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  • encode
  • A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions. (wikipedia.org)
  • Gene transcripts that encode 30 proteins important in the detection of semiochemicals, including sex pheromones, were identified and characterized. (usda.gov)
  • This work provides a source of DNA sequences and the proteins that they encode which are important in the detection of semiochemicals such as pheromones. (usda.gov)
  • The human and the murine GPR84 ORFs both encode proteins of 396 amino acid residues length with 85% identity and are therefore considered as orthologs. (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)
  • tandem mass spectro
  • Coding sequences for 16 of the inhibitors were unequivocally associated with specific proteins identified by tandem mass spectrometry (MS/MS) in a previous proteomic analysis of milled white flour from Butte 86. (biomedcentral.com)
  • Our laboratory has previously characterized the proteomes of conditioned media (CM) from 44 cancer cell lines, three near normal cell lines and 11 relevant biological fluids (for example, pancreatic juice and ascites) using multidimensional liquid chromatography tandem mass spectrometry, identifying between 1,000 and 4,000 proteins per cancer site [ 22 - 33 ] (unpublished work). (biomedcentral.com)
  • secretory
  • 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)
  • Genomic
  • Genomic tools (e.g., whole genome sequencing and SNP genotyping arrays) can rapidly provide insight in species whose genetics have been historically under-studied. (biomedcentral.com)
  • Here, we devise a phylogenomic falsification of the chromalveolate hypothesis that estimates signal strength across the three genomic compartments: If the four chlorophyll c-containing lineages indeed derive from a single photosynthetic ancestor, then similar amounts of plastid, mitochondrial, and nuclear sequences should allow to recover their monophyly. (jove.com)
  • Given an mRNA sequence, it is trivial to derive a unique genomic DNA sequence from which it had to have been transcribed. (wikipedia.org)
  • cDNA library
  • More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. (biomedcentral.com)
  • In 1979 teams at Harvard and Caltech extended the basic idea of making DNA copies of mRNAs in vitro to amplifying a library of such in bacterial plasmids In 1982, the idea of selecting random or semi-random clones from such a cDNA library for sequencing was explored by Greg Sutcliffe and coworkers. (wikipedia.org)
  • orthologs
  • Characteristics of the experimentally identified lumenal proteins and their orthologs were used for a genome-wide prediction of the lumenal proteome. (plantcell.org)
  • Although there are few eukaryote [FeFe]-H(2)ase maturase orthologs characterized, phylogenies of these proteins do recover eukaryote monophyly, although a consistent eubacterial sister group for eukaryotic homologs could not be determined. (jove.com)
  • The list of proteins below is not a comprehensive listing of UPF0762 orthologs. (wikipedia.org)
  • tissues
  • The immunoblot analyses with antisera raised against recombinant SguaOBP1, OBP2, and CSP1, respectively, indicate that two SguaOBPs are specific to antennae, whereas SguaCSP1, which are more abundant than OBPs and detected in both male and female wasps, expresses ubiquitously across different tissues. (ijbs.com)
  • Researchers at the USDA-ARS Yakima Agricultural Research Laboratory (Wapato, WA) and Corn Insect and Crop Genetics Research Unit (Ames,IA), and Washington State University (Pullman, WA) have used next generation sequencing to determine gene expression in various codling moth tissues that respond to semiochemicals. (usda.gov)
  • Cumulatively, the CASS4 transcripts are most highly expressed in spleen and lung among normal tissues, and are highly expressed in ovarian and leukemia cell lines. (wikipedia.org)
  • Genomics
  • We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. (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)
  • orthologous
  • DUF781, which is the singular identifiable domain in UPF0762, is tied to liver development in an orthologous protein in zebrafish. (wikipedia.org)
  • UPF0762 shows high homology in primates and orthologous proteins can be traced back as far as trichoplax adhaerens. (wikipedia.org)
  • molecular
  • Wheat grains accumulate a variety of low molecular weight proteins that are inhibitors of alpha-amylases and proteases and play an important protective role in the grain. (biomedcentral.com)
  • Wheat kernels accumulate a variety of low molecular weight proteins that inhibit amylases and/or proteases from different sources. (biomedcentral.com)
  • This protein has a calculated molecular mass of 47.219kDa. (biochemj.org)
  • In molecular biology, the protein domain SUI1 is a translation initiation factor often found in the fungus, Saccharomyces cerevisiae (Baker's yeast) but it is also found in other eukaryotes and prokaryotes as well as archaea. (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)
  • receptor
  • Three transcription units were identified within the candidate interval, including Toll-like receptor 4 ( Tlr4 ), part of a protein family with members that have been implicated in LPS-induced cell signaling. (rupress.org)
  • Probable G-protein coupled receptor 160 is a protein that in humans is encoded by the GPR160 gene. (wikipedia.org)
  • In their papers they described the sequence and expression profile of five new members of GPC receptor family. (wikipedia.org)
  • The product of this gene, P2Y14 belongs to the family of G-protein coupled receptors, which contains several receptor subtypes with different pharmacological selectivity for various adenosine and uridine nucleotides. (wikipedia.org)
  • This receptor is a P2Y purinergic receptor for UDP-glucose and other UDP-sugars coupled to G-proteins. (wikipedia.org)
  • Succinate receptor 1 is a protein that in humans is encoded by the SUCNR1 gene. (wikipedia.org)
  • specific proteins
  • The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics. (biomedcentral.com)
  • We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies. (biomedcentral.com)
  • We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. (biomedcentral.com)
  • Despite the presence of a universal core import mechanism, there are specific proteins found only in a few groups of organisms. (jove.com)
  • translocation
  • It was identified in 1996 through positional cloning of the reciprocal chromosomal t(8;16)(p11;p13) translocation with CREB-binding protein (CBP) associated with a subset of acute myeloid leukemia (AML) (Borrow et al. (springer.com)
  • Lumenal proteins with a typical twin-arginine translocation motif were predicted with good accuracy and sensitivity and included additional isomerases and proteases. (plantcell.org)
  • transiently expressed
  • When transiently expressed, MyoB, MyoC, as well as the common motor domain lacking the tail did not distribute evenly between daughter cells, suggesting some impairment in proper segregation. (rupress.org)
  • Soluble
  • Calvello M, Guerra N, Brandazza A et al (2003) Soluble proteins of chemical communication in the social wasp Polistes dominulus . (springer.com)
  • Soluble thylakoid proteins were separated by two-dimensional electrophoresis and identified by mass spectrometry. (plantcell.org)
  • gene expression
  • Importantly, the sequenced genome also makes it possible to take advantage of the dramatic improvements in biological mass spectrometry to study gene expression directly at the protein level and to determine protein localization and post-translational modifications efficiently in a systematic manner. (plantcell.org)
  • ORFs
  • Long ORFs are often used, along with other evidence, to initially identify candidate protein-coding regions or functional RNA -coding regions in a DNA sequence. (wikipedia.org)
  • On the other hand, it has been proven that some short ORFs (sORFs) that lack the classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides. (wikipedia.org)
  • The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, and provides their locations in the sequence. (wikipedia.org)
  • identification
  • Detailed study of the merozoite stage will support the identification of proteins important to key biological processes in the parasite including host invasion, replication, pathogenicity and the stimulation of host immunity. (biomedcentral.com)
  • Identification of a human histone acetyltransferase related to monocytic leukemia zinc finger protein. (springer.com)
  • The improved mass accuracy, mass resolution, and sensitivity of the latest generation of mass spectrometers allow the rapid identification of picomole to femtomole amounts of proteins and peptides. (plantcell.org)
  • Previous studies have focused on either gene or protein expression databases for the identification of candidates. (biomedcentral.com)
  • Prolactin-induced protein has also been used for identification and detection of disseminated breast cancer cells. (wikipedia.org)
  • helminth
  • A helminth protein, or helminthic antigen, is a protein derived from a parasitic worm that causes an immune reaction. (wikipedia.org)
  • Helminth proteins can result in a deregulated response to infection, and are implicated in reduced reactivity to other antigens. (wikipedia.org)
  • Other helminth proteins promote parasite survival in other ways, particularly since parasites must depend on hosts for the supply of essential nutrients. (wikipedia.org)
  • Despite their pathogenic properties, helminth proteins have potential to be co-opted to treat a number of other human diseases. (wikipedia.org)
  • Helminth proteins modulate the immune response of their hosts, but do not suppress it entirely. (wikipedia.org)
  • Additionally, the database can also be used to develop protein targets for new drugs to treat helminth infections. (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)
  • antigens
  • results have recently been obtained using membrane-spanning protein antigens from the tegument of Schistosoma mansoni . (labome.org)
  • complementation
  • Using a combination of bioinformatics, genetic complementation, and immunofluorescence microscopy analyses, we demonstrate that this protein functions as a typical Tom70 in Blastocystis mitochondrion-related organelles. (jove.com)
  • partial
  • Once candidate DNA sequences have been determined, it is a relatively straightforward algorithmic problem to efficiently search a target genome for matches, complete or partial, and exact or inexact. (wikipedia.org)
  • evolutionary
  • The presence of Tom70 in these lineages significantly expands the evolutionary spectrum of eukaryotes that contain this protein and suggests that it may have been part of the core mitochondrial protein import apparatus of the last common ancestral eukaryote. (jove.com)
  • SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii. (wikipedia.org)
  • Evolutionary divergence of the CAS proteins family members is discussed by Singh et al. (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)
  • in 2008 following in silico screening of databases describing expressed sequence tags from an evolutionarily diverse group of organisms, using the CAS-related proteins (p130Cas, NEDD9/HEF1 and EFS) mRNAs as templates. (wikipedia.org)
  • chromosome
  • Hgpr84 locates to chromosome 12q13.13, and its coding sequence is not interrupted by introns. (wikipedia.org)
  • The protein encoded by this gene forms a heterotrimeric motor complex with kinesin family member 3A and KAP3 (kinesin accessory protein 3) to drive intra-flagellar transport and possibly to aid in chromosome movement during mitosis and meiosis. (wikipedia.org)
  • similarity
  • Sequence identity and similarity were determined using BLAST with the reference human sequence as the query. (wikipedia.org)
  • 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)
  • Amino acid sequence homology of this isoform of human CASS4 with other family members is 26% overall identity and 42% 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)
  • The CASS4 C-terminus has a short region of CAS family homology, but lacks obvious similarity at the level of primary amino acid sequence. (wikipedia.org)
  • motif
  • Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. (biomedcentral.com)
  • CAS proteins have an amino terminal SH3 domain enabling interaction with poly-proline motif-containing proteins such as FAK. (wikipedia.org)
  • It also lacks a YDYVHL sequence at the N-terminal end of the FAT-like carboxy-terminal domain, even though this motif is conserved among the other three CAS family proteins and is an important binding site for the Src SH2 domain. (wikipedia.org)
  • peptides
  • At 20 h after induction with 12.5 ng/mL of inducing peptide in MRS media containing 20 g/L glucose, the yields and secretion efficiencies of the proteins with their native signal peptides were 50 kU/L and 84 % for ManB, and 79 kU/L and 56 % for CsnA, respectively. (biomedcentral.com)
  • precursor
  • In both invertebrates and mammals, Numb is localized using the Pins/GαI complex and the PAR complex of Bazooka (Par3 in mammals), Par6, and aPKC (atypical protein kinase C). In the sensory organ precursor (SOP) cell, the PAR proteins localize to the posterior pole of the cell, and the Pins/GαI complex is localized to the anterior pole of the cell. (wikipedia.org)
  • Enzymes
  • For comparative purposes, these enzymes were overproduced in three forms: with no signal peptide, with their native ( Bacillus ) signal peptide, and with a signal peptide derived from the Escherichia coli OmpA protein. (biomedcentral.com)
  • Protein folding steps involve a range of enzymes and molecular chaperones to coordinate and regulate reactions, in addition to a range of substrates required in order for the reactions to take place. (wikipedia.org)
  • Favoured by the highly oxidizing environment of the ER, protein disulfide isomerases facilitate formation of disulfide bonds, which confer structural stability to the protein in order for it to withstand adverse conditions such as extremes of pH and degradative enzymes. (wikipedia.org)
  • lysate
  • ab94065 is a 293T cell transfected lysate in which Human IKK beta has been transiently over-expressed using a pCMV-IKK beta plasmid. (abcam.com)
  • polymerase
  • They require RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid as template There has long been uncertainty over how viroids induce symptoms in plants without encoding any protein products within their sequences. (wikipedia.org)
  • mutations
  • this technique is able to establish point mutations, gene deletions, and short sequence insertions in several genomic loci with increased efficiency and time sensitivity. (wikipedia.org)
  • novel
  • Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. (embopress.org)
  • In this study, we developed and applied a novel method utilizing biochemistry, quantitative proteomics and computational approaches in order to characterize the organization of proteins in a complex. (embopress.org)
  • interacts
  • MoaD, which is involved in molybdenum cofactor biosynthesis, interacts with MoeB, which acts like an E1 ubiquitin-activating enzyme for MoaD, strengthening the link between these prokaryotic proteins and the ubiquitin system. (wikipedia.org)
  • cellular
  • Determining the architectures of protein complexes improves our understanding of protein cellular functions. (embopress.org)
  • The traditional central dogma of biology states that the DNA of a cell is transcribed to RNA, which is translated to proteins, which perform cellular processes and functions. (wikipedia.org)
  • With Diener's 1989 hypothesis that viroids may represent "living relics" from the widely assumed, ancient, and non-cellular RNA world--extant before the evolution of DNA or proteins--viroids have assumed significance beyond plant pathology to evolutionary science, by representing the most plausible RNAs capable of performing crucial steps in abiogenesis, the evolution of life from inanimate matter. (wikipedia.org)
  • The unfolded protein response (UPR) is a cellular stress response related to the endoplasmic reticulum (ER) stress. (wikipedia.org)
  • purification
  • The key of our method is the systematic purification of several tagged components of the protein complex in multiple genetic deletion strains, which serve to compromise the integrity of the complex. (embopress.org)
  • binds
  • Binds to DNA in a sequence-independent manner. (abcam.com)
  • It is expressed on lymph node endothelia, whereas the L-selectin to which it binds is on the T cell. (wikipedia.org)
  • The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence independent manner and may anchor the U2 snRNP to the pre-mRNA. (wikipedia.org)
  • Another member of this protein family binds to microtubules. (wikipedia.org)
  • Molecular
  • In this scenario, the UPR has three aims: initially to restore normal function of the cell by halting protein translation, degrading misfolded proteins, and activating the signalling pathways that lead to increasing the production of molecular chaperones involved in protein folding. (wikipedia.org)
  • Mammals
  • The numb gene protein product controls binary cell fate decisions in the peripheral and central nervous systems of both invertebrates and mammals during neurogenesis. (wikipedia.org)
  • In mammals, there are four alternatively spliced forms of the Numb protein. (wikipedia.org)
  • Numb proteins in mammals are not as well understood as their fly counterparts. (wikipedia.org)
  • Regulatory
  • Regulatory proteins that bind to DNA, RNA, and/or proteins are key effectors in these processes and function by positively or negatively regulating specific protein level and function in a cell. (wikipedia.org)
  • Ubiquitin is a small (8.5 kDa) regulatory protein found in most tissues of eukaryotic organisms i.e. it occurs ubiquitously. (wikipedia.org)
  • plasmid
  • In addition, to avoid using antibiotics, the erythromycin resistance gene was replaced on the expression plasmid with the alanine racemase ( alr ) gene, which led to comparable levels of protein production and secretion efficiency in a suitable, alr -deficient L. plantarum host. (biomedcentral.com)
  • In this system, sequences matching foreign bacteriophage or plasmid DNA are incorporated as "spacer" sequences into the bacterial genome located between repeating CRISPR loci. (wikipedia.org)
  • nascent
  • The term protein folding incorporates all the processes involved in the production of a protein after the nascent polypeptides have become synthesized by the ribosomes. (wikipedia.org)
  • clones
  • When expressing the Tet-On 3G transactivator protein from the EF-1 alpha promoter, 83% of the Jurkat Tet-On 3G clones showed strong inducible expression and 33% demonstrated very high inducibility (greater than 2,000-fold). (clontech.com)
  • suggests
  • Since these family members can form heterodimers, this suggests that these proteins may serve as a link between titin kinase and microtubule-dependent signal pathways in muscle. (wikipedia.org)
  • complexes
  • Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild‐type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. (embopress.org)
  • The chaperone EDEM guides the retrotranslocation of the misfolded protein back into the cytosol in transient complexes with PDI and Grp784. (wikipedia.org)
  • plasma membrane
  • These targeting signals are thought to be recognized in the TGN or endosomes, which leads to the sorting of cargo proteins into transport vesicles destined for the apical or basolateral plasma membrane. (rupress.org)