Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin

The distribution of the archaeal communities in deep subseafloor sediments [0–36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average ∼3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0–1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene ( amoA ) sequences affiliated to a group of uncultured sedimentary Crenarchaeota . However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales , Marine Benthic Group D and other lineages probably involved in the methane cycle ( Methanosarcinales , ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota , DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.     

Validation and Application of a Custom-Designed Targeted Next-Generation Sequencing Panel for the Diagnostic Mutational Profiling of Solid Tumors

The inevitable switch from standard molecular methods to next-generation sequencing for the molecular profiling of tumors is challenging for most diagnostic laboratories. However, fixed validation criteria for diagnostic accreditation are not in place because of the great variability in methods and aims. Here, we describe the validation of a custom panel of hotspots in 24 genes for the detection of somatic mutations in non-small cell lung carcinoma, colorectal carcinoma and malignant melanoma starting from FFPE sections, using 14, 36 and 5 cases, respectively. The targeted hotspots were selected for their present or future clinical relevance in solid tumor types. The target regions were enriched with the TruSeq approach starting from limited amounts of DNA. Cost effective sequencing of 12 pooled libraries was done using a micro flow cell on the MiSeq and subsequent data analysis with MiSeqReporter and VariantStudio. The entire workflow was diagnostically validated showing a robust performance with maximal sensitivity and specificity using as thresholds a variant allele frequency >5% and a minimal amplicon coverage of 300. We implemented this method through the analysis of 150 routine diagnostic samples and identified clinically relevant mutations in 16 genes including KRAS (32%), TP53 (32%), BRAF (12%), APC (11%), EGFR (8%) and NRAS (5%). Importantly, the highest success rate was obtained when using also the low quality DNA samples. In conclusion, we provide a workflow for the validation of targeted NGS by a custom-designed pan-solid tumor panel in a molecular diagnostic lab and demonstrate its robustness in a clinical setting.     

Production of bio-ethanol from soybean molasses by Saccharomyces cerevisiae at laboratory, pilot and industrial scales

The aim of this work was to develop an economical bioprocess to produce the bio-ethanol from soybean molasses at laboratory, pilot and industrial scales. A strain of Saccharomyces cerevisiae (LPB-SC) was selected and fermentation conditions were defined at the laboratory scale, which included the medium with soluble solids concentration of 30% (w/v), without pH adjustment or supplementation with the mineral sources. The kinetic parameters - ethanol productivity of 8.08g/Lh, Y(P/S) 45.4%, Y(X/S) 0.815%, m 0.27h(-1) and mu(X) 0.0189h(-1) - were determined in a bench scale bioreactor. Ethanol production yields after the scale-up were satisfactory, with small decreases from 169.8L at the laboratory scale to 163.6 and 162.7L of absolute ethanol per ton of dry molasses, obtained at pilot and industrial scales, respectively.     

Regulation of Endothelial Nitric-oxide Synthase (NOS) S-Glutathionylation by Neuronal NOS: EVIDENCE OF A FUNCTIONAL INTERACTION BETWEEN MYOCARDIAL CONSTITUTIVE NOS ISOFORMS*

Myocardial constitutive No production depends on the activity of both endothelial and neuronal NOS (eNOS and nNOS, respectively). Stimulation of myocardial β₃-adrenergic receptor (β₃-AR) produces a negative inotropic effect that is dependent on eNOS. We evaluated whether nNOS also plays a role in β₃-AR signaling and found that the β₃-AR-mediated reduction in cell shortening and [Ca²⁺]_i transient amplitude was abolished both in eNOS^−/− and nNOS^−/− left ventricular (LV) myocytes and in wild type LV myocytes after nNOS inhibition with S-methyl-l-thiocitrulline. LV superoxide (O₂^˙̄) production was increased in nNOS^−/− mice and reduced by l-N^ω-nitroarginine methyl ester (l-NAME), indicating uncoupling of eNOS activity. eNOS S-glutathionylation and Ser-1177 phosphorylation were significantly increased in nNOS^−/− myocytes, whereas myocardial tetrahydrobiopterin, eNOS Thr-495 phosphorylation, and arginase activity did not differ between genotypes. Although inhibitors of xanthine oxidoreductase (XOR) or NOX2 NADPH oxidase caused a similar reduction in myocardial O₂^˙̄, only XOR inhibition reduced eNOS S-glutathionylation and Ser-1177 phosphorylation and restored both eNOS coupled activity and the negative inotropic and [Ca²⁺]_i transient response to β₃-AR stimulation in nNOS^−/− mice. In summary, our data show that increased O₂^˙̄ production by XOR selectively uncouples eNOS activity and abolishes the negative inotropic effect of β₃-AR stimulation in nNOS^−/− myocytes. These findings provide unequivocal evidence of a functional interaction between the myocardial constitutive NOS isoforms and indicate that aspects of the myocardial phenotype of nNOS^−/− mice result from disruption of eNOS signaling.     

Cardiolipin and its metabolites move from mitochondria to other cellular membranes during death receptor-mediated apoptosis

We previously reported that during death receptor-mediated apoptosis, cardiolipin (CL) relocates to the cell surface, where it reacts with autoantibodies from antiphospholipid syndrome sera. Here, we analysed the intracellular distribution of CL and its metabolites during the early phase of cell death signalling triggered by Fas stimulation in U937 cells and mouse liver. We found a redistribution of mitochondrial CL to the cell surface by using confocal microscopy and flow cytometry. Mass spectrometry revealed that CL and its metabolites relocated from mitochondria to other intracellular organelles during apoptosis, with a conversion into non-mitochondrial lipids. Concomitantly, cytosolic Bid relocated to the light membranes comprised in fraction P100, including the plasma membrane and associated vesicular systems. A direct Bid-CL interaction was demonstrated by the observation that CL and monolysoCL coimmunoprecipitated with Bid especially after Fas stimulation, suggesting a dynamic interaction of the protein with CL and its metabolites.     

La diatomée marine Chaetoceros simplex calcitransPaulsen et son environnement. VI. Capture et métabolisme du cholestérol

An 8-day culture was made of the marine diatom Chaetoceros simplex calcitrans Paulsen in the presence of cholesterol-4 ¹⁴C. The collected cells were then introduced into a replacement medium for a new period of 8 days. The capture and metabolism of the sterol were followed and information was obtained concerning the exchanges between the cells and the medium; for this purpose, hydrocarbons and fatty acids have been analysed. Evidence for the degradation of cholesterol into acetate is established. The observed phenomena are rapid, complex, and apparently modulated at all levels of the exchanges.     

Resistance of the honey bee, Apis mellifera to the acarian parasite Varroa destructor: behavioural and electroantennographic data

Abstract. One way in which Apis mellifera honey bees resist Varroa destructor is by detection and elimination of nestmates. This study uses behavioural tests and electroanntennography to assess the role of chemostimuli in recognition by honey bees of this acarian ectoparasite. Behavioural tests using living or dead parasites involved observation of honey bee grooming activity (antennation) under controlled conditions in Petri dishes, and removal behaviour (uncapping and elimination of parasitized and unparasitized control brood cells) under natural conditions. Some bees from colonies with both small and large parasite populations showed aggressive behaviour (biting). No difference was observed according to whether the mite was dead or alive. Under natural conditions, bees uncapped more parasitized cells than control cells. Electroantennographic tests were performed to measure sensitivity to various Varroa extracts at three concentrations (10, 20 and 30 Varroa Equivalents). Only 30 Varroa Equivalent methanol extracts made from Varroa collected from brood cells elicited significantly greater antennal response than controls (pure solvent). All three methanol extracts elicited significantly greater antennal response than controls. No response was observed using Varroa extracts made with acetone or hexane. These findings suggest that polar products may act as chemostimuli for recognition of V. destructor by honey bees. Further study will be necessary to determine which polar products are involved in this recognition and assess grooming and removal behaviour using these products.     

Biochemical alterations in human cells irradiated with alpha particles delivered by macro- or microbeams

Irradiation of individual cell nuclei with charged-particle microbeams requires accurate identification and localization of cells using Hoechst staining and UV illumination before computer-monitored localization of each cell. Using Fourier-transform infrared microspectroscopy (FT-IRM), we investigated whether the experimental conditions used for cell recognition induce cellular changes prior to irradiation and compared biochemical changes and DNA damage after targeted and nontargeted irradiation with alpha particles delivered by macro- or microbeams, using gamma radiation as a reference. Molecular damage in single HaCaT cells was studied by means of FT-IRM and comet assay (Gault et al., Int. J. Radiat. Biol. 81, 767-779, 2005). Hoechst 33342-stained HaCaT cells were exposed to single doses of 2 Gy (239)Pu alpha particles from a broad-beam irradiator, five impacted alpha particles from a microbeam irradiator, or 6 Gy gamma rays from (137)Cs, each of which resulted in about 5% clonogenic survival. FT-IRM of control cells indicated that Hoechst binding to nuclear DNA induced subtle changes in DNA conformation, and its excitation under UV illumination induced a dramatic shift of the DNA conformation from A to B as well as major DNA damage as measured by the comet assay. Comparison of the FT-IRM spectra of cells exposed to gamma rays or alpha particles specifically targeted to the nucleus, alpha particles from a broad-beam irradiator revealed spectral changes corresponding to all changes in constitutive bases in nucleic acids, suggesting oxidative damage in these bases, as well as structural damage in the deoxyribose-phosphate backbone of DNA and the osidic structure of nucleic acids. Concomitantly, spectral changes specific to protein suggested structural modifications. Striking differences in IR spectra between targeted microbeam- and nontargeted macrobeam-irradiated cells indicated greater residual unrepaired or misrepaired damage after microbeam irradiation. This was confirmed by the comet assay data. These results show that FT-IRM, together with the comet assay, is useful for assessing direct radiation-induced damage to nucleic acids and proteins in single cells and for investigating the effects of radiation quality. Significantly, FT-IRM revealed that Hoechst 33342 binding to DNA and exposure to UV light induce a dramatic change in DNA conformation as well as DNA damage. These findings suggest that fluorochrome staining should be avoided in studies of ionizing radiation-induced bystander effects based on charged-particle microbeam irradiation. An alternative cell nucleus recognition system that avoids nuclear matrix damage and its possible contribution to propagation of biological effects from irradiated cells to neighboring nontargeted cells needs to be developed.     

Anti-predator defence mechanisms in sawfly larvae of Arge (Hymenoptera, Argidae)

Larvae of the sawfly Arge (Hymenoptera, Argidae) are exposed to predators such as ants. Their defence mechanisms, which have been almost unstudied, were investigated by behavioural observations coupled to a morphological approach and by testing the bioactivity of several body parts. Arge larvae raised their abdomen when contacted by Myrmica rubra workers. The ants rarely bit a larva and generally retreated immediately, sometimes without contacting it. Most of those few ants that bit a larva then showed an uncoordinated walk. Crude hemolymph from a common species, A. pagana, was a feeding deterrent towards ants. Hemolymph extracts remained active up to a concentration of 0.8 microg DW extract per microlitre solution, and were more active than integument and gut extracts. We also observed ants paralysed by extracts, especially from the gut. It is likely that this toxicity is due to a polypeptide, lophyrotomin, which is known to occur in A. pullata. Six or seven non-eversible ventro-abdominal glands occurred in all species studied (A. fuscipes, A. nigripes, A. ochropus, A. pagana, A. pullata, A. ustulata). These glands contain volatiles. We consider both types of chemicals to be important in defence, and we propose that the paralysing effect is a common feature among Arge species.     

Unexpected inhibition of peptidoglycan LD-transpeptidase from Enterococcus faecium by the beta-lactam imipenem

The beta-lactam antibiotics mimic the D-alanyl(4)-D-alanine(5) extremity of peptidoglycan precursors and act as "suicide" substrates of the DD-transpeptidases that catalyze the last cross-linking step of peptidoglycan synthesis. We have previously shown that bypass of the dd-transpeptidases by the LD-transpeptidase of Enterococcus faecium (Ldt(fm)) leads to high level resistance to ampicillin. Ldt(fm) is specific for the L-lysyl(3)-D-alanine(4) bond of peptidoglycan precursors containing a tetrapeptide stem lacking D-alanine(5). This specificity was proposed to account for resistance, because the substrate of Ldt(fm) does not mimic beta-lactams in contrast to the D-alanyl(4)-D-alanine(5) extremity of pentapeptide stems used by the DD-transpeptidases. Here, we unexpectedly show that imipenem, a beta-lactam of the carbapenem class, totally inhibited Ldt(fm) at a low drug concentration that was sufficient to inhibit growth of the bacteria. Peptidoglycan cross-linking was also inhibited, indicating that Ldt(fm) is the in vivo target of imipenem. Stoichiometric and covalent modification of Ldt(fm) by imipenem was detected by mass spectrometry. The modification was mapped into the trypsin fragment of Ldt(fm) containing the catalytic Cys residue, and the Cys to Ala substitution prevented imipenem binding. The mass increment matched the mass of imipenem, indicating that inactivation of Ldt(fm) is likely to involve rupture of the beta-lactam ring and acylation of the catalytic Cys residue. Thus, the spectrum of activity of beta-lactams is not restricted to transpeptidases of the DD-specificity, as previously thought. Combination therapy with imipenem and ampicillin could therefore be active against E. faecium strains having the dual capacity to manufacture peptidoglycan with transpeptidases of the LD- and DD-specificities.