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At least 289 records · Page 16Linked to original sources
PubMed1993

An antigen processing polymorphism revealed by HLA-B8-restricted cytotoxic T lymphocytes which does not correlate with TAP gene polymorphism.

In previous studies of antigen presentation through HLA-B27, we identified a healthy person whose lymphoblastoid cells do not present three B27-restricted viral epitopes to specific cytotoxic T lymphocytes (CTL), despite adequate cell surface expression of HLA-B2702 of normal sequence. Similar findings were observed in all members of his family sharing the HLA-A3-B2702 haplotype. The original donor, NW, carries HLA-B8 on his other class I haplotype, which his daughter, HW, has inherited. We now report a failure to present an HLA-B8-restricted epitope from influenza nucleoprotein following viral infection of NW cells, although exogenous added peptide is still presented normally. However, cells from HW, which do not carry the A3-B2702 haplotype, present the expected epitope after viral infection. Another B8-restricted epitope, from human immunodeficiency virus-gag, is presented equally well by both cell lines when infected with gag-vaccinia. This antigen processing phenotype does not correlate with any of the known human TAP-1 and TAP-2 polymorphisms.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1991

Application of silver staining to the rapid typing of the polymorphism of HLA-DQ alleles by enzymatic amplification and allele-specific restriction fragment length polymorphism.

A rapid and highly sensitive silver staining method, originally developed for the detection of proteins, was slightly modified to detect nucleic acids in polyacrylamide gels. The second exons of the histocompatibility antigen HLA-DQA 1 and DQB 1 genes were selectively amplified from genomic DNA by the polymerase chain reaction (PCR). Digestion of the PCR products by endonucleases, followed by their size-separation on polyacrylamide gels and visualization by silver staining, allowed us to define the HLA-DQ alleles of the genomic DNA. The intensity of staining of digested PCR-amplified DNA is linear from at least 8 to 18 ng for fragments of lengths ranging from approximately 40 to 200 bp. Thus, silver staining in combination with PCR and allele-specific restriction fragment length polymorphism provides a simple, safe, and rapid method for accurate definition of HLA-DQ alleles at the nucleotide level in the clinical typing laboratory.

Base Sequence↗
PubMed1987

Adaptive significance of amylase polymorphism in Drosophila. I. The geographical pattern of allozyme polymorphism at the amylase locus in Drosophila subobscura.

Allelic variation at the Amy locus was studied in eight natural populations from the central and northern range of D. subobscura, and the geographical pattern of Amy polymorphism over the range of this species was described. Even though regional and local differences in gene frequencies were found, in general the same alleles occur at high, intermediate and low frequencies, in nearly all populations. There are no significant differences in allele frequencies, but there is significant difference in the degree of heterozygosity among groups of populations from the northern, central and southern range. An analysis of population subdivision indicates that heterogeneity within populations is higher than between populations. Genetic distance values indicate that there is a variable degree of geographical differentiation between local populations. Variability within and between continental and insular populations is also discussed.

Adaptation, Physiological↗
PubMed1991

Detection of frequent BglII polymorphism by polymerase chain reaction and TaqI restriction fragment length polymorphism for 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase at the human HSD beta 3 locus (1p11-p13).

Analysis of amplified polymerase chain reaction products of 575 bp from the fourth exon of the human type I 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase gene at locus HSD beta 3 1p11-p13, reveals a frequent two-allele polymorphism at codon Leu338 due to a silent substitution of T by C, thus creating a BglII site leading to 371- and 204-bp fragments. Southern blot analysis of BglII-digested DNA from 57 individuals using a genomic probe detects two allelic fragments of 5.3 kb and 0.77 kb, respectively, while two allelic fragments of 3.7 kb and 3.4 kb are obtained in TaqI digests with multiple constant bands, as also observed with BglII digests.

Bacterial Proteins↗
PubMed1982

Human chromosomal polymorphism. II. Chromsomal C polymorphism in Mongoloid populations of Central Asia.

C polymorphism of chromosomes 1, 9 and 16 was studied in 447 Mongoloids of Central Asia living under different ecological conditions; two highland (Kirghiz) and three steppe (Kazakh, Mongolian, and Dungan) populations. C band sizes were estimated according to the semiquantitative 5-level method of Patil and Lubs (1977). All the ethnic groups studied showed statistically significant homogeneity in the frequency of C variants. It is suggested that chromosomal C-heterochromatin material has no selective value in the process of human adaptation to extreme high-altitude factors.

Adolescent↗
PubMed1994

New murine polymorphisms detected by random amplified polymorphic DNA (RAPD) PCR and mapped by use of recombinant inbred strains.

Oligonucleotide primers of random sequence that were 12 bases in length, 58% in GC content, and lacking internal palindromes were designed. By random amplified polymorphic DNA (RAPD) PCR, these primers were used to survey for DNA variations between the progenitors of the mouse AXB and BXA recombinant inbred sets (A/J and C57BL/6J). We identified 17 DNA variants detected by 10 primers. Map positions for these variants were determined by comparing their strain distribution patterns in the AXB, BXA recombinant inbred sets with strain distribution patterns of previously published loci. When necessary, BXD and NXSM recombinant inbred sets were also used. These 17 new loci mapped to 12 chromosomes. The 10 primers were also used to survey 20 inbred mouse strains including the progenitors of other recombinant inbred sets and four mouse strains recently inbred from the wild (CAST/Ei, MOLF/Ei, PERA/Ei, and SPRET/Ei).

Animals↗
PubMed1980

An electrophoretic polymorphism that mimics a true genetic polymorphism in Triturus cristatus carnifex (Amiphibia, Urodela).

Phosphoglucomutase electrophoretic patterns have been studied in 60 tail homogenates of Triturus cristatus carnifex. Our results show that the same sample produces a different electrophoretic pattern with homogenate ageing; a new band of intermediate mobility appears, together with the one produced by the fresh preparation. The phenomenon can mimic a true genetic polymorphism when differently stored samples are analyzed.

Animals↗
PubMed1995

Alpha-1-antichymotrypsin bi-allele polymorphism, apolipoprotein-E tri-allele polymorphism and genetic risk of Alzheimer's syndrome.

The alpha1-antichymotrypsin and apolipoprotein-E polymorphisms were investigated in patients suffering from Alzheimer's syndrome and non-demented psychiatric inpatients as controls. The apolipoprotein E allele 4, well known as risk factor, tended to be elevated in the index group. The frequency of the alpha1-antichymotrypsin allele A was significantly increased in patients with Alzheimer's syndrome: 0.647 vs. 0.483 (chi-square test, p < 0.05). We conclude that, apart from the apolipoprotein E allele 4, the alpha1-antichymotrypsin allele A possibly represents a second genetic factor increasing individual's risk for Alzheimer's syndrome.

Aged↗
PubMed2003

Detection of single nucleotide polymorphism (SNP) controlling the waxy character in wheat by using a derived cleaved amplified polymorphic sequence (dCAPS) marker.

We investigated a single nucleotide polymorphism (SNP) in the Wx-D1 gene, which was found in a mutant waxy wheat, and which expressed the Wx-D1 protein (granule-bound starch synthase I) as shown by immunoblot analysis. We also assayed starch synthase activity of granule-bound proteins. Using 22 doubled-haploid (DH) lines and 172 F(5) lines derived from the wild type x the mutant, we detected SNP via a PCR-based (dCAPS) marker. Amplified PCR products from Wx-D1 gene-specific primers, followed by mismatched primers designed for dCAPS analysis, were digested with the appropriate restriction enzyme. The two alleles, and the heterozygote genotype were easily and rapidly discriminated by gel-electrophoresis resolution to reveal SNP. All progeny lines that have the SNP of the mutant allele were waxy. Integrating the results of dCAPS analysis, immunoblot analysis and assays of starch synthase activity of granule-bound proteins indicates that the SNP in the Wx-D1 gene was responsible for its waxy character. This dCAPS marker is therefore useful as a marker to introduce the mutant allele into elite breeding lines.

Alleles↗
PubMed1998

Genetic polymorphism of Leishmania species using kinetoplast DNA restriction fragment length polymorphism and cDNA probe of Leishmania donovani.

Leishmaniasis represents a group of diseases that range from simple cutaneous lesions through metastasizing diffused cutaneous to severe systemic infection depending upon the taxon to which the causative parasite belongs. Therefore, it is important to identify the infecting Leishmania. Methods presently being used, including immunology, biochemistry and molecular biology have one or the other limitations, leaving scope for the search for newer probes. This study reports the characterization of leishmania isolates both by restriction fragment length polymorphism of kinetoplast DNA (kDNA) and genomic DNA. The genomic DNA was probed with a cDNA probe B2a1. Using a kDNA restriction pattern technique, different isolates of Leishmania donovani could be differentiated from the UR6 strain of L. tropica, but it was not possible to differentiate between newer local isolates of L. donovani with most of the restriction enzymes except AluI. However, the B2a1 cDNA probe was able to differentiate these isolates effectively. Both of these techniques could differentiate newer local isolates of L. donovani from the older isolates of L. donovani from India, i.e., DD8, RMRI and SS. The Indian isolates of L. donovani could also be differentiated from isolates of L. donovani from Jeddah and Germany using both techniques. The present study indicates that the cDNA probe B2a1 can be used as an important adjunct to kDNA restriction analysis for the characterization of Leishmania species.

Animals↗
PubMed1992

Polymerase chain reaction--amplification of the coding sequence of the type X collagen gene from genomic DNA and identification of a polymorphism that changes Gly to Arg at position 545 by single-strand conformation polymorphism analysis.

Type X collagen is a specific product of hypertrophic growth plate chondrocytes and it has been suggested that mutations in the corresponding gene (COL1OA1) may be responsible for certain heritable disorders affecting growth plate cartilage such as the epiphyseal dysplasias. We have amplified the coding region of COL1OA1 employing polymerase chain reaction (PCR) of genomic DNA. Single-strand conformation polymorphism (SSCP) analysis of PCR products followed by direct sequencing identified a G to C transition that results in a Gly to Arg substitution at position 545 of the polypeptide chain. The sequence variation was confirmed by restriction enzyme analysis with BsaJ 1. Analysis of a family with multiple epiphyseal dysplasia ruled out this sequence change as a cause of the disease. This is the first report showing application of SSCP for detection of a sequence variant in COL1OA1.

Arginine↗
PubMed2003

In polymorphic genomic regions indels cluster with nucleotide polymorphism: Quantum Genomics.

Previously, we have described polymorphic frozen blocks (PFBs) within the Major Histocompatibility Complex (MHC) as regions of several hundred kilobases characterised by high nucleotide diversity, little or no recombination, duplicated segments, disease susceptibility, and human endogenous retroviruses. The nucleotide diversity profile within these PFBs shows peaks and troughs outside of the Class I genes, reflecting other important genes (or sequences) in the region. Here we show that indel density is also clustered with similar peaks and troughs. In fact, SNPs and indels are co-located within PFBs.

Databases, Nucleic Acid↗
PubMed1999

Angiotensin converting enzyme gene insertion/deletion polymorphism, angiotensinogen gene polymorphisms, family history of hypertension, and childhood blood pressure.

Earlier epidemiologic studies have yielded inconsistent results on the extent and timing of the blood pressure (BP) increase in offspring of hypertensive parents. We hypothesized that a familial influence on the BP of the offspring exists from birth on, but becomes significant only later in childhood. We studied the influence of familial occurrence of hypertension on the BP of 3596 children aged 6 to 18 years during a 6-year follow-up. In addition, we examined the possible associations of BP variations with polymorphisms of two candidate genes for hypertension, ie, those coding for the angiotensin converting enzyme (ACE) and those coding for angiotensinogen. A positive family history of hypertension was reflected as the occurrence of higher systolic BP values from the age of 9 years and upward among the females and from the age of 12 years and upward among the males. The mean differences in BP varied from 3.2 to 5.8 mm Hg (systolic) and 2.1 to 5.9 mm Hg (diastolic) between the female offspring of normotensive and hypertensive parents and grandparents. The systolic BP values were significantly higher among females with a hypertensive history in two generations in comparison with females from normotensive families. Among the male offspring of hypertensive and normotensive families, the BP differences were inconsistent. The deletion/deletion males had higher systolic BP values than those with other ACE genotypes. In contrast, variation at the angiotensinogen gene locus was not significantly associated with BP. We conclude that parental history of hypertension is a risk factor for high blood pressure among the offspring from the ages of 9 to 12 years and upward, and hypertension within two generations may enhance this effect. Although the common genetic variation of ACE may influence blood pressure in male children and adolescents, our data do not suggest a role for the common variation of the angiotensinogen gene as a BP regulator during childhood.

Adolescent↗
PubMed1992

The alcohol dehydrogenase polymorphism in natural populations of Drosophila melanogaster: ADH activity variation restriction site polymorphism and the Adh cline.

Alcohol dehydrogenase activity has been measured in 186 iso-second chromosome lines--104 from seven Australian populations and 82 from six Chinese populations. Restriction endonuclease variation in the Adh gene region in these lines has previously been described (Jiang & Gibson, 1991). The mean ADH activity of AdhF and AdhS lines was significantly higher in the Chinese samples than in the Australian samples. In each population on both continents the mean activity of the AdhF lines is significantly higher than that of the AdhS lines. Six lines homozygous for a thermostability variant, AdhFChD (detected in four of the Chinese populations), had intermediate levels of ADH activity and protein amount. In a subset of the lines with the highest and lowest levels of ADH, there was a correlation of 0.69 between ADH activity and ADH CRM. None of the restriction site variants was consistently associated with the amount of ADH activity. Associations between BamHI (-7.2), the Adh polymorphism and ADH activity suggest that there are modifiers of ADH 5' to the gene. The deletion (0.2) at position -2.8 on the restriction map (Jiang & Gibson, 1991) was associated with increased levels of ADH activity in AdhS lines from China. Two unique insertions in the gene region were associated with low activity in AdhF lines and a null activity allele had a deletion removing most of exon 2. A single line with a duplication of a part of the Adh coding region and of the 5' regulatory section had relatively high ADH activity. Considering all the data, the main factor affecting ADH activity levels in populations is the frequency of AdhF.

Alcohol Dehydrogenase↗
PubMed2002

Anorexia nervosa (restrictive subtype) is associated with a polymorphism in the novel norepinephrine transporter gene promoter polymorphic region.

Long-term weight-restored patients with anorexia nervosa (AN) have lower norepinephrine levels than controls. Since this may reflect altered reuptake by the norepinephrine transporter (NET), we hypothesised that the NET gene was involved in the genetic component of AN. PCR-amplification of an AAGG repeat island (AAGG1) in the NET gene promoter region revealed a novel 343-bp sequence with five additional AAGG repeat islands (AAGG2-AAGG6). We named the sequence from AAGG1 to AAGG6 inclusive, the NET gene promoter polymorphic region (NETpPR). A 4-bp deletion (S4) or insertion (L4) in AAGG4 resulted in the net loss or gain, respectively, of a putative Elk-1 transcription factor site. The transmission disequilibrium test(TDT) with 87 Australian trios (patient plus parents) demonstrated significant preferential transmission of L4 (McNemar's chi(2) = 7.806, df = 1, P = 0.0052, odds ratio: 2.1) from parent to child with restricting AN (AN-R), suggesting that L4 or a DNA variant in linkage disequilibrium with it, doubles the risk for developing AN-R.

Adolescent↗
PubMed1998

Random amplified polymorphic DNA and amplified ribosomal DNA spacer polymorphism: powerful methods to differentiate Streptococcus thermophilus strains.

Streptococci from different collections and dairy materials were characterized by conventional and molecular methods. After amplification of the 16S-23S rDNA spacer region, all the strains referable to the genus Streptococcus exhibited a single polymerase chain reaction (PCR) product, allowing their differentiation from enterococci. Cleaving this PCR product with Hae III, two different restriction patterns could be observed, allowing Streptococcus salivarius DSM 20560T, Strep. thermophilus NCDO 822 and two strains of Streptococcus spp. to be gathered in one group and all the other strains in another. In order to achieve strain typing, all the cultures were investigated by random amplified polymorphic DNA (RAPD)-PCR analysis employing two selected primers. The results were treated by cluster analysis, appearing significantly consistent with both the taxonomic position and the origin of the strains. Pulsed-field gel electrophoresis (PFGE) of Sma I digests of the genomic DNA from 11 representative strains with decreasing levels of RAPD similarity allowed their diversity to be confirmed, even though RAPD-PCR proved to be less discriminating than PFGE analysis. The results are discussed with reference to the capability of the analytical procedures used to aid both identification and strain typing of streptococci, as well as the taxonomic structure of the species Strep. thermophilus.

Bacterial Typing Techniques↗
PubMed2000

Rapid detection of dihydropteroate polymorphism in AIDS-related Pneumocystis carinii pneumonia by restriction fragment length polymorphism.

Sulpha agents, which act by inhibiting the enzyme dihydropteroate synthase (DHPS), are used widely for the treatment and prophylaxis of Pneumocystis carinii pneumonia (PCP). Recently, we have shown that mutations in the dihydropteroate synthase (DHPS) gene of Pneumocystis carinii f.sp hominis are associated with failure of sulpha prophylaxis and increased mortality in HIV-1 positive patients with PCP, suggesting that DHPS mutations may cause sulpha resistance. To facilitate detection of DHPS mutations we developed a restriction fragment length polymorphism (RFLP) assay, detecting mutations at codon 55 and 57 of the P. carinii DHPS gene. The RFLP-assay was compared with direct DNA sequencing on 27 PCP isolates from HIV-1 positive patients with a mixture of wildtype and mutant DHPS types. In all samples the RFLP-assay correctly identified wildtype or DHPS mutation at codon 55 or 57. Combined with DNA extraction by a Chelex-based method, this method can be performed within 1 d and allows a fast, cost-efficient and reliable method of detection of DHPS mutations in P. carinii.

AIDS-Related Opportunistic Infections↗