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    The contribution of Anatolia to European phylogeography: the centre of origin of the meadow grasshopper, Chorthippus parallelus
    (WILEY-BLACKWELL, 2014) Korkmaz, E. Mahir; Lunt, David H.; Ciplak, Battal; Degerli, Naci; Basibuyuk, Hasan H.
    Aim Chorthippus parallelus is one of the classic model systems for studying genetic structure and phylogeography in the Western Palaearctic. Here, we investigate the regional genetic differentiation of C. parallelus and evaluate the historical and evolutionary processes responsible for such genetic structuring, test the nature of the Turkish Straits system as a barrier to dispersal, and explore the contribution of Anatolian populations to the biodiversity of the Western Palaearctic. Location Western Palaearctic. Methods We incorporated sequence data from dense sampling of the phylogeographically important Anatolian region with both previous and newly obtained data of the nuclear fragment cpnl-1 and the mitochondrial fragment COI-tRNALeu-COII. In total, 1049 sequences of cpnl-1 from 33 regions were analysed to investigate the genetic diversity, genetic structuring and phylogeography of C. parallelus across its distributional range. The mtDNA region was additionally used to test whether the Turkish Straits system acts as a barrier. Results The analyses revealed that not all southern refugial populations of C. parallelus have contributed equally to the post-glacial recolonization of Europe. Four genetic clusters across the species' range were recovered: cluster A (eastern part of the Anatolian Diagonal); cluster B (western part of the Anatolian Diagonal); cluster C (Spain, Italy, southern Balkans, west part of Anatolia and Russia); and cluster D (covering the entire distributional range of the species). The Turkish Straits system has been a weak barrier to dispersal by C. parallelus, allowing gene flow from Anatolia to the Balkans. Main conclusions The current patterns of genetic structuring of C. parallelus were best explained by multiple expansion and contraction events. Anatolia has been well connected to the Balkans, contributing genetically to the establishment of central and northern European populations prior to the Holocene. The Anatolian refugium is suggested to be the centre of origin for Western Palaearctic C. parallelus diversity rather than a Balkan refugium.
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    Genetic Diversity of Cyprinion macrostomus Heckel, 1843 (Teleostei: Cyprinidae) in Anatolia
    (CENTRAL FISHERIES RESEARCH INST, 2012) Dastan, Sevgi Durna; Bardakci, Fevzi; Degerli, Naci
    In this study, the phylogenetic and phylogeographic relationships among Cyprinion macrostomus HECKEL, 1843, Cyprinion kais HECKEL, 1843 and Carasobarbus chantrei SAUVAGE, 1882 samples from Anatolia were analysed. While doing this, mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Nuclear DNA inter-simple sequence repeat (ISSR) were used. PCR amplified the complete mtDNA NADH 3/4 dehydrogenase (ND-3/4) gene. Amplified fragment was digested by 14 restriction enzymes that produced 14 composite haplotypes for these populations. All identified mtDNA haplotypes differed from each other having a specific genetic profile. The genetic diversity among the mtDNA haplotypes of C. macrostomus, C. kais, and C. chantrei populations from drainage basins of the Mediterranean and those from the drainage basin of the Persian Gulf was purported by the extrapolation of mtDNA PCR-RFLP data. This result is also supported by the data explaining the geological history of Anatolia. Broadly, the data from mtDNA and from nDNA was consistent.
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    Genotyping by Sequencing of Acanthamoeba and Naegleria Isolates from the Thermal Pool Distributed Throughout Turkey
    (Springer Int Publ Ag, 2020) Degerli, Serpil; Degerli, Naci; Camur, Derya; Dogan, Ozgul; Ilter, Huseyin
    Purpose The main goal of this study was genotyping of free-living parasites and sub-grouping of pathogenic or non-pathogenic amebae obtained from Turkey's thermal springs. In so doing, distribution and abundance of possible pathogenic or causative strain for humans, which are caused by Acanthamoeba and Naegleria strains, would be elaborated. The number of extensive studies on the general occurrence and distribution of parasitic strains is very high worldwide, but there has been a paucity of information with regard to Turkey. Methods From a total of 434 obtained thermal pool samples, free-living amebas were isolated from 148 water samples using the non-nutrient agar (NNA) culture method. Subsequently, the cultivated samples were used for DNA isolation; then 102 obtained DNA samples were subjected to PCR amplification using various primers for samples of genera Acanthamoeba and Naegleria. Ultimately, estimation of genotype or subtype was evaluated by sequencing. Results About 29 samples that belong to Acanthamoeba and Naegleria were estimated from a total of 102 amplified PCR samples. These eukaryotic PCR products which have Acanthamoeba genus appearance, generated 26 subtypes and 3 Naegleria samples. Among the 26 Acanthamoeba genotypes, 22 aligned sequences were matched with various GenBank reference samples, while the 4 divergent genotypes were not elaborated and marked as ND. Most of the Acanthamoeba genera were determined as likely dominating groups and clustered as T form within totally eight groups. Eight, seven and three subtypes were found as T4A, T15 and T11 genotypes, respectively while the remainings were ultimately found in four groups. Results confirming the predominance of T4A, which is known the most causative form, the presence in the pools. Despite being uncommon, N. fowleri, lovaniensis and australiensis were also observed among the surveyed pools. Conclusion The present study is descriptive and is not unique. However, this is the most comprehensive study of the molecular distribution sampling of thermophilic Acanthamoeba and Naegleria that confirmed and demonstrated their ubiquitous presence throughout Turkey. By this estimation, in some spas, the most and likely causative form Acanthamoeba including T4 and Naegleria fowleri has also been confirmed.
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    Genotyping of Giardia intestinalis isolated from people living in Sivas, Turkey
    (TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY, 2012) Degerli, Serpil; Degerli, Naci; Celiksoz, Ali; Ozcelik, Semra
    Aim: The technique of polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) genotyping was used to characterise morphologically identical isolates of Giardia intestinalis from human stool samples. Materials and methods: In this study a total of 17 trophozoite samples, obtained either directly from stool samples or after excystation, or by duodenal aspiration, were used. A set of primers was chosen to amplify the different regions of triose phosphate isomerase (tpi) and a segment of the glutamate dehydrogenase (gdh) genes. A single-stranded conformational polymorphism technique was also used in an attempt to discriminate among some subgroups. Results: Only primers of the 683-bp segment of the tpi gene from the trophozoite samples were suitable for obtaining a PCR product. In the total of 17 trophozoite DNAs where the tpi gene segment was amplified, 9 belonged to assemblage A (53%) and 4 to assemblage B (23.5%). It was not possible to identify assemblages for the remaining 4 samples (23.5%). Conclusion: PCR RFLP tpi gene application was able to discriminate between G. intestinalis assemblage A and B, but not the other subgroups. Since assemblage A is the more prevalent subgroup compared with assemblage B, this subgroup can be said to be responsible for common Giardia infections in Turkey.
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    Phenylthiocarbamide taste perception as a possible genetic association marker for nutritional habits and obesity tendency of people
    (UNIV KARACHI, 2015) Dastan, Sevgi Durna; Degerli, Naci; Dastan, Taner; Yildiz, Fazilet; Yildir, Yavuz; Durna, Yusuf Muhammed; Atessahin, Dilek; Karan, Tunay
    Ability to taste Phenylthiocarbamide (PTC) a bitter molecule, is usually used to know the heritable characteristic in both genetic and physiological studies. So far, no research has yet attested whether PTC blindness relation with obesity and some nutrition behaviors of human. This stu.dy is the first attempt on a large scale to examine PTC sensitivity in healthy and overweight people in Turkish population to define in the perception of bitter senses which is associated with nutrition habits, body mass index, age, gender, and to be in stable weight. PTC taste perception was measured by tasting PTC solution filtered in a paper. The results showed that tasters were significantly more frequent (81,8%) than nontasters (18,2%) in all population. A "higher proportion of nontasters were observed in the quite fat individual group (BMI >= 40kg/m(2)). Alterations explained these differences in basic taste sensitivity, age, gender, BMI, individuals' family obesity situations, vegetarian nourishment. Increased frequency of nontasters allele is evident with obesity condition. This could be due to lack of preference for nutrition among nontasters. So the phenotypic variation in PTC sensitivity is genetic in origin; it may represent an association with obesity, dietary habits, regular weight, gender, and age.