RAPD and essential oil characterization of Turkish basil (Ocimum basilicum L.)

Sweet basil (Ocimum basilicum L., Lamiaceae), an important medicinal plant and culinary herb due to its delicate aroma and fragrance, shows great variation in both morphology and essential oil components. Genetic variation among basil accessions in Turkey has not been extensively examined with molecular markers. Genetic diversity was determined using random amplified polymorphic DNA (RAPD) markers of 14 genotypes of basil. A total of 375 bands were obtained from the RAPD analysis, and 273 of them (70.3 %) were polymorphic. The RAPD analysis allowed the grouping of samples into two main clusters. Genetic similarity values among the basil genotypes ranged between 0.46 and 0.87. Considerable genetic diversity was determined among basil genotypes. Essential oils were obtained by hydro-distillation and were characterized by gas chromatography. A total of 17 chemical components were identified. The evaluated genotypes of O. basilicum can be classified into seven chemotypes: (1) Linalool (7, 12, 16, 22, 25A and 33), (2) Methyl chavicol (6, 10A), (3) Citral/methyl chavicol (10L, 17), (4) Methyl eugenol (11), (5) Methyl cinnamate/linalool (23), (6) Linalool/methyl eugenol (25K), and (7) Methyl chavicol/linalool (Let). The chemical variability obtained from the essential oil composition of the genotypes in the study was remarkable. The chemical characterization of genotypes 10L and 17 was rich in citral (42.17 and 44.80 %) and methyl chavicol (30.56 and 32.03 %). Citral/methyl chavicol can be assessed as a new chemotype of basil cultivated in Turkey. The basil genotypes were grouped into two major clusters for both the RAPD analysis and chemical characterization with very few exceptions (genotype n. 6). A correlation analysis of the genetic distance matrix and the Euclidian distance matrix showed relatively low values (r = ?0.40). The results demonstrated a certain degree of correspondence between chemical and molecular data.     

Is Sp1 binding site polymorphism within COL1A1 gene associated with tennis elbow?

Tennis elbow defines a condition of pain and tenderness over the lateral epicondyle of the humerus. The exact aetiology of the injury is not yet fully understood. The major constituent of tendons is type 1 collagen which is encoded by COL1A1 gene. The aim of the study was to determine whether Sp1 binding site polymorphism (SNP rs1800012; 1546G/T) within the intronic region of COL1A1 gene is associated with tennis elbow. One hundred and three tennis elbow patients and one hundred and three healthy subjects without any history of previous ligament or tendon injuries were recruited for this genetic association study. All participants were genotyped for the COL1A1 Sp1 binding site polymorphism by using PCR–RFLP method. There were no observed statistical differences in the genotype (p = 0.17) or allele (p = 0.11) distributions between the groups. G allele frequency in patients and controls was 82.5% and 76.21%, and T allele frequency was 17.5% and 23.79% respectively. This study has shown that there is no association between this polymorphism and tennis elbow within the population studied.     

Genetic structure and diversity analysis revealed by AFLP on different Echinochloa spp. from northwest Turkey

Rice is one of the most economically important cereal crops in the world. The genus Echinochloa is the most competitive and difficult to control weeds in the rice fields. Improving the knowledge on the genetic diversity and structure of Echinochloa spp. can supply crucial information for designing effective management strategies for weed control in rice breeding. In the study, 28 Echinochloa spp. genotypes were subjected to the analysis of genetic diversity using four amplified fragment length polymorphism selective primer combinations. The number of polymorphic fragments per primer combination detected ranged from 28 to 50 bands with an average of 41.5 bands. Average polymorphic information content (PIC) was 0.26 in overall primer combinations. E_ACA-M_CAG primer combination showed the highest PIC (0.52) which can be a good candidate primer combination to verify genetic diversity in Echinochloa spp. The unweighted pair-group method of the arithmetic average and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of two populations. The accessions were clearly assigned to a single population in which >70 % of their inferred ancestry was derived from one of the model-based populations. However, three genotypes (10.7 %) in the sample were categorized as having admixed ancestry. The study showed that genetic variation and population structure are determined among genotypes collected from different locations. High level of genetic variation in both intra and inter species was detected.     

CRF-based models of protein surfaces improve protein-protein interaction site predictions

Background

The identification of protein-protein interaction sites is a computationally challenging task and important for understanding the biology of protein complexes. There is a rich literature in this field. A broad class of approaches assign to each candidate residue a real-valued score that measures how likely it is that the residue belongs to the interface. The prediction is obtained by thresholding this score.Some probabilistic models classify the residues on the basis of the posterior probabilities. In this paper, we introduce pairwise conditional random fields (pCRFs) in which edges are not restricted to the backbone as in the case of linear-chain CRFs utilized by Li et al. (2007). In fact, any 3D-neighborhood relation can be modeled. On grounds of a generalized Viterbi inference algorithm and a piecewise training process for pCRFs, we demonstrate how to utilize pCRFs to enhance a given residue-wise score-based protein-protein interface predictor on the surface of the protein under study. The features of the pCRF are solely based on the interface predictions scores of the predictor the performance of which shall be improved.

Results

We performed three sets of experiments with synthetic scores assigned to the surface residues of proteins taken from the data set PlaneDimers compiled by Zellner et al. (2011), from the list published by Keskin et al. (2004) and from the very recent data set due to Cukuroglu et al. (2014). That way we demonstrated that our pCRF-based enhancer is effective given the interface residue score distribution and the non-interface residue score are unimodal.Moreover, the pCRF-based enhancer is also successfully applicable, if the distributions are only unimodal over a certain sub-domain. The improvement is then restricted to that domain. Thus we were able to improve the prediction of the PresCont server devised by Zellner et al. (2011) on PlaneDimers.

Conclusions

Our results strongly suggest that pCRFs form a methodological framework to improve residue-wise score-based protein-protein interface predictors given the scores are appropriately distributed. A prototypical implementation of our method is accessible at http://ppicrf.informatik.uni-goettingen.de/index.html.     

Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

Human driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern cattle. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying domestication-related genes that ultimately may help to further genetically improve this economically important animal. To this end, we employed a panel of more than 15 million autosomal SNPs identified from re-sequencing of 43 Fleckvieh animals. We mainly applied two somewhat complementary statistics, the integrated Haplotype Homozygosity Score (iHS) reflecting primarily ongoing selection, and the Composite of Likelihood Ratio (CLR) having the most power to detect completed selection after fixation of the advantageous allele. We find 106 candidate selection regions, many of which are harboring genes related to phenotypes relevant in domestication, such as coat coloring pattern, neurobehavioral functioning and sensory perception including KIT, MITF, MC1R, NRG4, Erbb4, TMEM132D and TAS2R16, among others. To further investigate the relationship between genes with signatures of selection and genes identified in QTL mapping studies, we use a sample of 3062 animals to perform four genome-wide association analyses using appearance traits, body size and somatic cell count. We show that regions associated with coat coloring significantly (P<0.0001) overlap with the candidate selection regions, suggesting that the selection signals we identify are associated with traits known to be affected by selection during domestication. Results also provide further evidence regarding the complexity of the genetics underlying coat coloring in cattle. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to identify specific regions targeted by selection during speciation, domestication and breed formation of cattle. We also show that Linkage Disequilibrium (LD) decays in cattle at a much faster rate than previously thought.     

The effects of resveratrol on tissue injury,oxidative damage,and pro-inflammatory cytokines in an experimental model of acute pancreatitis

Acute pancreatitis (AP) is an acute inflammatory condition that results from the digestion of pancreatic tissue by its own enzymes released from the acinar cells. The objective of this study was to investigate the effects of resveratrol on oxidative damage, pro-inflammatory cytokines, and tissue injury involved with AP induced in a rat model using sodium taurocholate (n?=?60). There were three treatment groups with 20 rats per group. Groups I and II received 3 % sodium taurocholate solution, while group III underwent the same surgical procedure yet did not receive sodium taurocholate. In addition, group II received 30 mg/kg resveratrol solution. Rats were sacrificed at 2, 6, 12, and 24 h time points following the induction of AP. Blood and pancreatic tissue samples were collected and subjected to biochemical assays, Western blot assays, and histopathologic evaluations. Resveratrol did not reduce trypsin levels and prevent tissue damage. Resveratrol prevented IκB degradation (except for 6 h) and decreased nuclear factor-κB (NF-κB), activator protein-1 (AP-1) (except for 24 h), and levels of TNF-α, IL-6 (except for 24 h), and iNOS in the pancreatic tissue at all time points (P?<?0.05). Serum nitric oxide (NO) levels were reduced as well (P?<?0.05). Thus, we concluded that resveratrol did not reduce trypsin levels and did not prevent tissue injury despite the reduction in oxidative damage and pro-inflammatory cytokine levels detected in this model of AP.     

Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories

The increasing input of anthropogenically derived nitrogen (N) to ecosystems raises a crucial question: how does available N modify the decomposer community and thus affects the mineralization of soil organic matter (SOM). Moreover, N input modifies the priming effect (PE), that is, the effect of fresh organics on the microbial decomposition of SOM. We studied the interactive effects of C and N on SOM mineralization (by natural ¹³C labelling adding C₄‐sucrose or C₄‐maize straw to C₃‐soil) in relation to microbial growth kinetics and to the activities of five hydrolytic enzymes. This encompasses the groups of parameters governing two mechanisms of priming effects – microbial N mining and stoichiometric decomposition theories. In sole C treatments, positive PE was accompanied by a decrease in specific microbial growth rates, confirming a greater contribution of K‐strategists to the decomposition of native SOM. Sucrose addition with N significantly accelerated mineralization of native SOM, whereas mineral N added with plant residues accelerated decomposition of plant residues. This supports the microbial mining theory in terms of N limitation. Sucrose addition with N was accompanied by accelerated microbial growth, increased activities of β‐glucosidase and cellobiohydrolase, and decreased activities of xylanase and leucine amino peptidase. This indicated an increased contribution of r‐strategists to the PE and to decomposition of cellulose but the decreased hemicellulolytic and proteolytic activities. Thus, the acceleration of the C cycle was primed by exogenous organic C and was controlled by N. This confirms the stoichiometric decomposition theory. Both K‐ and r‐strategists were beneficial for priming effects, with an increasing contribution of K‐selected species under N limitation. Thus, the priming phenomenon described in ‘microbial N mining’ theory can be ascribed to K‐strategists. In contrast, ‘stoichiometric decomposition’ theory, that is, accelerated OM mineralization due to balanced microbial growth, is explained by domination of r‐strategists.     

Measuring Cognitive Errors Using the Cognitive Distortions Scale (CDS): Psychometric Properties in Clinical and Non-Clinical Samples

The Cognitive Distortions Scale was developed to assess thinking errors using case examples in two domains: interpersonal and personal achievement. Although its validity and reliability has been previously demonstrated in non-clinical samples, its psychometric properties and scoring has not yet been evaluated. The aim of the current study was to evaluate the psychometric properties of the Cognitive Distortions Scale in two Turkish samples and to examine the usefulness of the categorical scoring system. A total of 325 individuals (Sample 1 and Sample 2) were enrolled in this study to assess those psychometric properties. Our Sample 1 consisted of 225 individuals working as interns at the Diskapi Yildirim Beyazit Teaching and Research Hospital and Sample 2 consisted of 100 patients diagnosed with depression presenting to the outpatient unit of the same Hospital. Construct validity was assessed using the Beck Depression Inventory, the State Trait Anxiety Inventory, the Dysfunctional Attitude Scale, and the Automatic Thought Questionnaire. Factor analyses supported a one-factor model in these clinical and non-clinical samples. Cronbach''s α values were excellent in both the non-clinical and clinical samples (0.933 and 0.918 respectively). Cognitive Distortions Scale scores showed significant correlation with relevant clinical measures. Study Cognitive Distortions Scale scores were stable over a time span of two weeks. This study showed that the Cognitive Distortions Scale is a valid and reliable measure in clinical and non-clinical populations. In addition, it shows that the categorical exists/does not exist scoring system is relevant and could be used in clinical settings.