Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.Exome: That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.Formaldehyde: A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)Tissue Fixation: The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements.Prostate: A gland in males that surrounds the neck of the URINARY BLADDER and the URETHRA. It secretes a substance that liquefies coagulated semen. It is situated in the pelvic cavity behind the lower part of the PUBIC SYMPHYSIS, above the deep layer of the triangular ligament, and rests upon the RECTUM.Prostatic Neoplasms: Tumors or cancer of the PROSTATE.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.North CarolinaCancer Care Facilities: Institutions specializing in the care of cancer patients.Comprehensive Health Care: Providing for the full range of personal health services for diagnosis, treatment, follow-up and rehabilitation of patients.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.National Cancer Institute (U.S.): Component of the NATIONAL INSTITUTES OF HEALTH. Through basic and clinical biomedical research and training, it conducts and supports research with the objective of cancer prevention, early stage identification and elimination. This Institute was established in 1937.Oncology Service, Hospital: The hospital department responsible for the administration and provision of diagnostic and therapeutic services for the cancer patient.Oncology Nursing: A nursing specialty concerned with the care provided to cancer patients. It includes aspects of family functioning through education of both patient and family.Sunburn: An injury to the skin causing erythema, tenderness, and sometimes blistering and resulting from excessive exposure to the sun. The reaction is produced by the ultraviolet radiation in sunlight.South DakotaSunscreening Agents: Chemical or physical agents that protect the skin from sunburn and erythema by absorbing or blocking ultraviolet radiation.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Sunlight: Irradiation directly from the sun.Skin Neoplasms: Tumors or cancer of the SKIN.Protective Clothing: Clothing designed to protect the individual against possible exposure to known hazards.Phycodnaviridae: A family of DNA plant viruses that infect eukaryotic algae.Chlorella: Nonmotile unicellular green algae potentially valuable as a source of high-grade protein and B-complex vitamins.Phaeophyta: A division of predominantly marine EUKARYOTA, commonly known as brown algae, having CHROMATOPHORES containing carotenoid PIGMENTS, BIOLOGICAL. ALGINATES and phlorotannins occur widely in all major orders. They are considered the most highly evolved algae because of their well-developed multicellular organization and structural complexity.Paramecium: A genus of ciliate protozoa that is often large enough to be seen by the naked eye. Paramecia are commonly used in genetic, cytological, and other research.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Haptophyta: A group (or phylum) of unicellular EUKARYOTA (or algae) possessing CHLOROPLASTS and FLAGELLA.DNA, Algal: Deoxyribonucleic acid that makes up the genetic material of algae.Polyomaviridae: A family of small, non-enveloped DNA viruses, infecting mainly MAMMALS, and containing a single genus: POLYOMAVIRUS.Papilloma: A circumscribed benign epithelial tumor projecting from the surrounding surface; more precisely, a benign epithelial neoplasm consisting of villous or arborescent outgrowths of fibrovascular stroma covered by neoplastic cells. (Stedman, 25th ed)Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Papillomaviridae: A family of small, non-enveloped DNA viruses infecting birds and most mammals, especially humans. They are grouped into multiple genera, but the viruses are highly host-species specific and tissue-restricted. They are commonly divided into hundreds of papillomavirus "types", each with specific gene function and gene control regions, despite sequence homology. Human papillomaviruses are found in the genera ALPHAPAPILLOMAVIRUS; BETAPAPILLOMAVIRUS; GAMMAPAPILLOMAVIRUS; and MUPAPILLOMAVIRUS.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Magnesium Chloride: Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys.Taq Polymerase: A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.Magnesium: A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Amides: Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed)Cell Line, Tumor: A cell line derived from cultured tumor cells.Antineoplastic Agents: Substances that inhibit or prevent the proliferation of NEOPLASMS.Drug Screening Assays, Antitumor: Methods of investigating the effectiveness of anticancer cytotoxic drugs and biologic inhibitors. These include in vitro cell-kill models and cytostatic dye exclusion tests as well as in vivo measurement of tumor growth parameters in laboratory animals.Stomach Neoplasms: Tumors or cancer of the STOMACH.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Autoradiography: The making of a radiograph of an object or tissue by recording on a photographic plate the radiation emitted by radioactive material within the object. (Dorland, 27th ed)Genetic Code: The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).ArtSculptureThymine

*DNA vaccination

... while CpG motifs occurring in eukaryotes are methylated at the cytosine nucleotide. In contrast, nucleotide sequences that ...

*Regulation of gene expression

DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called " ... Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences ...

*Genome evolution

Many promoters contain CpG islands, areas of the genome where a cytosine nucleotide occurs next to a guanine nucleotide at a ... The genetic code is made up of sequences of four nucleotide bases: Adenine, Guanine, Cytosine and Thymine, commonly referred to ... Mutations can either change the identity of one or more nucleotides, or result in the addition or deletion of one or more ... A higher GC-content confers a benefit because a Guanine-Cytosine bond is made up of three hydrogen bonds while an Adenine- ...

*Molybdenum cofactor cytidylyltransferase

... residues of molybdopterin dinucleotide transferases that determine specificity for binding of guanine or cytosine nucleotides ... "MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli". J. ...

*Abiogenesis

As of 1994[update], there were difficulties in the explanation of the abiotic synthesis of the nucleotides cytosine and uracil ... November 2007). "Nucleotide synthetase ribozymes may have emerged first in the RNA world". RNA. Cold Spring Harbor, NY: Cold ... Eigen built on Spiegelman's work and produced a similar system further degraded to just 48 or 54 nucleotides - the minimum ... The hypercycle theory requires the existence of complex biochemicals, such as nucleotides, which do not form under the ...

*CTP synthetase

... glutamate It is the rate-limiting enzyme for the synthesis of cytosine nucleotides from both the de novo and uridine salvage ... Mutations in the CTP synthase have been seen to confer resistance to cytotoxic drugs such as cytosine arabinoside (ara-C) in a ... Whelan J, Smith T, Phear G, Rohatiner A, Lister A, Meuth M (1994). "Resistance to cytosine arabinoside in acute leukemia: the ... This acts to balance the relative amounts of purine and pyrimidine nucleotides. The reaction product CTP also serves as an ...

*CTPS2

This protein is the rate-limiting enzyme in the synthesis of cytosine nucleotides, which play an important role in various ...

*List of MeSH codes (D13)

... cytosine nucleotides MeSH D13.695.827.232.115 --- cyclic cmp MeSH D13.695.827.232.150 --- cytidine diphosphate MeSH D13.695. ... cytosine nucleotides MeSH D13.695.740.246.050 --- arabinofuranosylcytosine triphosphate MeSH D13.695.740.246.115 --- cyclic cmp ... thymine nucleotides MeSH D13.695.740.706.788 --- thymidine monophosphate MeSH D13.695.740.850 --- uracil nucleotides MeSH ... deoxyadenine nucleotides MeSH D13.695.201.150 --- deoxycytosine nucleotides MeSH D13.695.201.150.200 --- deoxycytidine ...

*Promoter (genetics)

50%, and have regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide and this occurs frequently in the ... In humans, DNA methylation occurs at the 5' position of the pyrimidine ring of the cytosine residues within CpG sites to form 5 ... These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific ... and 35 nucleotides upstream from the transcription start site. The sequence at -10 (the -10 element) has the consensus sequence ...

*Regulation of transcription in cancer

... and have regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide and this occurs frequently in the ... In humans, DNA methylation occurs at the 5' position of the pyrimidine ring of the cytosine residues within CpG sites to form 5 ... where the CpG island-containing promoter is located about 5,400 nucleotides upstream of the coding region of the ERCC1 gene. ...

*Canine circovirus

Guanine-Cytosine nucleotide base pairing makes up a little over half of the total pairs that are present in CaCV and the most ... The genome of CaCV is made up of a single circular strand of DNA 2,063 nucleotides in length. DNA in general is made up of four ... An interesting note about the genome of CaCV is that one of the intergenic noncoding regions shares 91% nucleotide identity ... The two intergenic noncoding portions of the genome are made up of 135 and 203 nucleotides. These regions contain distinctive ...

*CpG site

The CpG sites or CG sites are regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide in the linear ... For example, in the human genome, which has a 42% GC content, a pair of nucleotides consisting of cytosine followed by guanine ... A C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the cytosines in such ... Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. In mammals, methylating the cytosine within a gene ...

*Herpes B virus

Cytosine and guanine nucleotides represent 75% of the sequence. Sequence analyses suggest that B virus and HSV types 1 and 2 ...

*Gene polymorphism

A major and the cause of this SNPs is the replacement of the nucleotide cytosine (C) with thymine (T) in a part of the DNA. ... For example, a polymorphic variant of the enzyme CYP4A11 in which thymidine replaces cytosine at the gene's nucleotide 8590 ... SNPs are a single nucleotide changes that happen in the genome in a particular location. The single nucleotide polymorphism is ... single nucleotide polymorphisms, small-scale insertions and deletions, polymorphic repetitive elements and microsatellite ...

*DNA methylation

... while DNA methylation in mammals mainly occurs on the cytosine nucleotide in a CpG site, in plants the cytosine can be ... On the other hand, DNA cytosine methylase targets CCAGG and CCTGG sites to methylate cytosine at the C5 position (C meC(A/T) GG ... Cytosine methylation is widespread in both eukaryotes and prokaryotes, even though the rate of cytosine DNA methylation can ... of total cytosine Adenine or cytosine methylation is part of the restriction modification system of many bacteria, in which ...

*Hereditary gingival fibromatosis

There is an insertion of a cytosine between nucleotides 126,142 and 126,143 in codon 1083 of the SOS1 gene, meaning there is a ... In 2002, researchers described the SOS1 gene and proved for the first time that a single-nucleotide-insertion mutation of the ... A mutation in the SOS1 gene results in a single nucleotide insertion. Specific linkage studies have localized the mutation for ... SOS1 is a guanine nucleotide-exchange factor that functions in the transduction of signals that control cell growth and ...

*Leslie Orgel

However, in lab experiments, this only worked when the DNA template strands were rich in the nucleotide cytosine, and ... The imidazole would be a good leaving group for the condensation of nucleotides. Orgel also theorised that one single strand of ... To counteract this energy barrier, he proposed a nucleotide with an imidazole ring attached to the phosphate group. ... Orgel suggested a solution to the problem of condensing nucleotides to form nucleic acid polymers, an energy-demanding process ...

*Tiling array

DNA is methylated on cytosine in CG di-nucleotides in many places in the genome. This modification is one of the best- ...

*D-loop replication

The L (light) strand comprises lighter nucleotides (pyrimidines: thymine and cytosine). Replication begins with replication of ... In many organisms, one strand of DNA in the plasmid comprises heavier nucleotides (relatively more purines: adenine and guanine ...

*B recognition element

The next four nucleotides are always the same: cytosine, guanine, cytosine, cytosine. G/C G/C G/A C G C C. The Transcription ... in 1998 by Richard Ebright and co-workers The first two nucleotides of the BRE sequence can be either guanine or cytosine. The ... The BRE is a cis-regulatory element that is found immediately upstream of the TATA box, and consists of 7 nucleotides. The BRE ... third nucleotide is either guanine or adenine. ...

*EteRNA

The player can change the sequence by placing any of the four RNA nucleotides (adenine, cytosine, guanosine and uracil) at ...

*GC skew

... is when the nucleotides Guanine and Cytosine are over- or under-abundant in a particular region of DNA or RNA. In ... Deamination of cytosine and ultimately mutation of cytosine to thymine in one DNA strand can increase the relative number of ... The nucleotide composition skew spectra ranges from -1, which corresponds to G = 0 or A = 0, to +1, which corresponds to T= 0 ... This unique nucleotide composition is thought to be due to selection pressure of adenine over thymine in the coding region. ...

*Organism

The particular sequence of the four different types of nucleotides (adenine, cytosine, guanine, and thymine) dictate many ... The sequence is divided up into codons, each of which is a particular sequence of three nucleotides and corresponds to a ... However, the universal use of the same genetic code, same nucleotides, and same amino acids makes the existence of such an ... Nucleic acids (specifically deoxyribonucleic acid, or DNA) store genetic data as a sequence of nucleotides. ...

*Bisulfite sequencing

The objective of this analysis is therefore reduced to differentiating between single nucleotide polymorphisms (cytosines and ... the subsequent analysis will incorrectly interpret the unconverted unmethylated cytosines as methylated cytosines, resulting in ... Only cytosines in single-stranded DNA are susceptible to attack by bisulfite, therefore denaturation of the DNA undergoing ... Primers are designed to be strand-specific as well as bisulfite-specific (i.e., primers containing non-CpG cytosines such that ...

*Mutation

Radiation Ultraviolet light (UV) (non-ionizing radiation). Two nucleotide bases in DNA-cytosine and thymine-are most vulnerable ... Nucleotide substitution (e.g., 76A>T) - The number is the position of the nucleotide from the 5' end; the first letter ... it should be made publicly available for a straightforward nucleotide-by-nucleotide comparison, and agreed upon by the ... For example, if the 100th base of a nucleotide sequence mutated from G to C, then it would be written as g.100G>C if the ...
Press Release issued Sep 24, 2014: Whole exome sequencing (WES) refers to a technique for sequencing the coding region of the genome (exon). Whole exome sequencing helps to detect rare variants in the exome for identifying genomic cause of various diseases such as cancer, genetic disorders, monogenic disorders and others. Whole exome sequencing is used by research centers, pharmaceutical companies, hospitals, clinics, biotechnology companies and government institutions for sequencing of genome. Some of the application areas for whole exome sequencing are drug discovery and development, agriculture, cancer, personalized medicine, monogenic disorders, diagnostics and others.
...Cambridge MA and Shenzhen China July 22 2014 BGI Tech Solutions C...Complete Genomics highly regarded in the industry for providing propr...Whole exome sequencing on Complete Genomics platform available beginn... With the launch of whole exome sequencing on Complete Genomics platfo...,BGI,Tech,launches,human,whole,exome,sequencing,service,on,complete,genomics,advanced,platform,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Whole exome sequencing (WES) has recently emerged as an effective approach for identifying genetic variants underlying human diseases. However, considerable time and labour is needed for careful investigation of candidate variants. Although filtration based on population frequencies and functional prediction scores could effectively remove common and neutral variants, hundreds or even thousands of rare deleterious variants still remain. In addition, current WES platforms also provide variant information in flanking noncoding regions, such as promoters, introns and splice sites. Despite of being recognized to harbour causal variants, these regions are usually ignored by current analysis pipelines. We present a novel computational method, called Glints, to overcome the above limitations. Glints is capable of identifying disease-causing SNVs in both coding and flanking noncoding regions from exome sequencing data. The principle behind Glints is that disease-causing variants should manifest their effect at
TY - JOUR. T1 - RefCNV. T2 - Identification of gene-based copy number variants using whole exome sequencing. AU - Chang, Lun Ching. AU - Das, Biswajit. AU - Lih, Chih Jian. AU - Si, Han. AU - Camalier, Corinne E.. AU - McGregor, Paul M.. AU - Polley, Eric. PY - 2016/4/27. Y1 - 2016/4/27. N2 - With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we ...
Distal renal tubular acidosis is a rare renal tubular disorder characterized by hyperchloremic metabolic acidosis and impaired urinary acidification. Mutations in three genes (ATP6V0A4, ATP6V1B1 and SLC4A1) constitute a monogenic causation in 58-70% of familial cases of distal renal tubular acidosis. Recently, mutations in FOXI1 have been identified as an additional cause. Therefore, we hypothesized that further monogenic causes of distal renal tubular acidosis remain to be discovered. Panel sequencing and/or whole exome sequencing was performed in a cohort of 17 families with 19 affected individuals with pediatric onset distal renal tubular acidosis. A causative mutation was detected in one of the three "classical" known distal renal tubular acidosis genes in 10 of 17 families. The seven unsolved families were then subjected to candidate whole exome sequencing analysis. Potential disease causing mutations in three genes were detected: ATP6V1C2, which encodes another kidney specific subunit of ...
The falling cost of DNA sequencing has made the technology affordable to many research groups, enabling researchers to link genomic variants to observed phenotypes in a range of species. This review focusses on whole exome sequencing and its applications in humans and other species. The exome has traditionally been defined to consist of only the protein coding portion of the genome; a region where mutations are likely to affect protein structure and function. There are several commercial kits available for exome sequencing in a number of species and, owing to the highly conserved nature of exons, many of these can be applied to other closely related species. The data set produced from exome sequencing is many times smaller than that of whole genome sequencing, making it more easily manageable and the analysis less complex. Exome sequencing for disease gene discovery in humans is well established and has been used successfully to identify mutations that are causative of complex and rare diseases. ...
We developed a sequence context based model of de novo mutations to create per-gene probabilities of mutation. We noticed a high correlation (0.94) between the probability of a synonymous mutation in a gene and the number of rare synonymous variants identified in that same gene first using the NHLBI. s Exome Sequencing Project data (evs.gs.washington.edu), then with 25,000 exomes analyzed simultaneously (see abstract by MacArthur et al). We predicted the number of variants that we would expect to see in the dataset and, in order to quantify deviations, created a Z score of the chi-squared difference between observation and expectation for both synonymous and missense variation. While the distribution of these Z scores for the synonymous variants was normal, there is a marked shift in the missense distribution towards having fewer variants than predicted ...
Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common form of deafness: adult-onset progressive hearing loss. Despite several genome-wide association studies of adult hearing status, it remains unclear whether the genetic architecture of this common sensory loss consists of multiple rare variants each with large effect size or many common susceptibility variants each with small to medium effects. As next generation sequencing is now being utilised in clinical diagnosis, our aim was to explore the viability of diagnosing the genetic cause of hearing loss using whole exome sequencing in individual subjects as in a clinical setting. We performed exome sequencing of thirty patients selected for distinct phenotypic sub-types from well-characterised cohorts of 1479 people with adult-onset hearing loss. Every individual carried predicted pathogenic variants
Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common form of deafness: adult-onset progressive hearing loss. Despite several genome-wide association studies of adult hearing status, it remains unclear whether the genetic architecture of this common sensory loss consists of multiple rare variants each with large effect size or many common susceptibility variants each with small to medium effects. As next generation sequencing is now being utilised in clinical diagnosis, our aim was to explore the viability of diagnosing the genetic cause of hearing loss using whole exome sequencing in individual subjects as in a clinical setting. We performed exome sequencing of thirty patients selected for distinct phenotypic sub-types from well-characterised cohorts of 1479 people with adult-onset hearing loss. Every individual carried predicted pathogenic variants
We developed and optimized technical, bioinformatic and interpretive whole exome sequencing (WES) pipelines in a CAP and CLIA certified lab to identify causative mutations underlying disease phenotypes in undiagnosed patients being evaluated clinically for genetic disorders. Approximately 13 Gb of data were generated for each clinical sample and a mean coverage of 160X was achieved with ,95% of the targeted bases covered at 20X or higher. Of the 18773 genes in our exome capture 90% have ,90% of the coding regions covered by WES. Since October 2011, over 1700 WES tests have been submitted to our clinical lab on a fee-for-service basis. The majority of ordering physicians are medical geneticists and neurologists evaluating pediatric-aged patients with neurologic phenotypes who previously had a variety of genetic and other(e.g. imaging) tests without an etiologic diagnosis. To date, 1000 WES tests have been completed and results reported. We identified 367 causative mutant alleles in 265 patients, ...
Aim: To compare clonal T cell receptor γ (TCRγ) gene rearrangements in frozen and formalin-fixed paraffin wax-embedded (FFPE) tissue, using capillary electrophoresis for use in diagnostics, as T cell lymphomas may be difficult to diagnose by conventional methods.. Methods: The DNA for PCR was extracted from frozen and FFPE tissue, cell lines and blood. PCR primers Vγ1-8, Vγ9, Vγ10 or Vγ11 (5′ end labelled) combined with a mixture of JγP1/JγP/JγP2/Jγ2 (unlabelled) were used. Monoclonal cases were sequenced and clonality, reproducibility, sensitivity and specificity analyses were carried out.. Results: In all cases the molecular test was found to be in agreement with the histological diagnosis. Discrepancies were found between frozen and FFPE tissue in 18 of 56 (32%) tests. The method was highly reproducible. The sensitivity was found to be 0.5% for cell lines and 1% for patient specimens and the specificity 100%. The junctional region between the Vγ and Jγ segments was specific for ...
Whole exome sequencing (WES) identification of a rare, damaging, de novo germline MYH9 variant with the IDT xGen Exome Research Panel
Aims In recent years the genetic aberrations associated with diffuse large B-cell lymphoma and the new subtype described in the 2008 revision of the WHO classification, B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma have been increasingly well defined. Recurrent genetic abnormalities include rearrangements involving MYC (8q24), BCL2 (18q21) and BCL6 (3q27); as the prognostic and therapeutic implications associated with these abnormalities are clarified their accurate identification at diagnosis is becoming increasingly critical. We describe our experience of using a panel of fluorescence in situ hybridisation (FISH) probes on formalin-fixed paraffin-embedded tissue sections in the diagnostic work-up of 162 patients with non-Burkitt high grade B-cell non-Hodgkins lymphomas (HG-BNHL). ...
A number of reports have recently emerged with focus on extraction of proteins from formalin-fixed paraffin-embedded (FFPE) tissues for MS analysis; however, reproducibility and robustness as compared to flash frozen controls is generally overlooked. The goal of this study was to identify and validate a practical and highly robust approach for the proteomics analysis of FFPE tissues. FFPE and matched frozen pancreatic tissues obtained from mice (n = 8) were analyzed using 1D-nanoLC-MS(MS)2 following work up with commercially available kits. The chosen approach for FFPE tissues was found to be highly comparable to that of frozen. In addition, the total number of unique peptides identified between the two groups was highly similar, with 958 identified for FFPE and 1070 identified for frozen, with protein identifications that corresponded by approximately 80%. This approach was then applied to archived human FFPE pancreatic cancer specimens (n = 11) as compared to uninvolved tissues (n = 8), where ...
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE) tissue. This studys aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE) tissue. This studys aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The
FISH images of formalin fixed paraffin embedded sections of BAC. Red signals (white arrow heads) are indicative of the p53 gene probe, while green signals (yell
This video covers off on the challenging samples in cancer research, specifically formalin-fixed paraffin-embedded tissues. Presented by Beckman Coulter Life Sciences.
The identification of recurrent driver mutations by whole-exome sequencing (WES) of fresh-frozen human cancers and the subsequent development of novel targeted therapies have recently transformed the treatment of many cancers including melanoma. In routine clinical practice, fresh-frozen tissue is rarely available and mutation testing usually needs to be carried out on archival formalin fixed, paraffin embedded (FFPE) tissue, from which DNA is typically fragmented, cross-linked and of lower quality. In this study we aimed to determine whether WES data generated from genomic DNA (gDNA) extracted from FFPE tissues can be produced reliably and of clinically-actionable standard. In this study of ten melanoma patients, we compared WES data produced from analysis of gDNA isolated from FFPE tumour tissue with that isolated from fresh-frozen tumour tissue from the same specimen. FFPE samples were sequenced using both Illuminas Nextera and NimbleGen SeqCap exome capture kits. To examine mutations between the
The promising results of anaplastic lymphoma kinase (ALK) inhibitors have changed the significance of ALK fusions in several types of cancer. These fusions are no longer mere research targets or diagnostic markers, but they are now directly linked to the therapeutic benefit of patients. However, most available tumor tissues in clinical settings are formalin-fixed and paraffin-embedded (FFPE), and this significantly limits detailed genetic studies in many clinical cases. Although recent technical improvements have allowed the analysis of some known mutations in FFPE tissues, identifying unknown fusion genes by using only FFPE tissues remains difficult. We developed a 5-rapid amplification of cDNA ends-based system optimized for FFPE tissues and evaluated this system on a lung cancer tissue with ALK rearrangement and without the 2 known ALK fusions EML4-ALK and KIF5B-ALK. With this system, we successfully identified a novel ALK fusion, KLC1-ALK. The result was confirmed by reverse transcription
The storage and collection of fresh frozen tissue is by no means an easy task. Tissue sample collection and storage must conform to strict industry
Optimal reference genes for normalization of qRT-PCR data from archival formalin-fixed, paraffin-embedded breast tumors controlling for tumor cell content and decay of ...
TY - JOUR. T1 - p53 Overexpression and bcl-2 persistence in endometrial carcinoma. T2 - Comparison of papillary serous and endometrioid subtypes. AU - Zheng, Wenxin -. AU - Cao, Peiqin. AU - Zheng, Mei. AU - Kramer, Elmer E.. AU - Godwin, Thomas A.. PY - 1996/5. Y1 - 1996/5. N2 - Forty-two cases, including 21 uterine papillary serous carcinomas (UPSC) and 21 age-, nuclear-grade-, and clinical-stage-matched uterine endometrioid carcinomas (UEC), were studied immunohistochemically for p53 and bcl-2 in archival paraffin-embedded tissue. Compared to UEC (28.6% positive), UPSC (71.4% positive) had a significantly higher frequency of p53 overexpression (P = 0.005); furthermore, in a clinical-stage-matched fashion, a higher frequency of p53 overexpression was found in early-stage cases (P = 0.032), but not in late-stage cases. In a nuclear-grade-matched comparison, no statistical difference in p53 overexpression was identified between the two subtypes, although UPSC had stronger p53 immunoreactivity ...
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The goal of this study is to study NIS expression in benign and malignant breast and thyroid samples using archival formalin-fixed paraffin-embedded tissue sections.
Human-human hybridoma technology was evaluated for the study of humoral immune reactions of colorectal cancer patients against their own tumors. Six fusions were carried out with lymphocytes from mesenteric lymph nodes from patients with colorectal cancer, using the human B-lymphoma cell line LICR-LON-HMy-2 as fusion partner. A total of 294 wells with cell growth were obtained. Supernatants from 26 of these reacted in enzyme-linked immuno-sorbent assay (ELISA) with one or more colon cancer cell lines. Cells from only one of these wells (D 4213) could be cloned. The clone was shown to produce antibody which by immunocytochemical analysis reacted with a panel of colon cancer cell lines and melanoma cell lines but not with several other cancer cell lines or normal human leukocytes. By immunohistochemical analysis on formalin-fixed paraffin-embedded tissue this antibody reacted strongly with antigen expressed by autologous and allogeneic colorectal cancers. Faint staining could occasionally be ...
Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a long tail of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective ...
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Endometrial cancer is one of the most common malignancies of the reproductive female tract, with endometrioid endometrial cancer being the most frequent type. Despite the relatively favourable prognosis in cases of endometrial cancer, there is a necessity to evaluate clinical and prognostic utility of new molecular markers. MiRNAs are small, non-coding RNA molecules that take part in RNA silencing and post-transcriptional regulation of gene expression. Altered expression of miRNAs may be associated with cancer initiation, progression and metastatic capabilities. MiRNA-205 seems to be one of the key regulators of gene expression in endometrial cancer. In this study, we investigated clinical and prognostic role of miRNA-205 in endometrioid endometrial cancer. After total RNA extraction from 100 archival formalin-fixed paraffin-embedded tissues, real-time quantitative RT-PCR was used to define miRNA-205 expression levels. The aim of the study was to evaluate miRNA-205 expression levels in regard to
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); or 10% buffered formalin (3F ...
Formalin fixed, paraffin embedded (FFPE) whole tissue sections are ideal candidates for localizing DNA, RNA and protein markers. The tissues were fixed by formalin less than 48 hours, and then processed and sectioned. Two tissue sections with 5 µm (micro, micrometer) thickness are mounted on a SuperFrost Plus glass slide. US Biomax, Inc. paraffin tissue section is suitable for detection of genes and proteins expression in specific tissues of different species.. Features ...
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Effect of formalin fixation on thermal conductivity of the biological tissues is presented. A self-heated thermistor probe was used to measure the tissue thermal conductivity. The thermal conductivity of porcine aorta, fat, heart, and liver was measured before the formalin fixation and then 1 day, 4 days, and 11 days after formalin fixation. The results indicate that the formalin fixation does not cause a significant change in the tissue thermal conductivity of the tissues studied. In the clinical setting, tissues removed surgically are often fixed in formalin for subsequent pathological analysis. These results suggest that, in terms of thermal properties, it is equally appropriate to perform in vitro studies in either fresh tissue or formalin-fixed tissue.. ...
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The first reported miRNA gene, lin-4, was described in C. elegans in 1993 [22]; the same year that the first surgical samples in this study were isolated. In a perfect world these samples would remain unchanged over time; however, it is well known that processing and storage can lead to significant RNA degradation [5, 6]. The influence of such parameters on miRNA detection and stability remains debatable.. A recent study of six miRNAs in colorectal tissue blocks stored for up to 28 years found no significant effects of sample block age on miRNA detection [12]. Similar observations were reported for miR-181b and 5S ribosomal RNA from blocks as old as ten years [8]. Deep sequencing analyses of miRNAs from multiple different types of tissue, stored for 2 to 9 years, have also found no significant change in miRNA detection with sample age [9]. In contrast, others have reported significant miRNA loss with extended FFPE block storage times. Comparison of miRNA expression from 1 to 11 year old FFPE ...
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Background: Colorectal adenomas are precursor lesions of colorectal cancer. About 5% of colorectal adenomas are estimated to progress to colorectal cancer (CRC). The currently used histo-pathological characteristics to identify adenomas at risk of malignant progression, i.e. scoring of size ≥ 10mm, villous component or high grade dysplasia, are not sufficiently sensitive and specific and prone to inter-observer variability. Integrating molecular markers reflecting the underlying biology of CRC into the current classification system is expected to better characterize adenomas at high-risk of progression.. Aim: Here we compared the prevalence of genetic changes, in particular DNA copy number changes, between advanced and non-advanced adenomas.. Methods: Formalin-fixed paraffin-embedded tissue samples from 121 patients (mean age 65.4±11.6, 52.9% male) with colorectal adenomas (63 non-advanced adenomas and 58 advanced adenomas) were retrospectively collected from the archives of the department of ...
Urgently looking for CD14 antibody that would work on formalin fixed paraffin embedded tissues of cynomolgus monkeys. Has anybody worked with one ...
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Human bladder cancer specimens. Tumor samples from 109 patients of primary UCC were collected at cystectomy or transurethral resection, and snap frozen in liquid nitrogen. Use of tissues for this study was approved by Cambridgeshire Local Research Ethics Committee (Ref 03/018). A total of 30 sections of 30 μm of fresh frozen tissue were homogenized for DNA and RNA extraction. "Sandwich" H&E sections were prepared for cellularity and grade assessment by a reference urohistopathologist (A.W.). Tumors were staged and graded according to the American Joint Committee on Cancer and WHO/International Society of Urologic Pathology classifications (34, 35). Samples showing tumor cellularity of ,70% and significant inflammatory cell contamination were excluded.. Tissue microarray. For our custom-made tissue microarray (TMA), an independent cohort of 123 formalin-fixed, paraffin-embedded tissue samples of primary UCC was obtained from the pathology archives of Addenbrookes Hospital, Cambridge University ...
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Oral squamous cell carcinoma (OSCC) can remain undiagnosed until in an advanced, and sometimes lethal, state. It is often preceded by a potentially malignant lesion, which may manifest as a white patch leukoplakia of the oral mucosa. Previous research has implicated an association between the presence of Candida albicans and the progression of leukoplakias to OSCC. Alcohol may contribute to oral cancer via its conversion to acetaldehyde, a known carcinogen, which is also a product of C. albicans metabolism. The reversible conversion of ethanol to acetaldehyde is catalysed by enzymes known as alcohol dehydrogenases (ADHs) and in C. albicans, it is not known which ADH is responsible for acetaldehyde production. Aims of this study: To investigate expression of the CaADH genes in vitro and to identify the C. albicans genes responsible for acetaldehyde production. It is also the aim of this study to detect the expression of the CaADH genes in archival formalin-fixed paraffin-embedded (FFPE) samples ...
Dear Sally, , Has anyone ever performed IF on formalin fixed paraffin embedded tissue? If , yes. Is there an enzyme digesting agent that is better to use for IF? Also I , think I read somewhere that 10% Neutral Buffered Formalin autofluoresces. , Has anyone heard this? You can do IF on formalin fixed tissue just like a regular IPX (it is only the label that is different). Use enzyme or antigen retrieval as usual. IF on formalin fixed skin and renal (like IPX) is difficult but not impossible. Collagen will fluoresce after formalin fixation and of course melanin will as well (basis of the formalin induced fluorescence test). The appropriate use of filters will decrease this problem. Regards, Tony Tony Henwood Senior Scientist Anatomical Pathology Royal Prince Alfred Hospital Sydney, AUSTRALIA http://www2.one.net.au/~henwood http://www.pathsearch.com/homepages/TonyHenwood/default.html ...
Recent studies have suggested that Epstein-Barr virus (EBV) may play a role in the etiology of Hodgkins disease (HD). In a previous study, we used a latent membrane protein 1 (LMP1)-specific antibodies to examine archival material from 74 British children with HD and found 50% of cases to be positive. It is known that there are geographic and ethnic variations in the incidence of HD. We have investigated LMP1 status in formalin-fixed, paraffin wax-embedded lymph nodes with HD involvement from 53 children and 48 adults from Kenya using immunohistochemical staining. We also developed sensitive and specific in vitro gene amplification protocols for examining the EBV strain type in such material using several combinations of primers derived from the EBNA 2 and EBNA 3 coding regions. LMP1 positivity was present in 100% of the pediatric cases (two lymphocyte-predominant, 25 nodular sclerosis, 16 mixed cellularity, 5 lymphocyte depletion, and 5 unclassified) and in 66% of the adult cases (two of three ...
Background: The Human Papillomavirus (HPV) is a DNA tumor virus that causes epithelial proliferation. There are more than 100 HPV subtypes, of which 13 subtypes are regarded as high risk subtypes that can cause cancers of epithelial mucosal surfaces. High risk human papilloma viruses (HR-HPV) subtypes 16 and 18 plays a major role in the etiology of cervical cancer worldwide. Therefore, the aim of this study was to screen for the existence of HPV16 and HPV18 among Yemeni women with cervical lesions. Methodology: Formalin fixed paraffin wax processed tissue blocks were retrieved for 200 patients (150 were previously diagnosed with cervical cancer and the remaining 50 were diagnosed with different benign conditions). Results: Of the 200 cervical cancer tissue specimens, HR-HPV 16 was identified in 74/200 (37%) samples and couldnt be recognized in 126/200(63%) tissue samples. HR-HPV 18 was identified in 32/200 (16%) specimens and couldnt be recognized in 168/200(84%) tissue specimens. Conclusion: HR-HPV
Tissue autofluorescence frequently hampers visualization of immunofluorescent markers in formalin-fixed paraffin-embedded tissues tissues. Focused specifically on human respiratory tissues, we sought to identify endogenous elements contributing to autofluorescence through multi-photon microscopic separation of elastin from collagen with immunofluorescent labeling for validation. We then assessed nine treatments reported to have efficacy in reducing autofluorescence in other tissue types. The three most efficacious were eriochrome black T, Sudan black and sodium borohydride as measured using white light laser confocal multi-lambda analysis. We also assessed the impact of steam antigen retrieval and serum application on human tracheal tissue autofluorescence. Functionally fitting this multi-lambda data to 2-dimensional Guassian surfaces revealed that steam antigen retrieval and serum application contribute minimally to autofluorescence and that the three treatments are disparately efficacious. ...
Background Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of renal cell carcinoma. In patients with ccRCC several prognostic markers have been suggested, enclosing epidermal growth factor receptor (EGFR) expression and chromosome 7 polysomy (C7p). Cancer cells addicted to EGFR bear activated mutations in the EGFR gene, and these mutations are useful in predicting susceptibility of ccRCC to EGFR inhibitors. The aim of this study was to evaluate the prognostic value of EGFR overexpression and C7p.. Patients and methods Archival specimens, coupled with clinical and survival data of 34 patients (20 men, 14 women, median age 58, range 42-79 years) who had undergone radical nephrectomy for ccRCC were analyzed. Immunohistochemistry and fluorescence in situ hybridization (FISH) specimens were sections of formalin-fixed paraffin-embedded tissue. EGFR expression was detected as membranous and cytoplasmic staining of neoplastic cells > 1%, and a ratio between ...
Background and Objective: BRAF mutations were studied in various populations for prostate carcinoma (PC); however, mutations in BRAF gene are unusual compared to KRAS. Oncogenic activating of BRAF mutations were studied lately in almost 0%-10% of prostate cancer cases. Methods: In this retrospective study, we gathered 100 formalin-fixed paraffin-embedded samples of prostate adenocarcinoma. A hundred archived samples of adjacent benign prostatic hyperplasia were chosen as normal control. This study was done in pathology laboratory of Qaem Hospital during 2013-2015.Results: Total number of 200 PC and normal cases was investigated for BRAF V600E mutation. The BRAF V600E mutation was found in only 4 patients but it was not detected in normal cases. There were no significant differences between patient and control groups for this mutation (P|0.99). The frequency of BRAF V600E mutation was not significant in different age groups (P|0.285); the most frequency was related to the age range of 71-80. No
Background: MicroRNAs are small non-coding RNAs that play crucial roles in the pathogenesis of different cancer types. The aim of this study was to identify miRNAs that are differentially expressed in endometrial adenocarcinoma compared to healthy endometrium. These miRNAs can potentially be used to develop a panel for classification and prognosis in order to better predict the progression of the disease and facilitate the choice of treatment strategy.. Methods Formalin fixed paraffin embedded endometrial tissue samples were collected from the Örebro university hospital. QPCR was used to quantify the expression levels of 742 miRNAs in 30 malignant and 20 normal endometrium samples. After normalization of the qPCR data, miRNAs differing significantly in expression between normal and cancer samples were identified, and hierarchical clustering analysis was used to identify groups of miRNAs with coordinated expression profiles.. Results: In comparisons between endometrial adenocarcinoma and normal ...
Context:Multiple genes and proteins have been shown to be important in treatment and prognosis of breast cancer, including the estrogen and progesterone receptors and Her-2 neu. Vascular endothelial growth factor (VEGF) subtypes have been shown to be associated with lympho-vascular invasion, lymph node metastases and prognosis in multiple types of cancer, including colon cancer, gastric cancer and breast cancer. The goal of this project was to observe and quantify the protein expression of VEGF subtypes in human breast cancer, then correlate this with known clinicopathologic information. Design:Ninety grade three (high grade) invasive ductal carcinomas received over a four year period (1997-2001) were selected from our files. Immunohistochemistry was performed on formalin fixed paraffin embedded tissue of both primary tumor and lymph node metastasis when applicable using VEGF-A, VEGF-C, VEGF-D and VEGF-R (the VEGF receptor) antibodies. The staining was graded from zero (no expression) to 3+ (high
Ronz, P., et al. Immunohistochemical expression of E-cadherin in different tissues of the teleost fish Scophthalmus maximus. Aquaculture. 501, 465-472. 25/2/2019.. E-cadherin is an evolutionary conserved protein, whose main role as the principal component of adherens junctions is supporting epithelial cell-cell adhesion. It is an essential molecule for the maintenance of the epithelial barrier function and the analysis of its immunohistochemical expression is a valuable resource in morphopathological, ontogenetic and pathogenesis studies in mammals. As well, there is an increasing understanding of the importance of E-cadherin in the physiology of the immune system and the development of the immune response. Mucosal health is a primary issue in aquaculture research; nevertheless, there is a lack of immunohistochemical studies of cell junction proteins in fish species. In this work, an immunohistochemical technique was optimized in Bouin- and formalin-fixed paraffin-embedded tissues of turbot ...
Abstract. Diagnosis of dengue virus (DENV) infection in fatal cases is challenging because of the frequent unavailability of blood or fresh tissues. For formalin-fixed, paraffin-embedded (FFPE) tissues immunohistochemistry (IHC) can be used; however, it may not be as sensitive and serotyping is not possible. The application of reverse transcription-polymerase chain reaction (RT-PCR) for the detection of DENV in FFPE tissues has been very limited. We evaluated FFPE autopsy tissues of 122 patients with suspected DENV infection by flavivirus and DENV RT-PCR, sequencing, and DENV IHC. The DENV was detected in 61 (50%) cases by RT-PCR or IHC. The RT-PCR and sequencing detected DENV in 60 (49%) cases (DENV-1 in 16, DENV-2 in 27, DENV-3 in 8, and DENV-4 in 6 cases). No serotype could be identified in three cases. The IHC detected DENV antigens in 50 (40%) cases. The RT-PCR using FFPE tissue improves detection of DENV in fatal cases and provides sequence information useful for typing and epidemiologic studies.
Inflammatory breast cancer (IBC) is a distinct clinicopathologic entity that carries a worse prognosis relative to non-IBC breast cancer even when matched for standard biomarkers (ER/PR/HER2). The objective of this study was to identify opportunities for benefit from targeted therapy, which are not currently identifiable in the standard workup for advanced breast cancer. Comprehensive genomic profiling on 53 IBC formalin-fixed paraffin-embedded specimens (mean, 800× + coverage) using the hybrid capture-based FoundationOne assay. Academic and community oncology clinics. From a series of 2208 clinical cases of advanced/refractory invasive breast cancers, 53 cases with IBC were identified. The presence of clinically relevant genomic alterations (CRGA) in IBC and responses to targeted therapies. CRGA were defined as genomic alterations (GA) associated with on label targeted therapies and targeted therapies in mechanism-driven clinical trials. For the 44 IBCs with available biomarker data, 19 (39 %) ...
Childrens Hospital Los Angeles has launched OncoKids, a next-generation sequencing-based panel that detects mutations, gene amplification, and gene fusions for a full range of pediatric cancers including leukemias, bone and soft tissue tumors, and brain tumors. It only requires a small amount of DNA and RNA (20ng) isolated from fresh, frozen, or formalin-fixed paraffin-embedded tissue. The test was developed in collaboration with Thermo Fisher Scientific and uses the Ion Torrent S5 sequencing platform and Ion AmpliSeq technology.
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Background A T cell costimulatory molecule with dipeptidyl peptidase IV (DPPIV) activity in its extracellular area, Compact disc26 is a multifunctional molecule connected with various protein such as for example adenosine deaminase, caveolin-1, CXCR4, collagen, and fibronectin, while using a significant function in the regulation of inflammatory tumor and replies biology. molecule in the formalin-fixed paraffin-embedded tissue is critical. SOLUTIONS TO develop book anti-CD26 mAbs with the capacity of binding towards the denatured Compact disc26, we immunized mice with Compact disc26 proteins denatured in urea buffer. Following the fusion of myeloma and splenocytes cells, the mAbs had been screened for particular reactivity with individual Compact disc26 by stream cytometry, enzyme-linked immunosorbent assay, and immunohistochemistry. The binding competitiveness of novel anti-CD26 mAbs using the humanized anti-CD26 mAb YS110 was also analyzed. Results Weve been successful in developing book ...
Background: Expression of p53, cyclin D1, p21 (WAF1) and Ki-67 (MIB1) was evaluated in oral squamous cell carcinoma (OSCC) to test whether levels of these markers at invasive tumour fronts (ITFs) could predict the development of local recurrence. Materials and Methods: Archived paraffin-embedded specimens from 51 patients with T1/T2 tumours were stained immunohistochemically and analysed quantitatively. Local recurrence-free survival was tested with Kaplan-Meier survival plots (log-rank test) using median values to define low and high expression groups and with a Coxs proportional hazards model in which the expression scores were entered as continuous variables. Results: The assessment of expression of all markers was highly reliable, univariate analysis showing that patients with clear surgical margins, with low cyclin D1 and high p21 expression at the ITF had the best local recurrence-free survival. Multivariate analysis showed that these three parameters were independent prognostic factors but that
The limited number of available treatments for patients with small-cell lung cancer (SCLC) has prompted us to further investigate the biology of SCLC by molecular profiling. We collected formalin-fixed paraffin-embedded tumor samples from 127 patients with SCLC, who had undergone surgery at 16 institutions between January 2003 and January 2013, and analyzed the association between disease-specific survival and protein expression of c-kit, c-Met, epidermal growth factor receptor, human EGFR-related 2, vascular endothelial growth factor receptor II, anaplastic lymphoma kinase, mediator complex subunit 12 (MED12), and transforming growth factor beta receptor II (TGF-βRII) by immunohistochemistry (IHC ...
article{1cb77357-aca8-4b11-9d70-6a2e46c89bc9, abstract = {We report the association of an inherited variant located upstream of the poly(adenosine diphosphate-ribose) polymerase 1 (PARP1) gene (rs2249844), with survival in 11 BioGenoMEL melanoma cohorts. The gene encodes a protein involved in a number of cellular processes including single-strand DNA repair. Survival analysis was conducted for each cohort using proportional hazards regression adjusting for factors known to be associated with survival. Survival was measured as overall survival (OS) and, where available, melanoma-specific survival (MSS). Results were combined using random effects meta-analysis. Evidence for a role of the PARP1 protein in melanoma ulceration and survival was investigated by testing gene expression levels taken from formalin-fixed paraffin-embedded tumors. A significant association was seen for inheritance of the rarer variant of PARP1, rs2249844 with OS (hazard ratio (HR) = 1.16 per allele, 95% confidence interval ...
The overall goal of this application is to deliver a highly multiplexed, quantitative, and automated system for the rapid identification of diffuse large B-cell lymphoma (DLBCL) subgroups using formalin-fixed paraffin-embedded (FFPE) material as the sample source; a technology that is not yet available to the research and clinical communities. DLBCL accounts for ~30% of all non-Hodgkin lymphomas and thus is the most common subtype of this cancer in the United States. While many patients respond well to treatment, there is a sizable subset that remains refractory or suffers relapse. Gene expression profiling has revealed that this difference in response is reflected in the biology of the tumor an two subgroups have been defined based on the origin of the tumor cell. Molecular signatures within a panel of 17 genes can differentiate these subgroups. Technologies to detect gene expression patterns currently center around two existing formats: microarrays and real-time PCR. The former, although able ...
Molecular detection and analysis of virulence factors of Helicobacter pylori depends on the specificity of cell selection in the gastric biopsies. The laser microdissection (LM) instruments combine mi
Gene Expression Profiling of Cutaneous Melanoma The DecisionDx-Melanoma test (Castle Bioscience, Inc., Friendswood, TX) is a multigene expression assay designed to predict metastasis in individuals with stage I or stage II cutaneous melanoma who have no sign of disease beyond the original tumor. The laboratory test is a signature of 31 genes, 28 discriminating genes and 3 control genes, that classifies tumors as class 1 (low risk of metastasis) or class 2 (high risk of metastasis), using reverse transcription polymerase chain reaction (RT-PCR) on formalin-fixed paraffin-embedded (FFPE) primary tumor tissue specimens obtained from either biopsy or excision of a cutaneous melanoma.. There is wide variability in metastatic rates within and across Tumor-Node-Metastasis (TNM) stage groupings in individuals with cutaneous melanoma. The DecisionDx-Melanoma test is purported to predict the risk of tumor metastasis in confirmed melanoma independent of currently used metrics of risk assessment such as ...
Regulatory T cells (Tregs) exert various suppressive mechanisms to dampen the host immune response which can help tumor cells to escape immune surveillance. However, the prognostic value of tumor-infiltrating Tregs (Ti-Tregs) is controversial based on the expression of FoxP3 marker in cancer patients. Here, we decipher the phenotype of Tregs infiltrating human lung cancer to determine their role in shaping the immune response against tumor cells. Our aim was to study the differentiation, activation, and immunosuppression status of Ti-Tregs in different areas of human lung tumors. Immunohistochemistry was performed on paraffin-embedded tissue sections for CD3 and FoxP3 stainings, and phenotypic analysis was carried out on fresh human lung cancer specimens (n=50) by flow cytometry. In lung cancer patients, Ti-Tregs localize in the different part of the tumor i.e. tumor nests, stroma, and tertiary lymphoid structures (TLS). Ti-Tregs are CD4+ and show central-memory and effector-memory phenotype. ...
The U.S. Food and Drug Administration (FDA) has permitted marketing of the Philips IntelliSite Pathology Solution (PIPS, Philips Medical Systems Nederland B.V.), as an aid to pathologists to review and interpret digital images of surgical pathology slides prepared from formalin-fixed paraffin embedded tissue.. PIPS is an automated digital slide creation, viewing, and management system that will allow pathologists to review and interpret digital images of surgical pathology slides prepared from formalin-fixed paraffin embedded tissue, rather than having to look directly under a conventional light microscope at a tissue sample mounted on a glass slide. This is the first FDA-authorized digital pathology whole-slide imaging system available for these purposes.. The FDA reviewed the data for the PIPS through the de novo premarket review pathway to provide a reasonable assurance of safety and effectiveness of the device. During this process, the FDA evaluated data from a multisite, multireader, ...
Human papillomavirus (HPV) infection has been etiologically linked to oropharyngeal squamous cell carcinoma (OPSCC). The prevalence of HPV-positive OPSCC varies between studies, ranging from 20 to 90%. This may be related to the lack of a standardized HPV detection assay as well as to the time period in which HPV prevalence is investigated, as rising incidence rates are reported over the last decades. Here, we validated our previously defined test algorithm for HPV detection in formalin-fixed paraffin-embedded (FFPE) tumor specimen consisting of p16INK4A immunostaining followed by high-risk HPV DNA detection by GP5+/6+ PCR on the positive cases (Smeets et al., Int J Cancer 2007;121:2465-72). In addition, we analyzed HPV prevalence rates in OPSCCs in the years 1990-2010. The test algorithm was validated on a consecutive series of 86 OPSCCs collected during 2008-2011, of which both fresh frozen and FFPE samples were available. We performed HPV-E6 RT-PCR on the frozen samples as gold standard and ...
OBJECTIVES:. I. Validation of the 15-gene prognostic and predictive messenger (m) ribonucleic acid (RNA) signature on Lung Adjuvant Cisplatin Evaluation (LACE)-Bio formalin-fixed, paraffin-embedded tissue (FFPE) tumor samples.. II. Exploratory evaluation of the prognostic and predictive values of known potential oncogenic mutations using LACE-Bio FFPE tumor samples.. III. Exploratory evaluation of the prognostic and predictive values of gene copy variations using LACE-Bio FFPE tumor samples.. IV. Exploratory identification and evaluation of prognostic and predictive value of novel genomic aberrations discovered by Next Generation Sequencing on LACE-Bio tumor samples.. OUTLINE:. Archived RNA and DNA samples are analyzed for gene expression, mutations, and variations by reverse transcriptase (RT)-polymerase chain reaction (qPCR), mass spectrometry (MassARRAY), molecular inversion probe assay, and microarray assays. Results are then compared with patients clinical outcomes. ...
Background. DNA methylation is one of the best studied epigenetic modifications and one major constituent of the epigenome of a cell. It contributes to normal development as well to carcinogenesis. Nowadays, many efforts are being made in order to use DNA methylation as a biomarker. The aim of our work is to characterize the expression and methylation of SIRT1, HIC1, BCL6, KLF4 and other genes relevant for Non-Hodgkin lymphomas (NHL) pathogenesis. Methods. Immunohistochemistry (IHC) on 72 formalin-fixed paraffin embedded tissue sections (FFPE). B-lymphocytes were purified from 36 biopsies of follicular hyperplasias (non-malignant B-lymphocytes), follicular lymphomas (FL) and diffuse large B-cell lymphomas (DLBCL). Gene expression were analysed by quantitative retrotranscribedPCR (qRTPCR). Quantitative CpG promoter methylation analysis was performed by pyrosequencing after bisulfite conversion or by Methyl II array qPCR on genomic DNA. Results. In a total of 72 FFPE samples of follicular ...
USP6 rearrangement is the most common genetic abnormality in primary aneurysmal bone cyst, and SS18 rearrangement has not been previously described in any type of tumor where synovial sarcoma was excluded from the differential diagnosis. We report a case of solid aneurysmal bone cyst in which fluorescence in situ hybridization (FISH) analysis indicated rearrangements of both USP6 and SS18, but histologic features were consistent with aneurysmal bone cyst throughout the lesion. Reverse-transcription polymerase chain reaction (RT-PCR) for the SS18-SSX1 and SS18-SSX2 translocations, identity testing, and SS18 FISH were performed on cytogenetic monolayer cultures and formalin-fixed paraffin-embedded (FFPE) tissue. Genomic microarray, FISH, and immunohistochemistry were performed on follow-up studies of the FFPE specimen. The karyotype was 45,X,add(X)(p11.2),add(4)(q13),add(8)(p21),-13,add(17)(p11.2),add(18)(q11.2) in all 20 cells analyzed from monolayer cultures. The karyotype showed no ...
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Here, the protein-coding genes expressed in the bone marrow are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the bone marrow. Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 172 individual samples corresponding to 37 different human normal tissue types. RNA sequencing results of 4 fresh frozen tissues representing normal bone marrow was compared to 168 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in bone marrow. A tissue-specific score, defined as the ratio between mRNA levels in bone marrow compared to the mRNA levels in all other tissues, was used to divide the genes ...
Here, the protein-coding genes expressed in the thyroid gland are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the thyroid gland. Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 124 individual samples corresponding to 32 different human normal tissue types. RNA sequencing results of 4 fresh frozen tissues representing normal thyroid gland was compared to 120 other tissue samples corresponding to 31 tissue types, in order to determine genes with elevated expression in thyroid gland. A tissue-specific score, defined as the ratio between mRNA levels in thyroid gland compared to the mRNA levels in all other tissues, was used to divide ...
Here, the protein-coding genes expressed in the gallbladder are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the gallbladder. Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 124 individual samples corresponding to 32 different human normal tissue types. RNA sequencing results of 3 fresh frozen tissues representing normal gallbladder was compared to 121 other tissue samples corresponding to 31 tissue types, in order to determine genes with elevated expression in gallbladder. A tissue-specific score, defined as the ratio between mRNA levels in gallbladder compared to the mRNA levels in all other tissues, was used to divide the genes ...
Human frozen tissue section matched pair products include: Primary Pair (PP), Primary and Metastasis Pair (PM). PP consists of frozen tissue section of primary tumor and its adjacent normal tissue; PM consists of frozen tissue section of primary tumor and corresponding metastatic tumor. The frozen tissue sections in each pair are prepared from the same donor ...
OPUS (Open Publications of UTS Scholars) is the UTS institutional repository. It showcases the research of UTS staff and postgraduate students to a global audience. For you, as a researcher, OPUS increases the visibility and accessibility of your research by making it openly available regardless of where you choose to publish.. Items in OPUS are enhanced with high quality metadata and seeded to search engines such as Google Scholar as well as being linked to your UTS research profile, increasing discoverability and opportunities for citation of your work and collaboration. In addition, works in OPUS are preserved for long-term access and discovery.. The UTS Open Access Policy requires UTS research outputs to be openly available via OPUS. Depositing your work in OPUS also assists you in complying with ARC, NHMRC and other funder Open Access policies. Providing Open Access to your research outputs through OPUS not only ensures you comply with these important policies, but increases opportunities ...
The scope and overall interpretation of our report on the re-evaluation of the fixed, paraffin-embedded tissue samples taken at patient BIs autopsy are necessarily limited by the absence of diagnostic results of any serological or other tests for candidate infective organisms at the time of the "viral encephalitis" in 1986 (see review [17]). Nevertheless, taken together, the extended laboratory tests with C.b. specific monoclonal antibodies and PCR (COM1 and IS1111a genes) on a range of post mortem specimens suggest that the most compelling and coherent explanation of BIs illness from 1986 to 1996, is one of a severe attack of primary Q fever and a subsequent multisystem organ dysfunction with dissemination of the coxiella throughout the body, ending in 1996 with cardiac and cerebral dysfunction i.e., a complex, severe idiopathic illness labelled descriptively at the time as "post (viral) infection fatigue syndrome" (PIFS).. An epidemiological and clinical association between ...
Molecular subtype classification of formalin-fixed, paraffin-embedded diffuse large B-cell lymphoma samples on the ICEPlex® system.
Gene expression profiling classifies individual tumors by their gene expression patterns and may also describe and predict therapeutic resistance and sensitivity patterns. Profiling in several cancers, such as breast cancer, colon cancer, lymphoma, leukemia, and melanoma [3], has already identified molecular subclasses of tumors. Identification of tumor subtypes may be predictive for prognosis or response to drug therapy [6, 7, 28-31].. The potential of routine gene expression profiling to predict clinical outcomes for cancer patients has yet to be determined. The Evaluation of Genomic Applications in Practice and Prevention Working Group stated in 2009 that there was "insufficient evidence to make a recommendation for or against the use of tumor gene expression profiles to improve outcomes in defined populations of women with breast cancer" [32]. Clearly, more work needs to be done to translate promising research findings into clinically relevant results.. Comparison of FFPET sample-derived ...
Background. The CHER-LOB randomized phase II study showed that the combination of lapatinib and trastuzumab plus chemotherapy increases the pathologic complete re- mission (pCR) rate compared with chemotherapy plus either trastuzumab or lapatinib. A biomarker program was prospectively planned to identify potential predictors of sensitivity to different treatments and to evaluate treatment effect on tumor biomarkers. Materials and Methods. Overall, 121 breast cancer patients positive for human epidermal growth factor 2 (HER2) were randomly assigned to neoadjuvant chemotherapy plus trastu- zumab, lapatinib, or both trastuzumab and lapatinib. Pre-and post-treatment samples were centrally evaluated for HER2, p95- HER2, phosphorylated AKT (pAKT), phosphatase and tensin homolog, Ki67, apoptosis, and PIK3CA mutations. Fresh-frozen tissue samples were collected for genomic analyses. Results. A mutation in PIK3CA exon 20 or 9 was documented in 20% of cases. Overall, the pCR rates were similar in PIK3CA ...
TY - JOUR. T1 - Different methylation profiles between intestinal and diffuse sporadic gastric carcinogenesis. AU - Yang, Misuk. AU - Kim, Hyunsoo. AU - Cho, Meeyon. PY - 2014/1/1. Y1 - 2014/1/1. N2 - Objective: Gastric cancer (GC) is histologically classified into intestinal type and diffuse type, and diffuse type cancer can be further subdivided into poorly differentiated carcinoma (PDC) and signet ring cell carcinoma (SRCC). Recent evidence suggests that early SRCC is an initial, differentiated form of diffuse GC that may evolve into PDC. This study aimed at identifying the molecular features of epigenetic methylation changes in histologic differentiation status of GC. Methods: Included in this study are 149 samples of paraffin-embedded tissues and 115 fresh endoscopically biopsied tissues. Multiple paraffin tissues involving normal (n=. 22), dysplasias (GDs, n=. 39), differentiated cancers (DCs, n=. 35), PDCs (n=. 33) and SRCCs (n=. 20) were included as an experimental group. For the ...
Twenty autopsy cases with 2009 pandemic influenza A (2009 H1N1) virus infection, performed between August 2009 and February 2010, were histopathologically analyzed. Hematoxylin-eosin staining, immunohistochemistry for type A influenza nucleoprotein antigen, and real-time reverse transcription-PCR assay for viral RNA were performed on formalin-fixed and paraffin-embedded specimens. In addition, the D222G amino acid substitution in influenza virus hemagglutinin, which binds to specific cell receptors, was analyzed in formalin-fixed and paraffin-embedded trachea and lung sections by direct sequencing of PCR-amplified products. There were several histopathological patterns in the lung according to the most remarkable findings in each case: acute diffuse alveolar damage (DAD) with a hyaline membrane (four cases), organized DAD (one case), acute massive intra-alveolar edema with variable degrees of hemorrhage (three cases), neutrophilic bronchopneumonia (five cases) and tracheobronchitis with limited ...
A microscopic appearance slide review showed a mixoid matrix surrounded by a small strand of meningotelial cells areas, resembling chordoma histology. This was diagnosed as a chordoid meningioma.. Histopathological findings - Multiple fragments of tumor were fixed for classical histological study in 10% formalin; the sections were included in paraffin block, and stained with hematoxylin-eosin (HE). Immunohistochemistry was performed on paraffin sections using monoclonal antibodies to epithelial membrane antigen (EMA) and vimentin. All antisera were used with the avidin biotin complex technique and were visualized using 3,3 diaminobenzidine tetrahydrochloride substrate. Appropriate positive and negative controls were also used. Light microscopy examination revealed tumor characterized by cohesive strands of epithelial cells in a myxoid Alcian-blue positive matrix and a chronic inflammatory response consisting of lymphocytes and plasma cells but without the formation of follicles or germinal ...
The invention provides a device, assembly, and method for transoral endoscopic restoration of a gastroesophageal flap valve. The invention also provides a self-steering and self-closing tissue fixation device for tissue fixation, and an invaginator device for gripping and maneuvering tissue. The restoration device includes a longitudinal member arranged for transoral placement into a stomach, a tissue shaper carried on the longitudinal member that causes stomach tissue to assume a shape related to a gastroesophageal flap, and a tissue fixation device that maintains the shaped stomach tissue in a shape approximating a gastroesophageal flap. The tissue shaper may include a mold. The device may include the invaginator device for gripping and maneuvering esophageal tissue to aid restoration of the gastroesophageal flap, and may include the tissue fixation device.
Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Biocartis has launched two new research-use-only products for its Idylla molecular diagnostics platform. The first product, the Idylla ctBRAF Mutation Assay, uses blood plasma as a sample, and according to the company is the first fully automated liquid biopsy assay that can potentially act as a substitute for tissue biopsy testing in melanoma, colorectal, and lung cancers, as well as conditions such as hairy cell leukemia and histiocytosis. The assay has a turnaround time of approximately 90 minutes with less than one minute of hands-on time.The second product, the Idylla NRAS-BRAF-EGFR S492R Mutation Assay complements the already CE-marked Idylla KRAS Mutation Test. Together, these provide complete metastatic colorectal cancer mutation analysis using two slices of formalin-fixed, paraffin-embedded tumor tissue.
The small, single-stranded positive-sense RNA astroviruses are mostly known to be enteric viruses. In recent years, though, different astroviruses were reported in association with neurological disease in various species. In cattle, two distinct neurotropic astrovirus genotype species were described in numerous cases of nonsuppurative encephalomyelitis, with one of these viruses also reported in similar circumstances in several sheep. Here, we retrieved archived formalin-fixed, paraffin-embedded brain tissues of a muskox diagnosed with a comparable disease pattern in 1982 and investigated them for the presence of neurotropic astroviruses with various techniques. Initially, tissue samples scored positive for both neurotropic astroviruses by immunohistochemistry; however, unexpected results with further immunohistochemical testing, in situ hybridization and qRT-PCR prompted us to submit an RNA extract from the animals brain material to next-generation sequencing. We were thus able to obtain the full
Introduction: Integration of genetics and epigenetics has emerged as a powerful approach to studying cellular differentiation (Mikkelsen et al, 2009) and tumorigenesis (Shen et al, 2007). The study of DNA methylation is of particular importance in cancer, as causal involvement has been demonstrated and it is the most stable of all epigenetic modifications, making it a desirable marker for both early detection and treatment of tumors. Hypermethylation of CpG sites in gene promoter regions leads to decreased gene expression; if such a gene is a tumor suppressor, this leads to carcinogenesis. To date, there have been no studies of genome-wide DNA methylation profiling of NETs. This study sets out to determine the DNA methylation profiles of low, intermediate and high grade pancreatic NET liver metastases with the intention of identifying dysregulated biological pathways in the development of these tumors. A protocol for the analysis formalin-fixed paraffin embedded tissue (FFPE) has also been ...
Introduction: Integration of genetics and epigenetics has emerged as a powerful approach to studying cellular differentiation (Mikkelsen et al, 2009) and tumorigenesis (Shen et al, 2007). The study of DNA methylation is of particular importance in cancer, as causal involvement has been demonstrated and it is the most stable of all epigenetic modifications, making it a desirable marker for both early detection and treatment of tumors. Hypermethylation of CpG sites in gene promoter regions leads to decreased gene expression; if such a gene is a tumor suppressor, this leads to carcinogenesis. To date, there have been no studies of genome-wide DNA methylation profiling of NETs. This study sets out to determine the DNA methylation profiles of low, intermediate and high grade pancreatic NET liver metastases with the intention of identifying dysregulated biological pathways in the development of these tumors. A protocol for the analysis formalin-fixed paraffin embedded tissue (FFPE) has also been ...
Purpose: The current study evaluated associative effects of breast cancer cells with the tumor microenvironment and its influence on tumor behavior. Experimental design: Formalin-fixed paraffin embedded tissue and matched protein lysates were evaluated from two independent breast cancer patient data sets (TCGA and MD Anderson). Reverse-phase protein arrays (RPPA) were utilized to create a proteomics signature to define breast tumor subtypes. Expression patterns of cell lines and normal breast tissues were utilized to determine markers that were differentially expressed in stroma and cancer cells. Protein localization and stromal contents were evaluated for matched cases by imaging. Results: A subtype of breast cancers designated "Reactive," previously identified by RPPA that was not predicted by mRNA profiling, was extensively characterized. These tumors were primarily estrogen receptor (ER)-positive/human epidermal growth factor receptor (HER)2-negative, low-risk cancers as determined by ...
TY - JOUR. T1 - High rate of neoplastic cells with genetic abnormalities in proliferation centers of chronic lymphocytic leukemia. AU - Balogh, Zsófia. AU - Reiniger, Lilla. AU - Rajnai, Hajnalka. AU - Csomor, Judit. AU - Szepesi, Ágota. AU - Balogh, Anikó. AU - Deák, Linda. AU - Gagyi, Éva. AU - Bödör, Csaba. AU - Matolcsy, A.. PY - 2011/6. Y1 - 2011/6. N2 - In lymph nodes, chronic lymphocytic leukemia (CLL) cells (prolymphocytes and paraimmunoblasts) form proliferation centers (PCs), which are also known as pseudofollicles. To reveal whether PCs play a role in the accumulation of genetic alterations in CLL, we compared deletion at 11q22.3, 13q14.3, and 17p13.1 loci and trisomy 12 by the fluorescence in situ hybridization (FISH) technique in PCs versus surrounding small lymphocytes (SLs) in 12 formalin-fixed paraffin-embedded (FFPE) lymph nodes. The FFPE sections were stained with methylene blue and PCs were marked by laser beam. Subsequent FISH analysis was performed, relocalizing the ...
Use this spray-on wax paraffin repellent on microtomes, countertops and laboratory equipment. Spray a small amount on a paper towel or gauze pad and apply a thin film to desired surfaces. It saves cleaning time, eliminates the need for harsh solvents such as xylene and keeps your equipment looking shiny new. Because PARA/GardTM repellent is formulated to dissolve paraffin, it is not recommended for use on microtome blades, blade holders or base molds ...
Inclusion Criteria: - Patients with a histologically confirmed diagnosis of high-grade nonmucinous epithelial ovarian (serous, endometrial, clear cell, carcinosarcoma, an mixed pathologies), fallopian tube, or primary peritoneal cancer that is Stage III or IV according to the International Federation of Gynecology and Obstetrics (FIGO) or tumor, node and metastasis staging criteria. - All patients with Stage IV disease are eligible. This includes those with inoperable disease, those who undergo primary debulking surgery (complete cytoreduction (CC0) or macroscopic disease), or those for whom neoadjuvant chemotherapy is planned. - Patients with Stage III are eligible if they meet one or more of the following criteria: 1. High risk Stage IIIC disease. 2. Planning to receive neoadjuvant chemotherapy. - Patients must provide a blood sample for research at Screening. - Patient must provide sufficient tumor tissue sample (a minimum of 2 formalin-fixed paraffin embedded blocks) at Screening for ...
Our reviewed data demonstrated that Streptococcus pneumoniae (S. pneumoniae) is an important pathogen and death of pyogenic meningitis, pneumonia, and other infectious diseases in children. The distribution of serotypes of S. pneumoniae showed great diversity in several studies. The penicillin nonsusceptibility rates demonstrated an increase over time in China. The prevalence of resistance to erythromycin was very high. A total of 202 paraffin-embedded lung autopsy tissues of children aged 1 month to 5 years old who died of CAP were selected at random from a hospital. Conventional PCR, southern blotting and ISPCR were used to detect S. pneumoniae in lung tissues for a mouse pneumonia model and in 202 autopsy samples from fatal childhood CAP cases, 1 month to 5 years old, between 1953-2002. Southern blotting and ISPCR detected S. pneumoniae in 107/202 (53.0%) and 106/202 (52.5%) human samples respectively. A combined total of 116/202 (57.4%) samples were found to be positive by both methods. ...
Tissue protein expression of IMP3 is emerging as a promising prognostic factor in renal cell carcinoma (RCC). The most commonly used immunohistochemical (IHC) antibody has been criticized for its low specificity. In addition, blood levels of IMP3 have not yet been analyzed in RCC. Therefore, we compared the prognostic performance of two different IMP3 IHC antibodies and assessed the prognostic relevance of IMP3 plasma levels in RCC. IMP3 levels were assessed in an overall number of 425 RCC (344× clear cell [ccRCC], 63× papillary [pRCC], 18× chromophobe [chRCC]) patients in three partly overlapping cohorts. Plasma IMP3 concentrations were determined by ELISA in 98 RCC (79× ccRCC, 15× pRCC, 4× chRCC) patients and 20 controls. IMP3 mRNA expression levels were analyzed in 73 frozen tissue samples (55× ccRCC, 12× pRCC, 6× chRCC), while protein expressions were assessed in 366 FFPE samples (294× ccRCC, 56× pRCC, 16× chRCC) using the M3626 and N-19 antibodies. IMP3 plasma and mRNA ...
For FFPE Specimens: Specimens subject to this FISH testing should be fixed in 10% neutral buffered formalin for at least 6 hours and no longer than 48 hours. The volume of formalin should be at least 10 times the volume of the specimen. Decalcification solutions with strong acids should not be used. Specimens fixed for less than 6 or longer than 48 hours may show false negative results ...
A single human tumor tissue with 5-10 m thickness is mounted on a positively charged glass slide. The slides are fixed and dehydrated with acetone for consistent results with in situ hybridization and immunohistochemistry. More tumors maybe available upon request ...

Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-MethylcytosineModified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-Methylcytosine

... * Home ... Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-Methylcytosine. Publikationstyp:. ... Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-Methylcytosine. ... Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-Methylcytosine. In: Angewandte Chemie ...
more infohttps://kops.uni-konstanz.de/handle/123456789/33590

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos | ScienceCytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos | Science

Cytosine, but not adenine, base editors induced numerous single-nucleotide variants in both mouse and rice. ... Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos ... Cytosine base editing in mouse embryos generates numerous off-target single-nucleotide variants. ... Cytosine base editing in mouse embryos generates numerous off-target single-nucleotide variants. ...
more infohttps://science.sciencemag.org/content/364/6437/289

Transfer RNA genes experience exceptionally elevated mutation rates | PNASTransfer RNA genes experience exceptionally elevated mutation rates | PNAS

AID accompanies RNA polymerase II and deaminates cytosine nucleotides. To resolve the resulting base-pair mismatch, the ... Among the histone protein-coding genes less than 1,000 nucleotides in length, the average PhyloP score per nucleotide across ... tRNA transcripts include leader and trailer sequences extending roughly two to five nucleotides upstream and 5-15 nucleotides ... 1). Furthermore, virtually all active tRNA loci differ at this nucleotide between human and M. mulatta, and 25% have a low- ...
more infohttp://www.pnas.org/content/115/36/8996

How Aging Is Recorded in Our Genes | WIREDHow Aging Is Recorded in Our Genes | WIRED

... which has no effect on cytosines with methyl groups bound to them but turns nonmethylated cytosines into another nucleotide ... DNA is made up of four basic building blocks - adenine, thymine, guanine, and cytosine - and the sequence of these nucleotides ... binding to a nucleotide, usually cytosine. In general, this binding, called methylation, turns off the gene in question. ... 80.5 percent of all cytosine nucleotides, compared with 73 percent. To look at an intermediate case, the team also performed ...
more infohttps://www.wired.com/2012/06/aging-dna-damage/

The CpG Dinucleotide and Human Genetic Disease - PubMedThe CpG Dinucleotide and Human Genetic Disease - PubMed

Cytosine Nucleotides / genetics *. Actions. * Search in PubMed * Search in MeSH * Add to Search ... From nucleotide sequences of more than 70 histones genes in 15 species of eucaryotes the probable frequency was determined for ... Cytosine methylation in vertebrate genomes occurs predominantly at the dinucleotide CpG. This dinucleotide is deficient in ... The frequency of neighboring base pairs in nucleotide sequences of over 80 genes and pseudogenes of low molecular weight RNAs ...
more infohttps://pubmed.ncbi.nlm.nih.gov/3338800/

Methyltransferase and DNA - Stock Image - C015/5703 - Science Photo LibraryMethyltransferase and DNA - Stock Image - C015/5703 - Science Photo Library

... to DNA nucleotides. HhaI methyltransferase catalyses the transfer to cytosine nucleotides. Methylation of the nucleotides ...
more infohttps://www.sciencephoto.com/media/507761/view/methyltransferase-and-dna

Could someone please help?
1.	Which of the fol... - OpenStudyCould someone please help? 1. Which of the fol... - OpenStudy

Could someone please help? 1. Which of the following best identifies base 1? purine pyrimidine cytosine nucleotide 2. Which of ... Could someone please help? 1. Which of the following best identifies base 1? purine pyrimidine cytosine nucleotide 2. Which of ... Could someone please help? 1. Which of the following best identifies base 1? purine pyrimidine cytosine nucleotide 2. Which of ... What does guanine pair with? Cytosine. And what is cytosine? Its a pyrimidine. So there, #2 would be a pyrimidine ...
more infohttp://openstudy.com/updates/503e5b58e4b0074824ff7c38

The Clinical Aspects of Inherited Defects in Pyrimidine Degradation | SpringerLinkThe Clinical Aspects of Inherited Defects in Pyrimidine Degradation | SpringerLink

1). Cytosine nucleotides undergo deamination to form uracil nucleotides before entering the pyrimidine degradation pathway. ...
more infohttps://link.springer.com/chapter/10.1007/978-3-642-84962-6_23

Environment-Sensitive Epigenetics and the Heritability of Complex Diseases | GeneticsEnvironment-Sensitive Epigenetics and the Heritability of Complex Diseases | Genetics

Such modifications include methylation of cytosine nucleotides at CpG sites and histone protein modification. Such epigenetic ... 2002 The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355-363. ... of a cytosine at a particular autosomal CpG site (Figure 1). Therefore, a disease whose risk depends solely on nonheritable ... Large-scale single-nucleotide polymorphism (SNP) genotyping was hoped to reveal DNA variants that would explain much of the ...
more infohttp://www.genetics.org/content/189/4/1377

INFLUENZA VACCINES INCLUDING COMBINATIONS OF PARTICULATE ADJUVANTS AND IMMUNOPOTENTIATORS - NOVARTIS VACCINES AND DIAGNOSTICS...INFLUENZA VACCINES INCLUDING COMBINATIONS OF PARTICULATE ADJUVANTS AND IMMUNOPOTENTIATORS - NOVARTIS VACCINES AND DIAGNOSTICS...

132), and/or it may have a nucleotide composition with ,25% cytosine (e.g.,35%, ,40%, ,50%, ,60%, ,80%, etc.). These ... it may comprise more than one consecutive cytosine nucleotide (e.g. CCCC, as disclosed in ref. ... 9. The composition of claim 5, wherein the composition contains less than 10 ng of DNA that is 100 nucleotides or longer. 10. ... For example, it may comprise more than one consecutive thymidine nucleotide (e.g. TTTT, as disclosed in ref. 132), and/or it ...
more infohttp://www.freepatentsonline.com/y2009/0304739.html

RCSB PDB - URF Ligand Summary PageRCSB PDB - URF Ligand Summary Page

Fluorouracil blocks an enzyme which converts the cytosine nucleotide into the deoxy derivative. In addition, DNA synthesis is ... further inhibited because Fluorouracil blocks the incorporation of the thymidine nucleotide into the DNA strand. ...
more infohttps://www.rcsb.org/ligand/URF

The nasal methylome as a biomarker of asthma and airway inflammation in children | Nature CommunicationsThe nasal methylome as a biomarker of asthma and airway inflammation in children | Nature Communications

DNA methylation (DNAm) of cytosine nucleotides (CpG sites) is one of the most widely studied epigenetic modifications3. DNAm ... The Infinium MethylationEPIC BeadChip quantifies DNAm in over 850,000 CpGs at a single-nucleotide resolution for each sample. ...
more infohttps://www.nature.com/articles/s41467-019-11058-3?error=cookies_not_supported&code=f91b97d0-1be4-4c1d-9794-78a0b5aa14c9

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution | ScienceQuantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution | Science

A sequencing method can discriminate epigenetically modified cytosine nucleotides within embryonic stem cell DNA. ... A sequencing method can discriminate epigenetically modified cytosine nucleotides within embryonic stem cell DNA. ... Methylation of the cytosine base in eukaryotic DNA (5mC) is an important epigenetic mark involved in gene silencing and genome ... Methylated cytosine can be enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), which may function as a distinct ...
more infohttps://science.sciencemag.org/content/336/6083/934.abstract

Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation | PNASRole of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation | PNAS

Local DNA repair then removes the abasic nucleotide and adds back an unmethylated cytosine nucleotide (11). Using chicken ... Methylated cytosine is underlined. (B) Methyl-DNA cleavage activity of ROS1 using the substrates shown in A. (C) Comparison of ... DNA cytosine methylation is important for many epigenetic processes including X chromosome inactivation, genomic imprinting, ... Overexpression of ROS1 in transgenic plants led to a reduced level of cytosine methylation and increased expression of a target ...
more infohttps://www.pnas.org/content/103/31/11796?ijkey=78cdf3f29e95eddd8f9241201f74c3daf718ce62&keytype2=tf_ipsecsha

Transcriptional and physiological analyses of short-term Iron deficiency response in apple seedlings provide insight into the...Transcriptional and physiological analyses of short-term Iron deficiency response in apple seedlings provide insight into the...

GC content is proportion of guanidine and cytosine nucleotides among the total nucleotides ... Q20% is the proportion of the nucleotide quality value larger than 20; ...
more infohttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4846-z

Cytidine-5-Triphosphate - DrugBankCytidine-5'-Triphosphate - DrugBank

A cytosine nucleotide containing three phosphate groups esterified to the sugar moiety. [PubChem] ... Cytidine 5-(tetrahydrogen triphosphate). A cytosine nucleotide containing three phosphate groups esterified to the sugar ... Adds these three nucleotides in the order of C, C, and A to the tRNA nucl.... Gene Name. cca. Uniprot ID. Q7SIB1. Uniprot Name ... Nucleotide binding. Specific Function. Involved in the biosynthesis of the tyvelose, a 3,6-dideoxyhexose found in the O-antigen ...
more infohttps://www.drugbank.ca/drugs/DB02431

nucleotide facts, information, pictures | Encyclopedia.com articles about nucleotidenucleotide facts, information, pictures | Encyclopedia.com articles about nucleotide

Make research projects and school reports about nucleotide easy with credible articles from our FREE, online encyclopedia and ... In the double helix of DNA, guanine nucleotides are base-paired opposite cytosine nucleotides. Adenine nucleotides are base- ... The most important nucleotides are those derived from the bases adenine, guanine, cytosine, thymine, and uracil. ... nucleotide (nōō´klēətīd´, nyōō´-), organic substance that serves as a monomer in forming nucleic acids. Nucleotides consist of ...
more infohttp://www.encyclopedia.com/science-and-technology/biochemistry/biochemistry/nucleotide

Frontiers | Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and...Frontiers | Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and...

... phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide ... phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide ... A, T, G, and C alleles represent adenine, thymine, guanine and cytosine nucleotide calls, respectively. S, R, and K alleles ... A, T, G, and C alleles represent adenine, thymine, guanine and cytosine nucleotide calls, respectively. Differences in leaf ...
more infohttps://www.frontiersin.org/articles/10.3389/fpls.2018.01487/full

IJMS  | Free Full-Text | A Specific Oligodeoxynucleotide Promotes the Differentiation of Osteoblasts via ERK and p38 MAPK...IJMS | Free Full-Text | A Specific Oligodeoxynucleotide Promotes the Differentiation of Osteoblasts via ERK and p38 MAPK...

... and contained successive thymidine-cytosine nucleotides. In our previous studies [13,14], we found that ODN FC003 is inactive ... MT01 is a cytosine-rich ODN and contains five successive cytosines in each of its 9-mer motifs (5′-ACCCCCTCT-3′) [19]. To ... Oligodeoxynucleotides (ODNs) containing unmethylated nucleotide motifs are immunostimulatory in vertebrates, and some ODNs ...
more infohttp://www.mdpi.com/1422-0067/13/7/7902/htm

JoVE | Peer Reviewed Scientific Video Journal - Methods and ProtocolsJoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA ... Methylated cytosines are protected from deamination and thus remain as cytosines, enabling identification of DNA methylation at ... The chemistry of cytosine deamination by sodium bisulphite involves three steps (Figure 2). (1) Sulphonation: The addition of ... Bisulphite preferentially deaminates cytosine to uracil in single stranded DNA, whereas 5-MeC, is refractory to bisulphite- ...
more infohttps://www.jove.com/visualize/abstract/22295098/microrna-152-mediates-dnmt1-regulated-dna-methylation-estrogen

JoVE | Peer Reviewed Scientific Video Journal - Methods and ProtocolsJoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA ... The chemistry of cytosine deamination by sodium bisulphite involves three steps (Figure 2). (1) Sulphonation: The addition of ... Bisulphite preferentially deaminates cytosine to uracil in single stranded DNA, whereas 5-MeC, is refractory to bisulphite- ... Upon PCR amplification, uracil is amplified as thymine while 5-MeC residues remain as cytosines, allowing methylated CpGs to be ...
more infohttps://www.jove.com/visualize/abstract/24039035/engineering-the-ph-responsive-catalytic-behavior-of-aunps-by-dna

Mitochondrial DNA Hypomethylation Is a Biomarker Associated with Induced Senescence in Human Fetal Heart Mesenchymal Stem CellsMitochondrial DNA Hypomethylation Is a Biomarker Associated with Induced Senescence in Human Fetal Heart Mesenchymal Stem Cells

Regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide separated by only one phosphate. ... After treatment with sodium bisulfate, unmethylated cytosines were converted to uracils, and the TTGA and ATGT sites are not ... After treatment with sodium bisulfate, unmethylated cytosines were converted to uracils [43, 44]. As a result, methylated mtDNA ... It predominantly catalyzes methylation at hemimethylated CpG di-nucleotides [66]. Homozygous deletion of DNMT1 is lethal for ...
more infohttps://www.hindawi.com/journals/sci/2017/1764549/

US20130337034A1 - Biofunctionalized magnetic nanowires 
        - Google PatentsUS20130337034A1 - Biofunctionalized magnetic nanowires - Google Patents

The T7 RNA polymerase used for this transcription incorporates cytosine nucleotides already conjugated with Cy5. After that the ...
more infohttps://patents.google.com/patent/US20130337034A1/en

Regulation of gene expression - WikipediaRegulation of gene expression - Wikipedia

DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called " ... Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences ...
more infohttps://en.wikipedia.org/wiki/Gene_regulation

Regulation of gene expression - WikipediaRegulation of gene expression - Wikipedia

DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called " ... Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences ...
more infohttps://en.wikipedia.org/wiki/Regulation_of_gene_expression
  • Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). (frontiersin.org)
  • Esteller and his colleagues then took a closer look at the differences between the DNA of the newborn and of the centenarian, but restricted the comparison to regions of the genome where the DNA nucleotide sequences were identical so that only the epigenetic differences would stand out. (wired.com)
  • One of the most common of these epigenetic changes involves a methyl group - one carbon atom and three hydrogen atoms - binding to a nucleotide, usually cytosine. (wired.com)
  • Methylated cytosine can be enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), which may function as a distinct epigenetic mark-possibly involved in pluripotency-and it may also be an intermediate in active DNA demethylation. (sciencemag.org)
  • In addition, the methyl CpG-binding protein MBD2 was reported to be a DNA demethylase that hydrolyzes 5-methylcytosine to cytosine and methanol ( 19 ). (pnas.org)
  • Earlier work has shown that 5-methylcytosine was replaced by labeled cytosine during the demethylation reaction in erythroleukemia cells, indicating a replacement of the entire nucleotide or base alone ( 9 ). (pnas.org)
  • While the base portion does have weakly basic properties, the nucleotide as a whole acts as an acid, due to the phosphate group. (encyclopedia.com)
  • Finally, single nucleotide change from cytosine to uridine at base 158 in this short fragment of 5′-UTR was proven to reduce viral translation and EV71 virulence in mice. (ncku.edu.tw)
  • Aptamers that are identified through the standard SELEX process usually comprise ~80 nucleotides (nt), since they are typically selected from nucleic acid libraries with ~40 nt long randomized regions plus fixed primer sites of ~20 nt on each side. (jove.com)
  • In addition, DNA synthesis is further inhibited because Fluorouracil blocks the incorporation of the thymidine nucleotide into the DNA strand. (rcsb.org)
  • Nucleotides are the building blocks of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). (encyclopedia.com)