• Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. (nih.gov)
  • Learn to identify homologs of known genes of interest in your newly sequenced genome. (slideshare.net)
  • Frameshifts and indel errors - Split genes across scaffolds - Highly repetitive sequences To face these challenges, we train annotators in recovering coding sequences in agreement with all available biological evidence. (slideshare.net)
  • Taking a single DNA sample from an individual's blood, researchers can pass the nucleic acids through a protein nanopore , using changes in electrical current arising from the molecular interactions to decode in real time the sequences from 40 genes known to be connected to 25 tandem repeat diseases. (sciencealert.com)
  • Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. (ox.ac.uk)
  • 1300 copies) of mucin-associated surface protein (MASP) genes. (ox.ac.uk)
  • In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. (nature.com)
  • There are between 60 and 120 genes in the large herpesvirus genome, which encodes at least 100 distinct proteins. (doctor-dr.com)
  • The best method for examin- evolution of groups of genes, and assemble information from ing M. tuberculosis complex genotyping data gathered over genome sequencing projects. (cdc.gov)
  • Deep sequencing has revealed thousands of eukaryotic protein-coding genes that defy the central dogma, producing circular noncoding RNAs rather than linear messenger RNAs. (bcm.edu)
  • For some genes, the abundance of the circular RNA exceeds that of the associated linear mRNA by a factor of 10, raising the interesting possibility that the function of some protein-coding genes may actually be to produce circular noncoding RNAs, not proteins. (bcm.edu)
  • Using RNAi screening in Drosophila cells, we identified many hnRNPs, SR proteins, core spliceosome, and transcription termination factors that control the outputs of reporter and endogenous genes. (bcm.edu)
  • In total, these results indicate that inhibition or slowing of canonical pre-mRNA processing events shifts the steady-state output of protein-coding genes towards circular RNAs, which likely helps explain why and how circular RNAs show tissue-specific expression profiles. (bcm.edu)
  • Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. (openwetware.org)
  • Identification of immune-relevant genes by expressed sequence tag analysis of head kidney from grass carp (Ctenopharyngodon idella). (openwetware.org)
  • Equally important to most researchers, however, is obtaining high yields of mRNA and ultimately protein from synthetic genes. (thermofisher.com)
  • Then 50 human genes were chosen from the NCBI database to represent the five protein classes. (thermofisher.com)
  • For comparison, the corresponding wild type genes were subcloned using native sequences available from the NCBI database. (thermofisher.com)
  • In addition, ASP-gyrA3 and ASP-parC2, which bind to the FRE-specific coding sequence within the gyrA and parC structural genes, respectively, showed selective bactericidal effects against FRE isolates. (bvsalud.org)
  • This protocol describes methods to design, assemble, and validate tools for targeted activation or repression of single-copy and multi-copy genes, including repetitive and transposable elements. (springer.com)
  • Maeder ML, Angstman JF, Richardson ME et al (2013) Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. (springer.com)
  • The above-mentioned ab, of repetitive sequences in plant genomes (up to 99%), makes difficult the application of this technique for, mapping individual plant genes [40]. (centrocardiobogota.com)
  • In a first-of-its-kind study [ 1 ], five important protein classes were selected for optimization: protein kinases, transcription factors, ribosomal proteins, cytokines, and membrane proteins. (thermofisher.com)
  • Telomeres are repetitive sequences at the ends of chromosomes protected by DNA binding proteins of the shelterin complex that form capping structures. (ttu.edu)
  • Telomeres are long, repetitive DNA sequences at the ends of chromosomes that serve a protective function analogous to that of the plastic tips on shoelaces. (medicalxpress.com)
  • results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome chromosomes and for, To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. (centrocardiobogota.com)
  • The genomes of several other phytopathogenic species in the Magnaporthales have thereafter been sequenced 8 . (nature.com)
  • To this end, we recently sequenced the genomes of five species and generated transcriptomes from 21 species of Magnaporthales, including saprobes and plant pathogens 9 . (nature.com)
  • We now examine the organization of mitochondrial genomes in a human cell line that contains mitochondria tagged with the yellow fluorescent protein (YFP). (biomedcentral.com)
  • Proteins that specifically bind to TELOMERES. (lookformedical.com)
  • A ubiquitously expressed telomere-binding protein that is present at TELOMERES throughout the CELL CYCLE. (lookformedical.com)
  • Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). (embl.de)
  • This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22). (biomedcentral.com)
  • A sophisticated high-order framework nucleic acid (FNA) was engineered for the targeted delivery and responsive release of environment tolerant antisense peptide nucleic acids (asPNAs). (bvsalud.org)
  • Peptide nucleic acids (PNAs) are synthesized by attaching modified peptide backbones generally derived from repetitive N-2-aminoethyl glycine units in place of the regular phosphodiester backbone and represent synthetic impersonator of nucleic acids that offers an exciting research field due to their fascinating spectrum of biotechnological, diagnostic and potential therapeutic applications. (bvsalud.org)
  • The semi-rigid peptide nucleic acid backbone serves as a nearly-perfect template for attaching complimentary base pairs on DNA or RNA in a sequence-dependent manner as described by Watson-Crick models. (bvsalud.org)
  • Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. (bvsalud.org)
  • OBJECTIVES: To examine the bactericidal effect of antisense peptide-peptide nucleic acids (P-PNAs) that can block the expression of DNA gyrase or topoisomerase IV in FQ-resistant Escherichia coli (FRE). (bvsalud.org)
  • We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein mod- ifications. (lu.se)
  • The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. (lu.se)
  • The goal is to assign acquired spectra to known peptide sequences and potential co- and post-translational modifica- tions. (lu.se)
  • The need to keep track of protein modifications is readily recognized by the proteomics community, and few repositories of known peptide modifications have been created. (lu.se)
  • Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. (muni.cz)
  • A 'profile' (defined as a consensus primary structure model consisting of position-specific residue scores and insertion or deletion penalties) is an intuitive step beyond the pairwise sequence alignment methods. (biopred.net)
  • We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. (biomedcentral.com)
  • Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. (biomedcentral.com)
  • sequence) of the whole genome or its separate parts. (centrocardiobogota.com)
  • Herpesviruses contain a variety of virus-specific enzymes involved in the control of protein synthesis, gene expression, nucleic acid metabolism, and DNA synthesis (DNA polymerase, helicase-primase, thymidine kinase, transcription factors, protein kinases). (doctor-dr.com)
  • Although the segregation of RNA into phase-separated condensates broadly affects RNA metabolism 3,4 , whether and how specific RNAs use phase separation to regulate interacting factors such as RNA-binding proteins (RBPs), and the phenotypic consequences of such regulatory interactions, are poorly understood. (elsevierpure.com)
  • Protein-coding regions of the resulting RNAs are translated by ribosomes within the mitochondrion. (biomedcentral.com)
  • Almost any sequence can now be efficiently circularized in eukaryotic cells, which has enabled us (and others) to begin to ask how circular RNAs function. (bcm.edu)
  • To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. (biomedcentral.com)
  • This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. (biomedcentral.com)
  • We now know that the evolution of multidomain proteins has frequently involved genetic duplication events. (embl.de)
  • The newly developed assessment is based on nanopore technology, which can analyze long DNA or RNA fragments in known repetitive regions of the human genome. (sciencealert.com)
  • An increase of a single percentage point may mean learning something useful about an additional 700 human proteins by the time elucidation of the sequence of the human genome nears completion round about the year 2002. (biopred.net)
  • Since 1992, M. tuberculosis complex DNA of DNA sequencing by hybridization. (cdc.gov)
  • Sequence alignments and phylogenetic trees of these domains allow us to interpret the evolutionary relationship between these proteins, concluding that spectrin evolved from alpha-actinin by an elongation process that included two duplications of a block of seven repeats. (embl.de)
  • In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. (nature.com)
  • I'm interested in how evolutionary analyses can be combined with experimental research to reconstruct functional evolution of proteins, and to generate testable hypotheses about unknown aspects of protein function. (lu.se)
  • Digestion of genomic DNA of Trichinella spiralis with EcoRI reveals the presence of several families of repetitive DNA. (elsevierpure.com)
  • OTEs are undesired changes to genomic DNA sequences with some sequence similarity to the target site. (idtdna.com)
  • A goal of molecular genetics is to understand the relationship between basic nuclear processes, epigenetic changes and the numerous proteins that orchestrate these effects. (ox.ac.uk)
  • These findings have implications for understanding the molecular mechanisms of telomere-associated proteins and enzymes involved in the unfolding reaction, as well as for rational design of anti-cancer drugs, Stone said. (medicalxpress.com)
  • In my group we use and develop bioinformatics tools for analysing molecular sequence data. (lu.se)
  • The ZFP36 proteins regulate post-transcriptional gene expression at the level of mRNA stability in. (fsu.edu)
  • Our GeneOptimizer algorithm enables true multiparametric optimization, dealing with a large number of sequence-related parameters involved in different aspects of gene expression, such as transcription, splicing, translation, and mRNA degradation. (thermofisher.com)
  • PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. (bvsalud.org)
  • Recently, the newly identified embryonic stem cell marker, Zinc finger and SCAN domain-containing 4 gene (Zscan4), was shown to be a telomere-associated protein, co-localizing to the shelterin complex. (ttu.edu)
  • Protein synthesis. (unipv.it)
  • The tegument is made up of enzymes like VP16, which subverts cellular proteins, enzymes involved in viral nucleic acid reproduction, and VHS (Virion Host Shut off), which stops the host cell's cytoplasmic protein synthesis. (doctor-dr.com)
  • Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis. (lookformedical.com)
  • Rationally weighing the combination of the optimization parameters (e.g., codon adaptation, mRNA de novo synthesis and stability, transcription and translation efficiency) is important in order to achieve the most efficient expression of a given protein. (thermofisher.com)
  • Sequence optimization using the GeneOptimizer software is included as an optional step with all GeneArt Gene Synthesis and DNA fragments services. (thermofisher.com)
  • 7. In a eukaryotic cell, protein synthesis occurs in the A. nuclear envelope. (nursingdons.com)
  • Nucleic acids are formed when nucleotides come together through phosphodiester linkages between the 5' and 3' carbon atoms. (wikipedia.org)
  • The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. (lookformedical.com)
  • The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. (ox.ac.uk)
  • During the past year, applications of these powerful new HMM-based profiles have begun to appear in the fields of protein-structure prediction and large-scale genome-sequence analysis. (biopred.net)
  • In this review, I will explain what HMMs are, describe their strengths and limitations, and highlight how HMM-based profiles are beginning to be used in protein structure prediction and large-scale genome sequence analysis. (biopred.net)
  • Spectrin repeats [ ( PUBMED:8266097 ) ] are found in several proteins involved in cytoskeletal structure. (embl.de)
  • We examined spoligotype data using a bioin- formatic tool (sequence logo analysis) to elucidate undisclosed phylogenetic relationships and gain insights into the global dissemination of strains of tuberculosis. (cdc.gov)
  • The first section introduces sequence-basedanalyses,includinggenefind-ing, gene family and phylogenetic analy-ses, and comparative genomics approaches. (centrocardiobogota.com)
  • HSV has at least 11 glycoproteins that are used for various functions, including (a) virus attachment proteins (gB, gC, gD, and gH), (b) fusion proteins (gB), (c) structural proteins, (d) immune escape proteins (gE, and gI), and (e) other fractions. (doctor-dr.com)
  • Experimental methods of multi-dimensional NMR spectroscopy, dynamics and theoretical description of spin system evolution, multiple resonance NMR technique for structural studies of proteins and nucleic acids by NMR spectroscopy, contemporary methods of structural biology, studies of complex biomolecular systems. (muni.cz)
  • One is faced with a number of difficult problems: what are the best ways to set the position-specific residue scores, to score gaps and insertions, and to combine structural and multiple sequence information? (biopred.net)
  • The results, published in Nucleic Acids Research , showed that a relatively small structural displacement causes the G-quadruplex to unfold. (medicalxpress.com)
  • Biopolymers include the polysaccharides such as cellulose, starch, the carbohydrate polymers produced by bacteria and fungi and animal protein-based biopolymers such as wool, silk, gelatin and collagen: biopolymers, especially the carbohydrate origin, have been found very promising industrial application in … This group consists of naturally occurring polymers and chemical modifications of these polymers. (cichlidresearch.com)
  • The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. (biomedcentral.com)
  • Sequence logo analysis suspected TB transmission and suspected laboratory cross- can find motifs in potentially related nucleic acid or protein contamination. (cdc.gov)
  • We applied sequence direct DNA fingerprinting studies are relatively simple to logo analysis to find motifs based on the presence or absence design, we are still learning how best to use in toto the large of specific spacer sequences. (cdc.gov)
  • Here we show that mutations in ATRX give rise to changes in the pattern of methylation of several highly repeated sequences including the rDNA arrays, a Y-specific satellite and subtelomeric repeats. (ox.ac.uk)
  • Two small repeats of 516 and 604 bp, respectively, have been cloned and sequenced. (elsevierpure.com)
  • The two repeats are related to each other and to a 1.1-kb repetitive DNA. (elsevierpure.com)
  • Although mechanistically simple, this step occurs in a highly selective manner, as the sequence of the repeats can drastically alter the efficiency of circular RNA production. (bcm.edu)
  • We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. (stanford.edu)
  • The paucity of studies and the lack of sequence data from non-model species in Magnaporthales results in a poor understanding of the phylogeny and an unstable taxonomy of Magnaporthales species. (nature.com)
  • Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation. (ox.ac.uk)
  • Codon preference (codon usage bias) differs in each organism, and it can create challenges for expressing recombinant proteins in heterologous expression systems, resulting in low and unreliable expression. (thermofisher.com)
  • We analyzed the organization and function of mitochondrial DNA in a stable human cell line (ECV304, which is also known as T-24) containing mitochondria tagged with the yellow fluorescent protein. (biomedcentral.com)
  • Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes. (biomedcentral.com)
  • abstract = "The Escherichia coli MelR protein is a melibiose-triggered transcription factor, belonging to the AraC family, that activates transcription initiation at the melAB promoter. (birmingham.ac.uk)
  • Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. (embl.de)
  • It is structurally different from TELOMERIC REPEAT BINDING PROTEIN 2 in that it contains acidic N-terminal amino acid residues. (lookformedical.com)
  • Multiple alignments of protein sequence families indicate residues that are more conserved than others, and the points at which insertions and deletions are more frequent. (biopred.net)
  • Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary. (wikipedia.org)
  • One further advantage of synthetic sequences is that you won't be dependent on available DNA templates, and you can design your sequence exactly according to your requirements. (thermofisher.com)
  • Design your synthetic gene by uploading your sequence, selecting your expression system, and specifying your cloning vector and your sequence details (including open reading frames, untranslated regions, and cloning sites). (thermofisher.com)
  • These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (embl.de)
  • OTEs occur when the Cas enzyme is directed to the wrong site by the gRNA due to such sequence similarity. (idtdna.com)
  • Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bond. (wikipedia.org)
  • One such protein, ATRX, contains a highly conserved plant homeodomain (PHD)-like domain, present in many chromatin-associated proteins, and a carboxy-terminal domain which identifies it as a member of the SNF2 family of helicase/ATPases. (ox.ac.uk)
  • from Int J Paediatr Dent 2000 Dec;10(4):328-34) The X-linked form is also known as Zinsser-Cole-Engman syndrome and involves the gene which encodes a highly conserved protein called dyskerin. (lookformedical.com)
  • Repression of IL-1beta-induced PGE2 release, COX activity, and COX-2 protein by actinomycin D was only effective within the first hour following IL-1beta treatment, while dexamethasone was effective when added up to 10 h later, suggesting a functional role for post-transcriptional mechanisms of repression. (mdc-berlin.de)
  • Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion. (openwetware.org)
  • These approaches promise to enable researchers to assess, on a large scale, both expression level and functional state of the proteins that carry out most functions in a cell. (lu.se)
  • This analysis shows how a modular protein unit can be used in the evolution of large cytoskeletal structures. (embl.de)
  • Basic techniques for the analysis of nucleic acids. (unipv.it)
  • Logo analysis combines these data on a select regions was used to evaluate if genotyping every new graphic that illustrates the location and degree of sequence patient isolate from a particular region was useful. (cdc.gov)
  • Computational analysis is increasingly important for inferring the functions and structures of proteins [1] because the speed of DNA sequencing has long since surpassed the rate at which the biological function of sequences can be elucidated experimentally. (biopred.net)
  • Dive into the research topics of 'Binding of the Escherichia coli MelR protein to the melAB promoter: orientation of MelR subunits and investigation of MelR-DNA contacts. (birmingham.ac.uk)
  • and Public Health Research Insti- differentiation achieved with each spacer sequence. (cdc.gov)
  • Nucleic Acids Research. (openwetware.org)
  • Once you submit your request, the GeneOptimizer software generates the DNA sequence that best suits your research requirements, based on consideration of all parameters that are relevant for the given host organism plus your individual sequence requirements. (thermofisher.com)
  • Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)
  • The focus of my research is the evolution of protein function and structure. (lu.se)
  • Established sequence comparison algorithms detect significant similarities between known database sequences and 35-80% of new proteins, depending on the organism. (biopred.net)
  • Profiles' of protein structures and sequence alignments can detect subtle homologies. (biopred.net)
  • Within the HMM formalism, it is possible to apply formal, fully probabilistic methods to profiles and gapped sequence alignments. (biopred.net)
  • Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. (wikipedia.org)
  • It is this linear sequence of nucleotides that make up the primary structure of DNA or RNA. (wikipedia.org)
  • Sequences are presented from the 5' to 3' end and determine the covalent structure of the entire molecule. (wikipedia.org)
  • The secondary structure is responsible for the shape that the nucleic acid assumes. (wikipedia.org)
  • The present status of erythrocyte spectrin structure: the 106-residue repetitive structure is a basic feature of an entire class of proteins. (embl.de)
  • Polymers, including biopolymers, are made of repetitive units called monomers.Biopolymers inherently have a well defined structure: The exact chemical composition and the sequence in which these units are arranged is called the primary structure. (cichlidresearch.com)
  • Groundbreaking work in biochemistry has led to our knowledge of the structure of DNA, RNA and proteins and it holds the promise of further breakthroughs in treatment in the future. (hud.ac.uk)
  • The sequences also show an The conventional and marker-assisted breeding (MAB) are the two approaches used to accomplish plant breeding (Breseghello and Coelho, 2013). (centrocardiobogota.com)
  • The method can be used for automated detection of chemical/post- translational modifications, quality control of experiments and labelling approaches, and to control the modification settings of protein identification tools. (lu.se)
  • These approaches depend on sequence databases that are used by the engines to match real spectra to theoretical in silico spectra. (lu.se)
  • Biopolymer definition is - a polymeric substance (such as a protein or polysaccharide) formed in a biological system. (cichlidresearch.com)
  • The second helix is interrupted by proline in some sequences. (embl.de)