Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.

Halopiger djelfamassiliensis strain IIH2^T sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.     

Molecular Evidence for the Presence of Rickettsia Felis in the Feces of Wild-living African Apes

Background

Rickettsia felis is a common emerging pathogen detected in mosquitoes in sub-Saharan Africa. We hypothesized that, as with malaria, great apes may be exposed to the infectious bite of infected mosquitoes and release R. felis DNA in their feces.

Methods

We conducted a study of 17 forest sites in Central Africa, testing 1,028 fecal samples from 313 chimpanzees, 430 gorillas and 285 bonobos. The presence of rickettsial DNA was investigated by specific quantitative real-time PCR. Positive results were confirmed by a second PCR using primers and a probe targeting a specific gene for R. felis. All positive samples were sequenced.

Results

Overall, 113 samples (11%) were positive for the Rickettsia-specific gltA gene, including 25 (22%) that were positive for R. felis. The citrate synthase (gltA) sequence and outer membrane protein A (ompA) sequence analysis indicated 99% identity at the nucleotide level to R. felis. The 88 other samples (78%) were negative using R. felis-specific qPCR and were compatible with R. felis-like organisms.

Conclusion

For the first time, we detected R. felis in wild-living ape feces. This non invasive detection of human pathogens in endangered species opens up new possibilities in the molecular epidemiology and evolutionary analysis of infectious diseases, beside HIV and malaria.     

Nanowire-Based Electrode for Acute In Vivo Neural Recordings in the Brain

We present an electrode, based on structurally controlled nanowires, as a first step towards developing a useful nanostructured device for neurophysiological measurements in vivo. The sensing part of the electrode is made of a metal film deposited on top of an array of epitaxially grown gallium phosphide nanowires. We achieved the first functional testing of the nanowire-based electrode by performing acute in vivo recordings in the rat cerebral cortex and withstanding multiple brain implantations. Due to the controllable geometry of the nanowires, this type of electrode can be used as a model system for further analysis of the functional properties of nanostructured neuronal interfaces in vivo.     

A signaling cascade mediated by ceramide,src and PDGFRβ coordinates the activation of the redox-sensitive neutral sphingomyelinase-2 and sphingosine kinase-1

Stress-inducing agents, including oxidative stress, generate the sphingolipid mediators ceramide (Cer) and sphingosine-1-phosphate (S1P) that are involved in stress-induced cellular responses. The two redox-sensitive neutral sphingomyelinase-2 (nSMase2) and sphingosine kinase-1 (SK1) participate in transducing stress signaling to ceramide and S1P, respectively; however, whether these key enzymes are coordinately regulated is not known. We investigated whether a signaling link coordinates nSMase2 and SK1 activation by H₂O₂. In mesenchymal cells, H₂O₂ elicits a dose-dependent biphasic effect, mitogenic at low concentration (5 μM), and anti-proliferative and toxic at high concentration (100 μM).     

Structural comparison of substrate entry gate for rhomboid intramembrane peptidases

Rhomboids are intramembrane serine peptidases conserved in all kingdoms of life. Their general role is to cleave integral membrane proteins to release signalling molecules. These signals, when disrupted, can contribute to various diseases. Crystal structures of H. influenzae (hiGlpG) and E. coli GlpG (ecGlpG) rhomboids have revealed a structure with six transmembrane helices and a Ser-His catalytic dyad buried within the membrane. One emerging issue was the identification of the mobile element in the protein that allows substrate docking. It has been proposed that the substrate entry gate is composed of helix 5 and loop 5. The present review studies the structures of these two orthologs. In ecGlpG structures, different conformations of loop 5 and helix 5 are observed. Open and closed conformations of ecGlpG structures are compared with each other and with hiGlpG, surveying differences in hydrophobic interactions within loop 5 and helix 5. Furthermore, a comparison of the ecGlpG and hiGlpG structures reveals differences in loop 4. Overall, less variation is observed in loop 4, suggesting this region acts as an anchor for the substrate gate. Functional and regulatory implications of these variations are discussed.     

Effects of a phosphorus amendment and the pH of water used for watering on the mobility and phytoavailability of Cd, Pb and Zn in highly contaminated kitchen garden soils

Studies on two lead and zinc smelters in Northern France (Metaleurop Nord and Umicore) showed that the level of metallic contamination of kitchen garden soils is higher than the agricultural soils located in the same environment. This results most particularly from cropping practices and the addition of various products. Due to the physical and chemical parameters of these soils, the behaviour and transfer of pollutants towards various plants (grass, trees, and vegetables) may be perceptibly different than what is observed on agricultural soils.For a better understanding of pollutant behaviour in kitchen garden topsoils, the Cd, Pb and Zn was fractionated using the SM&T protocol and various extracting solutions (CaCl₂, acetic acid, and citric acid) to evaluate their mobility in two highly contaminated soils chosen in the area affected by the past atmospheric emissions of the two smelters. In addition, agricultural topsoil was sampled in a non-massively contaminated area and was therefore chosen as the control soil.The three soils were amended with a mixture of hydroxyapatite (HA) and diammonium phosphate (DAP). At 6 months, extracting procedures were carried out to evaluate the effects of the amendment on the mobility of Cd, Pb and Zn. This step was then supplemented by an evaluation of the impact of the amendment on the phytoavailability of pollutants, which was determined in plant uptake studies with ryegrass (Lolium perenne L.) by considering only the pollutant concentrations in their shoots. Two experiments were carried out. In the first one, unamended and amended soils and ryegrass were watered with distilled water (pH = 7). In the second one, osmosed water (pH = 5.5) was used to evaluate the effects of the acid water-phosphate amendment system on the mobility and phytoavailability of Cd, Pb and Zn. Six months after the start of the experiments, the selective extractions showed that the effectiveness of the amendment studied depended on the element, the soil and the water's pH. Reductions of metal eluted from the contaminated soils were 1.5-37.9% for Cd, and 9.1-80.9% for Pb. Application of P amendment to the combination of osmosed water was generally the most effective for immobilising Cd and Pb elution. In contrast, the mixture of HA and DAP was ineffective for reducing Zn elution. The plant-fresh biomass yield was significantly (p < 0.05) increased by the combination of P amendment and distilled water, whereas a reduction of biomass was recorded with the combined amendment and osmosed water. Addition of P amendment generally reduced Pb uptake in ryegrass shoots (1-47%), while both Cd and Zn were increased by 17.9-79% and 0.45-100%, respectively.     

Zinc(II) modulates specifically amyloid formation and structure in model peptides

Metal ions such as zinc and copper can have dramatic effects on the aggregation kinetics of and the structures formed by several amyloidogenic peptides/proteins. Depending on the identity of the amyloidogenic peptide/protein and the conditions, Zn(II) and Cu(II) can promote or inhibit fibril formation, and in some cases these metal ions have opposite effects. To better understand this modulation of peptide aggregation by metal ions, the impact of Zn(II) binding to three amyloidogenic peptides (Aβ14-23, Aβ11-23, and Aβ11-28) on the formation and structure of amyloid-type fibrils was investigated. Zn(II) was able to accelerate fibril formation for all three peptides as measured by thioflavin T fluorescence and transmission electron microscopy. The effects of Zn(II) on Aβ11-23 and Aβ11-28 aggregation were very different compared with the effects of Cu(II), showing that these promoting effects were metal-specific. X-ray absorption spectroscopy suggested that the Zn(II) binding to Aβ11-23 and Aβ11-28 is very different from Cu(II) binding, but that the binding is similar in the case of Aβ14-23. A model is proposed in which the different coordination chemistry of Zn(II) compared with Cu(II) explains the metal-specific effect on aggregation and the difference between peptides Aβ14-23 and Aβ11-23/Aβ11-28.     

Current trends in the structure-activity relationships of sialyltransferases

Sialyltransferases (STs) represent an important group of enzymes that transfer N-acetylneuraminic acid (Neu5Ac) from cytidine monophosphate-Neu5Ac to various acceptor substrates. In higher animals, sialylated oligosaccharide structures play crucial roles in many biological processes but also in diseases, notably in microbial infection and cancer. Cell surface sialic acids have also been found in a few microorganisms, mainly pathogenic bacteria, and their presence is often associated with virulence. STs are distributed into five different families in the CAZy database (http://www.cazy.org/). On the basis of crystallographic data available for three ST families and fold recognition analysis for the two other families, STs can be grouped into two structural superfamilies that represent variations of the canonical glycosyltransferase (GT-A and GT-B) folds. These two superfamilies differ in the nature of their active site residues, notably the catalytic base (a histidine or an aspartate residue). The observed structural and functional differences strongly suggest that these two structural superfamilies have evolved independently.