Contributions of catchment and in-stream processes to suspended sediment transport in a dominantly groundwater-fed catchment

Suspended sediments impact stream water quality by increasing the turbidity and acting as a vector for strongly sorbing pollutants. Understanding their sources is of great importance to developing appropriate river management strategies. In this study, we present an integrated sediment transport model composed of a catchment-scale hydrological model to predict river discharge, a river-hydraulics model to obtain shear stresses in the channel, a sediment-generating model, and a river sediment-transport model. We use this framework to investigate the sediment contributions from catchment and in-stream processes in the Ammer catchment close to Tübingen in southwestern Germany. The model is calibrated to stream flow and suspended-sediment concentrations. We use the monthly mean suspended-sediment load to analyze seasonal variations of different processes. The contributions of catchment and in-stream processes to the total loads are demonstrated by model simulations under different flow conditions. The evaluation of shear stresses by the river-hydraulics model allows the identification of hotspots and hot moments of bed erosion for the main stem of the Ammer River. The results suggest that the contributions of suspended-sediment loads from urban areas and in-stream processes are higher in the summer months, while deposition has small variations with a slight increase in summer months. The sediment input from agricultural land and urban areas as well as bed and bank erosion increase with an increase in flow rates. Bed and bank erosion are negligible when flow is smaller than the corresponding thresholds of 1.5 and 2.5 times the mean discharge, respectively. The bed-erosion rate is higher during the summer months and varies along the main stem. Over the simulated time period, net sediment trapping is observed in the Ammer River. The present work is the basis to study particle-facilitated transport of pollutants in the system, helping to understand the fate and transport of sediments and sediment-bound pollutants.</p

A Potential Role for Drosophila Mucins in Development and Physiology

Vital vertebrate organs are protected from the external environment by a barrier that to a large extent consists of mucins. These proteins are characterized by poorly conserved repeated sequences that are rich in prolines and potentially glycosylated threonines and serines (PTS). We have now used the characteristics of the PTS repeat domain to identify Drosophila mucins in a simple bioinformatics approach. Searching the predicted protein database for proteins with at least 4 repeats and a high ST content, more than 30 mucin-like proteins were identified, ranging from 300–23000 amino acids in length. We find that Drosophila mucins are present at all stages of the fly life cycle, and that their transcripts localize to selective organs analogous to sites of vertebrate mucin expression. The results could allow for addressing basic questions about human mucin-related diseases in this model system. Additionally, many of the mucins are expressed in selective tissues during embryogenesis, thus revealing new potential functions for mucins as apical matrix components during organ morphogenesis

The high affinity selectin glycan ligand C2-O-sLex and mRNA transcripts of the core 2 β-1,6-N-acetylglusaminyltransferase (C2GnT1) gene are highly expressed in human colorectal adenocarcinomas

<p>Abstract</p> <p>Background</p> <p>The metastasis of cancer cells and leukocyte extravasation into inflamed tissues share common features. Specialized carbohydrates modified with sialyl Lewis x (sLe^x) antigens on leukocyte membranes are ligands for selectin adhesion molecules on activated vascular endothelial cells at inflammatory sites. The activity of the enzyme core 2 β1,6 <it>N</it>-acetylglucosaminyltransferase (C2GnT1) in leukocytes greatly increases their ability to bind to endothelial selectins. C2GnT1 is essential for the synthesis of core 2-branched O-linked carbohydrates terminated with sLe^x(C2-O-sLe^x). Our goal was to determine the expression profiles of C2-O-sLe^xin the malignant progression and metastasis of colorectal adenocarcinomas. The well characterized CHO-131 monoclonal antibody (mAb) specifically recognizes C2-O-sLe^xpresent in human leukocytes and carcinoma cells. Using CHO-131 mAb, we investigated whether C2-O-sLe^xwas present in 113 human primary colorectal adenocarcinomas, 10 colorectal adenomas, 46 metastatic liver tumors, 28 normal colorectal tissues, and 5 normal liver tissues by immunohistochemistry. We also examined mRNA levels of the enzyme core 2 β1,6-<it>N</it>-acetylglucosaminyltransferase (C2GnT1) in 20 well, 15 moderately, and 2 poorly differentiated colorectal adenocarcinomas, and in 5 normal colorectal tissues by using quantitative real-time polymerase chain reactions (RT-PCR).</p> <p>Results</p> <p>We observed high reactivity with CHO-131 mAb in approximately 70% of colorectal carcinomas and 87% of metastatic liver tumors but a lack of reactivity in colorectal adenomas and normal colonic and liver tissues. Positive reactivity with CHO-131 mAb was very prominent in neoplastic colorectal glands of well to moderately differentiated adenocarcinomas. The most intense staining with CHO-131 mAb was observed at the advancing edge of tumors with the deepest invasive components.</p> <p>Finally, we analyzed C2GnT1 mRNA levels in 37 colorectal adenocarcinomas and 5 normal colorectal tissues by RT-PCR. Significantly, we observed a greater than 15-fold increase in C2GnT1 mRNA levels in colorectal adenocarcinomas compared to normal colorectal tissues.</p> <p>Conclusion</p> <p>C2-O-sLe^x, detected by the CHO-131 mAb, is a tumor associated antigen whose expression is highly upregulated in colorectal adenocarcinomas and metastatic liver tumors compared to normal tissues. C2-O-sLe^xis a potentially useful early predictor of metastasis.</p

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner–Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.This work was supported by the Swedish Research Council (Grant Numbers 2012-4592 to AE and 2012-3892 to SB) and the Communiy Sequencing Programme of the US Department of Energy Joint Genome Institute. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, freeliving bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages. comparative genomics | marine microbiology | microbial ecology | microbial microevolution | operational taxonomic uni

Particle bound pollutants in rivers: Results from suspended sediment sampling in Globaqua River Basins

Transport of hydrophobic pollutants in rivers such as polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals is often facilitated by suspended sediment particles, which are typically mobilized during high discharge events. Suspended sediments thus represent a means of transport for particle related pollutants within river reaches and may represent a suitable proxy for average pollutant concentrations estimation in a river reach or catchment. In this study, multiple high discharge/turbidity events were sampled at high temporal resolution in the Globaqua River Basins Sava (Slovenia, Serbia), Adige (Italy), and Evrotas (Greece) and analysed for persistent organic pollutants such as PAHs (polycyclic aromatic hydrocarbons) or PCBs (polychlorinated biphenyls) and heavy metals. For comparison, river bed sediment samples were analysed as well. Further, results are compared to previous studies in contrasting catchments in Germany, Iran, Spain, and beyond. Overall results show that loadings of suspended sediments with pollutants are catchment-specific and relatively stable over time at a given location. For PAHs, loadings on suspended particles mainly correlate to urban pressures (potentially diluted by sediment mass fluxes) in the rivers, whereas metal concentrations mainly display a geogenic origin. By cross-comparison with known urban pressure/sediment yield relationships (e.g. for PAHs) or soil background values (for metals) anthropogenic impact – e.g. caused by industrial activities – may be identified. Sampling of suspended sediments gives much more reliable results compared to sediment grab samples which typically show a more heterogeneous contaminant distribution. Based on mean annual suspended sediment concentrations and distribution coefficients of pollutants the fraction of particle facilitated transport versus dissolved fluxes can be calculated