• A mutation within the β subunit of Escherichia coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters. (nih.gov)
  • Pathway-level mutation analysis in primary high-grade serous ovarian cancer and matched brain metastases. (cdc.gov)
  • Our analyses of IDH1 mutations in for R132C mutations in astrocytes or glioblastomas from a population- precursor cel s that already carry a based study (407 cases) showed that germline TP53 mutation. (who.int)
  • Next\generation sequencing of 416 malignancy\relevant genes in 139 resected lung cancers exposed the co\mutational panorama with background mutation. (accessibletech4all.org)
  • This study reported the mutational analysis of one Chinese family with Crouzon syndrome at the gene level, along with related clinical features, and identified one heterozygous mutation. (molvis.org)
  • Every mutation detected on the DNA level causes an amino acid substitution within one of the functional domains of the tumor suppressor protein. (nih.gov)
  • To gain a better understanding of the role of MMP-20 in normal and defective enamel formation, we developed and used a strategy for mutational analyses of the human MMP20 gene and have identified the first MMP20 gene mutation in a family with amelogenesis imperfecta. (bmj.com)
  • The results may indicate a common ancient origin for the 999del5 mutation in Iceland and in Finland, but distinct mutational events cannot be ruled out. (nih.gov)
  • PCR amplification and DNA sequence analysis or allele-specific PCR for BRAF V600E mutation status are performed on formalin-fixed, paraffin-embedded tissue from the primary tumor or a metastasis. (medscape.com)
  • This analysis showed that at any given time 20.1% of the mutants from Hodgkin's disease patients and 17.5% of the mutants from squamous cell carcinoma patients consisted of siblings, identified as having identical polymerase chain reaction/single-stranded conformation polymorphism patterns. (cdc.gov)
  • The remaining mutants had unique polymerase chain reaction/single-stranded conformation polymorphism patterns and therefore can be presumed to have arisen from independent mutational events. (cdc.gov)
  • A total of 41 β-thalassaemia carriers and 40 control subjects without haemoglobinopathies were screened for the C282Y, H63D and S65C mutations by polymerase chain reaction-restriction fragment-length polymorphism. (who.int)
  • Unlike proteins and RNA , DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. (wikipedia.org)
  • DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage. (wikipedia.org)
  • The mediator complex physically links transcription factors, which are proteins that influence whether genes are turned on or off, with an enzyme called RNA polymerase II. (medlineplus.gov)
  • Once transcription factors are attached, this enzyme initiates gene transcription, the process by which information stored in a gene's DNA is used to build proteins. (medlineplus.gov)
  • Specifically, while Cas10 has a known DNA nuclease domain, it also encodes two Palm domains (with similarity to nucleotide polymerase and cyclase proteins) of unknown function. (nature.com)
  • A genome contains coding information that specifies protein and RNA sequences and structural information that specifies local DNA conformation involved in interactions with proteins. (biomedcentral.com)
  • DNA polymerase δ (Polδ) plays an essential role in replication from yeast to humans. (utmb.edu)
  • We investigated the effect of BP-3 and PP on estrogen receptor-dependent transactivation and DNA damage at concentrations relevant to exposures in humans. (nih.gov)
  • Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. (biorxiv.org)
  • This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
  • 2. New Perspectives on the Recurrent Monoallelic Germline Mutations of DNA Repair and Checkpoint Genes and Clinical Variability. (nih.gov)
  • Ten nanograms of DNA from each sample was tested for mutations in the hotspot regions of 46 cancer-related genes using a 318-chip on Ion PGM Sequencer. (nih.gov)
  • Genomic Landscape of Primary and Recurrent Anal Squamous Cell Carcinomas in Relation to HPV Integration, Copy-Number Variation, and DNA Damage Response Genes. (cdc.gov)
  • DNA was extracted from formalin-fixed, paraffin-embedded sections and analyzed for mutations using a 21-gene panel (including 13 well-known HRR genes) by next-generation sequencing. (frontiersin.org)
  • A customized xGen lockdown probe panel (Integrated DNA Systems, Skokie, IL) was utilized for targeted enrichment of 416 predefined genes. (accessibletech4all.org)
  • Many genes that were initially shown to influence life span have turned out to be involved in DNA damage repair and protection. (wikipedia.org)
  • The phytochemical 3,3'-diindolylmethane decreases expression of AR-controlled DNA damage repair genes through repressive chromatin modifications and is associated with DNA damage in prostate cancer cells. (oregonstate.edu)
  • We obtained an average of 81 million reads per sample from the RNA-Seq data, of which 90% were retained for further analysis based on the mapping results, the vast majority (94.0%) of which localized to protein coding genes. (nature.com)
  • Use of restriction endonucleases to analyze and generate a physical map of genomes, genes , or other segments of DNA . (lookformedical.com)
  • 5. Tumor immune microenvironment is influenced by frameshift mutations and tumor mutational burden in gastric cancer . (nih.gov)
  • Analysis of DNA Damage Response Gene Alterations and Tumor Mutational Burden Across 17,486 Tubular Gastrointestinal Carcinomas: Implications for Therapy. (cdc.gov)
  • Pathogenic alterations, molecular signatures, tumor mutational burden (TMB), and copy number alterations (CNA) were correlated with pattern of invasion.45 HPVA (11 pattern A, 17 pattern B and 17 pattern C tumors) were included. (stanford.edu)
  • Genetic analyses of mutations in these PIPs have revealed that in the absence of functional Pol32 PIP domain, PCNA binding by both the Pol3 and Pol31 subunits becomes essential for cell viability. (utmb.edu)
  • Based on our biochemical and genetic studies we infer that yeast Polδ can simultaneously utilize all three PIP motifs during PCNA-dependent DNA synthesis, and suggest that Polδ binds the PCNA homotrimer via its three subunits. (utmb.edu)
  • Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. (cancerindex.org)
  • Molecular and genetic analysis demonstrated that PDXs rely primary tumor characteristics, making them suitable models to study pathogenesis and to test anti-cancer drugs activity. (biomedcentral.com)
  • METHODS: We analyzed the mutational spectra associated with somatic BRCA1/2 truncations in multiple genomic cohorts (N = 2,335). (nih.gov)
  • Molecular markers such as mutational spectra or mRNA expression patterns may give some indication of the mechanisms of carcinogenesis induced by fibers and other carcinogens. (nih.gov)
  • 2021. UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin. (nih.gov)
  • Each 5' end is covalently linked to a terminal protein, which is essential in the replication process by acting as a primer for the viral DNA polymerase. (wikipedia.org)
  • Individual products of DNA damage are incorporated into viral genomes for in vivo mutagenesis experiments. (vanderbilt.edu)
  • It is being increasingly used in molecular biology for multiple displacement DNA amplification procedures, and has a number of features that make it particularly suitable for this application. (wikipedia.org)
  • Φ29 polymerase enzyme is already used in multiple displacement amplification (MDA) procedures (including in a number of commercial kits) whereby fragments tens of kilobases in length can be produced from non-specific hexameric primers annealing at intervals along the genome. (wikipedia.org)
  • Polymerase mistakes during pre-amplification generate point mutations resulting from base mis-incorporations and rearrangements due to template switching [26, 27]. (justia.com)
  • The library was then subjected to polymerase chain reaction (PCR) amplification and purification before targeted enrichment. (accessibletech4all.org)
  • To exclude culture- cloning assay with direct analysis of nested reverse tran- derived artifacts and estimate mutational heterogeneity, scription-polymerase chain reaction products in sequence. (cdc.gov)
  • In vitro experiments have shown that Φ29 replication can proceed to completion with the sole phage protein requirements of the polymerase and the terminal protein. (wikipedia.org)
  • The polymerase catalyses the formation of the initiation complex between the terminal protein and the chromosome ends at an adenine residue. (wikipedia.org)
  • The polymerase is a monomeric protein with two distinct functional domains. (wikipedia.org)
  • A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing. (nih.gov)
  • A 3D puzzle approach to building protein-DNA structures. (nih.gov)
  • Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program. (nih.gov)
  • Mutational analysis of the T4 gp59 helicase loader reveals its sites for interaction with helicase, single-stranded binding protein, and DNA. (nih.gov)
  • Here we show that PCNA interacting protein (PIP) motifs in all three subunits contribute to PCNA-stimulated DNA synthesis by Polδ, and mutational inactivation of all three PIP motifs abrogates its ability to synthesize DNA with PCNA. (utmb.edu)
  • PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein. (umassmed.edu)
  • Single molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions. (umassmed.edu)
  • Structure and Function of the PriC DNA Replication Restart Protein. (umassmed.edu)
  • Development of a single-stranded DNA-binding protein fluorescent fusion toolbox. (umassmed.edu)
  • Interaction with single-stranded DNA-binding protein localizes ribonuclease HI to DNA replication forks and facilitates R-loop removal. (umassmed.edu)
  • From an analysis of a limited number (9 to 36) of bacterial chromosomes, it has been proposed that there is an overall excess of purines ('purine excess') or keto bases G and T ('keto excess') in the protein coding sequences (CDS) [ 7 - 9 ]. (biomedcentral.com)
  • RNA sequencing and expression analysis reveal a role for Lhx9 in the haploinsufficient adult mouse ovary. (otago.ac.nz)
  • The advent of affordable benchtop next-generation sequencing platforms such as the semiconductor-based Ion Personal Genome Machine (PGM) Sequencer has facilitated multi-gene mutational profiling using only nanograms of DNA. (nih.gov)
  • of these, 31 specimens yielded sufficient DNA for next-generation sequencing testing. (nih.gov)
  • The results of this study show that next-generation sequencing-based mutational profiling can be performed on fine needle aspiration cytological smears and cell blocks. (nih.gov)
  • Next-generation sequencing can be performed with only nanograms of DNA and has better sensitivity than traditional sequencing platforms. (nih.gov)
  • Polymerase chain reaction followed by direct sequencing was used to detect mutations in the M1S1 gene. (nih.gov)
  • Sequencing results were confirmed with restriction analysis. (nih.gov)
  • Using whole-exome and RNA sequencing we demonstrate that PHF6 and BCORL1 mutations, IKZF1 deletions, and AID/RAG-mediated rearrangements are enriched in RUNX1 mut BP-CML leading to typical mutational signature. (nature.com)
  • Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. (justia.com)
  • However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. (justia.com)
  • This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. (justia.com)
  • The advent of massively parallel DNA sequencing has ushered in a new era of genomic exploration by making simultaneous genotyping of hundreds of billions of base-pairs possible at small fraction of the time and cost of traditional Sanger methods [1]. (justia.com)
  • Although, in theory, DNA subpopulations of any size should be detectable when deep sequencing a sufficient number of molecules, a practical limit of detection is imposed by errors introduced during sample preparation and sequencing. (justia.com)
  • Library Preparation and Sequencing Genomic DNA was fragmented into 300350 base pairs using the Covaris M220 (Covaris, Woburn, MA). (accessibletech4all.org)
  • The assay has a mean target coverage of 180X for the normal (germline) and 400X for tumor DNA including enhanced probe design to facilitate the sequencing of difficult regions. (oncotarget.com)
  • Limouse C, Jukam D, Smith OK, Fryer KA and Straight AF, 2020, Mapping Transcriptome-Wide and Genome-Wide RNA-DNA Contacts with Chromatin-Associated RNA Sequencing (ChAR-seq). (stanford.edu)
  • Peripheral blood was obtained from them to detect hMLHI and hMLH2 mutations using PCR-SSCP analysis and direct sequencing. (ox.ac.uk)
  • 2002. Sequencing of the rat beta-catenin gene (Ctnnb1) and mutational analysis of liver tumors induced by 2-amino-3-methylimidazo[4,5-f]quinoline. . (oregonstate.edu)
  • Here we present the results of a whole-genome sequencing (WGS) study of ccRCC patients from four European countries (Czech Republic, United Kingdom, Romania and Russia), and we identify a specific mutational pattern that is predominant in the patients from Romania but not elsewhere. (nature.com)
  • Previous studies utilizing targeted sequencing have shown a correlation between mutational profiles and invasive pattern. (stanford.edu)
  • Highly efficient DNA synthesis by the phage Φ29 DNA polymerase. (wikipedia.org)
  • 1990. Cell replication and unscheduled DNA synthesis (UDS) activity of low molecular weight chlorinated paraffins in the rat liver in vivo. (cdc.gov)
  • DNA synthesis is completed once the two forks fuse in a region diametrically opposite the origin. (frontiersin.org)
  • WebImmediately after DNA synthesis, any remaining mispaired bases can be detected and replaced in a process called mismatch repair. (keyworddensitychecker.com)
  • Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases. (nih.gov)
  • Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. (biorxiv.org)
  • Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
  • A relatively high amount of WT1 mRNA was measured by quantitative competitive reverse transcription-polymerase using RNA extracted from crocidolite-induced tumors. (nih.gov)
  • Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)
  • These systems are particularly curious because they target not only DNA but also RNA to offer transcription-mediated cleavage. (nature.com)
  • In contrast to type I and type II (of Cas9 fame) systems, which directly target DNA, the type III systems find RNA targets during phage transcription. (nature.com)
  • 1970. Tumors of the urinary bladder: An analysis of the occupations of 1030 patients in Leeds, England. (cdc.gov)
  • Because the anatomic pathologist's analysis of tissue from a patient's tumor is absolutely critical in sarcoma treatment, sarcoma pathologists are specially trained in the diagnosis of these rare tumors. (sarcomahelp.org)
  • DNA and RNA of these tumors were subjected to analysis of point mutations and to investigation of mRNA expression patterns. (nih.gov)
  • The analysis of point mutations in the tumor suppressor gene p53 revealed mutations in the B[a]P-induced tumors. (nih.gov)
  • 2003. Mutational analysis of Ctnnb1 and Apc in tumors from rats given 1,2-dimethylhydrazine or 2-amino-3-methylimidazo[4,5-f]quinoline: mutational 'hotspots' and the relative expression of beta-catenin and c-jun. . (oregonstate.edu)
  • APOBEC mutational signature was detected only in Silva pattern C tumors (5/17), and pathogenic PIK3CA changes were detected only in destructively invasive HPVA (patterns B and C). When cases were grouped as low-risk (pattern A and pattern B without LVI) and high-risk (pattern B with LVI and pattern C), high-risk tumors were enriched in mutations in PIK3CA, ATRX, and ERBB2. (stanford.edu)
  • One hundred thirteen sequence variations with nine recur- ples, and a TA-cloning assay was used with direct analysis rent variant sites were identified in analyzed S-gene of reverse transcriptase-polymerase chain reaction (RT- sequences compared with the BJ01 strain of SARS-CoV. (cdc.gov)
  • Despite this lack of sequence identity, cross-species transgenesis has identified some cases where non-coding DNA from invertebrates drives reporter gene expression in transgenic vertebrates in patterns reminiscent of the expression of vertebrate orthologues. (ox.ac.uk)
  • [2] Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. (wikipedia.org)
  • The therascreen KRAS RGQ (Rotor-Gene Q) PCR (polymerase chain reaction) Kit tests for 7 mutations in codons 12 or 13 of the KRAS gene on formalin-fixed, paraffin-embedded tissue from the primary tumor or a metastasis. (medscape.com)
  • DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encodes its genome . (wikipedia.org)
  • The DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal functionality of that organism. (wikipedia.org)
  • In addition to the WGS analysis of somatic variations, we also present results from a genome-wide transcriptome analysis in a subset of the study samples. (nature.com)
  • Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome . (lookformedical.com)
  • Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F 2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. (biomedcentral.com)
  • included in the sequence analysis. (cdc.gov)
  • Because these technologies digitally tabulate the sequence of many individual DNA fragments, unlike conventional techniques which simply report the average genotype of an aggregate collection of molecules, they offer the unique ability to detect minor variants within heterogeneous mixtures [2]. (justia.com)
  • 6. Expression and prognostic significance of the DNA damage response pathway and autophagy markers in gastric cancer . (nih.gov)
  • 8. Comprehensive Analysis of Prognostic and Immune Infiltr ate s for RAD51 in Human Breast cancer . (nih.gov)
  • Effect of DNA damage response mutations on prostate cancer prognosis: a systematic review. (cdc.gov)
  • We studied the demographic characteristics and clinical presentation of patients with breast cancer and conducted survival analyses based on various factors. (who.int)
  • In 1977, scientists identified the presence of abnormally high levels of cell-free DNA (cfDNA) in the plasma and serum of cancer patients relative to healthy control patients and this cfDNA was presumed to represent mainly circulating tumor DNA (ctDNA) 1,5 . (cap.org)
  • The integration of structural, biochemical and computational studies of DNA replication fidelity requires a collaborative approach, where the theoretical analysis should be treated as an integral part of the experimental effort. (grantome.com)
  • Somatic mutations in the DNA repairome in prostate cancers in African Americans and Caucasians. (cdc.gov)
  • Baseline serum Ca125 was 1615 U/mL, and prior cytological analysis of ascitic fluid in October 2016 confirmed a diagnosis of high grade serous carcinoma, likely ovarian origin. (bmj.com)
  • Citation: Cruz M. Á, Arias S. & Terrazas T. 2016: Molecular phylogeny and taxonomy of the genus Disocactus (Cactaceae), based on the DNA sequences of six chloroplast markers. (researchgate.net)
  • Validated by signature analyses of tumor exomes and in vivo assays, the classifier accurately reassigned multiple POLE variants of unknown significance as pathogenic and identified MSS hypermutant samples without POLE exonuclease domain mutations. (nih.gov)
  • citation needed] The isolated enzyme has no intrinsic helicase activity but may carry out an equivalent function by way of its strong binding to single stranded DNA, particularly in preference to double stranded nucleic acid. (wikipedia.org)
  • The enzyme facilitates the "debranching" of double stranded DNA. (wikipedia.org)
  • This method uniquely capitalizes on the redundant information stored in double-stranded DNA, thus overcoming technical limitations of prior methods utilizing data from only one of the two strands. (justia.com)
  • Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. (lookformedical.com)
  • The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells. (lookformedical.com)
  • Genomic DNA was extracted using the QIAamp DNA FFPE Cells Kit (Qiagen, Hilden, Germany). (accessibletech4all.org)
  • Genomic DNA was extracted from leukocytes of peripheral blood collected from the family and 100 unrelated control subjects from the same population. (molvis.org)
  • Phylogenetic reconstruction was carried out with data from DNA sequences using the maximum parsimony and Bayesian inference criteria to explore the monophyly of the genus, its subgenera and its position within Hylocereeae. (researchgate.net)
  • They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA . (lookformedical.com)
  • Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. (lookformedical.com)
  • Additionally, the comparative studies will help in selecting the most effective approach for computational inhibitor and mutational screening. (grantome.com)
  • Immunostaining of mouse mammary epithelium was performed to quantify R-loops and DNA damage in vivo . (nih.gov)
  • Produces more DNA than PCR-based methods, by about an order of magnitude. (wikipedia.org)
  • different scientific genres and experimental sciences in gen- est, the improvement brought by argumentative features for eral (chemistry, anthropology, computer sciences, linguis- text categorization confirms that discourse analysis methods tics. (nih.gov)
  • R-loops and DNA damage were also detected in mammary epithelial cells of mice treated with BP-3 and PP. (nih.gov)
  • While the current focus is predominantly on detection of cfDNA, additional components of a liquid biopsy could include DNA methylation patterns, DNA fragment sizes, ribonucleic acids (RNA), circulating tumor cells, extracellular vesicles or exosomes, and tumor educated platelets. (cap.org)
  • DNA mismatch repair (MMR) is a conserved mechanism that corrects both base-base mispairs (G-T rather than G-C, for example) and small insertion/deletion loops that are caused by DNA polymerase slippage. (keyworddensitychecker.com)
  • Functional analysis of COX-2 by structure-guided mutagenesis has uncovered new strategies for synthesizing COX-2 inhibitors and has suggested new biological roles for the enzyme. (vanderbilt.edu)
  • DNA Extraction Serial formalin\fixed paraffin\inlayed (FFPE) sections were microdissected to ensure that each sample comprised at least 70% tumor content. (accessibletech4all.org)
  • A technique to generate restriction maps from single large DNA molecules by spreading the DNA onto a glass surface, digesting with DNA RESTRICTION ENZYMES , staining with FLUORESCENT DYES, and visualizing the DNA cleavage sites by FLUORESCENCE MICROSCOPY. (lookformedical.com)
  • Formation of R-loops was determined with DNA: RNA hybrid-specific S9.6 antibody. (nih.gov)
  • Analysis of 185 representative bacterial chromosomes showed diverse and characteristic patterns of skews among different clades. (biomedcentral.com)
  • this involves two replication origins and two distinct polymerase monomers. (wikipedia.org)
  • Analysis of the Finnish families revealed two distinct haplotypes. (nih.gov)