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Berlin Brandenburg

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  • 2018  (9)
  • Directory of Open Access Journals (DOAJ)  (9)
  • 1
    In: mBio, 2018, Vol.9(6)
    Description: The alphaproteobacterium Agrobacterium tumefaciens is able to infect various eudicots causing crown gall tumor formation. Based on its unique ability of interkingdom gene transfer, Agrobacterium serves as a crucial biotechnological tool for genetic manipulation of plant cells. The presence of hundreds of putative sRNAs in this organism suggests a considerable impact of riboregulation on A. tumefaciens physiology. Here, we characterized the biological function of the sRNA PmaR that controls various processes crucial for growth, motility, and virulence. Among the genes directly targeted by PmaR is ampC coding for a beta-lactamase that confers ampicillin resistance, suggesting that the sRNA is crucial for fitness in the competitive microbial composition of the rhizosphere. ABSTRACT Small regulatory RNAs play an important role in the adaptation to changing conditions. Here, we describe a differentially expressed small regulatory RNA (sRNA) that affects various cellular processes in the plant pathogen Agrobacterium tumefaciens . Using a combination of bioinformatic predictions and comparative proteomics, we identified nine targets, most of which are positively regulated by the sRNA. According to these targets, we named the sRNA PmaR for peptidoglycan biosynthesis, motility, and ampicillin resistance regulator. Agrobacterium spp. are long known to be naturally resistant to high ampicillin concentrations, and we can now explain this phenotype by the positive PmaR-mediated regulation of the beta-lactamase gene ampC . Structure probing revealed a spoon-like structure of the sRNA, with a single-stranded loop that is engaged in target interaction in vivo and in vitro . Several riboregulators have been implicated in antibiotic resistance mechanisms, such as uptake and efflux transporters, but PmaR represents the first example of an sRNA that directly controls the expression of an antibiotic resistance gene.
    Keywords: Research Article ; Molecular Biology And Physiology ; Antibiotic Resistance ; Gene Regulation ; Plant-Microbe Interaction ; Posttranscriptional Control ; Regulatory Rna
    ISSN: 21612129
    E-ISSN: 2150-7511
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  • 2
    In: mBio, 2018, Vol.9(6)
    Description: P. aeruginosa is a soil dwelling bacterium and a plant pathogen, and it also causes life-threatening infections in humans. Thus, P. aeruginosa thrives in diverse environments and over a broad range of temperatures. Some P. aeruginosa strains rely on the CRISPR-Cas adaptive immune system as a phage defense mechanism. Our discovery that low temperatures increase CRISPR adaptation suggests that the rarely occurring but crucial naive adaptation events may take place predominantly under conditions of slow growth, e.g., during the bacterium’s soil dwelling existence and during slow growth in biofilms. ABSTRACT Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) systems are adaptive defense systems that protect bacteria and archaea from invading genetic elements. In Pseudomonas aeruginosa , quorum sensing (QS) induces the CRISPR-Cas defense system at high cell density when the risk of bacteriophage infection is high. Here, we show that another cue, temperature, modulates P. aeruginosa CRISPR-Cas. Increased CRISPR adaptation occurs at environmental (i.e., low) temperatures compared to that at body (i.e., high) temperature. This increase is a consequence of the accumulation of CRISPR-Cas complexes, coupled with reduced P. aeruginosa growth rate at the lower temperature, the latter of which provides additional time prior to cell division for CRISPR-Cas to patrol the cell and successfully eliminate and/or acquire immunity to foreign DNA. Analyses of a QS mutant and synthetic QS compounds show that the QS and temperature cues act synergistically. The diversity and level of phage encountered by P. aeruginosa in the environment exceed that in the human body, presumably warranting increased reliance on CRISPR-Cas at environmental temperatures.
    Keywords: Research Article ; Molecular Biology And Physiology ; Crispr ; Phage ; Pseudomonas ; Quorum Sensing ; Growth Rate
    ISSN: 21612129
    E-ISSN: 2150-7511
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  • 3
    Language: English
    In: Vadose Zone Journal, 01 March 2018, Vol.17(1)
    Description: X-ray radiography is a suitable approach to study water dynamics in undisturbed soil. However, beam hardening impairs the deduction of soil moisture changes from X-ray attenuation, especially when studying infiltration of water into cylindrical soil columns. We developed a calibration protocol to correct for beam hardening effects that enables the quantitative determination of changing average water content in two-dimensional projections. The method works for a broad range of materials and is easy to implement. Moreover, we studied the drift of X-ray attenuation values due to the detector latency and eliminated its contribution to the quantitative analysis. Finally we could visualize the dynamics of infiltrating water into undisturbed cylindrical soil samples.
    Keywords: Agriculture
    ISSN: 1539-1663
    E-ISSN: 1539-1663
    Source: Directory of Open Access Journals (DOAJ)
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  • 4
    Language: English
    In: Frontiers in Environmental Science, 01 April 2018, Vol.6
    Description: Soil-borne nitrous oxide (N2O) emissions have a high spatial and temporal variability which is commonly attributed to the occurrence of hotspots and hot moments for microbial activity in aggregated soil. Yet there is only limited information about the biophysical processes that regulate the production and consumption of N2O on microscopic scales in undisturbed soil. In this study, we introduce an experimental framework relying on simplified porous media that circumvents some of the complexities occuring in natural soils while fully accounting for physical constraints believed to control microbial activity in general and denitrification in particular. We used this framework to explore the impact of aggregate size and external oxygen concentration on the kinetics of O2 consumption, as well as CO2 and N2O production. Model aggregates of different sizes (3.5 vs. 7 mm diameter) composed of porous, sintered glass were saturated with a defined growth medium containing roughly 109 cells ml−1 of the facultative anaerobic, nosZ-deficient denitrifier Agrobacterium tumefaciens with N2O as final denitrification product and incubated at five different oxygen levels (0–13 vol-%). We demonstrate that the onset of denitrification depends on the amount of external oxygen and the size of aggregates. Smaller aggregates were better supplied with oxygen due to a larger surface-to-volume ratio, which resulted in faster growth and an earlier onset of denitrification. In larger aggregates, the onset of denitrification was more gradual, but with comparably higher N2O production rates once the anoxic aggregate centers were fully developed. The normalized electron flow from the reduced carbon substrate to N-oxyanions (edenit-/etotal- ratio) could be solely described as a function of initial oxygen concentration in the headspace with a simple, hyperbolic model, for which the two empirical parameters changed with aggregate size in a consistent way. These findings confirm the important role of soil structure on N2O emissions from denitrification by shaping the spatial patterns of microbial activity and anoxia in aggregated soil. Our dataset may serve as a benchmark for constraining or validating spatially explicit, biophysical models of denitrification in aggregated soil.
    Keywords: Greenhouse Gas Emissions ; Denitrification Kinetics ; Microbial Hotspots ; Microsites ; Anoxic Aggregate Centers ; Agrobacterium Tumefaciens ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 5
    Language: English
    In: PLoS Genetics, 01 June 2018, Vol.14(6), p.e1007401
    Description: Invasion of epithelial cells by Salmonella enterica requires expression of genes located in the pathogenicity island I (SPI-1). The expression of SPI-1 genes is very tightly regulated and activated only under specific conditions. Most studies have focused on the regulatory pathways that induce SPI-1 expression. Here, we describe a new regulatory circuit involving CRP-cAMP, a widely established metabolic regulator, in silencing of SPI-1 genes under non-permissive conditions. In CRP-cAMP-deficient strains we detected a strong upregulation of SPI-1 genes in the mid-logarithmic growth phase. Genetic analyses revealed that CRP-cAMP modulates the level of HilD, the master regulator of Salmonella invasion. This regulation occurs at the post-transcriptional level and requires the presence of a newly identified regulatory motif within the hilD 3'UTR. We further demonstrate that in Salmonella the Hfq-dependent sRNA Spot 42 is under the transcriptional repression of CRP-cAMP and, when this transcriptional repression is relieved, Spot 42 exerts a positive effect on hilD expression. In vivo and in vitro assays indicate that Spot 42 targets, through its unstructured region III, the 3'UTR of the hilD transcript. Together, our results highlight the biological relevance of the hilD 3'UTR as a hub for post-transcriptional control of Salmonella invasion gene expression.
    Keywords: Biology
    ISSN: 1553-7390
    E-ISSN: 1553-7404
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  • 6
    Language: English
    In: Frontiers in Microbiology, 2018, Vol.9, p.1929
    Description: Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gases. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale). For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. In terms of microbial aspects, whereas a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because relevant experimental data are extremely scarce. For the overall research to move forward, it will be crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead.Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
    Keywords: Life Sciences ; X-Ray Computed ; Upscaling ; Biodiversity ; Soil Microbiology ; Tomography ; Single-Cell Genomics ; Nanosims Imaging ; Biology
    ISSN: 1664-302X
    E-ISSN: 1664-302X
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  • 7
    Language: English
    In: SOIL, 2018, Vol.4(1), pp.83-92
    Description: The central importance of soil for the functioning of terrestrial systems is increasingly recognized. Critically relevant for water quality, climate control, nutrient cycling and biodiversity, soil provides more functions than just the basis for agricultural production. Nowadays, soil is increasingly under pressure as a limited resource for the production of food, energy and raw materials. This has led to an increasing demand for concepts assessing soil functions so that they can be adequately considered in decision-making aimed at sustainable soil management. The various soil science disciplines have progressively developed highly sophisticated methods to explore the multitude of physical, chemical and biological processes in soil. It is not obvious, however, how the steadily improving insight into soil processes may contribute to the evaluation of soil functions. Here, we present to a new systemic modeling framework that allows for a consistent coupling between reductionist yet observable indicators for soil functions with detailed process understanding. It is based on the mechanistic relationships between soil functional attributes, each explained by a network of interacting processes as derived from scientific evidence. The non-linear character of these interactions produces stability and resilience of soil with respect to functional characteristics. We anticipate that this new conceptional framework will integrate the various soil science disciplines and help identify important future research questions at the interface between disciplines. It allows the overwhelming complexity of soil systems to be adequately coped with and paves the way for steadily improving our capability to assess soil functions based on scientific understanding.
    Keywords: Soil Stability ; Evaluation ; Agricultural Production ; Modelling ; Agricultural Management ; Biodiversity ; Soil Stability ; Food Production ; Water Quality ; Raw Materials ; Biological Activity ; Decision Making ; Soil Improvement ; Soil Science ; Terrestrial Environments ; Interactions ; Water Quality ; Soil Management ; Modelling ; Raw Materials ; Raw Materials ; Soil Sciences ; Water Quality ; Soils ; Framework ; Stability ; Nutrient Cycles ; Biological Diversity ; Mathematical Models ; Agricultural Production ; Biodiversity ; Nutrients (Mineral) ; Soils ; Decision Making ; Water Quality ; Biological Diversity;
    ISSN: SOIL
    ISSN: 21993971
    E-ISSN: 2199-398X
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  • 8
    Language: English
    In: BMC Medical Education, 01 June 2018, Vol.18(1), pp.1-10
    Description: Abstract Background The German quality assurance programme for evaluating work capacity is based on peer review that evaluates the quality of medical experts’ reports. Low reliability is thought to be due to systematic differences among peers. For this purpose, we developed a curriculum for a standardized peer-training (SPT). This study investigates, whether the SPT increases the inter-rater reliability of social medical physicians participating in a cross-institutional peer review. Methods Forty physicians from 16 regional German Pension Insurances were subjected to SPT. The three-day training course consist of nine educational objectives recorded in a training manual. The SPT is split into a basic module providing basic information about the peer review and an advanced module for small groups of up to 12 peers training peer review using medical reports. Feasibility was tested by assessing selection, comprehensibility and subjective use of contents delivered, the trainers’ delivery and design of training materials. The effectiveness of SPT was determined by evaluating peer concordance using three anonymised medical reports assessed by each peer. Percentage agreement and Fleiss’ kappa (κm) were calculated. Concordance was compared with review results from a previous unstructured, non-standardized peer-training programme (control condition) performed by 19 peers from 12 German Pension Insurances departments. The control condition focused exclusively on the application of peer review in small groups. No specifically training materials, methods and trainer instructions were used. Results Peer-training was shown to be feasible. The level of subjective confidence in handling the peer review instrument varied between 70 and 90%. Average percentage agreement for the main outcome criterion was 60.2%, resulting in a κm of 0.39. By comparison, the average percentage concordance was 40.2% and the κm was 0.12 for the control condition. Conclusion Concordance with the main criterion was relevant but not significant (p = 0.2) higher for SPT than for the control condition. Fleiss’ kappa coefficient showed that peer concordance was higher for SPT than randomly expected. Nevertheless, a score of 0.39 for the main criterion indicated only fair inter-rater reliability, considerably lower than the conventional standard of 0.7 for adequate reliability.
    Keywords: Training Curriculum ; Peer Review ; Quality Assurance ; Work Capacity Evaluation ; Inter-Rater Reliability ; Medicine
    E-ISSN: 1472-6920
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  • 9
    Language: English
    In: Cell Reports, 23 October 2018, Vol.25(4), pp.1027-1039.e6
    Description: Cdkn1a, which encodes p21, functions as a major route for p53-mediated cell-cycle arrest. However, the consequence of Cdkn1a gene dosage on tumor suppression has not been systematically investigated. Here, we employed BAC transgenesis to generate a Cdkn1aSUPER mouse, which harbors an additional Cdkn1a allele within its natural genomic context. We show that these mice display enhanced cell-cycle arrest and reduced apoptosis in response to genotoxic stress. Furthermore, using a chemically induced skin cancer model and an autochthonous Kras-driven lung adenocarcinoma model, we show that Cdkn1aSUPER mice display a cancer protection phenotype that is indistinguishable from that observed in Tp53SUPER animals. Moreover, we demonstrate that Tp53 and Cdkn1a cooperate in mediating cancer resistance, using a chemically induced fibrosarcoma model. Overall, our Cdkn1aSUPER allele enabled us to assess the contribution of Cdkn1a to Tp53-mediated tumor suppression. •An extra p21 copy enforces cell-cycle arrest and protects from DNA-damaging agents•Increased p21 gene expression delays epithelial regeneration and blocks apoptosis•Mice harboring a third Cdkn1a allele display cancer protection•The tumor suppressors p21 and p53 cooperate in mediating cancer resistance Torgovnick et al. create a mouse model, carrying a third copy of Cdkn1a (p21), which shows enhanced cell-cycle arrest capacity and protection against DNA damage-induced apoptosis. The Cdkn1aSUPER animals display delayed epithelial regeneration and a robust cancer resistance phenotype, highlighting the importance of p21 in p53-dependent tumor suppression.
    Keywords: Cdkn1a ; P21 ; P53 ; Mouse Model ; Cancer ; Tumor Suppressor ; Cell Cycle Arrest ; Apoptosis ; Cancer Protection
    ISSN: 2211-1247
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