• We developed genomic locus proteomics (GLoPro), in which we combine CRISPR-based genome targeting, proximity labeling, and quantitative proteomics to discover proteins associated with a specific genomic locus in native cellular contexts. (nature.com)
  • ETS proteins share a conserved ETS domain that mediates specific DNA binding. (wikipedia.org)
  • p53 is up-regulated in response to stress signals and stimulated to activate transcription of specific genes, resulting in expression of p21waf1 and other proteins involved in G1 or G2/M arrest. (thermofisher.com)
  • In a previous study, the researchers found that in estrogen receptor-positive and estrogen receptor-negative mammary cell lines of women who have been affected with breast cancer, the tumor-suppressing gene pRb2/p130 binds to a specific region of the estrogen receptor gene alpha and forms molecular complexes recruiting and/or interacting with several proteins. (sciencedaily.com)
  • They discovered that in estrogen receptor-negative cells - which are able to silence the expression of the estrogen receptor - pRb2/p130 forms a specific molecular complex recruiting a different sequence of proteins than in the estrogen receptor-positive cells. (sciencedaily.com)
  • Our hypothesis is that the sequence of epigenetic events for establishing and maintaining the silenced state of the estrogen receptor gene alpha during the breast cancer progression is mediated by pRb2/p130 in association with specific proteins that modified the DNA structure through specific mechanisms," said Giordano, who discovered the Rb2 gene while working at Temple's Fels Cancer Institute in the early 1990s. (sciencedaily.com)
  • 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)
  • Regulatory proteins, namely the Transcription Factors (TFs), bind in a sequence-specific manner to TFBSs to activate or suppress gene transcription (gene expression). (biomedcentral.com)
  • 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)
  • At least four phylogenetically distinct groups of bacteria encode repeat proteins with the common ability to bind specific DNA sequences with a unique but conserved code. (uni-muenchen.de)
  • Repeat arrays of these proteins have been demonstrated or predicted to form almost identical tertiary structures: a right-handed super helix that wraps around the DNA double strand with the base specifying residue of each repeat positioned in the major groove next to its cognate target base. (uni-muenchen.de)
  • In addition the TALEs and RipTALs may simply represent one face of the TALE-likes, a protein family mediating as yet unknown biological roles as bacterial DNA binding proteins. (uni-muenchen.de)
  • Now, "RedChIP" has us stampeding in anticipation towards the exploration of the complex interactions taking place between RNA, DNA, and proteins in the nucleus. (epigenie.com)
  • While RNA-DNA proximity ligation techniques map genome-wide ncRNA interactions , they don´t describe the proteins involved. (epigenie.com)
  • His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)
  • Cytosine modifications directly affect the positioning of nucleosomes (the first level of chromatin organization into chromosome involving the DNA chain wound around a core of 8 histone proteins), and recruit chromatin-modifying complexes that modify histones. (i-sis.org.uk)
  • Therefore, specific localization patterns of GEFs and GTPase-activating proteins, and a molecular network of their regulation underlie the spatiotemporal control of Rho GTPases activities in the cells. (life-science-alliance.org)
  • DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
  • PIAS1, but not other PIAS proteins, blocked the DNA binding activity of Stat1 and inhibited Stat1-mediated gene activation in response to interferon. (nih.gov)
  • This process, known as mating pair stabilization (MPS), is mediated by interactions between the plasmid-encoded outer membrane (OM) protein TraN in the donor and chromosomally-encoded OM proteins in the recipient. (bvsalud.org)
  • These two elements of vector design are critical for the expression efficacy, safety and specificity of the AAV mediated gene therapy. (brighttalk.com)
  • Gene probes are used in various blotting and in situ hybridization (ISH) techniques for the detection of nucleic acid sequences in food industry, environmental, medical, and veterinary applications to improve the specificity of the analyses. (enzolifesciences.com)
  • Each repeat binds a single DNA base, and specificity is determined by the amino acid residue at position 13 of each repeat. (uni-muenchen.de)
  • These HDI-responsive T cells expressed unique oligoclonal gamma/delta rather than alpha/beta T-cell receptors, with characteristics suggestive of antigen-mediated selection and specificity. (cdc.gov)
  • AlphaFold2 predictions suggested that this specificity is mediated by a single amino acid difference in loop 3 of OmpW, which we confirmed experimentally. (bvsalud.org)
  • Furthermore, single-cell-based proteomic and transcriptomic analysis of D4-IgG4H-CD28TM CAR T cells reveals specific genes (e.g. (nature.com)
  • In terms of the therapeutic gene of choice, a single AAV virion can only carry about 4.7KB of cargo DNA, therefore, for large genes, dual AAV vector designs are a necessity. (brighttalk.com)
  • Regions of the L. killicki ( L. tropica ) and L. major genes sequences were scanned using BLAST program and subsequently compared using appropriate bioinformatic tools Chromas and MEGA. (who.int)
  • Tyrosine phosphorylated STATs dimerize and translocate into the nucleus to activate specific genes. (nih.gov)
  • Sequencing and genomic localization of a library of chromatin-DNA fragments bound by Pax7 has identified 34 candidate Pax7 target genes, with occupancy of a selection confirmed with independent chromatin enrichment tests (ChIP-PCR). (edu.au)
  • In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. (biomedcentral.com)
  • Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. (lu.se)
  • Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli. (cdc.gov)
  • Genes are arranged linearly along the DNA of chromosomes. (msdmanuals.com)
  • The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)
  • Encoded by one of two nearly indentical genes: FCGR3A and FCGR3B which are expressed in a tissue-specific manner. (lu.se)
  • Reduction of functional NMDA Receptor in neurons by RNase P-mediated cleavage of the NR1 mRNA. (bcm.edu)
  • Sequence-specific cleavage of Huntington mRNA by catalytic DNA. (bcm.edu)
  • The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. (harvard.edu)
  • We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. (cdc.gov)
  • Although an sgRNA design consisting of a truncated crRNA and tracrRNA had been previously shown to mediate efficient cleavage in vitro 12 , it failed to achieve detectable cleavage at several loci that were efficiently modified by crRNA-tracrRNA duplexes bearing identical guide sequences 1 . (cdc.gov)
  • sgRNAs with +67 or +85 nucleotide (nt) tracrRNA tails mediated DNA cleavage at all target sites tested, with up to fivefold higher levels of indels than the corresponding crRNA-tracrRNA duplexes ( Fig. 1b and Supplementary Fig. 1a ). (cdc.gov)
  • We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)
  • The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
  • This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. (nih.gov)
  • PGC7/Dpp3a/Stella is targeted to the genome via binding to the heterochromatic histone mark H3K9me2 (this refers to a specific amino acid lysine in position 9 on histone H3 that has 2 methyl groups added). (i-sis.org.uk)
  • The genome-wide activity of transcription factors (TFs) on multiple regulatory elements precludes their use as gene-specific regulators. (jci.org)
  • Adeno-associated virus (AAV) vector-mediated ectopic expression of KLF15 in rod photoreceptors of pigs enables Rho silencing with limited genome-wide transcriptional perturbations. (jci.org)
  • Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. (bvsalud.org)
  • To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses. (cdc.gov)
  • Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. (lu.se)
  • We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. (lu.se)
  • Scientists can now sequence an entire genome overnight. (cdc.gov)
  • We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. (lu.se)
  • We want to understand differences in life stage-specific gene expression in the peacock fly and relate these patterns to signatures of selection across the genome. (lu.se)
  • The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. (imperial.ac.uk)
  • After a systematic evaluation of DNA analogs for improved triple helix formation in cells, we have focused on peptide nucleic acids (PNAs), which have a neutral polyamide backbone and bind DNA with high affinity. (yale.edu)
  • Many new nucleic acid-based diagnostic tools or assays have been developed that allow analysis of DNA and RNA molecules in clinical samples. (enzolifesciences.com)
  • Nucleic acid probes are either a single stranded DNA or RNA with a strong affinity towards a specific DNA or RNA target sequence. (enzolifesciences.com)
  • In theory, any nucleic acid can be used as a probe provided it can be labeled to permit detection and quantitation of the hybrid molecules formed between the probe and sequence to be identified. (enzolifesciences.com)
  • NcRNAs such as those involved in RNA interference can be independently inherited, and can also direct chromatin modification and DNA methylation see [7, 8] RNA Inheritance of Acquired Characters , and Nucleic Acid Invaders from Food Confirmed , SiS 63). (i-sis.org.uk)
  • Multi-parameter Chlamydia trachomatis and Neisseria gonorrhea (CT/NG) Nucleic Acid Amplification combination test uses PCR or Ligase chain reaction methods to amplify nucleic acid sequences of C. trachomatis and N. gonorrhea, by targeting specific nucleic acid sequences. (medicaldevice-network.com)
  • DNA or RNA is used as a template for transcription and reverse transcription reactions in series also known as transcription mediated amplification or nucleic acid sequence-based amplification. (medicaldevice-network.com)
  • Detection of the rRNA amplification product sequences is achieved using nucleic acid hybridization (HPA). (cdc.gov)
  • Understanding how signals might inform cells of their positional identity, directionality, and interactions and organize these functions in diverse tissue-specific patterns is critical to understanding morphogenesis. (biorxiv.org)
  • Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
  • As a parallel to HiChIP , which takes a protein-centric view of mapping DNA-DNA interactions , RedChIP evaluates RNA-DNA interactions occurring with a given protein. (epigenie.com)
  • Finally, RNA-DNA sequencing reports on RNA-DNA interactions mediated by the protein and protein-DNA interactions mediated by RNAs. (epigenie.com)
  • Indeed, the identification of Kcnq1ot1, which targets Polycomb complexes to repressed genomic domains, and the significant overlap of ncRNAs isolated via a conventional technique suggest that RedChIP represents the way forward for studies of RNA-protein-DNA interactions in live cells. (epigenie.com)
  • Amplification initiates from strand invasion by one of the inner primers and a stand displacing DNA polymerase extends the primer and separates the target DNA duplex. (neb.com)
  • This annealing and displacement cycle repeats on the opposite end of the target sequence and the resulting product is a short dumbbell structure that forms a seed for exponential lamp amplification. (neb.com)
  • The result is a rapid accumulation of double-stranded DNA and the amplification by-products that can be detected by a variety of methods. (neb.com)
  • Mediated Isothermal Amplification based assays for the selective and/or specific identification of, and discrimination among the two (2) Leishmania species encountered in Tunisia. (who.int)
  • We opted for conserved sequences between species, presenting enough sequence heterogeneities to be considered for the design of species- specific LAMP primers: such primers would allow the selective amplification of the DNA targets. (who.int)
  • The sequences identified in the previous section of the work were used to design a combinations of 6 primers in 8 distinct regions of the target sequences for the amplification of a selection of reference DNAs belonging to the different Old World Leishmania species. (who.int)
  • The GEN-PROBE APTIMA M. genitalium assay combines the technologies of target capture, Transcription-Mediated Amplification (TMA), and Dual Kinetic Assay (DKA). (cdc.gov)
  • SPIB and SPI1 bind to a purine-rich sequence, the PU box (5-prime-GAGGAA-3-prime). (wikipedia.org)
  • Mutants of p53 that frequently occur in a number of different human cancers fail to bind the consensus DNA binding site, and cause the loss of tumor suppressor activity. (thermofisher.com)
  • The DNA binding domain(s) of a TF can recognize and bind to a collections of similar TFBSs, from which a conserved pattern called motif can be obtained. (biomedcentral.com)
  • However, RBPJL can bind to canonical RBPJ DNA elements and shows migration dynamics comparable to that of RBPJ in the nuclei of living cells. (uni-ulm.de)
  • During the hybridization step, the sequence specific regions of the capture oligomers bind to specific regions of the target molecules. (cdc.gov)
  • Specific molecular probes and primers are designed for this purpose. (enzolifesciences.com)
  • DNA/RNA probe assays are faster and sensitive so that many conventional diagnostic tests for viruses and bacteria involving culturing of the organisms are being fast replaced by molecular probe assays. (enzolifesciences.com)
  • Molecular probes can be broadly categorized into DNA probes and RNA probes, cDNA probes, and synthetic oligonucleotide probes. (enzolifesciences.com)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • Using molecular modeling, biochemical and functional assays, as well as single-molecule time-lapse imaging, we show that RBPJL and RBPJ, despite limited sequence homology, possess a high degree of structural similarity. (uni-ulm.de)
  • Most enzyme-mediated labeling techniques are very much dependent on polymerase activity, which is responsible for incorporation of the labeled nucleotides. (enzolifesciences.com)
  • The annealed primers ultimately become part of the probe itself, because the Klenow fragment of DNA polymerase I extends the primers in the 3′ direction and, in so doing, incorporates the label. (enzolifesciences.com)
  • Next, the enzyme DNA polymerase I removes the native nucleotides from the probe molecules in the 5′→3′ direction (exonuclease activity) while replacing them with labeled dNTP precursors by virtue of its 5′→3′ polymerase activity. (enzolifesciences.com)
  • The process involves a polymerase chain reaction or ligase chain reaction with specific primers, nucleotide triphosphates, and taq polymerase leading to the production of detectable amounts of DNA or RNA. (medicaldevice-network.com)
  • 5fC and 5caC are excised by mammalian DNA glycosylase TDG, implicating 5mC oxidation in DNA demethylation. (nih.gov)
  • Our results reveal roles of active 5mC/5hmC oxidation and TDG-mediated demethylation in epigenetic tuning at regulatory elements. (nih.gov)
  • Moreover, in the ketamine group, the level of Ten‑Eleven‑Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription‑quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. (spandidos-publications.com)
  • In contrast, the Ten-Eleven-Translocation (TET) dioxygenase family, including TET1, TET2 and TET3, mediates active DNA demethylation and hydroxylate-methylated DNA by converting 5-methylcyto-sine to 5-hydroxymethylcytosine to regulate DNA methylation status. (spandidos-publications.com)
  • Here we show that in young proliferating embryonic fibroblasts (MEFs) the Polycomb Repressive Complex 2 (PRC2) member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD) identified as a DNA replication origin. (plos.org)
  • The structure of p53 comprises an N-terminal transactivation domain, a central DNA-binding domain, an oligomerisation domain, and a C-terminal regulatory domain. (thermofisher.com)
  • Transcription Factor Binding Sites (TFBSs) are small nucleotide fragments (usually ≤ 30 bp) in the cis-regulatory/intergenic regions in DNA sequences. (biomedcentral.com)
  • We are currently pursuing studies of the dominant signaling and gene regulatory networks that control this process, including the Ras/MAPK cascade, which is required for stem cell-mediated self-renewal and the p53 transcription factor family member, p63, which is required for epidermal differentiation. (stanford.edu)
  • This disruption can be prevented by the inhibition of viral DNA synthesis, suggesting the existence of novel and potent regulatory mechanisms linked to either viral DNA replication or late gene expression. (nih.gov)
  • Recurrent chimeric RNAs enriched in human prostate cancer identified by deep-sequencing. (bcm.edu)
  • instead, they combined RNA-DNA proximity ligation ( Red-C ) with chromatin immunoprecipitation (ChIP) to create RedChIP, which identifies RNAs associated with a DNA-bound protein of interest. (epigenie.com)
  • The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)
  • The ssRNA(+), likely transferred into the nucleolus, is finally processed by a type III RNase and a DNA LIGASE into unit-length circular RNAs (8) ( Figure 1 ). (degruyter.com)
  • Cyclin-dependent kinase 2 (CDK2) is a key mediator for EGF-induced cell transformation mediated through the ELK4/c-Fos signaling pathway. (nih.gov)
  • These results identify PIAS1 as a specific inhibitor of Stat1-mediated gene activation and suggest that there may exist a specific PIAS inhibitor in every STAT signaling pathway. (nih.gov)
  • An ASNA1 point mutant identified using CRISPR-mediated mutagenesis abolishes both the cytoprotective effect of Retro-2 against ricin and its inhibitory effect on ASNA1-mediated ER-targeting. (elifesciences.org)
  • The CRISPR/Cas9 system has been implemented in a variety of model organisms to mediate site-directed mutagenesis. (harvard.edu)
  • Furthermore, the use of Taq or other thermostable DNA polymerases permits labeling reactions to be performed at higher temperatures via PCR, thereby reducing the incidence of enzyme-mediated point mutations during probe synthesis. (enzolifesciences.com)
  • protein sequences were analysed with a major concern [1,2]. (who.int)
  • The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
  • Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. (biomedcentral.com)
  • A DNA probe is a labeled fragment of DNA that contains a nucleotide sequence specific for the gene or chromosomal region of interest. (enzolifesciences.com)
  • Additionally, the tissue-specific promotors allow for targeted expression of the transgene in the disease tissues. (brighttalk.com)
  • This process is mediated by 2 mutually exclusive programs of gene expression: 1) an undifferentiated program supporting proliferation by stem cells within the basal layer and 2) a differentiation program instructing growth arrest and differentiation-associated programmed cell death in suprabasal layers. (stanford.edu)
  • Epigenetic control of gene expression lasts through multiple cell divisions without alterations in primary DNA sequence and can occur via mechanisms that include histone modification and DNA methylation. (stanford.edu)
  • Upon depletion of RBPJ using CRISPR/Cas9, we observed specific upregulation of Notch target gene expression. (mdpi.com)
  • Here we show that ectopic expression of a TF in a cell-specific context can be used to silence the expression of a specific gene as a therapeutic approach to regulate gene expression in human disease. (jci.org)
  • We selected the TF Krüppel-like factor 15 (KLF15) based on its putative ability to recognize a specific DNA sequence motif present in the rhodopsin (RHO) promoter and its lack of expression in terminally differentiated rod photoreceptors (the RHO-expressing cells). (jci.org)
  • Moreover, DNA hypomethylation of the COX‑2 promoter region located from ‑1,522 to ‑829 bp might contribute to transcriptional regulation of COX‑2 expression and induce a pro‑inflammatory response in KIC. (spandidos-publications.com)
  • To assess the capacity of Pax7 to regulate transcription from these loci, we have cloned alternate transcripts of Pax7 (differing significantly in their DNA binding domain) into expression vectors and transfected cultured cells with these constructs, then analyzed target gene expression levels using RT-PCR. (edu.au)
  • We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant correlation with gene expression profiles. (lu.se)
  • Changes in gene expression mediate growth and development in all living organisms. (lu.se)
  • The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)
  • Targeting DNA methylation with small molecules: what's next? (google.fr)
  • In this work, we use isotope incorporation within DNA molecules to model taxon-specific population growth in the presence of 18 O-labeled water. (osti.gov)
  • Nick translation is efficient for both linear and covalently closed DNA molecules, and labeling reaction are completed in less than an hour. (enzolifesciences.com)
  • At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
  • The capture oligomers contain sequences complementary to specific regions of the target molecules as well as a string of deoxyadenosine residues. (cdc.gov)
  • The GEN-PROBE TMA reaction replicates a specific region of the small ribosomal subunit from T. vaginalis via DNA and RNA intermediates and generates RNA amplicon molecules. (cdc.gov)
  • This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. (cancerindex.org)
  • When designing a LAMP experiment, four to six primers are required, specific to identified regions of target DNA or RNA sequence. (neb.com)
  • Random priming is a type of primer extension in which a mixture of small oligonucleotide sequences, acting as primers, anneal to a heat-denatured double-stranded template. (enzolifesciences.com)
  • Detection of the IS Ecp1B sequence munity, mostly in hospitals and often in ité de l'Antibiogramme de la Société was performed by PCR using primers intensive care units (ICUs) [3]. (who.int)
  • When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. (osti.gov)
  • In this review we discuss recent advances in our understanding of the function of the TraN sensor at the donor-recipient interface, used by F-like plasmids to select bacterial hosts within polymicrobial communities prior to DNA transfer. (bvsalud.org)
  • The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. (who.int)
  • data for specific Pacific Island coun- in SXT elements for insertion of 8. (cdc.gov)
  • Importantly, RBPJL is not able to interact with Notch−1 to −4 and it does not support Notch-mediated transactivation. (uni-ulm.de)
  • However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists' understanding of how microbial populations interact to regulate ecosystem processes. (osti.gov)
  • The labeled DNA probe combines with amplicon to form stable RNA: DNA hybrids. (cdc.gov)
  • During the detection step, light emitted from the labeled RNA: DNA hybrids is measured as photon signals in a luminometer, and are reported as Relative Light Units (RLU). (cdc.gov)
  • It involves randomly nicking the backbone of a double-stranded DNA with dilute concentrations of DNase I. At extremely low concentrations, this enzyme nicks a template at four or five sites, producing a free 3′-OH group that can act as a primer at each nicking location. (enzolifesciences.com)
  • The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. (imperial.ac.uk)
  • These host LANA-binding sites are generally found within transcriptionally active promoters and display striking overrepresentation of a consensus DNA sequence virtually identical to the LBS1 motif in KSHV DNA. (nih.gov)
  • Following crRNA and tracrRNA hybridization, SpCas9 is targeted to genomic loci matching a 20-nt guide sequence within the crRNA, immediately upstream of a required 5′-NGG protospacer adjacent motif (PAM) 11 . (cdc.gov)
  • Conjugation has been regarded as a promiscuous mechanism of DNA transfer, with host range determined by the recipient downstream of plasmid transfer. (bvsalud.org)
  • Moreover, we show that single amino acids insertions into loop 3 of OmpK36 affect TraNß-mediated conjugation efficiency of the K. pneumoniae resistance plasmid pKpQIL. (bvsalud.org)
  • According to a procedure that has been previously validated for the identification of species - specific targets among which some fragments would fit into the second category of sequences expected. (who.int)
  • In case of homologies identified with the other Leishmania species, these sequences were compared to L. major and/or L. tropica using MEGA software. (who.int)
  • The objective here is to develop LAMP assays specific for each of the Leishmania species so far encountered in Tunisia. (who.int)
  • First of all we proceeded to an alignment using the CLUSTAL W program to each Leishmania species and for the selected gene (cysteine protase b) (the alignment use published sequences and sequences which were sequenced in our laboratory). (who.int)
  • Cytosine methylation of DNA involves a subset of genomic cytosines methylated at the C5 position in some species. (i-sis.org.uk)
  • One of the methods that does seem to work well is TargetScan, which relies on both pairing of seed sequences (a subset of the 18-23 bp that make up a miRNA) and phylogenetic conservation of sites. (lu.se)
  • A single-stranded chemiluminescent DNA probe, which is complementary to a region of the target amplicon, is labeled with different acridinium ester molecule. (cdc.gov)
  • allow proceeding to the in silico comparative genomics analysis of Leishmania DNAs and annotating the sequences identified. (who.int)
  • The sequences were analyzed in silico by BLAST searching for homologies with other DNAs deposited in the local and public data bases. (who.int)
  • Here, we characterized the function of RBPJL, a pancreas-specific paralog of RBPJ. (mdpi.com)
  • In the pancreas, a specific paralog of RBPJ, called RBPJL, is expressed and found as part of the heterotrimeric PTF1-complex. (uni-ulm.de)
  • Agherbi H, Gaussmann-Wenger A, Verthuy C, Chasson L, Serrano M, Djabali M (2009) Polycomb Mediated Epigenetic Silencing and Replication Timing at the INK4a/ARF Locus during Senescence. (plos.org)
  • Click "Sequence Details" to view all sequence information for this locus, including that for other strains. (yeastgenome.org)
  • Using the SURVEYOR nuclease assay 13 , we assessed the ability of each Cas9-sgRNA complex to generate indels in human embryonic kidney (HEK) 293FT cells through the induction of DNA doublestranded breaks (DSBs) and subsequent nonhomologous end joining (NHEJ) DNA damage repair (Online Methods). (cdc.gov)
  • This affinity and complementary sequence allow binding to specific regions of a target sequence of nucleotides. (enzolifesciences.com)
  • In eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. (degruyter.com)
  • DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
  • Together, these results demonstrate subtype- and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis. (lu.se)
  • 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)
  • Biotin can be installed subsequently for specific enrichment of 5fC. (nih.gov)
  • In F-like plasmids, efficient DNA transfer is mediated by close association between donor and recipient bacteria. (bvsalud.org)
  • In the current study, lead by Antonio Giordano, M.D., Ph.D., director of the Sbarro Institute, the researchers showed that the presence of specific pRb2/p130 multimolecular complexes bound to the estrogen receptor gene strongly correlates with the methylation (chemical modification) of the gene. (sciencedaily.com)
  • then, a specific antibody immunoprecipitates protein-associated RNA-DNA complexes. (epigenie.com)
  • As it is displaced, the end of the product forms a self-hybridizing loop structure, due to inclusion of a reverse complementary sequence in the inner primer sequence. (neb.com)
  • 2. Develop additional strategies to deliver affordable, simple DNA based tools and protocols for the rapid, sensitive and specific Leishmania parasites detection concomitant to their identification/ differentiation. (who.int)
  • We also report the development and application of a single-base resolution method for the detection of 5fC in genomic DNA by hydroylamine mediated protection of 5fC from deamination during bisulfite treatment, or 5fC Chemical Assisted Bisulfite Sequencing (fCAB-Seq). (nih.gov)
  • Cooperative activity of GR with other transcription factors and a plethora of coregulators contribute to the tissue- and context-specific response toward the endogenous and pharmacological glucocorticoids (GCs). (uni-ulm.de)
  • In this review, we take a wide view of this problem by analyzing the strategies involved in setting up normal DNA methylation patterns and understanding how this stable epigenetic mark works to prevent gene activation during development. (aacrjournals.org)
  • Sequencing and other techniques may reveal the actual genetic defects in these patients. (medscape.com)
  • In other words, the presence of a specific pRb2/p130 multimolecular complex may dictate a local change of the DNA structure of the estrogen receptor alpha gene and influence its susceptibility to chemical modification (DNA methylation), as well as to different epigenetic alterations leading to estrogen receptor alpha silencing," added Marcella Macaluso, research assistant professor at the Sbarro Institute and the study's lead author. (sciencedaily.com)
  • Here, we show that FGF is Glycosylphosphatidylinositol-anchored to the producing cell surface and that this modification both inhibits free FGF secretion and activates target-specific bidirectional FGF-FGFR signaling through cytonemes. (biorxiv.org)
  • In this review article, we have adopted a developmental approach for understanding what DNA methylation actually does, and this suggests new concepts for the role of this modification in tumorigenesis. (aacrjournals.org)
  • Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. (plos.org)
  • Furthermore, by investigating the impact of hinge (CD8 and IgG4) and TM (CD8 and CD28) on D4 CAR T cells, we discover that IgG4H-CD28TM mediated D4 CAR dimerization, leading to enhanced T-cell signaling and tumor regression in pancreatic cancer models with low antigen density. (nature.com)
  • Contact-mediated FGF-FGFR binding induces bidirectional signaling, which, in turn, promotes ASP and source cells to polarize cytonemes toward each other and reinforce signaling contacts. (biorxiv.org)
  • Thus, GPI-anchored FGF organizes both source and recipient cells and self-regulates its cytoneme-mediated tissue-specific dispersion and signaling. (biorxiv.org)
  • The discrete tissue-specific organization of morphogen signaling is known to be dependent on the ability of signal-receiving cells to selectively sense and respond to a specific signal 3 . (biorxiv.org)
  • DNA sequence analysis of T-cell receptors was used to further define clonal populations of HDI-responsive T cells. (cdc.gov)
  • HDI antigen preparations but not "mock exposed" control antigens lead to increased proliferation of specific cell types, CD3+CD4-CD8(dim) and/ or CD3+CD4-CD8- cells, from HDI-exposed but not from HDI-unexposed subjects. (cdc.gov)