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    Determination the Subtypes of Blastocystis sp. and Evaluate the Effect of These Subtypes on Pathogenicity
    (Springer International Publishing Ag, 2019) Cakir, Fatih; Cicek, Mutalip; Yildirim, Ibrahim Halil
    PurposeThe present study aimed to determine the frequency of subtypes of Blastocystis sp. in the immunosuppressed individuals, in patients with chronic urticaria, and in patients with GIS complaints to investigate the difference of Blastocystis sp. subtype distribution between patient and control groups.MethodsA total of 345 stool samples were collected from the patients and samples were studied by native-Lugol, trichrome staining, and Jones medium culture method. Positively detected samples were subjected to PCR to determine the subtypes. ResultsThis is the first study of nine subtypes of Blastocystis sp. investigated in our country and the most frequently found subtype was ST3, and then, the other subtypes were ST1, ST2, ST5, and ST6, respectively. Mix subtype was detected in the 11.6% and no subtype was detected in the 17.4% of the samples. The ST5 was detected first time in the control group and ST6, which is reported limitedly in our country, was found in patients with GIS complaints. ST1 and ST2 were found higher in the patient group.ConclusionThis study confirmed that the subtype (ST) differences are an important factor affecting the pathogenesis of Blastocystis sp.
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    Effects of melatonin on apoptosis and cell differentiation in MCF-7 derived cancer stem cells
    (C M B Assoc, 2018) Kocak, Nadir; Donmez, Huseyin; Yildirim, Ibrahim Halil
    Melatonin is a hormone of the pineal gland that has a wide range of biological effects such as antioxidant, anti-inflammatory, and anti-tumor activity. Previous studies have shown that melatonin also affects survival, proliferation, and apoptosis of the cells. In this study, we investigated the effect of melatonin on apoptosis, self-renewal, and differentiation. For this purpose, MCF-7 and HEK293 cells were subjected to melatonin treatment. Expression of genes related to apoptosis (Bax and Bcl2) and self-renewal and differentiation (Oct4, Sox2, and Nanog) analyzed after the sorting of cancer stem cells from MCF-7 cells. Results showed that the effect of melatonin is dependent on the melatonin concentration and treatment periods. Melatonin treatment decreased the cell proliferation rate of MCF-7 in contrast to HEK293. Also, this treatment increased apoptosis in MCF-7 cells and decreased in HEK293 cells. Gene expression of Nanog was decreased and Sox2 was increased in both cell groups after the melatonin treatment. Expression of Oct4 was decreased in MCF-7 cells and increased in HEK293 cells. We determined that melatonin decreases apoptosis and differentiation of stem cells in normal HEK293 stem cells, but increases apoptosis and differentiation in the MCF-7 cancer stem cells.
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    Gene expression of ING4 gene in pancreatic cancers and splice forms of ING4 gene
    (C M B Assoc, 2018) Yildirim, Ibrahim Halil; Cakmak, Ecir Ali; Camci, Celaleddin
    Pancreatic cancer is characterized by rapid metastasis and resistant to medical treatments. As the other cancers, mutations of tumor suppressor genes that involved in suppression of cell growth are observed in pancreatic cancers. ING4 protein is one of the proteins involved in the regulation of p53 tumor suppressor gene functions. ING4 involved in suppression of cell proliferation, chromosome rearrangement, cell migration, and angiogenesis. In this study, gene expressions and splicing variants of ING4 gene were investigated. Fresh tumor and normal specimens of the same pancreatic cancer patients were used. Gene expression study carried out by calculating the brightness of the bands on agarose gel and splicing variants were detected by direct sequencing. According to the results, three splice forms of ING4 and a decrease in gene expression of ING4 were determined. Splicing type of ING4 affects the translocation of ING4 proteins into the nucleus. To determine the gene expression of each splicing variant, will further clarify the role of ING4 in pancreatic cancers.
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    Investigation of autophagic effects of melatonin on breast cancer stem cells
    (Allied Acad, 2017) Donmez, Huseyin; Kocak, Nadir; Yildirim, Ibrahim Halil
    Autophagy plays important roles in physiologic cellular events and also in cancers. It has been reported that cells escaped from death via autophagy and if autophagy inhibited, cells conducted to apoptosis. In some studies, protective effects of the melatonin on induced autophagy in cancer cells reported. In this study, we aimed to evaluate the autophagic effect of melatonin in cancer stem cells. For this purpose, CD44+/CD24-phenotype cells sorted from melatonin-treated and untreated MCF-7 and HEK293 cells. Effect of melatonin on autophagy was analysed by immunofluorescence and western blot analysis. Results showed that melatonin-induced LC3 (Microtubule-associated protein 1A/1B-light chain 3) aggregation and formation of autophagic vacuoles in MCF-7 derived cancer stem cells and also induced LC3-I to LC3-II conversion in these stem cells when compared to untreated control group. In conclusion, melatonin showed a pro-autophagic effect in CD44+/CD24-stem cells derived from MCF-7 cells and anti-autophagic effect in CD44+/CD24-stem cells obtained from HEK293 cells.
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    Prevalence and Antibiotic Resistance of Arcobacter spp. Isolates from Meats, Meat Products, and Giblets
    (Aves, 2022) Yesilmen, Simten; Vural, Aydin; Erkan, Mehmet Emin; Yildirim, Ibrahim Halil; Guran, Husnu Sahan
    In this study, the presence and the species distribution of Arcobacter spp. were determined in ground beef, ground lamb, meatballs, chicken meat, and chicken giblet samples (470 samples in total) using the 16S rDNA polymerase chain reaction-restriction fragment length polymorphism method. The presence of Arcobacter spp. was found to be 36.38% (n =171) in all samples analyzed; 23.3% (n=63) in ground beef, ground lamb, and meatball samples; 51.3% (n = 77) in chicken meat, and 62% (n -= 31) in giblet samples. Chicken wings had the highest Arcobacter spp. contamination level (72%), and the lowest contamination was found in ground lamb (20%) samples. A higher prevalence of Arcobacter spp. was found in chicken meat and giblets than in other samples, and chicken leg and chicken breast with skin had higher prevalence of Arcobacter spp. than those without skin. A. butzleri was the most isolated species in all samples. In neck, leg, breast, and wings samples, A. cryaerophilus was the second most isolated species. In addition, we assessed antibiotic resistance of the isolates found in this study using 14 different antibiotics. All A. butzleri and A. skirrowii isolates, as well as most of the A. cryaerophilus isolates (96.7%), showed resistance to cefoperazone. A. butzleri isolates were mostly susceptible to norfloxacin (61.5%), florphenicol (60.5%), and amoxicillin/ clavulanic acid. A. skirrowii isolates showed susceptibility to ciprofloxacin (91.6%), norfloxacin (88.8%), and chloramphenicol (83.3%). A. cryaerophilus isolates showed susceptibility to chloramphenicol (96.7%), streptomycin (83.8%), cefoperazone (83.8%), and florphenicol (80.6%). We have identified that many food samples examined in this study were contaminated with Arcobacter species. Arcobacter contamination poses a human health concern and multiple antibiotic resistance in the isolates and this may pose a risk to public health.
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    Prevalence and antimicrobial susceptibility of Arcobacter species in cow milk, water buffalo milk and fresh village cheese
    (Elsevier Science Bv, 2014) Yesilmen, Simten; Vural, Aydin; Erkan, Mehmet Emin; Yildirim, Ibrahim Halil
    In this study, the presence of Arcobacter spp. was examined in cow milk (n = 50), water buffalo (WB) milk (n = 50) and fresh village cheese (n = 50) samples. The 165 rDNA-RFLP method was used for the identification of Arcobacter spp. The disc diffusion method was used to investigate the susceptibility of all strains identified to 18 different antimicrobial substances. The most commonly isolated Arcobacter species were found to be Arcobacter butzleri (38.89%), Arcobacter cryaerophilus (22.23%) and Arcobacter skirrowii (11.12%) in cow milk; A. cryaerophilus (33.33%), Arcobacter cibarius (20.83%) and A. butzleri (12.50%) in WB milk; and A. skirrowii (28.57%),A. butzleri (21.43%) and A. cryaerophilus (14.29%) in fresh village cheese. This is the first study to identify the presence of Arcobacter nitrofigilis, Arcobacter cloacae, Arcobacter halophilus, Arcobacter bivalviorum and A. cibarius species in analyzed samples. It was found that all of the A. cryaerophilus (n:16) isolates were resistant to cefoperazone, cloxacillin and penicillin G; all of the A. skirrowii (n:12) and A. butzleri (n:10) isolates were resistant to cefoperazone, tetracycline, ampicillin, erythromycin, cloxacillin and penicillin G. It was concluded that cow milk, WB milk and fresh village cheese samples are an important source of Arcobacter species and pose a risk to public health. (C) 2014 Elsevier B.V. All rights reserved.
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    The Prevalence of MEFV Gene Mutations in Rheumatoid Arthritis Patients Inhabiting the Van Province and Surroundings
    (Baycinar Medical Publ-Baycinar Tibbi Yayincilik, 2014) Ozkol, Halil; Yildirim, Ibrahim Halil; Tuluce, Yasin; Ediz, Levent; Delen, Veysel; Gulcu, Elif
    Objective: An inhibitory protein of inflammation pyrin/marenostrin is encoded by the Mediterranean fever (MEFV) gene. Mutations of this gene are known to cause familial Mediterranean fever (FMF) disease. A relation between mutations of the MEFV gene and rheumatic diseases was also suggested. The aim of the present study was to investigate the frequency of four common mutations of the MEFV gene in 110 rheumatoid arthritis (RA) patients and 98 healthy controls (HC) inhabiting a region of eastern Turkey. Material and Methods: DNA extraction was realized by salting out method from peripheral blood lymphocytes of all subjects included in the study. Polymerase chain reactions (PCR) amplification of exon 10 was performed by the appropriate primers, and single-nucleotide polymorphisms (SNPs) were detected by specific restriction endonucleases recognizing the mutational DNA or wild-type DNA regions. Results: Mutation frequency of RA patients was higher than in HC, but this result was not statistically significant (p>0.05). Conclusion: The MEFV mutation rate of RA patients living in eastern Turkey was not significantly different from HC. Further studies are needed to investigate other gene mutations that may affect RA etiopathogenesis.
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    Single-strand conformation polymorphism-based genetic characterization of the Cyclospora cayetanensis strains collected from different provinces in Turkey
    (Inst Agricultural Medicine, 2021) Cicek, Muttalip; Yildirim, Ibrahim Halil; Cengiz, Zeynep Tas; Karaman, Ulku
    Introduction and objective. Cyclospora cayetanensis, a coccidian protozoan species, has been recently found to cause diarrhea in all age groups in immunocompetent and immunocompromised individuals in most regions of the world. This study aimed to conduct the molecular detection of C. cayetanensis and to determine the genetic diversity of the 18S ribosomal RNA (rRNA) gene sequence of C. cayetanensis isolated from individuals living in different provinces in Turkey by using PCR-single-strand conformation polymorphism (SSCP). Materials and method. A total of 22 subjects were included in the study. Fourteen of the subjects were female and eight were male, with ages ranging between 7-65 years. Stool specimens were examined using wet mount and modified acid-fast staining methods, which revealed the presence of oocysts in the samples. The 18S rRNA ITS-1 Ccits37f-GCTTGCTATGTTTTAGCATGTGG and Ccits501r-GCACAATGAATGCACACACA gene regions were used as primers. The PCR products were analyzed by agarose gel electrophoresis and visualized on a UV transilluminator. For the SSCP, the PCR products were denatured with formamide, run for 16 h in 6% (49:1) polyacrylamide gel, and then imaged with silver staining. Results. SSCP assay was performed given that the DNA strands demonstrated different folds; the DNA strands contain different nucleotides based on the PCR-SSCP results for the Cyclospora strains collected in 4 provinces. Moreover, 3 different band profiles were observed in the investigated samples. A slight mutation difference was observed among the strains collected. Conclusions. Further comprehensive studies involving more C. cayetanensis-positive specimens and utilizing different mutation screening methods are warranted to demonstrate mutation differences in Cyclopora strains in Turkey.
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    TLR4 Asp299Gly and Thr399Ile and TLR2 intron 2 microsatellite gene polymorphism in patients with acute biliary pancreatitis: Does it cause the disease?
    (Aves, 2018) Anilir, Ender; Ozen, Filiz; Ozemir, Ibrahim Ali; Yildirim, Ibrahim Halil; Bilgic, Cagri; Alimoglu, Orhan
    Objectives: There has been coverage of Toll-like receptor 4 and Toll-like receptor 2 gene polymorphisms in inflammatory episodes in a number of studies. In view of the inflammatory nature of acute pancreatitis, we aimed to determine the predictive value of mutations in Asp299Gly and Thr399Ile of the Toll-like receptor 4 gene, and the intron 2 microsatellite polymorphism of the Toll-like receptor 2 gene on the occurrence of acute biliary pancreatitis. Material and Methods: The study included 86 patients for the Toll-like receptor 4 Thr399Ile polymorphism, 100 patients for the Toll-like receptor 4 Asp299Gly polymorphism with acute biliary pancreatitis, and 101 healthy volunteers. At the same time, 93 patients and 92 healthy volunteers were included in the study to research the Toll-like receptor 2 intron 2 microsatellite polymorphism. Genotypes were determined using the restriction fragment length polymorphism analysis of PCR products and by an allele-specific PCR. Results: The Toll-like receptor 4 Thr399Ile homozygotes mutant variants (p=0.005) and Toll-like receptor 2 MM genotype (p<0.001) were detected with a significantly higher frequency in patients with acute biliary pancreatitis than in the healthy blood donors. Conclusion: The Toll-like receptor 4 Asp299Gly and Thr399Ile polymorphisms and the Toll-like receptor 2 intron 2 microsatellite polymorphism are statistically associated with ABP.