Expanding the cerebrospinal fluid endopeptidome

Biomarkers of neurodegenerative disorders are needed to assist in diagnosis, to monitor disease progression and therapeutic interventions, and to provide insight into disease mechanisms. One route to identify such biomarkers is by proteomic and peptidomic analysis of cerebrospinal fluid (CSF). In the current study, we performed an in-depth analysis of the human CSF endopeptidome to establish an inventory that may serve as a basis for future targeted biomarker studies. High-pH RP HPLC was employed for off-line sample prefractionation followed by low-pH nano-LC-MS analysis. Different software programs and scoring algorithms for peptide identification were employed and compared. A total of 18 031 endogenous peptides were identified at a FDR of 1%, increasing the number of known endogenous CSF peptides 10-fold compared to previous studies. The peptides were derived from 2 053 proteins of which more than 60 have been linked to neurodegeneration. Notably, among the findings were six peptides derived from microtubule-associated protein tau, three of which span the diagnostically interesting threonine-181 (Tau-F isoform). Also, 213 peptides from amyloid precursor protein were identified, 58 of which were partially or completely within the sequence of amyloid β 1-40/42, as well as 109 peptides from apolipoprotein E, spanning sequences that discriminate between the E2/E3/E4 isoforms of the protein

Controls on methane concentration and stable isotope (δ2H-CH4 and δ13C-CH4) distributions in the water columns of the Black Sea and Cariaco Basin

Methane (CH4) concentration and stable isotope (δ2H-CH4 and δ13C-CH4) depth distributions show large differences in the water columns of the Earth's largest CH4-containing anoxic basins, the Black Sea and Cariaco Basin. In the deep basins, the between-basin stable isotope differences are large, 83‰ for δ2H-CH4 and 9‰ for δ13C-CH4, and the distributions are mirror images of one another. The major sink in both basins, anaerobic oxidation of CH4, results in such extensive isotope fractionation that little direct information can be obtained regarding sources. Recent measurements of natural 14C-CH4 show that the CH4 geochemistry in both basins is dominated (∼64 to 98%) by inputs of fossil (radiocarbon-free) CH4 from seafloor seeps. We derive open-system kinetic isotope effect equations and use a one-dimensional (vertical) stable isotope box model that, along with isotope budgets developed using radiocarbon, permits a quantitative treatment of the stable isotope differences. We show that two main factors control the CH4 concentration and stable isotope differences: (1) the depth distributions of the input of CH4 from seafloor seeps and (2) anaerobic oxidation of CH4 under open-system steady state conditions in the Black Sea and open-system non-steady-state conditions in the Cariaco Basin

The effect of pH, grain size, and organic ligands on biotite weathering rates

Biotite dissolution rates were determined at 25 °C, at pH 2–6, and as a function of mineral composition, grain size, and aqueous organic ligand concentration. Rates were measured using both open- and closed-system reactors in fluids of constant ionic strength. Element release was non-stoichiometric and followed the general trend of Fe, Mg > Al > Si. Biotite surface area normalised dissolution rates (ri) in the acidic range, generated from Si release, are consistent with the empirical rate law: ri=kH,iaxiH+ where kH,i refers to an apparent rate constant, aH+ designates the activity of protons, and xi stands for a reaction order with respect to protons. Rate constants range from 2.15 × 10−10 to 30.6 × 10−10 (molesbiotite m−2 s−1) with reaction orders ranging from 0.31 to 0.58. At near-neutral pH in the closed-system experiments, the release of Al was stoichiometric compared to Si, but Fe was preferentially retained in the solid phase, possibly as a secondary phase. Biotite dissolution was highly spatially anisotropic with its edges being ∼120 times more reactive than its basal planes. Low organic ligand concentrations slightly enhanced biotite dissolution rates. These measured rates illuminate mineral–fluid–organism chemical interactions, which occur in the natural environment, and how organic exudates enhance nutrient mobilisation for microorganism acquisition

Adsorption of hydroxamate siderophores and EDTA on goethite in the presence of the surfactant sodium dodecyl sulfate

Siderophore-promoted iron acquisition by microorganisms usually occurs in the presence of other organic molecules, including biosurfactants. We have investigated the influence of the anionic surfactant sodium dodecyl sulfate (SDS) on the adsorption of the siderophores DFOB (cationic) and DFOD (neutral) and the ligand EDTA (anionic) onto goethite (α-FeOOH) at pH 6. We also studied the adsorption of the corresponding 1:1 Fe(III)-ligand complexes, which are products of the dissolution process. Adsorption of the two free siderophores increased in a similar fashion with increasing SDS concentration, despite their difference in molecule charge. In contrast, SDS had little effect on the adsorption of EDTA. Adsorption of the Fe-DFOB and Fe-DFOD complexes also increased with increasing SDS concentrations, while adsorption of Fe-EDTA decreased. Our results suggest that hydrophobic interactions between adsorbed surfactants and siderophores are more important than electrostatic interactions. However, for strongly hydrophilic molecules, such as EDTA and its iron complex, the influence of SDS on their adsorption seems to depend on their tendency to form inner-sphere or outer-sphere surface complexes. Our results demonstrate that surfactants have a strong influence on the adsorption of siderophores to Fe oxides, which has important implications for siderophore-promoted dissolution of iron oxides and biological iron acquisition

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness

Systemic infection induces conserved physiological responses that include both resistance and ‘tolerance of infection’ mechanisms. Temporary anorexia associated with an infection is often beneficial, reallocating energy from food foraging towards resistance to infection or depriving pathogens of nutrients. However, it imposes a stress on intestinal commensals, as they also experience reduced substrate availability; this affects host fitness owing to the loss of caloric intake and colonization resistance (protection from additional infections). We hypothesized that the host might utilize internal resources to support the gut microbiota during the acute phase of the disease. Here we show that systemic exposure to Toll-like receptor (TLR) ligands causes rapid α(1,2)-fucosylation of small intestine epithelial cells (IECs) in mice, which requires the sensing of TLR agonists, as well as the production of interleukin (IL)-23 by dendritic cells, activation of innate lymphoid cells and expression of fucosyltransferase 2 (Fut2) by IL-22-stimulated IECs. Fucosylated proteins are shed into the lumen and fucose is liberated and metabolized by the gut microbiota, as shown by reporter bacteria and community-wide analysis of microbial gene expression. Fucose affects the expression of microbial metabolic pathways and reduces the expression of bacterial virulence genes. It also improves host tolerance of the mild pathogen Citrobacter rodentium. Thus, rapid IEC fucosylation appears to be a protective mechanism that utilizes the host’s resources to maintain host–microbial interactions during pathogen-induced stress

Investigation of how observed methane concentrations in Ny-Ålesund are influenced by atmospheric flow patterns

International audienceLong-range atmospheric transport to Svalbard has been studied with a compilation of 4 years of daily trajectories to determine how the atmospheric flow patterns influence the observed methane (CH4) at Mt. Zeppelin station (475 m.a.s.l.) in Ny-Ålesund (78&deg54' N, 11°53' E). The flow patterns were determined through cluster analysis of 5-day back-trajectories arriving at Ny-Ålesund twice a day (00:00 and 12:00 UTC) for the period 2000?2003. Eight cluster patterns were obtained and used in the analysis of the continuous methane measurements at Mt. Zeppelin station. The analysis shows a shift in frequencies eastward into the Arctic compared to identical studies of transport for 1992?2001. Higher concentrations of methane are mainly seen in clusters with transport from Europe and Russia in contrast to air following transport pathways within the Arctic Basin. The vertical motion of the trajectories has been investigated and shows that it has an effect on the methane concentration at the Mt. Zeppelin station. This is consistent with previous similar studies of CO2 and of other anthropogenic species. Seasonal variation in trajectory frequency can be seen, like for instance more trajectories from Europe and Siberia during winter, and short trajectories from the Arctic region in summer. The identified seasonal and indications of decadal shifts in transport pathways translate into shifts in source areas sampled by a single station. To determine shifts in regional source (and sink) strengths it is necessary to correct for transport pathway shifts when interpreting time series data

Yes, now we can: Technological change and the exploitation of entrepreneurial opportunities

The paper investigates how technological change in an industry influence which individuals will identify and exploit entrepreneurial opportunities. We propose that the introduction of new development tools will change knowledge-barriers to entry because they enable the abstraction of specialized knowledge that was previously needed for development. Empirically we test the argument using data from the web design industry in a Nordic country during the period 1992-2003. We compare the education and experience of founders before and after the introduction of web administration tools in 1998 and find a significant difference, which supports the main thesis of our argument

A microwave radiometer for the remote sensing of nitric oxide and ozone in the middle atmosphere

Nitric oxide, which reacts catalytically to destroy ozone, can be produced in great abundance in the middle atmosphere during energetic particle precipitation triggered by solar storms. During the Antarctic winter, the strong polar vortex can rapidly transport nitric oxide downward, and this process has been identified as a mechanism that can link ozone recovery in,the upper stratosphere with solar activity. As part of the Sun Earth Connection programme at the British Antarctic Survey (BAS), a new, state-of-the-art microwave radiometer is being developed in collaboration with the MaxPlanck Institute (MPI) and the Norwegian Polar Institute (NPI) to simultaneously measure profiles of ozone and nitric oxide between 30 and 80 km deep within the Antarctic polar vortex. Operating in the 250 GHz spectral region, the semi-autonomous instrument will be coupled to moderate- and high-resolution chirp spectrometers to provide simultaneous spectra of the nitric oxide and ozone. In addition, a second local oscillator will be used to periodically examine carbon monoxide at 230.538 GHz to infer the vertical descent rate within the Antarctic vortex. Here, we present the science rationale for the observation programme as well as the instrument specifications, design and performance