with the target database. (wikipedia.org)
  • BLAT then builds a list of all overlapping k-mers from the query sequence and searches for these in the target database, building up a list of hits where there are matches between the sequences (Figure 1 illustrates this process). (wikipedia.org)
  • Additional protein-related data is imported from the UniProtKB database. (wikipedia.org)
  • molecular
  • Progress in understanding molecular mechanisms of longan embryogenesis, which is the primary influence on fruit quality and yield, is slowed by lack of transcriptomic and genomic information. (biomedcentral.com)