Protein dna mutational analysis. Medical search. Frequent questions

We studied the influence of histological subtype on protein expression with reverse phase protein array (RPPA) and assessed proteomic changes associated with ARID1A mutation/BAF250a expression in EC and CCC. (biomedcentral.com)
SAM (Significance Analysis of Microarrays) was performed to determine differential protein expression by histological subtype and ARID1A mutation status. (biomedcentral.com)
We propose to assess the use of a multiple mutation-based assay, using DNA from exfoliated cells in the urine of patients, to establish the sensitivity and specificity in tumor detection compared to cystoscopy and cytology. (centerwatch.com)
Mutation and in vitro DNA binding studies completed on a subset of the CRMs provide evidence for a direct regulatory relationship. (sdbonline.org)
In vitro analyses of apoptosis through flow cytometry and confocal microscopy show that NANOS3 capacity to prevent apoptosis was impaired by this mutation. (hindawi.com)
The identification of an inactivating missense mutation in NANOS3 suggests a mechanism for POI involving increased primordial germ cells (PGCs) apoptosis during embryonic cell migration and highlights the importance of NANOS proteins in human ovarian biology. (hindawi.com)
Mutation analysis did not detect causal mutations in exons 9 to 13 encoding the microtubule-binding domains involved in FTD, however, two novel polymorphisms were detected in exon 9. (ox.ac.uk)
Depending on the substitution, this type of mutation can change the encoded amino acid (missense mutation) to produce a different protein or an incomplete protein (nonsense mutation) which can lead to a diseased state. (bio-rad.com)
Over the past couple of decades, mutation detection techniques, such as denaturing gradient gel electrophoresis (DGGE), constant denaturing gel electrophoresis (CDGE), temporal temperature gradient gel electrophoresis (TTGE), single-strand conformation polymorphism (SSCP), and protein truncation test (PTT), have assisted researchers with analyzing mutations. (bio-rad.com)
More recently, high resolution melt (HRM) analysis has also become a technique of choice for mutation detection. (bio-rad.com)
DNA sequencing can be used to verify the mutation after any of these techniques. (bio-rad.com)
Since the T m of a particular melting domain is sequence specific, the presence of a mutation will alter the melting profile of that DNA when compared to wild type. (bio-rad.com)
A mutational signature of aristolochic acid was observed in the tumour DNA, and the principal aristolochic acid-specific mutation spectra and deleterious mutations were present in the mRNA of up to 50% of genes that were active in tumours. (who.int)

Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. (lookformedical.com)
Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. (lookformedical.com)

The aryl hydrocarbon receptor (also known as AhR, AHR, ahr, ahR, AH receptor, or dioxin receptor) is a protein that in humans is encoded by the AHR gene. (wikipedia.org)
However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
Analysis of protein-coding genetic variation in 60,706 humans. (ox.ac.uk)

RESULTS: The analysis indicated that the zebrafish crx gene consisted of three exons and 2 introns, and spans 3.8 kb of genomic DNA. (zfin.org)
The EGFR gene status and protein expression were investigated by direct DNA sequencing of the hot-spot regions in exons 18, 19 and 21, fluorescence in situ hybridisation (FISH), and immunohistochemistry in tumour tissues from 23 patients with ATC. (bmj.com)
PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)

Due to the advancement of genomic analysis, a vast literature characterizing cancer-associated molecular aberrations and relative therapeutic relevance has been published. (nih.gov)
By using published DNA binding specificity data for five transcription factors active in the early Drosophila embryo, genomic regions containing unusually high concentrations of predicted binding sites were identified for these factors. (sdbonline.org)
METHODS: Overlapping fragments were PCR amplified from genomic DNA isolated from homozygous mutant embryos and wild-type siblings (sibs). (zfin.org)
They use integrative genomic and molecular analyses to identify frequent DDR alterations across 33 cancer types, correlate gene- and pathway-level alterations with genome-wide measures of genome instability and impaired function, and demonstrate the prognostic utility of DDR deficiency scores. (elsevierpure.com)
The Cancer Genome Atlas Research Network 2018, ' Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas ', Cell reports , vol. 23, no. 1, pp. 239-254.e6. (elsevierpure.com)
We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. (biorxiv.org)
Thus, BRCA2 maintains genomic integrity both through homologous recombination and by the protection of nascent strands during DNA replication. (biomedcentral.com)
The search for unknown mutations in genomic DNA is important for a broad spectrum of research studies, including fundamental research on gene structure and function, the study of genetic diseases and disorders, and species identification. (bio-rad.com)

Scope includes mutations and abnormal protein expression. (cancerindex.org)
Double and triple mutants F16W/I24Q, F16W/N27D, and F16W/I24Q/N27D all showed defects in DNA binding, strand transfer, and helix destabilization, suggesting that the I24Q and N27D mutations have a "dominant negative" effect and abolish the positive influence of F16W. (umd.edu)
Sarcoma tissue samples and cell lines are subjected to a multiplatform genome-wide characterization of expression of protein-coding genes and microRNAs, DNA copy number changes, activating mutations, gene rearrangements and methylation profiling. (mskcc.org)
Consistent with the absence of identified mutations, linkage analysis excluded linkage of the mutant phenotypes to crx. (zfin.org)
On mutational analysis and FISH, neither mutations in the hot-spots nor gene amplification was observed. (bmj.com)
Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. (elsevierpure.com)
Meanwhile, their analysis of the cryoelectronic microscopy structures of the enhanced enzymes revealed that their mutations stabilized dimer formation and enabled robust interaction with nucleic acids, enhancing their ability to make snips in DNA. (genomeweb.com)
In any living cell, mutations occur when there is a failure in DNA repair. (bio-rad.com)
Mutational analysis assists with identifying unknown mutations as well as identifying precursors to diseases and disorders by allowing researchers to study these mutations in a control environment. (bio-rad.com)
Typically, site-directed mutagenesis is used to create mutant control samples by introducing mutations into some DNA fragments. (bio-rad.com)
DNA containing mutations will encounter mobility shifts at different positions in the gel than the wild type. (bio-rad.com)
Most of these mutations change single DNA building blocks (nucleotides) in the gene. (medlineplus.gov)
Analysis of these large elucidatinG the etioloGical role sites, and also patterns of genetic genome-wide studies also includes a of obeSity and related riSk factorS mutations that are observed in tumours. (who.int)

For example, most human tissues in healthy individuals acquire somatic nucleotide substitutions, insertions, deletions and DNA rearrangements, leading to the production of variant protein isoforms. (biorxiv.org)

They're based on the analysis of DNA methylation, a biological process by which CH3 methyl groups are added to the DNA molecule and that determines gene expression. (medscape.com)
To address this aim we have designed the lungNENomics study, an international cohort of over 250 cases of pulmonary carcinoids, with clinical data and central pathology review, as well as whole-genome sequencing, RNA sequencing, DNA methylation array, and digital spatial profiling data. (who.int)
DNA methylation and copy number variation profiling of T-cell lymphoblastic leukemia and lymphoma. (cancercentrum.se)

Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm. (lookformedical.com)

Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. (scilifelab.se)

In the yeast Saccharomyces cerevisiae , DNA polymerase ε (Pol ε) synthesizes primarily the leading strand, while DNA polymerase δ (Pol δ) synthesizes primarily the lagging strand and the genes encoding the catalytic subunits of these two polymerases are essential for life. (biomedcentral.com)
Reference: Structure and mechanism of DNA polymerase Beta. (neb.com)
The herpes simplex virus DNA polymerase is composed of two subunits, a large catalytic subunit (Pol) and a smaller subunit (UL42) that increases the processivity of the holoenzyme. (ed.ac.uk)
The functional importance of the interaction was confirmed by the finding that a pol mutant defective for UL42 binding retained polymerase activity, but did not synthesize longer DNA products in the presence of UL42. (ed.ac.uk)

Results from two other forms of HIV-1 NC (NCp9 and NCp15) and NC proteins from Simian Immunodeficiency Virus and Murine Leukemia Virus are also reported. (umd.edu)

In a dominant family segregated with late-onset, progressive, nonsyndromic hearing impairment, linkage analysis revealed a 2.07 Mb candidate region on chromosome 16p13.3 that contains TBC1D24. (nih.gov)
In prokaryotes, this process has been proposed to involve the RecN protein, a member of the structural maintenance of chromosome (SMC) protein family, which include key eukaryotic and prokaryotic proteins such as cohesin, condensin, and Rad50. (rcsb.org)
The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. (scilifelab.se)
We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. (scilifelab.se)

Also contained with the AhR are two PAS domains, PAS-A and PAS-B, which are stretches of 200-350 amino acids that exhibit a high sequence homology to the protein domains that were originally found in the Drosophila genes period (Per) and single-minded (Sim) and in AhR's dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT). (wikipedia.org)
The scientists noted that, although functional, the extra gene lacks certain parts of the DNA code, called introns, found in normal genes. (nih.gov)
Figure 3: Protein locations of private disruptive variants in new candidate NDD risk genes. (nature.com)
Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines. (zfin.org)
10 Similarly, in recent studies, at least one third of genes in diverse organisms can exhibit alternative transcription, leading to the production of N-terminally extended proteins or alternative reading frames. (biorxiv.org)
Here a global analysis of exon usage in AML samples revealed distinct molecular subsets containing alternative spliced isoforms of inflammatory and immune genes. (cancer-genetics.org)
identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. (ox.ac.uk)
Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes. (ox.ac.uk)

What pathways are this gene/protein implicaed in? (cancerindex.org)
These included PI3K/AKT pathway proteins, those regulating the cell cycle, apoptosis, transcription, and other signaling pathways including steroid hormone signaling. (biomedcentral.com)
The overall goal of the lab is to perform a comprehensive molecular genetic and functional analysis of soft tissue sarcoma, so as to elucidate the mutational programs and pathways involved in sarcomagenesis and to identify novel therapeutic targets. (mskcc.org)
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. (elsevierpure.com)
It encodes a large nuclear protein that is a component of DNA repair pathways. (lookformedical.com)
The BRCA2 protein is an essential component of DNA repair pathways, suppressing the formation of gross chromosomal rearrangements. (lookformedical.com)
It encodes a large, nuclear protein that is an essential component of DNA repair pathways, suppressing the formation of gross chromosomal rearrangements. (lookformedical.com)
The IRS proteins (IRS1-4) are the family of adaptors regulating metabolic and mitogenic signaling pathways ( Hanke and Mann , 2009 Hanke S and Mann M (2009) The phosphotyrosine interactome of the insulin receptor family and its substrates IRS-1 and IRS-2. (scielo.br)
Molecular chaperones are essential for stabilizing the fragile structures of many receptors, protein kinases, and transcription factors that participate in the pathways of normal cellular growth. (biomedcentral.com)

Complex population structure of the Atlantic puffin revealed by whole genome analyses. (scilifelab.se)

The RNA-binding protein NANOS3 poses as an interesting candidate gene for POI since members of the Nanos family have an evolutionarily conserved function in germ cell development and maintenance by repressing apoptosis. (hindawi.com)
We all have fragments of DNA from dead cells in our plasma (apoptosis), but cancer cells release more of these than others, and most importantly, their DNA has distinctive characteristics. (medscape.com)

Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). (ox.ac.uk)
This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. (ox.ac.uk)

Pathogenicity assessment of PMS2 VUS was performed evaluating clinicopathological data, frequency in control population and in silico and in vitro analyses at the RNA and protein level. (bmj.com)

Biochemical identification of mutational changes in a nucleotide sequence. (lookformedical.com)
These results, together with a thorough biochemical and mutational study of RecN, allow us to propose a model for the role of RecN in DSB repair. (rcsb.org)

The aim of this study was to evaluate the role of PMS2 in LS by assessing the pathogenicity of variants of unknown significance (VUS) detected in the mutational analysis of PMS2 in a series of Spanish patients. (bmj.com)
Results Overall 25 different PMS2 DNA variants were detected. (bmj.com)
The compact size of the new enzyme variants means that a greater quantity of the gene editing protein can be packaged into vectors such as adeno-associated viruses (AAVs) commonly used to infect living human cells requiring DNA editing. (genomeweb.com)
As reported in Cell on Friday, investigators from the University of Tokyo, Kyoto Prefectural University of Medicine, Jichi Medical University, and elsewhere used deep mutational scanning (DMS) and structural analysis to create the small and efficient Cas12f variants. (genomeweb.com)
Genetic bioinformatic techniques to complement combines large population-based studies analysis comprises either candidate more traditional approaches for the study with laboratory and bioinformatics gene or genome-wide genotyping of rare genetic variants. (who.int)

The remaining urine will be stored to evaluate biomarkers for the detection of tumor presence or progression using protein-based analyses. (centerwatch.com)
Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. (lookformedical.com)

This results in overproduction of the FGF4 protein, which the researchers hypothesize may turn on key growth receptors at the wrong times during fetal development. (nih.gov)
The IRS proteins function as adaptors and transmit signals from multiple receptors. (scielo.br)

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. (ox.ac.uk)
We examined the coding sequence of 518 protein kinases, approximately 1.3 Mb of DNA per sample, in 25 breast cancers. (uea.ac.uk)
A base is exchanged for another (for example, C to T) in the DNA sequence. (bio-rad.com)
Single or multiple base-pairs are incorporated or deleted from a DNA sequence. (bio-rad.com)

For the future, a more detailed understanding of the paths of the leading and lagging DNA strands running through the CMG helicase complex towards the DNA polymerases is needed. (biomedcentral.com)

The comprehensive functional analysis shown here has been useful in the classification of PMS2 VUS and contributes to refining the role of PMS2 in LS. (bmj.com)
Looking for an experienced Postdoctoral Fellow to join an NIH funded laboratory dedicated to gene target identification and drug discovery in soft tissue sarcoma through a genome-wide genetic and functional analysis. (mskcc.org)
The cancer assays to be tested use DNA analysis and antibodies to specific proteins as well as functional assays for proteins to attempt to identify bladder tumor presence. (centerwatch.com)

Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the whole proteome-scale. (biorxiv.org)
Through 2D-DIGE and mass spectrometry of granulocyte protein from 20 MPN samples, showed differential expression of HSP70 in PV and ET besides other 60 proteins. (biomedcentral.com)
Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. (scilifelab.se)

The researchers applied an integrative multi-omics analysis of upper urinary tract urothelial carcinomas arising in the context of nephropathy linked to environmental exposure to the herbal carcinogen aristolochic acid. (who.int)
These data have been combined with previously published LNET data to perform integrative analysis using multi-omics factor analysis (MOFA), resulting in a molecular map of lung neuroendocrine neoplasms for exploration. (who.int)

Hyperphosphorylated microtubule associated protein tau, present in neurofibrillary tangles, is a prominent pathological feature of Alzheimer's disease (AD). (ox.ac.uk)

Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. (scilifelab.se)

Torres, F., Barbosa, M. & Maciel, P. Recurrent copy number variations as risk factors for neurodevelopmental disorders: critical overview and analysis of clinical implications. (nature.com)

The breast cancer suppressor protein BRCA2 has an important role in double-strand break repair via homologous recombination. (biomedcentral.com)
The purification of BRCA2 will allow the study of the functions of the different domains in this large protein. (biomedcentral.com)
Katharina Schlacher (Memorial Sloan-Kettering Cancer Center, New York, USA), presented elegant single-molecule DNA fiber analysis demonstrating that BRCA2 protects newly synthesized DNA from degradation by the nuclease MRE11 when replication forks are stalled by hydroxyurea. (biomedcentral.com)
Mutational analysis of BRCA2 by Schlacher and her colleagues enabled the separation of functions required for homologous recombination and for fork protection. (biomedcentral.com)

CHAC encodes a large, novel protein with a yeast homologue implicated in protein sorting. (ox.ac.uk)

The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. (lookformedical.com)

GEP analyses were performed on highly purified, flow-cytometry sorted tumor-cells from eight subgroups of BCLs. (lu.se)

Comparisons with the structures of yeast and bacterial Pif1 reveal a conserved ssDNA binding channel in hPIF1 that we show is critical for single-stranded DNA binding during unwinding, but not the binding of G quadruplex DNA. (rcsb.org)
Structural differences, in particular in the DNA strand separation wedge region, highlight significant evolutionary divergence of the human PIF1 protein from bacterial and yeast orthologues. (rcsb.org)
Botchan's work further indicates that Cdc45 has a structure similar to the bacterial recombination protein RecJ, linking replication and recombination. (biomedcentral.com)
Stephen Kowalczykowski (University of California, Davis, USA) described for the first time the purification of this impressive 3,418-amino-acid protein and reported that it binds RAD51 (the human homolog of bacterial RecA) and promotes RAD51 assembly onto single-stranded DNA. (biomedcentral.com)

Using mutational data and structural information, Botchan suggested that the leading strand of the DNA passes through the central channel of the CMG complex. (biomedcentral.com)
An extensive high- and low-resolution structural analysis of Deinococcus radiodurans RecN using a combination of protein crystallography and small-angle X-ray scattering enabled us to assemble a quasi-atomic model of the entire RecN protein, representing the complete structure of a SMC-like protein. (rcsb.org)

Mutational analysis suggests that while the ssDNA-binding channel is important for helicase activity, it is not used in DNA annealing. (rcsb.org)
The substituted amino acid is located within the second C2HC motif in the conserved zinc finger domain of NANOS3 and in silico molecular modelling suggests destabilization of protein-RNA interaction. (hindawi.com)
Cdc45 might be able to bind single-stranded DNA, which suggests that the lagging strand is channeled through Cdc45, whereas the leading strand passes through the center of the MCM ring. (biomedcentral.com)
Klapholz-Brown Z, Walmsley GG, Nusse YM, Nusse R, Brown PO "Transcriptional program induced by wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments. (openwetware.org)

In normal cells the BRCA1 protein is localized in the nucleus, whereas in the majority of breast cancer cell lines and in malignant pleural effusions from breast cancer patients, it is localized mainly in the cytoplasm. (lookformedical.com)

Repair of DNA double-strand breaks (DSBs) is essential for cell survival and maintaining genome integrity. (rcsb.org)

We show that Igf2 P3 is transactivated by AP-1 in a transient expression assay, and that this effect is mediated through two non-consensus AP-1 binding sites characterised by DNA-protein interaction studies. (bath.ac.uk)
The interaction between the two polypeptides is of interest both for the mechanism by which it enables the enzyme to synthesize long stretches of DNA processively and as a possible target for the rational design of novel antiviral drugs. (ed.ac.uk)
al describe, and carefully characterise through point mutational analysis, the direct physical interaction between IHO1 and REC114-MEI4. (sciety.org)

Proteomic assessment of CCC and EC demonstrates remarkable differences in protein expression that are dependent on histotype, thereby further characterizing these cancers. (biomedcentral.com)

Rad51 is involved in DNA REPAIR of double-strand breaks. (lookformedical.com)
Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), essential for fertility and genetic diversity. (sciety.org)

C.P. tion stage, why much more detailed molecular analysis is contributed to the design of the study, discussions on statistical analysis of called for [2]. (lu.se)

Gene Expression Analysis , Gene Cloning and Analysis , and Epigenetics and Chromatin Structure . (bio-rad.com)

The AhR protein contains several domains critical for function and is classified as a member of the basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) family of transcription factors. (wikipedia.org)
The bHLH motif is located in the N-terminal of the protein and is a common entity in a variety of transcription factors. (wikipedia.org)
The first is the basic-region (b), which is involved in the binding of the transcription factor to DNA. (wikipedia.org)
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)

Anatomy11

Organisms17

Diseases3

Chemicals and Drugs89

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Phenomena and Processes94

Information Science3

Mutation13

Neoplasm Proteins2

Humans3

Exons3

Genomic8

Mutations13

Somatic1

Methylation3

Tumor Suppress1

Polymorphism1

Polymerase4

Murine Leuke1

Chromosome4

Genes8

Pathways9

Whole genome1

Apoptosis2

Exome2

Vitro1

Biochemical2

Variants5

Progression2

Receptors2

Sequence4

Polymerases1

Functional3

Mass spectrometry3

Integrative2

Microtubule-associated1

Eukaryotic1

Risk Factors1

BRCA24

Encodes a large1

Mismatch1

Flow cytometry1

Bacterial4

Structural2

Suggests4

BRCA11

Survival1

Interaction3

Cancers1

Double-strand2

Statistical analysis1

Gene Expression1

Transcription4