Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variable sites”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources

The use of recombinant DNA techniques for the diagnosis of familial hypercholesterolaemia.

In the UK, about 5% of patients with familial hypercholesterolaemia have a detectable deletion or rearrangement of part of the LDL-receptor gene. This results in the detection of shorter or abnormal sized fragments of the LDL-receptor gene in a Southern blot hybridization. This can be used to follow the inheritance of the defective gene, and for diagnosis in the families of these individuals. In the families of the rest of the patients, diagnosis may be possible using linked restriction fragment length polymorphisms (RFLPs) detected with the LDL-receptor probe. There are now ten common RFLPs of the LDL-receptor gene, with variable sites in the 3' half of the gene. Over 80% of patients are heterozygous for at least one of these RFLPs, and therefore potentially informative for DNA diagnosis. For a foetus at risk of homozygous familial hypercholesterolaemia, antenatal diagnosis may also be possible using these methods. However, family studies require samples to be available from affected or unaffected relatives of the patient, and this limits the applicability of the tests. For some mutations, the base pair change causing the defect in the LDL-receptor itself creates or destroys a site for a restriction enzyme. Such 'mutation-specific' RFLPs could be used for population screening, but so far have only been reported for the familial hypercholesterolaemia mutation that is common in Lebanon. In the future it may be possible to develop mutation-specific oligonucleotide probes for the diagnosis of familial hypercholesterolaemia. These would be appropriate for population screening or screening patients with hyperlipidaemia. This information may be useful if different mutations require different therapeutic strategies.

DNA, Recombinant↗

Clinical anatomy of the suprarenal arteries: a quantitative approach by aortography.

The angiographic visualization, arterial origin and mean diameter per age group (20-40, 41-60 years) of the suprarenal arterial vessels have been quantitatively investigated by aortography in 100 patients without suprarenal disease. Visualization of the various arteries was achieved in a percentage substantially comparable to the anatomic data of the literature, though with lower detection of the superior suprarenal vessels. A variable site of origin was present particularly for the superior and middle suprarenal vessels compared to the inferior suprarenal arteries and possible embryological reasons and clinical implications are discussed. Statistically significant differences were found in the mean diameter of each arterial vessel in all the subjects examined, thus substantiating the concept of differential arterial supply to various portions of the gland. Age-related changes were demonstrated in the right middle suprarenal artery, suggesting a predominant role of this vessel in the physiological adaptation of the blood supply to the gland with increasing age.

Adrenal Glands↗

A novel mitochondrial intergenic spacer reflecting population structure of Pacific oyster.

Nucleotide sequence divergence in a novel major mitochondrial DNA intergenic spacer (IGS) of Pacific oyster Crassostrea gigas was analyzed for 29 cultured individuals within the Goseong population (Korea). A total of 7 variable sites were detected within the IGS, and the relative frequency of nucleotide alteration was determined to be 1.16%;. All alterations were due to a single nucleotide substitution, and 5 transitions and 2 transversions were observed. Among 29 specimens, only 8 haplotypes could be identified, and 6 of the haplotypes were unique to particular specimens. Pairwise genetic diversity of all 8 haplotypes was calculated to be 0.412+/-0.134 from multiple sequence substitutions based on the two-parameter model. The phylogenetic tree obtained for these haplotypes according to the neighbor-joining method illustrated a single cluster of linkages, which comprised 5 haplotypes associated with 23 specimens, while the other 3 haplotypes associated with 6 specimens were scattered. The results indicate that the IGS is higher polymorphic and thus more suitable as a genetic marker for population structure analysis of Pacific oyster than the mtDNA coding regions, such as cytochrome c oxidase I and 16S ribosomal RNA genes.

Animals↗

The power of relative rates tests depends on the data.

One of the most useful features of molecular phylogenetic analyses is the potential for estimating dates of divergence of evolutionary lineages from the DNA of extant species. But lineage-specific variation in rate of molecular evolution complicates molecular dating, because a calibration rate estimated from one lineage may not be an accurate representation of the rate in other lineages. Many molecular dating studies use a "clock test" to identify and exclude sequences that vary in rate between lineages. However, these clock tests should not be relied upon without a critical examination of their effectiveness at removing rate variable sequences from any given data set, particularly with regard to the sequence length and number of variable sites. As an illustration of this problem we present a power test of a frequently employed triplet relative rates test. We conclude that (1) relative rates tests are unlikely to detect moderate levels of lineage-specific rate variation (where one lineage has a rate of molecular evolution 1.5 to 4.0 times the other) for most commonly used sequences in molecular dating analyses, and (2) this lack of power is likely to result in substantial error in the estimation of dates of divergence. As an example, we show that the well-studied rate difference between murid rodents and great apes will not be detected for many of the sequences used to date the divergence between these two lineages and that this failure to detect rate variation is likely to result in consistent overestimation the date of the rodent-primate split.

Evolution, Molecular↗

Polymorphisms of the glucocorticoid receptor gene in laboratory and wild rats: steroid binding properties of trinucleotide CAG repeat length variants.

The polyglutamine tract, beginning at codon 75 in the N-terminal modulatory domain of rat glucocorticoid receptor (rGR), was analyzed in 61 inbred strains and 155 wild caught Rattus norvegicus. A discontinuous distribution of repeat lengths was found (7, 17-23 repeats). To investigate the possible significance of this distribution, full-length rGR cDNAs with 7, 18, 20, and 21 CAG repeats were expressed in CV-1 cells, and the resulting GR protein analyzed by Western blots and extensive Scatchard analyses. The quantity and steroid binding capacity of GR, together with the binding affinities for dexamethasone and corticosterone, were found to be indistinguishable for the four repeat alleles. From the sequencing of four inbred strains CAG repeat variants were found to be flanked by silent allelic substitutions at nucleotide positions 198, 531, and 711. The four variable sites extended over 471-519 bp of coding sequence, forming six Grl haplotypes. The results are discussed in the light of genetic studies on the Milan hypertensive and normotensive strains of rat. Codon sequence of rat GR required amendment at the following residues: D98, G226, D260, P600, and F602.

Alleles↗

Genotype of Giardia intestinalis isolates from children and dogs and its relationship to host origin.

The presence of human Giardia in several animals suggests a zoonotic transmission. We studied G. Intestinalis isolates obtained from: children with diarrhea (n=6), asymptomatic children (n=7), axenic cultures (n=7) and dogs (n=11). The sequence corresponding to 16 S rRNA was amplified by PCR, sequenced and compared with genotypes A, B and Dog sequences reported in the Gene Bank database. Results show that 9/20 (45%) of children isolates belonged to genotype A and 11/20 (55%) showed some variable sites, allowing classification in three arbitrary clusters: A1, A2 and A3. In addition 7/11 (63%) of dog isolates were genotype A, including those dogs that lived in the same locality as the children lived, while 4/11 (37%) belonged to an arbitrary A4 cluster living in a different locality. In this study, genotype A was associated with samples from children and dogs, and, therefore, we could infer zoonotic transmission as a way of getting the disease.

Animals↗

Genetic variation in alpha(1)-antichymotrypsin and its association with Alzheimer's disease.

Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by extracellular neuritic plaques and intracellular neurofibrillary tangles in brain parenchyma. Alpha-1-antichymotrypsin (ACT) is a component of plaque cores, can bind to Abeta, and has been proposed as a possible candidate gene for AD susceptibility. The genetic association between the ACT codon -17*A allele of the signal peptide polymorphism and AD has been shown in some, but not in all studies. One hypothesis is that the ACT codon -17*A allele is in linkage disequilibrium with unknown functional mutation(s) in the ACT gene. This study was undertaken to identify new mutation(s) in the ACT gene by PCR-SSCP-sequencing and, in conjunction with known mutations, to assess their role in affecting the risk of AD. A total of seven new point mutations were observed: 5'UTR(A-->G), Asp128Asn(G-->A), Ser250Ser(C-->T), Leu301Pro(T-->C), Thr324Thr(A-->G), G-->A in intron 4, and 3'UTR C-->A. Of these, mutations at codon 250, codon 324, intron 4 and 3'UTR showed a frequency of 1% or more. Of the known mutations, Thr-17Ala(A-->G), Lys76Lys(A-->G) and Leu241Leu(G-->A) occur at a polymorphic level. The ACT codon -17*A allele was associated with increased risk of AD (OR for AA vs TT: 1.71; 95% CI: 1.16-2.53; P=0.007), especially in the presence of the APOE*4 allele (OR for AA vs TT: 2.35; 95% CI: 1.13-4.85; P=0.02). The codon 241*A allele and the codon 250*T allele were associated with protective effects against AD (OR: 0.36; 95% CI: 0.13-0.86; P=0.02) (OR:0.39; 95% CI: 0.18-0.85; P=0.02). irrespective of the APOE*4 status. The codon 324*G allele was associated with a marginal protective effect (OR:0.57; 95% CI: 0.26-1.26; P=0.17). While the codon 241*A allele was in linkage disequilibrium with the codon -17*A allele, the codon 250*T and codon 324*G alleles were non-randomly associated with the codon -17*T allele. In contrast, the codon 76*G (OR:1.34; 95% CI: 0.92-1.95; P=0.13), codon 227*G (OR:3.96; 95% CI: 0.83-18.8; P=0.08) and intron 4*G (OR:1.47; 95% CI: 0.88-2.29; P=0.15) alleles were associated with a modest risk of AD, and all were in linkage disequilibrium with the codon -17*A allele. EH-based haplotype analysis showed that certain haplotypes are associated with either higher or lower risk of AD. Our data indicate that the ACT gene harbors several potentially important variable sites, which are associated with either an increased or decreased risk of AD. The non-random combination of risk and protective alleles may explain, in part, why the association studies regarding the ACT codon -17*A have been inconsistent, especially if the frequency of other ACT mutations varies between populations.

3' Untranslated Regions↗

Sequence polymorphism at the human apolipoprotein AII gene ( APOA2): unexpected deficit of variation in an African-American sample.

A 3.3-kb region, encompassing the APOA2 gene and 2 kb of 5' and 3' flanking DNA, was re-sequenced in a "core" sample of 24 individuals, sampled without regard to the health from each of three populations: African-Americans from Jackson (Miss., USA), Europeans from North Karelia (Finland), and non-Hispanic European-Americans from Rochester, (Minn., USA). Fifteen variable sites were identified (14 SNPs and one multi-allelic microsatellite, all silent), and these sites segregated as 18 sequence haplotypes (or nine, if SNPs only are considered). The haplotype distribution in the core African-American sample was unusual, with a deficit of particular haplotypes compared with those found in the other two samples, and a significantly (P<0.05) low level of nucleotide diversity relative to patterns of polymorphism and divergence at other human loci. Six of the 14 SNPs, whose variation captured the haplotype structure of the core data, were then genotyped by oligonucleotide ligation assay in an additional 2183 individuals from the same three populations (n=843, n=452, and n=888, respectively). All six sites varied in each of the larger "epidemiological" samples, and together, they defined 19 SNP haplotypes, seven with relative frequencies greater than 1% in the total sample; all of these common haplotypes had been identified earlier in the core re-sequencing survey. Here also, the African-American sample showed significantly lower SNP heterozygosity and haplotype diversity than the other two samples. The deficit of polymorphism is consistent with a population-specific non-neutral increase in the relative frequency of several haplotypes in Jackson.

Alleles↗

Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1.

Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degree of linkage disequilibrium in a candidate gene region. In this study, we scanned sequence variants in a 2.2-kb promoter sequence and all 13 exons (totalling 3.3 kb) of the matrix metalloproteinase-9 gene, which is associated with coronary heart disease and a candidate for other diseases involving connective tissue remodelling, such as cancer metastasis. The sequences had a total of ten variable sites, four in the promoter, five in the coding region (three of which alter the amino acid encoded) and one in the 3' untranslated sequence. Sequence inspection suggests that some of the variants will have a functional impact on either level of expression or enzymatic activity. Tight linkage disequilibrium was detected between variants across the entire length of the gene (approximately 9 kb), and frequencies of different haplotypes were determined. The data provide an essential tool for studies of the possible contribution of genetic variation at the matrix metalloproteinase-9 locus to genetically determined susceptibility to a number of important diseases. The results also provide experimental data on the extent of linkage disequilibrium in the general population, which is yet to be resolved.

3' Untranslated Regions↗

Phylogeny and molecular evolution of Tetraogallus in China.

In total, 535 nucleotides in the mtDNA cytochrome b have been sequenced in Tetraogallus. The 53 variable sites define 16 haplotypes in 53 Tetraogallus himalayensis samples, 1 haplotype in 2 T. altaicus samples, and 6 haplotypes in 19 T. tibetanus samples. The lowest genetic distance is between T. himalayensis and T. altaicus (0.011). The divergent time is 0.69 Ma BP between T. himalayensis and T. altaicus, 4.06 Ma BP between T. himalayensis and T. tibetanus, and 4.19 Ma BP between T. altaicus and T. tibetanus. The evidence of this work showed that T. altaicus should fall under the dark-bellied group of Tetraogallus. The dark-bellied and white-bellied speciation first occurred along with the uplift of the Qinghai-Tibet Plateau. A maximum glacier (0.80-0.60 Ma BP) led to the formation of T. altaicus.

Animals↗

Genetic variations of 13 indigenous Chinese goat breeds based on cytochrome B gene sequences.

Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F (st)=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.

Animals↗

[125I]iodotamoxifen cytotoxicity in cultured human (MCF-7) breast cancer cells.

We evaluated the uptake and radiotoxicity of [125I]iodotamoxifen (125ITAM) in MCF-7 human breast cancer cells in the presence or absence of excess non-radioactive estradiol (E2) or iodotamoxifen (ITAM). Studies in cells under wash-out conditions and in nuclei isolated from previously exposed cells showed that 125ITAM binds estrogen receptor (ER) and antiestrogen binding sites (AEBS) and has the capacity for considerable non-specific binding. The radiotoxicity of 125ITAM was a complex function related to ER content and/or function as well as interactions with ER, AEBS and non-specific binding. Addition of E2 or ITAM abolished ER mediated cell killing. ITAM but not E2 abolished AEBS mediated cytotoxicity. Non-specific binding accounted for considerable cytotoxicity. Although these studies confirm the radiotoxicity of nuclear bound 125I, multiple nuclear binding sites, variability in ER content and function and non-specific binding will all adversely influence ultimate clinical efficacy.

Breast Neoplasms↗

Molecular characterization of carrier rabies isolates.

We compared the genomes of nine dog rabies virus isolates using two molecular methods. The viruses used in the comparison included three Ethiopian rabies strains from carrier dogs, a street strain from a rabid dog from the same geographic area, two saliva isolates made from an experimentally infected carrier dog, the virus isolated from the tonsil of this carrier dog at necropsy, and two laboratory strains. We produced overlapping polymerase chain reaction (PCR) segments spanning 97% of the genome. Restriction analysis of these PCR products with AvaII, Bcll, and BamHI detected 39 variable sites representing 668 nucleotides (nt) or 5.5% of the genome. We also compared the DNA and the deduced peptide sequences of a 200-nt segment of the 3' end of the rabies nucleoprotein gene. Previous work with these Ethiopian carrier viruses and the endemic street strain had failed to show any differences among them. Both restriction mapping and sequence analysis of 200 nt of the nucleoprotein gene allowed us to individually identify these isolates. Phylogenetic analyses of these data sets showed only the two saliva isolates of the experimentally infected carrier dog to be identical. Each of the viruses in this study, including the one isolated from the tonsil of the experimentally infected carrier dog, could be distinguished by these techniques.

Animals↗

Tumor necrosis factor microsatellites in four European populations.

The human genome contains a large number of interspersed simple repeat sequences that vary in length among individuals and can therefore serve as highly informative polymorphic markers. Several such variable sites (microsatellites) have been described within the TNF genes within the MHC. In this study, individuals from four Caucasian populations have been typed for three TNF-associated microsatellites in order to define their haplotypes. Of the 208 possible haplotypes, eight exist at a high frequency in all populations and account for approximately 60% of the haplotypes studied, but with marked variations in their frequencies among populations. A few population/sample-specific haplotypes have been identified. The ability of alleles to define haplotypes uniquely varies not only among the loci, but also among the alleles: some alleles displaying complete gametic association (linkage disequilibrium) and others displaying very little.

Alleles↗

Quality of life in patients treated for head and neck cancer: a follow-up study 7 to 11 years after radiotherapy.

PURPOSE: To compare health-related quality of life factors in 845 head and neck cancer patients randomized to receive either conventional radiotherapy (2 Gy, 5 days-a-week) or a hypofractionated regimen (2.35 Gy, 4 days-a-week), a follow-up study was carried out 7 to 11 years after treatment in the surviving patients, representing 30% of the original patient number. METHODS AND MATERIALS: The cancer-specific EORTC Core Quality of Life Questionnaire (30 item version; the EORTC QLQ-C30) and a 19 item head and neck cancer-specific questionnaire were mailed to the 245 surviving patients of the trial. The EORTC QLQ-C30 is comprised of six multi-item function scales, three symptom scales, and six single items which assess both symptoms and economic consequences of the disease. Two hundred and four patients (83%) completed the questionnaire. The two groups of patients (N = 103 and N = 101) treated by different fractionating schedules, were comparable with regard to sociodemographic variables, tumor site, treatment variables (including different types of surgical treatment), and secondary primary cancers. Patients in the conventional group had more advanced disease and a higher recurrence rate compared to patients in the hypofractionated group. RESULTS: Unexpectedly, patients in the hypofractionated group, reported similar or better quality of life compared to patients in the conventional fractionated group. Patients in both groups described a high level of symptoms, like dryness in the mouth and mucus production. Clinical and sociodemographic variables did not explain variance in social function, emotional function or fatigue, except for the type of surgery performed, which significantly influenced the patients' emotional function. CONCLUSION: Long-term survivors of head and neck cancer reported a high level of disease and treatment related symptoms. Emotional function was significantly influenced by the type of surgical procedure. Strategies for future trials in head and neck cancer should continue to attempt to stress conservative surgical approaches and coordinated adjuvant therapy to maximize local regional control and quality of life. Functional and emotional outcome are important parameters which should prospectively be evaluated in future clinical trials in head and neck cancer.

Adult↗

The hemolysin/bacteriocin produced by enterococci is a marker of pathogenicity.

The hemolysin/bacteriocin produced by some strains of Enterococcus faecalis is active in the lysis of human, rabbit, and horse erythrocytes, but not those from sheep. In this study, we determined that 20% of clinical enterococcal isolates tested in the clinical microbiology laboratory produced hemolysin and that pathogenic human E. faecalis were more likely to be hemolysin-producing isolates. Among the organisms isolated from different anatomic sites, variability in the degree of hemolysin production existed. We used an isogenic pair of E. faecalis organisms to demonstrate that hemolysin production was due to a hemolysin/bacteriocin determinant transmissible by a plasmid and was not strain dependent. This determinant may be linked to antibiotic resistance genes in some instances. Also, the erythrocyte lysis occurred only when hemolysin was in the presence of E. faecalis organisms, suggesting a bacterial cell dependency for activity of the hemolysin.

Bacteremia↗

Convergence in ascospore discharge mechanism among pyrenomycete fungi based on 18S ribosomal RNA gene sequence.

Fungi of the class Pyrenomycetes (Ascomycotina) form a morphological series ranging from those that shoot ascospores (sexual spores) forcibly from the ascus (spore sac) to fungi that ooze ascospores or have no obvious mechanism for ascospore release. Did forcible ascospore discharge evolve within these pyrenomycetes, or has it been lost in the group? We determined the sequences of the 18S ribosomal RNA gene from three fungi and used these, along with six sequences from our previous work and three sequences from GenBank, to infer the phylogeny of 12 ascomycetes with various ascospore discharge mechanisms. The 1720 base pairs of sequence data per fungus yielded 361 variable sites, 198 phylogenetically informative sites, and a single most parsimonious tree requiring 562 nucleotide changes. The tree shows that the capacity to shoot ascospores into the air has been lost or, less probably, gained repeatedly and independently. Species lacking forcible ascospore discharge are intercalated among three lineages of species with forcible discharge. In this tree, seven of the nine internal branches appeared in 95% or more of 500 bootstrap replicates. A tree uniting the fungi with forcible ascospore discharge into a monophyletic group required 45 additional steps and fit significantly less well with the data than the most parsimonious tree, based on a maximum likelihood test. Two of the fungi whose sequence we determined, Pseudallescheria boydii and Sporothrix schenckii, are not closely related to one another, even though both are human pathogens and both are from pyrenomycete lineages lacking forcible ascospore discharge. Using the well-resolved, most parsimonious tree, we inferred base substitution patterns in the 18S rRNA. The transition-to-transversion ratio was 1.9. Of all 12 possible substitutions, 29% were from U to C. At sites corresponding to yeast stem positions, A to G transitions were frequent, perhaps compensating for some of the U to C changes, and maintaining secondary structure base pairing (A to G:U to C = 3:4). In loop or bulge positions without secondary structure base pairing, U to C transitions were still frequent, but A to G transitions were rare (A to G:U to C = 1:5).

Ascomycota↗

Molecular characterization and evidencing of the porcine CRH gene as a functional-positional candidate for growth and body composition.

Corticotropin-releasing hormone (CRH), a major regulator of neuroendocrine response to stress, is involved in the control of energy balance and thus may affect body composition and growth. The porcine CRH (pCRH) gene was studied as a comparative-positional candidate for QTL for longissimus muscle area, average backfat thickness, carcass length, and average daily gain on test on porcine chromosome 4. Sequence of the complete transcriptional unit of pCRH gene spanning 2068bp was determined along with 582bp of the 5'-flanking region. Cross-species sequence comparison revealed a number of potential regulatory regions including an intronic evolutionary conserved region and an adjacent CpG island that may control cell-type specific expression of the CRH gene. A SNP in exon 2 (c.+83G>A) leading to a non-conservative amino acid exchange (p.28Arg>Gln) in the prohormone was identified that is segregating in the DUMI resource population. Linkage and association analysis based on this SNP revealed that for all four traits the pCRH gene falls in the QTL peak area and that the c.+83G>A SNP shows a highly significant additive effect (p<0.0001). Physical mapping using the IMpRH panel assigned the pCRH gene to interval SW724-S0107, promoting the gene as a positional candidate also for QTL identified in other porcine resource populations. Additional four variable sites were identified that segregate in commercial pig breeds. Particularly interesting is a SNP (g.233C>T) in the 5'-flanking region that occurred in an evolutionary conserved motif. The knowledge of the DNA-variation of pCRH gene will facilitate follow-up studies necessary to provide definite genetic evidence of the effect of pCRH gene on body composition and growth.

Amino Acid Sequence↗