Bayesian network model informs on the impact of biotic and abiotic factors on the population characteristics of an endangered plant species

Preservation of the endangered plant species requires knowledge of the impact of environmental factors on their populations. This study was undertaken to evaluate the potential of a Bayesian network (BN) model to analyze the impact of habitat conditions on the current characteristics of Pulsatilla patens (L.) Mill. population in NE Poland. The model was based on field data collected in 2011–2015 from 47 sites in the four largest forest complexes of NE Poland. The causal network between (1) the biotic and (2) abiotic factors as well as morphological-developmental features of individuals and demographic features of populations (20 attributes, 1573 records) was made using the Bayesian Search Algorithm in GeNIe 2.0. The results indicate that the greatest impact on the population features had the number of competing species in forest undergrowth and exposition of slopes. Diagnostic testing and sensitivity analysis revealed that these factors were the major variables determining the size of the population, developmental phase, and the size of individuals. Tenfold cross-validation revealed that this model was the most effective to analyze the impact of habitat conditions on the presence of generative shoots, developmental phase, and juvenile shoots. The optimal levels of factors following from the BN modeling of the impact of habitat conditions on the characteristics of the population will allow regular growth (size of individuals) and development (life cycle of individuals) of a given endangered species.     

Functional characterization of two melanocortin (MC) receptors in lamprey showing orthology to the MC1 and MC4 receptor subtypes

Background  

The melanocortin (MC) receptors have a key role in regulating body weight and pigmentation. They belong to the rhodopsin family of G protein-coupled receptors (GPCRs). The purpose of this study was to identify ancestral MC receptors in agnathan, river lamprey.     

Application of enzymatic apple pomace hydrolysate to production of 2,3-butanediol by alkaliphilic <Emphasis Type="Italic">Bacillus licheniformis</Emphasis> NCIMB 8059

2,3-Butanediol (2,3-BD) synthesis by a nonpathogenic bacterium Bacillus licheniformis NCIMB 8059 from enzymatic hydrolysate of depectinized apple pomace and its blend with glucose was studied. In shake flasks, the maximum diol concentration in fed-batch fermentations was 113 g/L (in 163 h, from the hydrolysate, feedings with glucose) while in batch processes it was around 27 g/L (in 32 h, from the hydrolysate and glucose blend). Fed-batch fermentations in the 0.75 and 30 L fermenters yielded 87.71 g/L 2,3-BD in 160 h, and 72.39 g/L 2,3-BD in 94 h, respectively (from the hydrolysate and glucose blend, feedings with glucose). The hydrolysate of apple pomace, which was for the first time used for microbial 2,3-BD production is not only a source of sugars but also essential minerals.     

Influence of tail versus cardiac sampling on blood glucose and lipid profiles in mice

Blood is collected during animal experimentation to measure haematological and metabolic parameters. It cannot be assumed that circulating blood has the same composition irrespective of its location, and indeed, differences in the composition of blood sampled from the arterial and venous compartments have been reported. Here we investigated whether blood collected by cardiac puncture (CP) versus that collected following removal of the distal 1 mm of the tail tip (TT) differs with respect to glucose and lipid profiles in male C57BL/6J mice at 4, 7, 20 and 28 weeks of age. Blood was first collected from the TT of unanaesthetized mice, which were then immediately anaesthetized using ketamine/xylazine, and a second blood sample was collected by CP. The CP glucose concentration was significantly higher than TT glucose by a positive bias averaging +80% (P < 0.01), irrespective of the age of the mice. Conversely, the concentrations of the CP lipids, including total cholesterol, high-density lipoprotein cholesterol and triglyceride were lower than TT lipids by a negative bias averaging -25% (P < 0.05). These observations highlight the difficulty in measuring and comparing metabolic parameters such as glucose and lipid between one blood compartment and another. They illustrate the need to standardize sampling sites, especially when repeated blood sampling is required.     

Synthesis and SAR of pyridothiazole substituted pyrimidine derived HCV replication inhibitors

Introduction of a nitrogen atom into the benzene ring of a previously identified HCV replication (replicase) benzothiazole inhibitor 1, resulted in the discovery of the more potent pyridothiazole analogues 3. The potency and PK properties of the compounds were attenuated by the introductions of various functionalities at the R(1), R(2) or R(3) positions of the molecule (compound 3). Inhibitors 38 and 44 displayed excellent potency, selectivity (GAPDH/MTS CC(50)), PK parameters in all species studied, and cross genotype activity.     

Redescriptions of two frequently recorded but poorly known hemiurid digeneans, Lecithochirium musculus (Looss, 1907) (Lecithochiriinae) and Ectenurus lepidus Looss, 1907 (Dinurinae), based on material from the western Mediterranean

Two frequently reported but poorly known hemiurid digeneans, Lecithochirium musculus (Looss, 1907) (Lecithochiriinae), from the stomach of Trachinus draco and Citharus linguatula, and Ectenurus lepidus Looss, 1907 (Dinurinae), from the stomach of Spicara maena, are redescribed based on material from off the Barcelona coast of the western Mediterranean. The two species are commented upon, and Lecithochirium israelense Fischthal, 1980 is considered a synonym of L. musculus. Records of the two species in the Mediterranean Basin and North East Atlantic region are summarised.     

Pressure as a denaturing agent in studies of single-point mutants of an amyloidogenic protein human cystatin c

Recently, we presented a convenient method combining a deuterium‐hydrogen exchange and electrospray mass spectrometry for studying high‐pressure denaturation of proteins (Stefanowicz et al., Biosci Rep 2009; 30:91–99). Here, we present results of pressure‐induced denaturation studies of an amyloidogenic protein—the wild‐type human cystatin C (hCC) and its single‐point mutants, in which Val57 residue from the hinge region was substituted by Asn, Asp or Pro, respectively. The place of mutation and the substituting residues were chosen mainly on a basis of theoretical calculations. Observation of H/D isotopic exchange proceeding during pressure induced unfolding and subsequent refolding allowed us to detect differences in the proteins stability and folding dynamics. On the basis of the obtained results we can conclude that proline residue at the hinge region makes cystatin C structure more flexible and dynamic, what probably facilitates the dimerization process of this hCC variant. Polar asparagine does not influence stability of hCC conformation significantly, whereas charged aspartic acid in 57 position makes the protein structure slightly more prone to unfolding. Our experiments also point out pressure denaturation as a valuable supplementary method in denaturation studies of mutated proteins. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

N-glycosylation affects the molecular organization and stability of E-cadherin junctions

Epithelial cell-cell adhesion is mediated by E-cadherin, an intercellular N-glycoprotein adhesion receptor that functions in the assembly of multiprotein complexes anchored to the actin cytoskeleton named adherens junctions (AJs). E-cadherin ectodomains 4 and 5 contain three potential N-glycan addition sites, although their significance in AJ stability is unclear. Here we show that sparse cells lacking stable AJs produced E-cadherin that was extensively modified with complex N-glycans. In contrast, dense cultures with more stable AJs had scarcely N-glycosylated E-cadherin modified with high mannose/hybrid and limited complex N-glycans. This suggested that variations in AJ stability were accompanied by quantitative and qualitative changes in E-cadherin N-glycosylation. To further examine the role of N-glycans in AJ function, we generated E-cadherin N-glycosylation variants lacking selected N-glycan addition sites. Characterization of these variants in CHO cells, lacking endogenous E-cadherin, revealed that site 1 on ectodomain 4 was modified with a prominent complex N-glycan, site 2 on ectodomain 5 did not have a substantial oligosaccharide, and site 3 on ectodomain 5 was decorated with a high mannose/hybrid N-glycan. Removal of complex N-glycan from ectodomain 4 led to a dramatically increased interaction of E-cadherin-catenin complexes with vinculin and the actin cytoskeleton. The latter effect was further enhanced by the deletion of the high mannose/hybrid N-glycan from site 3. In MDCK cells, which produce E-cadherin, a variant lacking both complex and high mannose/hybrid N-glycans functioned like a dominant positive displaying increased interaction with gamma-catenin and vinculin compared with the endogenous E-cadherin. Collectively, our studies show that N-glycans, and complex oligosaccharides in particular, destabilize AJs by affecting their molecular organization.