EPAS1 gene variants are associated with sprint/power athletic performance in two cohorts of European athletes

BACKGROUND: The endothelial PAS domain protein 1 (EPAS1) activates genes that are involved in erythropoiesis and angiogenesis, thus favoring a better delivery of oxygen to the tissues and is a plausible candidate to influence athletic performance. Using innovative statistical methods we compared genotype distributions and interactions of EPAS1 SNPs rs1867785, rs11689011, rs895436, rs4035887 and rs1867782 between sprint/power athletes (n = 338), endurance athletes (n = 254), and controls (603) in Polish and Russian samples. We also examined the association between these SNPs and the athletes’ competition level (‘elite’ and ‘sub-elite’ level). Genotyping was performed by either Real-Time PCR or by Single-Base Extension (SBE) method. RESULTS: In the pooled cohort of Polish and Russian athletes, 1) rs1867785 was associated with sprint/power athletic status; the AA genotype in rs1867785 was underrepresented in the sprint/power athletes, 2) rs11689011 was also associated with sprint/power athletic status; the TT genotype in rs11689011 was underrepresented sprint/power athletes, and 3) the interaction between rs1867785, rs11689011, and rs4035887 was associated with sprint/power athletic performance; the combinations of the AA genotype in rs4035887 with either the AG or GG genotypes in rs1867785, or with the CT or CC genotypes in rs11689011, were underrepresented in two cohorts of sprint/power athletes. CONCLUSIONS: Based on the unique statistical model rs1867785/rs11689011 are strong predictors of sprint/power athletic status, and the interaction between rs1867785, rs11689011, and rs4035887 might contribute to success in sprint/power athletic performance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-382) contains supplementary material, which is available to authorized users

Changes of Gene Expression Patterns from Aquatic Organisms Exposed to Metal Nanoparticles

Metal nanoparticles are used in various branches of industry due to their physicochemical properties. However, with intensive use, most of the waste and by-products from industries and household items, and from weathering of products containing nanoparticles, end up in the waters. These pollutants pose a risk to aquatic organisms, one of which is a change in the expression of various genes. Most of the data that focus on metal nanoparticles and their effects on aquatic organisms are about copper and silver nanoparticles, which is due to their popularity in general industry, but information about other nanoparticulate metals can also be found. This review aims to evaluate gene expression patterns in aquatic organisms by metal nanoparticles, specifying details about the transcription changes of singular genes and, if possible, comparing the changes in the expression of the same genes in different organisms. To achieve this goal, available publications tackling this problem are studied and summarized. Nanometals were found to have a modulatory effect on gene expression in different aquatic organisms. Data show both up-regulation and down-regulation of genes. Nano silver, nano copper, and nano zinc show a regulatory effect on genes involved in inflammation and apoptosis, cell cycle regulation and ROS defense as well as in general stress response and have a negative effect on the expression of genes involved in development. Nano gold, nano titanium, nano zinc, and nano iron tend to elevate the transcripts of genes involved in response to ROS, but also pro-apoptotic genes and down-regulate DNA repair-involved genes and anti-apoptotic-involved genes. Nano selenium showed a rare effect that is protective against harmful effects of other nanoparticles, but also induced up-regulation of stress response genes. This review focuses only on the effects of metal nanoparticles on the expression of various genes of aquatic organisms from different taxonomic groups

Bioinformatics analysis of the promoter sequence of the 9f-2.8 gene encoding germin

Bioinformatics is a field of study having an enormous potential, allowing to solve a number of problems arising as a result of dynamic development of natural sciences with the use of computer science methodologies. It is widely used and constitutes a basis for most scientific research conducted in the field of molecular biology. The aim of this study was in silico analysis of the promoter sequence of the 9f-2.8 gene encoding isoform of the germin protein considered as a germination marker in common wheat’s (Triticum aestivum L.). The gene mentioned above has already been characterized, however, with the use of experimental methods instead of bioinformatics. Analysis with the use of TSSP and TSSPlant software identified the promoter region and classified it as the TATA-box containing promoter. For 9f-2.8 gene including 2.8 kbp, the TSSP software indicated that the TATA-box sequence was located in the position 1665 nt, while the TSSPlant tool showed that TSS [+1] was located in the position 1699 nt. At the second stage, transcription factors were analyzed. Four main families of transcription factors were detected within the analyzed region: MADS, AP2, bZIP and NAC. The most common were MADS-box and bZIP motifs. In the final step of analysis the presence of CpG islands have been checked using the PlantPAN software. The region which could be potentially considered as CpG island have been detected and localized. Software used in analysis above is free online tool.Bioinformatyka jest dyscypliną nauki, w której tkwi olbrzymi potencjał. Dyscyplina ta rozwiązuje wiele problemów powstałych w wyniku dynamicznego rozwoju nauk przyrodniczych przy użyciu metodologii nauk informatycznych. Ma szerokie zastosowanie i jest bazą dla prowadzenia większości badań naukowych z dziedziny biologii molekularnej. Celem artykułu jest analiza in silico promotora genu 9f-2.8 kodującego izoformę (9f-2.8) białka germiny uważaną za marker kiełkowania u pszenicy zwyczajnej (Triticum aestivum L.). Gen ten był już wcześniej scharakteryzowany, jednak do jego analizy korzystano z metod eksperymentalnych, nie obliczeniowych. Analiza bioinformatyczna za pomocą programów TSSP i TSSPlant pozwolila zidentyfikować promotor i potwierdziła jego klasyfikacje do grupy promotorów z motywem TATA-box. W genie 9f-2.8 liczącym 2.8 kpz program TSSP wykazał, że sekwencja TATA-box znajduje się w pozycji 1665 nt, zaś narzędzie TSSPlant wskazało, że TSS [+1] znajduje się w pozycji 1699 nt. Drugim etapem była analiza czynników transkrypcyjnych. W analizowanym obszarze wyróżniono cztery główne rodziny czynników transkrypcyjnych: MADS, AP2, bZIP oraz NAC, z których najliczniejsze były motywy MADS-box oraz bZIP. Ostatnią częścią analiz była kontrola obecności wysp CpG. Zastosowano program PlantPAN, dzięki któremu zlokalizowano region spełniający warunki, pozwalające uznać go za wyspę CpG. Programy, których użyto do scharakteryzowania tych sekwencji są darmowe i ogólnodostępne online

“Expression of genes encoding protein disulfide isomerase (PDI) in cultivars and lines of common wheat with different baking quality of flour”

Abstract Background The subject of this research was to investigate the level of expression of genes encoding protein disulfide isomerase (PDI) in cultivars and lines of wheat with different baking value of flour. PDI plays a key role in the formation of disulfide bonds in newly formed proteins. Each of cultivars and lines had a specific set of high molecular weight glutenin subunits (HMW-GS). Based on the presence of individual subunits, the potential baking value is predicted. Sometimes this value is not confirmed during technological analysis. Since there are cases where flour has a better or worse value than expected on the basis of the genotype, the expression of PDI genes was considered as a potential cause for discrepancies mentioned. Results Analysis focused on three stages of grain development. The expression level of PDI genes was compared between wheat cultivars and lines with different genotype-phenotype combinations, which means diversified sets of HMW-GS combined with diversified qualitative classification. The highest expression level of PDI was noticed at early stage of grain development, which is consistent with the function of PDI. The expression level was evaluated by the real-time PCR technique. Conclusion Results obtained in this work did not allow for a clear statement of decisive significance of PDI in the context of shaping the final baking value. The results of this work contribute to an ever more in-depth understanding of the mechanisms governing baking value, and thus to the progress of the selection of new varieties with more beneficial properties

Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis.

The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated

Enhanced Cd Phytoextraction by <i>Solanum nigrum</i> L. from Contaminated Soils Combined with the Application of N Fertilizers and Double Harvests

It is very important to increase phytoremediation efficiency in practice in suitable climatic conditions for plant growth through multiple harvests. Solanum nigrum L. is a Cd hyperaccumulator. In the present experiment, after applying different types of N fertilizers (NH4HCO3, NH4Cl, (NH4)2SO4, CH4N2O), root and shoot biomasses and Cd phytoextraction efficiency of S. nigrum effectively improved (p S. nigrum harvested at the first florescence stage plus the amounts at the second florescence stage were higher than those harvested at the maturation stage, which indicates that S. nigrum Cd phytoaccumulation efficiency was higher in the former compared to the latter as there was no clear change in Cd concentration (p 2O2 and malondialdehyde (MDA) contents in S. nigrum in vivo were lower compared to those that had not received N addition (CK); similarly, the concentration of proline was decreased as well (p S. nigrum shoots, while peroxidase (POD) and superoxide dismutase) (SOD) activities increased (p 4)2SO4 treatment exerted the most positive effect and CH4N2O the second most positive effect on S. nigrum Cd phytoremediation efficiency in double harvests at florescence stages, and the growth conditions were better than others

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3&ndash;8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species