Browsing by Subject "Polymerase Chain Reaction"
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Item Open Access Analysis of skewed X-chromosome inactivation in females with rheumatoid arthritis and autoimmune thyroid diseases(BioMed Central, 2009) Chabchoub, G.; Uz, E.; Maalej, A.; Mustafa, C. A.; Rebai, A.; Mnif, M.; Bahloul, Z.; Farid, N. R.; Ozcelik, T.; Ayadi, H.Introduction The majority of autoimmune diseases such as rheumatoid arthritis (RA) and autoimmune thyroid diseases (AITDs) are characterized by a striking female predominance superimposed on a predisposing genetic background. The role of extremely skewed X-chromosome inactivation (XCI) has been questioned in the pathogenesis of several autoimmune diseases.Item Open Access Copy number variation of individual cattle genomes using next-generation sequencing(2012) Bickhart, D.M.; Hou, Y.; Schroeder, S.G.; Alkan C.; Cardone, M.F.; Matukumalli L.K.; Song J.; Schnabel, R.D.; Ventura M.; Taylor J.F.; Garcia J.F.; Van Tassell, C.P.; Sonstegard, T.S.; Eichler, E. E.; Liu G.E.Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome - wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence-476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ 2 test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome. © 2012 by Cold Spring Harbor Laboratory Press.Item Open Access DNA repair gene polymorphisms and bladder cancer susceptibility in a Turkish population(International Institute of Anticancer Research, 2006) Karahalil, B.; Kocabas, N. A.; Özçelik, T.Background: Occupational exposure and life style preferences, such as smoking are the main known environmental susceptibility factors for bladder cancer. A growing list of chemicals has been shown to induce oxidative DNA damage. Base excision repair (BER) genes (X-ray repair cross complementing 1, XRCC1 and human 8-oxoguanine DNA glycosylase 1, OGG1) may play a key role in maintaining genome integrity and preventing cancer development. Materials and Methods: We tested whether polymorphisms in XRCC1 and OGG1 are associated with bladder cancer risk by using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay. In addition, the possible modifying affect of cigarette smoking was evaluated. Results: No studies, to date, have examined the association between genetic polymorphisms in DNA repair genes and bladder cancer susceptibility, in the Turkish population. We found the OGG1 Cys326Cys genotype to be more frequent among bladder cancer patients (odds ratio (OR): 2.41 (95% CI, 1.36-4.25)). However, in the case of XRCC1, there was no significant difference in susceptibility to bladder cancer development between patients with the Arg399 and these with the Gln399 allele (OR: 0.72 (95% CI, 0.41-1.26)). Conclusion: Our data showed that OGG1 genetic polymorphisms might be useful as prognostic genetic markers for bladder cancer in the clinical setting.Item Open Access Polymorphisms of glutathione S-transferase genes (GSTM1, GSTP1 and GSTT1) and bladder cancer susceptibility in the Turkish population(Springer, 2001) Törüner, G. A.; Akyerli, C.; Uçar, A.; Aki, T.; Atsu, N.; Özen, H.; Tez, M.; Çetinkaya, M.; Özçelik, T.We investigated the effect of the GSTM1 and GSTT1 null genotypes, and GSTP1 313 A/G polymorphism on bladder cancer susceptibility in a case control study of 121 bladder cancer patients, and 121 age- and sex-matched controls of the Turkish population. The adjusted odds ratio for age, sex, and smoking status is 1.94 [95% confidence intervals (CI) 1.15-3.26] for the GSTM1 null genotype, and 1.75 (95% CI 1.03-2.99) for the GSTP1 313 A/G or G/G genotypes. GSTT1 was shown not to be associated with bladder cancer. Combination of the two high-risk genotypes, GSTM1 null and GSTP1 313 A/G or G/G, revealed that the risk increases to 3.91-fold (95% CI 1.88-8.13) compared with the combination of the low-risk genotypes of these loci. In individuals with the combined risk factors of cigarette smoking and the GSTM1 null genotype, the risk of bladder cancer is 2.81 times (95% CI 1.23-6.35) that of persons who both carry the GSTMl-present genotype and do not smoke. Similarly, the risk is 2.38-fold (95% CI 1.12-4.95) for the combined GSTP1 313 A/G and G/G genotypes and smoking. These findings support the role for the GSTM1 null and the GSTP1 313 AG or GG genotypes in the development of bladder cancer. Furthermore, gene-gene (GSTM1-GSTP1) and gene-environment (GSTMl-smoking, GSTP1-smoking) interactions increase this risk substantially.Item Open Access Strain-and region-specific gene expression profiles in mouse brain in response to chronic nicotine treatment(Wiley-Blackwell Publishing, 2008) Wang, J.; Gutala, R.; Hwang, Y. Y.; Kim J. -M.; Konu, O.; Ma, J. Z.; Li, M. D.A pathway-focused complementary DNA microarray and gene ontology analysis were used to investigate gene expression profiles in the amygdala, hippocampus, nucleus accumbens, prefrontal cortex (PFC) and ventral tegmental area of C3H/HeJ and C57BL/6J mice receiving nicotine in drinking water (100 μg/ml in 2% saccharin for 2 weeks). A balanced experimental design and rigorous statistical analysis have led to the identification of 3.5-22.1% and 4.1-14.3% of the 638 sequence-verified genes as significantly modulated in the aforementioned brain regions of the C3H/HeJ and C57BL/6J strains, respectively. Comparisons of differential expression among brain tissues showed that only a small number of genes were altered in multiple brain regions, suggesting presence of a brain region-specific transcriptional response to nicotine. Subsequent principal component analysis and Expression Analysis Systematic Explorer analysis showed significant enrichment of biological processes both in C3H/HeJ and C57BL/6J mice, i.e. cell cycle/proliferation, organogenesis and transmission of nerve impulse. Finally, we verified the observed changes in expression using real-time reverse transcriptase polymerase chain reaction for six representative genes in the PFC region, providing an independent replication of our microarray results. Together, this report represents the first comprehensive gene expression profiling investigation of the changes caused by nicotine in brain tissues of the two mouse strains known to exhibit differential behavioral and physiological responses to nicotine.