The pathophysiologies of bronchopulmonary dysplasia (BPD) are inflammation, infection, tissue damage, angiogenesis defects and genetic susceptibility. Because of the role of the vitamin D binding protein (Gc globulin) on these factors, we investigated the relationship between Gc globulin polymorphisms and BPD. This case-control study was performed with 160 neonates (⩽32 gestational ages, ⩽1500 g). PCR DNA sequence analyses were used for GC gene rs4588 and rs7041 single-nucleotide polymorphisms. In the univariate analyses, it was observed that Gc2 was the only variant that was protective against BPD (Odd ratio (OR)=0.47, 95% coinfidence interval (CI)=0.24 to 0.89, P=0.020). In the multivariate analyses, Gc2 decreased the risk of disease (OR=0.15, 95% CI=0.029 to 0.79, P=0.026) independent of gestational age, birth weight, 5-min Appearance, Pulse, Grimace, Activity, and Respiration scores, respiratory distress syndrome and sepsis. The Gc2 variant was, after adjusting for confounders, associated with a decrease in the frequency of BPD. Our study adds Gc globulin to the list of candidate genes that potentially contribute to the etiology of the disease.

Many immunologic and inflammatory mechanisms play a role in asthma etiology. The aim of this study was to investigate the susceptibility of asthma patients in the Turkish population with demonstrating genes for polymorphisms in TIM1, TSLP and IL18R1. All of the genomic DNA samples were isolated from blood samples according to a standard salting-out protocol. DNA samples were stored at -20 degrees C until the genotype analysis was performed. rs3806933 (TSLP -847 C > T) and TIM1 -416G > C were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The rs3806933 (TSLP -847 C > T) was genotyped by PCR using our new primers and HphI restriction enzyme digestion. rs2287033 (IL18R1 c. 1270+150 A > G), rs3213733 (IL18R1 c. 626-196 G > T), and rs3771166 (IL18R1-c. 302+1694 C > T) were genotyped using SYBR green dye based real time PCR assay. Results: The allele frequencies of 5 SNPs in TSLP, TIM-1, and IL18R1 genes were determined in 139 asthmatic patients and 126 healthy controls of in Turkish population. The investigated SNPs are as follows; rs3806933 (TSLP -847 C > T), TIM1 -416G > C, rs2287033 (IL18R1 c. 1270+150 A > G), rs3213733 (IL18R1 c. 626-196 G > T), and rs3771166 (IL18R1-c. 302+1694 C > T). Results suggest that IL18R1 c. 626-196 G > T (rs3213733) and TIM1 -416G > C are significantly associated with asthma in patients in Turkish population. Patients with AA genotypes of rs2287033 (IL18R1 c. 1270+150 A > G), have significantly less total serum IgE levels when compared with patients having GG or GA genotypes (p < 0.012; 381.77 +/- 239.46 vs 557.52 +/- 549.96, respectively). Conclusion: This study showed that IL18R1 c. 626 -196 G > T (rs3213733) and TIM1 -416G > C are significantly associated with asthma patients in Turkish population.

Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T(m) discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.

Aneurysm and microorganism relationship, which is urged to be a cause of atherosclerotic and non atherosclerotic pathogenesis, is a subject that has been discussed for years. In addition to many known microorganisms about this relationship, in recent years Chlamydophila pneumoniae, anaerobic bacteria and Helicobacter pylori are the most emphasized microorganisms suggested as a possible factors influencing the development and expansion especially of abdominal aortic aneurysm. In this study, we aimed to evaluate the potential etiopathogenetic relationship between abdominal and ascending aneurysm and H. pylori. The study was conducted between January 2010 and December 2010 as a cross-sectional, case-control study with 50 cases admitted to TR Ministry of Health, Dr. Siyami Ersek Thoracic and Cardiovascular Surgery Training and Research Hospital, Department of Cardiovascular Surgery and diagnosed with abdominal aortic aneurysm (AAA) and ascendıng aortıc aneurysm (AsAA) according to their clinical findings and their radiodiagnostic data. Laboratory studies of the research were performed in Serology-enzyme linked immunosorbent assay (ELISA) and Molecular Biology laboratories of the Depatment of Medical Microbiology in Istanbul University, Cerrahpasa Faculty of Medicine and in private Burc Molecular Diagnostic Center. The study was performed in three groups. The first group was the patient group (PG) including 50 patients with aneurysm (40 ascending, 10 abdominal), the second group was the patient control group (PCG) including 30 patients with post-stenotic aneurysm (PSAG) and the third group was the healthy control group (HCG) with 47 healthy individuals selected among the people admitted to Computed Tomography (CT) laboratory of the department of radiodiagnostics of Istanbul University (IU) Cerrahpasa Faculty of Medicine (CFM) according to their particular complaint, but not having abdominal or cardiovascular complaints resembling the AAA and AsAA. H. pylori IgG test was applied to the serum samples taken from all people of the three groups by enzyme immunoassay method. Additionaly, DNA extraction was applied using a commercial tissue extraction kit in the tissue specimens of the patient group and in the tissue specimens of patients with post-stenotic aneurysm. H. pylori DNA was determined by real-time PCR method using a commercial kit (WAY2GENE® Helicobacter pylori, Genmar, Turkey) according to the manufacturer’s protocol. H. pylori IgG positivity was detected in PG, PSAG and HCG as 76, 57 and 57%, respectively. H. pylori DNA was detected only in one male patient with atherosclerotic abdominal aneurysm and could not be detected in other 49 cases. While these strain’s genotype was identified as VagA s1b/m1, it was found to be negative for all other genes. In conclusion, however, VagA s1b1 type H. pylori was detected in vascular tissue of a case with atherosclerotic abdominal aneurysm and not detected in PCG with post-stenotic aneurysm, these data are not enough to support an etiopathogenetic relationship between aneurysm and H. pylori. The presence of H. pylori DNA in only one case suggests that H. pylori is not a primer agent and probably has an affinity to the vascular tissues. Key words: Helicobacter pylori, aneurysm, PCR.

Linezolid which is the first member of oxazolidinone class of synthetic antimicrobial agents, was licensed for the treatment of gram-positive coccal infections in Turkey in 2006. In recent years, multidrug-resistant pathogens, especially vancomycin-resistant enterococci (VRE), have emerged rapidly worldwide and linezolid exhibited good clinical efficacy against VRE. However, linezolid-resistant bacteria have been reported from Turkey. In April 2011, a 66-year-old paraplegic woman was admitted to our hospital because of an infected decubitis ulcer and empirical antibiotic therapy was started. Since the patient's condition worsened during treatment, she was moved to the intensive care unit. Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium were recovered from tracheal aspirates and blood, respectively. Following three weeks of linezolid therapy blood culture yielded linezolid and vancomycin resistant E.faecium. Linezolid resistance in the VRE strain was confirmed by polymerase chain reaction and sequence analysis, subsequently. Linezolid-resistant two isolates were identified as E.faecium by 16S rRNA sequencing and both isolates had G2576U mutation in 23S rRNA gene. Linezolid resistance which was identified in a vancomycin-resistant E.faecium isolate is a new problem for Turkey. Last year another mutation related to linezolid resistance was reported from Istanbul, Turkey. The isolate had G2576T mutated 23S rRNA genes. Resistance should be considered and closely followed-up during linezolid treatment.

The single nucleotide polymorphism (SNP) genotyping is currently considered as a particularly valuable tool for the diagnosis of different pathologies. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. Although a large number of distinct approaches has been reported each laboratory use one of the published methods based on their technical and economical capacity. This article presents an application of an in-house assay, tetra-primer ARMS PCR assay, and its application in SNP genotyping. We have shown that this assay could be more advantageous when compared with PCR-RFLP, real time PCR, and DNA sequencing. We have shown that the assay is successful in genotyping using archived paraffin-embedded tissues, heparinated samples and amniotic fluids with meconium. These low-costed (3$/reaction) assays could be completed within 3-4 h after specimen receipt allowing for a reasonable turn-around time in the laboratory. Since tetra-primer ARMS PCR assay does not require any special equipment, the assay could be set up in most clinical diagnostic laboratories. (C) 2011 Elsevier Ltd. All rights reserved.

We evaluated the genotypes of the serotonin transporter gene (5-HTT) in patients with premature ejaculation (PE) to determine the role of genetic factors in the etiopathogenesis of PE and possibly to identify the patient subgroups. A total of 70 PE patients and 70 controls were included in this study. All men were heterosexual, had no other disorders and were either married or in a stable relationship. PE was defined as ejaculation that occurred within 1 min of vaginal intromission. Genomic DNA from patients and controls was analyzed using polymerase chain reaction, and allelic variations of the promoter region of the serotonin transporter gene (5-HTTLPR) were determined. The 5-HTTLPR (serotonin transporter promoter gene) genotypes in PE patients vs. controls were distributed as follows: L/L 16% vs. 17%, L/S 30% vs. 53% and S/S 54% vs. 28%. We examined the haplotype analysis for three polymorphisms of the 5-HTTLPR gene: LL, LS and SS. The appropriateness of the allele frequencies in the 5-HTTLPR gene was analyzed by the Hardy-Weinberg equilibrium using the chi(2)-test. The short (S) allele of the 5-HTTLPR gene was significantly more frequent in PE patients than in controls (P < 0.05). We suggest that the 5-HTTLPR gene plays a role in the pathophysiology of all primary PE cases. Further studies are needed to evaluate the relationship between 5-HTTLPR gene polymorphism and patient subgroup (such as primary and secondary PE) responses to selective serotonin reuptake inhibitors as well as ethnic differences.

Despite numerous studies in many laboratories over several years, the etiology of Multiple Sclerosis (MS) is still unknown. It was suggested that some infectious agents play a role in the etiology of MS. This study included 39 patients with MS, 10 patients with other neurological disorders (OND) and a control group of 42 healthy people. There was no significant difference between MS, OND and HC groups for

Spinal muscular atrophy (SMA), the leading genetic cause of death in childhood, is an autosomal recessive neuromuscular disorder characterized by progressive muscle weakness, associated with deletions of the survival motor neuron 1 (SMN1) gene. Approximately 94% of SMA patients carry homologous deletions of SMN1 exon(s) 7 (and 8). Because of the high incidence and severity of the disease, precise detection and quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. We have developed a reliable single-tube tetra-primer PCR assay to simultaneously detect both the SMN1 and SMN2 exon 7 deletion using the advantage of C/T difference at nucleotide position of 840 in exon 7. The assay has been optimized and tested in 48 healthy controls, 20 known patients with SMA, 12 carriers (one SMN1 copy), and 8 amniotic fluids suspected of having SMA for whom we had determined the SMN1/SMN2 deletion by an additional PCR-RFLP method. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for simultaneous detection of both SMN1 and SMN2 deletion, which could be used even in "low-tech" laboratories.

Background As reported recently, some gene polymorphisms are suspected to determine susceptibility to sarcoidosis and are held responsible for the extent and progression of the disease. Polymorphism at -857 locus of tumor necrosis factor (TNF)-alpha gene is considered to be a predisposition factor in sarcoidosis and held responsible for pathogenesis of the disease. We compared these polymorphisms in healthy Turkish control subjects and Turkish patients with sarcoidosis.Methods We examined gene polymorphisms in 90 cases which were histopathologically diagnosed as sarcoidosis and 110 healthy subjects without any history of a chronic disease. TNF-alpha-857 gene polymorphisms were determined using a polymerase chain reaction (PCR)-based method after DNA isolation. Genotype distributions of the groups were evaluated by the Hardy-Weinberg equilibrium test.Results Genotype distributions were in agreement with the Hardy-Weinberg equilibrium both in sarcoidosis patients and healthy subjects. TNF-alpha gene (C/T) polymorphism, at position -857, revealed no differences in genotype and allele frequency between patients and control subjects but more relapses and more frequently involvement of three or more organs were found in sarcoidosis patients who have this polymorphism (p < 0.05, p < 0.01 respectively).Conclusion T allele at -857 locus of TNF gene is a marker for more extensive disease in Turkish sarcoidosis patients.

Polymorphism at +813 locus of vascular endothelial growth factor (VEGF) gene is considered to decrease predisposition to sarcoidosis. Our study aimed to investigate the roles of this polymorphism in the development and extent of sarcoidosis. We examined polymorphisms of the VEGF gene in 90 cases with histopathological diagnosis of sarcoidosis and in 110 healthy subjects. VEGF +813 gene polymorphisms were determined using a polymerase chain reaction-based method after DNA isolation. A significant increase in the frequency of the T allele was found in healthy subjects (odds ratio 0.55; 95% confidence interval 0.32-0.97, P<0.05). Our results suggest that increase in rarer T allele at + 813 locus of VEGF gene may diminish susceptibility to sarcoidosis in Turkish population.

Background. Helicobacter pylori infection leads to different clinical outcomes depending on both host and bacterial factors. In a recent study, we identified H. pylori cagE and babA2 genotypes as independent predictors of duodenal ulcer (DU) and gastric cancer (GC) in dyspepsia patients, but no previous studies have examined the role of host-related genetic factors in Turkey. This time our aim was to evaluate whether polymorphisms of the interleukin 1B (IL-1B) and the interleukin 1 receptor antagonist (IL-1RN) genes are important factors in the differential expression of gastroduodenal diseases in H. pylori-positive dyspepsia patients. Methods. Ninety-three H. pylori-positive patients, 30 with nonulcer dyspepsia (NUD), 30 with DU, and 33 with GC, were investigated. The IL-1B-511 and IL-1B-31 biallelic polymorphisms, and the IL-1RN intron 2 variable number tandem repeat were genotyped by polymerase chain reaction and single-strand confirmation polymorphism analysis. Results. The IL-1RN-1/1 genotype was significantly more prevalent among patients with NUD than among those with GC (chi(2) = 9.270; P = 0.002), and the IL-1RN-1/2 genotype was significantly more common in patients with GC (chi(2) = 6.01; P = 0.014). Multivariate regression analysis showed that cagE, babA2, and IL-1RN-1/2 genotypes were independent predictors of GC, but when patients with benign disorders were grouped together (NUD + DU) and compared with patients with GC, regression analysis disclosed that babA2 (P = 0.000) and IL-1B-31 gene polymorphisms (CC or CT) (P = 0.01) were the only independent markers of GC. Conclusions. When analyzed together with host genetic factors, the wellestablished bacterial risk factor babA2 seems to be the most important predictor of malignant disorders, and the presence of the IL-1B-31TT genotype emerges as a protective factor against them.

Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500. In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles. The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories.

INTRODUCTION:To investigate the association of 1G/2G polymorphism in matrix metalloproteinase-1 (MMP-1) promoter with susceptibility to prostate carcinoma in the Turkish population.MATERIALS AND METHODS:MMP-1 promoter polymorphism was genotyped by PCR-RFLP analysis in 55 prostate cancer patients and 43 healthy controls.RESULTS:The frequency of 1G/2G genotypes in prostate cancer patients was similar to that of the controls (all p values were >0.05). Compared with the 1G/1G genotype, neither the 2G/2G nor a combination with the 1G/2G genotype significantly modified the risk of developing prostate cancer and metastasis status. In addition, the frequencies of genotypes were not significantly different among patients stratified by smoking status and family history of prostate cancer.CONCLUSIONS:The 2G allele of the MMP-1 promoter polymorphism might not modify the risk of prostate cancer development and might not be used as a putative marker to predict the potential of metastasis in this cancer type, at least in the Turkish population.

We previously reported that change, with age, in plasma levels of total cholesterol (TC) and LDL cholesterol (LDL-C) differed between apolipoprotein E (APOE) genotypes e3e3 and e3e4, in a sample of 77 older, unrelated males. By use of a larger sample from that cohort, followed longitudinally during 1969–87, the change in TC and in LDL-C, between the e3e3 and e3e4 APOE genotypes, over three exams, was reanalyzed. Additionally, the change in triglycerides (TG) and in HDL-choles-terol (HDL-C), between the e3e3 and e3e4 APOE genotypes—as well as the differences between the e3e3 and e3e2 genotypes, for TC, LDL-C, TG, and HDL-C—were contrasted over the three exams. At exam 1 TG was higher in the e3e4 group than in the e3e3 group (mean age 48 years), and at exams 2 and exam 3 (mean ages 58 and 63 years, respectively) it was similar (P = .009 for the exam-by-genotype-interaction effect in the repeated-measures analysis). A similar trend was seen for TC (P = .03), yet previously detected LDL-C effects were not apparent (P = .46). Those with the e3e2 genotype had higher TG and lower LDL-C and TC at each exam than were seen in those with the e3e3 genotype, although the differences in the values were not always statistically significant. Differences in TC, LDL-C, and TG, between the e3e2-genotype and e3e3-genotype groups, did not significantly change over the three exams. HDL-C levels were relatively stable over the exams; however, the exam-by-genotype interaction was significant for the e3e2 genotype versus the e3e3 genotype (P = .02). The e4 allele effects on TG and TC changed between longitudinal exams and may be age dependent. Changes, with age, in the effect of the e3e4 genotype on lipids may impact the risk of developing atherosclerotic disease.

OBJECTIVE To explore the association between the promoter polymorphism (that influences the transcriptional level) of matrix metalloproteinase‐1 (MMP‐1, associated with tumour cell invasion and metastasis) and bladder cancer in a Turkish population. PATIENTS, SUBJECTS AND METHODS The MMP‐1 polymorphism was assessed in 102 transitional cell carcinomas of the bladder (50 Ta, 52 T2–4) and in 94 age‐, smoking‐ and gender‐matched healthy volunteers. The polymerase chain reaction (PCR) assay was used to determine the MMP‐1 genotypes. Genomic DNA used for the assay was extracted from peripheral blood lymphocytes. RESULTS The frequency of the MMP‐1 2G/2G genotype, which results in the highest MMP‐1 transcriptional level, was compared to that of the 1G/1G plus 1G/2G genotypes. Of the 102 cases with bladder cancer, 49 (48%) showed the 2G/2G genotype, whereas it was found in 22 of the 94 controls (23%); this difference was statistically significant ( P < 0.01; odds ratio 2.79, 95% confidence interval, CI, 1.53–5.60). However, there was no significant association between the 2G/2G genotype and tumour grade and pathological stage. We assessed the interaction between smoking status (former and current smokers, by their median pack years) and 2G/2G genotype; there was a significantly increased risk in heavy smokers ( P < 0.001; odds ratio 3.21; 95% CI 1.33–5.60). CONCLUSION These results suggest that the MMP‐1 promoter polymorphism might be linked to susceptibility for bladder cancer.