Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities

Microbial communities in hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) were studied by using 16S rRNA sequencing and carbon isotopic analysis of archaeal and bacterial lipids. The Guaymas sediments harbored uncultured euryarchaeota of two distinct phylogenetic lineages within the anaerobic methane oxidation 1 (ANME-1) group, ANME-1a and ANME-1b, and of the ANME-2c lineage within the Methanosarcinales, both previously assigned to the methanotrophic archaea. The archaeal lipids in the Guaymas Basin sediments included archaeol, diagnostic for nonthermophilic euryarchaeota, and sn-2-hydroxyarchaeol, with the latter compound being particularly abundant in cultured members of the Methanosarcinales. The concentrations of these compounds were among the highest observed so far in studies of methane seep environments. The delta-(13)C values of these lipids (delta-(13)C = -89 to -58 per thousand) indicate an origin from anaerobic methanotrophic archaea. This molecular-isotopic signature was found not only in samples that yielded predominantly ANME-2 clones but also in samples that yielded exclusively ANME-1 clones. ANME-1 archaea therefore remain strong candidates for mediation of the anaerobic oxidation of methane. Based on 16S rRNA data, the Guaymas sediments harbor phylogenetically diverse bacterial populations, which show considerable overlap with bacterial populations of geothermal habitats and natural or anthropogenic hydrocarbon-rich sites. Consistent with earlier observations, our combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy. Anaerobic methane oxidation likely represents a significant and widely occurring process in the trophic ecology of methane-rich hydrothermal vents. This study stresses a high diversity among communities capable of anaerobic oxidation of methane.     

Seasonal dynamics and depth distribution of belowground biomass carbon and nitrogen of extensive grassland and a Miscanthus plantation

Plant and Soil - Belowground carbon (C) inputs are a major source of soil organic carbon (SOC) in terrestrial ecosystems, and substrate C:N ratios drive SOC stabilisation. In perennial systems,...     

Comparison of Plasma and Urine Biomarker Performance in Acute Kidney Injury

Background

New renal biomarkers measured in urine promise to increase specificity for risk stratification and early diagnosis of acute kidney injury (AKI) but concomitantly may be altered by urine concentration effects and chronic renal insufficiency. This study therefore directly compared the performance of AKI biomarkers in urine and plasma.

Methods

This single-center, prospective cohort study included 110 unselected adults undergoing cardiac surgery with cardiopulmonary bypass between 2009 and 2010. Plasma and/or urine concentrations of creatinine, cystatin C, neutrophil gelatinase-associated lipocalin (NGAL), liver fatty acid-binding protein (L-FABP), kidney injury molecule 1 (KIM1), and albumin as well as 15 additional biomarkers in plasma and urine were measured during the perioperative period. The primary outcome was AKI defined by AKIN serum creatinine criteria within 72 hours after surgery.

Results

Biomarkers in plasma showed markedly better discriminative performance for preoperative risk stratification and early postoperative (within 24h after surgery) detection of AKI than urine biomarkers. Discriminative power of urine biomarkers improved when concentrations were normalized to urinary creatinine, but urine biomarkers had still lower AUC values than plasma biomarkers. Best diagnostic performance 4h after surgery had plasma NGAL (AUC 0.83), cystatin C (0.76), MIG (0.74), and L-FAPB (0.73). Combinations of multiple biomarkers did not improve their diagnostic power. Preoperative clinical scoring systems (EuroSCORE and Cleveland Clinic Foundation Score) predicted the risk for AKI (AUC 0.76 and 0.71) and were not inferior to biomarkers. Preexisting chronic kidney disease limited the diagnostic performance of both plasma and urine biomarkers.

Conclusions

In our cohort plasma biomarkers had higher discriminative power for risk stratification and early diagnosis of AKI than urine biomarkers. For preoperative risk stratification of AKI clinical models showed similar discriminative performance to biomarkers. The discriminative performance of both plasma and urine biomarkers was reduced by preexisting chronic kidney disease.     

Effects of land use in the drainage area on phosphorus binding and mobility in the sediments of four drinking-water reservoirs

The study of four drinking-water reservoirsdemonstrates how the anthropogenic land use of acatchment may affect binding and mobility ofphosphorus in the sediment. P_diss concentrationgradients at the sediment–water interface weremeasured to calculate potential diffusive releaserates. P binding forms were determined by sequentialextraction of fresh sediment and settling seston. Mainstudy sites were Saidenbach Reservoir (mesotrophic,densely populated drainage area with 73% agriculturalland use) and Neunzehnhain Reservoir (oligotrophic,unpopulated drainage area forested to 80%) in thesilicate-rich Erzgebirge mountains of eastern Germany.Tot-P concentrations and P binding forms of typicalerosive matter from each catchment were similar to thesediment of both pre-reservoirs and reservoirs' mouth.In Saidenbach Reservoir, diatoms responded to highnutrient loading by incorporating ortho-P. Whilesettling, the org-P was partly transformed toFe(OOH)P. Apart from hypolimnetic O₂depletion, this P binding form dominated in thesurface sediment mainly in front of the dam. Withincreasing sediment depth, org-P and Fe(OOH)Pnot only redissolved into the pore water, but alsoadsorbed onto Al compounds. In Neunzehnhain Reservoir,acidification of the low buffered catchment favouredloading of humic compounds and Al³+ ions, whichprecipitated and redox-independently adsorbed ortho-Pdue to a pH increase in the lake. Neunzehnhainsediment was able to immobilize Fe(OOH)P fromSaidenbach sediment in a batch experiment. Comparativesequential P extraction of sediment from SosaReservoir (oligo-mesotrophic, sparsely populateddrainage area forested to 94%) and Kleine KinzigReservoir (nearly unpopulated drainage area forestedto 98%) also demonstrated effective P immobilizationby Al-/humic compounds.It is concluded that the absence of settlements in thecatchment, together with forestry as dominating landuse, favour not only oligotrophic conditions in thereservoir but also confine internal P loading from thesediment. But attention should be paid toacidification problems.     

Antipredator Behavioral Traits of some <Emphasis Type="Italic">Agriotes</Emphasis> Wireworms (Coleoptera: Elateridae) and their Potential Implications for Species Identification

Many insects show a typical antipredator behavior. The two simplest tactics are immobilization and flight. The antipredator behavior of wireworms, the soil-dwelling polyphagous larvae of click beetles, has not yet been investigated. Birds are known to attack wireworms. Our experimental method (picking up and dropping wireworms) mimics the first attack of a predator, such as a bird. In Europe, some Agriotes species are of particular importance as crop pests. As these species differ considerably, in ecology, damage threshold, and pathogen resistance, knowing more about the species specific biology and behavior will support the establishment of successful control measures. In an extensive microcosm study, we observed the antipredator behavior of wireworms belonging to four different Agriotes species (A. lineatus, A. obscurus, A. sordidus, and A. ustulatus) before and during digging into the soil after a startle-stimulus. We recorded wireworm immobility frequency and duration, and locomotor activity at three temperatures. We also analyzed genetic and morphologic attributes of A. lineatus larvae from two different origins. Following behavior types were found reflecting different escape tactics: (a) distinct tonic immobility (A. lineatus), (b) brief/inconsistent tonic immobility (A. obscurus, A. sordidus), and (c) immediate fleeing/burying (A. ustulatus). Additionally, we found small but significant differences in morphology, behavior, and genetics (PCR results) between A. lineatus larvae originating from the Netherlands and those originating from Germany. The biological information we gathered about each species will further increase the understanding of these insects and improve interpretation of future experimental data. In addition, the described behavioral differences between Agriotes obscurus and A. lineatus wireworms may represent a useful additional criterion in morphological species identification.     

Hypoxia signalling in the control of erythropoietin gene expression in rat hepatocytes

This study aimed to investigate the sequence of events involved in the stimulation of erythropoietin (EPO) gene expression by hypoxia in hepatocytes. To this end, primary cultures of rat hepatocytes were kept at either high (40% O₂) or low (3% O₂) oxygen tensions for 2.5 h. Hypoxia increased EPO mRNA about fifteen-fold, whilst the divalent cation cobalt (50–100 μM) or the iron chelator desferrioxamine (10–200 μM) did not increase EPO mRNA levels. Addition of hydrogen peroxide (100–500 μM) to the culture medium did also not change EPO mRNA levels at high or low oxygen tension. Addition of catalase (50–200 μg/ml) to the culture medium resulted in a lower level of hypoxia-induced EPO mRNA. Inhibition of protein synthesis by cycloheximide (100 μM) completely abolished the increase of EPO mRNA in response to hypoxia. Hypoxia but not cobalt increased the appearance of the hypoxia-inducible factor 1 (HIF-1), and this increase was blunted by cycloheximide. Taken together, these findings suggest that a classic heme protein and a related oxygen-dependent production of oxygen radicals is less likely to be involved in the regulation of the EPO gene by oxygen in hepatocytes. On the other hand, intact protein synthesis is an absolute requirement for the hypoxia-induced appearance of HIF-1 and for hypoxia-stimulated expression of the EPO gene in hepatocytes. © 1996 Wiley-Liss, Inc.     

Scaffold hopping approach towards various AFQ-056 analogs as potent metabotropic glutamate receptor 5 negative allosteric modulators

The metabotropic glutamate receptor subtype 5 has evolved into a promising target for the treatment of various diseases of the central nervous system, such as Fragile X and l-DOPA induced dyskinesia. One of the most advanced clinical compound is Novartis’ AFQ-056 (Mavoglurant), which served us as a template for a scaffold hopping approach, generating a structurally diverse set of potent analogs. Both the limited aqueous solubility and the relatively poor metabolic stability of AFQ-056 were improved with hexahydrocyclopenta[c]pyrrole derivative 54a, which proved to be a valuable candidate for further development.     

SPRED: A machine learning approach for the identification of classical and non-classical secretory proteins in mammalian genomes

Eukaryotic protein secretion generally occurs via the classical secretory pathway that traverses the ER and Golgi apparatus. Secreted proteins usually contain a signal sequence with all the essential information required to target them for secretion. However, some proteins like fibroblast growth factors (FGF-1, FGF-2), interleukins (IL-1 alpha, IL-1 beta), galectins and thioredoxin are exported by an alternative pathway. This is known as leaderless or non-classical secretion and works without a signal sequence. Most computational methods for the identification of secretory proteins use the signal peptide as indicator and are therefore not able to identify substrates of non-classical secretion. In this work, we report a random forest method, SPRED, to identify secretory proteins from protein sequences irrespective of N-terminal signal peptides, thus allowing also correct classification of non-classical secretory proteins. Training was performed on a dataset containing 600 extracellular proteins and 600 cytoplasmic and/or nuclear proteins. The algorithm was tested on 180 extracellular proteins and 1380 cytoplasmic and/or nuclear proteins. We obtained 85.92% accuracy from training and 82.18% accuracy from testing. Since SPRED does not use N-terminal signals, it can detect non-classical secreted proteins by filtering those secreted proteins with an N-terminal signal by using SignalP. SPRED predicted 15 out of 19 experimentally verified non-classical secretory proteins. By scanning the entire human proteome we identified 566 protein sequences potentially undergoing non-classical secretion. The dataset and standalone version of the SPRED software is available at http://www.inb.uni-luebeck.de/tools-demos/spred/spred.