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Item RAPD-PCR analysis of cultured type olives in Turkey(2009) Sesli M.; Yeǧenoǧlu E.D.The aim of this study was to detect genetic similarities and distances among cultured type olive trees by RAPD-PCR technique. Olives are raised in a high range from the Aegean, Mediterranean, Marmara and Black Sea to Southeast Anatolia regions of Turkey. Olive breeding had a rapid increase in Turkey during recent years, among the agricultural products. Finding the genetic relationships between cultured type olives may help to improve genetic resources and our knowledge of their evolutionary background and to determine genetic relationships with wild type relatives. In this study, samples were obtained from the Olive Production Research Institute (Manzanilla, Domat, Gemlik and Memecik) and sapling producers in Manisa, Akhisar (Uslu, Edremit). Genomic DNA's were extracted from young leaves and PCR was used generate RAPD bands. Sixty random primers obtained from Operon Tech. were tested by RAPD-PCR (OP-A, OP-I, OP-Q). A total of 36 primers among 60 Operon random primers (Kit OP-A, OP-I, OP-Q) yielded clear and firm bands. The electrophoretic patterns of olive samples showed that 291 highly polymorphic loci. Averages of 8.08 scorable bands per primer were determined from RAPD-PCR analysis. © 2009 Academic Journals.Item Comparison of Manzanilla and wild type olives by RAPD-PCR analysis(Academic Journals, 2010) Sesli M.; Yeǧenoǧlu E.D.The object of this study was to detect genetic similarities and distances between cultivated Manzanilla and wild type olives by random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) technique. In this study, the cultivated type olive Manzanilla was supplied from Olive Research Institute of Turkey and the wild type olives from the villages of Manisa, Izmir and Mugla provinces. Genomic DNA's were extracted from young leaves and PCR was used to generate RAPD bands. Sixty random primers obtained from Operon technology were tested by RAPD-PCR (OP-A, OP-I, OP-Q). Forty one of 60 primers used in the study provided 346 considerably polymorphic bands and the average number of bands was defined as 8.43. Comparisons of cultivated and wild type olives are important for understanding genetic relation. It was determined that the genetic distance values varied between 0.0665 and 0.2863 and genetic similarity values varied between 0.9356 and 0.7511. It was observed that the samples most close to each other were wild 8 and wild 3 and the samples most distant from each other were wild 5 and Manzanilla, in accordance with such genetic distance and similarity values. © 2010 Academic Journals.Item Oxidative DNA damage: The thyroid hormone-mediated effects of insulin on liver tissue(Humana Press Inc., 2010) Altan N.; Sepici-Dinçel A.; Şahin D.; Kocamanoǧlu N.; Kosova F.; Engin A.Thyroid hormone affects glucose homeostasis with its actions between the skeletal muscle and liver and the altered oxidative and non-oxidative glucose metabolism. In our study three chemicals are considered biomarkers associated with oxidative stress for protein modifications were measured; 8-hydroxy-2-deoxyyguanosine (8-OHdG), a major lesion that can be generated by reactive oxygen species for DNA damage, protein carbonyl content (PCO), products of protein oxidation and advanced oxidation protein products (AOPPs) a dithyrosine containing cross-linked protein products. The purpose of the recent study was to determine the effects of insulin and T4 or their combination in diabetic, thyroidectomized, or diabetic-thyroidectomized rats and possible relations with oxidative DNA and protein damages. For this purpose, rats were assigned to eight groups: Group 1; control, Group 2; diabetes, Group 3; diabetes + insulin, Group 4; surgically thyroidectomized control, Group 5; thyroidectomized + diabetes, Group 6; thyroidectomized + diabetes + insulin, Group 7; thyroidectomized + diabetes + insulin + thyroid hormone, levothyroxin sodium, 2.5 μg/kg and Group 8; thyroidectomized + diabetes + insulin + thyroid hormone, levothyroxin sodium, 5.0 μg/kg for 5 weeks. After the genomic DNA of liver tissues was extracted, the ratio of 8-OHdG to deoxyguanosine and liver tissue protein oxidation markers was determined. The main findings of our recent study were the increased 8-OHdG levels during the diabetes, hypothyroidism, and hypothyroidism with diabetes, which can be regulated in different percentages with the treatment of 2.5 and 5.0 μg/kg doses of thyroid hormone and the altered protein carbonyl and AOPP levels of liver tissue. Consequently, it was observed that the DNA and protein damage induced by oxidative stress in diabetes could be regulated by dose-dependent thyroid hormone-mediated effects to insulin treatment. © 2010 Springer Science+Business Media, LLC.Item Determination of the genetic relationships between wild olive (Olea europaea oleaster) varieties grown in the aegean region(Fundacao de Pesquisas Cientificas de Ribeirao Preto, 2010) Sesli M.; Yeǧenoǧlu E.D.The RAPD technique was used for determining genetic differences between 12 wild-olive varieties grown in the Aegean provinces of Izmir, Mugla, and Manisa in Turkey. Wild olives obtained from the same provinces were included in the same plot. Twenty of 25 operon primers (OP-I 4, OP-I 14, OP-I 15, OP-I 16, OP-I 17, OP-Q1, OP-Q2, OP-Q3, OP-Q4, OP-Q11, OP-Q12, OP-Q13, OP-Q14, OP-Q15, OP-Q16, OP-Q17, OP-Q18, OP-Q19, OP-Q20, OP-F1, OP-F2, OP-F3, OP-F6, OP-F7, OP-F8) yielded bands. The differences between the varieties were determined based on their genetic similarities, using principal coordinate analysis; genetic distances were determined using neighbor-joining analysis. The varieties wild 7 and wild 12 had the lowest genetic similarity (0.97, Jaccard similarity index); they also had the greatest genetic distance between them (0.3606, Nei's genetic distance). It was concluded that the RAPD technique is adequate for the evaluation of genetic relationships among wild olives. Principal coordinate analysis and neighbor-joining analysis gave results that support the Genetic relationships between wild olive varietie use of this type of analysis to help understand the genetic background of olives and for further genetic studies. ©FUNPEC-RP.Item High-resolution melting analysis for screening of Turkish germline mutations in BRCA1 and BRCA2; [Türk hasta popülasyonunda BRCA1 ve BRCA2 germline mutasyonlarïnïn high resolution melting analizi ile taranması](UHOD - Uluslararasi Hematoloji Onkoloji Dergisi, 2010) Purcu D.U.; Karaca B.; Kapkac M.; Ozdemir N.; Uzunoglu S.; Uslu R.The germline mutations of breast cancer susceptibility genes 1 (BRCA1) and 2 (BRCA2) are the two most frequently mutated genes in inherited breast and ovarian cancer. Among the most known mutations in these tumor suppressor genes are 5382insC and 185delAG in BRCA1 and 6174delT in BRCA2. The aim of the current study was to investigate the frequency of these BRCA1 and BRCA2 mutations in Western Turkish population. Twenty-five women with a history of self breast cancer and family history, 25 women with a familial history of breast cancer in their first degree-relatives and five healthy women formed the studied groups. DNA from peripheral blood was extracted and analyzed by high-resolution melting (HRM) analysis. None of the 50 patients and five healthy individuals was found to carry 185delAG mutation in BRCA1 and the 6174delT mutation in BRCA2. But, we found the 5382insC mutation in exon 20 of BRCA1 in five patients, having a strong family history. Four of these five patients were from the same family. Our preliminary results indicate that penetrance of 5382insC mutation in BRCA1 mutations is dominant in Turkish population; however, it seems there might be some other genes that contribute more significantly to familial breast carcinoma in Turkish population in BRCA.Item RAPD assay of wild-type olives in Turkey(Fundacao de Pesquisas Cientificas de Ribeirao Preto, 2010) Sesli M.; Yeǧenoǧlu E.D.Genetic similarities and distances between wild-type olives in Turkey were studied using an RAPD-PCR assay. Seven wild olive tree samples were collected from villages in Manisa and Izmir provinces. Genomic DNA was extracted from young leaves and the RAPD-PCR assay was used to generate RAPD markers. Sixty-five random primers obtained from Operon Technologies were tested for the assay (OP-A 1-20, OP-I 1-20, OP-Q 1-20, and OP-J 1-5). Thirty-two of these primers yielded 115 highly polymorphic bands. The mean number of usable bands per primer for all the samples was 3.59. The genetic distance values ranged from 0.1498 to 0.6845, and genetic similarity values varied from 0.8609 to 0.5043. We found that the closest samples based on their genetic distance and similarity values were from Harlak and Sabancilar; the most distant samples were from Bornova and Bademli, © FUNPEC-RP.Item Alterations of copy number of methylation pattern in mismatch repair genes by methylation specific-multiplex ligation-dependent probe amplification in cases of colon cancer(2011) Onrat S.T.; Çeken I.; Ellidokuz E.; Kupelioǧlu A.Genetic alterations and changes in genomic DNA cytosine methylation patterns are associated with all types of cancer and are caused by germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1 (MutL homolog 1, 19 exons) and MSH2 (MutS homolog 2, 16 exons). Genomic DNA was extracted from tissue samples embedded in paraffin from 49 patients with adenocarcinoma and from 21 patients with carcinoma for the study group; genomic DNA was extracted from lymphocytes from 10 healthy donors for the control group. We used methylation specific multiplex ligation-dependent probe amplification (MS-ML-PA), which allows the detection of copy number changes and unusual methylation levels of 10 to 50 different sequences in one reaction by use of the methylationsensitive restriction enzyme HhaI and sequence-specific capillary electrophoresis for the study of 24 genes.We found the mean methylation rates for MLH1 (97.14%), MSH2 (24.28%), MSH6 (MutS homolog 6) (67.14%), MSH3 (MutS homolog 3) (78.57%), MLH3 (MutL homolog 3) (75.71%), PMS2 (postmeiotic segregation increased 2) (65.71%), MGMT(O-6-methylguanine-DNA methyltransferase) (82.85%). We conclude that the mismatch repair (MMR) system is critical for the maintenance of genomic stability.Item Association between idiopathic generalized epilepsy and EFHC1 gene mutations of 662 G>A and 685 T>C; [İdiyopatik Jeneralize Epilepsi ile EFHC1 Genindeki 662 G>A ve 685 T>C Mutasyonu Arasındaki İlişkinin Araştırılması](Turkiye Klinikleri, 2012) Büyük I.; Tuǧrul B.; Yilmaz H.; Onur E.; Vatandaş G.; Doǧan BozyIǧIt F.Objective: Idiopathic generalized epilepsy (IGE) is an epilepsy form without an underlying brain lesion or neurological indication or symptom. Recent investigations on the genetic origins of IGE and its subtypes report that certain mutations of various ion and non-ion channel genes in the central nervous system may be associated with IGE. Among these mutations, the ones related to the non-ionic channel gene EFHC1 are controversial (545G>A, 685T>C, 628G>A 757G>T, 229C>A, 662G>A, 520A>G, 776G>A, 829C>T). In this study we investigated the relationship between IGE and 662G>A (R221H) and 685T>C (F229L) mutations in EFHC1 gene in a Turkish population. Material and Methods: The study enrolled 96 healthy volunteers (47 male, 49 female) and 96 IGE patients (41 male, 55 female). IGE diagnosis was confirmed in the neurology department. After venous blood sampling, DNA extractions were performed. The presence of 662G>A (R221H) and 685T>C (F229L) mutations in the exon 4 of EFHC1 gene were analyzed using Real-Time polymerase chain reaction (PCR) (Cobas, Roche Diagnostics, Germany). The results of the control and patient groups were compared statistically. Results: In the patient group there was one heterozygous male with 685T>C mutation. In the control group, there were two subjects with 685T>C mutation; one heterozygous male and one heterozygous female. The control and the patient groups did not have the 662G>A mutation. The difference between the patient and the control groups were not significant (p value for 685 T>C mutation=0.56062; p value for 662G>A mutation=1.00). Conclusion: We found no evidence that EFHC1 is a major genetic factor for the development of IGE in Turkish patients. Our results indicated that 685T>C and 662G>A mutations might not be associated with IJE. © 2012 by Türkiye Klinikleri.Item Genetic screening in adolescents with steroid-resistant nephrotic syndrome(Nature Publishing Group, 2013) Lipska B.S.; Iatropoulos P.; Maranta R.; Caridi G.; Ozaltin F.; Anarat A.; Balat A.; Gellermann J.; Trautmann A.; Erdogan O.; Saeed B.; Emre S.; Bogdanovic R.; Azocar M.; Balasz-Chmielewska I.; Benetti E.; Caliskan S.; Mir S.; Melk A.; Ertan P.; Baskin E.; Jardim H.; Davitaia T.; Wasilewska A.; Drozdz D.; Szczepanska M.; Jankauskiene A.; Higuita L.M.S.; Ardissino G.; Ozkaya O.; Kuzma-Mroczkowska E.; Soylemezoglu O.; Ranchin B.; Medynska A.; Tkaczyk M.; Peco-Antic A.; Akil I.; Jarmolinski T.; Firszt-Adamczyk A.; Dusek J.; Simonetti G.D.; Gok F.; Gheissari A.; Emma F.; Krmar R.T.; Fischbach M.; Printza N.; Simkova E.; Mele C.; Marco Ghiggeri G.; Schaefer F.Genetic screening paradigms for congenital and infantile nephrotic syndrome are well established; however, screening in adolescents has received only minor attention. To help rectify this, we analyzed an unselected adolescent cohort of the international PodoNet registry to develop a rational screening approach based on 227 patients with nonsyndromic steroid-resistant nephrotic syndrome aged 10-20 years. Of these, 21% had a positive family history. Autosomal dominant cases were screened for WT1, TRPC6, ACTN4, and INF2 mutations. All other patients had the NPHS2 gene screened, and WT1 was tested in sporadic cases. In addition, 40 sporadic cases had the entire coding region of INF2 tested. Of the autosomal recessive and the sporadic cases, 13 and 6%, respectively, were found to have podocin-associated nephrotic syndrome, and 56% of them were compound heterozygous for the nonneutral p.R229Q polymorphism. Four percent of the sporadic and 10% of the autosomal dominant cases had a mutation in WT1. Pathogenic INF2 mutations were found in 20% of the dominant but none of the sporadic cases. In a large cohort of adolescents including both familial and sporadic disease, NPHS2 mutations explained about 7% and WT1 4% of cases, whereas INF2 proved relevant only in autosomal dominant familial disease. Thus, screening of the entire coding sequence of NPHS2 and exons 8-9 of WT1 appears to be the most rational and cost-effective screening approach in sporadic juvenile steroid-resistant nephrotic syndrome. © 2013 International Society of Nephrology.Item Histopathological and genetic features of patients with limb girdle muscular dystrophy type 2C; [Kavşak tipi müsküler distrofi tip 2C hastalari{dotless}ni{dotless}n histopatolojik ve genetik özellikleri](Federation of Turkish Pathology Societies, 2014) Diniz G.; Hazan F.; Tosun Yildirim H.; Ünalp A.; Polat M.; Serdaroǧlu G.; Güzel O.; Baǧ Ö.; SeçIl Y.; Özgönül F.; Türe S.; Akhan G.; Tükün A.Objective: In this study, it was aimed to describe the clinical, histopathological and genetic features of 20 patients with gamma sarcoglycanopathy confirmed by muscle biopsies and genetic analysis. Material and Method: We retrospectively reviewed 20 patients from whom muscle biopsy specimens were obtained between 2007 and 2012. All patients were clinically diagnosed as muscular dystrophy and biopsy materials were collected from five different centers of neurological disorders. All DNAs were extracted from muscle tissues or blood samples of patients and genetic tests (mutation analyses for gamma sarcoglycan gene and deletion-duplication analyses for all 4 sarcoglycan genes) were performed. Results: The mean age of the patients was 7.6 years (2 -21 years). Only one case (5%) was older than 14 years. The mean CPK level was 10311 U/L (1311 - 35000 U/L). There were 4 siblings in these series. Expression defects of gamma sarcoglycan staining were determined in (15 males, and 5 females) all patients with muscle biopsy specimens. But only in 9 of them, disease-causing defects could be determined with genetic analyses. Conclusion: The present study has demonstrated that both examination of muscle biopsy specimens and DNA analysis remain important methods in the differential diagnosis of muscular dystrophies. Because dystrophinopathies and sarcoglycanopathies have similar clinical manifestation.Item No relation between EFHC2 gene polymorphism and idiopathic generalized epilepsy(Makerere University, Medical School, 2015) Berrin T.; Hikmet Y.; Gülşen V.; Ferda B.; Erdal B.; Ece O.Background: Idiopathic generalized epilepsy (IGE) is an epilepsy form without an underlying brain lesion or neurological indication or symptom. Recent investigations on the genetic origins of IGE and its subtypes report that certain mutations of various ion and non-ion channels genes in the central nervous system may be associated with IGE. Purpose: In this study we evaluated the relation between IGE and S430Y polymorphism in EFHC2 gene in a Turkish population. Material/methods: The study enrolled 96 healthy volunteers (47 male, 49 female), served as controls, and 96 IGE patients (41 male, 55 female), IGE diagnosis was confirmed in the neurology department. DNA extractions were performed. The presence of S430Y polymorphism in the exon 9 of EFHC2 gene were analyzed by Real-Time PCR. The findings obtained from the control and patient groups were compared. Results: In the patient group there was one heterozygous male with 685 T>C mutation. In the control group, there were two objects with 685 T>C mutation; one heterozygous male, one heterozygous female. 662 G>A mutation was determined in neither controls nor patients. Conclusion: In our series of 96 IGE patients and 96 healthy controls, there was no relation between S430Y polymorphism in EFHC2 gene and IGE presence. © 2015, Makerere University, Medical School. All rights reserved.Item Molecular detection and identification of Leishmania spp. in naturally infected Phlebotomus tobbi and Sergentomyia dentata in a focus of human and canine leishmaniasis in western Turkey(Elsevier B.V., 2016) Özbel Y.; Karakuş M.; Arserim S.K.; Kalkan Ş.O.; Töz S.Human visceral leishmaniasis (VL) is reported from 38 provinces of Turkey and dogs are accepted as main reservoir hosts. Kuşadasi town, belonging to Aydin province and located in western part of Turkey, is endemic for human and canine visceral leishmaniasis caused by Leishmania infantum MON1 and MON98.In this study, phlebotomine survey was conducted to determine the vector sand fly species and to identify sand fly blood meal sources. In August and September 2012, 1027 sand fly specimens were caught using CDC light traps. Eight Phlebotomus and two Sergentomyia species with the dominancy of Phlebotomus tobbi (61.34%) were detected. A total of 622 female sand flies (571 Phlebotomus; 51 Sergentomyia) were checked for Leishmania infection by direct dissection of the midgut. The half of the midgut content was inoculated into NNN culture for isolation of the parasite. Leishmania species-specific ITS1 real time PCR, conventional PCR assays of ITS1 and hsp70 genes and subsequent sequencing were performed from extracted DNAs. A region of cytochrome b (cyt-b) gene of vertebrates based PCR was used to determine the source of blood meal of sand flies.In microscopical examinations, two female specimens (0.32%) were found naturally infected with high number and different stages of promastigotes. No growth was observed in NNN culture but Leishmania DNA was obtained from both specimens. First positive specimen was identified as P. tobbi and L. infantum DNA was detected. Second specimen was Sergentomyia dentata, but Leishmania DNA could not be identified on species level. A total of 16 blood-fed female P. tobbi specimens were used for blood meal analysis and eight, three and one specimens were positive for human, dog and mouse, respectively.This is the first detection of Leishmania promastigotes using microscopical examination in P. tobbi and S. dentata in human and canine visceral leishmaniasis endemic area in western part of Turkey. Our results indicate that, (i) P. tobbi is the principal vector species and (ii) human and dogs are main blood sources. The detection of Leishmania sp. in Sergentomyia species may be an evidence for natural cycle of Sauro-leishmania agents in the area. © 2016 Elsevier B.V.Item Discrimination of Paederus fuscipes and Paederus littoralis by mtDNA-COI PCR-RFLP(Tehran University of Medical Sciences, 2016) Bazrafkan S.; Vatandoost H.; Heydari A.; Bakhshi H.; Panahi-Moghadam S.; Hashemi-Aghdam S.; Mohtarami F.; Rahimiforoushan A.; Anlas S.; Shayeghi M.; Oshaghi M.A.; Abtahi S.M.Background: Linear dermatitis is endemic in Iran where most cases occur in the Caspian Sea coast and Fars province. The disease is caused by beetles of the genus Paederus which are active from early spring to beginning of autumn although its incidence rises from May to August. The classic taxonomy of Paederus spp. is based on the male genitalia that is very complex and needs expertise. In this study, we report a DNA-based method to discriminate Paederus fuscipes and Paederus littoralis (=syn: P. lenkoranus, P. ilsae). Methods: Type specimens were collected from north and south of Iran. Molecular typing of the species was performed using restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified fragments of mtDNA-COI. Results: Sequence analyses of the data obtained in this study showed significant DNA polymorphisms. There were 89 substitutions between COI sequences of the two species. The mtDNA-COI fragment comprises several useful species-specific restriction sites comprising HaeIII that could result in distinctively different species-specific PCR- RFLP profiles. The HaeIII enzyme cuts the 872 bp PCR amplicon of P. littoralis into 737 and 100 bp and two small nonvisible bands whereas it does not cut P. fuscipes amplicon into fragments. Conclusion: This study demonstrates that molecular typing is useful method and allows one to differentiate between two species and is recommended for discrimination of other Paederus species, which morphologically are indistinguishable or very difficult to be distinguished.Item Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT)(Public Library of Science, 2017) Karakuş M.; Nasereddin A.; Onay H.; Karaca E.; Özkeklikçi A.; Jaffe C.L.; Kuhls K.; Özbilgin A.; Ertabaklar H.; Demir S.; Özbel Y.; Töz S.Turkey is located in an important geographical location, in terms of the epidemiology of vector-borne diseases, linking Asia and Europe. Cutaneous leishmaniasis (CL) is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey, 45% of CL patients originate from Şanlıurfa province located in southeastern Turkey. Herein, the epidemiological status of CL, caused by L. tropica, in Turkey was examined using multilocus microsatellite typing (MLMT) of strains obtained from Turkish and Syrian patients. A total of 38 cryopreserved strains and 20 Giemsa-stained smears were included in the present study. MLMT was performed using 12 highly specific microsatellite markers. Delta K (ΔK) calculation and Bayesian statistics were used to determine the population structure. Three main populations (POP A, B and C) were identified and further examination revealed the presence of three subpopulations for POP B and C. Combined analysis was performed using the data of previously typed L. tropica strains and Mediterranean and Şanlıurfa populations were identified. This finding suggests that the epidemiological status of L. tropica is more complicated than expected when compared to previous studies. A new population, comprised of Syrian L. tropica samples, was reported for the first time in Turkey, and the data presented here will provide new epidemiological information for further studies. © 2017 Karakuş et al.Item Clinicopathological characteristics and mutation profile of BRAF and NRAS mutation in cutaneous melanomas in the Western Turkish population(Turkiye Klinikleri Journal of Medical Sciences, 2018) Evrenos M.K.; Temiz P.; Çam F.S.; Yaman M.; Yoleri L.; Ermertcan A.T.Background/aim: Malignant melanoma is the most common cause of death due to skin cancers. The most common mutations in RAFRAS pathway from tumor oncogenes are BRAF and NRAS. In this study, we analyzed the frequency of BRAF and NRAS gene mutations and investigated their association with clinicopathological features of melanomas in the Turkish population. Materials and methods: 65 primary cutaneous melanoma were included in the study. The mutations were evaluated with real-time PCR-based PCR-array through allele-specific amplification, and the results were correlated with various clinicopathological characteristics. Results: 52.3% of the patients were female and 47.7% were male. The mean age of the patients with a mutation was lower than those without mutation. 16 patients had BRAF mutation. 12 patients had NRAS mutation. NRAS mutation was statistically more common in men (P = 0.036). The number of mitoses increased with the increase of the tumor thickness (P = 0.003). There was more mitosis in the presence of ulceration (P = 0.05). A total of 41.7% of NRAS mutations had adjuvant chemotherapy. Conclusion: We found lower mutation rate when compared to regional studies. NRAS mutation was common in men. This is the first study from our region evaluating the prognostic value of clinical stage and necessity of adjuvant treatment with the presence of BRAF and NRAS mutations. © TÜBİTAK.Item First isolation of Mycobacterium bovis SIT 482 BOV from beef cattle in Turkey(Hellenic Veterinary Medical Society, 2020) Avsever M.L.; Çavuşoğlu C.; Çamkerten İ.Bovine tuberculosis is a zoonotic disease which should be emphasized in our country as in many countries. A large number of genotypes have been revealed by spoligotyping method of M. bovis in the world. M. bovis SIT 482. BOV is one of these genotypes and it is also M. bovis genotype in which BCG vaccine is administered in humans. The BCG vaccine is obtained through multiple passages of this genotype. However, this genotype, like other genotypes, can cause serious infections in humans and animals. There are data on the isolation of M. bovis SIT 482 BOV from animal and human tuberculosis cases in the world. In our country, the isolation of this genotype has been reported only in humans and no data have been found in the animals. In this study, M. bovis SIT 482. BOV was isolated from the samples of six cattle with internal organ samples obtained from licensed slaughterhouses in Aksaray. While isolation is carried out with BACTEC MGIT 960 liquid media, spoligotyping was carried out according to the manufacturer’s with kit (Isogen LifeScience, The Netherlands). This study aims to report M. bovis SIT 482 BOV from cattle in Turkey for the first time, to draw attention a very limited number reported in M. bovis cases in Turkey, highlight the importance of genotyping of tuberculosis factors and contribute to epidemiological studies. These and similar studies will contribute to the creation of genetic maps for eradication of M. bovis from cattle in our country. The study was also conducted to investigate whether M. bovis SIT 482. BOV isolated from cattle in Aksaray province is BCG strain or another strain giving the same pattern. © 2020 M.L. Avsever, C. Çavuşoğlu, I. ÇamkertenItem Full-mouth disinfection effects on gingival fluid calprotectin, osteocalcin, and N-telopeptide of Type I collagen in severe periodontitis(Wiley-Blackwell, 2020) Afacan B.; Çınarcık S.; Gürkan A.; Özdemir G.; İlhan H.A.; Vural C.; Köse T.; Emingil G.Background: To compare the effects of full-mouth disinfection (FMD) and full-mouth ultrasonic debridement (FMUD) on clinical, microbiological and biochemical parameters with conventional quadrant-wise scaling and root planning (Q-SRP) in severe chronic periodontitis. Methods: In the present prospective randomized controlled clinical trial with three parallel arms (#NCT04038801), 60 chronic periodontitis patients were randomly assigned to three study groups by a consecutive number in ascending order: FMD (n = 20), FMUD (n = 20), and Q-SRP (n = 20). All measurements and treatments were performed by the same investigator. At baseline, gingival crevicular fluid (GCF) and subgingival plaque were collected and clinical periodontal parameters were recorded. Ultrasonic debridement was completed within 24 hours in FMD and FMUD groups. Chlorhexidine gluconate was used for FMD. Q-SRP was performed by hand instruments per quadrant at 1-week-intervals. Clinical measurements and sampling were repeated at 1, 3, and 6 months after treatment. Real-time PCR was used for quantitative analysis of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, Fusobacterium nucleatum, and total bacteria count. GCF Calprotectin, osteocalcin, and N-telopeptide of type I collagen (NTx) levels were analyzed by ELISA. The changes of GCF biomarker levels after treatment between groups were the primary outcomes. Results: No harm was observed. All treatment strategies resulted in significant improvements in all clinical parameters (P < 0.05), with no significant differences between study groups at all time-points (P ˃ 0.05). Aggregatibacter actinomycetemcomitans was significantly decreased in FMD compared to FMUD and Q-SRP at 6 months (P < 0.05). Although GCF NTx total amounts increased in all groups during the study period, this increase was less prominent in full-mouth groups at three time points after treatment (P < 0.05). Conclusions: Present results represent the short-term effects. Full-mouth treatment approaches offered limited beneficial effects on microbiological and biochemical parameters over quadrant-wise approach. All three treatment strategies can be recommended in the management of severe chronic periodontitis. © 2020 American Academy of PeriodontologyItem Determination of sand fly fauna and molecular detection of Leishmania in sand flies in Antalya Province, Southern Turkey(Springer Science and Business Media Deutschland GmbH, 2021) Arserim S.K.; Çetin H.; Karakuş M.; Demir S.; Ser Ö.; Töz S.; Balcioğlu I.C.; Ölgen M.K.; Yilmaz B.; Özbel Y.Visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL) are diseases transmitted by infected female sand flies. Since the eradication of malaria in Turkey, CL is the main vector-borne disease in the country, with more than 2000 cases per year, making it a significant public health problem. The aims of this study were to carry out an entomological survey in Antalya Province, an endemic area for CL in the Mediterranean Region of Turkey, to identify sand fly fauna and to screen female specimens for the presence of Leishmania parasites (Leishmania infantum, L. tropica, L. major, and L. donovani) using molecular analysis. Sand flies were collected in 42 localities of seven districts in Antalya Province using CDC miniature light traps in two different periods, June 2012 and September 2013. The specimens were kept in 96% ethanol until the dissection was done. The head and genitalia of the specimens were cut for preparing individual slides for species identification. The rest of the body of female specimens was kept separately. The specimens were identified at the species level, and 27 pools were generated according to the locations and species for screening the presence of Leishmania. A commercial kit was used for DNA extractions. Real-time and conventional polymerase chain reaction (PCR) targeting the internal transcribed spacer region (ITS1) were then performed. In total, 1306 specimens comprising nine species belonging to the Phlebotomus genus were collected in the study region, with Phlebotomus neglectus/syriacus (38.82%) the most abundant, followed by P. alexandri (21.67%) and P. tobbi (20.44%). In the 27 pools, Leishmania infantum DNA was detected in four pools containing P. neglectus/syriacus and one pool containing P. tobbi. In conclusion, the sand fly fauna in the Antalya Province is diverse. The probable vector sand fly species are P. neglectus/syriacus and P. tobbi with high dominance (59.26%), which indicates a high risk of CL transmission. The data presented here may help to shed more light on the transmission cycles of the Leishmania parasite in this CL endemic area. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Item Investigation of the role of stray cats for transmission of toxoplasmosis to humans and animals living in Izmir, Turkey(Journal of Infection in Developing Countries, 2021) Karakavuk M.; Can H.; Selim N.; Yesilsiraz B.; Atli E.; Sahar E.A.; Demir F.; Gül A.; Özdemir H.G.; Alan N.; Yalçin M.; Özkurt O.; Aras M.; Çelik T.; Can S.; Döskaya A.D.; Gürüz A.Y.; Döskaya M.Introduction: Toxoplasma gondii is a protozoan parasite that has a widespread distribution among mammalians and birds. One of the reasons for the high prevalence may be due to ingesting oocyst disseminated by stray cats' feces. In Turkey, most of the citizens are closely associated with stray cats and they love to pet and feed them on the streets. In this study, we aimed to determine the prevalence of T. gondii DNA in feces of stray cats living in Izmir, Turkey in order to identify the transmission potential to humans and other animals. Methodology: Feces and blood samples of 465 stray cats were investigated for the presence of T. gondii oocysts by microscopy and for the presence of T. gondii DNA by two real time PCR methods. Furthermore, serum samples were analyzed for anti-T. gondii IgG antibodies using an ELISA. Results: Oocysts were detected in 0.43% of the stray cats by microscopy. T. gondii DNA was detected in 14.37% of the stray cats' feces samples. The seroprevalence rate was 37.84%. In the feces and/or blood PCR positive group, 35.89% of them were seropositive. Among the 176 seropositive cats, T. gondii DNA was detected in feces of 27 cats (15.34%). Conclusions: This study first time showed the inter relation of T. gondii DNA in feces and blood samples and seropositivity. In sum, over 14% of the stray cats living outdoor may have an important role in transmission of toxoplasmosis to humans in Izmir as well as to other animals. © 2021 Journal of Infection in Developing Countries. All rights reserved.Item Population structure and gene flow of the syntopic turtles Emys and Mauremys from coastal and inland regions of Anatolia (Turkey): results from mitochondrial and microsatellite data(Springer Science and Business Media B.V., 2021) Ilhan S.; Vamberger M.; Ayaz D.; Fritz U.Revealing the genetic basis of the existence of different species living together in different geographic regions provides clarification of this phylogeographic differentiation. In this study, we investigated the population genetics and evaluated the level of genetic variation of inland and coastal populations of Mauremys and Emys in Turkey. Tissue samples of 196 terrapins were studied which were collected from syntopic coastal (Gölbent-Söke/Aydın; M. rivulata and E. orbicularis) and inland populations (Bahçesaray/Aksaray; M. caspica and E. orbicularis). DNA was isolated using the InnuPREP DNA Mini Kit. Mitochondrial DNA sequences and allelic variation at 13 microsatellite loci for Mauremys and 12 microsatellite loci for Emys were examined. Three haplotypes were found for Emys orbicularis (Im, Ip and Iw) collected from the coastal region and two haplotypes for Emys orbicularis (Ig and Im) collected from inland. Two haplotypes were identified for M. caspica (Cmt8 and Cmt9) and three haplotypes were identified for M. rivulata (Rmt3, Rmt24 and Rmt26). Using microsatellites and the software STRUCTURE the most probable value for K was revealed as two 2 for both species. The FST value between M. rivulata and M. caspica was 0.39, and between the coastal and inland populations of E. orbicularis 0.09. It can be concluded that Emys populations tend to evolve by somehow preserving the allelic richness they have and Mauremys populations continue to differentiate so that new species emerge in the evolutionary process to reach the ideal allelic structure. © 2021, The Author(s), under exclusive licence to Springer Nature B.V.