• Our broad analysis demonstrates that the qBiomarker's performance is on par with that of other labour-intensive and expensive methods of cancer mutation detection of frequently altered cancer-associated genes, and provides a foundation for supporting its consideration as an option for molecular diagnostics. (nature.com)
  • Mutational analysis of NPHS2 and WT1 genes in Saudi children with nephrotic syndrome. (alliedacademies.org)
  • Up to date, several causative genes related to NS have been identified by either using direct DNA sequencing approaches or next-generation sequencing technology [ 6 - 12 ]. (alliedacademies.org)
  • DNA phosphorothioation, conferred by dnd genes, was originally discovered in the soil-dwelling bacterium Streptomyces lividans , and thereafter found to exist in various bacterial genera. (frontiersin.org)
  • RNA-seq experiments revealed that, catalase and organic hydroperoxide resistance gene expression were not up-regulated in the wild type strain, suggesting that the resistance to oxidative stress was not due to the up-regulation of these genes by DNA phosphorothioation. (frontiersin.org)
  • Quantitative RT-PCR analysis was conducted to trace the expression of the catalase and the organic hydroperoxide resistance genes after peroxides treatments. (frontiersin.org)
  • In this study, molecular genetic analysis was performed on all these 12 genes in 25 Chinese families with congenital cataract. (molvis.org)
  • The establishment of the mutational spectrum for NDMA in endogenous mammalian genes is necessary if exposure to NDMA, based on its mutational specificity, is going to be assessed in human tissues. (epa.gov)
  • The studies seek to identify the signal transduction pathways, specific DNA elements and transcription factors which are required for the tissue-specific, regulated expression of these pituitary hormone genes. (ohsu.edu)
  • The Lawrence Laboratory focuses on using computation as a powerful microscope to study the processes of DNA damage and repair, gene expression and genome replication, and cancer driver genes. (massgeneral.org)
  • Segments of the DNA molecule carrying genetic information are called genes. (differencebetween.net)
  • In modern research, genetics provides important tools for studying the functions of individual genes, analysis of genetic interactions, etc. (differencebetween.net)
  • Here we had used various bioinformatic tools and statistical analyses to understand the compositional features, expression level and codon usage bias in the genes of these two species.After estimating the effective number of codon (ENC) in both the species, codon usage bias was found to be low and gene expression was high. (degruyter.com)
  • Whole exome sequencing allows for thorough genetic analysis of candidate genes as well as novel gene discovery. (dovepress.com)
  • We extracted cfDNA from 500 μL of plasma, which is sufficient for target mutation analysis using dPCR. (springer.com)
  • Garcia-Murillas I, Schiavon G, Weigelt B et al (2015) Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. (springer.com)
  • Further analysis of markers in the 4154delA mutation carriers from all three populations allows us to assert that all analysed mutation carriers share a common ancestry. (arctichealth.org)
  • By direct DNA sequencing and digestion with Surveyor nuclease one heterozygous mutation in the 5' untranslated region of exon 1, transcript variant 3 was detected. (medsci.org)
  • Methods: Mutation analysis was accomplished by direct sequencing of the complete 8 exons of NPHS2 and exons 8 and 9 of WT1 in 20 patients with steroid-resistant nephrotic syndrome, 25 with steroid-dependent nephrotic syndrome, and 13 with frequently-relapse nephrotic syndrome. (alliedacademies.org)
  • This assay is also available as PCR-based pyrosequencing of DNA to examine codons 595 to 600 from exon 15 (the most common mutation site) and codons 468 to 474 from exon 11 of the BRAF gene. (mdanderson.org)
  • Another common mutation involved amino acids that are thought to make specific contacts with DNA. (elsevier.com)
  • G-to-C frequencies varied substantially (up to ≈80-fold) depending upon sequence position, but surprisingly, mutational hot spots (defined as upper outliers within the mutation frequency distribution) were not observed. (asm.org)
  • The nucleobase A and T were used most often than C and G. From neutrality plot and correspondence analysis it was found that both natural selection and mutation pressure played an important role in shaping the codon usage pattern of both species. (degruyter.com)
  • In circulating tumor DNA (ctDNA), mutant MEK1 levels declined with treatment, but a previously unrecognized KRAS Q61H mutation was also identified that increased despite therapy. (aacrjournals.org)
  • Seven percent had a single heterozygous mutation identified that would cause recessive disease and 13% had no obviously pathogenic variants and no family members available to perform segregation analysis. (dovepress.com)
  • It allows for an unbiased analysis of genetic variants to reduce the chance that the pathogenic mutation will be missed due to incomplete or inaccurate family history or analysis at the early stage of a syndromic form of retinal degeneration. (dovepress.com)
  • The Cre/loxP system has been used in transgenic models primarily to excise DNA flanked by loxP sites for gene deletion. (nih.gov)
  • Reporter gene expression analysis, electrophoretic mobility shift assays and chromatin immunoprecipitation studies were utilized to examine the functional effects of the deletion. (arctichealth.org)
  • DNA methylation is an epigenetic process involved in gene regulation that is key for cell differentiation and viability. (purdue.edu)
  • To determine the role of Acr-DNA adducts in p53 mutagenesis in CS-related lung cancer we mapped the distribution of Acr-DNA adducts at the sequence level in the p53 gene of lung cells using the UvrABC incision method in combination with ligation-mediated PCR. (pnas.org)
  • The tumor suppressor gene p53 is frequently mutated in human cancers ( 1 , 2 ), and its mutational patterns often bear the fingerprints of the etiological carcinogens. (pnas.org)
  • We did not observe a statistical association between clinical response and the mutational status of the EGFR gene ( 2 ). (aacrjournals.org)
  • In all patients, the HESX1 gene was analyzed by direct sequence analysis and in cases of CPHD the PROP1 gene was also sequenced. (scielo.br)
  • Mutational analysis of the HvDWARF gene with the "reverse genetics" approach allowed for its detailed functional analysis at the level of protein functional domains. (mdpi.com)
  • This assay is available as PCR-based DNA pyrosequencing for codons 338 in exon 2 of the CXCR4 gene. (mdanderson.org)
  • The MT-TL1 gene provides instructions for making a molecule called a transfer RNA (tRNA), which is a chemical cousin of DNA. (medlineplus.gov)
  • Identification of a poxvirus gene encoding a uracil DNA glycosylase. (ebi.ac.uk)
  • In addition to their role in base excision repair, DNA glycosylase enzymes have been implicated in the repression of gene silencing in A. thaliana, N. tabacum and other plants by active demethylation. (wikipedia.org)
  • The results from a single locus analysis in IL1B gene were reflected also in a haplotype level: The IL1B −511/ +3962 TC haplotype tended to be more frequent in PJI patients by comparison to those without infection after TJA. (nih.gov)
  • Functional analysis of the transcriptional promoter for the CYP1A1 gene. (stanford.edu)
  • We hypothesize that unlike Dnmt3a, Dnmt3b does not oligomerize and to test this hypothesis, we performed mutational analysis of the conserved residues in Dnmt3b that are critical for Dnmt3a tetrameric structure. (purdue.edu)
  • On the basis of amino acid sequence alignments and structural data of related enzymes, we have performed a mutational analysis of 14 amino acid residues in the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. (cf.ac.uk)
  • The target residues are located within the ten conserved amino acid sequence motifs characteristic for cytosine-C5 methyltransferases and in the putative DNA recognition domain of the enzyme (TRD). (cf.ac.uk)
  • This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues), pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. (frontiersin.org)
  • Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. (ebi.ac.uk)
  • Nevertheless, its clinical application is limited due to the high cost and long turnaround time (3 weeks) required for the data analysis. (nature.com)
  • Our investigations into this subject were prompted by the striking clinical and histopathologic similarities between EN and aristolochic acid nephropathy (AAN) ( 14 , 15 ). (pnas.org)
  • and (3) the evidence related to the relationship between KRAS genetic intratumoural heterogeneity, clinical sensitivity of mutational detection tools and anti-EGFR treatment outcome. (jove.com)
  • Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest. (biomedcentral.com)
  • This pathology has nuclear heterogeneous genetic origins, and at present, molecular diagnostic tests on nuclear DNA cover only 30% of BrS patients. (cdc.gov)
  • Using 32 P-postlabeling/PAGE and authentic standards, we identified dA-aristolactam (AL) and dG-AL DNA adducts in the renal cortex of patients with EN but not in patients with other chronic renal diseases. (pnas.org)
  • The accuracy of plasma RAS mutational status determined by OncoBEAM RAS kit was confirmed for Japanese mCRC patients. (oncoletter.ch)
  • The concordance rate between plasma- and tissue-based analyses was 86.4% in overall, rising to 89.2% in patients excluding lung metastasis alone, with 13.6% of discordant cases being potentially attributed to variables of tissue heterogeneity, a longer interval in sample collection from archived tissue to plasma and a lower amount of ctDNA shed into plasma. (oncoletter.ch)
  • this study analyses the impact of using an NGS platform for molecular diagnosis of mCRC patients. (oncoletter.ch)
  • Mutational analysis of patients with X-linked adrenoleukodystrophy. (nih.gov)
  • For the case-control analysis of OGG1 R154H, a total of 625 hereditary or sporadic colorectal cancer patients and 527 normal controls were screened. (springer.com)
  • The mutational signatures are specific and therapy-related, as they are only present in the genomes of relapsed ALL patients but not in other pediatric or adult cancer genomes," Zhang said. (newswise.com)
  • The analysis also included targeted deep sequencing of leukemic cells collected regularly during treatment of 16 patients. (newswise.com)
  • Thus, DNA molecular targets to stratify patients for targeted therapy are often evaluated on cytology. (jove.com)
  • Analysis of the role of the mitogen-activated protein kinase in mediating cyclic-adenosine 3′,5′-Monophosphate effects on prolactin promoter activity. (ohsu.edu)
  • Based on the sequence alignment of promoters recognized by FliA and genome in silico analysis, we propose that P. putida sigma 28 recognizes a TCAAG-t-N-12-GCCGATA consensus sequence located between -34 and -8 and that this sequence is preferentially associated with an AT-rich upstream region. (diva-portal.org)
  • Application of deconstructSigs identifies samples with DNA repair deficiencies and reveals distinct and dynamic mutational processes molding the cancer genome in esophageal adenocarcinoma compared to squamous cell carcinomas. (biomedcentral.com)
  • They underwent whole genome sequencing of leukemic cells collected at the diagnosis and relapse as well as normal DNA. (newswise.com)
  • Ligases are versatile and ubiquitous enzymes that join the 3' hydroxyl and 5' phosphate ends to form a phosphodiester bond, making them essential in nicked DNA repair, and ultimately genome fidelity. (wikipedia.org)
  • DNA mismatch repair (MMR) is an important DNA repair system that helps maintain genome plasticity by correcting mismatches, or non Watson-Crick base pairs in the a DNA duplex. (wikipedia.org)
  • There are many challenges in processing the raw DNA sequencing reads from a patient's resected tumor or biopsy material, aligning them accurately to the reference human genome, and then scanning for loci where the tumor DNA differs from the patient's bulk "normal" DNA (e.g. from a blood draw). (massgeneral.org)
  • By using DNA probes and microscopy-based methods, we explore the structure of the nucleus and the organization of the genome. (umanitoba.ca)
  • Furthermore, we found that Acr can greatly reduce the DNA repair capacity for damage induced by benzo[ a ]pyrene diol epoxide. (pnas.org)
  • Together these results suggest that Acr is a major etiological agent for CS-related lung cancer and that it contributes to lung carcinogenesis through two detrimental effects: DNA damage and inhibition of DNA repair. (pnas.org)
  • PAHs have been shown to be strong carcinogens, and thus PAH-induced DNA damage may shape the p53 mutational pattern in lung cancer and may also represent a strong molecular link between lung cancer and cigarette smoking ( 1 , 2 , 5 - 7 ). (pnas.org)
  • In this study, we report for the first time that a proportion of human lung cancer cell lines did not properly arrest before entering mitosis in the presence of a catalytic, circular cramp-forming topoisomerase II inhibitor ICRF-193, whereas the decatenation G 2 checkpoint impairment was present independently of the impaired DNA damage G 2 checkpoint. (aacrjournals.org)
  • (11) previously reported that in contrast to DNA damage checkpoint, decatenation G 2 checkpoint activation relies on ataxia telangiectasia and Rad3-related (ATR) activity and nuclear exclusion of cyclin B1 instead of ataxia-telangiectasia mutated (ATM)-dependent down-regulation of cdc2/cyclin B1 activity. (aacrjournals.org)
  • Independent of replicative age, factors such as oncogenic activation, DNA damage, chromatin remodeling, cellular stress, overexpression of cyclin-dependent kinase (Cdk) inhibitors, and deprotection of chromosome ends can also induce a phenotype resembling senescence ( 11 -16 ). (aacrjournals.org)
  • A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action. (wikipedia.org)
  • Nicked DNA can be the result of DNA damage or purposeful and carefully regulated biomolecular reactions carried out in the cell. (wikipedia.org)
  • Thus, SMUG1 is a new member of DNA glycosylases involved in the repair of oxidative damage. (nii.ac.jp)
  • Sequence analysis of the URA3 mutants revealed approximately 48% frameshifts, approximately 44% base substitutions and approximately 8% complex events. (biomedsearch.com)
  • To gain insights into the biology of thymomas and thymic carcinomas, we did a comprehensive genomic analysis of 45 resected thymic tumors. (aacrjournals.org)
  • deconstructSigs confers the ability to define mutational processes driven by environmental exposures, DNA repair abnormalities, and mutagenic processes in individual tumors with implications for precision cancer medicine. (biomedcentral.com)
  • DNA Alterations in Primary and Circulating Tumors, Non-Coding RNAs for Cancer Classification, Detection, and Monitoring, Identifying Pred. (utah.edu)
  • As a contribution to a better understanding of the developmental processes that are specific to plants, we have begun a genetic analysis of leaf ontogeny in the model system Arabidopsis thaliana by performing a large-scale screening for mutants with abnormal leaves. (genetics.org)
  • As a contribution to the causal analysis of plant leaf development, we first performed a large-scale screen for EMS-induced mutants with aberrantly shaped or sized leaves. (genetics.org)
  • Analysis of their impact on phenotype of the mutants was performed. (mdpi.com)
  • In this study, we have analyzed the crystal structures, DNA binding and the response to ATP binding of three Glu38 mutants. (rcsb.org)
  • Human thymine DNA glycosylase (TDG) was discovered as an enzyme that can initiate base excision repair at sites of 5-methylcytosine- or cytosine deamination in DNA by its ability to release thymine or uracil from G.T and G.U mismatches. (uzh.ch)
  • Current evidence suggests that, in human cells, TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs caused by spontaneous cytosine deamination, whereas uracil arising in DNA through dU misincorporation is mainly dealt with by UNG. (wikipedia.org)
  • This entry represents various uracil-DNA glycosylases and related DNA glycosylases (EC), such as uracil-DNA glycosylase, thermophilic uracil-DNA glycosylase, G:T/U mismatch-specific DNA glycosylase (Mug), and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1). (wikipedia.org)
  • Previously we demonstrated that DNA adducts induced by diol epoxides of polycyclic aromatic hydrocarbons (PAHs), a major category of cigarette smoke (CS) carcinogens, preferentially occur at p53 mutational hotspots in CS-related lung cancers and that adducts formed at these locations are poorly repaired ( 5 - 7 ). (pnas.org)
  • However, since in vitro diagnostic tests are licensed only for paraffin-tissue, all mutational assays on cytology are "home brew," requiring a rigorous validation process. (jove.com)
  • Authoritative and cutting-edge, Cell-free DNA as Diagnostic Markers: Methods and Protocols aims to ensure successful results in the further study of this vital field. (springer.com)
  • Four different uracil-DNA glycosylase activities have been identified in mammalian cells, including UNG, SMUG1, TDG, and MBD4. (wikipedia.org)
  • The structure of human UNG in complex with DNA revealed that, like other glycosylases, it flips the target nucleotide out of the double helix and into the active site pocket. (wikipedia.org)
  • 4) Analysis of repair activity of E.coli Endo IV and yeast APN1 suggests that they initiate nucleotide incision repair (NIR) for free radical-induced DNA lesions. (nii.ac.jp)
  • Mutational and deletion analyses narrowed the region essential for elicitor activity to the 23-amino-acid peptide (H 2 N-NQGISEKQLDQLLTQLIMALLQQ-COOH). (asm.org)
  • The p53 binding pattern of carcinogenic polycyclic aromatic hydrocarbons (PAHs) found in CS coincides with the p53 mutational pattern found in lung cancer, and PAHs have thus been considered to be major culprits for lung cancer. (pnas.org)
  • DNA methyltransferase 3a and 3b (Dnmt3a andDnmt3b) are two enzymes that establish this epigenetic modification during early cell development. (purdue.edu)
  • Thermostable uracil-DNA glycosylase from Thermotoga maritima a member of a novel class of DNA repair enzymes. (ebi.ac.uk)
  • DNA can be nicked by physical shearing, over-drying or enzymes. (wikipedia.org)
  • DNA glycosylases are a family of enzymes involved in base excision repair, classified under EC number EC 3.2.2. (wikipedia.org)
  • Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the arthrodontous mosses, studies of hybridization using molecular and morphological markers, and investigations of cryptic speciation within geographically widespread species. (duke.edu)
  • The sequence of uracil-DNA glycosylase is extremely well conserved [ PMID: 2555154 ] in bacteria and eukaryotes as well as in herpes viruses. (ebi.ac.uk)
  • Utilizing lambda integrase, mutant loxP sites were placed at the E. coli attB site and the excision-insertion ratios of incoming DNA plasmids carrying a second, complementary mutant loxP site were determined. (nih.gov)
  • Diehl F, Schmidt K, Choti MA et al (2008) Circulating mutant DNA to assess tumor dynamics. (springer.com)
  • Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9)AAA) in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. (nih.gov)
  • DNA Mutational Analysis" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (sickkids.ca)
  • Monofunctional glycosylases have only glycosylase activity, whereas bifunctional glycosylases also possess AP lyase activity that permits them to cut the phosphodiester bond of DNA, creating a single-strand break without the need for an AP endonuclease. (wikipedia.org)
  • The first crystal structure of a DNA glycosylase was obtained for E. coli Nth. (wikipedia.org)
  • 2) DNA glycosylase activity for 5-formyluracil (fU) was isolated from rat liver and identified as SMUG1. (nii.ac.jp)
  • In order to ligate these fragments together, the ligase progresses through three steps: Addition of an adenosine monophosphate (AMP) group to the enzyme, referred to as adenylylation, Adenosine monophosphate transfer to the DNA and Nick sealing, or phosphodiester bond formation. (wikipedia.org)
  • To investigate this, we performed Illumina high-throughput sequencing of multiple amplicons prepared from proviral DNA that was recovered from decitabine-treated cells infected with HIV-1. (asm.org)
  • Mathematical modeling, mutational analysis and other evidence indicated that earlier relapse was likely caused by drug-resistant tumor cells present at diagnosis. (newswise.com)
  • Analysis of specific cells can give insight into a variety of diseases. (google.com)
  • The DNA molecules in the cells are in the form of double helices. (differencebetween.net)
  • Inside the cells, DNA forms long structures called chromosomes. (differencebetween.net)
  • With respect to histology, most cytological samples have the advantages of a purer population of tumor cells, with low stromal component, a better preserved DNA, and assessing at the same time of sample collection cellular adequacy for DNA testing. (jove.com)
  • Trainees will learn how to prepare cells and tissues for 3D imaging, and how to perform fluorescent in situ hybridization (FISH) followed by 3D imaging and analysis. (umanitoba.ca)
  • Hindson BJ, Ness KD, Masquelier DA et al (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. (springer.com)