• Although high-throughput analysis of liquid biopsies has uncovered many differentially expressed genes in the context of cancer, the functional connection between these genes is not investigated in depth. (frontiersin.org)
  • Our analysis revealed a number of genes previously associated with hepatocellular carcinoma and uncovered their association network in the blood. (frontiersin.org)
  • In comparison to the frequently used differential gene expression analysis the approach offers additional insights by incorporating information about the relationship between genes detected in a given sample. (frontiersin.org)
  • Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. (biomedcentral.com)
  • Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci. (biomedcentral.com)
  • At least 50,000 lncRNAs are expressed from intergenic regions of the human genome, more than twice the number of protein-coding genes [ 5 ]. (biomedcentral.com)
  • Streamlining Regulon Identification in Bacteria Regulons are a group of genes that can be turned on or off by the same regulatory protein. (doe.gov)
  • RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. (nature.com)
  • This entailed mining available transcriptomic and/or genomic sequence datasets for the presence of homologues of known TIMPs, predicting secondary structures of defined protein sequences, systematic phylogenetic analyses and assessment of differential expression of genes encoding putative TIMPs in the developmental stages of A. suum , N. americanus and Schistosoma haematobium which infect the mammalian hosts. (biomedcentral.com)
  • A detailed understanding of the molecular biology of parasitic helminths, and in particular of the structure and function of key genes and gene products playing essential roles in host-parasite interactions, could provide a basis for the design of novel therapeutics. (biomedcentral.com)
  • The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. (datadryad.org)
  • Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. (datadryad.org)
  • Conclusions: In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses. (datadryad.org)
  • Furthermore, we discuss recent findings on EBV associated gastric carcinogenesis by focusing on the roles of latent genes, epigenetic abnormalities, genomic alterations, and post-transcriptional regulation by cellular and viral microRNAs (miRNAs). (spandidos-publications.com)
  • 1] "Construction and properties of Escherichia coli mutants defective in two genes encoding homologous membrane proteins with putative roles in anaerobic C4-dicarboxylic acid transport. (tcdb.org)
  • Nucleotide sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli K12. (tcdb.org)
  • Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. (ncbs.res.in)
  • Sequencing of ToxA genes from a world wide collection of isolates of P. tritici-repentis and S. nodorum showed that all the P. tritici-repentis sequences were identical but that the S. nodorum sequences were highly variable. (usda.gov)
  • These include the effect of toxin possession and expression on the fecundity and survival of fungal strains carrying the toxins, the history of the possession and expression of toxin receptor genes in the host wheat and the mechanisms of sequence diversification in toxin genes. (usda.gov)
  • Eleven candidate effector genes were identified based on features common to characterized fungal effectors, i.e. they encode small, soluble (lack of transmembrane domain), cysteine-rich proteins with a putative SP. (biomedcentral.com)
  • Sequencing multiple tumor genomes] enabled us to pick out which genes are significantly, recurrently mutated in ways that we couldn't have with a single genome," said Chapman, who is supported by a Clinician Scientist Fellowship from Leukaemia and Lymphoma Research. (broadinstitute.org)
  • In half of the study's patients, the researchers found mutations in genes that control two fundamental cellular processes: how RNA is processed and proteins are folded. (broadinstitute.org)
  • Two of these genes, DIS3 and FAM46C , appear to play important roles in the stability of RNA and hence its translation into protein. (broadinstitute.org)
  • This shows that there are entirely new cancer-causing genes that are going to be discovered through these sequencing efforts. (broadinstitute.org)
  • Expression analyses of the carrot E2F and DP genes reveal distinctive patterns and suggest that the functions of some of them are not necessarily linked to cell proliferation. (cardiff.ac.uk)
  • They then examined the mRNA expression pattern at a single cell level using so-called single-cell RNA sequencing analysis and found a subset of cardiac fibroblasts highly expressed genes activated by the transcription factor NF-kB and CCL2 mRNA. (kcl.ac.uk)
  • Multi-omics analyses based on genes associated with oxidative stress and phospholipid metabolism revealed the intrinsic molecular characteristics of pancreatic cancer. (cdc.gov)
  • Chromosome 10 likely contains 700 to 800 genes that provide instructions for making proteins. (medlineplus.gov)
  • The association of cancerous tumors with a loss of chromosome 10 suggests that some genes on this chromosome play critical roles in controlling the growth and division of cells. (medlineplus.gov)
  • Molecular neuroscience has largely focused on the functions of protein-coding genes, which account for less than 2% of our DNA. (lu.se)
  • Previous data for sequencing of 3 genes indicated that the Georgia 2007/1 isolate is closely related to isolates of genotype II, which has been identified in Mozambique, Madagascar, and Zambia. (cdc.gov)
  • The Georgia 2007/1 isolate was grouped within genotype II by partial sequencing of the B646L and B602L genes and complete sequencing of the CP204L gene. (cdc.gov)
  • Our research also focuses on the synthesis mechanisms of telomerase, and aims for the identification and functional analysis of the genes that regulate telomerase. (lu.se)
  • These results identify a subset of protein abundance and acetylation changes in muscle, mitochondrial, and structural proteins that appear to be essential in regulating diastolic function in old hearts. (springer.com)
  • What are the structural determinants of protein sequence evolution? (arxiv.org)
  • This four and a half-credit course will present an introduction to the Biophysical Chemistry and Structural Biology of proteins and nucleic acids. (columbia.edu)
  • The course includes a series of biophysical research-related topics including practical introductions to the software tools available for the visualization and modeling of biomolecular structures and the bioinformatic analysis of biomolecular sequence and structural homology. (columbia.edu)
  • Background: Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. (datadryad.org)
  • MATERIAL/METHODS: The polypeptide chains of all the proteins in the Protein Data Bank were transformed into their early-stage structural forms. (medscimonit.com)
  • RESULTS: High values of the rho-coefficient extracted sequences of strong structural determinability and structures of high sequence selectivity. (medscimonit.com)
  • proteins that break down the major structural component of fungal cell walls. (biomedcentral.com)
  • Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)
  • The minimal essential sequences of yeast U1 can be drawn in a secondary structure which resembles metazoan U1 in four of seven structural domains. (umn.edu)
  • CRISPRi genetic interaction analysis revealed Retro-2 activity resembles disruption of the transmembrane domain recognition complex (TRC) pathway, which mediates post-translational ER-targeting and insertion of tail-anchored (TA) proteins, including SNAREs required for retrograde transport. (elifesciences.org)
  • DNA and RNA sequencing analyses suggested that exon skipping did not result from genetic alterations in intronic or exonic cis-regulatory elements, but rather was associated with a single epigenetic modification downstream of exon 3a, and quantitative changes in the expression of trans-acting proteins that have known roles in the regulation of alternative splicing. (datadryad.org)
  • NEBCutter - 'This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. (fenteany.com)
  • Recent advances in genome-wide and comprehensive molecular analyses have demonstrated that both genetic and epigenetic changes contribute to EBVaGC carcinogenesis. (spandidos-publications.com)
  • Genetic analyses in yeast suggested a specific interaction between the TRAPP subunits Bet3p and Trs33p. (proteopedia.org)
  • It's going to take a lot of biological research to sort out whether these will make good drug targets," said co-senior author Todd Golub, director of the Broad's Cancer Program and Charles A. Dana Investigator in Human Cancer Genetics at the Dana-Farber Cancer Institute, "But this is an example of how genetic analysis can help point the field in the right direction very dramatically. (broadinstitute.org)
  • Efforts to collect, store, sequence, and analyze samples cut across many groups at the Broad, including the Biological Samples Platform, Genetic Analysis Platform, and Genome Sequencing Platform. (broadinstitute.org)
  • A study of genetic heterogeneity in autism spectrum disorders based on plasma proteomic and metabolomic analysis: multiomics study of autism heterogeneity. (cdc.gov)
  • Transposable elements (TEs) are mobile genetic sequences that comprise around 50% of our genomic DNA. (lu.se)
  • Analysis of the protein sequences of the three CpHsps indicated the presence of 83 amino acids with homology to the a-crystallin domain. (usda.gov)
  • A total of 15 protein sequences with high homology to known eukaryotic TIMPs were predicted from the complement of sequence data available for parasitic helminths and subjected to in-depth bioinformatic analyses. (biomedcentral.com)
  • Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNA consensus sequence required for binding. (embl.de)
  • Yeast U1 snRNA (568 nucleotides) is 3.5-fold larger than its mammalian counterpart (164 nucleotides) and contains apparent sequence homology only at the 5′ and 3′ ends. (umn.edu)
  • Published in the Journal of Proteins: Structure, Function, and Bioinformatics. (arxiv.org)
  • Bioinformatics analysis and luciferase reporter assay were used to validate interactions among hsa_circ_0046060, miR-338-3p, and G6PC2. (hindawi.com)
  • High-throughput RNA sequencing and bioinformatics analysis have led to the identification of several novel circRNAs that exhibit biological characteristics and regulatory functions [ 6 , 9 ]. (hindawi.com)
  • CBS Prediction Servers - Nucleotide and amino acid sequence-based bioinformatics tools for structure and function prediction. (fenteany.com)
  • The HESI Protein Allergens, Toxins, and Bioinformatics (PATB) Committee is co-hosting a virtual workshop in collaboration with the Society of Toxicology (SOT) Food Safety Specialty Section titled "From Protein Toxins to Applied Toxicological Testing" in the context of safety assessment of novel foods and feeds. (hesiglobal.org)
  • It will cover the state of the science in protein toxins biology (structure, activity, MOA, etc.), current bioinformatics approaches used to identify and characterize protein toxins, with the ultimate goal to leverage computational biology and in silico approaches for determining the potential of a protein to present toxic properties. (hesiglobal.org)
  • The Doxey lab focuses on bioinformatics, microbial genomics, and molecular evolution, and applies computational methods to discover new protein families and functions. (hesiglobal.org)
  • Since 2000, she has been working as a biocurator at the SIB Swiss Institute of Bioinformatics for the UniProt knowledgebase, the reference resource of protein sequences and functional annotation. (hesiglobal.org)
  • 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)
  • Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. (ncbs.res.in)
  • 2015. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. . (ncbs.res.in)
  • strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)
  • Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
  • Researchers determined the origin of a group of protein-based light sensors in land plants and a series of related phytoplankton by sequencing and comparing RNA in these genomes. (doe.gov)
  • Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. (datadryad.org)
  • This file includes the bZIPs protein sequences from Arabidopsis thaliana and six legume genomes (Glycine max,Medicago truncatula,Cajanus cajan,Cicer arietinum,Phaseolus vulgaris and Lotus japonicus). (datadryad.org)
  • For the study , published in the American Journal of Human Genetics , researchers sequenced and analyzed whole genomes of more than 1,100 people. (researchamerica.org)
  • Once the group had the sequencing results, they analyzed the genomes of 493 people with either Alzheimer's disease, amyotrophic lateral sclerosis (ALS), or frontotemporal dementia (FTD) and 671 healthy people. (researchamerica.org)
  • The data confirmed that variants in TET2, in both protein-coding and non-coding regions, were more likely to be present in the genomes of people with ALS, Alzheimer's, or FTD than in people without these diseases. (researchamerica.org)
  • RNA splicing plays important roles in viral replication and virus-host interactions 38 . (nature.com)
  • As a result, circRNAs exert important roles in numerous physiological and pathological processes [ 9 , 10 ]. (hindawi.com)
  • PTPases are enzymes that play important roles in phosphorylation by removing unneeded phosphate groups. (ucsd.edu)
  • These results indicate that DcE2F1 is involved in the control of cell proliferation and plays important roles in the regulation of embryo and plant development. (cardiff.ac.uk)
  • The adult heart contains many resident cardiac fibroblasts, which play important roles in maintaining tissue architecture. (kcl.ac.uk)
  • Using a newly developed enzyme-coupled continuous activity assay, we compare differing NAS proteins identified through multiple sequence alignments and phylogenetic analyses. (bvsalud.org)
  • Topics covered include various high-throughput genomics technologies (genome sequencing, DNA microarrays, proteomics), quantitative modeling of transcriptional and post-transcriptional regulatory networks, synthetic biology, and the world of RNA structure, dynamics, and function. (columbia.edu)
  • Topics covered will include high-throughput assay development, screening, chemical library creation, high-throughput chemistry, affinity purification of target proteins and target validation, protein microarrays, molecular evolution, protein engineering and synthetic biology. (columbia.edu)
  • The availability of next-generation sequencing technology has circumvented this barrier for non-model organisms by enabling transcriptome assembly from high-throughput RNA sequencing (RNA-seq) data [ 9 , 10 ]. (biomedcentral.com)
  • 2016. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. . (ncbs.res.in)
  • The annotation system is searchable and the user can select any annotations to be an experimental factors in analysis whereby it becomes available to analysis plugins and plot-tools. (lu.se)
  • The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [ ( PUBMED:9007998 ) ] involved in many biological processes. (embl.de)
  • ABSTRACT In order to define the protein expressional changes related to the process of meglumine antimoniate resistance in anthroponotic cutaneous leishmaniasis (CL), we performed a comparative proteomics analysis on sensitive and resistant strains of Leishmania tropica isolated from Iranian CL patients. (who.int)
  • The study shows the usefulness of proteomics in identifying proteins that may express differences between sensitive and resistant L. tropica isolates. (who.int)
  • We are proud to work together with the leading biotech company in Sweden for biomarker panel analyses in epidemiology, OLINK Proteomics AB, Uppsala, and its representatives! (lu.se)
  • In 2022, the percentage of E. coli sequence type (ST) 361 isolates sent to F-NRC doubled to 1.2% from 0.6% of CPE in 2021. (cdc.gov)
  • Phylogenetic analysis of 80 Escherichia coli ST361 isolates collected during 2015-2022 and used in a population analysis of E. coli ST361 and reduced cefiderocol susceptibility, France. (cdc.gov)
  • 2022) Mendelian randomization analysis of plasma levels of CD209 and MICB proteins and the risk of varicose veins of lower extremities. (plos.org)
  • Members of this family are membrane-anchored proteins structurally related to snake venom disintegrins, and have been implicated in a variety of biologic processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. (wikipedia.org)
  • This represents a new function for the SAM domain family, which is well characterized for mediating protein-protein interactions. (embl.de)
  • Mutational analysis suggests that yeast Trs33p facilitates other Bet3p protein-protein interactions. (proteopedia.org)
  • Deciphering protein–protein interactions. (crossref.org)
  • In contrast, the essential 5′ and 3′ terminal domains correspond to phylogenetically conserved sequences and/or structures previously implicated in RNA:RNA and RNA:protein interactions. (umn.edu)
  • The analysis of these results, in terms of a statistical-mechanical model that incorporates polymer flexibility as well as the excluded volume of the protein, shows that the dramatic enhancement of bovine pancreatic trypsin inhibitor self-association can be quantitatively rationalized in terms of hard repulsive interactions. (lu.se)
  • Sequencing of the α6 subunit cDNA from spinosad selected and unselected strains of T. absoluta revealed all Taα6 transcripts of the selected strain were devoid of exon 3, with comparison of genomic DNA and mRNA revealing this is a result of exon skipping. (datadryad.org)
  • While whole gene duplications and deletions are relatively well-studied, the biology of subexonic ( i.e. , within coding exon sequences), copy number variation remains elusive. (nature.com)
  • Our study thus demonstrates the feasibility of performing gene co-expression network analysis from cell-free RNA data and its utility in studying hepatocellular carcinoma. (frontiersin.org)
  • An underexplored way of analyzing the rich data obtained from sequencing liquid biopsy-derived cfRNA liquid biopsy is weighted gene co-expression network analysis (WGCNA). (frontiersin.org)
  • Quantification of protein expression changes in the aging left ventricle of Rattus norvegicus. (springer.com)
  • Capturing heterogeneity in gene expression studies by surrogate variable analysis. (springer.com)
  • Abstract Scaffold proteins are crucial regulators of signaling networks, and their abnormal expression may favor the development of tumors. (techscience.com)
  • To further reveal the pharmacokinetic mechanism of PEG-L repeated administration for the treatment of HCC, the protein expression of hepatic CYP3A and the concentration of CP in the liver and spleen of HCC mice by inhibiting CYP3A were analyzed. (bvsalud.org)
  • EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula . (biomedcentral.com)
  • Using potato virus X (PVX) based transient expression assays, we showed that one of the candidate effectors, i. e. contig 8 that encodes a cerato-platanin (CP) domain containing protein, unlike CP proteins from other fungal pathogens was unable to elicit a hypersensitive response (HR). (biomedcentral.com)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • Multiple sequence alignments and three-dimensional structure analysis of 14-3-3 proteins indicated all the members contained nine conservative antiparallel α-helices. (figshare.com)
  • Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways. (cdc.gov)
  • Tissue inhibitors of metalloproteases (TIMPs) are a multifunctional family of proteins that orchestrate extracellular matrix turnover, tissue remodelling and other cellular processes. (biomedcentral.com)
  • We have utilized mass spectrometry of purified bovine papillomavirus E1 protein to identify and characterize new sites of phosphorylation. (biomedcentral.com)
  • Mass spectrometry and in silico sequence analysis were used to identify phosphate sites on the BPV E1 protein and kinases that may recognize these sites. (biomedcentral.com)
  • Cell proteins were analysed with 2-dimensional electrophoresis and differentially expressed proteins were identified by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. (who.int)
  • After 4 weeks of conversion, we performed global analyses of RNA and protein levels by RNA-sequencing and mass spectrometry. (lu.se)
  • FASTA - 'Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. (fenteany.com)
  • Dixon's interest in phosphatases eventually led to analysis of the tumor suppressor protein PTEN, which shares sequence identity (the degree of similarity between two or more nucleotide sequences) with PTPases. (ucsd.edu)
  • 8] "Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12. (tcdb.org)
  • The work presented in this thesis focuses on the bioinformatic methods for a TE-centric analysis of next- and third-generation sequencing technologies. (lu.se)
  • Genomic and phenotypic analysis of Escherichia coli sequence type 361, a primary clone causing carbapenemase spread in France, revealed mutations leading to cefiderocol resistance. (cdc.gov)
  • SMC3 with retained acetylation is loaded onto chromatin, and chromatin immunoprecipitation sequencing analysis demonstrates decreased occupancy of cohesin localization sites that results in a consistent pattern of altered transcription seen in CdLS cell lines with either NIPBL or HDAC8 mutations. (nih.gov)
  • Previous work has demonstrated that changes in DNA methylation happen during aging, so the team hypothesized that mutations in the gene could lead to a faulty TET2 protein that disrupts how the brain ages and contributes to the development of neurodegenerative diseases. (researchamerica.org)
  • [ 8 ] Both mutations created stop codons leading to truncation of the PAX3 protein. (medscape.com)
  • Compared to fungal and moss NAS that comprise merely a core-NAS domain (class III), NA biosynthetic activities of the four paralogous Arabidopsis thaliana NAS proteins were far lower. (bvsalud.org)
  • Nearly 39% of the ESTs were predicted to encode proteins of fungal origin and among these, 162 ESTs were predicted to contain N-terminal signal peptides (SPs) in their deduced open reading frames (ORFs). (biomedcentral.com)
  • So as to generate an antibody directed enzyme prodrug remedy, right here we designed a chimeric protein by fusing the F8 antibody that acknowledges the EDA of fibronectin (expressed on the tumor neovasculature) and an developed variant of the ROS-generating enzyme D-amino acid oxidase (DAAO). (holliseden.com)
  • Sequencing the full genome of a tumor is still a feat of technical and analytical prowess and only a few studies to date have looked across more than one. (broadinstitute.org)
  • Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. (cdc.gov)
  • Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. (nature.com)
  • As increasing number of next-generation sequencing (NGS) datasets are being produced from various-omics initiatives, transcriptome sequencing of flora and fauna for a specific developmental stage/condition gains its popularity in biological research. (nature.com)
  • Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain-containing proteins, suggesting that the function of the domain is conserved from yeast to humans. (embl.de)
  • Pathway analysis was performed to gain further insights into the biological functions that are associated with the discovered modules. (frontiersin.org)
  • We will discuss the structure and function of both proteins and small molecules in biological systems. (columbia.edu)
  • Proteins are the primary class of biological macromolecules and serve to carry out most cellular functions. (columbia.edu)
  • The growing list of human syndromes associated with the immunophilin defect underscores the biological relevance of these proteins that are largely opportunistically exploited by cancer cells to support and enable the tumor's intrinsic properties. (techscience.com)
  • CircRNAs exert their biological effects by 4 different mechanisms: serving as sponges of microRNAs (miRNAs), serving as sponges of RNA binding proteins (RBPs), modulating parental gene transcription, and encoding functional proteins. (techscience.com)
  • BASE features a biomaterial LIMS tracking biological material from its source to hybridisation/sequencing and ultimately to raw data and analysis. (lu.se)
  • provided a biological motivation for studying the effects of This task is further complicated by the background of abun- nominally inert background macromolecules on protein as- dant macromolecular crowding agent. (lu.se)
  • Report of the third international workshop on human chromosome 10 mapping and sequencing 1999. (medlineplus.gov)
  • Liquid biopsy represents a promising alternative to invasive tissue biopsies in particular for cancer diagnosis as it enables the study of cell-free (cf) nucleic acids in the blood, which includes cfDNA and various cfRNAs (e.g., protein-coding, lncRNA, microRNA, etc. (frontiersin.org)
  • Molecular Toolkit - Utilities to analyze and manipulate nucleic acid and protein sequences. (fenteany.com)
  • EBI Services - Access to nucleic acid, protein and macromolecular structure databases, including the EMBL-Bank database. (fenteany.com)
  • Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation, and apoptosis. (nih.gov)
  • To exclude potential indirect targets of PKA, we built a computational model to characterize the kinase sequence specificity toward the substrate target site based on known kinase-substrate relationships. (nih.gov)
  • Most recently, Dixon's lab has identified a new group of enzymes in the protein kinase family that phosphorylate casein in the biomineralization of teeth and bone. (ucsd.edu)
  • The sequence has facilitated experiments that have defined roles for the Ca2+/calmodulin, MAP kinase and cAMP-dependant signalling pathways and for the metabolites mannitol, arabitol, xylitol, malate, trehalose and aminolevulinate. (usda.gov)
  • Image analysis of the matched maps identified 7 proteins that were either over- or down-expressed: activated protein kinase c receptor (LACK), alpha tubulin (×2), prostaglandin f2-alpha synthase, protein disulfide isomerase, vesicular transport protein and a hypothetical protein. (who.int)
  • Crystal structures are available for archaeal and bacterial NAS-like proteins that carry out simpler aminobutanoyl transferase reactions. (bvsalud.org)
  • Tetrapetide sequences and structures were expressed by letter codes. (medscimonit.com)
  • Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. (embl.de)
  • To date, many studies have focused on WGCNA analysis of bulk or single-cell RNA (scRNA) sequencing data from tissue samples. (frontiersin.org)
  • The majority of 14-3-3s had transcript accumulation in each detected potato tissue, implying their regulatory roles across all stages of potato growth and development. (figshare.com)
  • CONCLUSIONS: The results revealed sequence-to-structure (and vice versa) correlation in early-stage folding. (medscimonit.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)
  • Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine- F. circinatum interaction. (biomedcentral.com)
  • C. truncatum likely secretes an arsenal of proteins that are implicated in maintaining a compatible interaction with its host. (biomedcentral.com)
  • Some of these proteins may have a role in establishing compatible interaction with the host plant. (biomedcentral.com)
  • During the transition, C. truncatum probably secretes a range of proteins to establish a compatible interaction with its host, including some that may exclusively be involved in switching the pathogen to the necrotrophic phase. (biomedcentral.com)
  • Genome-wide interaction analysis of folate for colorectal cancer risk. (cdc.gov)
  • No detectable NA biosynthesis was mediated by two representative plant NAS proteins that naturally lack the C-terminal domain, class Ia Arabidopsis halleri NAS5 and Medicago truncatula NAS2 of class II which is found in dicots and diverged early during the evolution of flowering plants. (bvsalud.org)
  • Sequence comparisons indicate that DcE2F1 could be an ortholog of the AtE2FA factor of Arabidopsis thaliana. (cardiff.ac.uk)
  • 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)
  • 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)
  • 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)
  • 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)
  • During Adv DNA replication, host cellular proteins such as nuclear factor I and POU2F1 are used by Adv [ 13 , 14 ]. (hindawi.com)
  • The small heat shock proteins (sHsps) play a major role in cellular responses to environmental stressors. (usda.gov)
  • Phosphorylation plays critical roles in the regulation of many cellular processes, including cell cycle, growth, apoptosis and signal transduction pathways. (ucsd.edu)
  • 5] "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. (tcdb.org)
  • Our preliminary study using 2D isolates were recovered from liq- new cases throughout the world cu- gel electrophoresis in drug sensitive/ uid nitrogen, and sub-cultured in taneous leishmaniasis (CL) remains resistant strains of L. tropica showed RPMI1640 medium (Gibco/BRL) a serious public health problem in that some proteins were differentially supplemented with 10% fetal bovine numerous countries [1,2]. (who.int)
  • Updated criteria for enumerating a case of reinfection are included based on recent studies indicating that different sequenced SARS-CoV-2 strains can be detected at different time points from weeks to months after initial diagnosis. (cdc.gov)
  • The aim of the present study is to replicate the effects of the plasma levels of MHC class I polypeptide-related sequence B (MICB) and cluster of differentiation 209 (CD209) proteins reported in a previous hypothesis-free MR study. (plos.org)
  • The spliceosome complex, composed of at least 170 proteins and several small nuclear RNAs (snRNAs), is the key structure responsible for splicing in eukaryotes 10 . (nature.com)
  • This study identified the biochemical compositions of kimchi extracts from Korea and China by 1 H nuclear magnetic resonance (NMR) spectroscopy followed by multivariate data analysis. (go.jp)
  • Widespread domain in signalling and nuclear proteins. (embl.de)
  • The F8(scFv)-DAAO-Q144R recombinant protein is expressed by each CHO-S and E. coli cells. (holliseden.com)
  • Phylogeny based on concatenated sequences of 125 conserved ORFs showed that this isolate clustered most closely with the Mkuzi 1979 isolate. (cdc.gov)
  • Finally, by combining the sequence recognition model with the quantitative changes in phosphorylation measured in the two drug perturbation experiments, we identified 29 reliable candidates of PKA targeting residues in living cells including 8 previously known substrates. (nih.gov)
  • Quantitative analysis of NAD synthesis-breakdown fluxes. (springer.com)
  • siRNA Database - [A] comprehensive siRNA database that contains siRNA targets against all known mRNA sequences throughout a variety of organisms. (fenteany.com)
  • Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. (embl.de)
  • The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug. (embl.de)
  • We analyzed the effects of aging on protein abundance and acetylation, as well as the ability of the mitochondrial-targeted drugs elamipretide (SS-31) and nicotinamide mononucleotide (NMN) to reverse aging-associated changes in mouse hearts. (springer.com)
  • Both drugs had a modest effect on restoring the abundance and acetylation of proteins that are altered with age, while also inducing additional changes. (springer.com)
  • Age-related increases in protein acetylation were predominantly in mitochondrial pathways such as mitochondrial dysfunction, oxidative phosphorylation, and TCA cycle signaling. (springer.com)
  • These form a ring structure that is proposed to encircle sister chromatids to mediate sister chromatid cohesion and also has key roles in gene regulation. (nih.gov)
  • Furthermore, we augmented cell-free RNA network analysis with single-cell RNA sequencing data which enables the contextualization of the identified network modules with cell-type specific transcriptomes from the liver. (frontiersin.org)
  • Hence, we performed WGCNA analysis on cfRNA data derived from the blood of HCC patients. (frontiersin.org)
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
  • The European Ribosomal RNA Database - Ribosomal RNA (rRNA) sequence data listed by organism, secondary structure prediction programs and other software, links to related sites. (fenteany.com)
  • Dr. Matulka has more than a decade of experience in the analysis of toxicity data and conducting safety and risk assessments. (hesiglobal.org)
  • For MICB and CD209, we used data from a large-scale genome-wide association study (GWAS) for plasma protein levels (N = 3,301). (plos.org)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
  • A BASE project is used to group items (biomaterial, raw data, and experiments) into a logical entity, and a BASE experiment is a collection of bioassays, e.g., array data, grouped logically together for further analysis. (lu.se)
  • The file storage is an integral part of a strategy to store all experiment relevant data in BASE, even data types not already supported in analysis. (lu.se)
  • Collecting all data allows future reuse of the data as more data are produced, and new analysis tools becomes available. (lu.se)
  • BASE features a hierarchically organised analysis interface that allows data filtering, normalisation, transformation, and other analyses. (lu.se)
  • LC-MS/MS analyses identified 2755 and 3191 phosphopeptides from experiments with activator or inhibitor of PKA. (nih.gov)
  • TET2 encodes a protein that catalyzes DNA demethylation. (researchamerica.org)
  • Genotyping of ASFV isolates by partial sequencing of the B646L gene that encodes the major capsid protein p72 has identified 22 genotypes ( 6 ). (cdc.gov)
  • 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)
  • 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)
  • 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)
  • We have used deletion analysis to determine whether the yeast-specific U1 sequences play essential roles in vivo. (umn.edu)
  • The boundaries of the viable deletions define a dispensable internal domain which comprises sequences unique to yeast. (umn.edu)
  • The E1 helicase is regulated at least in part by protein phosphorylation, however no systematic approach to phosphate site mapping has been attempted. (biomedcentral.com)
  • A number of individual phosphorylation sites on BPV E1 have been identified by several groups, but no systematic effort to identify all of the phosphorylated amino acid positions of this protein has been undertaken. (biomedcentral.com)
  • In addition to accumulating more case series of EBV-associated gastric carcinoma (EBVaGC), the development of comprehensive molecular analyses has provided evidence that EBVaGC is a distinct subset both in terms of its clinicopathological and molecular features. (spandidos-publications.com)
  • Therefore, the aim of the present study was to identify a regulatory signaling pathway in cardiac inflammation based on the hypothesis that a distinct subset of inflammation-related activated fibroblasts plays crucial roles in the recruitment of inflammatory cells, especially monocytes/macrophages, and in the pathology of heart failure. (kcl.ac.uk)
  • 2021. Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting . (ncbs.res.in)
  • We report the complete genomic coding sequence of the Georgia 2007/1 isolate and comparison with other isolates. (cdc.gov)
  • 90,000 animals died or were destroyed (www.oie.int). Experimental infections of pigs confirmed that isolates obtained after introduction of ASF into Armenia and the Russian Federation cause acute disease and result in high mortality rates (www.efsa.europa.eu/en/scdocs/scdoc/1556.htm). (cdc.gov)
  • 172 Computational analysis and prediction of proteins that undergo domain swapping. (ncbs.res.in)