The 1.59 Å resolution structure of the minor pseudopilin EpsH of Vibrio cholerae reveals a long flexible loop

The type II secretion complex exports folded proteins from the periplasm to the extracellular milieu. It is used by the pathogenic bacterium Vibrio cholerae to export several proteins, including its major virulence factor, cholera toxin. The pseudopilus is an essential component of the type II secretion system and likely acts as a piston to push the folded proteins across the outer membrane through the secretin pore. The pseudopilus is composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. We determined the x-ray crystal structure of the head domain of EpsH at 1.59 Å resolution using molecular replacement with the previously reported EpsH structure, 2qv8, as the template. Three additional N-terminal amino acids present in our construct prevent an artifactual conformation of residues 160–166, present in one of the two monomers of the 2qv8 structure. Additional crystal contacts stabilize a long flexible loop comprised of residues 104–135 that is more disordered in the 2qv8 structure but is partially observed in our structure in very different positions for the two EpsH monomers in the asymmetric unit. In one of the conformations the loop is highly extended. Modeling suggests the highly charged loop is capable of contacting EpsG and possibly secreted protein substrates, suggesting a role in specificity of pseudopilus assembly or secretion function.     

Identification and Validation of Oncologic miRNA Biomarkers for Luminal A-like Breast Cancer

Introduction

Breast cancer is a common disease with distinct tumor subtypes phenotypically characterized by ER and HER2/neu receptor status. MiRNAs play regulatory roles in tumor initiation and progression, and altered miRNA expression has been demonstrated in a variety of cancer states presenting the potential for exploitation as cancer biomarkers. Blood provides an excellent medium for biomarker discovery. This study investigated systemic miRNAs differentially expressed in Luminal A-like (ER+PR+HER2/neu-) breast cancer and their effectiveness as oncologic biomarkers in the clinical setting.

Methods

Blood samples were prospectively collected from patients with Luminal A-like breast cancer (n = 54) and controls (n = 56). RNA was extracted, reverse transcribed and subjected to microarray analysis (n = 10 Luminal A-like; n = 10 Control). Differentially expressed miRNAs were identified by artificial neural network (ANN) data-mining algorithms. Expression of specific miRNAs was validated by RQ-PCR (n = 44 Luminal A; n = 46 Control) and potential relationships between circulating miRNA levels and clinicopathological features of breast cancer were investigated.

Results

Microarray analysis identified 76 differentially expressed miRNAs. ANN revealed 10 miRNAs for further analysis (miR-19b, miR-29a, miR-93, miR-181a, miR-182, miR-223, miR-301a, miR-423-5p, miR-486-5 and miR-652). The biomarker potential of 4 miRNAs (miR-29a, miR-181a, miR-223 and miR-652) was confirmed by RQ-PCR, with significantly reduced expression in blood of women with Luminal A-like breast tumors compared to healthy controls (p = 0.001, 0.004, 0.009 and 0.004 respectively). Binary logistic regression confirmed that combination of 3 of these miRNAs (miR-29a, miR-181a and miR-652) could reliably differentiate between cancers and controls with an AUC of 0.80.

Conclusion

This study provides insight into the underlying molecular portrait of Luminal A-like breast cancer subtype. From an initial 76 miRNAs, 4 were validated with altered expression in the blood of women with Luminal A-like breast cancer. The expression profiles of these 3 miRNAs, in combination with mammography, has potential to facilitate accurate subtype-specific breast tumor detection.     

Bacteria recovered from a high-altitude,tropical glacier in Venezuelan Andes

Glacial-ice microorganisms are intensively studied world-wide for a number of reasons, including their psychrophilic lifestyle, their usefulness in biotechnology procedures and their relationship with the search of life outside our planet. However, because of the difficulties for accessing and working at altitudes of >5.000 m above sea level, tropical glaciers have received much less attention than their arctic and antarctic counterparts. In the present work we isolated and characterized a total of forty-five pure isolates originating from direct plating of melted ice collected at the base of a rapidly-retreating, small glacier located at around 4.900 m.a.s.l. in Mount Humboldt (Sierra Nevada National Park, Mérida State, Venezuela). Initial examination of melted ice showed the presence of abundant- (>10⁶ cells ml^?1), morphologically diverse- and active bacterial cells, many of which were very small (“dwarf cells”). The majority of the isolates were psychrophilic or psychrotolerant and many produced and excreted cold-active extracellular enzymes (proteases and amylases). The antibiotic tests showed an elevated percentage of isolates resistant to high doses (100 μg/ml) of different antibiotics including ampicillin, penicillin, nalidixic acid, streptomycin, chloramphenicol, kanamycin and tetracycline. Multiresistance was also observed, with 22.22 % of the strains simultaneously resistant up to five of the antibiotics tested. Metal resistance against Ni⁺⁺, Zn⁺⁺ and Cu⁺⁺ was also detected. In accordance with these results, plasmids of low and high molecular weight were detected in 47 % of the isolates. Twenty-two partial 16S rDNA sequences analyzed allowed grouping the isolates within five different phyla/classes: Alpha-, Beta- and Gamma-proteobacteria, Actinobacteria and Flavobacteria. This is the first report concerning South American Andean glacial ice microorganisms.     

Plasma alpha natriuretic peptide in cardiac impairment.

Regional plasma alpha human atrial natriuretic peptide concentrations were measured, and their relation to intracardiac pressures assessed, in an unselected series of 45 patients undergoing diagnostic cardiac catheterisation. Arteriovenous gradients in plasma concentrations of alpha human atrial natriuretic peptide were consistent with its cardiac secretion and its clearance by the liver and kidneys. Plasma concentrations of the peptide in the pulmonary artery, aorta, and superior vena cava correlated closely with the mean right atrial and pulmonary arterial pressures, and similar, though weaker, positive relations were seen with the left ventricular end diastolic and pulmonary artery wedge pressures. Concentrations of both atrial natriuretic peptide and renin showed significant inverse relations with serum sodium concentrations. Plasma concentrations of alpha human atrial natriuretic peptide are an additional objective indicator of the severity of haemodynamic compromise in patients with cardiac impairment.     

Micro and macro-habitat associations in saproxylic beetles: implications for biodiversity management

Restoration of habitats is critically important in preventing full realization of the extinction debt owed as a result of anthropogenic habitat destruction. Although much emphasis has been placed on macrohabitats, suitable microhabitats are also vital for the survival of most species. The aim of this large-scale field experiment was to evaluate the relative importance of manipulated microhabitats, i.e., dead wood substrates of spruce (snags, and logs that were burned, inoculated with wood fungi or shaded) and macrohabitats, i.e., stand types (clear-cuts, mature managed forests, and forest reserves) for species richness, abundance and assemblage composition of all saproxylic and red-listed saproxylic beetles. Beetles were collected in emergence traps in 30 forest stands in 2001, 2003, 2004 and 2006. More individuals emerged from snags and untreated logs than from burned and shaded logs, but species richness did not differ among substrates. Assemblage composition differed among substrates for both all saproxylics and red-listed saproxylic species, mainly attributed to different assemblage composition on snags. This suggests that the practise of leaving snags for conservation purposes should be complemented with log supplementation. Clear-cuts supported fewer species and different assemblages from mature managed forests and reserves. Neither abundance, nor species richness or assemblage composition differed between reserves and mature managed forests. This suggests that managed stands subjected to selective cutting, not clear-felling, maintain sufficient old growth characteristics and continuity to maintain more or less intact assemblages of saproxylic beetles. Thus, alternative management methods, e.g., continuity forestry should be considered for some of these stands to maintain continuity and conservation values. Furthermore, the significantly higher estimated abundance per ha of red-listed beetles in reserves underlines the importance of reserves for maintaining viable populations of rare red-listed species and as source areas for saproxylic species in boreal forest landscapes.     

BON-BONs: cyclic molecules with a boron-oxygen-nitrogen backbone. Computational studies of their thermodynamic properties

Although they were first reported in 1963, molecules with a boron-oxygen-nitrogen dimeric backbone do not seem to have been investigated seriously in terms of thermodynamic properties. Here we report on the calculated structures and properties, including thermodynamics, of several so-called “BON-BON” molecules. With the popularity of nitrogen-containing substituents on new high-energy materials, nitro-substituted BON-BONs were a focus of our investigation. A total of 42 BON-BON molecules were evaluated, and thermochemical analysis shows a decrease in the specific enthalpy of combustion or decomposition with increasing NO₂ content, consistent with other systems.     

VopA inhibits ATP binding by acetylating the catalytic loop of MAPK kinases

The bacterial pathogen Vibrio parahemeolyticus manipulates host signaling pathways during infections by injecting type III effectors. One of these effectors, Vibrio outer protein A (VopA), inhibits MAPK signaling via a novel mechanism, distinct from those described for other bacterial toxins, that disrupts this signaling pathway. VopA is an acetyltransferase that potently inhibits MAPK signaling pathways not only by preventing the activation of MAPK kinases (MKKs) but also by inhibiting the activity of activated MKKs. VopA acetylates a conserved lysine found in the catalytic loop of all kinases and blocks the binding of ATP, but not ADP, on the MKKs, resulting in an inactive phosphorylated kinase. Acetylation of this conserved lysine inhibits kinase activity by a new mechanism of regulation that has not been observed previously. Identifying the target of VopA reveals a way that the reversible post-translational modification of lysine acetylation can be used to regulate the activity of an enzyme.