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  • 2018  (12)
  • ScienceDirect Journals (Elsevier)
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  • 2018  (12)
  • 1
    Language: English
    In: Molecular Cell, 07 June 2018, Vol.70(5), pp.785-799
    Description: Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over. RNA-seq-based approaches are revolutionizing how bacterial RNA biology can be studied. Hör, Gorski, and Vogel review the available global methods that can be used to chart the increasingly diverse number of RNA species and functions in any microbe of interest.
    Keywords: RNA-Seq ; Non-Coding RNA ; Small RNA ; Transcription ; RNA-Binding Protein ; Post-Transcriptional Control ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 2
    Language: English
    In: Molecular Cell, 07 June 2018, Vol.70(5), pp.971-982.e6
    Description: The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in and . Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3′ end of mRNAs. Using the mRNA as a model for 3′ end targeting, we reveal a function for ProQ in protecting mRNA against exoribonucleolytic activity. Taken together, our results underpin the notion that ProQ governs a post-transcriptional network distinct from those of the well-characterized sRNA-binding proteins, CsrA and Hfq, and suggest a previously unrecognized, sRNA-independent role of ProQ in stabilizing mRNAs. Using CLIP-seq, Holmqvist et al. map transcriptome-wide interactions of the emerging global RNA-binding protein ProQ in and . Their data suggest ProQ to target sRNAs and mRNA 3′ UTRs primarily through a structural code and to stabilize some mRNAs by counteracting 3′ exoribonuclease activity.
    Keywords: Proq ; Clip-Seq ; RNA-Binding Protein ; 3′ Utr ; Post-Transcriptional Control ; Exoribonuclease ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 3
    Language: English
    In: Science of the Total Environment, 15 December 2018, Vol.645, pp.192-204
    Description: Riverbank filtration systems are important structures that ensure the cleaning of infiltrating surface water for drinking water production. In our study, we investigated the potential risk for a breakthrough of environmentally aged silver nanoparticles (Ag NP) through these systems. Additionally, we identified factors leading to the remobilization of Ag NP accumulated in surficial sediment layers in order to gain insights into remobilization mechanisms. We conducted column experiments with Ag NP in an outdoor pilot plant consisting of water-saturated sediment columns mimicking a riverbank filtration system. The NP had previously been aged in river water, soil extract, and ultrapure water, respectively. We investigated the depth-dependent breakthrough and retention of NP. In subsequent batch experiments, we studied the processes responsible for a remobilization of Ag NP retained in the upper 10 cm of the sediments, induced by ionic strength reduction, natural organic matter (NOM), and mechanical forces. We determined the amount of remobilized Ag by ICP-MS and differentiated between particulate and ionic Ag after remobilization using GFAAS. The presence of Ag-containing heteroaggregates was investigated by combining filtration with single-particle ICP-MS. Single and erratic Ag breakthrough events were mainly found in 30 cm depth and Ag NP were accumulated in the upper 20 cm of the columns. Soil-aged Ag NP showed the lowest retention of only 54%. Remobilization was induced by the reduction of ionic strength and the presence of NOM in combination with mechanical forces. The presence of calcium in the aging- as well as the remobilizing media reduced the remobilization potential. Silver NP were mainly remobilized as heteroaggregates with natural colloids, while dissolution played a minor role. Our study indicates that the breakthrough potential of Ag NP in riverbank filtration systems is generally low, but the aging in soil increases their mobility. Remobilization processes are associated to co-mobilization with natural colloids.
    Keywords: Heteroaggregation ; Nanoparticle Transformation ; Breakthrough ; Mobility ; Reversibility ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 4
    Language: English
    In: Geoderma, 01 June 2018, Vol.319, pp.132-141
    Description: Irrigation with treated waste water (TWW) is a common practice in agriculture, mainly in arid and semiarid areas as it provides a sustainable water resource available at all-season in general and at freshwater shortage in particular. However, TWW still contains abundant organic material which is known to decrease soil wettability, which in turn may promote flow instabilities that lead to the formation of preferential flow paths. We investigate the impact of long-term TWW irrigation on water wettability and infiltration into undisturbed soil cores from two commercially used orchards in Israel. Changes of water content during infiltration were quantitatively analysed by X-ray radiography. One orchard (sandy clay loam) had been irrigated with TWW for more than thirty years. In the other orchard (loamy sand) irrigation had been changed from freshwater to TWW in 2008 and switched back in some experimental plots to freshwater in 2012. Undisturbed soil cores were taken at the end of the dry and the rainy season to investigate the seasonal effect on water repellency and on infiltration dynamics in the laboratory. The irrigation experiments were done on field moist samples. A test series with different initial water contents was run to detect the influence on water movement at different wettabilities. In this study we show that the infiltration front stability is dependent on the history of waste water irrigation at the respective site and on the initial water content.
    Keywords: Soil Water Repellency ; Treated Waste Water Irrigation ; Unstable Flow ; Preferential Flow ; Water Infiltration ; X-Ray Analysis ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 5
    Language: English
    In: Soil & Tillage Research, January 2018, Vol.175, pp.205-216
    Description: In recent years, there has been an increased application of conservation-oriented tillage techniques, where instead of being turned the soil is only loosened or not tilled at all. Strip tillage, a special form of conservation tillage, results in small-scale structural differences, since tillage is performed only within the seed row, while the soil between seed rows is not tilled. However, tillage always impacts upon physical soil properties and processes. A combined application of conventional soil mechanical methods and X-ray computed tomography (X-ray CT) is employed here in order to investigate small-scale structural differences in a chernozem (texture 0–30 cm: silt loam) located in central Germany under strip tillage (within and between seed rows) compared to no tillage and mulch tillage. Apart from recording changes over time (years: 2012, 2014, 2015) to dry bulk density and saturated conductivity at soil depths 2–8 and 12–18 cm, stress-strain tests were conducted to map mechanical behaviour for a load range of 5–550 kPa at a soil depth of 12–18 cm (year 2015). Mechanical precompression stress was determined from the stress-dry bulk density curves. In addition, computed tomography scans were created followed by quantitative image analysis of the morphometric parameters mean macropore diameter, macroporosity, connectivity and anisotropy of the same soil samples. For strip tillage between seed rows and no tillage, a significant increase in dry bulk density was observed over time compared to strip tillage within the seed row and mulch tillage. This was more pronounced at a soil depth of 2–8 cm than at 12–18 cm. Despite higher dry bulk density, strip tillage between the seed row displayed also an increasing saturated conductivity compared to strip tillage within the seed row and mulch tillage. The computed tomography scans showed that the macropores became more compressed and soil aggregates were pushed together as mechanical stress increased, with the aggregate arrangement being transformed down into a coherent soil mass. The soil mechanical and morphometric parameters supported each other in terms of what they revealed about the mechanical properties of the soil structures. For instance, in the strip tillage between seed rows and no tillage treatments, the lack of soil tillage not only resulted in higher dry bulk densities, but also higher aggregate densities, mechanical precompression stress values, mean macropore diameters as well as lower macroporosity and connectivity values compared to mulch tillage and strip tillage within the seed row. The computed tomography parameters are therefore highly suitable for providing Supplementary information about the compaction process. Overall, this study showed that strip tillage combines the advantages of no tillage and a deeper, soil conservation-oriented primary tillage because, on a small scale, it creates two distinct soil structures which are beneficial in terms of optimal plant growth as well as mechanical resistance by driving over the soil.
    Keywords: Pre-Compression Stress ; Dry Bulk Density ; Aggregate Density ; Image Analysis ; Soil Compaction ; Agriculture
    ISSN: 0167-1987
    E-ISSN: 1879-3444
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  • 6
    Language: English
    In: Geoderma, 01 September 2018, Vol.325, pp.37-48
    Description: Organic particles including microorganisms are a significant fraction of the mobile organic matter (MOM) pool that contributes to initial pedogenesis. Still, the dynamics and the interplay of the multitude of processes that control the mobilization, transport, and retention of MOM are vastly unclear. We studied this interplay using an ‘artificial soil’ as model for a young, unstructured soil with defined initial composition employing a novel two-layer column experiment. The upstream layer was composed of a mixture of well-defined mineral phases, a sterile organic matter source and a diverse, natural microbial inoculant mimicking an organic-rich topsoil. The downstream layer, mimicking the subsoil, was composed of the mineral phases, only. Columns were run under water-unsaturated flow conditions with multiple flow interruptions to reflect natural flow regimes and to detect possible non-equilibrium processes. Pore system changes caused by flow were inspected by scanning electron microscopy and computed micro-tomography. MOM-related physicochemical effluent parameters and bacterial community diversity and abundance were assessed by molecular analysis of the effluent and the solid phase obtained after the long-term irrigation experiment (75 d). Tomographic data showed homogeneous packing of the fine-grained media (sandy loam). During flow, the initially single-grain structured artificial soil showed no connected macropores. In total, 6% of the initial top layer organic matter was mobile. The release and transport of particulate (1.2%) and dissolved organic matter (4.8%) including bacteria were controlled by non-equilibrium conditions. Bacterial cells were released and selectively transported to downstream layer resulting in a depth-dependent and selective establishment of bacterial communities in the previously sterile artificial soil. This study underlines the importance of bacterial transport from the surface or topsoil for colonization and maturation of downstream compartments. This initial colonization of pristine surfaces is the major step in forming biogeochemical interfaces - the prominent locations of intensive biological activity and element turnover that seem to play a major role for the functioning of soil.
    Keywords: Mobile Organic Matter ; Unsaturated Two-Layer Column Experiment ; Experimental Pedogenesis ; Artificial Soil ; Computed Micro-Tomography ; Molecular Analysis ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 7
    Language: English
    In: The Journal of Urology, April 2018, Vol.199(4), pp.e366-e366
    Keywords: Medicine
    ISSN: 0022-5347
    E-ISSN: 1527-3792
    Source: ScienceDirect Journals (Elsevier)
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  • 8
    Language: English
    In: Critical Reviews in Oncology / Hematology, October 2018, Vol.130, pp.13-26
    Description: The use of immune checkpoint inhibitors constitutes an emerging therapeutic field for the therapy of gastrointestinal (GI) malignancies following the recent FDA approvals of PD-1 inhibitors for esophago-gastric adenocarcinoma, hepatocellular carcinoma and for microsatellite-instable tumors, which are mainly colorectal cancers. This paper reviews the clinical evidence end of 2017 and discusses the clinical development programs of atezolizumab, avelumab, durvalumab, nivolumab and pembrolizumab in GI-tract cancers. Since 2014, these antagonists of the PD-1/PD-L1 axis have gained approval for use in numerous other tumors. Phase II trials and phase I expansion cohorts demonstrate clinical activity in patients with oesophageal, gastric, colorectal, anal and hepatic cancer. Signals of outstanding efficacy are particularly observed in biomarker selected populations and for certain combination regimen. Comprehensive phase III development programs have been initiated in oesophageal and gastric cancer, with randomized trials ongoing in hepatocellular and colorectal cancer as well.
    Keywords: Medicine
    ISSN: 1040-8428
    E-ISSN: 1879-0461
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  • 9
    Language: English
    In: Journal of the European Ceramic Society, April 2018, Vol.38(4), pp.1600-1607
    Description: The sintering behavior and the thermoelectric performance of Ca Co O multilayer laminates were studied, and a multilayer thermoelectric generator was fabricated. Compacts and multilayer samples with anisotropic microstructure and residual porosity were obtained after conventional sintering at 920 °C, whereas dense and isotropic multilayer samples were prepared by firing at 1200 °C and reoxidation at 900 °C. A hot-pressed sample has a dense and anisotropic microstructure. Samples sintered at 920 °C exhibit low electrical conductivity due to the low density, whereas the Seebeck coefficient is not sensitive to preparation conditions. However, thermal conductivity of multilayers is very low, and, hence acceptable ZT values are obtained. A transversal multilayer thermoelectric generator (TMLTEG) was fabricated by stacking layers of Ca Co O green tapes, AgPd conductor printing, and co-firing at 920 °C. The TMLTEG has a power output of 3 mW at ΔT = 200 K in the temperature interval of 25 °C to 300 °C.
    Keywords: Thermoelectric Oxides ; Thermoelectric Generator ; Multilayer ; Engineering
    ISSN: 0955-2219
    E-ISSN: 1873-619X
    Source: ScienceDirect Journals (Elsevier)
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  • 10
    Language: English
    In: Journal of Pharmacological and Toxicological Methods, March 2018, Vol.90, pp.7-12
    Description: Quantitative assessment of renal function by measurement of glomerular filtration rate (GFR) is an important part of safety and efficacy evaluation in preclinical drug development. Existing methods are often time consuming, imprecise and associated with animal burden. Here we describe the comparison between GFR determinations with sinistrin (PS-GFR) and fluorescence-labelled sinistrin-application and its transcutaneous detection (TD-GFR) in a large animal model of chronic kidney disease (CKD). TD-GFR measurements compared to a standard method using i.v. sinistrin were performed in a canine model. Animals were treated with one-sided renal wrapping (RW) followed by renal artery occlusion (RO). Biomarker and remote hemodynamic measurements were performed. Plasma sinistrin in comparison to transcutaneous derived GFR data were determined during healthy conditions, after RW and RW + RO. RW alone did not led to any significant changes in renal function, neither with PS-GFR nor TD-GFR. Additional RO showed a rise in blood pressure (+ 68.0 mm Hg), plasma urea (+ 28.8 mmol/l), creatinine (+ 224,4 μmol/l) and symmetric dimethylarginine (SDMA™; + 12.6 μg/dl). Plasma sinistrin derived data confirmed the expected drop (− 44.7%, p 〈 0.0001) in GFR. The calculated transcutaneous determined Fluorescein Isothiocyanate (FITC)-sinistrin GFR showed no differences to plasma sinistrin GFR at all times. Both methods were equaly sensitive to diagnose renal dysfunction in the affected animals. Renal function assessment using TD-GFR is a valid method to improve preclinical drug discovery and development. Furthermore, TD-GFR method offers advantages in terms of reduced need for blood sampling and thus decreasing animal burden compared to standard procedures.
    Keywords: Animal Model ; Drug Development ; Glomerular Filtration Rate ; Kidney Disease ; Methods ; Pharmacy, Therapeutics, & Pharmacology ; Chemistry
    ISSN: 1056-8719
    E-ISSN: 1873-488X
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