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PubMed2004

Sequence characterization, polymorphism and chromosomal localizations of the porcine PSME1 and PSME2 genes.

The full-length cDNA of porcine genes (PSME1 and PSME2) encoding proteasome activators PA28alpha- and beta-subunits were obtained by the rapid amplification of cDNA ends (RACE). The nucleotide sequences and the predicted protein sequences share high sequence identity with their mammalian counterparts. The reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that porcine PSME1 and PSME2 genes are expressed in all eight tissues studied (liver, spleen, bladder, small intestine, kidney, heart, skeletal muscle and lung). The full-length genomic DNA of the porcine PSME1 and PSME2 genes were amplified by PCR. These two genes shared the same structure and were similar in size. A C/T single nucleotide polymorphism in PSME1 intron 8 detected as an SphI PCR-restriction fragment length polymorphism (PCR-RFLP) shows allele frequency differences between Meishan, Tibetan, Large White, Qingping, and Duroc pigs. The association analysis using two experimental GY selection lines selected for growth rate or leanness suggested that the PSME1 genotype was associated with weaning weight. Analyses of somatic cell hybrid (SCHP) and radiation hybrid (IMpRH) panels revealed that both genes map to SSC7q15.3-q21 and closely linked to the T-cell receptor alpha (TCRA) gene.

Animals↗
PubMed2005

Polymorphism, linkage mapping and expression pattern of the porcine skeletal muscle glycogen synthase (GYS1) gene.

The glycogen synthase gene (GYS1), which encodes the rate-limiting enzyme for glycogen synthesis of skeletal muscle, is a promising candidate gene for traits related to skeletal muscle in pigs. In this study, a G/A single nucleotide polymorphism in GYS1 intron 7 detected as a FokI PCR-restriction fragment length polymorphism (PCR-RFLP) showed allele frequency differences among five Chinese indigenous pig breeds and three western commercial pig breeds. Linkage analysis assigned the gene GYS1 to marker interval SW1302-SW1473 on SSC6 in a three-generation Meishan X Large White reference family. The results of association analysis and interval mapping suggested that the FokI PCR-RFLP polymorphism might be linked with the quantitative trait loci affecting carcass traits detected on SSC6 in the F2 intercross pedigree. The reverse transcriptase-polymerase chain reaction revealed that the porcine GYS1 gene was expressed in spleen, lung, liver, kidney, small intestine, skeletal muscle, heart and stomach, with the highest expression in skeletal muscle.

Animals↗
PubMed2006

Association of specific p53 polymorphisms with keratosis in individuals exposed to arsenic through drinking water in West Bengal, India.

Although, more than six million people are endemically exposed to inorganic arsenic in West Bengal, India by drinking heavily contaminated groundwater, only about 300,000 people show arsenic induced skin lesions. This suggests that genetic variability plays an important role in arsenic induced skin lesions and skin cancers. Arsenic induced keratosis is considered as a possible precancerous state of in situ carcinoma. Several reports have suggested the role of p53 polymorphisms as potential marker for risk assessment of different types of cancers. This prompted us to study the association of three p53 polymorphisms with arsenic induced keratosis in a population exposed to arsenic through drinking water. A total of 366 unrelated individuals (177 individuals with arsenic induced keratosis and 189 individuals with no arsenic induced skin lesions) were recruited from North 24 Parganas, Nadia and Murshidabad districts between January 2003 and February 2005 for the study of the genotypic distribution of three p53 polymorphisms (16bp duplication at intron 3, codon 72 Arg/Pro and G>A at intron 6 [nt 13,494]) by PCR-RFLP. The arginine homozygous genotype at codon 72, and homozygous genotype of no duplication polymorphism at intron 3 were over represented in the individuals with keratosis compared with individuals with no skin lesions (OR=2.086; 95% CI=1.318-3.299 and OR=2.086; 95% CI=1.257-3.457, respectively). This study indicates that individuals carrying the arginine homozygous genotype at codon 72, and/or no duplication homozygous genotype at intron 3 are at risk for the development of arsenic induced keratosis.

Adult↗
PubMed2006

Genetic susceptibility to Tardive Dyskinesia in chronic schizophrenia subjects: V. Association of CYP1A2 1545 C>T polymorphism.

Tardive dyskinesia (TD) is an iatrogenic disorder observed in approximately 20-30% of schizophrenia patients on long-term treatment with typical antipsychotic drugs. CYP1A2 is involved in the metabolism of atypical antipsychotic drugs such as clozapine and olanzapine. It is not directly involved in the metabolism of typical antipsychotic drugs, but gains importance when the schizophrenia patients are under long-term chronic treatment, acting as a low-affinity high-capacity metabolizing enzyme. In this study, we have completely sequenced the coding region to ascertain the presence of common coding polymorphisms and their role if any in susceptibility to TD and schizophrenia. Four previously reported polymorphisms, CYP1A2*1F (intron A), rs2472304 & rs3743484 (intron D) and rs2470890 (CYP1A2 1545 C>T) in exon 7 were identified. We further investigated whether the CYP1A2 1545 C>T polymorphism has any role to play in susceptibility to TD and in schizophrenia per se. Association of this single nucleotide polymorphism with TD (P=0.03) and schizophrenia (P=0.04) was observed, but was rendered insignificant after corrections for multiple comparisons.

Antipsychotic Agents↗
PubMed2004

Tubulin-based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species.

TBP (tubulin-based polymorphism) is a new molecular marker based tool that relies on the presence of intron-specific DNA polymorphisms of the plant beta-tubulin gene family. The multifunctional and essential role of the tubulin proteins is reflected in the conservation of regions within their primary amino acid sequence. The ubiquitous nature of this gene family can be exploited using primers that amplify the first intron of different beta-tubulin isotypes, revealing specific fingerprints. The method is rapid, simple, and reliable and does not require preliminary sequence information of the plant genome of interest. The ability of TBP to discriminate between accessions and species in oilseed rape, coffee, and lotus is shown. In all cases, TBP was able to detect specific genetic polymorphisms in the context of a simplified and readily appreciable pattern of DNA amplification. The application of TBP for assessing genetic diversity and genome origins in disseminated plant landraces rather than in highly inbred cultivated species is also discussed.

Brassica napus↗
PubMed1998

Nucleotide polymorphisms in the alpha2 gene define multiple alleles that are associated with differences in platelet alpha2 beta1 density.

Three allelic differences in the alpha2 gene are associated with expression levels of the alpha2beta1 integrin on the platelet surface. We have previously defined two linked silent polymorphisms in the alpha2 gene coding region at nucleotides 807 (C or T) and 873 (G or A). We have now identified one rarer nucleotide polymorphism in the coding region at nucleotide 837 (T or C) and four additional linked polymorphisms within the introns that flank these coding sequences. Moreover, we have determined that the alloantigenic Br polymorphism, which resides in a distal coding region at nucleotide 1648, is also linked to the 837 polymorphism. Thus, three alpha2 gene alleles, defined by eight nucleotide polymorphisms, have now been discovered. Allele 1 (807T/837T/873A/Brb) is associated with increased levels of alpha2beta1; allele 2 (807C/837T/873G/Brb) and allele 3 (807C/837C/873G/Bra) are each associated with lower levels of alpha2beta1. Finally, we also show here that the rate of platelet attachment to type I collagen in whole blood under conditions of high shear rate (1,500/s) is proportional to the density of alpha2beta1 receptors on the platelet surface. Thus, the density of platelet alpha2beta1 could have an important impact on platelet adhesion to collagen in whole blood and therefore on platelet function in vivo, contributing to an increased risk of thrombosis or to bleeding in relevant disease states.

Alleles↗
PubMed2001

Characterization of the annexin I gene and evaluation of its role in type 2 diabetes.

In a previous study, we identified suggestive linkage between type 2 diabetes and a locus on chromosome 9p13-q21. This region contains the gene annexin I (ANXA1), encoding a protein suggested to be involved in both insulin secretion and insulin action. In this study, we sequenced the exon/intron boundaries of the human ANXA1 gene and performed mutation screening in 41 individuals from the initial linkage study. We identified five single nucleotide polymorphisms A58G, A401G, intronic variance sequence (IVS)8-28A/G, IVS11 +31A/G, and IVS12-11T/G, which were further tested for association to diabetes in 197 parent/offspring trios using the transmission disequilibrium test. No significant association with type 2 diabetes was observed, although the common A allele of the +58A/G variant gave a 22:12 transmission distortion (P = 0.12). This variant was further genotyped in 481 case and control subjects, but no difference in allele, genotype, or haplotype frequencies were observed between the groups. Further, a novel polymorphic (CA)(15-25) repeat in intron 11 was genotyped in the subjects included in the initial linkage study. No improvement of the original finding was observed. We therefore concluded that the ANXA1 gene is unlikely to harbor variants that contribute to risk of type 2 diabetes.

Alleles↗
PubMed2004

[Association of p53 gene polymorphism with susceptibility to ovarian cancer].

OBJECTIVE: To investigate the association of p53 codon 72 and p53 intron 3 (PIN3) polymorphism with susceptibility to epithelial ovarian cancer in northern Chinese women. METHODS: p53 codon 72 and PIN3 genotyping was performed by DNA fragments with sequence specific primers among 124 patients with ovarian cancer and 128 healthy control women. RESULTS: The frequency of the Pro and Arg allele among ovarian cancer patients and healthy controls were 53.2%, 46.8% and 46.1%, 53.9%. No significant difference in distribution of allelotype was shown between the two groups (chi(2) = 2.563, P = 0.109). The genotype frequencies of Pro/Pro, Pro/Arg, and Arg/Arg among ovarian cancer and healthy controls were 29.0%, 48.4%, 22.6% and 21.1%, 50.0%, 28.9% respectively. No significant difference was shown between the cases and controls (chi(2) = 2.598, P = 0.273). When the epithelial ovarian cancer patients were grouped according to the pathological characteristics, no significant difference was observed between the patients with serous cystadenocarcinoma or endometrioid carcinoma and the control group or between the two carcinoma groups for p53 codon 72 Pro/Arg (P > 0.05). When the epithelial ovarian cancer patients were divided into two subgroups according to the International Federation of Gynecology and Obstetrics (FIGO) standard, there was a significant difference between the early group (I approximately II) and the late group (III approximately IV) for Arg allelotype and Arg/Arg genotype (chi(2) = 7.494, P = 0.006 and chi(2) = 8.318, P = 0.004). The frequency of A, A'allelotype among ovarian cancer patients and healthy controls was 94.8%, 5.2% and 94.5%, 5.5%, no significant difference was shown between two groups (chi(2) = 0.013, P = 0.91). The genotype frequency of AA, AA', A'A' was not significantly different between the ovarian cancer and healthy controls (chi(2) = 0.301, P = 0.583). There was no significant difference in the frequencies of allelotypes and genotypes between patients with serous systadenocarcinoma and those with endometrioid carcinoma and between patients with ovarian cancers and the control subjects (all P > 0.05). The frequencies of allelotypes and genotypes were not significantly different between early and late ovarian cancers (chi(2) = 0.014, P = 0.906 and chi(2) = 0.137, P = 0.711). CONCLUSIONS: In northern Chinese women, p53 codon 72 Pro/Arg and p53 PIN3 gene polymorphisms are not associated with development of ovarian cancer. Arg/Arg genotype may be used as a stratification marker according to the standards of FIGO for ovarian cancer.

Adult↗
PubMed2002

Investigation of bax, bcl-2, bcl-x and p53 gene polymorphisms in multiple sclerosis.

Clinical course, outcome, radiological features, severity, and histopathology are heterogenous in multiple sclerosis (MS). Since MS is considered to be a polygenic disease, the genetic background may at least partly be responsible for this variability. Some MS cases are histopathologically characterized by a dramatic oligodendrocyte loss that is in part caused by apoptosis. A dysregulated apoptotic elimination of self-reactive T cells may also contribute to disease susceptibility. To analyze genetic differences in the apoptosis regulating factors bcl-2, bax, bcl-x and p53 we investigated polymorphisms of these genes in 105 patients with a relapsing remitting disease course and 99 controls by PCR-SSCP and direct sequencing. We identified so far unpublished sequence alterations in the promotor region of the bxl-x gene, in exon 7 of the p53 gene, and in exon 1 of the bax gene. No differences were observed between MS patients and controls. Additional known polymorphisms were found in intron 3 of the bax gene and in exon 6 of the p53 gene. No significant differences in the frequency of gene sequence variations were found between MS patients and controls. The apoptosis genes studied here therefore appear less likely to be important effector genes in MS.

Apoptosis↗
PubMed2005

The polyAT, intronic IVS11-6 and Lys939Gln XPC polymorphisms are not associated with transitional cell carcinoma of the bladder.

Chemical carcinogens from cigarette smoking and occupational exposure are risk factors for bladder transitional cell carcinoma (TCC). The Xeroderma Pigmentosum Group C (XPC) gene is essential for repair of bulky adducts from carcinogens. The Xeroderma Pigmentosum Group C gene polymorphisms may alter DNA repair capacity (DRC), thus giving rise to genetic predisposition to bladder cancer. Recent studies have demonstrated linkage disequilibrium between three polymorphisms in the XPC gene (polyAT, IVS11-6 and Lys939Gln) and these have been shown to influence the DRC, as well as to be associated with bladder cancer risk. We analysed all three XPC polymorphisms in 547 bladder TCC patients and 579 cancer-free controls to investigate the association between these polymorphisms and bladder cancer susceptibility, and we also attempted to assess gene-environmental interactions. We confirmed strong linkage disequilibrium among the polymorphisms (Lewontin's D' > 0.99). Using logistic regression adjusting for smoking, occupational and family history, neither the heterozygote nor the homozygote variants of these polymorphisms were associated with increased bladder cancer risk (adjusted odds ratio [95% confidence interval] for heterozygote 0.82 [0.63-1.07], 0.82 [0.63-1.08] and 0.83 [0.63-1.08] for PolyAT, IVS11-6 and Lys939Gln, respectively and homozygote variant, 0.98 [0.68-1.42], 0.99 [0.69-1.43] and 1.01 [0.70-1.46]). Moreover, we did not find any significant interaction between these XPC polymorphisms and environmental exposure to cigarette smoking and occupational carcinogens.

Aged↗
PubMed2006

The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications.

We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic 'p-distance tree' using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes.

Ascomycota↗
PubMed2000

Rh gene evolution in primates: study of intron sequences.

By amplification and sequencing of RH gene intron 4 of various primates we demonstrate that an Alu-Sx-like element has been inserted in the RH gene of the common ancestor of humans, apes, Old World monkeys, and New World monkeys. The study of mouse and lemur intron 4 sequences allowed us to precisely define the insertion point of the Alu-Sx element in intron 4 of the RH gene ancestor common to Anthropoidea. Like humans, chimpanzees and gorillas possess two types of RH intron 4, characterized by the presence (human RHCE and ape RHCE-like genes) or absence (human RHD and ape RHD-like genes) of the Alu-Sx element. This led us to conclude that in the RH common ancestor of humans, chimpanzees, and gorillas, a duplication of the common ancestor gene gave rise to two genes, one differing from the other by a 654-bp deletion encompassing an Alu-Sx element. Moreover, most of chimpanzees and some gorillas posses two types of RHD-like intron 4. The introns 4 of type 1 have a length similar to that of human RHD intron 4, whereas introns 4 of type 2 display an insertion of 12 bp. The latest insertion was not found in the human genome (72 individuals tested). The study of RH intron 3 length polymorphism confirmed that, like humans, chimpanzees and gorillas possess two types of intron 3, with the RHD-type intron 3 being 289 bases shorter than the RHCE intron 3. By amplification and sequencing of regions encompassing introns 3 and 4, we demonstrated that chimpanzee and gorilla RH-like genes displayed associations of introns 3 and 4 distinct to those found in man. Altogether, the results demonstrate that, as in humans, chimpanzee and gorilla RH genes experienced intergenic exchanges.

Animals↗
PubMed2002

Fine mapping of the chromosome 2p12-16 dyslexia susceptibility locus: quantitative association analysis and positional candidate genes SEMA4F and OTX1.

A locus on chromosome 2p12-16 has been implicated in dyslexia susceptibility by two independent linkage studies, including our own study of 119 nuclear twin-based families, each with at least one reading-disabled child. Nonetheless, no variant of any gene has been reported to show association with dyslexia, and no consistent clinical evidence exists to identify candidate genes with any strong a priori logic. We used 21 microsatellite markers spanning 2p12-16 to refine our 1-LOD unit linkage support interval to 12cM between D2S337 and D2S286. Then, in quantitative association analysis, two microsatellites yielded P values<0.05 across a range of reading-related measures (D2S2378 and D2S2114). The exon/intron borders of two positional candidate genes within the region were characterized, and the exons were screened for polymorphisms. The genes were Semaphorin4F (SEMA4F), which encodes a protein involved in axonal growth cone guidance, and OTX1, encoding a homeodomain transcription factor involved in forebrain development. Two non-synonymous single nucleotide polymorphisms were found in SEMA4F, each with a heterozygosity of 0.03. One intronic single nucleotide polymorphism between exons 12 and 13 of SEMA4F was tested for quantitative association, but no significant association was found. Only one single nucleotide polymorphism was found in OTX1, which was exonic but silent. Our data therefore suggest that linkage with reading disability at 2p12-16 is not caused by coding variants of SEMA4F or OTX1. Our study outlines the approach necessary for the identification of genetic variants causing dyslexia susceptibility in an epidemiological population of dyslexics.

Chromosome Mapping↗
PubMed1998

Sequence polymorphism in the beta-tubulin gene reveals heterogeneous and variable population structures in Cryptosporidium parvum.

Restriction fragment length polymorphism (RFLP) analysis of isolates of Cryptosporidium parvum has revealed two subgroups, termed H and C. The limited resolution of the RFLP method precludes an in-depth study of the genetic structure of C. parvum populations. Published C. parvum restriction polymorphisms lie within protein-coding regions known to be more homogeneous than noncoding sequences. To better assess the degrees of heterogeneity between and within C. parvum isolates, sequence polymorphism in the beta-tubulin intron, the only C. parvum intron described to date, was investigated. In contrast to the two genotypes distinguished by multilocus RFLP, several alleles were detected by sequence and RFLP analysis of the beta-tubulin intron and adjacent exon 2. Isolates carrying different beta-tubulin alleles were found. Significantly, one of the beta-tubulin alleles present in two geographically unrelated isolates combined features of C- and H-type isolates, suggesting that it might have arisen from a recombination event. A comparison of multiple samples of a calf-propagated laboratory isolate showed that the ratio of different beta-tubulin alleles fluctuated during serial passage.

Animals↗
PubMed2006

Relationship of ENOS and RAS gene polymorphisms to initial peritoneal transport status in peritoneal dialysis patients.

BACKGROUND: Peritoneal membrane permeability is of major importance for adequate dialysis and fluid balance in peritoneal dialysis (PD) therapy. The peritoneal capillary endothelium plays a key role in peritoneal transport. Nitric oxide derived from endothelial cells is related to the maintenance of vascular permeability. We investigated the relationship between the endothelial nitric oxide synthase (ENOS) gene polymorphism, the renin-angiotensin system (RAS) gene polymorphisms, and initial peritoneal transport type in PD patients. METHODS: This study included 74 incident continuous ambulatory PD patients. The ENOS gene polymorphism was identified at the 4a/b variable number of tandem repeats in intron 4. Genetic polymorphisms of the renin-angiotensin system were performed for the angiotensin-converting enzyme I/D, angiotensinogen M235T, and angiotensin II type 1 receptor A1166C and type 2 receptor C3123A by polymerase chain reaction. Patients were divided into two groups according to the initial peritoneal equilibration test results performed within 3 months of PD therapy: group 1 consisted of high/high average transporters (n = 41), and group 2 consisted of low/low average transporters (n = 33). RESULTS: Demographic, clinical, and laboratory data were similar between the two groups (p > 0.05). Group 1 had a significantly higher prevalence of the ENOS b/b genotype than group 2 (78% vs. 48.5%, p < 0.008). In contrast, group 2 had a significantly greater prevalence of the ENOS a/a+a/b genotype than group 1 (51.5% vs. 22%, p < 0.008). Genetic polymorphisms of the renin-angiotensin system were not associated with initial peritoneal transport type (p > 0.05). CONCLUSIONS: Modulation of the nitric oxide activity via the ENOS a/b polymorphism may have a considerable effect on the basal peritoneal permeability.

Adult↗
PubMed2005

Association of the OSCAR promoter polymorphism with BMD in postmenopausal women.

UNLABELLED: In an effort to identify genetic polymorphisms in potential candidate genes for osteoporosis, 10 variants were identified in the OSCAR gene using direct DNA sequencing, and 560 postmenopausal women were genotyped at five SNP loci, using the TaqMan method. The rare allele (G allele) of OSCAR-2322A>G (SNP in the 5' flanking region) showed significant association with lower BMD at various bone sites in postmenopausal women (n = 560). INTRODUCTION: BMD is the major factor for determining bone strength and osteoporotic fracture risk and is determined by both environmental and multiple genetic factors. The osteoclast-associated receptor (OSCAR) plays a critical role in osteoclast differentiation and thus is an important candidate gene for the modulation of BMD. MATERIALS AND METHODS: Through direct sequencing in 24 Korean individuals, 10 sequence variants were identified: 2 in the 5' flanking region, 7 in the exons (including 6 nonsynonymous single-nucleotide polymorphisms [SNPs]), and 1 in an intron. Five of these polymorphisms were selected for larger-scale genotyping in postmenopausal women (n = 560). Areal BMD (g/cm2) of the anterior-posterior lumbar spine and the nondominant proximal femur was measured using DXA (Lunar Expert XL and Hologic QDR 4500-A). Lateral thoracolumbar radiographs were obtained in all subjects. RESULTS: Using multiple regression analysis and controlling for age, years since menopause, height, weight, and evaluation machine as covariates, the rare allele (G allele) of OSCAR-2322A>G showed significant association with lower BMD at various bone sites in postmenopausal women. CONCLUSION: These findings suggest that the promoter variant in OSCAR gene (OSCAR-2322A>G) might be one of genetic determinants of BMD in postmenopausal women.

Absorptiometry, Photon↗