The determinants of stability in the human prion protein: insights into folding and misfolding from the analysis of the change in the stabilization energy distribution in different conditions

The dynamic evolution of the PrP(C) from its NMR-derived conformation to a beta-sheet-rich, aggregation-prone conformation is studied through all-atom, explicit solvent molecular dynamics in different temperature and pH conditions. The trajectories are analyzed by means of a recently introduced energy decomposition approach aimed at identifying the key residues for the stabilization and folding of the protein. It is shown that under native conditions the stabilization energy is concentrated in regions of the helices H1 and H3, whereas under misfolding conditions (low pH, high temperature, or mutations in selected sites) it is spread out over helix H2. Misfolding appears to be a rearrangement of the chain that disrupts most of the native secondary structure of the protein, producing some beta-rich conformations with an energy distribution similar to that of the native state.     

Activity and Diversity of Sulfate-Reducing Bacteria in a Petroleum Hydrocarbon-Contaminated Aquifer

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO₄²⁻ reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day⁻¹ for sulfate reduction and from 0.13 to 0.60 day⁻¹ for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.     

Phylogenetic island disequilibrium: evidence for ongoing long‐term population dynamics in two Mediterranean butterflies

Aim Our aims were to verify the existence of phylogenetic disequilibrium between butterfly lineages at the subcontinental scale for islands and the nearest mainland and to test the capacity of islands for hosting ancestral populations of butterflies and the significance of such relict populations. Location The western Mediterranean continental area of Europe and North Africa together with several large and small islands (Balearics, Tuscan Archipelago, Aeolian Archipelago, Capri, Sardinia, Sicily, Corsica). Methods Using geometric morphometrics, the shape of male genitalia was analysed in two common butterflies (Pyronia cecilia and Pyronia tithonus), whose spatial heterogeneity in the Mediterranean region has recently been described. Observed patterns in genital shapes were compared with shapes predicted for islands and fossil islands to assess the contribution of historical and current events in accounting for the transition from a refugial model to an equilibrium model. Measurements were taken for 473 specimens in 90 insular and mainland sites. Results The shape of the genitalia of populations of most islands differed substantially from that predicted by the equilibrium hypothesis while closely fitting the refugial hypothesis. The comparison between different models strongly suggests that islands maintain ancestral lineages similar to those living in Spain (P. cecilia) and France (P. tithonus). A high correlation between observed and predicted patterns on islands and fossil islands occurs during the first steps of modelled introgressive hybridization while the following steps exposed a successively lower fit, suggesting that the process from a refugial to an equilibrium situation is highly skewed towards an earlier non‐equilibrium. Main conclusions The observed non‐equilibrium pattern supports the refugial hypothesis, suggesting that an ancestral lineage was originally distributed from Spain to Italy, and also occupied offshore islands. This lineage, replaced in Italy, has persisted on the islands owing to their isolation. A comparison of the distribution patterns for genetic and morphometric markers in several species indicates that the situation highlighted for Pyronia may represent a common biogeographic feature for many Mediterranean butterflies.     

Biogeneration of 2-phenylethanol and 2-phenylethylacetate important aroma components

Summary 2-Phenylethanol and 2-phenylethylacetate important aroma components are obtained in substantial amounts whenHansenula anomala CBS 110 andKloeckera saturnus CBS 5761 are grown with L-phenylalanine as sole nitrogen source. Up to 2 g/L of mixtures of alcohol and ester are obtained. While in the first microorganism the alcohol predominates, in the second the acetate is formed almost exclusively. Experiments with 1-¹³C-d-Glucose show complete incorporation of the label into the methyl group of the acetate.     

Maternal Control of PIN1 Is Required for Female Gametophyte Development in Arabidopsis

Land plants are characterised by haplo-diploid life cycles, and developing ovules are the organs in which the haploid and diploid generations coexist. Recently it has been shown that hormones such as auxin and cytokinins play important roles in ovule development and patterning. The establishment and regulation of auxin levels in cells is predominantly determined by the activity of the auxin efflux carrier proteins PIN-FORMED (PIN). To study the roles of PIN1 and PIN3 during ovule development we have used mutant alleles of both genes and also perturbed PIN1 and PIN3 expression using micro-RNAs controlled by the ovule specific DEFH9 (DEFIFICENS Homologue 9) promoter. PIN1 down-regulation and pin1-5 mutation severely affect female gametophyte development since embryo sacs arrest at the mono- and/or bi-nuclear stages (FG1 and FG3 stage). PIN3 function is not required for ovule development in wild-type or PIN1-silenced plants. We show that sporophytically expressed PIN1 is required for megagametogenesis, suggesting that sporophytic auxin flux might control the early stages of female gametophyte development, although auxin response is not visible in developing embryo sacs.     

Single‐Ion Conducting Electrolyte Based on Electrospun Nanofibers for High‐Performance Lithium Batteries

Herein, a novel electrospun single‐ion conducting polymer electrolyte (SIPE) composed of nanoscale mixed poly(vinylidene fluoride‐co‐hexafluoropropylene) (PVDF‐HFP) and lithium poly(4,4′‐diaminodiphenylsulfone, bis(4‐carbonyl benzene sulfonyl)imide) (LiPSI) is reported, which simultaneously overcomes the drawbacks of the polyolefin‐based separator (low porosity and poor electrolyte wettability and thermal dimensional stability) and the LiPF₆ salt (poor thermal stability and moisture sensitivity). The electrospun nanofiber membrane (es‐PVPSI) has high porosity and appropriate mechanical strength. The fully aromatic polyamide backbone enables high thermal dimensional stability of es‐PVPSI membrane even at 300 °C, while the high polarity and high porosity ensures fast electrolyte wetting. Impregnation of the membrane with the ethylene carbonate (EC)/dimethyl carbonate (DMC) (v:v = 1:1) solvent mixture yields a SIPE offering wide electrochemical stability, good ionic conductivity, and high lithium‐ion transference number. Based on the above‐mentioned merits, Li/LiFePO₄ cells using such a SIPE exhibit excellent rate capacity and outstanding electrochemical stability for 1000 cycles at least, indicating that such an electrolyte can replace the conventional liquid electrolyte–polyolefin combination in lithium ion batteries (LIBs). In addition, the long‐term stripping–plating cycling test coupled with scanning electron microscope (SEM) images of lithium foil clearly confirms that the es‐PVPSI membrane is capable of suppressing lithium dendrite growth, which is fundamental for its use in high‐energy Li metal batteries.     

Genotyping of Polyomavirus BK by Real Time PCR for VP1 Gene

Polyomavirus BK latently persist in different sites, including the renourinary tract, and may reactivate causing nephropathy in renal transplant recipients or hemorrhagic cystitis in bone marrow recipients. Based on the sequence of the VP1 gene, four genotypes have been described, corresponding to the four serologically differentiated subtypes I–IV, with different prevalence and geographic distribution. In this study, the development and clinical validation of four different Real-Time PCR assays for the detection and discrimination of BKV genotypes as a substitute of DNA sequencing are described. 379 BK VP1 sequences, belonging to the main four genotypes, were aligned and “hot spots” of mutation specific for all the strains or isolates were identified. Specific primers and probes for the detection and discrimination of each genotype by four Real-Time PCR assays were designed and technically validated. Subsequently, the four Real-Time PCR assays were used to test 20 BK-positive urine specimens from renal transplant patients, and evidenced a prevalence of BK genotype I, as previously reported in Europe. Results were confirmed by sequencing. The availability of a rapid and simple genotyping method could be useful for the evaluation of BK genotypes prevalence and studies on the impact of the infecting genotype on viral biological behavior, pathogenic role, and immune evasion strategies.     

Novel polymorphic microsatellite loci for the protogynous hermaphrodite slinger sea bream (Chrysoblephus puniceus, Sparidae)

As a result of the global decline of fish stocks, an increasing number of fish species are becoming targets of heavy exploitation, often concomitantly with a lack of biological knowledge on their structure and demographics. Here we present 11 new polymorphic microsatellite loci, isolated from the slinger sea bream (Chrysoblephus puniceus, Sparidae), a relatively recent target of coastal fisheries in eastern South Africa. Levels of genetic diversity were assessed in 39 individuals collected from the KwaZulu-Natal coast (Park Rynie, South Africa). Observed and expected heterozygosities varied between 0.39 and 0.97 and between 0.53 and 0.96, respectively. One locus (SL35) showed significant heterozygote deficiency and linkage disequilibrium was detected between SL35 and SL1. Importantly, five of these microsatellites cross-amplify in Cheimerius nufar, a sympatric species also subjected to exploitation.