Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.
Peptide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Learning to make a series of responses in exact order.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
Any method used for determining the location of and relative distances between genes on a chromosome.
The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."
Genetic loci associated with a QUANTITATIVE TRAIT.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
A subclass of DIABETES MELLITUS that is not INSULIN-responsive or dependent (NIDDM). It is characterized initially by INSULIN RESISTANCE and HYPERINSULINEMIA; and eventually by GLUCOSE INTOLERANCE; HYPERGLYCEMIA; and overt diabetes. Type II diabetes mellitus is no longer considered a disease exclusively found in adults. Patients seldom develop KETOSIS but often exhibit OBESITY.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
The capacity of a normal organism to remain unaffected by microorganisms and their toxins. It results from the presence of naturally occurring ANTI-INFECTIVE AGENTS, constitutional factors such as BODY TEMPERATURE and immediate acting immune cells such as NATURAL KILLER CELLS.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
Lipid-containing polysaccharides which are endotoxins and important group-specific antigens. They are often derived from the cell wall of gram-negative bacteria and induce immunoglobulin secretion. The lipopolysaccharide molecule consists of three parts: LIPID A, core polysaccharide, and O-specific chains (O ANTIGENS). When derived from Escherichia coli, lipopolysaccharides serve as polyclonal B-cell mitogens commonly used in laboratory immunology. (From Dorland, 28th ed)
Toxins closely associated with the living cytoplasm or cell wall of certain microorganisms, which do not readily diffuse into the culture medium, but are released upon lysis of the cells.
A pattern recognition receptor that interacts with LYMPHOCYTE ANTIGEN 96 and LIPOPOLYSACCHARIDES. It mediates cellular responses to GRAM-NEGATIVE BACTERIA.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
A form of CARDIAC MUSCLE disease, characterized by left and/or right ventricular hypertrophy (HYPERTROPHY, LEFT VENTRICULAR; HYPERTROPHY, RIGHT VENTRICULAR), frequent asymmetrical involvement of the HEART SEPTUM, and normal or reduced left ventricular volume. Risk factors include HYPERTENSION; AORTIC STENOSIS; and gene MUTATION; (FAMILIAL HYPERTROPHIC CARDIOMYOPATHY).
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
A form of CARDIAC MUSCLE disease that is characterized by ventricular dilation, VENTRICULAR DYSFUNCTION, and HEART FAILURE. Risk factors include SMOKING; ALCOHOL DRINKING; HYPERTENSION; INFECTION; PREGNANCY; and mutations in the LMNA gene encoding LAMIN TYPE A, a NUCLEAR LAMINA protein.
The abrupt cessation of all vital bodily functions, manifested by the permanent loss of total cerebral, respiratory, and cardiovascular functions.
An autosomal dominant inherited form of HYPERTROPHIC CARDIOMYOPATHY. It results from any of more than 50 mutations involving genes encoding contractile proteins such as VENTRICULAR MYOSINS; cardiac TROPONIN T; ALPHA-TROPOMYOSIN.
Molecules on the surface of some B-lymphocytes and macrophages, that recognize and combine with the C3b, C3d, C1q, and C4b components of complement.
Molecular sites on or in some B-lymphocytes and macrophages that recognize and combine with COMPLEMENT C3B. The primary structure of these receptors reveal that they contain transmembrane and cytoplasmic domains, with their extracellular portion composed entirely of thirty short consensus repeats each having 60 to 70 amino acids.
Molecular sites on or in B-lymphocytes, follicular dendritic cells, lymphoid cells, and epithelial cells that recognize and combine with COMPLEMENT C3D. Human complement receptor 2 (CR2) serves as a receptor for both C3dg and the gp350/220 glycoprotein of HERPESVIRUS 4, HUMAN, and binds the monoclonal antibody OKB7, which blocks binding of both ligands to the receptor.
A glycoprotein that is central in both the classical and the alternative pathway of COMPLEMENT ACTIVATION. C3 can be cleaved into COMPLEMENT C3A and COMPLEMENT C3B, spontaneously at low level or by C3 CONVERTASE at high level. The smaller fragment C3a is an ANAPHYLATOXIN and mediator of local inflammatory process. The larger fragment C3b binds with C3 convertase to form C5 convertase.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
An adhesion-promoting leukocyte surface membrane heterodimer. The alpha subunit consists of the CD11b ANTIGEN and the beta subunit the CD18 ANTIGEN. The antigen, which is an integrin, functions both as a receptor for complement 3 and in cell-cell and cell-substrate adhesive interactions.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Persistently high systemic arterial BLOOD PRESSURE. Based on multiple readings (BLOOD PRESSURE DETERMINATION), hypertension is currently defined as when SYSTOLIC PRESSURE is consistently greater than 140 mm Hg or when DIASTOLIC PRESSURE is consistently 90 mm Hg or more.
A highly specific (Leu-Leu) endopeptidase that generates ANGIOTENSIN I from its precursor ANGIOTENSINOGEN, leading to a cascade of reactions which elevate BLOOD PRESSURE and increase sodium retention by the kidney in the RENIN-ANGIOTENSIN SYSTEM. The enzyme was formerly listed as EC 3.4.99.19.
Sodium channels found on salt-reabsorbing EPITHELIAL CELLS that line the distal NEPHRON; the distal COLON; SALIVARY DUCTS; SWEAT GLANDS; and the LUNG. They are AMILORIDE-sensitive and play a critical role in the control of sodium balance, BLOOD VOLUME, and BLOOD PRESSURE.
PRESSURE of the BLOOD on the ARTERIES and other BLOOD VESSELS.
Drugs used in the treatment of acute or chronic vascular HYPERTENSION regardless of pharmacological mechanism. Among the antihypertensive agents are DIURETICS; (especially DIURETICS, THIAZIDE); ADRENERGIC BETA-ANTAGONISTS; ADRENERGIC ALPHA-ANTAGONISTS; ANGIOTENSIN-CONVERTING ENZYME INHIBITORS; CALCIUM CHANNEL BLOCKERS; GANGLIONIC BLOCKERS; and VASODILATOR AGENTS.
Increased VASCULAR RESISTANCE in the PULMONARY CIRCULATION, usually secondary to HEART DISEASES or LUNG DISEASES.
A hormone secreted by the ADRENAL CORTEX that regulates electrolyte and water balance by increasing the renal retention of sodium and the excretion of potassium.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Abnormal growths of tissue that follow a previous neoplasm but are not metastases of the latter. The second neoplasm may have the same or different histological type and can occur in the same or different organs as the previous neoplasm but in all cases arises from an independent oncogenic event. The development of the second neoplasm may or may not be related to the treatment for the previous neoplasm since genetic risk or predisposing factors may actually be the cause.
A carcinoma derived from stratified SQUAMOUS EPITHELIAL CELLS. It may also occur in sites where glandular or columnar epithelium is normally present. (From Stedman, 25th ed)
Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.

Expression of vascular endothelial growth factor in human oral squamous cell carcinoma: its association with tumour progression and p53 gene status. (1/2565)

AIMS: To correlate vascular endothelial growth factor (VEGF) expression in oral squamous cell carcinoma with the clinicopathological characteristics and prognosis; and to assess whether p53 gene status is associated with VEGF expression in human cancers. METHODS: Tumour specimens from 45 patients with oral squamous cell carcinomas were examined. Expression of VEGF was determined using an immunohistochemical method, and a tumour was considered positive when more than 5% of the neoplastic cells showed VEGF immunoreactivity. The p53 gene status was screened using a polymerase chain reaction--single strand conformation polymorphism analysis. RESULTS: VEGF positive staining was detected in 19 (42.2%) of the 45 cases. VEGF immunoreactivity did not correlate with the histological degree of tumour differentiation, clinical stages, or lymph node metastasis. The patients with VEGF positive tumours had a significantly worse prognosis than those with VEGF negative tumours. The five year overall survival rate of the VEGF negative patients was 76.5%, as compared with 48.8% for the VEGF positive patients. No significant association between VEGF expression and the p53 gene status of the tumours was found. CONCLUSIONS: VEGF is a good prognostic indicator of the survival of patients with oral squamous cell carcinoma. The p53 gene status does not seem to be associated with VEGF expression in these cancers.  (+info)

Inactivation of the glucose 6-phosphate transporter causes glycogen storage disease type 1b. (2/2565)

Glycogen storage disease type 1b (GSD-1b) is proposed to be caused by a deficiency in microsomal glucose 6-phosphate (G6P) transport, causing a loss of glucose-6-phosphatase activity and glucose homeostasis. However, for decades, this disorder has defied molecular characterization. In this study, we characterize the structural organization of the G6P transporter gene and identify mutations in the gene that segregate with the GSD-1b disorder. We report the functional characterization of the recombinant G6P transporter and demonstrate that mutations uncovered in GSD-1b patients disrupt G6P transport. Our results, for the first time, define a molecular basis for functional deficiency in GSD-1b and raise the possibility that the defective G6P transporter contributes to neutropenia and neutrophil/monocyte dysfunctions characteristic of GSD-1b patients.  (+info)

Mutations and allelic deletions of the MEN1 gene are associated with a subset of sporadic endocrine pancreatic and neuroendocrine tumors and not restricted to foregut neoplasms. (3/2565)

Endocrine pancreatic tumors (EPT) and neuroendocrine tumors (NET) occur sporadically and rarely in association with multiple endocrine neoplasia type 1 (MEN1). We analyzed the frequency of allelic deletions and mutations of the recently identified MEN1 gene in 53 sporadic tumors including 30 EPT and 23 NET (carcinoids) of different locations and types. Allelic deletion of the MEN1 locus was identified in 18/49 (36.7%) tumors (13/30, 43.3% in EPT and 5/19, 26.3% in NET) and mutations of the MEN1 gene were present in 8/52 (15.3%) tumors (4/30 (13.3%) EPT and 4/22 (18.1%) NET). The somatic mutations were clustered in the 5' region of the coding sequence and most frequently encompassed missense mutations. All tumors with mutations exhibited a loss of the other allele and a wild-type sequence of the MEN1 gene in nontumorous DNA. In one additional patient with a NET of the lung and no clinical signs or history of MEN1, a 5178-9G-->A splice donor site mutation in intron 4 was identified in both the tumor and blood DNA, indicating the presence of a thus far unknown MEN1 syndrome. In most tumor groups the frequency of allelic deletions at 11q13 was 2 to 3 times higher than the frequency of identified MEN1 gene mutations. Some tumor types, including rare forms of EPT and NET of the duodenum and small intestine, exhibited mutations more frequently than other types. Furthermore, somatic mutations were not restricted to foregut tumors but were also detectable in a midgut tumor (15.2% versus 16.6%). Our data indicate that somatic MEN1 gene mutations contribute to a subset of sporadic EPT and NET, including midgut tumors. Because the frequency of mutations varies significantly among the investigated tumor subgroups and allelic deletions are 2 to 3 times more frequently observed, factors other than MEN1 gene inactivation, including other tumor-suppressor genes on 11q13, may also be involved in the tumorigenesis of these neoplasms.  (+info)

Maroteaux-lamy syndrome: five novel mutations and their structural localization. (4/2565)

Maroteaux-Lamy syndrome (mucopolysaccharidosis type VI, MPS VI) is an autosomal recessive disorder due to the deficiency of the lysosomal enzyme N-acetylgalactosamine-4-sulfatase (arylsulfatase B, ASB). Mutation analysis in Maroteaux-Lamy syndrome resulted in the identification of approximately 40 molecular defects underlying a great genetic heterogeneity. Here we report five novel mutations in Italian subjects: S65F, P116H, R315Q, Q503X, P531R; each defect was confirmed by restriction enzyme or amplification refractory mutation system (ARMS) analysis. We also performed a three-dimensional (3-D) structure analysis of the alterations identified by us, and of an additional 22 point mutations reported by other groups, in an attempt to draw helpful information about their possible effects on protein conformation.  (+info)

Missense mutations in SGLT1 cause glucose-galactose malabsorption by trafficking defects. (5/2565)

Glucose-galactose malabsorption (GGM) is an autosomal recessive disorder caused by defects in the Na+/glucose cotransporter (SGLT1). Neonates present with severe diarrhea while on any diet containing glucose and/or galactose [1]. This study focuses on a patient of Swiss and Dominican descent. All 15 exons of SGLT1 were screened using single stranded conformational polymorphism analyses, and aberrant PCR products were sequenced. Two missense mutations, Gly318Arg and Ala468Val, were identified. SGLT1 mutants were expressed in Xenopus laevis oocytes for radiotracer uptake, electrophysiological experiments, and Western blotting. Uptakes of [14C]alpha-methyl-d-glucoside by the mutants were 5% or less than that of wild-type. Two-electrode voltage-clamp experiments confirmed the transport defects, as no noticeable sugar-induced current could be elicited from either mutant [2]. Western blots of cell protein showed levels of each SGLT1 mutant protein comparable to that of wild-type, and that both were core-glycosylated. Presteady-state current measurements indicated an absence of SGLT1 in the plasma membrane. We suggest that the compound heterozygote missense mutations G318R and A468V lead to GGM in this patient by defective trafficking of mutant proteins from the endoplasmic reticulum to the plasma membrane.  (+info)

The haplotype distribution of two genes of citrus tristeza virus is altered after host change or aphid transmission. (6/2565)

Genetic variability of citrus tristeza virus (CTV) was studied using the haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of genes p18 and p20 in six virus populations of two origins. The Spanish group included a CTV isolate and subisolates obtained by graft-transmission to different host species. The other included two subisolates aphid-transmitted from a single Japanese isolate. The homozygosity observed for gene p20 was always significantly higher than that expected under neutral evolution, whereas only three populations showed high homozygosity for p18, suggesting stronger host constraints for p20 than for p18. Sequential transmissions of a Spanish isolate to new host species increased the difference between its population and that of the successive subisolates for gene p18, as estimated by the F statistic. Analysis of molecular variance indicated that variation between both groups of populations was not statistically significant, whereas variations between populations of the same group or within populations were significant for both genes studied. Our data indicate that selection affects the haplotype distribution and that adaptation to a new host can be as important or more as the geographical origin. Variation of the CTV populations after host change or aphid transmission may explain in part the wide biological variability observed among CTV isolates.  (+info)

No association between the -308 polymorphism in the tumour necrosis factor alpha (TNFalpha) promoter region and polycystic ovaries. (7/2565)

The tumour necrosis factor (TNF)2 allele appears to be linked with increased insulin resistance and obesity, conditions often found in overweight patients with polycystic ovary syndrome (PCOS). The significance of TNFalpha polymorphism in relation to the clinical and biochemical parameters associated with PCOS was investigated in 122 well-characterized patients with polycystic ovaries (PCO). Of these, 84 had an abnormal menstrual cycle and were classified as having PCOS, while the remaining 38 had a normal menstrual cycle and were classified as having PCO. There were a further 28 individuals without PCO (non-PCO) and 108 individuals whose PCO status was undetermined (reference population). The promoter region of the TNFalpha gene was amplified by polymerase chain reaction (PCR), and the presence or absence of the polymorphism at -308 was determined by single-strand conformational polymorphism (SSCP) analysis. The less common TNF allele (TNF2) was found as TNF1/2 or TNF2/2 in 11/38 (29%) of PCO subjects, 25/84 (30%) of PCOS subjects, 7/28 (25%) of non-PCO subjects, and 45/108 (42%) of the reference population. There was no significant difference in the incidence of the TNF2 allele between the groups. The relationship of TNF genotype to clinical and biochemical parameters was examined. In both the PCO group and the PCOS group, the presence of the TNF2 allele was significantly associated with lower glucose values obtained from the glucose tolerance testing (P<0.05). The TNF genotype was not significantly associated with any clinical or biochemical parameter measured in the PCO, PCOS or non-PCOS groups. Thus, the TNFalpha -308 polymorphism does not appear to strongly influence genetic susceptibility to polycystic ovaries.  (+info)

A common MSH2 mutation in English and North American HNPCC families: origin, phenotypic expression, and sex specific differences in colorectal cancer. (8/2565)

The frequency, origin, and phenotypic expression of a germline MSH2 gene mutation previously identified in seven kindreds with hereditary non-polyposis cancer syndrome (HNPCC) was investigated. The mutation (A-->T at nt943+3) disrupts the 3' splice site of exon 5 leading to the deletion of this exon from MSH2 mRNA and represents the only frequent MSH2 mutation so far reported. Although this mutation was initially detected in four of 33 colorectal cancer families analysed from eastern England, more extensive analysis has reduced the frequency to four of 52 (8%) English HNPCC kindreds analysed. In contrast, the MSH2 mutation was identified in 10 of 20 (50%) separately identified colorectal families from Newfoundland. To investigate the origin of this mutation in colorectal cancer families from England (n=4), Newfoundland (n=10), and the United States (n=3), haplotype analysis using microsatellite markers linked to MSH2 was performed. Within the English and US families there was little evidence for a recent common origin of the MSH2 splice site mutation in most families. In contrast, a common haplotype was identified at the two flanking markers (CA5 and D2S288) in eight of the Newfoundland families. These findings suggested a founder effect within Newfoundland similar to that reported by others for two MLH1 mutations in Finnish HNPCC families. We calculated age related risks of all, colorectal, endometrial, and ovarian cancers in nt943+3 A-->T MSH2 mutation carriers (n=76) for all patients and for men and women separately. For both sexes combined, the penetrances at age 60 years for all cancers and for colorectal cancer were 0.86 and 0.57, respectively. The risk of colorectal cancer was significantly higher (p<0.01) in males than females (0.63 v 0.30 and 0.84 v 0.44 at ages 50 and 60 years, respectively). For females there was a high risk of endometrial cancer (0.5 at age 60 years) and premenopausal ovarian cancer (0.2 at 50 years). These intersex differences in colorectal cancer risks have implications for screening programmes and for attempts to identify colorectal cancer susceptibility modifiers.  (+info)

Detection of TP53 gene mutation in human meningiomas: A study using immunohistochemistry, polymerase chain reaction/single-strand conformation polymorphism and DNA sequencing techniques on paraffin-embedded samples ...
Minisatellite isoallelism, i.e. the occurrence of minisatellite alleles with different internal sequence composition but indistinguishable length, is a common limitation of minisatellite allele length analysis. Internal sequence variation can be used to distinguish such isoalleles, provided that detailed sequence knowledge of its basis is available. We now show that minisatellite isoalleles can also be simply resolved by single-stranded conformational polymorphisms (SSCP) arising during agarose gel electrophoresis. SSCP on agarose gels can be used to distinguish minisatellite isoalleles either after PCR amplification, or by standard Southern blot analysis of genomic DNA ...
OBJECTIVE: In this study, we examined the mutational spectrum of K-ras in cases of gallbladder and gallbladder carcinoma with an anomalous junction of the pancreaticobiliary duct (AJPBD). METHODS: We examined 35 gallbladders with AJPBD (20 with hyperplasia, 15 with carcinoma) and 38 gallbladders without AJPBD (lour normal gallbladders, four with hyperplasia, six with adenoma, 24 with carcinoma). Polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) and direct sequencing were performed to detect mutations in codon 12 or 13 of K-ras. RESULTS: In the eases with AJPBD, the prevalences of K-ras imitation were 15% (3/20) in hyperplasia, 60% (6/10) in stage I carcinoma, and 100% (5/5) in stage II-IV carcinoma. In the eases without AJPBD, the prevalences of K-ras mutation were 0% (0/4) in normal gallbladder, 0% (0/4) in hyperplasia, 17% (1/6) in adenoma, 7% (1/16) in stage I carcinoma, and 38% (3/8) in stage II-IV carcinoma. Prevalences of K-ras mutation in hyperplasia and ...
Longevity in livestock is a valuable trait. When productive animals live longer, fewer replacement animals need to be raised. However, selection for longevity is not commonly the focus of breeding programs as direct selection for long-lived breeding stock is virtually impossible until late in the reproductive life of the animal. Additionally the underlying genetic factors or genes associated with longevity are either not known, or not well understood. In humans, there is evidence that IGF 1 receptor (IGF1R) is involved in longevity. Polymorphism in the IGF1R gene has been associated with longevity in a number of species. Recently, 3 alleles of ovine IGF1R were identified, but no analysis of the effect of IGF1R variation on sheep longevity has been reported. In this study, associations between ovine IGF1R variation, longevity and fertility were investigated. Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) was used to type IGF1R variation in 1,716 New Zeal ...
Background: DNA polymerases (Pols) represent potential candidates for cancer genes because of their central functions in DNA metabolism. Defects of some DNA Pols have shown cancer associations, but data on DNA polymerase (Pol) ε is limited. Materials and Methods: Twenty-four human breast cancer DNA samples and four control DNA samples were examined for possible mutation in the entire coding region of the 55 kDa small subunit of the human DNA Pol ε gene using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis of the DNA and sequence analysis. In addition, 20 control DNAs were studied with PCR-SSCP for the end of intron 18 and exon 19 region. Results: An AATT deletion was found at one location in intron 18 in 2 out of the 24 breast cancer cases (8%), but in none of the control cases. In addition, a single base transition was found in the cancer DNAs in intron 14, but the same changes were also found in the control DNAs, suggesting polymorphism. Conclusion: ...
BACKGROUND Inactivation of the p53 tumor suppressor gene (also known as TP53) through a point mutation and/or loss of heterozygosity is one of the most common genetic changes found in various types of human tumors. PURPOSE Our purpose was to investigate the relationship between the presence of p53 gene mutations and survival of patients with non-small-cell lung cancer (NSCLC) of all stages who underwent surgery with preoperative curative intent as a routine therapeutic intervention. The prognostic significance of factors like sex, age, tumor histology, and the stage of the disease was also evaluated. METHODS We analyzed 120 tumor specimens from patients with histologically confirmed NSCLC for p53 mutations occurring in exons 5 through 8 by polymerase chain reaction-single-strand conformation polymorphism assay of genomic DNA. Univariate and multivariate analyses were performed to assess the association between p53 mutations and the survival of the NSCLC patients. RESULTS Fifty-one (43%) of 120
TY - JOUR. T1 - Cell cycle regulators in multiple myeloma. T2 - Prognostic implications of p53 nuclear accumulation. AU - Pruneri, Giancarlo. AU - Carboni, Nadia. AU - Baldini, Luca. AU - Intini, Daniela. AU - Colombi, Mariangela. AU - Bertolini, Francesco. AU - Valentini, Stefano. AU - Maisonneuve, Patrick. AU - Viale, Giuseppe. AU - Neri, Antonino. PY - 2003/1/1. Y1 - 2003/1/1. N2 - Multiple myeloma (MM) is characterized by a multistep process of tumorigenesis involving genes that control cell cycle progression. The prevalence and clinical implications of p53, p21, HDM-2, p27, and cyclin E immunoreactivity in MM patients, however, have not been fully elucidated. We evaluated the immunoreactivity (IR) for p53, p21, HDM-2, p27, cyclin E, and Ki-67 in bone marrow biopsies from 48 patients. In 34 (70.8%) cases, TP53 gene mutations and HDM-2 gene amplification were analyzed by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and Southern blot densitometric analyses in ...
Alterations in the FHIT gene region have been previously associated with smoking status and the occurrence of lung tumors. In the current study, we examined the nature of the mutations that occur at FHIT and the types of carcinogen exposures that are associated with FHIT alterations. We screened 40 primary lung tumors for the presence of point mutations within the coding exons of FHIT using PCr-single-strand conformational polymorphism. Tumors were also analyzed for allelic loss using microsatellite markers located in or near FHIT. No tumors contained point mutations within the coding region of the FHIT gene. However, several samples failed to generate a PCR product, suggesting that regions of the gene are homozygously deleted. Samples were reanalyzed for exon loss using PCR; 13 of 30 tumors failed to generate a PCR product, and 20 of 30 tumors were missing at least one FHIT exon or had loss (loss of heterozygosity or deletion) of one microsatellite marker, suggesting that regions of the gene ...
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TY - JOUR. T1 - Endoglin gene polymorphism as a risk factor for sporadic intracerebral hemorrhage. AU - Alberts, M. J.. AU - Davis, J. P.. AU - Graffagnino, C.. AU - McClenny, C.. AU - Delong, D.. AU - Granger, C.. AU - Herbstreith, M. H.. AU - Boteva, K.. AU - Marchuk, D. A.. AU - Roses, A. D.. PY - 1997/5. Y1 - 1997/5. N2 - Intracerebral hemorrhage (ICH) is a common and serious type of stroke. Recent studies have shown that inherited factors that affect the development of the vessel wall can increase the risk of ICH. We studied endoglin as a candidate gene in patients with sporadic ICH, since mutations in this gene can cause telangiectasia formation. One hundred three patients with sporadic ICH and 202 controls were studied. The polymerase chain reaction and single- strand conformational polymorphism analysis were used to screen for mutations in exon 7 of the endoglin gene. No coding mutations in exon 7 were identified in the ICH patients or controls. A 6-base intronic insertion was found 26 ...
Alterations of the p53 gene and the p53 protein are common in a wide spectrum of human malignancies. In several tumor types, p53 gene mutation and/or p53 protein overexpression correlate with a more clinically aggressive phenotype as judged by worse patient survival. This has not been clearly demonstrated to be the case in colorectal cancer. Herein, we report results of the prognostic significance of p53 protein accumulation and gene mutation in a large series of colorectal cancers (n = 541) with long patient follow-up (mean, 87 months). The large majority of patients (95%) received no postoperative systemic adjuvant therapy. The incidence of p53 accumulation detected by immunohistochemistry with the monoclonal antibody DO-7 was 30%, whereas the incidence of p53 gene mutation in exons 5-8 detected using PCR-single strand conformation polymorphism was 36%. Accumulation of p53 protein was associated with improved patient survival independent of tumor stage or grade (hazard ratio, 0.66; 95% ...
The aetiology and detection of human herpes virus type 8 (HHV-8) DNA sequences in Kaposis sarcoma (KS) is a matter of intense investigation. We report on the detection of HHV-8 DNA and sequence polymorphism in different clinicopathological subtypes of cutaneous KS samples from South Africa. The diagnosis was confirmed by histological examination in all cases. Six patients had classic KS (CKS), 3 epidemic KS (EKS), and 3 iatrogenic KS (IKS). A nested polymerase chain reaction (PCR) assay was used to detect HHV-8 DNA in cell lysates, prepared from formalin fixed, paraffin embedded sections. We investigated polymorphism in the HHV-8 DNA using single-stranded conformational polymorphism (SSCP) analysis on the PCR products, followed by direct sequencing. HHV-8 DNA was detected in all the patients with KS, irrespective of the clinicopathological subtype. Direct sequencing was performed on 5 selected cases and showed single base pair substitutions in all. The spectrum of mutations was similar to those ...
The Mycobacterium tuberculosis H37Rv efpA gene encodes a putative efflux protein, EfpA, of 55,670 Da. The deduced EfpA protein was similar in secondary structure to Pur8, MmrA, TcmA, LfrA, EmrB, and other members of the QacA transporter family (QacA TF) which mediate antibiotic and chemical resistance in bacteria and yeast. The predicted EfpA sequence possessed all transporter motifs characteristic of the QacA TF, including those associated with proton-antiport function and the motif considered to be specific to exporters. The 1,590-bp efpA open reading frame was G+C rich (65%), whereas the 40-bp region immediately upstream had an A+T bias (35% G+C). Reverse transcriptase-PCR assays indicated that efpA was expressed in vitro and in situ. Putative promoter sequences were partially overlapped by the A+T-rich region and by a region capable of forming alternative secondary structures indicative of transcriptional regulation in analogous systems. PCR single-stranded conformational polymorphism ...
Hybridization analysis showed a p27 gene region, which exhibits different patterns with two probes derived from two biological distinct CTV isolates. In an attempt to screen whether that gene region differs in mild and severe strains, six CTV isolates belonging to different biogroups were compared for variations in their p27 gene by analysis of single-strand conformation polymorphism (SSCP). The p27 gene was reverse transcribed and amplified by PCR and thirty clones of each isolate were obtained. From each clone, two fragments of the gene were amplified by PCR: fragment (a), 459 bp long, and fragment (b), 281 bp long. Sequence variations in both gene fragments were studied by SSCP analysis. A variety of SSCP patterns was obtained from each isolate, being isolates belonging to the groups II-IV and III those with the higher and lower number of them. Moreover, SSCP analysis provided a rapid procedure to screen the genetic heterogeneity of the viral isolate reducing considerably the amount of ...
Aim: To determine the frequency and nature of mutations in the gene ABCA4 in a cohort of patients with bulls-eye maculopathy (BEM).. Methods: A panel of 49 subjects (comprising 40 probands/families, 7 sibling pairs and a set of three sibs) with BEM, not attributable to toxic causes, was ascertained. Blood samples from each patient were used to extract genomic DNA, with subsequent mutation screening of the entire coding sequence of ABCA4, using single-strand conformational polymorphism (SSCP) analysis and direct sequencing.. Results: Fourteen probands (35%) were found to have a potentially disease-causing ABCA4 sequence variant on at least one allele. Three patients had a Gly1961Glu missense mutation, the most common variant in Stargardt disease (STGD), with 2 of these subjects having a macular dystrophy (MD) phenotype and a second ABCA4 variant previously associated with STGD. The second most common STGD mutation, Ala1038Val, was seen in one patient with cone-rod dystrophy (CORD). Five novel ...
TY - JOUR. T1 - The dithiacyclooctane cation (DTCO+). T2 - Conformational analysis, interconversion barriers and bonding. AU - Stowasser, Ralf. AU - Glass, Richard S. AU - Hoffmann, Roald. PY - 1999/7. Y1 - 1999/7. N2 - A theoretical conformation analysis of the dithiacyclooctane radical cation (DTCO+) suggests that the lowest energy conformer is a chair-boat, with a partial but significant S-S σ bond. For the ring flip process of this molecule we calculate a barrier of 40 kJ mol-1 and two possible pathways: one involves a boat-boat conformer and an untwisted transition structure, the other a chair-chair conformer and a twisted transition structure.. AB - A theoretical conformation analysis of the dithiacyclooctane radical cation (DTCO+) suggests that the lowest energy conformer is a chair-boat, with a partial but significant S-S σ bond. For the ring flip process of this molecule we calculate a barrier of 40 kJ mol-1 and two possible pathways: one involves a boat-boat conformer and an ...
The present study was aimed at evaluating random bred broiler and layer lines maintained at Directorate of Poultry Research, Rajendranagar, Hyderabad with respect to expression profiling, epigenetic and functionality of promoter of BMP3 and BMP4 genes. BMP3 acts as a negative regulator for osteogenesis and as a modulator of osteogenic activity of other BMPs in vivo while BMP4 shows osteogenetic activity in vivo and in vitro. The functionality of promoters was elucidated by means of reporter GFP marker in vivo. BMP3 gene promoter was divided into two fragments of 501 and 786 bp while that of BMP4 was divided into fragments of 541 bp and 1.1 kb size. Larger fragments were better promoters. Both the promoters displayed polymorphism by means of single strand conformation polymorphism study using blood samples of broiler (286) and layer (270) birds. For BMP3 gene promoter, haplotype, h1 was predominant (0.735 and 0.62) and h3 was the least frequent (0.046 and 0.04) in broiler and layer lines, ...
We have previously found an inverse association of childhood asthma and fungal diversity by classical culturing (Ege et al. NEJM 2011;364:701-9), which covers only a small minority of taxa.. The aim of the present analysis was to include also non-cultivable fungi by a molecular technique. For this purpose we applied single strand conformation polymorphism polymerase chain reaction (SSCP-PCR) targeting the internal transcribed spacer region (ITS) of fungi (Janke et al. Curr Microbiol 2013;67:156-69).. We used data from the GABRIELA study and analysed mattress dust samples from 844 Bavarian children age 6-10 years. DNA was extracted from dust samples, and the fungus-specific ITS region was amplified by PCR. The amplicons were subjected to non-denaturing gel-electrophoresis, and the resulting band patterns were digitized and normalized. We applied a factor analysis for the identification of the relevant gel positions and explored associations with a lifetime physicians diagnosis of asthma by ...
We reported an association of smoking-induced lung cancer susceptibility with the human cytochrome P450 1A1 (CYP1A1) polymorphisms in our previous studies. To investigate a relationship between genetically determined individual predispositions and mutations of target genes in the early stage of lung carcinogenesis, we examined p53 mutations in relation to germ line polymorphisms of the CYP1A1 and GSTM1 genes, using surgical specimens of 148 non-small cell lung cancer patients who were smokers. The frequency of p53 mutations among heavy smokers was higher than in patients who had never smoked [P , 0.01; odds ratio (OR), 3.74; 95% confidence interval (CI), 1.46-9.56]. By single-strand conformational polymorphism, aberrant migration bands of p53 gene fragments were detected in 56 cases (38%). Smokers with susceptible rare homozygous alleles of either the MspI or Ile-Val polymorphism of the CYP1A1 gene have a 4.5-fold (P , 0.005; OR, 4.48; 95% CI, 1.64-12.26) or 5.5-fold (P , 0.01; OR, 5.52; 95% CI, ...
Features of our method make it inherently robust. First, double-end labeling allows for independent detection of the two cleavage products in different fluorescence channels, which guards against false positives. Second, we reamplify and retest each individual from a pool in the same way, which further eliminates false positives. Third, from fragment mobilities we estimate the position of the mutation within the fragment; we find that this estimation is accurate to ±10 bp (data not shown). We use both the near certainty of a mutation being in the fragment and the mobility information to help in identifying the heterozygous changes. Other technologies have been applied to single test samples and have demonstrated high accuracy in detection of heterozygotes (Spiegelmanet al. 2000; Kwok 2001; Liet al. 2002). However, methods that simply report the presence of a migration or retention anomaly, such as single-strand conformational polymorphism, temperature-gradient capillary electrophoresis, and ...
The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial ...
Highlights Helical Molecules and Aggregates Molecules with Helical Structure: How To Build a Molecular Spiral Staircase Carsten Schmuck* Keywords: arenes · conformation analysis · foldamers · helical structures Helical Compounds Molecules with helical structure have fascinated chemists for may years now. Due to their nonplanar structure, such molecules are inherently chiral and exhibit interesting optical and electronic properties. In principle, molecules with such unusual topologies[1] can be synthesized through three different approaches: First, in rigid molecules steric effects can be used to enforce a helical structure. This is the case, for example, in the long-known and well-studied helicenes and their derivatives.[2] An increasing ortho annulation of aromatic ring systems first causes an increasing steric interaction between the H atoms on the terminal rings, leading to a nonplanar conformation. When the number of annulated arenes further increases, the terminal rings will overlap, ...
زمینه مطالعاتی: انتخاب به وسیله ژنتیک مولکولی روی ژن-های منحصر بفرد یک روش مطمئن برای بهبود ژنتیکی صفات مهم اقتصادی در حیوانات اهلی می-باشد. صفت چندقلوزایی یکی از صفات مهم اقتصادی در صنعت گوسفندداری می-باشد که در سال-های اخیر توجه متخصصین اصلاح نژاد را به خود جلب کرده است. ژن فاکتور رشد و تمایز شماره 9 (GDF9) از مهم-ترین ژن-های کاندیدای موثر بر صفت چندقلوزایی در گوسفند می-باشد. هدف: این آزمایش جهت بررسی وجود چند شکلی در جایگاه نیمه دوم (منتهی به3) اگزون 2 ژن GDF9 گوسفند نژاد کرمانی انجام شد. روش کار: در این مطالعه، از 102 رأس گوسفند خونگیری شد. پس از استخراج DNA، تعیین
Pyrazinamide is a first-line drug for treating tuberculosis, but pyrazinamide resistance testing is usually too slow to guide initial therapy, so some patients receive inappropriate therapy. We therefore aimed to optimize and evaluate a rapid molecular test for tuberculosis drug resistance to pyrazinamide. Tuberculosis polymerase chain reaction single strand conformational polymorphism (PCR-SSCP) was optimized to test for mutations causing pyrazinamide resistance directly from sputum samples and Mycobacterium tuberculosis isolates. The reliability of PCR-SSCP for sputum (n=65) and Mycobacterium tuberculosis isolates (n=185) from 147 patients was compared with four tests for pyrazinamide resistance: Bactec-460 automated-culture; the Wayne biochemical test; DNA sequencing for pncA mutations; and traditional microbiological broth culture. PCR-SSCP provided interpretable results for 96% (46/48) of microscopy-positive sputum samples, 76% (13/17) of microscopy-negative sputa and 100% of Mycobacterium ...
Acetyl-coenzyme A carboxylase α (ACC-alpha) is considered as the key regulatory enzyme in fatty acid biosynthesis. ACC-alpha gene is located on Caprine chromosome 11 and is polymorphic in many goat breeds. In the current study, we aimed to find possible single nucleotide polymorphisms (SNPs) in the exon 1 region of the ACC-alpha gene in Iranian Mahabadi goat breed. Genomic DNA was extracted from blood samples of 150 Mahabadi does. The exon 1 region of the ACC-alpha gene was amplified to produce a 390 bp fragment. The PCR products were analyzed by both polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques. RFLP was performed utilizing HinfI endonuclease enzyme. No polymorphism was observed after digestion of the PCR products using HinfI. However, SSCP of the PCR products revealed two conformation patterns at the exon 1 region of goat ACC-alpha gene with frequencies of 86% and 14%,
Marfan syndrome is a dominantly inherited connective tissue disorder with a wide range of phenotypic severity. The condition is the result of mutations in FBN1, a large gene composed of 65 exons encoding the fibrillin-1 protein. While mutations causing classic manifestations of Marfan syndrome have been identified throughout the FBN1 gene, the six previously characterized mutations resulting in the severe, perinatal lethal form of Marfan syndrome have clustered in exons 24-32 of the gene. We screened 8 patients with either neonatal Marfan syndrome or severe cardiovascular complications of Marfan syndrome for mutations in this region of the gene. Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. This analysis documented mutations in exons 25-27 of the FBN1 mutations in 6 of these patients. These results, taken together with previously published FBN1 ...
TY - JOUR. T1 - Mutation analysis of neurofilament-light gene in Chinese Charcot-Marie-Tooth disease. AU - Luo, Wei. AU - Tang, Bei Sha. AU - Zhao, Guo Hua. AU - Li, Qi. AU - Xiao, Jianfeng. AU - Yang, Qi Dong. AU - Xia, Jia Hui. PY - 2003/4/1. Y1 - 2003/4/1. N2 - Objective: To study the characteristic of the mutation of neurofilament-light (NF-L) gene in Chinese Charcot-Marie-Tooth disease (CMT) patients. Methods: Mutation analysis of NF-L gene was made by use of polymerase chain reaction-single strand conformation polymorphsim combined with DNA direct sequencing in 32 CMT probands from the Hans of five provinces in China who had been diagnosed by clinical feature and electromyography and/or biopsy of sural nerve. Results: In 32 CMT probands, only one sporadic case was found to display variant banding pattern, and this case was confirmed as 1329C to T (Tyr443Tyr) single nucleotide polymorphism by sequencing. Conclusion: Mutation of NF-L gene may be rare in Chinese CMT patients.. AB - Objective: ...
TY - JOUR. T1 - Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots. AU - Simon, Holly M.. AU - Jahn, Courtney E.. AU - Bergerud, Luke T.. AU - Sliwinski, Marek K.. AU - Weimer, Paul J.. AU - Willis, David K.. AU - Goodman, Robert M.. PY - 2005/8. Y1 - 2005/8. N2 - Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two ...
The Ataxia-telangiectasia mutated (ATM) gene encodes a multifunctional kinase, which is linked to important cellular functions. Women heterozygous for ATM mutations have an estimated relative risk of developing breast cancer of 3.8. However, the pattern of ATM mutations and their role in breast cancer etiology has been controversial and remains unclear. In the present study, we investigated the frequency and spectrum of ATM mutations in a series of sporadic breast cancers and controls from the Brazilian population. Using PCR-Single Strand Conformation Polymorphism (SSCP) analysis and direct DNA sequencing, we screened a panel of 100 consecutive, unselected sporadic breast tumors and 100 matched controls for all 62 coding exons and flanking introns of the ATM gene. Several polymorphisms were detected in 12 of the 62 coding exons of the ATM gene. These polymorphisms were observed in both breast cancer patients and the control population. In addition, evidence of potential ATM mutations was observed in 7
BACKGROUND. Microsatellite instability (MI) is a frequent occurrence in endometrioid carcinoma of the endometrium (EC). Several genes known to contain mononucleotide short tracts in their coding sequences (TGF-β RII, IGFIIR, BAX, hMSH6, and hMSH3) are likely targets for mutations in these tumors. METHODS. DNA from 24 patients with EC and MI was extracted from blood and from fresh-frozen and paraffin embedded tumor tissue. Seven of these patients were found to have metastatic spread to paraaortic lymph nodes. DNA also was studied from 10 patients with EC without MI. RESULTS. Frameshift mutations at coding mononucleotide repeats were detected by single strand conformation polymorphism analysis and DNA sequencing. Frameshift mutations were detected more frequently in BAX (11 of 24 MI positive (+) tumors; 45.8%) than in TGF-β RII (0 of 24 tumors; 0%), IGFIIR (3 of 24 tumors; 12.5%), hMSH3 (6 of 24 tumors; 25%), or hMSH6 (0 of 24 tumors; 0%). The mutations frequently were distributed ...
Background: Folylpolyglutamate synthetase (FPGS), an important enzyme in the folate metabolic pathway,plays a central role in intracellular accumulation of folate and antifolate in several mammalian cell types. Loss ofFPGS activity results in decreased cellular levels of antifolates and consequently to polyglutamatable antifolatesin acute lymphoblastic leukemia (ALL). Materials and Methods: During May 1997 and December 2003, 134children diagnosed with ALL were recruited from one hospital in Thailand. We performed a mutation analysis inthe coding regions of the FPGS gene and the association between single nucleotide polymorphisms (SNPs) withinFPGS in a case-control sample of childhood ALL patients. Mutation screening was conducted by polymerasechain reaction-single strand conformation polymorphism (PCR-SSCP) and subsequently with direct sequencing(n=72). Association analysis between common FPGS variants and ALL risk was done in 98 childhood ALL casesand 95 healthy volunteers recruited as controls.
We have recently isolated a human gene, ROX, encoding a new member of the basic helix-loop-helix leucine zipper protein family. ROX is capable of heterodimerizing with Max and acts as a transcriptional repressor in an E-box-driven reporter gene system, while it was found to activate transcription in HeLa cells. ROX expression levels vary during the cell cycle, being down-regulated in proliferating cells. These biological properties of ROX suggest a possible involvement of this gene in cell proliferation and differentiation. The ROX gene maps to chromosome 17p13.3, a region frequently deleted in human malignancies. Here we report the genomic structure of the human ROX gene, which is composed of six exons and spans a genomic region of less than 40 kb. In an attempt to identify possible inactivating mutations in the ROX gene in human breast cancer, we performed a single-strand conformation polymorphism analysis of its coding region in 16 sporadic breast carcinomas showing loss of heterozygosity in ...
Background. Human and animal studies support the role of MC4R and MC3R in human obesity, but limited data are available on the genetic contribution to obesity in South African populations. Objective. To screen obese-overweight South African pupils for MC3R and MC4R polymorphisms that may play a role in the development of obesity. Design. A cross-sectional study screened 227 obese-overweight (115 black and 112 coloured) and 204 normal weight (94 black, 110 coloured) school pupils for the presence of MC4R and MC3R polymorphisms using a single strand conformation polymorphism, subsequent sequencing, and allele specific restriction enzyme analysis. Results. Two polymorphisms were detected in the MC3R (T6K and V81I) but none in MC4R. After adjusting for age, gender and case-control status, the frequency distributions of T6K and V81I genotype and allele varied significantly between the ethnic groups. The frequency of the V81I A allele was significantly lower in coloured overweight-obesity than normal pupils
Conclusions Imagine • Innovate • Integrate The NSET procedure is effective for uterine transfer of blastocyst stage embryos. Surgery causes a significant.Neutering companion exotic mammals (Proceedings). Once the uterine horn has been. A single interrupted suture.Alpaca Article. An Introduction to. The uterus has a short body with two horns,. Administered as a single 1ml IM injection it will allow return to normal.uterine body and uterine horn) were taken at slaughter for the analysis of gene ex-. (Single Strand Conformation Polymorphism), HRM (High Resolution Melting), se-.. ovarian duct definition, meaning, English dictionary, synonym, see also Ontarian,ovary,ovaritis,ova, Reverso dictionary, English definition, English vocabulary.Open pulled straw vitrification of murine and caprine embryos and timed deep uterine insemination of goats Dissertation to obtain the Ph. D. degree.proliferate rapidly and, as a result, large numbers of cells can be produced from a single embryo within. ...
Principal Investigator:MORISHITA Fujio,一瀬 光之尉, Project Period (FY):1993 - 1994, Research Category:Grant-in-Aid for General Scientific Research (B), Research Field:工業分析化学
Epithelial (E)-cadherin and its associated cytoplasmic proteins (alpha-, beta-, and gamma-catenins) are important mediators of epithelial cell-cell adhesion and intracellular signaling. Much evidence exists suggesting a tumor/invasion suppressor role for E-cadherin, and loss of expression, as well as mutations, has been described in a number of epithelial cancers. To investigate whether E-cadherin gene (CDH1) mutations occur in colorectal cancer, we screened 49 human colon carcinoma cell lines from 43 patients by single-strand conformation polymorphism (SSCP) analysis and direct sequencing. In addition to silent changes, polymorphisms, and intronic variants in a number of the cell lines, we detected frameshift single-base deletions in repeat regions of exon 3 (codons 120 and 126) causing premature truncations at codon 216 in four replication-error-positive (RER+) cell lines (LS174T, HCT116, GP2d, and GP5d) derived from 3 patients. In LS174T such a mutation inevitably contributes to its lack of E
Although postoperative chemotherapy is widely accepted as the standard modality for Dukes stage C or earlier stage colorectal cancer (CRC) patients, biomarkers to predict those who may benefit from the therapy have not been identified. Previous in vitro and clinical investigations reported that CRC patients with wild-type p53 gene (TP53)-tumors benefit from 5-fluorouracil (5-FU) based chemotherapy, while those with mutated TP53-tumors do not. However, these studies evaluated the mutation-status of TP53 by immunohistochemistry with or without single-strand conformation polymorphism, and the mutation frequency was different from study to study. In addition, the polymorphic status at p53 codon 72, which results in arginine or proline residues (R72P) and is thought to influence the function of the protein significantly, was not examined. To evaluate the significance of the TP53 mutation as a molecular marker to predict the prognosis of CRC patients, especially those who received postoperative chemotherapy,
The growth hormone gene could be an attractive candidate gene for milk production in goats. Single-strand conformation polymorphism was used to identify polymorphism at the goat growth hormone (gGH) gene. For this purpose, genotyping of 90 Talli goat breeds was performed. Nine conformational patterns were observed in exon 4 of the gGH gene, with frequencies of 27.7% for the homozygous pattern (AA) and 72.2% for all of other heterozygous patterns (A\B, A\C, A\B\C, A\B\D\E, A\B\C\F, A\C\F, A\B\E, A\B\F). The results showed that exon 4 of the GH gene in Talli goats is highly polymorphic ...
What you need to do is cut out the individual SSCP bands out of hte acrylamide gel and rePCR them and then sequence those PCR products. Mark the original gel with some radioactive ink and reexpose it on film. Using the marks, align the film and the gel to precisely cut out the gel bands. Soak the cut out bands in 50 ul 10 mM Tris and use 5 ul in a new PCR reaction. When you sequence these reactions, you will only be seeing one allele instead of two, so heterozygosity wont hide the mutation. Also, you should try MDE gel solution + 5% glycerol for SSCP gels instead of acrylamide - your mutations will show up a lot easier. beth : , I am new to this newsgroup, please forgive me if my behavir is wrong : , or : , rude. : , I am looking for a mutation site of BRCA1 and BRCA2 gene, the : , material : , of DNA is mostly coming from paraffin. : , I have done SSCP for hundreds of times ,some of them indicate the : , mutation definitaly. However, the results of DNA sequence always beat : , me:there is no ...
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COL4A3/COL4A4 mutations: From familial hematuria to autosomal-dominant or recessive Alport syndrome. BACKGROUND: Mutations of the type IV collagen COL4A5 gene cause X-linked Alport syndrome (ATS). Mutations of COL4A3 and COL4A4 have been reported both in autosomal-recessive and autosomal-dominant ATS, as well as in benign familial hematuria (BFH). In the latter conditions, however, clinical features are less defined, few mutations have been reported, and other genes and non-genetic factors may be involved. METHODS: We analyzed 36 ATS patients for COL4A3 and COL4A4 mutations by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) and direct sequencing. Sporadic patients who had tested negative for COL4A5 mutations were included with typical cases of autosomal recessive ATS to secure a better definition of the phenotype spectrum. RESULTS: We identified seven previously undescribed COL4A3 mutations: in two genetic compounds and three heterozygotes, and one in COL4A4. In ...
BACKGROUND AND PURPOSE: Plasma glutathione peroxidase (GPx-3)-deficiency increases extracellular oxidant stress, decreases bioavailable nitric oxide, and promotes platelet activation. The aim of this study is to identify polymorphisms in the GPx-3 gene, examine their relationship to arterial ischemic stroke (AIS) in a large series of children and young adults, and determine their functional molecular consequences. METHODS: We studied the GPx-3 gene promoter from 123 young adults with idiopathic AIS and 123 age- and gender-matched controls by single-stranded conformational polymorphism and sequencing analysis. A second, independent population with childhood stroke was used for a replication study. We identified 8 novel, strongly linked polymorphisms in the GPx-3 gene promoter that formed 2 main haplotypes (H1 and H2). The transcriptional activity of the 2 most prevalent haplotypes was studied with luciferase reporter gene constructs. RESULTS: The H2 haplotype was over-represented in both patient ...
Background: The X-linked form of chronic granulomatous disease (CGD) is a primary immunodeficiency that affects phagocytes of the innate immune system and is characterized by an increased susceptibility to severe bacterial and fungal infections. It is caused by mutations in the CYBB gene, which encodes the 91-kD subunit of phagocyte NADPH oxidase. Aim: To identify the mutation in the CYBB gene in two unrelated patients from Chile with, the diagnosis of X-linked CGD and their families. Patients and methods: The molecular genetic defects of two unrelated patients from Chile with X-linked CGD caused by defects in the CYBB gene were investigated. The underlying mutation was investigated by single strand conformation polymorphism (SSCP) analysis of PCR-amplified genomic DNA and by sequencing of the affected gene region. Results: We found an insertion c.1267_1268insA in exon 10 leading to a frameshift mutation. This mutation is a novel report. We also identified a splice site mutation in the other ...
Abstract: : Purpose: Define the role of MYOC, CYP1B1 and PITX2 in patients with juvenile open angle glaucoma. Methods: We undertook mutational analysis of three glaucoma-related genes (MYOC, CYP1B1 and PITX2)using a combination of single strand conformation polymorphism (SSCP), and direct cycle sequencing. The patient population included 60 unrelated cases affected with JOAG or early onset glaucoma (onset age 5-40 years). Results: MYOC mutations were identified in 8/60 individuals (13.3%); CYP1B1 mutations in 3/60 (5%) and none in PITX2. Individuals with MYOC mutations showed greater phenotypic variability than expected, and included pigment dispersion syndrome and a mixed-mechanism glaucoma. Mutations in CYP1B1 were identified in three cases that did not have features suggestive of congenital glaucoma. Study of one large pedigree with autosomal dominant glaucoma demonstrated segregation of both MYOC and CYP1B1 mutations with the disease. Those who carried the MYOC mutation alone had an average ...
2-Amino-3-methylimidazo[4,5-f]quinoline (IQ), a strong mutagen/carcinogen, belongs to a group of heterocyclic amines that are formed (ng/g amounts) during the cooking of protein containing food. The mutational specificity of IQ in Escherichia coli was determined in a forward mutation assay using the yeast URA3 gene as a target. The plasmid pTU-AC, containing the target URA3, was randomly modified in vitro using N-hydroxy-IQ, and subsequently transformed into an E. coli pyrF strain (DB6656). Mutant clones were directly selected by their ability to grow on medium containing 5-fluoro-orotic acid which is toxic to URA3+ clones and thereby selects for URA3- mutants. Single Strand Conformation Polymorphism (SSCP) was used to map the mutation-containing regions of URA3, so that it was necessary to sequence only the relevant, mutation-containing fragment and not the entire gene. At a modification level of 7 IQ-lesions/URA3 gene, the predominant mutations were base substitutions (approximately 70%), ...
Background: The PARK2 gene at 6q26 encodes parkin, whose inactivation is implicated in an early-onset autosomal recessive form of Parkinson disease (PD). Objective: To evaluate the influence of heterozygosity for parkin mutation on onset age in a sample of families with at least 2 PD-affected members. Design: Clinical and genetic study. Setting: Twenty collaborative clinical sites. Patients: Patients with familial PD collected in the GenePD study. Studied families were selected for (1) affected sibling pairs sharing 2 alleles identical by state at PARK2 (D6S305) or (2) 1 or more family members with onset age younger than 54 years, regardless of D6S305 status. At least 1 member from each of 183 families underwent comprehensive screening for deletion/insertion variants and point mutations in PARK2. Main Outcome Measures: Mutations in the parkin gene were screened by means of single-stranded conformation polymorphism and sequencing in all 12 coding exons and flanking intronic sequences for point ...
The glp-1 gene product mediates cell-cell interactions required for cell fate specification during development in Caenorhabditis elegans. To identify genes that interact with glp-1, we screened for dominant suppressors of two temperature-sensitive glp-1 alleles and recovered 18 mutations that suppress both germline and embryonic glp-1 phenotypes. These dominant suppressors are tightly linked to glp-1 and do not bypass the requirement for a distal tip cell, which is thought to be the source of a signal that is received and transduced by the GLP-1 protein. Using single-strand conformation polymorphism (SSCP) analysis and DNA sequencing, we found that at least 17 suppressors are second-site intragenic revertants. The suppressors, like the original glp-1(ts) mutations, are all located in the cdc10/SWI6/ankyrin domain of GLP-1. cdc10/SWI6/ankyrin motifs have been shown to mediate specific protein-protein interactions in other polypeptides. We propose that the glp-1(ts) mutations disrupt contact between GLP-1
Mutations in the p53 tumor suppressor gene and K-ras oncogene have been frequently found in sputum and bronchoalveolar lavage (BAL) samples of lung cancer patients and also in those of patients prior to presenting clinical symptoms of lung cancer, suggesting they may provide useful biomarkers for early lung cancer diagnosis. However, the detection of these gene mutations in sputum and BAL samples has been complicated by the fact that they often occur in only a small fraction of epithelial cells among sputum cells and, in the case of p53 gene, at many codons. In this study, sputum cells were collected on a filter membrane by sputum cyto-centrifugation and morphologically analyzed. Epithelial cells were selectively taken by using a laser capture microdissection microscope and analyzed by polymerase chain reaction (PCR) and single-stranded conformational polymorphism (SSCP), for p53 mutations, and PCR and denaturing gradient gel electrophoresis (DGGE), for K-ras mutations. This method was applied ...
AIMS: To attempt to detect p53 gene mutations in the plasma of patients with large bowel carcinoma. METHODS: Plasma was collected from 20 control patients with no history of cancer and from 17 patients with large bowel carcinoma. Corresponding tumour and benign lymph node (control) samples for each of the carcinoma patients were obtained from paraffin blocks. A Dukes stage was determined for each tumour. DNA was extracted from the plasma samples and the paraffin embedded tissue using previously described methods. A nested primer polymerase chain reaction protocol was used for the amplification of exons 5 to 8 of the p53 gene. Cold single strand conformational polymorphism (SSCP) was performed on mini gels and silver stained. Abnormal bands were excised, the DNA eluted, and reamplified for automated dye termination sequencing. Any sample showing an apparent mutation was rechecked from the original extracted DNA sample at least three times. RESULTS: p53 gene mutations were not found in the ...
Includes bibliographical references and index. Nucleic acid methods: The manipulation of nucleic acids : basic tools and techniques / Gayle Corkill and Ralph Rapley. Restriction enzymes : tools in clinical research / Gareth J.S. Jenkins. Principles and medical applications of the polymerase chain reaction / Bimal D.M. Theophilus. Probe design, production, and applications / Marilena Aquino de Muro. Southern blotting as a diagnostic method / Bronwen M. Harvey and Pirkko Soundy. Capillary electrophoresis of DNA : biomedical applications / Beatriz Sanchez-Vega. Denaturing high-performance liquid chromatography (DHPLC) for nucleic acid analysis / Kim Hung Leung and Shea Ping Yip. Denaturing gradient gel electrophoresis (DGGE) / Jeroen H. Roelfsema and Dorien J.M. Peters. Single strand conformation polymorphism (SSCP) analysis / Kim Hung Leung and Shea Ping Yip. Randomly amplified polymorphic DNA (RAPD) : a useful tool for genomic characterization of different organisms / Lúcia Maria da Cunha ...
To confirm the diagnosis of CAA at the molecular level, a mutational analysis of the ALB was carried out as described in Materials and methods. In this case the combination of heteroduplex analysis and single-strand conformation polymorphism did not allow an unambiguous localisation of the mutation site. Therefore all the fourteen coding exons and their adjacent intron regions were submitted to DNA sequence analysis, which clearly indicated the presence of a single mutation in the region encompassing exon 12 and the intron 11 - exon 12 and exon 12 - intron 12 junctions, that escaped our electrophoretic analysis. The electropherogram of the proband revealed that she is homozygous for a G,A transition at position c.1652+1, the first base of intron 12 in a 5 GT consensus sequence (Figure 3a). Both parents were heterozygous for the wild-type and mutated alleles, as the sequencing electropherograms showed the presence of two superimposed peaks at nucleotide c.1652+1 (Figure 3b and 3c). To establish ...
Long QT syndrome (LQT) is an inherited cardiac disorder that causes syncope, seizures and sudden death from ventricular tachyarrhythmias. We used single-strand conformation polymorphism (SSCP) and DNA sequence analyses to identify mutations in the cardiac sodium channel gene, SCN5A, in affected members of four LQT families. These mutations include two identical intragenic deletions and two missense mutations. These data suggest that SCN5A mutations cause LQT. The location and character of these mutations suggest that this form of LQT results from a delay in cardiac sodium channel fast inactivation or altered voltage-dependence of inactivation. ...
Background: Overexpression of the human epidermal growth factor receptor (HER) 2 is associated with poor prognosis and shortened survival in breast cancer patients. HER2 is a potent activator of several signaling pathways that support cell survival, proliferation and metabolism. In HER2- positive breast cancer there are most likely unexplored proteins that act directly or indirectly downstream of well established pathways and take part in tumor development and treatment response.. Methods: In order to identify novel copy number variations (CNVs) in HER2-positive breast cancer whole-genome single nucleotide polymorphism (SNP) arrays were used. A PCR-based loss of heterozygosis (LOH) assay was conducted to verify presence of deletion in HER2-positive breast cancer cases but also in HER2 negative breast cancers, cervical cancers and lung cancers. Screening for mutations was performed using single-strand conformation polymorphism (SSCP) followed by PCR sequencing. Protein expression was evaluated ...
TY - JOUR. T1 - Identification of seven novel mutations in LH β-subunit gene by SSCP. AU - Roy, Ashim C.. AU - Liao, Wu Xiang. AU - Chen, Ying. AU - Arulkumaran, Sabaratnam. AU - Ratnam, Shan S.. PY - 1996. Y1 - 1996. N2 - Seven new point mutations have been identified from LH β-subunit gene by PCR-mediated SSCP, and sequencing. One mutation was found changing amino acid from Gln102 to Ser102. The remaining six mutations, which did not change the codings, were in complete linkage disequilibrium. SSCP can be used in the diagnosis of LH-related disorders.. AB - Seven new point mutations have been identified from LH β-subunit gene by PCR-mediated SSCP, and sequencing. One mutation was found changing amino acid from Gln102 to Ser102. The remaining six mutations, which did not change the codings, were in complete linkage disequilibrium. SSCP can be used in the diagnosis of LH-related disorders.. KW - Luteinizing hormone. KW - Mutation. KW - Polymerase chain reaction. KW - Restriction enzyme ...
Figure 2. Mutation analysis of the MYO7A gene in the family. A: Sequencing chromatograms of PCR products of exon 22 from a normal individual and the affected individual IV-4; insertion of an A residue is marked by an arrow. B: Partial nucleotide and amino acid sequences of wild type (normal) and mutant alleles; insertion site of an A residue is marked above by a pipe (,) in the wild type allele; a missense run of 18 amino acids are shown in purple in the mutant protein; premature stop codon in exon 23 is shown in red. C: PCR-SSCP analysis of all 13 individuals from the family, note all five affected individuals (IV-1, IV-2, IV-3, IV-4, and IV-6) are homozygous for the mutant allele (M) and their parents (II-1, III-1, III-2, and III-3) are heterozygous for the mutant and the wild type (W) alleles. D: Schematic representation of mutant (above) and normal MYO7A (below) proteins. Note the truncation of MYO7A protein in affected individuals. The normal protein has a head domain with an ATP binding ...
PubMed journal article: p53 gene abnormalities are closely related to hepatoviral infections and occur at a late stage of hepatocarcinogenesis. Download Prime PubMed App to iPhone, iPad, or Android
摘要 试验旨在研究DQB2基因外显子2多态性与哈萨克羊布鲁氏菌病易感性的相关性。通过PCR-SSCP技术对146只布鲁氏菌阴性哈萨克羊血液样本和28只布鲁氏菌阳性哈萨克羊血液样本中的白细胞表面抗原DQB2基因外显子2的多态性进行研究,挑取不同的等位基因进行克隆测序,经卡方检验分析每个SNP位点的基因频率、基因型频率及其多态性与布鲁氏菌病易感性的相关性,应用生物信息学软件分析与哈萨克羊布鲁氏菌病易感性相关的不同等位基因的mRNA二级结构及蛋白质的二级结构、三级结构和抗原表位。结果发现,在270 ...
"Six new mutations in the ornithine transcarbamylase gene detected by single-strand conformational polymorphism". Pediatric ... The human OTC gene is located on the short arm of chromosome X (Xp21.1). The gene is located in the Watson (plus) strand and is ... The binding of CP induces a global conformational change, while the binding of L-ornithine only induces movement of the SMG ... Yamaguchi S, Brailey LL, Morizono H, Bale AE, Tuchman M (July 2006). "Mutations and polymorphisms in the human ornithine ...
in human faecal samples and subtype assignment using single strand conformational polymorphism and sequencing". Molecular and ... Blastocystis is a protozoal, single-celled parasite that inhabits the gastrointestinal tracts of humans and other animals. Many ... Blastocystis hominis was the most frequently detected parasite in single and multiple infections, with Cryptosporidium parvum ...
Donnelly JG, Detombe S, Hindmarsh JT (2002). "Single-strand conformational polymorphism and denaturing gradient gel ... complete genomic sequence and polymorphisms in the human gene". Biochemical and Biophysical Research Communications. 226 (1): ...
... polymorphism, single-stranded conformational MeSH G13.920.795.800 - polymorphism, single nucleotide The list continues at List ... polymorphism, genetic MeSH G13.920.795.595 - polymorphism, restriction fragment length MeSH G13.920.795.600 - ...
... for example melting temperature-based systems such as Single-stranded conformational polymorphism analysis (SSCP) and ... These methods are simple to run using standard laboratory techniques and equipment, and can detect polymorphisms, single base ... The PCR reaction should be optimized to create a single, strong PCR band, as non-specific bands will increase the background ... Since then the method has been used to detect mutations and polymorphisms in many different organisms and cell types (see ...
... (SSCP), or single-strand chain polymorphism, is defined as a conformational difference ... "Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and ... "Detection of the polymorphisms of human DNA by gelelectrophoresis as single-strand conformation polymorphisms". Proc. Natl. ... After denaturation, single-stranded DNA undergoes a characteristic 3-dimensional folding and may assume a unique conformational ...
... or inactive Cas9 One of several human vitamin D receptor gene variants is caused by a single nucleotide polymorphism in the ... the first strand 9 nucleotides downstream and the second strand 13 nucleotides upstream of the nearest nucleotide of the ... the endonuclease domain is sequestered by the DNA-binding domain and is released through a conformational change in the DNA- ... 2003). "Vitamin D receptor start codon polymorphism (Fok1) is related to bone mineral density in healthy adolescent boys". J ...
Single-stranded DNA (ssDNA) folds into a tertiary structure. The conformation is sequence dependent and most single base pair ... SNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms (SNPs) between members of a species ... This conformational change permits the fluorophore and quencher to be free of their tight proximity due to the hairpin ... The key to DHPLC is the solid phase which has differential affinity for single and double-stranded DNA. In DHPLC, DNA fragments ...
So far, more than 4580 single nucleotide polymorphisms (SNPs) for this gene have been identified. SLC46A3 is expressed at ... More precisely, the protein is predicted to be composed of 62.9% α-helix, 33.8% random coil, and 3.3% extended strand. The ... The substrate translocation pores have access to both sides of the membrane in an alternating fashion through a conformational ... Cite journal requires ,journal= (help) Shen LX, Basilion JP, Stanton VP (July 1999). "Single-nucleotide polymorphisms can cause ...
... the protein preferably binds to double-stranded DNA rather than single-stranded DNA. The ability of lactoferrin to bind DNA is ... Gene polymorphism between species is much more diverse than the intraspecific polymorphism of lactoferrin. There are ... Refinement and analysis of ligand-induced conformational change". Acta Crystallogr. D. 54 (Pt 6 Pt 2): 1319-35. doi:10.1107/ ... such as agarose with the immobilized single-stranded DNA. Lactoferrin's primary role is to sequester free iron, and in doing so ...
Chiu CF, Tsai MH, Tseng HC, Wang CL, Tsai FJ, Lin CC, Bau DT (2008). "A novel single nucleotide polymorphism in ERCC6 gene is ... CSB also accumulates at sites of DNA double-strand breaks in a transcription dependent manner and influences double-strand ... Lewis R, Durr H, Hopfner KP, Michaelis J (2008). "Conformational changes of a Swi2/ Snf2 ATPase during its mechano-chemical ... Single-nucleotide polymorphisms in the ERCC6 gene have been correlated with significantly increased risk of certain forms of ...
... sense strand - sequence - sequence motif - sequence polymorphism - sequence-tagged site - sequential epitope - severe combined ... single nucleotide polymorphism - siRNA - site-directed mutagenesis - site-specific recombination - slot blot - SNP - snRNA - ... coding strand - codon - codon usage bias - competent - complementary - conformational epitope - congenital - consensus sequence ... anti-sense strand - antibiotic resistance - antibody - antisense - antisense strand - AP-1 site - apoptosis - assembled epitope ...
... single-stranded RNA viruses. In the Baltimore classification system, which groups viruses together based on their manner of ... A series of uncoating steps and conformational changes accompany cell entry and replication. High-resolution structures are ... 13 shell that influences the inherent structural polymorphism of pVP2. The virus-encoded RNA-dependent RNA polymerase, VP1, is ... The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome. Double-stranded RNA ...
... and single strands composed of only extended bases can recognize and bind to single strands of natural DNA, making them useful ... This conformational preference is seen primarily in pyrimidines, and purines display minimal preference for orientation. ... Natural bases can be bound directly to fluorophores for use in microarrays, in situ hybridization, and polymorphism analysis. ... Similar to B-DNA, xDNA can recognize and bind complementary single-stranded DNA or RNA sequences. Duplexes formed from xDNA are ...
Down syndrome patients with a single valine substitution have been linked to earlier cognitive decline. Several polymorphisms ... NMR shows copper binding results in a conformational change at the N-terminus. PrPSc is a conformational isoform of PrPC, but ... The human protein structure consists of a globular domain with three α-helices and a two-strand antiparallel β-sheet, an NH2- ... The mechanism for conformational conversion to the scrapie isoform is speculated to be an elusive ligand-protein, but, so far, ...
Each individual protein molecule can contribute one to several β-strands in each protofilament and the strands can be arranged ... August 2000). "Nucleated conformational conversion and the replication of conformational information by a prion determinant". ... Paravastu AK, Leapman RD, Yau WM, Tycko R (25 November 2008). "Molecular structural basis for polymorphism in Alzheimer's beta- ... that of a single protofilament) and are up to 30 nm wide; more often protofilaments twist around each other to form the ...
... the protein preferably binds to double-stranded DNA rather than single-stranded DNA. The ability of lactoferrin to bind DNA is ... Gene polymorphism between species is much more diverse than the intraspecific polymorphism of lactoferrin. There are ... Refinement and analysis of ligand-induced conformational change". Acta Crystallographica Section D. 54 (Pt 6 Pt 2): 1319-35. ... "Characterisation of single nucleotide polymorphisms identified in the bovine lactoferrin gene sequences across a range of dairy ...
SMUG1 prefers single-stranded DNA as substrate, but also removes U from double-stranded DNA. In addition to unmodified uracil, ... UDG undergoes a conformational change from an ''open'' unbound state to a ''closed'' DNA-bound state. Lindahl was the first to ... Xiong XD, Luo XP, Liu X, Jing X, Zeng LQ, Lei M, Hong XS, Chen Y (2012). "The MBD4 Glu346Lys polymorphism is associated with ... NEIL1 is also capable of removing lesions from single-stranded DNA as well as from bubble and forked DNA structures. A ...
This single nucleotide polymorphism (SNP) results in an arginine-to-cysteine substitution in a phosphate recognition domain ... The glycine rich P-loop is between the β1 and β2 strands, forming a classical β-strand-turn-β-strand motif that anchors and ... Phosphorylation also hinders PER's ability to enter the nucleus by inducing a conformational change in its nuclear localization ... Certain kinase-related structural motifs were subsequently confirmed, such as a β-strand-turn-β-strand motif that anchors ATP, ...
... the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double- ... Lu XJ, Shakked Z, Olson WK (July 2000). "A-form conformational motifs in ligand-bound DNA structures". Journal of Molecular ... Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL (October 1980). "Polymorphism of DNA double helices". Journal of Molecular ... The two strands can come apart-a process known as melting-to form two single-stranded DNA (ssDNA) molecules. Melting occurs at ...
Antisense oligonucleotides are single strands of DNA or RNA that are complementary to a chosen sequence. In the case of ... Spingler B (January 2012). "Chapter 3. Metal-Ion-Promoted Conformational Changes of Oligonucleotides". In Sigel A, Sigel H, ... which do not activate RNase-H but can reduce gene expression or modify RNA splicing Polymorphism, the appearance in a ... these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are ...
The observed hypercalciuria phenotypes from animal studies and studies on TRPV6 single nucleotide polymorphisms (SNPs) suggest ... This conformational change moves the lower portion of the helix gating the pore and thereby widens the pore size. The ... a β-hairpin structure linker domain made up two β-strands, a helix-turn-helix motif, a pre-SI helix, TM domain made up of six ... The TRPV6 protein is constitutive with a single-channel conductance of 42-58 ps. At low Ca2+ concentrations, a single Ca2+ ion ...
Representative Cas2 proteins have been characterised and possess either (single strand) ssRNA- or (double strand) dsDNA- ... During the same interval the phage developed single nucleotide polymorphisms that became fixed in the population, suggesting ... In type I systems correct base pairing between the crRNA and the protospacer signals a conformational change in Cascade that ... Cas13 is an RNA-guided RNA endonuclease, which means that it does not cleave DNA, but only single-stranded RNA. Cas13 is guided ...
In addition to masking key elements within single-stranded RNA, the formation of double-stranded RNA duplexes can also provide ... Recently, a number of association studies examining single nucleotide polymorphisms (SNPs) associated with disease states have ... The authors found that this activation involves a conformational alteration to the structure of HSR-1 in response to rising ... "Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells". Nature Structural & Molecular Biology ...
Most posit balancing selection (see polymorphism (biology)), which is any natural selection process whereby no single allele is ... α1 and α2 form deep peptide-binding groove between two long α-helices and the floor of the groove formed by eight β-strands. ... and nucleic acid-and recognize conformational epitopes, which have three-dimensional structure.) MHC molecules enable immune ... The polymorphism is so high, in a mixed population (nonendogamic), no two individuals have exactly the same set of MHC ...
Yi G, Brendel VP, Shu C, Li P, Palanathan S, Cheng Kao C (2013). "Single nucleotide polymorphisms of human STING can affect ... cGAS is found at the plasma membrane and is responsible for detecting cytosolic double stranded DNA, normally found in the cell ... Upon binding dsDNA, cGAS dimerizes and undergoes conformational changes that open up a catalytic nucleotide binding pocket, ... This pathway plays a critical role in mediating immune defense against double-stranded DNA viruses. The innate immune system ...
Common single nucleotide polymorphisms in the scaffold impair conformational change". The Journal of Biological Chemistry. 282 ... Since the RCL is still intact, the first strand of the C-sheet has to peel off to allow full RCL insertion. Regulation of the ... The conformational change involves the RCL moving to the opposite end of the protein and inserting into β-sheet A, forming an ... A single fungal serpin has been characterized to date: celpin from Piromyces spp. strain E2. Piromyces is a genus of anaerobic ...
"Effects of MDM2 promoter polymorphisms and p53 codon 72 polymorphism on risk and age at onset of squamous cell carcinoma of the ... In some cases, single missense mutations in p53 have been shown to disrupt p53 stability and function. Suppression of p53 in ... Second, a conformational change forces p53 to be activated as a transcription regulator in these cells. The critical event ... Cuddihy AR, Wong AH, Tam NW, Li S, Koromilas AE (April 1999). "The double-stranded RNA activated protein kinase PKR physically ...
In the UCK2 monomer, the active site is composed of a five-stranded β-sheet, surrounded by five α-helices and a β-hairpin loop ... Studies have shown that the binding of the cytidine/uridine sugar moiety results in the conformational change to reduce the ... Komatsu N, Kimura Y, Kido A, Oya M (December 1990). "Polymorphism of uridine monophosphate kinase: population study in Japanese ... "Structure of human uridine-cytidine kinase 2 determined by SIRAS using a rotating-anode X-ray generator and a single samarium ...
... has a positive sense single-stranded RNA genome. The genome consists of a single open reading frame that is ... The substantial proportion of this lack of response to treatment is proposed to be caused by a single-nucleotide polymorphism ( ... Although HVR1 is quite variable in amino acid sequence, this region has similar chemical, physical, and conformational ... The hepatitis C virus (HCV) is a small (55-65 nm in size), enveloped, positive-sense single-stranded RNA virus of the family ...
Single nucelotide polymorphism (rs1800629)[edit]. Empty section References[edit]. *^ a b c ENSG00000230108, ENSG00000223952, ... This binding causes a conformational change to occur in the receptor, leading to the dissociation of the inhibitory protein ... are composed of two antiparallel β-pleated sheets with antiparallel β-strands, forming a 'jelly roll' β-structure, typical for ... 2tun: CONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROSIS FACTOR ...
Polymorphisms at sites 136, 154, and 171 are associated with varying susceptibility to ovine scrapie. Polymorphisms of the PrP- ... The human protein structure consists of a globular domain with three α-helices and a two-strand antiparallel β-sheet, an NH2- ... The mechanism for conformational conversion to the scrapie isoform is speculated to be an elusive ligand-protein, but, so far, ... Some PRNP mutations lead to a change in single amino acids (the building-blocks of proteins) in the prion protein. Others ...
"Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG ... Caspi, A. (18 July 2003). "Influence of Life Stress on Depression: Moderation by a Polymorphism in the 5-HTT Gene". Science. ... In other words, as a single fertilized egg cell - the zygote - continues to divide, the resulting daughter cells change into ... The yeast prion PSI is generated by a conformational change of a translation termination factor, which is then inherited by ...
ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily". Cell. 101 (7): 789-800. ... involved in several diseases that arise from polymorphisms in ABC genes and rarely due to complete loss of function of single ... The conformational transition from MsbA-closed-apo to MsbA-AMP-PNP involves two steps, which are more likely concerted: a ~10° ... The closed NBD dimer induces a conformational change in the TMDs such that the TMD opens, forming a chamber with an opening ...
... single strand) ssRNA-[84] or (double strand) dsDNA-[85][86] specific endoribonuclease activity. ... During the same interval the phage developed single nucleotide polymorphisms that became fixed in the population, suggesting ... Sashital DG, Jinek M, Doudna JA (June 2011). "An RNA-induced conformational change required for CRISPR RNA cleavage by the ... binding double-stranded fragments of invading DNA, while Cas1 binds the single-stranded flanks of the DNA and catalyses their ...
... conformational changes in RNA polymerase, conformational changes in DNA, binding of nucleoside triphosphate (NTP) to the ... Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 3' ... In the case of a transcription factor binding site, there may be a single sequence that binds the protein most strongly under ... β Promoter Polymorphisms in Allergies and Asthma". American Journal of Respiratory and Critical Care Medicine. 158 (6): 1958- ...
In other words, as a single fertilized egg cell - the zygote - continues to divide, the resulting daughter cells change into ... Caspi, A. (18 July 2003). "Influence of Life Stress on Depression: Moderation by a Polymorphism in the 5-HTT Gene". Science. ... The yeast prion PSI is generated by a conformational change of a translation termination factor, which is then inherited by ... If this enzyme reaches a "hemimethylated" portion of DNA (where 5-methylcytosine is in only one of the two DNA strands) the ...
... conformational changes in RNA polymerase, conformational changes in DNA, binding of nucleoside triphosphate (NTP) to the ... In genetics, a promoter is a sequence of DNA to which proteins bind that initiate transcription of a single RNA from the DNA ... refers to two adjacent genes coded on opposite strands, with their 5' ends oriented toward one another.[15] The two genes are ... "Interleukin-10 and transforming growth factor-beta promoter polymorphisms in allergies and asthma". American Journal of ...
For synthesis of a DNA strand from the RNA template only the reverse primer is required since the RNA is a single strand ... A single nucleotide polymorphism-based technique for specific characterization of YO and YN isolates of Potato virus Y (PVY). J ... In terms of potato plant viruses, mutations within the CP gene may cause the CP to undergo conformational changes rendering ... During the extension step the strands are amplified beyond the target DNA. This means that each newly synthesized strand of DNA ...
September 2010). "A synonymous single nucleotide polymorphism in DeltaF508 CFTR alters the secondary structure of the mRNA and ... Normally, the three DNA base pairs A-T-C (paired with T-A-G on the opposite strand) at the gene's 507th position form the ... ATP-driven conformational changes in CFTR open and close a gate to allow transmembrane flow of anions down their ... Carriers of a single CF mutation have a higher prevalence of chronic rhinosinusitis than the general population. Approximately ...
An increase in pKa of cytosine N3 showed that these conditions favored quadruplex and i-motif over double and single-stranded ... The conformational change from B DNA to i-motif under acidic conditions makes it useful as a colormetric sensor for glucose ... Saxena, Sarika; Bansal, Aparna; Kukreti, Shrikant (March 2008). "Structural polymorphism exhibited by a homopurine· ... This result reflects the transcription process in which supercoiled DNA is unwound into single-stranded structures, which ...
In addition, single nucleotide polymorphisms (SNPs) on the gene encoding FTO have been associated with increased risk of breast ... This modification results in the melting of double-stranded RNA, due to alterations in the RNA structure. The N1- ... Väre VY, Eruysal ER, Narendran A, Sarachan KL, Agris PF (March 2017). "Chemical and Conformational Diversity of Modified ... Moreover, m6A is more abundant in mRNAs that undergo alternative splicing compared to genes that code a single isoform. This is ...
Most mutations that occur are single nucleotide polymorphisms which modify single bases of the DNA sequence, resulting in point ... Damaged bases are first excised, the damaged strand is then aligned with an undamaged homolog, and DNA synthesis repairs the ... Hanukoglu I (2017). "ASIC and ENaC type sodium channels: Conformational states and the structures of the ion selectivity ... Mutation rates for single nucleotide sites for most organisms are very low, roughly 10−9 to 10−8 per site per generation, ...
Polymorphism, Single-Stranded Conformational*Polymorphism, Single-Stranded Conformational. *Polymorphism, Single Stranded ... Single-Stranded Conformational" by people in Harvard Catalyst Profiles by year, and whether "Polymorphism, Single-Stranded ... Conformational Polymorphism, Single-Stranded. *Conformational Polymorphisms, Single-Stranded. *Polymorphisms, Single-Stranded ... "Polymorphism, Single-Stranded Conformational" is a descriptor in the National Library of Medicines controlled vocabulary ...
Mycobacterium tuberculosis Identified by Polymerase Chain Reaction Single-Stranded Conformational Polymorphism Miriam Bobadilla ... Mycobacterium tuberculosis Identified by Polymerase Chain Reaction Single-Stranded Conformational Polymorphism. ...
... of extended-spectrum beta-lactamases of the SHV family using a combination of PCR-single strand conformational polymorphism ( ... to extend the identification of SHV beta-lactamases previously characterised by PCR-single strand conformational polymorphism ( ... Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) has been developed ... PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP).. Chanawong A1, MZali FH, Heritage J, Lulitanond A, ...
... in Streptococcus pneumoniae by PCR-Restriction Fragment Length Polymorphism and Single-Strand Conformational Polymorphism. ... method of using a combination of PCR-restriction fragment length polymorphism and single-strand conformational polymorphism ( ... in Streptococcus pneumoniae by PCR-Restriction Fragment Length Polymorphism and Single-Strand Conformational Polymorphism ... in Streptococcus pneumoniae by PCR-Restriction Fragment Length Polymorphism and Single-Strand Conformational Polymorphism ...
We now show that minisatellite isoalleles can also be simply resolved by single-stranded conformational polymorphisms (SSCP) ... Minisatellite isoalleles can be distinguished by single-stranded conformational polymorphism analysis in agarose gels. ...
"Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and ... Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and ... Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and ... was investigated by single-strand conformational polymorphism (SSCP) analysis and nucleotide sequencing. Forty-eight samples of ...
DETECTION OF MISSENSE MUTATIONS BY SINGLE-STRAND CONFORMATIONAL POLYMORPHISM (SSCP) ANALYSIS IN 5 DYSFUNCTIONAL VARIANTS OF ... 1993) DETECTION OF MISSENSE MUTATIONS BY SINGLE-STRAND CONFORMATIONAL POLYMORPHISM (SSCP) ANALYSIS IN 5 DYSFUNCTIONAL VARIANTS ...
Detection of mutations in the factor VIII gene using single-stranded conformational polymorphism (SSCP). Genomics. 1992;13(3): ... Detection of mutations in the factor VIII gene using single-stranded conformational polymorphism (SSCP). / Economou, Effrosini ... title = "Detection of mutations in the factor VIII gene using single-stranded conformational polymorphism (SSCP)", ... T1 - Detection of mutations in the factor VIII gene using single-stranded conformational polymorphism (SSCP) ...
... is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs ... In contrast, SSCP and pyrosequencing of an unrelated single SNP (rs1835740:C > T), showed 94% concordance. Our data suggest ... Single-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the ... Detection of three closely located single nucleotide polymorphisms in the EAAT2 promoter: comparison of single-strand ...
single-stranded conformational polymorphisms;. LOH,. loss of heterozygosity;. MSP,. methylation-specific PCR. ... Single-Stranded Conformational Polymorphisms (SSCP) and Sequencing.. PCR was performed as described previously by using primers ... Four additional cases had intragenic p53 LOH (determined by using polymorphisms in exon 2, 3, or 4 of the gene) but no ... Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations ...
Rapid detection of K-ras gene mutations in canine lung cancer using single-strand conformational polymorphism analysis. / ... Rapid detection of K-ras gene mutations in canine lung cancer using single-strand conformational polymorphism analysis. ... title = "Rapid detection of K-ras gene mutations in canine lung cancer using single-strand conformational polymorphism analysis ... T1 - Rapid detection of K-ras gene mutations in canine lung cancer using single-strand conformational polymorphism analysis ...
We tested the use of a modified method of single-strand conformational polymorphism (SSCP) analysis for the detection of point ... We tested the use of a modified method of single-strand conformational polymorphism (SSCP) analysis for the detection of point ... Strand-separating conformational polymorphism analysis: efficacy of detection of point mutations in the human ornithine delta- ...
Single-Stranded Conformational Polymorphism (SSCP) and Sequence Analysis of HNF-4α.. One individual from each of 64 type 2 ... Single locus MLSs and heterozygosities are presented for each marker in Table 1. Using multipoint analysis under an additive ... Although the second and third peaks could be explained by a single susceptibility locus, evidence for linkage on both arms on ... Of these rare variants found in single diabetic families, three occurred near splice junctions, but not in the conserved donor ...
Single-strand Conformational Polymorphism Analysis.. To detect single nucleotide changes in alleles of different inbred mouse ... The nucleotide sequences of polymorphisms detected by single-strand conformational polymorphism (SSCP) analysis were determined ... single-strand conformational polymorphism. SSLP. simple sequence length repeat. STS. sequence-tagged site. TIR. Toll IL-1 ... First-strand cDNA synthesis was carried out using 2 μg of total RNA, 100 ng of random hexamers, and 200 U of Moloney murine ...
... single strand conformational polymorphism (SSCP) etc. are either costly or technically cumbersome and requires the use of ... Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem. 2004;50( ... n UDP-glucuronosyltransferase 1A1 promoter polymorphism in Nigerian neonates. Pediatr. Res. 2008;63(1):109.CrossRefPubMedGoogle ... The frequency of UDP-glucuronosyltransferase 1A1 promoter region (TA) 7 polymorphism in newborns and its relation with ...
RNA Single-Stranded Conformational Polymorphism.. To determine whether modifications in the ATG of the uORF in the 5′-UTR of ... 1992) Screening for mutations by single strand conformation polymorphism (rSSCP): Comparison with DNA-SSCP. Nucleic Acid Res 20 ... To determine whether mutation of the upstream ATG influences the secondary structure of the mRNA, single-stranded radiolabeled ... As shown in Fig.8, RNA produced from the native 5′-UTR of CRHR1 migrated as a single band. A similar mobility was observed for ...
Polymorphism, Single-Stranded Conformational Substances * MYH7 protein, human * Cardiac Myosins * Myosin Heavy Chains ... Methods: Single-strand conformation polymorphism analysis and sequencing of fragments with abnormal MYH7 gene mobility were ...
The use of polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) to study rpoB gene mutations in ... The use of polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) to study rpoB gene mutations in ... One such method is single-stranded conformational polymorphism (SSCP) analysis, which involves amplification by PCR of a ... Detection of polymorphisms of human DNA by gel electrophoresis single-strand conformation polymorphisms. Proc Natl Acad Sci U S ...
The use of polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) to study rpoB gene mutations in ... Representative polymerase chain reaction single-stranded conformational polymorphism (SSCP) patterns of rifampin resistance in ... Mycobacterium tuberculosis Identified by Polymerase Chain Reaction Single-Stranded Conformational Polymorphism Miriam Bobadilla ... Mycobacterium tuberculosis Identified by Polymerase Chain Reaction Single-Stranded Conformational Polymorphism. ...
A method and a package for identifying single nucleotide polymorphisms in complement receptor is useful in identifying ... single strand conformational polymorphism analysis (SSCP); "HOT" cleavage; denaturing gradient gel electrophoresis (DVGE) and ... CR1 is a single polypeptide chain that exhibits a size polymorphism derived from four codominant inherited alleles. The alleles ... The single nucleotide polymorphism at position 5932 results in a missense codon, which translates to an alanine (A) to ...
Single-strand conformational polymorphism. MLPA. Multiplex ligation-dependent probe amplification. HSF. Human splicing finder ... Krawczak M, Thomas NST, Hundrieser B et al (2007) Single base-pair substitutions in exon-intron junctions of human genes: ... Buhard O, Cattaneo F, Wong YF et al (2006) Multipopulation analysis of polymorphisms in five mononucleotide repeats used to ... Capriotti E, Calabrese R, Casadio R (2006) Predicting the insurgence of human genetic diseases associated to single point ...
Development of single-strand conformational polymorphism to screen for mutations in hotspot regions of beta-globin gene of beta ... Development of single-strand conformational polymorphism to screen for mutations in hotspot regions of beta-globin gene of beta ... Single strand conformational polymorphism (SSCP) technique was developed as an adjunct for the previously developed allele- ...
Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis is a kind of sensitive mutation ... n in Mitochondrial D-loop using Polymerase Chain Reaction-single Strand Conformational Polymorphism (PCR-SSCP) / 체질인류학회지 ... A single DNA strand with a mutation or nucleotide polymorphism has a different conformation from its wild-type counterpart, and ... In type 1 and 4, positions of the lower single stand of both were same but those of upper strand were different. In sequencing ...
Using single-strand conformational polymorphism, we screened for mutations in exons 5, 6, 7 and 8 of gene TP53 in the ... Investigation of single-strand conformational polymorphism of the TP53 gene in women with a family history of breast cancer ... Investigation of single-strand conformational polymorphism of the TP53 gene in women with ... Full text: Available Index: LILACS (Americas) Main subject: Breast Neoplasms / Genes, p53 / Polymorphism, Single-Stranded ...
Using single strand conformational polymorphisms (SSCP) to identify Phytophthora species in Oregon forests affected by sudden ...
polymorphism, single-stranded conformational. *oocytes. *hypertension, essential. The ENaC constitutes the rate-limiting step ... Uracyl-containing single-strand DNA was precipitated using 5% PEG 6000 and 0.95 mol/L ammonium acetate and then purified using ... β Single-strand DNA (500 ng) and 10 pmol phosphorylated mutagenic primer were denatured together for 10 minutes at 95°C, slowly ... That single purpose drives all we do. The need for our work is beyond question. Find Out More about the American Heart ...
Single-strand conformational polymorphism. *Denaturing gradient gel electrophoresis analysis. *DNA sequencing. Alternative ... Tumor DNA strands and normal DNA are compared in neighboring lanes. Tumors are considered MSI-H (high instability) if two or ... Strand M, Prolla TA, Liskay RM, et al. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA ... Testing for a single point mutation (rather than sequencing the entire gene) makes BRAF mutation analysis economically ...
The abbreviations used are: APC, adenomatous polyposis coli; SSCP, single-strand conformational polymorphism. ... The samples were sectioned with a cryostat, and a single section was quick stained to identify the hepatoblastomas. Then, the ...
For mapping of the H60 gene, a single strand conformational polymorphism (SSCP) that distinguished parental B6 and SPRET/Ei ... single strand conformational polymorphism; TFA, trifluoroacetic acid; NCBI, National Center for Biotechnology Information. ... Polymorphisms of H loci. The ability of H loci to induce T cell immunity suggested that they were polymorphic between the donor ... 3⇓A). Neither the strong (4.7, 7.2 kb) nor weakly (∼9 kb) hybridizing bands in the BALB.B DNA matched the single 5-kb band in ...
Single-Stranded Conformational Polymorphism. *Up-Regulation. *Breast Cancer. *Disease Progression. *Oligonucleotide Array ... and single nucleotide polymorphism (SNP) array copy number analysis.. METHODS: We used conventional cytogenetics, FISH, and ... potentially functional single nucleotide polymorphisms (SNPs) located in the microRNA binding sites of the 3 untranslational ... which was generated by fusing a HER2-specific single-chain Ab, a single-chain Pseudomonas exotoxin A and an active caspase-6 ...
  • Characterisation of extended-spectrum beta-lactamases of the SHV family using a combination of PCR-single strand conformational polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP). (nih.gov)
  • Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) has been developed to extend the identification of SHV beta-lactamases previously characterised by PCR-single strand conformational polymorphism (PCR-SSCP) analysis alone. (nih.gov)
  • A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in Streptococcus pneumoniae . (asm.org)
  • Methods for detection of known mutations in the QRDRs have included PCR-restriction fragment length polymorphism (PCR-RF) ( 1 ), oligonucleotide probe assay ( 6 ), TaqMan assay ( 8 ), and single-strand conformational polymorphism (SSCP) ( 27 ). (asm.org)
  • We now show that minisatellite isoalleles can also be simply resolved by single-stranded conformational polymorphisms (SSCP) arising during agarose gel electrophoresis. (le.ac.uk)
  • Kitajima, E. 2009-06-01 00:00:00 The variability of a fragment of the nucleocapsid gene of orchid fleck virus (OFV) was investigated by single-strand conformational polymorphism (SSCP) analysis and nucleotide sequencing. (deepdyve.com)
  • Antonarakis, Stylianos E. / Detection of mutations in the factor VIII gene using single-stranded conformational polymorphism (SSCP) . (elsevier.com)
  • Single-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs) due to its simplicity, requirement for basic equipment accessible in most laboratories and low cost. (biomedcentral.com)
  • The SSCP process involves PCR amplification of the target fragment, denaturation of the double-stranded PCR product with heat and formamide and electrophoresis on a non-denaturing polyacrylamide gel. (biomedcentral.com)
  • We tested the use of a modified method of single-strand conformational polymorphism (SSCP) analysis for the detection of point mutations in the human ornithine-delta-aminotransferase gene. (nih.gov)
  • A total of 126 spontaneous lung tumors from pet dogs were examined for K-ras mutations within exon 1 and exon 2 using a non-radioisotope single-strand conformational polymorphism analysis (SSCP) detection method on PCR products. (elsevier.com)
  • The use of polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) to study rpoB gene mutations in rifampin-resistant (RIFr) Mycobacterium tuberculosis has yielded contradictory results. (cdc.gov)
  • One such method is single-stranded conformational polymorphism (SSCP) analysis, which involves amplification by PCR of a segment of the gene encoding for the specific drug target and comparison of PCR products of drug-sensitive and drug- resistant strains by SSCP, in which mutations usually result in an altered pattern ( 9 , 10 ). (cdc.gov)
  • Representative polymerase chain reaction single-stranded conformational polymorphism (SSCP) patterns of rifampin resistance in Mycobacterium tuberculosis strains. (cdc.gov)
  • Single strand conformational polymorphism (SSCP) technique was developed as an adjunct for the previously developed allele-specific PCR (ASP) technique to screen the presence of mutationsin beta-globin gene. (ac.lk)
  • Polymerase chain reaction -single strand conformational polymorphism ( PCR - SSCP ) analysis is a kind of sensitive mutation detection method that has been usually used in field of medical genetics . (bvsalud.org)
  • A49G polymorphism in position 49 of exon-1 of the CTLA-4 gene was studied by the polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) method. (biomedsearch.com)
  • Southern blots, PCR-SSCP assays using primers specific for Rfp-Y genes, and Rfp-Y class I allele-specific sequencing show that the polymorphisms observed in B19H1, B19H2 and B19H3 are due to the presence of three different Rfp-Y haplotypes. (biomedsearch.com)
  • Single-stranded conformation polymorphism (SSCP) analysis is a widely used screening method that allows you to identify different genomic variants in a large number of samples and in a broad range of organisms, from microorganisms to humans. (thermofisher.com)
  • SSCP analysis detects sequence variations (single-point mutations and other small-scale changes) through electrophoretic mobility differences. (thermofisher.com)
  • METHODS An alteration in CYP27 of the proband was searched for by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis and subsequent sequencing. (bmj.com)
  • Blood samples from each patient were used to extract genomic DNA, with subsequent mutation screening of the entire coding sequence of ABCA4 , using single-strand conformational polymorphism (SSCP) analysis and direct sequencing. (bmj.com)
  • In the present study the existence of genetic variation in the nested multiplex polymerase chain reaction (NM-PCR) amplified region of the 16S-like ribosomal RNA genes of E. histolytica, E. dispar and E. moshkovskii was investigated by riboprinting and single strand conformation polymorphism (SSCP) analysis. (nih.gov)
  • We initiated this study to clarify whether a reduction of Vα24JαQ NK T cells in the periphery may be seen in the relapsing/remitting type of multiple sclerosis (MS). 4 To detect the presence of NK T cells, we used a novel method relying on single-strand conformation polymorphism (SSCP) of TCR nucleotide chains ( 21 , 22 , 23 ). (jimmunol.org)
  • 1 The more frequently used mutation screening methods are DGGE and Single-Strand Conformational Polymorphism (SSCP). (bio-medicine.org)
  • Some of these techniques include Single-Stranded Conformational Polymorphisms (SSCP) (Orita et al. (google.com)
  • To improve detection of commercial seafood fraud, a variety of DNA‐based techniques have been developed, including Multiplex PCR, FINS, PCR‐RFLP, PCR‐RAPD, PCR‐AFLP, and PCR‐SSCP, which are all based on polymorphisms in the genetic codes of different species. (deepdyve.com)
  • Cold" single strand conformational polymorphism (SSCP) was performed on mini gels and silver stained. (bmj.com)
  • The gene was analyzed by polymerase chain reaction (PCR), single-strand conformational polymorphism (SSCP), and 3'RACE for mutations. (cdc.gov)
  • PCR-SSCP screening of cell line cDNAs identified one silent polymorphism in cell line SK-LU-1. (cdc.gov)
  • p53 mutations were identified with single-strand conformational polymorphism (SSCP) and DNA sequencing in selected cases. (ovid.com)
  • We performed initial screening for five unrelated Korean patients using single strand conformation polymorphism (SSCP) and then selective sequencing for the regions involving the abnormal bands. (nih.gov)
  • Analysis of single strand conformation polymorphism (SSCP) by CE was also developed. (nii.ac.jp)
  • Whole blood provides high quality genomic DNA in microgram quantities sufficient for current applications including genome scans using SNPs or STRs, polymorphism discovery using methods such as denaturing gel electrophoresis, single strand conformational polymorphisms (SSCP), or sequencing, and for genotyping loci using methods such as allele specific oligonucleotides, RFLPs, or sequencing. (cdc.gov)
  • Griffey, SM , Kraegel, SA & Madewell, BR 1998, ' Rapid detection of K-ras gene mutations in canine lung cancer using single-strand conformational polymorphism analysis ', Carcinogenesis , vol. 19, no. 6, pp. 959-963. (elsevier.com)
  • Using single-strand conformational polymorphism, we screened for mutations in exons 5, 6, 7 and 8 of gene TP53 in the peripheral blood of 8 young non-affected members (17 to 36 years old) of families with a history of breast cancer . (bvsalud.org)
  • TILLING searches the genomes of mutagenized organisms for mutations in a chosen gene, typically single base-pair substitutions. (wiley.com)
  • Screening for the presence of known mutations or polymorphisms is the simpler task, because screening reagents can be customized to the individual lesion. (wiley.com)
  • The single-stranded conformational polymorphism identification of CaR mutations may help in the distinction of FBH from mild primary hyperparathyroidism which can be clinically difficult. (nih.gov)
  • All such mutations result in conformational changes that lead to increased sensitivity to tyrosine kinase inhibitors. (nature.com)
  • Six new mutations in the ornithine transcarbamylase gene detected by single-strand conformational polymorphism. (proteopedia.org)
  • Use of formalin-fixed paraffin-embedded tissue and single-strand conformation polymorphism analysis for polymerase chain reaction of antigen receptor rearrangements in dogs. (harvard.edu)
  • The methodology to study polymorphisms is simple, requiring only access to a polymerase chain reaction machine, funding for reagents, and DNA samples from cases and controls (Fig. 1 illustrates the methods used to detect polymorphisms). (biomedcentral.com)
  • Publications] Hidetoshi Arakawa: 'Analysis of polymerase chain reaction product by capillary electrophoresis and its application to the detection of single base substitution in genes' J.Chromatogr. (nii.ac.jp)
  • The seemingly unlimited potential of genetics to help predict who will get lung disease or who, once diagnosed with disease, will have an unfavorable prognosis has inspired many investigators to jump on the bandwagon of studying genetic polymorphisms. (biomedcentral.com)
  • demonstrated that a single base pair deletion or alteration is detectable by analyzing single-stranded conformational polymoφhisms evident in nucleic acid gel electrophoresis (Orita, et al. (google.com)
  • Terminated strands are separated by denaturing gel or capillary electrophoresis and are detected using fluorescence. (biomedcentral.com)
  • Publications] 荒川秀俊: 'Analysis of single strand conformation polymorphism by capillary electrophoresis' Journal of chromatography. (nii.ac.jp)
  • Publications] 荒川秀俊: 'Analysis of Single-Strand Conformation Polymorphisms by Capillary Electrophoresis with Laster Induced Fluorescence Detection' J.Pharm.Biomed.Anal. (nii.ac.jp)
  • The binding of CP induces a global conformational change, while the binding of L-ornithine only induces movement of the SMG loop to close and isolate the activation site. (wikipedia.org)
  • Comparison of these structures with the structures of OTCase complexed with the bisubstrate analogue PALO or CP and L-norvaline reveals that binding of the first substrate, CP, induces a global conformational change involving relative domain movement, whereas the binding of the second substrate brings the flexible SMG loop, which is equivalent to the 240s loop in aspartate transcarbamylase, into the active site. (proteopedia.org)
  • Changes to a single nucleotide, known as single nucleotide polymorphism (SNP) is one of the major types of variants identified in the human genome. (biomedcentral.com)
  • A single DNA strand with a mutation or nucleotide polymorphism has a different conformation from its wild-type counterpart, and these conformational differences result in different electrophoretic mobility. (bvsalud.org)
  • Because these markers flank the BRCA2 gene, we intensively examined a mutation of the gene through all coding exons and exon-intron junctions by PCR-single-strand conformational polymorphism analysis under two different assays. (aacrjournals.org)
  • p53 mutational status was determined for 1458 incident cases of colon cancer using single-strand conformational polymorphism/sequencing of exons 5-8. (aacrjournals.org)
  • Using intron-based exon-specific primers, we amplified exons 23-32 from genomic DNAs, screened these fragments by single-stranded conformational polymorphism analysis, and sequenced indicated exons. (osti.gov)
  • Genetic polymorphism of CYP4A11 and CYP4A22 genes and in silico insights from comparative 3D modelling in a French population. (harvard.edu)
  • We show, however, that plants of this genus possess two other linked genes that exhibit patterns of polymorphism and expression that are characteristic of an S locus. (plos.org)
  • Here, we performed intra- and inter-species comparative analyses of wheat and its relatives to dissect polymorphism and differentiation of the TaGW2 genes. (frontiersin.org)
  • Consequently, single locus amplification of MHC genes is hard to carry out in species with recently duplicated genes in the same MHC class, and multiple MHC loci have to be genotyped simultaneously. (biomedcentral.com)
  • Reference Strand-Mediated Conformational Analysis (RSCA), which is increasingly used in studies of natural populations with multiple MHC genes, is a genotyping method capable to provide high resolution and accuracy in such cases. (biomedcentral.com)
  • The procedure is to mutagenize a large population of worms with trimethylpsoralen and UV irradiation, set up 1152 subpopulations, screen DNA made from this library for deletions in specific genes by nested PCR , and then to recover single worms carrying the deletions through a sib-selection process. (protocol-online.org)
  • Single-strand conformation polymorphism analysis and sequencing of fragments with abnormal MYH7 gene mobility were carried out in 128 consecutive index patients with HCM. (nih.gov)
  • Abstract Single-strand conformational polymorphism analysis of the lipoprotein lipase promoter identified a T→G transition at position −93. (ahajournals.org)
  • POP™ Conformational Analysis Polymer. (thermofisher.com)
  • The technique of DNA restriction fragment length polymorphism (RFLP) analysis and linkage mapping was applied to wheat in the 1980s (Chao et al . (fao.org)
  • Genetic mapping of 262 loci derived from expressed sequences in a murine interspecific cross using single-strand conformational polymorphism analysis. (jax.org)
  • However, in a single strand conformational polymorphism analysis, direct sequencing with assistance of the heart. (nrha.org)
  • Whether the observed association results from linkage imbalance with other loci on chromosome 2 or other polymorphisms of the CTLA-4 gene or even from a preferential transfer and/or expression of one allele from a heterozygous mother to the fetus will be the subject of future investigations. (biomedsearch.com)
  • We conclude that Rfp-Y has an intermediate role in allograft rejection, likely to be attributable to polymorphism at the class I loci within this region. (biomedsearch.com)
  • Analyses of 235 polymorphic amplified fragment length polymorphisms (AFLP) loci and 700 base pairs of mitochondrial DNA control region provide the first account of genetic variation and geographical partitioning (east and west coasts of Australia, South Africa) in C. taurus . (royalsocietypublishing.org)
  • To identify susceptibility loci, association studies involve typing a genetic polymorphism in unrelated affected individuals and in a group of healthy, ethnically matched controls. (biomedcentral.com)
  • Genomic markers including restriction fragment length polymorphisms (RFLPs), short tandem repeats (STRs, also called microsatellites), insertion-deletion polymorphisms, single nucleotide polymorphisms (SNPs) and groups of markers inherited together on one chromosome as haplotypes are being used to locate disease-associated genetic loci, and studies of the association between these loci and disease are elucidating the genetic basis for disease. (cdc.gov)
  • Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. (harvard.edu)
  • A nucleic acid is combined with a double stranded nucleic acid-specific dye to form a detectable complex between the dye and one or more double stranded structures within the nucleic acid. (google.com)
  • The combination is then exposed to varying temperatures and the fluorescence emission of the dye is measured to determine the melting temperature(s) for the double stranded structures. (google.com)
  • After denaturation and bisulfite modification, double-stranded DNA is obtained by primer extension and the fragment of interest is amplified by PCR . (protocol-online.org)
  • Blastocystis is a protozoal, single-celled parasite that inhabits the gastrointestinal tracts of humans and other animals. (wikipedia.org)
  • The highly sensitive LIF-CE was applied to detection of allele specific PCR for medium-chain acyl-CoA dehydrogenase deficiency and phenylketonuria mutation, and of PCR-restriction fragment length polymorphism for mutant dive E gene. (nii.ac.jp)
  • A method and a package for identifying single nucleotide polymorphisms in complement receptor is useful in identifying individual susceptibility to a disease. (google.com)
  • The present invention relates generally to compounds and methods for identifying polymorphism in a cellular receptor, and more particularly, to compounds and methods for identifying and typing single nucleotide polymorphisms that code for a complement receptor and applying these polymorphisms to delineation of disease susceptibility and severity. (google.com)
  • The conformational change of the single strand DNA is caused by a mutation in DNA fragment. (nii.ac.jp)
  • Genetic polymorphisms may alter protein structure and function through a single nucleotide base substitution in a gene's coding region, and may increase or decrease gene expression either by affecting mRNA stability when occurring in a gene's 3´ untranslated region or by altering transcription factor binding when occurring in the 5´ promoter region. (biomedcentral.com)
  • Allelic loss, comparative genomic hybridization (CGH), single-stranded conformational polymorphism screening, CpG island methylation status, and X chromosome inactivation clonality analyses were performed. (thejns.org)
  • Because it can detect both sequence and size polymorphisms, we hypothesized that HTA is more sensitive than current methods. (ajtmh.org)
  • A single nt change in dsDNA, hard to detect. (studystack.com)
  • (a) Several methods to detect specific nucleotide changes (polymorphisms) exist. (biomedcentral.com)
  • Allele-specific oligonucleotides are then used to detect single base changes in the DNA samples. (biomedcentral.com)
  • (d) DNA sequencing can also be used to detect polymorphisms but is the most labor intensive. (biomedcentral.com)
  • Starting with a homozygous population is desirable, because DHPLC will detect polymorphisms. (plantphysiol.org)
  • Although the testing methods have undergone extensive refinements, idiosyncrasies and unexpected issues during the conduct of these studies are not unusual due to the plethora of new vehicles available for formulating test substances, changing regulatory requirements, and introducting new strain and/or species of laboratory animals as no single species or method seems to suffice for evaluating skin toxicity. (jove.com)
  • Methods: This is a retrospective single institution cohort study of 410 patients who underwent pre-transplant PFT and were followed up to 10 years post-transplant. (jove.com)
  • By using the single-strand conformational polymorphism-PCR technique and sequencing methods, we determined that 59 IRT enzymes corresponded to previously described IRT enzymes whereas 8 were new. (asm.org)
  • 24, 1998 entitled "Genetic Polymorphism in the Receptor for IgA," and U.S. provisional application Ser. (google.com)
  • No. 60/106,643 filed Nov. 2, 1998 entitled "Genetic Polymorphism in a Complement Receptor. (google.com)
  • Different alleles of the ND1 protein differed by a single amino acid substitution within this peptide sequence and were recognized bidirectionally by T cells in appropriate donor/host strain combinations. (jimmunol.org)
  • HSP90 is essential for posttranslational conformational maturation and stability of client proteins including protein kinases and transcription factors, many of which are important for the proliferation and survival of cancer cells. (plos.org)
  • Alternatively, a polymorphism may have no discernable effect on the protein product and may lie within DNA regions that are not involved in gene transcription or translation. (biomedcentral.com)
  • To provide further insight into the roles of the multiple isoforms, we mapped polymorphisms, deletions, and P -element insertions in the locus, identifying several that are largely, if not completely, isoform specific in their effects. (genetics.org)
  • Mendelian disorders result from a mutation at a single genetic locus. (glowm.com)
  • Designing primers that amplify a single MHC locus is therefore a difficult task. (biomedcentral.com)
  • A polymorphism of HRH2 (rs2607474) on the severity of gastric mucosal atrophy. (curehunter.com)
  • Most daf-2 reduction-of-function (hypomorphic) alleles form a single, approximate allelic series over a range of severity. (genetics.org)
  • Using a single-strand conformation polymorphism method, we demonstrate that a great reduction of Vα24JαQ NK T cells in the peripheral blood is an immunological hallmark of multiple sclerosis, whereas it is not appreciable in other autoimmune/inflammatory diseases such as chronic inflammatory demyelinating polyneuropathy. (jimmunol.org)
  • (b) Another means of rapid screening for DNA variations relies on detecting conformational changes in secondary structure caused by the nucleotide sequence alteration. (biomedcentral.com)
  • This graph shows the total number of publications written about "Polymorphism, Single-Stranded Conformational" by people in Harvard Catalyst Profiles by year, and whether "Polymorphism, Single-Stranded Conformational" was a major or minor topic of these publication. (harvard.edu)
  • Despite sharing identical MHC, polymorphisms among the minor histocompatibility (H) 4 Ags cause T cell-mediated chronic graft rejection and graft-vs-host disease ( 1 ). (jimmunol.org)
  • We attempted to clarify the associations of this polymorphism with the progression of gastric mucosal atrophy . (curehunter.com)
  • The H Ag polymorphisms are therefore reflected in quantitative or qualitative differences in the processed peptide/MHC ligands that profoundly influence the T cell response. (jimmunol.org)
  • Polymorphism, Single-Stranded Conformational" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)
  • Genetic polymorphisms in lung disease: bandwagon or breakthrough? (biomedcentral.com)
  • DNA that contains a sequence mutation (even a single base pair change) has a measurable mobility difference compared to wild type DNA when subjected to nondenaturing (or partially denaturing) conditions. (thermofisher.com)
  • A single nucleotide change in an enzyme recognition site would be readily detectable, because the enzyme would no longer recognize the nucleotide sequence as a cut site. (glowm.com)
  • A homozygous missense point mutation resulting in a single amino acid substitution, Arg160Cys (R160C), is associated with a heritable form of the human condition of septo-optic dysplasia (SOD). (biologists.org)