• Here, we report positional cloning of Pairing homoeologous 2 (Ph2) and functional validation of the wheat DNA mismatch repair protein MSH7-3D as a key inhibitor of homoeologous recombination, thus solving a half-century-old question. (nature.com)
  • Similar to ph2 mutant phenotype, we show that mutating MSH7-3D induces a substantial increase in homoeologous recombination (up to 5.5 fold) in wheat-wild relative hybrids, which is also associated with a reduction in homologous recombination. (nature.com)
  • ZIP4 is a ZMM protein involved in homologous recombination and may act as a hub through physical interactions with components of the chromosome axis and other ZMMs 19 . (nature.com)
  • Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. (nature.com)
  • We show that C-terminally truncated Redβ, whilst still able to promote annealing and nucleoprotein filament formation, is unable to mediate homologous recombination. (nature.com)
  • As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. (nature.com)
  • As opposed to single strand (ss) DNA binding proteins such as SSB and RPA, which protect and occlude ssDNA from recombination, RAD52/Redβ SSAPs promote recombination and share several biochemical similarities. (nature.com)
  • Also, they share a similar protein architecture based on an N-terminal ssDNA binding domain of ~180 amino acids and a C-terminal extension that in the case of RAD52 is required for homologous recombination (HR) through specific protein-protein interactions 6 . (nature.com)
  • Both homologous recombination, in which the ends of the broken DNA seek out intact templates with the same sequence, and nonhomologous end-joining pathways are found in Saccharomyces as they are in humans. (brandeis.edu)
  • Analysis of homologous recombination. (brandeis.edu)
  • Recombination between homologous sequences is a fundamentally important process both in meiosis and in mitotic cells. (brandeis.edu)
  • We are interested in understanding at the molecular level how recombination occurs and what roles are played by the many proteins involved in DNA recombination, repair and replication. (brandeis.edu)
  • Using synchronized cells undergoing recombination that is initiated at a specific site on a chromosome by an inducible endonuclease, we use physical monitoring techniques (Southern blots, PCR analysis) to follow the sequence of molecular events that occur in real time. (brandeis.edu)
  • We are interested in determining what are the specific biochemical roles played by the many proteins implicated in DNA recombination, repair and replication. (brandeis.edu)
  • This "in vivo biochemistry" approach has enabled us to demonstrate that there are in fact several independent, competing pathways of homologous recombination, each with its own genetic requirements. (brandeis.edu)
  • We have shown that the invasion of DNA strands into a donor template region requires the action of the chromatin remodeling protein Rad54 that enables the recombination machinery to gain access to "closed" regions of DNA. (brandeis.edu)
  • We have shown that this regulation involves the action of a small Recombination Enhancer (RE) sequence that enables a donor on the left chromosome arm to recombine preferentially in MATa cells. (brandeis.edu)
  • Genes to be inserted by legitimate recombination need to be flanked by short sequences of the gene at the insertion site. (i-sis.org.uk)
  • Homologous recombination inserts the DNA and disrupts the target gene, allowing rapid selection of cells with the inserted gene. (i-sis.org.uk)
  • When a HEG is integrated into its recognition sequence in the genome, its protein product acts to cleave its cognate site on the homologous chromosome and gene conversion or homologous recombination can result in a new copy of the HEG being inserted. (plos.org)
  • To reduce the risk of analyzing cell line- pathway can be divided into distinct stages based on the specific features, we used several representative cell lines for recombination status of the Ig genes and on the expression each of four major stages in B cell development: pro-B, pre-B, pattern of surface markers and the presence of intracellular proteins [1- 6]. (lu.se)
  • To track differentiating cell populations, reporter cell lines generated by homologous recombination (knock-in) or via BAC transgenes have been widely used in mouse cells (5-8 ). (lu.se)
  • Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the shared ancestor. (wikipedia.org)
  • citation needed] Given their tremendous importance for biology and bioinformatics, orthologous genes have been organized in several specialized databases that provide tools to identify and analyze orthologous gene sequences. (wikipedia.org)
  • ANNOUNCEMENT ================================================================================ HOVERGEN Homologous Vertebrate Genes Data Base Release 6 (May 9 1994) from GenBank Release 82 (April 15 1994) ================================================================================ The new release is available by anonymous FTP at biom3.univ-lyon1.fr (134.214.100.42) in the directory /pub/hovergen HOVERGEN is a database of homologous vertebrate genes. (bio.net)
  • HOVERGEN allows one to easily select sets of homologous genes among a given set of vertebrate species. (bio.net)
  • Users have directly access to all information attached to sequences (either from GenBank or specific of HOVERGEN), or multiple alignments simply by clicking on genes. (bio.net)
  • This graphical tool gives thus a rapid and simple access to all data necessary to interpret homology relationships between genes: phylogenetic trees of gene families, taxonomy, GenBank information and protein multiple alignments. (bio.net)
  • Oligonucleotide primers, designed on the basis of amino acid sequences of 2 tryptic peptides derived from 1 such protein and conserved regions of the C and B genes from members of the repeats in the structural toxin (RTX) family of bacterial toxins, were used to amplify cytotoxin-specific genes from M bovis genomic DNA. (avma.org)
  • Bioinformatics strategies were used to find other homologous genes and proteins, which can also degrade HCH present in various bacteria for controlling of pollution and offer clue to prevent its entry in the food chain. (ispub.com)
  • Burt proposed that such methods could be applied to engineer HEGs that recognise and cleave sequences within coding sequences of genes in insect genomes, with the subsequent invasion of these HEGs into a population leading to the inactivation of target genes and the subsequent decline in fitness of the targeted population [2] . (plos.org)
  • Twenty-two of the pairs, chromosome numbers 1 to 22, the autosomes, are normally homologous (identical in size, shape, and position and number of genes). (msdmanuals.com)
  • Membrane proteins encoded by the BCL-2 GENES and serving as potent inhibitors of cell death by APOPTOSIS. (bvsalud.org)
  • Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. (wikipedia.org)
  • Coding sequences have been classified in gene families. (bio.net)
  • HOVERGEN is particularly useful for: - comparative sequence analysis - phylogeny - molecular evolution studies More generaly, HOVERGEN gives an overall view of what is known about a particular gene family. (bio.net)
  • In comparison to Ph1 , the causative gene sequence for Ph2 is yet to be determined. (nature.com)
  • Brg1 (Brahma-related gene 1) is an ATPase subunit of SWI2/SNF2-like chromatin-remodeling complexes that enable access of regulatory and effector proteins in transcription, DNA repair and DNA replication. (thermofisher.com)
  • We have been fascinated by the process of yeast mating-type gene switching, in which cells replace about 700 bp of Ya or Y-specific DNA sequences at the MAT locus by recombining with one of two donor loci, called HMLDescription: image3 and HMRa. (brandeis.edu)
  • Cloning and sequencing of the pancreatic islet neogenesis associated protein (INGAP) gene and its expression in islet neogenesis in hamsters. (jci.org)
  • Islet neogenesis associated protein (INGAP) is a product of a novel gene expressed in regenerating hamster pancreas. (jci.org)
  • A portion of human INGAP gene was cloned and appears to be highly homologous to the hamster gene. (jci.org)
  • This data suggests that the INGAP gene is a novel pancreatic gene expressed during islet neogenesis whose protein product is a constituent of Ilotropin and is capable of initiating duct cell proliferation, a prerequisite for islet neogenesis. (jci.org)
  • In the case of the regulatory protein gene targeted to the uracil locus, the transformed yeast colonies would be identified using replica plating on growth medium lacking uracil. (i-sis.org.uk)
  • Conclusions and Clinical Relevance -A gene was identified in M bovis that encodes a protein with sequence homology to other RTX toxins. (avma.org)
  • Because many yeast proteins are similar in sequence and function to those found in other organisms, studies performed in yeast can help us to determine how a particular gene or protein functions in higher eukaryotes (including humans). (jove.com)
  • according to morphological, physiological and its 16S rRNA gene sequence. (researchgate.net)
  • The protein product of the translocase gene demonstrated characteristics typical for members in this family of proteins, including 12 transmembrane helices and an isoelectric point of 9.4. (usda.gov)
  • We have isolated and completely sequenced the gene encoding human rhodopsin. (nih.gov)
  • The amino acid sequence of human rhodopsin, deduced from the nucleotide sequence of its gene, is 348 residues long and is 93.4% homologous to that of bovine rhodopsin. (nih.gov)
  • The Arc gene, which contains remnants of a structural GAG retrotransposon sequence, produces a protein that self-assembles into capsid-like structures harboring Arc mRNA. (lu.se)
  • While nine spCas9 gene editing sites surround the Arc start codon, the accuracy of the editing was highly sequence-dependent, with only a single target resulting in an in-frame reporter integration. (lu.se)
  • One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
  • By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)
  • Although, the number of omic techniques is ever expanding, the most developed omics technologies are high throughput DNA sequencing, transcriptomics (focused on gene expression), epigenomics (focused on epigenetic regulation of gene expression), proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of metabolites, the metabolome). (who.int)
  • A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • Each gene has a specific location (locus), which is typically the same on each of the 2 homologous chromosomes. (msdmanuals.com)
  • A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)
  • Overexpression of bcl-2 proteins, due to a translocation of the gene, is associated with follicular lymphoma. (bvsalud.org)
  • However it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of genetic engineering. (wikipedia.org)
  • Genetic and cytogenetic studies have revealed the presence of several pairing homoeologous ( Ph ) loci that ensure wheat behaves as a diploid during meiosis, with only homologous chromosomes of the same sub-genome (AA, BB or DD) pairing and recombining. (nature.com)
  • The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
  • S. cerevisiae is an attractive model organism due to the fact that its genome has been sequenced, its genetics are easily manipulated, and it is very easy to maintain in the lab. (jove.com)
  • Because it's genome has been sequenced, its genetics are easily manipulated, and it is easy to maintain in the lab, this species of yeast has been an invaluable resource in the understanding of fundamental cellular processes such as cell division and cell death. (jove.com)
  • Sarah Gregory] Today, I'm talking with Dr. Kelly Oakeson about bioinformatics and genome sequencing in a public health lab. (cdc.gov)
  • I also do whole genome sequencing. (cdc.gov)
  • Kelly Oakeson] Well, whole genome sequence data provides a very high-resolution tool for everything from identifying what types of microbes or viruses you might have in any given sample to determining antimicrobial resistance and identifying clusters of related microbes in the case of a foodborne illness outbreak. (cdc.gov)
  • claiming that two homologous chromosomes paired between complementary sequences lead to the formation of a cross-stranded structure that physically links the two component helices. (iucr.org)
  • In meiosis, the genetic information inherited from a person's mother and father is recombined through crossing over (exchange between homologous chromosomes). (msdmanuals.com)
  • Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
  • An open reading frame encoding a 927-amino acid protein with a predicted molecular mass of 98.8 kd was amplified from M bovis genomic DNA. (avma.org)
  • A putative ATP/ADP translocase was uncovered during the genomic sequencing of the intracellular plant pathogen, Candidatus Liberibacter asiaticus (Las), the causal agent of citrus huanglongbing. (usda.gov)
  • He thanked CDC and KTL for their support in providing accurate genomic sequencing results of polioviruses in a timely manner, as this greatly facilitated planning and targeting the polio eradication activities. (who.int)
  • Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. (rochester.edu)
  • These low and high-resolution data sets originates from T3SSes from different species and can also be collected from other structurally homologous systems, such as the flagella. (lu.se)
  • The p40 subunit is homologous to the extracellular domains of the hematopoietic cytokine receptors. (rndsystems.com)
  • The multiple sequence alignment of 16 subunit VII homologues showsthat Bmuccr is very hydrophilic, has a characteristic charge distribution, and has a high helical content. (researchgate.net)
  • Definition of the homologous of bovine subunit VII of ubiquinol-cytochrome C reductaseshould facilitate further analysis of structure/function relationships of silkworm cytochrome bcl complex. (researchgate.net)
  • In particular, we are interested in a subclass of protein assemblies, homomeric assemblies, which are produced by the repetition of single type of subunit. (lu.se)
  • In the Fp subunit of SQR, and the closely related membrane-associated fumarate reductase of anaerobic organisms, FAD is covalently attached via an 8α-N(3)-histidyl linkage to a histidine (His) in a conserved sequence in the N-terminal part of the polypeptide. (lu.se)
  • As with morphological and anatomical structures, sequence similarity might occur because of convergent evolution, or, as with shorter sequences, by chance, meaning that they are not homologous. (wikipedia.org)
  • Align homologous protein sequences and structures. (simtk.org)
  • Sequoia is a command-line tool for the alignment of molecular protein sequences and atomic structures. (simtk.org)
  • In earlier work, we have applied novel bioinformatic methods to the comparison of protein sequences and protein structures, and used the resulting data to address problems at the foundations of bioinformatics. (rochester.edu)
  • The Structural Classification of Proteins - extended ( SCOPe ) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst all proteins of known structure, along with resources for analyzing the protein structures and their sequences. (berkeley.edu)
  • SCOPe undertakes to provide interfaces and data to support all users of protein structure and evolutionary relationships, for research, education, and policy, at scales ranging from interactive exploration of relationships of proteins of interest, including nuances of their individual structures and variations, to comprehensive studies and methods that draw on the entirety of the protein universe. (berkeley.edu)
  • The researchers aim to exploit the conservation of certain SARS-CoV-2 RNA motif sequences and structures. (news-medical.net)
  • To use this resource, a user provides the sequence information for each protein building block and available partial or homologous structures. (asbmb.org)
  • Mohammed AlQuraishi from Columbia University, US, who developed one of the competing algorithms , thinks that DeepMind's AI could help researchers understand the functions of proteins by comparing their predicted structures to proteins with known function and shape. (chemistryworld.com)
  • The software, which was trained on around 170,000 structures from the protein data bank , builds on a previous version that was presented at Casp13 in 2018. (chemistryworld.com)
  • The original AlphaFold had multiple separate pieces trained independently and only predicted interatomic distances - not 3D structures - that were used to fold the protein using more conventional approaches like Rosetta. (chemistryworld.com)
  • Many biological processes are controlled by large multi-component protein assemblies, the size and complexity of which typically precludes the determination of their high-resolution structures. (lu.se)
  • Currently we are working with development of methods to determine structures of fibrillar proteins by a combination of structure modeling and X-ray fiber diffraction interference. (lu.se)
  • Previous work in this area has been on modeling the assembly structure of the type III secretion system and prediction of the high-resolution structures of homo-oligomeric proteins using limited experimental data from Nuclear Magnetic Resonance (NMR) in order to speed up the process of structure determination. (lu.se)
  • This macromolecular assembly comprises more than 20 conserved proteins that form a series of ring-like structures and a needle-shaped protrusion, which allows the transport of proteins into a host cell. (lu.se)
  • Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. (wikipedia.org)
  • Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. (wikipedia.org)
  • The term "percent homology" is often used to mean "sequence similarity", that is the percentage of identical residues (percent identity), or the percentage of residues conserved with similar physicochemical properties (percent similarity), e.g. leucine and isoleucine, is usually used to "quantify the homology. (wikipedia.org)
  • Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. (wikipedia.org)
  • Alternative approach to protein structure prediction based on sequential similarity of physical properties. (rochester.edu)
  • Including such artifacts can result in similarity between non-homologous sequences. (berkeley.edu)
  • Here, we show that APP can coimmunoprecipitate NEEP21 from nontransgenic mouse brain and from mammalian cells stably coexpressing both proteins. (jneurosci.org)
  • These shared biochemical, protein sequence and functional similarities suggest the existence of an ancestral annealing mechanism involved in HR. (nature.com)
  • Their position in the 5' UTR suggests they contain homologous nucleotides with functional equivalency. (news-medical.net)
  • Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites. (ncbs.res.in)
  • These ribosomal sequences was functional for the phylogenetic analysis and molecular taxonomic of any bacteria. (ispub.com)
  • Here, we review the available structural and functional data on RCC1 superfamily members, paying special attention to the human proteins and their involvement in disease. (nih.gov)
  • It showed a high degree of homology with WRKY11 from Arabidopsis thaliana, containing a WRKY domain and a zinc finger structure and II-d WRKY characteristic domains of HARF, a calmodulin-binding domain (C-motif), and a putative nuclear localization signal (NLS) through sequence alignment and functional element mining. (bvsalud.org)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • Results -Several proteins ranging in molecular mass from 55 to 75 kd were unique to the hemolytic strain. (avma.org)
  • A popular technique used to validate direct interactions in protein complexes is cross-linking mass spectrometry, or XL-MS, which typically will detect linked residues while integrating these networks with structural techniques to generate accurate models of high-level molecular processes. (asbmb.org)
  • To overcome these shortcomings, Evelyn Ramberger, Lorena Suarez-Artiles, Daniel Perez-Hernandez and colleagues at Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Germany, have developed an optimized method for using protein interaction screen on a peptide matrix, or PRISMA, in combination with quantitative mass spectrometry. (asbmb.org)
  • Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. (genomicglossaries.com)
  • Human p19 cDNA encodes a 189 amino acid residue (aa) precursor protein with a putative 19 aa signal peptide and 170 aa mature protein. (rndsystems.com)
  • To investigate the APP in vivo interactome in an unbiased manner, we generated mice that harbor a mouse prion protein promoter-driven cDNA encoding human APP-695 fused to a C-terminal affinity tag. (jneurosci.org)
  • somewhat similar sequences of about 110 amino acids each. (wikipedia.org)
  • Interestingly, many proteins found in yeast share similar sequences with proteins from their fellow Eukaryotes. (jove.com)
  • These proteins are often homologous, and their similar sequences indicate that the organisms share a common ancestor. (jove.com)
  • We think this route is worthwhile because it may enable the design of proteins very different from naturally occurring ones and may be more sensitive to changes in individual sequences, for example, mutations. (chemistryworld.com)
  • Computational tools to study RNA-protein complexes. (ncbs.res.in)
  • DeepMind now wants to improve the algorithm further to make it figure out how proteins form complexes or how they interact with small molecules. (chemistryworld.com)
  • Purification of APP-AT protein complexes and identification of the constituents by mass spectrometry revealed several previously reported APP-interacting proteins as well as proteins involved in synaptic maintenance. (jneurosci.org)
  • The eukaryotic proteins are more complicated than the bacterial enzyme complexes. (tcdb.org)
  • In this study, chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq) was performed to identify the AmtR regulon in C. glutamicum ATCC 14067. (frontiersin.org)
  • Kelly Oakeson] Next Generation Sequencing is a very high throughput, massively parallel method for sequencing DNA. (cdc.gov)
  • Click "Sequence Details" to view all sequence information for this locus, including that for other strains. (yeastgenome.org)
  • Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • Procedure -Hemolytic and nonhemolytic strains of M bovis were compared by use of western blotting to identify proteins unique to hemolytic strains. (avma.org)
  • Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
  • In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. (cdc.gov)
  • Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. (wikipedia.org)
  • Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. (wikipedia.org)
  • Phylogenetic tree showed Bmuccr hadhigh homology with T. castaneum homologous. (researchgate.net)
  • Nucleotide sequence of cucumber-mosaic-virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses. (wikidata.org)
  • it is generally believed that all the copies in an organism are identical or nearly identical in nucleotide sequence. (ispub.com)
  • The horseshoe-shaped Hint domain contains a catalytic center for protein splicing, which involves both N and C-terminal residues. (rcsb.org)
  • The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. (nih.gov)
  • Using complementary approaches, i.e. controlled enzymatic hydrolysis and production of recombinant fusion proteins, we demonstrated that, for these patients, the allergenicity of the caprine β-casein could be abolished by substituting five amino acids residues. (cea.fr)
  • By analyzing its amino acid sequence, RCC1 was found to consist of seven homologous repeats of 51-68 amino acid residues, which were later shown to adopt a seven-bladed beta-propeller fold. (nih.gov)
  • We have extended our studies to encompass intrinsically disordered proteins, and are using the sequences of those proteins as an added resource in the study of folding and stability in proteins. (rochester.edu)
  • When protein interactions occur in intrinsically disordered regions, it's often through short linear motifs, known as SLiMs, which are both tedious and challenging to study. (asbmb.org)
  • Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. (wikipedia.org)
  • Protein multiple alignments and phylogenetic trees have been calculated for each family. (bio.net)
  • Bioinformatic analysis of the protein revealed 12 transmembrane helices and an isoelectric point of 9.4, both of which are characteristic of this family of proteins. (usda.gov)
  • One method developed for making high ethanol yeast, for example, involves site-specific mutagenesis (see below) of regulatory proteins controlling a metabolic network for ethanol production, to make the yeast tolerate high levels of ethanol and glucose [2]. (i-sis.org.uk)
  • Because recombinant antibody production involves sequencing the antibody light and heavy chains, it is a highly controlled and reliable process. (cellsignal.com)
  • They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. (genomicglossaries.com)
  • The basic format of the yeast-two hybrid system involves the creation of two hybrid molecules, one in which the " bait ' protein is fused with a transcription factor, and one in which the " prey " protein is fused with a related transcription factor . (genomicglossaries.com)
  • Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. (wikipedia.org)
  • These resources employ approaches that can be generally classified into those that use heuristic analysis of all pairwise sequence comparisons, and those that use phylogenetic methods. (wikipedia.org)
  • This is the process we have studied most intensively, but we are also interested in an alternative process known as break-induced replication (BIR), where only one end of a chromosome break locates a template sequence and assembles a complete replication fork and can copy sequences to the end of a chromosome, producing a nonreciprocal translocation. (brandeis.edu)
  • 2015. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. . (ncbs.res.in)
  • LC-MS/MS and bioinformatics analysis were performed to identify differentially expressed proteins. (frontiersin.org)
  • Bioinformatics analysis indicated the up-regulated proteins were significantly enriched in "GnRH secretion" and "Circadian rhythm" signaling pathway. (frontiersin.org)
  • Sarah Gregory] I understand that the ability of this sequencing to work optimally is dependent on bioinformatics. (cdc.gov)
  • So, bioinformatics combines computer science and biology in order to make heads or tails out of all of this sequence data we're making. (cdc.gov)
  • I think a general lack of understanding as to what bioinformatics is and how important it is, especially when dealing with next generation sequence data. (cdc.gov)
  • Researchers must incubate individual peptide spots with the protein extract on a cellulose membrane and then retrieve them for further analysis. (asbmb.org)
  • Using this tag, we prepared mild detergent lysates from transgenic mouse brain cortical membrane preparations and isolated a number of previously identified APP-interacting proteins. (jneurosci.org)
  • Aβ is liberated from type I integral membrane proteins, termed β-amyloid precursor proteins (APPs), by the concerted action of β-secretase (BACE1) and γ-secretase (for review, see Selkoe, 2002 ). (jneurosci.org)
  • If the membrane-anchor is missing or defective, Fp and Ip subunits accumulate as soluble proteins in the cytoplasm. (lu.se)
  • The proteins are found on mitochondrial, microsomal, and NUCLEAR MEMBRANE sites within many cell types. (bvsalud.org)
  • Proteins were validated with targeted proteomics using parallel reaction monitoring (PRM) in a validation set consisting of samples from the above patients. (frontiersin.org)
  • This report represents the first description of combined label-free quantitative proteomics and PRM analysis of targeted proteins for discovery of different proteins before and after IVR treatment in the same patient. (frontiersin.org)
  • These transport proteins appear to be unique to mitochondria, plant plastids, and obligate-intracellular bacteria. (usda.gov)
  • The addition of an affinity tag allowed us to avoid the use of antibodies targeted toward the intracellular C-terminal tail of APP, a region to which a number of reported interacting proteins bind ( King and Turner, 2004 ). (jneurosci.org)
  • The two donor loci are maintained in a chromatin configuration that prevents them from being transcribed or being cleaved by the HO endonuclease that cuts the same sequence at MAT to initiate switching. (brandeis.edu)
  • Sequence comparison methods were first pioneered in the COGs database in 1997. (wikipedia.org)
  • Thus, this study demonstrates that using proteomic methods on our transgenic model can uncover important in vivo APP-interacting proteins that will provide insights into the biology of APP. (jneurosci.org)
  • Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). (iucr.org)
  • They recognize long asymmetric nucleotide sequences and cleave both DNA strands in a monomer form. (rcsb.org)
  • Interestingly, those portions of the polypeptide chain predicted to form loops on the cytoplasmic face of rhodopsin are perfectly conserved between the human and bovine proteins. (nih.gov)
  • Despite sequence identities ranging from 87% to 91% between caprine and bovine caseins, these patients possess IgE antibodies that bind specifically to the caprine caseins without recognizing the bovine ones. (cea.fr)
  • Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences. (rochester.edu)
  • Nearly all proteins have structural similarities with other proteins, and in some of these cases, share a common evolutionary origin. (berkeley.edu)
  • SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
  • Keratin ( / ˈ k ɛr ə t ɪ n / [1] [2] ) is one of a family of structural fibrous proteins also known as scleroproteins . (wikipedia.org)
  • Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)
  • Allergenicity of food proteins has been correlated to their structural conformation and their resistance to proteolysis. (cea.fr)
  • As we show here, these RCC1 superfamily proteins can be subdivided in five subgroups based on structural criteria. (nih.gov)
  • Our goal is to use high-resolution structural modeling techniques guided by constraints taken from lower resolution experimental data to generate structural models of important biological protein assemblies for which high resolution structural determination is unfeasible. (lu.se)
  • A synthetic, specially- designed oligonucleotide with the ability to recognize and bind a protein ligand molecule or molecules with high affinity and specificity. (genomicglossaries.com)
  • 2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)
  • Oxidant damage to cellular DNA, proteins (including the epigenome), and lipids can occur when reactive oxygen species escape cell antioxidant and repair mechanisms. (who.int)
  • 2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)
  • Other sources of experimental information include X-ray diffraction, biotinylation, sequence mutation and deletion, solution binding and chemical cross-linking data. (lu.se)
  • Kelly Oakeson] Yeah, so Next Generation Sequencing generates a lot of sequence data that need to be translated into meaningful biological information. (cdc.gov)
  • 172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)
  • A team at Google offshoot DeepMind say that their artificial intelligence (AI) network has made a huge leap solving the 50-year-old protein folding problem after it outcompeted all other teams at in a protein structure prediction challenge. (chemistryworld.com)
  • Google's algorithm, called AlphaFold2 , was the clear winner of this year's Critical Assessment of Structure Prediction (Casp14) challenge - a biennial competition created to benchmark progress in the accuracy of computational protein structure prediction. (chemistryworld.com)
  • Taxonomic distribution of proteins containing CH domain. (embl.de)
  • The complete taxonomic breakdown of all proteins with CH domain is also avaliable . (embl.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing CH domain in the selected taxonomic class. (embl.de)
  • We are interested in computational studies of protein folding and dynamics, and particularly in the information about protein physics which is available through bioinformatic studies. (rochester.edu)
  • In recent work we developed the first bioinformatic representation of protein dynamics, and are currently using this tool, in combination with earlier studies of the static physical properties of amino acid sequences, to elucidate basic mechanisms of protein folding. (rochester.edu)
  • Small molecules that behave like drugs can be used to explore the function of various proteins and large molecules, acting as chemical probes. (news-medical.net)
  • It's likely not yet accurate enough for medical applications focused on small molecules, but it may help with designing antibodies for protein-based therapeutics,' he says. (chemistryworld.com)
  • By proximity ligation assay (PLA), we demonstrated that the mCherry-Arc fusion protein retains the Arc function by interacting with the transmembrane protein stargazin in postsynaptic spines. (lu.se)
  • From these studies, the emerging picture is that the RLD is a versatile domain which may perform many different functions, including guanine nucleotide exchange on small GTP-binding proteins, enzyme inhibition or interaction with proteins and lipids. (nih.gov)
  • By mechanism, DNA annealing proteins are divided into ATPases capable of strand invasion (RecA, RAD51) and single strand annealing proteins (SSAPs) that do not utilize ATP 4 . (nature.com)
  • Such regulation may occur through protein-RNA interactions or allosteric RNA-RNA effects between stem-loops on the 5'-UTR. (news-medical.net)
  • co-immunoprecipitation Used to determine protein- protein interactions . (genomicglossaries.com)
  • A census of actin-associated proteins in humans. (ncbs.res.in)
  • By investigating the function of a given protein in yeast, researchers gain insight into the protein's function in higher eukaryotes, such as us, humans. (jove.com)
  • It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. (nih.gov)
  • In addition, the CH domain occurs also in a number of proteins not known to bind actin, a notable example being the vav protooncogene. (embl.de)
  • Finally, the video describes some of the many ways in which yeast cells are put to work in modern scientific research, including protein purification and the study of DNA repair mechanisms and other cellular processes related to Alzheimer's and Parkinson's diseases. (jove.com)
  • We have identified the proteins necessary to carry out the initial steps in strand invasion and the beginning of new DNA synthesis, which is significantly different from the normal process of replication. (brandeis.edu)
  • Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
  • He adds that although the program wasn't developed for protein design, experience from other models like Rosetta suggests that it might be possible to adapt it for this purpose. (chemistryworld.com)
  • To examine the role of protein kinase C as a chronic regulator of proximal tubule Na/H antiporter activity, the effect of phorbol 12-myristate 13-acetate (PMA) on the Na/H antiporter was studied in cultured proximal tubule cells. (jci.org)
  • The activity-regulated cytoskeleton-associated (Arc) protein is essential for synaptic plasticity and memory formation. (lu.se)
  • In this study, three amino acid sites (Thr133, Ser134, Ser33) that may affect the function of PcPKS1 were identified by analyzing the sequences of PcPKS1, the BAS from Rheum palmatum and the CHS from Arabidopsis thaliana, as well as the conformation of the catalytic site of the enzyme. (bvsalud.org)
  • They are weak ssDNA binding proteins with no affinity for double-stranded (ds) DNA. (nature.com)
  • DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity. (ncbs.res.in)
  • An antibody ( Ab ), also known as an immunoglobulin ( Ig ), [1] is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses . (wikipedia.org)
  • An antibody is used to precipitate a protein along with bound proteins. (genomicglossaries.com)
  • Finally, we recorded mCherry-Arc interaction with presynaptic protein Bassoon in mCherry-negative surrounding neurons at close proximity to mCherry-positive spines of edited neurons. (lu.se)
  • When they subjected these samples to mass spectrometry, the researchers found 7,582 proteins, of which 143 were upregulated and 80 were downregulated in patients who had COVID-19. (asbmb.org)
  • We are also interested in understanding how oligomerization specificity is encoded in protein sequence and structure, in particular in coiled-coils. (lu.se)
  • In particular, the authors monitored two specific molecules, RIG-1 and STAT1, involved in interferon signaling and found that the levels of these proteins correlate with viral loads. (asbmb.org)