Hatice Mergen

Mitochondrial DNA sequence variation in the Anatolian peninsula (Turkey)

Throughout human history, the region known today as the Anatolian peninsula (Turkey) has served as a junction connecting the Middle East, Europe and Central Asia, and, thus, has been subject to major population movements. The present study is undertaken to obtain information about the distribution of the existing mitochondrial D-loop sequence variations in the Turkish population of Anatolia. A few studies have previously reported mtDNA sequences in Turks. We attempted to extend these results by analysing a cohort that is not only larger, but also more representative of the Turkish population living in Anatolia. In order to obtain a descriptive picture for the phylogenetic distribution of the mitochondrial genome within Turkey, we analysed mitochondrial D-loop region sequence variations in 75 individuals from different parts of Anatolia by direct sequencing. Analysis of the two hypervariable segments within the noncoding region of the mitochondrial genome revealed the existence of 81 nucleotide mutations at 79 sites. The neighbourjoining tree of Kimura’s distance matrix has revealed the presence of six main clusters, of which H and U are the most common. The data obtained are also compared with several European and Turkic Central Asian populations.

A Prospective Study of Serotonin Transporter Gene Promoter (5-HTT Gene Linked Polymorphic Region) and Intron 2 (Variable Number of Tandem Repeats) Polymorphisms as Predictors of Trauma Response to Mild Physical Injury

The aim of this study was to examine the effect of both promoter and intron polymorphisms of the serotonin transporter (5HTT) gene on posttraumatic stress disorder (PTSD) development. For this purpose, two polymorphisms of the 5-HTT gene, which are found in the promoter (5-HTT gene-linked polymorphic region) and second intron (variable number of tandem repeats) of the gene, were analyzed in 100 patients who were admitted to the Emergency Department after a mild physical trauma. None of the 5-HTT polymorphisms studied have an effect on PTSD development after a mild physical injury, but having L allele for 5-HTT gene-linked polymorphic region may cause milder hyperarousal symptoms in those patients who have developed PTSD.

Early sign of atherosclerosis in slow coronary flow and relationship with angiotensin-converting enzyme I/D polymorphism

Increase in carotid artery intima-media thickness (IMT) is an early sign of atherosclerosis. Slow coronary flow (SCF) is characterized by delay of opacification of coronary arteries in coronary angiography in the absence of any evident obstructive lesion, but its etiopathogenesis remains unclear. Genes that regulate the renin angiotensin system also play a role in developing cardiovascular system disorders. The presence of deletion (D) allele in angiotensin converting enzyme (ACE) gene polymorphism is associated with coronary artery disease. The aim of this study was to investigate the carotid artery IMT measurement, as an early sign of atherosclerosis, in patients with SCF and without SCF and also to assess the effect of the renin-angiotensin gene system on carotid IMT. Forty-four patients with angiographically proven SCF and 44 cases with normal coronary flow (NCF) pattern with similar risk profile were enrolled in the study. Coronary flow patterns of the cases were determined by thrombolysis in myocardial infarction (TIMI) frame count method. Intima-media thickness was measured by recording ultrasonographic images of both the left and right common carotid artery with a 12-MHz linear array transducer. ACE I/D polymorphism and Angiotensin II tip 1 receptor (AT1R) A/C gene polymorphism were determined by polymerase chain reaction (PCR) amplification. Demographic characteristics and coronary artery disease risk factors of SCF and NCF groups were similar. Mean TIMI frame count and carotid IMT (mm) were significantly higher in the SCF group than controls (45.9 ± 12 vs 23.3 ± 3.7, P = 0.0001; 0.75 ± 0.08 vs 0.69 ± 0.06, P = 0.0001, respectively). Mean TIMI frame count was positively correlated with IMT of carotid artery in correlation analysis (r = 0.45, P = 0.0001). When analyzed in regard to ACE genotype in all subjects, IMT values were statistically different (0.78 ± 0.06 for DD genotype, 0.72 ± 0.05 for ID genotype, and 0.64 ± 0.06 for II genotype, P = 0.0001). This difference remained significant in subgroup analyses for each genotype. No association could be observed between the AT1R A/C1166 polymorphism and IMT of carotid artery measurement (P > 0.05). Lack of association was still observed with analysis carried out when genotype effect was assumed to be inherited as additive (CC versus AA versus AC) or dominant (AA versus AC+CC). Increased IMT in patients with SCF shows that subclinical atherosclerosis may play role in this phenomenon. This increase was most marked in the presence of D allele of ACE genotype, which is associated with vascular hypertrophy.

Woodhouse and Sakati syndrome (MIM 241080): report of a new patient.

A 32-year-old male with Woodhouse Sakati syndrome (MIM 241080) is described. Two of the probands brothers also have diabetes mellitus and similar facial features, however they are not dysarthric. An affected older brother died of an unknown cause at age 30. This confirms autosomal recessive inheritance.

Assessment of ER Stress and Autophagy Induced by Ionizing Radiation in Both Radiotherapy Patients and Ex Vivo Irradiated Samples

Acute radiation leads to several toxic clinical states and triggers some molecular pathways. To shed light on molecular mechanisms triggered by ionizing radiation (IR), we examined the expression profiles of endoplasmic reticulum (ER) stress and autophagy‐related genes in individuals who were exposed to IR. Blood samples were collected from 50 cancer patients before radiotherapy and on the 5th, 15th, and 25th days of the treatment. Peripheral blood samples from 10 healthy volunteers were also obtained for ex vivo irradiation, divided into five and irradiated at a rate of 373 kGy/h to 0, 0.1, 0.5, 1, and 3Gy γ‐rays using a constant gamma source. GRP78, ATG5, LC3, ATF4, XBP1, and GADD153 genes were analyzed by quantitative real‐time polymerase chain reaction (QRT‐PCR) using beta 2 microglobulin (B2M) and glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) as references. In both groups, expressions of the selected genes have increased. It can be concluded that IR induces ER stress and related authophagy pathway in the peripheral lymphocyte cells proportionally by dose.

Mutations in the AVPR2, AVP-NPII, and AQP2 genes in Turkish patients with diabetes insipidus

The aim of this study was to identify mutations in three different genes, the arginine-vasopressin-neurophysin II (AVP-NPII) gene, the arginine-vasopressin receptor 2 (AVPR2) gene, and the vasopressin-sensitive water channel aquaporin-2 (AQP2) gene in Turkish patients affected by central diabetes insipidus or nephrogenic diabetes insipidus. This study included 15 patients from unrelated families. Prospective clinical data were collected for all patients including the patients underwent a water deprivation–desmopressin test. The coding regions of the AVPR2, AQP2, and AVP-NPII genes were amplified by polymerase chain reaction and submitted to direct sequence analysis. Of the 15 patients with diabetes insipidus referred to Gulhane Military Medical Academy, Department of Endocrinology and Metabolism, eight patients have AVPR2 mutations, five patients have AQP2 mutations and two patients have AVP-NPII mutations. Of the patients, which have AVPR2 mutations, one is compound heterozygous for AVPR2 gene. Seven of these mutations are novel. Comparison of the clinical outcomes of these mutations may facilitate in understanding the functions of AVP-NPII, AQP2, and AVPR2 genes in future studies.

Molecular variability of Schistonchus caprifici (Nematoda: Aphelenchoididae) from Ficus carica in Turkey

An extensive biogeographical survey was conducted from 2004 through part of 2007 of nematodes associated with the edible fig, Ficus carica, in seven different regions of Turkey. Figs (syconia) were collected, dissected and harvested for nematodes from 308 apparently wild or naturalised F. carica trees along roadsides and trails. Nematode specimens were examined morphologically and molecular analyses of sequences of the D2/D3 expansion segments of the large subunit (LSU) rDNA and partial mitochondrial DNA COI (mtCOI) were done. Of the 308 fig trees, 150 (49%) were positive for what was morphologically confirmed to be Schistonchus caprifici. Figs on one tree in Kahramanmaras city, South East Turkey, were found to contain S. caprifici and dauer juveniles of what appears to be a diplogastrid nematode. Molecular analyses produced congruent trees for both sequenced loci supporting the hypothesis that S. caprifici from different locations in Turkey are part of a well supported clade with some inherent variability. No geographic patterns were observed for either locus suggesting that the sequences generated represent inherent intraspecific variation for S. caprifici and that human activities related to the culture of the edible fig have allowed for mixing of any previously allopatric lineages.

Association of VNTR polymorphisms in DRD4, 5-HTT and DAT1 genes with obesity

Abstract Objective: To investigate the association between VNTR polymorphisms of DRD4, DAT1 and 5-HTT genes and obesity. Material and methods: Peripheral blood samples of 234 obese (BMI ≥ 30) and 148 healthy individuals (BMI ≤ 25) were objected to PCR to detect the VNTR of the 2nd intron of 5-HTT, 3rd exon of DRD4 and 3’UTR of DAT1 genes. Results: The association between obesity and genotype distributions of 5-HTT, DAT1 and DRD4 genes and between obesity and distributions of allele frequencies were tested by Chi Square (χ2) test and were not found statistically significant. BMI values for genotype of obese and morbidly obese (BMI > 40) individuals were analyzed by Kruskal-Wallis and not found statistically significant differences between BMI values for the most frequent genotypes of 5-HTT, DAT1 and DRD4 genes. Conclusions: As a conclusion, there was no association between 5-HTT, DAT1 and DRD4 genes VNTR polymorphisms and obesity.

A safer and relatively shorter method for Southern blot hybridization analysis

The study presented here describes a Southern blot hybridization technique which is performed in a shorter time and safer than the classical one. In this study DNA was isolated from a small amount of blood sample and the probe for hybridization was prepared with (35)S by polymerase chain reaction.

Promoter hypermethylation of p16 and APC in gastrointestinal cancer patients.

BACKGROUND/AIMS Cancer is a consequence of the disruption of cellular regulation. Epigenetic is one of the reasons of this disruption. Epigenetic factors play a role in the carcinogenesis by affecting proto-oncogenes and tumor suppressor genes and it is one of the most popular research areas in recent years. DNA methylation, which is an epigenetic mechanism, occurs in the early stages of tumorigenesis. Promoter methylation which causes the silence of tumor suppressor genes have been studied extensively in various tumor types. The aim of this study was to investigate promoter methylation of certain tumor suppressor genes, Cyclin-dependent kinase inhibitor 2A (p16) and Adenomatous polyposis coli (APC), which take part in gastrointestinal tumorigenesis. MATERIALS AND METHODS To detect the promoter methylation of p16 and APC genes, tissue samples from 20 gastrointestinal cancer patients and peripheral blood samples from 15 healthy individuals were collected for Methylation-Specific Polymerase Chain Reaction (MSP) analysis. RESULTS According to the statistical analysis, in tumor tissue, positive methylation ratio of p16 and APC genes was found respectively 30% (6/20) and 50% (10/20). The difference of promoter methylation of these genes between tumor tissues and control group was significantly observed (p=0.02 and 0.001, respectively). An alteration of promoter methylation of APC gene according to tumor localization was found (p=0.007), but there was no significant difference observed in p16. CONCLUSION In our study, promoter methylation which was considered to be occurred as an early event in gastrointestinal carcinogenesis was observed in p16 and APC genes.