Browsing by Author "Yildirim, H"
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Item A comparative anatomical study of the genus Puschkinia Adams in TurkeyYetisen, K; Yildirim, H; Özdemir, CIn the study, Puschkinia scilloides Adams, P. bilgineri Yildirim, and P. peshmenii Rix et B. Mathew were compared anatomically. Although the stem vascular bundles were arranged in two rows in P. peshmenii, they can observed in three rows in P. scilloides and P. bilgineri. In addition, some differences were found, such as the metaxylem number in the root, number of vascular bundles in the scape, presence of raphide crystals, and number of protruding epidermis cells at the tip of the leaf. These differences have been found to be taxonomically useful for distinguishing these species. Moreover, similarities and differences between Puschkinia Adams and the taxonomically closely related Scilla L. section Chionodoxa Boiss. and Scilla bifolia L. taxa were also discussed.Item AN ANATOMICAL STUDY OF Scilla (SCILLOIDEAE) SECTION Chionodoxa AND Scilla bifolia IN TURKEYYildirim, H; Yetisen, K; Özdemir, A; Özdemir, CIn the present study Scilla luciliae, S. forbesii, S. sardensis, S. siehei, Scilla x allenii and S. bifolia are compared anatomically. Some differences have been found in root, scape, and leaf anatomy of the taxa, and commented. S. luciliae, S. forbesii, S. sardensis and S. siehei have a metaxylem at the center of the root, others have 3-4 number metaxylem. Vascular bundles in two row in S. luciliae and S. forbesii in a single row in S. sardensis, Scilla x allenii and S. bifolia though in three rows in S. siehei. Aerenchyma tissue is present in mesophyll of five taxa leaf except S. sardensis. The anatomical variations in the taxa have been investigated by means of numerical methods (Analysis of variance and Pearson correlation). By the analysis of the investigated taxa from 12 anatomy related characters, it has been also found that the results from numerical analysis of anatomy characters can provide additional evidences, which correspond to the anatomy for the recognition of the taxa.Item Galium shinasii (Rubiaceae): a new species of Galium L. from Eastern TurkeySik, L; Yildirim, H; Pirhan, AF; Altioglu, Y; Gemici, MGalium shinasii Yildirim (Rubiaceae), is described as a new species from Malatya Province in eastern Anatolia, Turkey. The new species is morphologically related to Galium cornigerum Boiss. & Hausskn. G. lasiocarpum and G. sorgereae Ehrend. and Schnb. but clearly differs from them based on the morphological differences presented in the species description. In addition, the conservation status, the distribution map, and notes on the biogeography and ecology of the new species are given.Item Boron intake, osteocalcin polymorphism and serum level in postmenopausal osteoporosisBoyacioglu, O; Orenay-Boyacioglu, S; Yildirim, H; Korkmaz, MThe relationship between daily boron intake and osteocalcin-mediated osteoporosis was studied in boron-exposed postmenopausal women. It is known that boron and osteocalcin are important in bone metabolism, however the effect of boron in bone metabolism has not been fully discovered. The study was performed on 53 postmenopausal women aged 55-60 living in parts of Balikesir, Turkey, where the subjects are naturally exposed to high (>= 1 mg/L) or low (< 1 mg/L) boron concentration in drinking water. 24-h urine samples were collected from all participants and creatinine clearance was detected. Boron intake levels of the subjects whose clearance levels were between 80-124 mL/min were measured by inductively coupled plasma-optical emission spectrometry (ICP-OES) in urine samples. Serum osteocalcin levels of the subjects were measured by osteocalcin enzyme-linked immunosorbent assay (ELISA) kit. Osteocalcin polymorphism rs1800247 was detected using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Serum osteocalcin levels in boron-exposed postmenopausal women were significantly higher than that of control group (P <= 0.05) and the correlation between the serum osteocalcin level and rs1800247 polymorphism was not significant in both groups (P > 0.05). The differences in the distribution of osteocalcin genotypes and alleles in postmenopausal women were not significant between the boron exposed and the control groups (P > 0.05). Serum osteocalcin level in the CC genotype was significantly higher compared to the TC genotype in boron-exposed group (P <= 0.05). Our study suggests that daily boron intake of 1 mg/L may affect bone metabolism in postmenopausal women positively.Item Never in mitosis gene A-related kinase 6 and aurora kinase A: New gene biomarkers in the conversion from ulcerative colitis to colorectal cancerGerçeker, E; Boyacioglu, SO; Kasap, E; Baykan, A; Yuceyar, H; Yildirim, H; Ayhan, S; Ellidokuz, E; Korkmaz, MUlcerative colitis (UC) is an important risk factor for colorectal cancer (CRC). Histone modifications are one of the epigenetic mechanisms that may have key roles in the carcinogenesis of CRC. At present, there are no studies comparing histone modification patterns of UC and CRC in the literature. Therefore the aim of the present study was to investigate whether genes, particularly those involved in histone modification, have value in patient monitoring with regards to CRC development in UC. Key gene expressions of the histone modification enzyme were assessed and compared in CRC, UC and control groups using the RT-PCR array technique. Patients were divided into subgroups based on the extent and duration of the disease and inflammatory burden, which are considered risk factors for CRC development in UC patients. In UC and CRC groups, a significantly higher overexpression of the NEK6 and AURKA genes compared to the control group was identified. In addition, there was a significantly higher overexpression of HDAC1 and PAK1 genes in the UC group, and of HDAC1, HDAC7, PAKI and AURKB genes in the CRC group. NEK6, AURKA, HDAC1 and PAK1 were significantly overexpressed in patients with a longer UC duration. Overexpression of AURKA and NEK6 genes was significantly more pronounced in UC patients with more extensive colon involvement. HDAC1, HDAC7, PAK1, NEK6, AURKA and AURKB are important diagnostic and prognostic markers involved in the carcinogenesis of CRC. HDAC1, PAK1, NEK6 and AURKA may be considered as diagnostic markers to be used in CRC screening for UC patients.Item A Comparative Study for Selectivity of Micronuclei in Cervical Exfoliated Cells on Chronic Boron EffectsYildirim, H; Göker, A; Demirci, H; Güvenal, T; Korkmaz, MBackground: Cervical cancer is one of the most frequent malignancies in women. Micronucleus (MN) testing has gained popularity as a biomarker in early diagnosis of many types of cancer. Aims: This study aims to investigate the role of MN testing on early detection of cervical cancer and the effect of boron exposure on cervical cells. Settings and Design: The study population comprised women who were diagnosed to be human papillomavirus (HPV)-positive and had atypical squamous cells of undetermined significance (ASCUS) as cervical cytology in a cervical screening project. A total of 15 HPV-positive and 36 ASCUS patients were identified. Randomly selected 20 women were selected from boron-rich region (n = 10) and nonboron region (n = 10). Materials and Methods: Cervical swab specimens were dyed using Papanicolaou (PAP) and May-Grunwalds-Giemsa (MGG) techniques, and MN count in 1000 cells was performed. The results were statistically evaluated. Statistical Analysis Used: Data were analyzed using Statistical Package for the Social Sciences (SPSS) version 13. Quantitative data were presented as mean +/- standard deviation. MN test scoring was compared using Mann-Whitney U-test. Results: Boron content of urine was measured to be 3.02 +/- 1.45 and 0.98 +/- 0.42 mg/day in boron-rich and nonboron regions, respectively. When MN counts were compared according to PAP and MGG staining in HPV-and ASCUS-positive women, there was statistically no significant difference (P > 0.05). Disregarding regions, HPV/control and HPV/ASCUS cases stained with PAP and MGG had statistically significant difference in MN count (P < 0.05). Conclusion: These findings suggest that MGG and PAP staining gives similar results with regard to MN count. On the other hand, it has been shown again that HPV induces MN and causes genomic instability.Item Overexpressions of RHOA, CSNK1A1, DVL2, FZD8, and LRP5 genes enhance gastric cancer development in the presence of Helicobacter pyloriDemirci, U; Orenay-Boyacioglu, S; Kasap, E; Gerçeker, E; Bilgiç, F; Yüceyar, H; Yildirim, H; Baykan, AR; Ellidokuz, EB; Korkmaz, MBackground and study aims: Intestinal metaplasia (IM), and Helicobacter pylori (HP) infection can be shown as risk factors in the development of gastric cancer (GC). WNT signaling pathway plays a critical role in carcinogenesis. However, the literature studies are limited on the significance of this pathway for the transition from IM to GC. Patients and methods: We aimed to investigate the importance of the genes of WNT signaling pathways diagnostic and prognostic markers in the presence and absence of HP in conversion from IM to GC. 104 patients, (GC group n = 35, IM group n = 45, control group n = 25) were included in this case-control study. Expression of genes in WNT signalling were searched in study groups with qRT-PCR array and qRT-PCR method. Data were analysed using PCR array data analysis software. Results: Statistically significant overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes was detected in the GC and IM groups compared to the control group (p < 0.05). Statistically significant overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes was observed in patients with metastatic GC compared to patients with GC without metastasis (p < 0.05). It was found that the RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes were statistically significantly over-expressed in diffuse GC patients compared to non-diffuse GC patients (p < 0.05). Statistically significant overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes was detected in HP positive IM patients compared to HP negative IM patients (p < 0.05). Conclusion: Overexpression of RHOA, CSNK1A1, DVL2, FZD8 and LRP5 genes in IM may suggest that these genes are important markers in the development of IM and inflammation with HP. In addition, these genes are linked to tumor burden in the GC group. Consequently, we can conclude that these genes are poor prognosis biomarkers for GC and have the potential to be used as markers for future treatment monitoring.Item Are RHOA, CSNK1A1, DVL2, FZD8 and LRP5 Genes Novel Biomarkers in the conversion from Intestinal Metaplasia to Gastric Cancer?Demirci, U; Boyacioglu, SÖ; Kasap, E; Bilgiç, F; Gerçeker, E; Yildirim, H; Baykan, A; Ellidokuz, E; Yüceyar, M; Korkmaz, MItem Biological effects of tolerable level chronic boron intake on transcription factorsBoyacioglu, SO; Korkmaz, M; Kahraman, E; Yildirim, H; Bora, S; Ataman, OYThe mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57 +/- 0.06 mg/l for boron group while the corresponding value for the control group was 0.016 +/- 0.002 mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects. The RNA was then reverse transcribed into cDNA and analyzed using the Human Transcription Factors RT2 Profiler (TM) PCR Arrays. While the boron amount in urine was detected as 3.56 +/- 1.47 mg/day in the boron group, it was 0.72 +/- 0.30 mg/day in the control group. Daily boron intake of the boron and control groups were calculated to be 6.98 +/- 3.39 and 1.18 +/- 0.41 mg/day, respectively. The expression levels of the transcription factor genes were compared between the boron and control groups and no statistically significant difference was detected (P > 0.05). The data suggest that boron, intake at 6.98 +/- 3.39 mg/day, which is the dose at which beneficial effects might be seen, does not result in toxicity at molecular level since the expression levels of transcription factors are not changed. Although boron intake over this level will seem to increase RNA synthesis, further examination of the topic is needed using new molecular epidemiological data. (C) 2016 Elsevier GmbH. All rights reserved.Item Genetic diversity of Lilium candidum natural populations in Türkiye evaluated with ISSR and M13-tailed SSR markersTokgöz, HB; Çetin, Ö; Kaya, HB; Akkale, C; Yildirim, H; Pirhan, AF; Kaya, E; Altan, FThe Liliaceae family includes the perennial, herbaceous, monocotyledonous plant Lilium candidum (L. candidum). The cosmetics, fragrance, and pharmaceutical industries regularly use L. candidum. It has been widely used in traditional medicine for wound healing, and its anti-inflammatory, antidiabetic, antimicrobial, and anticancer effects have been demonstrated in various studies. Natural populations of L. candidum are significantly affected by biotic and abiotic factors such as anthropological pressure, diseases, pathogen attacks, fossil fuel pollution, and climate change. Overcollection and destruction of its habitat put L. candidum into the endangered category. Therefore, it is of great importance to preserve this plant's genetic diversity, which plays a crucial role in adapting to different conditions, preserving evolutionary potential, and breeding studies. Molecular markers are essential in breeding and evolution studies to conserve genetic resources. Because of its economic and medical importance, various DNA markers have been used to evaluate the genetic diversity of L. candidum accessions. In this study, the genetic diversity of L. candidum, which is native to Turkiye, was determined with ISSR and SSR molecular markers among accessions collected from seven different cities and 76 accessions (Mugla, Izmir, Aydin, Antalya, Balikesir, Denizli, and Manisa). Genetic distances and phylogenetic analysis were carried out using the software TASSEL 5.2.63. The assessment of genetic diversity was visualized through a UPGMA dendrogram. The resulting phylogenetic tree revealed two distinct groups. The closest and farthest accessions were determined according to the genetic distance matrix. It was determined that the highest genetic distance value was between 19 (Balikesir, Kepsut) and 76 (Mugla, Ula) accessions (0.5390946) and the lowest genetic distance value was between 53 (Mugla, Marmaris) and 54 (Mugla, Marmaris) accessions (0.1069968).Item Turkish Thoracic Society Early Career Members Task Force Group's Virtual Congress Notes: European Respiratory Society International Congress 2020Kizilirmak, D; Karadogan, D; Yildirim, H; Akyil, FT; Eyüboglu, TS; Emiralioglu, N; Sertçelik, ÜÖ; Günaydin, FE; Ataoglu, Ö; Oguz, MS; Çakmakci, S; Özçelik, N; Öncel, A; Firincioglulari, A; Kara, BY; Ömer, D; Karaoglanoglu, S; Cetin, N; Karakas, FG; Gurkan, CG; Marim, F; Önyilmaz, T; Yulug, DP; Öztürk, NAA; Güçlü, ÖA; Küsbeci, TÇ; Serifoglu, I; Arikan, H; Töreyin, ZN; Çelik, P; Akgün, MIn this article, Early Career Task Force Group members of the Turkish Thoracic Society summarize the European Respiratory Society 2020 virtual congress. Current developments in the field of respiratory diseases were compiled with the addition of sessions specific to coronavirus disease 2019 this year. Almost all of the congress sessions were examined, and the important and striking results of the congress were highlighted. Congress sessions were attended by expert researchers, and the prominent messages of each session were highlighted in short summaries. They were then grouped under relevant titles and ranked in order of meaning and relation. It was finalized by a team of researchers.