Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins

Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.     

Characterization of alkaline proteases from a novel alkali-tolerant bacterium Bacillus patagoniensis

Summary The extracellular proteolytic activity produced by a moderately alkaliphilic bacterium, Bacillus patagoniensis PAT 05^T, was characterized. This strain, grown in a highly alkaline and saline medium, produced important levels of proteolytic activity. SDS-PAGE and zymogram analyses revealed two proteolytic active bands. Through isoelectricfocusing (IEF)-zymogram, an active band with alkaline pI and two slighter active bands with acid pI values were detected. The alkaline active enzyme in the IEF was purified and characterized. It showed a molecular mass of 29.4 kDa and its pI value was >‰10.3. Proteolytic activity of the culture supernatant showed an optimal temperature of approximately 60 °C and a plateau of maximum activity between pH 9.0 and 12.0. Such activity was not affected by H₂O₂ (10% v/v), 1,10-phenanthroline (10 mM), Triton X-100 (1% v/v) and Tween 20 (1% v/v), under the assay conditions. More than 80% of the activity was retained in 10 mM EDTA, 73% in 1 % (w/v) SDS and 63% in 2 M NaCl. The enzyme was inhibited by PMSF, indicating serine-protease activity. The proteolytic activity of the crude supernatant was thermosensitive with a half-life of 2.3 min at 70 °C, while high activity was detected at moderate temperatures. Considering PAT 05^T proteolytic activity characteristics, such as high optimum pH, high stability and residual activity in presence of oxidant, surfactant and chelating agents, this strain could be a potential source of enzymes for use as additives in detergent formulations or in the leather industry.     

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure,hybridization and a role for humans in Andean parasite dispersal

An improved understanding of how a parasite species exploits its genetic repertoire to colonize novel hosts and environmental niches is crucial to establish the epidemiological risk associated with emergent pathogenic genotypes. Trypanosoma cruzi, a genetically heterogeneous, multi‐host zoonosis, provides an ideal system to examine the sylvatic diversification of parasitic protozoa. In Bolivia, T. cruzi I, the oldest and most widespread genetic lineage, is pervasive across a range of ecological clines. High‐resolution nuclear (26 loci) and mitochondrial (10 loci) genotyping of 199 contemporaneous sylvatic TcI clones was undertaken to provide insights into the biogeographical basis of T. cruzi evolution. Three distinct sylvatic parasite transmission cycles were identified: one highland population among terrestrial rodent and triatomine species, composed of genetically homogenous strains (A_r = 2.95; PA/L = 0.61; D_AS = 0.151), and two highly diverse, parasite assemblages circulating among predominantly arboreal mammals and vectors in the lowlands (A_r = 3.40 and 3.93; PA/L = 1.12 and 0.60; D_AS = 0.425 and 0.311, respectively). Very limited gene flow between neighbouring terrestrial highland and arboreal lowland areas (distance ~220 km; F_ST = 0.42 and 0.35) but strong connectivity between ecologically similar but geographically disparate terrestrial highland ecotopes (distance >465 km; F_ST = 0.016–0.084) strongly supports ecological host fitting as the predominant mechanism of parasite diversification. Dissimilar heterozygosity estimates (excess in highlands, deficit in lowlands) and mitochondrial introgression among lowland strains may indicate fundamental differences in mating strategies between populations. Finally, accelerated parasite dissemination between densely populated, highland areas, compared to uninhabited lowland foci, likely reflects passive, long‐range anthroponotic dispersal. The impact of humans on the risk of epizootic Chagas disease transmission in Bolivia is discussed.     

Biological activities of extracts from Chenopodium ambrosioides Lineu and Kielmeyera neglecta Saddi

ABSTRACT: BACKGROUND: Chenopodium ambrosioides and Kielmeyera neglecta are plants traditionally used in Brazil to treat various infectious diseases. The study of the biological activities of these plants is of great importance for the detection of biologically active compounds. METHODS: Extracts from these plants were extracted with hexane (Hex), dichloromethane (DCM), ethyl acetate (EtOAc) and ethanol (EtOH) and assessed for their antimicrobial properties, bioactivity against Artemia salina Leach and antifungal action on the cell wall of Neurospora crassa. RESULTS: Extracts from C. ambrosioides (Hex, DCM and EtOH) and K. neglecta (EtOAc and EtOH) showed high bioactivity against A. salina (LD50 < 1000 ug/mL), which might be associated with cytotoxic activity against cancer cells. C. ambrosioides Hex and DCM showed specific activity against yeasts, highlighting the activity of hexanic extract against Candida krusei (MIC = 100 ug/mL). By comparing the inhibitory concentration of 50% growth (IC 50%) with the growth control, extracts from K. neglecta EtOAc and EtOH have shown activities against multidrug-resistant bacteria (Enterococcus faecalis ATCC 51299 and Staphylococcus aureus ATCC 43300), with IC 50% of 12.5 ug/mL The assay carried out on N. crassa allowed defining that extracts with antifungal activity do not have action through inhibition of cell wall synthesis. CONCLUSIONS: Generally speaking, extracts from C. ambrosioides and K. neglecta showed biological activities that have made the search for bioactive substances in these plants more attractive, illustrating the success of their use in the Brazilian folk medicine.     

Use of Hydrogenophaga pseudoflava Penetration To Quantitatively Assess the Impact of Filtration Parameters for 0.2-Micrometer-Pore-Size Filters

Filters rated as having a 0.2-μm pore size (0.2-μm-rated filters) are used in laboratory and manufacturing settings for diverse applications of bacterial and particle removal from process fluids, analytical test articles, and gasses. Using Hydrogenophaga pseudoflava, a diminutive bacterium with an unusual geometry (i.e., it is very thin), we evaluated passage through 0.2-μm-rated filters and the impact of filtration process parameters and bacterial challenge density. We show that consistent H. pseudoflava passage occurs through 0.2-μm-rated filters. This is in contrast to an absence of significant passage of nutritionally challenged bacteria that are of similar size (i.e., hydrodynamic diameter) but dissimilar geometry.The 0.2-μm-pore-size filter class (0.2-μm-rated filters) includes a large and diverse set of products (22). They include air filters, particle reduction filters, filters used for bioburden reduction, lab-grade filters, and “sterilizing-grade” filters used in sterile-dosage-form manufacture. ASTM F 838-05, the Brevundimonas diminuta challenge test, is a standard for the “sterilizing-grade” filters (4), a subset of the 0.2-μm-rated filters. The “0.2-μm” designation is applied to the larger and more diverse set of products. This designation is based on physical measurements (e.g., the bubble point, the force necessary to extrude air through the capillary network of a wet filter) and mathematical extrapolations (5, 14, 29).The current filter validation approach for parenteral pharmaceuticals involves a demonstration of removal of 7 log₁₀ CFU/cm² of nutritionally starved B. diminuta from bulk drug product liquids (4, 8, 11, 29). B. diminuta can penetrate 0.2-μm-rated filters, but only sporadically and at low levels (12, 21). Larger bacteria (Listeria monocytogenes) have been demonstrated to be able to penetrate 0.2-μm filters after long-term exposure (27). Recently, a species of small waterborne bacteria, Hydrogenophaga pseudoflava, has been shown to penetrate 0.2-μm-rated filters (31-36) to a greater extent than the above-described bacteria. None of these bacteria are actually physically smaller than 0.2 μm, even H. pseudoflava (25, 37, 38).Because H. pseudoflava penetrates 0.2-μm-rated filters in a potentially quantifiable manner, it can be used to study filtration efficiency. In this report, we evaluate the impact of filtration process parameters and bacterial challenge density on passage. We benchmark H. pseudoflava passage against that of nutritionally challenged bacteria which are of similar size (i.e., hydrodynamic diameter) but dissimilar geometry.     

Le passage vers l’Atlantique : le processus de néolithisation en Algarve (sud du Portugal)

The late beginning of the research on the neolithisation in the Algarve (southern Portugal) has been providing, as a paradox, excellent conditions for the establishment of interdisciplinary research and the test of working hypotheses. The systematic projects put forward by the University of Algarve permit us today to conclude on a preliminary basis for the formation of a Neolithic enclave at ca. 5500 cal BC, centred in the coastal territories of the region. This enclave is fully Neolithic in economic terms and it is the westernmost extension of the Mediterranean Cardial. However, some specific features of these first Neolithic groups’ artefactual items (such as pottery morphology and style and some technological aspects of chipped stone production) indicate the existence of phenomena of partial reformulation of their material cultures. According to the presently available data, this complex process seems to have occurred in similar traits also in Andalucia and coastal Morocco, that is, at the moment of the passage to the Atlantic. This individualization within the Neolithic of Cardial tradition is the equivalent to the same general cultural phenomena that have been responsible for the formation, for example, of the so-called “Franco-Iberian Cardial” or “Tirrenic Cardial” at the time of settling of the Neolithic groups in these regions.