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    Evaluation of confidence limit estimates of cluster analysis on molecular marker data
    (WILEY, 2012) Kayis, Seyit A.
    BACKGROUND: Diversity studies employ cluster analysis as a statistical tool, whereby relationships between individuals are shown in a dendrogram, mostly accompanied by bootstrap support for merging branches to indicate confidence limits. The objective of this study was to evaluate the reliability of the currently applied method of obtaining confidence limit estimates in cluster analysis and to propose an improved alternative bootstrap method. RESULTS: It was illustrated via a simulation study that conventional bootstrap support for cluster analysis was affected by the sample size. The reliability of merging branches decreased with increasing number of individuals in the sample. Unlike the current bootstrap support for cluster analysis, the proposed method provides confidence intervals for the similarity coefficients between individuals. To facilitate the interpretation of similarity coefficients and confidence intervals, alternative graphical presentations are proposed for both 'similarity coefficients' and 'confidence interval range'. CONCLUSION: The proposed bootstrap method is not affected by the number of individuals in the sample. (C) 2011 Society of Chemical Industry
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    Expression of enzymes and receptors of leukotriene pathway genes in equine endometrium during the estrous cycle and early pregnancy
    (ELSEVIER SCIENCE INC, 2013) Guzeloglu, Aydin; Atli, Mehmet O.; Kurar, Ercan; Kayis, Seyit A.; Handler, Johannes; Semacan, Ahmet; Aslan, Selim
    The aims of the present study were to elucidate the expression profiles of leukotriene (LT) pathway mRNA transcription and to determine the possible interaction of LT and prostaglandin (PTG) pathways genes in equine endometrium during the estrous cycle and early pregnancy. Endometrial biopsies were obtained from mares on the day of ovulation (d0), at late diestrous (LD, n = 4), and after luteolysis in the estrus phase (AL n = 4) of the cycle. Biopsies were also taken on Days 14 (P14; n = 4), 18 (P18, n = 4), and 22 (P22, n = 4) during early pregnancy that were comparable days to cyclic sampling days. A mixed model was fitted on the normalized relative mRNA levels, quantified by qPCR in duplicate, and least significant difference test was employed to detect significantly different group(s). In addition, to determine the degree of contribution of each gene to separation of treatment groups, the multivariate projection method partial least square regression discriminant analysis was used. The expression of 5-lipoxygenase mRNA was greater on d0 and LD, declined at AL, and was suppressed by early pregnancy. Leukotriene A(4) hydrolase mRNA expression increased at LD and during early pregnancy, but Was significantly greater at LD compared with P14. The expression of LT C-4 synthase mRNA was only induced at LD. Cysteinyl leukotriene receptors (CysLT1 and CysLT2) mRNA expressions were decreased by both cyclic changes and early pregnancy, whereas 5-lipoxygenase-activating protein and B leukotriene receptor mRNA expressions were not affected by early pregnancy or stages of the estrous cycle. Partial least square discriminant analysis suggests that LT and PTG pathway enzymes and receptors appear to behave similarly in terms of mRNA expression. In conclusion, the expression profiles of LT pathway genes are demonstrated in equine endometrium for the first time by the present study, and the present data suggest that LT pathway mRNA transcriptions are tightly regulated during early pregnancy in mares. (C) 2013 Elsevier Inc. All rights reserved.
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    Inter simple sequence repeats separate efficiently hemp from marijuana (Cannabis sativa L.)
    (UNIV CATOLICA DE VALPARAISO, 2007) Hakki, Erdogan E.; Kayis, Seyit A.; Pinarkara, Emine; Sag, Ayla
    Cannabis sativa L. is a multiple-use plant that provides raw material for the production of seed oil, natural fiber for textiles, automotive and pulp industries. It has also been used in insulating boards, ropes, varnishes, animal feed, and as medicinal agents. Cannabis has potential to be used for phytoremediation: however, its cultivation is strictly controlled due to its psychoactive nature and usage in producing drugs such as marijuana, and hashish. In this study, psychoactive type Cannabis samples, which were seized from 23 different locations of Turkey, and nine hemp type Cannabis accessions, as well as an unknown accession were used. Our interest was to identify the genetic relatedness of the seized samples and to separate drug and hemp type plants. Inter Simple Sequence Repeats (ISSRs) were employed for analysis based on single plant material (SET1) and bulked samples of them (SET2). Data was analysed via cluster analysis and principal coordinate analysis (PCoA). PCoA analyses, by using SET1 and SET2, were able to efficiently discriminate the seized samples from the fiber type accessions. However, separation of the plants was not clear via unweighted pair-group method using arithmetic average (UPGMA) dendogram in SET1, while they were clearly separated in SET2. Hemp type accessions showed high levels of variation compared to drug type Cannabis both in SET1 and SET2.
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    Molecular and Elemental Characterization of Selected Turkish Durum Wheat Varieties
    (UNIV AGR SCI & VETERINARY MED CLUJ-NAPOCA, 2014) Hakki, Erdogan E.; Dograr, Nurdan; Pandey, Anamika; Khan, Mohd. Kamran; Hamurcu, Mehmet; Kayis, Seyit A.; Gezgin, Sait
    Combination of elemental and protein studies along with molecular data using microsatellite markers may lead CO the better and realistic determination of relatedness between the varieties and their populations. In this study, the extent of diversity among five Turkish durum wheat cultivars and their populations has been assessed using seven microsatellite markers and the elemental analysis together with the differences in their protein content. In molecular analysis, total 23 alleles have been obtained among all the genotypes with middling of 4.6 per primer. On employing UPGMA Dendrogram, Principle Coordinate Analysis (PCoA) and Winboot analyses, both inter and inn-a varietal polymorphic studies had shown similar clustering with minor differences. As a result of AMOVA performed, the extent of diversity was found to be higher among the genotypes (76%) in comparison to the variability within the genotypes (24%). In elemental analyses, 'Selcuklu-97' was found to be the most efficient variety with high content of several elements. Also, strong and positive correlation has been observed between magnesium-phosphorus, magnesium-sulphur and sulphur-sodium, while noteworthy negative correlation has been observed between sodium and zinc. The protein content of the genotypes was found in the range of 15.17-16.90%. The diversity revealed in durum genotypes can be employed in genetic expansion of the crop. These involved varieties may aid to avoid genetic attrition coming up from the landraces. The information provided can be utilized by breeders for appropriate selection of both, generically and nutritionally efficient durum wheat varieties.
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    PLS-DA approach for simultaneous evaluation of genes involved in luteolysis in equine endometrium during estrous cycle and early pregnancy
    (CURRENT BIOLOGY LTD, 2011) Guzeloglu, Aydin; Kayis, Seyit A.; Atli, Mehmet O.; Kurar, Ercan; Semacan, Ahmet; Aslan, Selim
    [Abstract not Available]
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    RAPD analysis of seized marijuana (Cannabis sativa L.) in Turkey
    (UNIV CATOLICA DE VALPARAISO, 2009) Pinarkara, Emine; Kayis, Seyit A.; Hakki, Erdogan E.; Sag, Ayla
    Cannabis sativa L. is a multiple-use plant. However, its cultivation is strictly controlled due to its psychoactive nature and usage in producing drugs such as marijuana, and hashish. In this study, psychoactive type Cannabis samples, which were seized from 29 different locations of Turkey, were used. Interests were to identify the genetic relatedness of the seized samples and to partition molecular variance between and within populations. Randomly Amplified Polymorphic DNAs were employed for analysis based on single plant material and bulked samples of them. Data were analysed via cluster and principal coordinate analyses (PCoA). Analysis of molecular variance (AMOVA) was performed to obtain variations between and within populations. Cannabis accessions were basically separated into two main groups by PCoA and cluster analyses according to geographical regions. One of them was made up of Cannabis plants, which were seized from mostly western part of Turkey (group 1). The other one was made up of Cannabis plants that were seized from mostly eastern part of Turkey (group 2). It is found that 20.23% of the genetic variation is due to differences between accessions groups while 79.77% of the genetic variation is due to between accessions within accessions groups. Compared to group 1, group 2 showed more variation.
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    Rating of putative housekeeping genes for quantitative gene expression analysis in cyclic and early pregnant equine endometrium
    (ELSEVIER SCIENCE BV, 2011) Kayis, Seyit A.; Atli, Mehmet O.; Kurar, Ercan; Bozkaya, Faruk; Semacan, Ahmet; Aslan, Selim; Guzeloglu, Aydin
    The aim was an evaluation of a set of housekeeping genes (HKGs) to be used in the normalization of gene expression in the equine endometrium. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hypoxanthine ribosyl transferase 1 (HPRT1), ubiquitin B (UBB), tubulin alpha 1 (TUBA1), ribosomal protein L32 (RPL32), beta-2-microglobulin (B2M), 18S rRNA (18S), and 285 rRNA (28S) HKGs were evaluated using real-time PCR and were compared in different physiological stages of the endometrium. Endometrial biopsies were obtained from mares on day of ovulation (d0, n = 4), at late diestrus (LD, n = 4), after luteolyis (AL, n = 4) of the cycle and on days 14 (P14; n = 3), 18 (P18, n = 3) and 22 (P22; n = 3) of pregnancy. A model based on REML with support of descriptive statistics was proposed in accordance with experimental design and was further confirmed with principal component analysis (PCA). Results were compared with widely used software including geNorm, BestKeeper, and NormFinder. Results indicated that GAPDH was the most stable HKG and RPL32 was ranked as the second best. 18S and 285 were found to be the least stable. The proposed model, PCA, geNorm, and BestKeeper were in agreement in detecting the most stable and the least stable HKGs in the equine endometrium during the estrous cycle and early pregnancy. (C) 2011 Elsevier B.V. All rights reserved.