Geographic and seasonal patterns and limits on the adaptive response to temperature of European <Emphasis Type="Italic">Mytilus</Emphasis> spp. and <Emphasis Type="Italic">Macoma balthica</Emphasis> populations

Seasonal variations in seawater temperature require extensive metabolic acclimatization in cold-blooded organisms inhabiting the coastal waters of Europe. Given the energetic costs of acclimatization, differences in adaptive capacity to climatic conditions are to be expected among distinct populations of species that are distributed over a wide geographic range. We studied seasonal variations in the metabolic adjustments of two very common bivalve taxa at European scale. To this end we sampled 16 populations of Mytilus spp. and 10 Macoma balthica populations distributed from 39° to 69°N. The results from this large-scale comprehensive comparison demonstrated seasonal cycles in metabolic rates which were maximized during winter and springtime, and often reduced in the summer and autumn. Studying the sensitivity of metabolic rates to thermal variations, we found that a broad range of Q ₁₀ values occurred under relatively cold conditions. As habitat temperatures increased the range of Q ₁₀ narrowed, reaching a bottleneck in southern marginal populations during summer. For Mytilus spp., genetic-group-specific clines and limits on Q ₁₀ values were observed at temperatures corresponding to the maximum climatic conditions these geographic populations presently experience. Such specific limitations indicate differential thermal adaptation among these divergent groups. They may explain currently observed migrations in mussel distributions and invasions. Our results provide a practical framework for the thermal ecophysiology of bivalves, the assessment of environmental changes due to climate change and its impact on (and consequences for) aquaculture. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Simultaneous LC-MS-MS determination of cyclosporine A, tacrolimus, and sirolimus in whole blood as well as mycophenolic acid in plasma using common pretreatment procedure

The purpose of the study was to develop rapid and simple procedure for simultaneous determination of cyclosporine A (CsA), tacrolimus (TCR), and sirolimus (SIR) in whole blood and mycophenolic acid (MPA) in plasma. Ascomycin (ASCO), cyclosporine D (CsD), and desmethoxysirolimus (DMSIR) were used as internal standards (IS) for TCR, CsA and MPA, and SIR, respectively. In the method development, six-level blood calibrators were used for CsA (range 47-1725 ng/ml), TCR (range 2.1-38.8 ng/ml), and SIR (range 2.4-39.6 ng/ml). Four-level calibrators were used for MPA (range 0.15-5.48 microg/ml). Four levels of quality control (QC) standards were used for blood samples, together with two levels of QC standards in plasma. All QC standards and calibrators were obtained from commercial sources. Sample preparation based on precipitation of 50 microl of sample in zinc sulfate-methanol-acetonitrile mixture containing IS, followed by centrifugation. HPLC was performed on ChromSpher pi column, 30 mm x 3 mm, in ballistic gradient of ammonium formate buffer-methanol at 0.8 ml flow rate. Following gradient elution profile was applied: 0-1.2 min at 30% methanol (divert valve to waste), 1.21-3.1 min 97% methanol (divert valve to detector), 3.11-3.7 min 30% methanol (divert valve to waste). ESI-MS-MS (MRM) was done on TSQ Quantum instrument with ESI source in positive ion mode. Ammoniated adducts of protonated molecules were used as precursor ions for all analytes but MPA. For this compound sodium adduct was used. Following transitions were monitored: for CsA m/z 1220-1203; for CsD 1234-1217; for SIR 931.6-864.5 and 882.6; for DMSIR 902-834.5; for TCR 821.5-768.5 and 785.5; for ASCO 809.5-756; for MPA 343-211.6; for MPA-glucuronide 514-306 and 211.6. The limits of quantitation were: 1 ng/ml for TCR and SIR, 20 ng/ml for CsA, and 0.1 microg/ml for MPA. Post-column infusion experiments showed that no positive or negative peaks appeared after injection of matrix in the elution range of target compounds. General signal suppression caused by matrix ranged from 20-40%, and was caused mainly by zinc sulfate present in deproteinizing solution. Extracted samples were stable for 2 days at 4 degrees C and for at least 20 days at -20 degrees C. MPA was fully separated from its glucuronide, which was eluted at around 0.7-0.8 min and directed to the waste. Some mutual cross-contribution of CsD and CsA was observed (below 1%), other IS did not contribute to target compounds and vice versa. Observations of chromatograms from patients taken single therapy demonstrated that possible metabolites of CsA, TCR, or SIR did not interfere with target compounds or IS.     

Variation among wheat (Triticum easativum L.) genotypes in response to the drought stress: I – selection approaches

The agronomic and physiological traits, drought tolerance indexes, principal component analysis and Ward`s method were applied to assess the differences among 20 wheat genotypes in response to drought. Statistically significant correlation was observed for measured traits. Drought susceptibility index (DSI), stress tolerance index (STI) and stress index (SI) were most useful to identify genotypes differing in their response to drought. Utility of the indexes was confirmed by physiological markers of drought tolerance i.e. membrane injury and leaf water status. Variation of the genotypes in biomass and grain yield during drought stress was also verified by clustering methods. Finally, integration of physiological and statistical methods presented in this work, allows to both, indicate that tolerance to drought in wheat has a common genetic background, and select the most diverse genotypes. Based on the results, we recommend a tool for breeders, useful to select the genotypes resistant and sensitive to drought.

Abbreviations: DM: dry matter; DSI: drought susceptibility index; FWC: field water capacity; GY: grain yield; GMP: geometric mean productivity index; H: plant height; LI: leakage index related to membrane injury; M_PRO: mean productivity index; M_HAR: harmonic mean index; NoT: number of tillers; NoG, W-1000: number of grains and weight of 1000 grains, respectively; NoL_MT, NoL_AT, NoL_T: number of leaves on main tiller, adventitious tillers and total leaf number, respectively; PCA: principal component analysis; RTC: relative trait change; RWC, RT, WD: relative water content, relative turgidity and water deficit, respectively SI: stress index; SPAD: leaf greening; STI: stress tolerance index; TI: tolerance index; WCA: Ward`s cluster analysis.     

MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids

Structural biology experiments and structure prediction tools have provided many high-resolution three-dimensional structures of nucleic acids. Also, molecular dynamics force field parameters have been adapted to simulating charged and flexible nucleic acid structures on microsecond time scales. Therefore, we can generate the dynamics of DNA or RNA molecules, but we still lack adequate tools for the analysis of the resulting huge amounts of data. We present MINT (Motif Identifier for Nucleic acids Trajectory) — an automatic tool for analyzing three-dimensional structures of RNA and DNA, and their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or nuclear magnetic resonance-derived structures). For each RNA or DNA conformation MINT determines the hydrogen bonding network resolving the base pairing patterns, identifies secondary structure motifs (helices, junctions, loops, etc.) and pseudoknots. MINT also estimates the energy of stacking and phosphate anion-base interactions. For many conformations, as in a molecular dynamics trajectory, MINT provides averages of the above structural and energetic features and their evolution. We show MINT functionality based on all-atom explicit solvent molecular dynamics trajectory of the 30S ribosomal subunit.     

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks

Background

Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implementations are programming libraries that require users to write code, which limits their accessibility.

Results

We have developed a tool called CyNetworkBMA for inferring gene networks from expression data that integrates with Cytoscape. Our application offers a graphical user interface for networkBMA, an efficient implementation of Bayesian Model Averaging methods for network construction. The client-server architecture of CyNetworkBMA makes it possible to distribute or centralize computation depending on user needs.

Conclusions

CyNetworkBMA is an easy-to-use tool that makes network inference accessible to non-programmers through seamless integration with Cytoscape. CyNetworkBMA is available on the Cytoscape App Store at http://apps.cytoscape.org/apps/cynetworkbma.

     

Incidence of microcystin‐producing cyanobacteria in Lake Tana,the largest waterbody in Ethiopia

The occurrence of toxic cyanobacterial blooms is a serious problem for fast‐developing countries in Africa, such as Ethiopia, that are struggling with significant degradation of the natural environment and limited access to water of good quality. Research undertaken on Lake Tana in Ethiopia between 2009 and 2011 was intended to assess the seasonal threat from cyanobacteria and to select methods for tracking of this threat in the future. The cyanobacterial genus Microcystis was found to be present throughout the monitoring period, and M. aeruginosa was determined as the dominant species. Moreover, in all samples, toxigenic cyanobacteria with the potential to produce microcystins were detected. High levels of microcystins, ranging from 0.58 to 2.65 μg L^?1, were detected each November, which indicates that in the postrainy season, water usage should be limited. The correlation between concentrations of chlorophyll‐a and microcystins suggested that chlorophyll‐a could be used as an indicator of the potential presence of cyanobacterial‐derived hepatotoxins in Lake Tana in the future. Furthermore, for quick quantitative confirmation of the presence of microcystins, a simple and rapid ELISA test was recommended.     

The Importance of Non-Native Prey,the Zebra Mussel Dreissena polymorpha,for the Declining Greater Scaup Aythya marila: A Case Study at a Key European Staging and Wintering Site

The European population of Greater Scaup Aythya marila has experienced an alarming, ~60% decline in numbers over the last two decades. The brackish lagoons of the Odra River Estuary (ORE) in the south-western Baltic Sea, represent an important area for the species during the non-breeding season in Europe. The lagoons regularly support over 20 000 Scaup, with peaks exceeding 100 000 (38%–70% of the population wintering in NW Europe and the highest number recorded in April 2011–105 700). In the ORE, Scaup feed almost exclusively on the non-native Zebra Mussel Dreissena polymorpha. This mussel was present in the ORE already in the 19^th century and continues to be superabundant. Using the results of 22 Scaup censuses (November to April 2002/2003 to 2013/2014) from the whole ORE (523 km² of water), we show that Scaup flocks follow areas with the greatest area of occurrence and biomass of the Zebra Mussel, while areas with low mussel densities are ignored. The numbers of Scaup in the ORE are primarily related to the area of Zebra Mussel occurrence on the lagoon’s bottom (km²) in a non-linear fashion. Zebra Mussels were absolutely prevalent (97% of biomass) in the digestive tracts of birds unintentionally by-caught in fishing nets (n = 32). We estimate that Scaup alone consume an average of 5 400 tons of Zebra Mussels annually, which represents 5.6% of the total resources of the mussel in the ORE. Our results provide a clear picture of the strong dependence of the declining, migratory duck species on the non-native mussel, its primary food in the ORE. Our findings are particularly important as they can form the basis for the conservation action plan aimed at saving the north-western European populations of Scaup.