Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe,Asia and Africa

Background

Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×).

Results

We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency.

Conclusion

This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-963) contains supplementary material, which is available to authorized users.     

Determination of microRNAs associated with adverse left ventricular remodeling after myocardial infarction

Molecular and Cellular Biochemistry - Increasing evidence indicates that microRNA (miRNA) regulated mechanisms in myocardial healing and ventricular remodeling following acute myocardial infarction...     

Efficacy and safety of canakinumab in adolescents and adults with colchicine-resistant familial Mediterranean fever

IntroductionThis open-label pilot study aimed to investigate the efficacy of canakinumab in colchicine-resistant familial Mediterranean fever (FMF) patients.MethodPatients with one or more attacks in a month in the preceding 3 months despite colchicine were eligible to enter a 30-day run-in period. Patients who had an attack during the first run-in period advanced to a second 30-day period. At the first attack, patients started to receive three canakinumab 150 mg subcutaneous injections at 4-week intervals, and were then followed for an additional 2 months. Primary efficacy outcome measure was the proportion of patients with 50 % or more reduction in attack frequency. Secondary outcome measures included time to next attack following last canakinumab dose and changes in quality of life assessed by SF-36.ResultsThirteen patients were enrolled in the run-in period and 9 advanced to the treatment period. All 9 patients achieved a 50 % or more reduction in attack frequency, and only one patient had an attack during the treatment period. C-reactive protein and serum amyloid A protein levels remained low throughout the treatment period. Significant improvement was observed in both physical and mental component scores of the Short Form-36 at Day 8. Five patients had an attack during the 2-month follow-up, occurring median 71 (range, 31 to 78) days after the last dose. Adverse events were similar to those observed in the previous canakinumab trials.ConclusionCanakinumab was effective at controlling the attack recurrence in patients with FMF resistant to colchicine. Further investigations are warranted to explore canakinumab’s potential in the treatment of patients with colchicine resistant FMF.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01088880","term_id":"NCT01088880"}}NCT01088880. Registered 16 March 2010.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0765-4) contains supplementary material, which is available to authorized users.     

Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon

Protoplasma - Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the...     

Effects of nitric oxide donor and inhibitor on prostaglandin E2-like activity, malondialdehyde and reduced glutathione levels after skeletal muscle ischemia-reperfusion.

Oxygen free radicals are implicated in the pathophysiology of ischemia-reperfusion (I/R) injury in skeletal muscle. Nitric oxide (NO) and prostaglandin E2 (PGE2) are important regulators of the microcirculation in skeletal muscle. The effects of L-arginine, substrate for NO, and N(G)-nitro L-arginine methyl ester (L-NAME) on PGE2 synthesis, lipid peroxidation and reduced glutathione (GSH) levels was investigated in the rat gastrocnemius muscle after 3 h of reperfusion following 2 h of ischemia. Lipid peroxidation and GSH levels showed a non-significant changes in the I/R groups compared to the control group. According to these results, it can be assumed that skeletal muscle can resist 2 h of ischemia followed by 3 h of reperfusion-induced oxidative stress. PGE2-like activity in the gastrocnemius muscle increased in the L-NAME treated and I/R groups. L-arginine administration reversed the increase in PGE2-like activity of reperfused skeletal muscle. These findings support the conclusion that endothelium-derived PGE2 synthesis increases during reperfusion and suggest that PGE2 may have a protective role in the maintenance of endothelial function.     

The effect of an anoxic zone on biological phosphorus removal by a sequential batch reactor

Nitrate can affect phosphate release and lead to reduced efficiency of biological phosphorus removal process. The inhibition effect of remaining nitrate at the anaerobic/anoxic phases was investigated in a lab scale sequencing batch reactor. In this study the influence of denitrification process on reactor performance and phosphorus removal was examined. The experiments were carried out through simultaneous filling and decanting, mixing, mixing-aeration and settling modes. Glucose and acetate were used as carbon sources. The proposed treatment system was capable of removing approximately 80% of the influent PO4-P, 98% NH4-N and 97% COD at a SRT of 25 days. In the fill/decant phase, anoxic and anaerobic conditions prevailed and a large quantity of nitrate was removed in this stage. In the anoxic phase the remaining nitrate concentration was quickly reduced and a considerable amount of phosphate was released. This was attributed to the availability of acetate in this stage. For effective nitrogen and phosphate removal, a short anoxic phase was beneficial before an aerobic phase.     

Anaerobic treatability and biogas production potential studies of different agro-industrial wastewaters in Turkey

The anaerobic treatability and methane generation potential of the wastewaters of the three important agro-industries in Turkey, namely, cheese-making, poultry breeding and the olive-oil mill industries were studied. Biochemical methane potential (BMP) experiments were conducted for different initial chemical oxygen demand (COD) concentrations. The results indicate that anaerobic treatment was possible for all the wastewaters studied and the biogas produced had a high methane content.     

Species richness effects on grassland recovery from drought depend on community productivity in a multisite experiment

Biodiversity can buffer ecosystem functioning against extreme climatic events, but few experiments have explicitly tested this. Here, we present the first multisite biodiversity × drought manipulation experiment to examine drought resistance and recovery at five temperate and Mediterranean grassland sites. Aboveground biomass production declined by 30% due to experimental drought (standardised local extremity by rainfall exclusion for 72–98 consecutive days). Species richness did not affect resistance but promoted recovery. Recovery was only positively affected by species richness in low‐productive communities, with most diverse communities even showing overcompensation. This positive diversity effect could be linked to asynchrony of species responses. Our results suggest that a more context‐dependent view considering the nature of the climatic disturbance as well as the productivity of the studied system will help identify under which circumstances biodiversity promotes drought resistance or recovery. Stability of biomass production can generally be expected to decrease with biodiversity loss and climate change.