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  • 2019  (34)
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  • 2019  (34)
  • 1
    Language: English
    In: Nucleic acids research, 28 February 2019, Vol.47(4), pp.2075-2088
    Description: Global RNA profiling studies in bacteria have predicted the existence of many of small noncoding RNAs (sRNAs) that are processed off mRNA 3' ends to regulate other mRNAs via the RNA chaperones Hfq and ProQ. Here, we present targets of SdhX (RybD), an Hfq-dependent sRNA that is generated by RNase E mediated 3' processing of the ∼10 000-nt mRNA of the TCA cycle operon sdhCDAB-sucABCD in enteric bacteria. An in silico search predicted ackA mRNA, which encodes acetate kinase, as a conserved primary target of SdhX. Through base pairing, SdhX represses AckA synthesis during growth of Salmonella on acetate. Repression can be achieved by a naturally occurring 38-nucleotide SdhX variant, revealing the shortest functional Hfq-associated sRNA yet. Salmonella SdhX also targets the mRNAs of fumB (anaerobic fumarase) and yfbV, a gene of unknown function adjacent to ackA. Instead, through a slightly different seed sequence, SdhX can repress other targets in Escherichia coli, namely katG (catalase) and fdoG (aerobic formate dehydrogenase). This study illustrates how a key operon from central metabolism is functionally connected to other metabolic pathways through a 3' appended sRNA, and supports the notion that mRNA 3'UTRs are a playground for the evolution of regulatory RNA networks in bacteria.
    Keywords: Rna And Rna-Protein Complexes;
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 2
    Article
    Article
    Language: English
    In: Vadose Zone Journal, 01 July 2019, Vol.18(1)
    Description: Soil hydrology is a key control for the functioning of the terrestrial environment. Many environmental issues that we need to tackle today are directly linked to soil water dynamics. This includes agricultural production and food security, nutrient cycling and carbon storage, prevention of soil degradation and erosion, and last but not least, clean water resources and flood protection. However, these problems need to be addressed at the scales of fields, regions, and landscapes, while soil water dynamics and soil hydraulic properties are well understood and typically measured at much smaller scales—the comfort zone of soil physics. An obvious problem is how to link these vastly different scales and how to profit from small-scale understanding to improve our capability to predict what is going on at the large scale. In this update, this problem is discussed based on insights gained during the last decades. As a synthesis, a two-step scaling approach is proposed for modeling soil water dynamics from local to landscape scales where the scale of the soil profile is the stepping stone.
    Keywords: Agriculture
    ISSN: 1539-1663
    E-ISSN: 1539-1663
    Source: Directory of Open Access Journals (DOAJ)
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  • 3
    Language: English
    In: RNA Biology, 03 April 2019, Vol.16(4), pp.390-396
    Description: Neisseria meningitidis, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. A recent genome-wide association study suggested an association of its type II-C CRISPR/Cas system with carriage and thus less invasive lineages....
    Keywords: Neisseria Meningitidis ; Crispr/Cas ; Cas9 ; Virulence ; Nasopharynx ; RNA-Seq ; RIP-Seq ; Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
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  • 4
    Language: English
    In: Vadose Zone Journal, 01 June 2019, Vol.18(1)
    Description: Biological activity in soil causes fluxes of O into and CO out of the soil with significant global relevance. Hence, the dynamics of CO concentrations in soil can be used as an indicator for biological activity. However, there is an enormous spatial and temporal variability in soil respiration, which has led to the notion of hotspots and hot moments. This variability is attributed to the spatiotemporal heterogeneity of both plant–soil–microbiome interactions and the local conditions governing gas transport. For the characterization of a given soil, the local heterogeneities should be replaced by some meaningful average. To this end, we introduce a line sensor based on tubular gas-selective membranes that is applicable at the field scale for a wide range in water content. It provides the average CO concentration of the ambient soil along its length. The new technique corrects for fluctuating external conditions (i.e., temperature and air pressure) and the impact of water vapor without any further calibration. The new line sensor was tested in a laboratory mesocosm experiment where CO concentrations were monitored at two depths during the growth of barley ( L.). The results could be consistently related to plant development, plant density, and changing conditions for gas diffusion toward the soil surface. The comparison with an independent CO sensor confirmed that the new sensor is actually capable of determining meaningful average CO concentrations in a natural soil for long time periods.
    Keywords: Agriculture
    ISSN: 1539-1663
    E-ISSN: 1539-1663
    Source: Directory of Open Access Journals (DOAJ)
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  • 5
    Language: English
    In: Scientific reports, 07 November 2019, Vol.9(1), pp.16236
    Description: Contradictory evidence exists regarding whether and to which extend roots change soil structure in their vicinity. Here we attempt to reconcile disparate views allowing for the two-way interaction between soil structure and root traits, i.e. changes in soil structure due to plants and changes in root...
    Keywords: Image Processing ; Porosity ; Soil Structure ; Roots ; Rhizosphere;
    E-ISSN: 2045-2322
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  • 6
    Language: English
    In: Journal of Water Process Engineering, December 2019, Vol.32, p.100903
    Description: Urea removal from aqueous solutions is a challenge in many field applications. Most available technologies are either energy intensive or complicated. Novel membrane-based processes such as forward osmosis (FO) present potentially desirable alternatives for energy efficient urea removal. Recently, aquaporin-based membranes (ABMs) gained attention due to their high water permeability and selectivity. In this study, a hollow fiber ABM module was investigated for both urea and ammonia/ammonium rejection under different conditions such as varying water recovery rates, initial feed solute concentrations, draw solution molarities and feed solution pH. The amount of water recovery significantly impacted urea rejection as a result of feed concentration increase and draw dilution over time. While only less than 37% of urea could be rejected for a water recovery rate of 80%, the rejection of urea for water recovery rates of 25% was above 82% when rejection was calculated via overall mass balance; however ammonium rejection at lower pH did exceed 90%, even under high water recovery rates. The increase of ammonium rejection at low pH is believed to be influenced by the decrease of bidirectional diffusion of sodium and ammonium cations favored by the less negative charge of carboxyl groups dominating the membrane surface’s active layer. Since rejection for uncharged urea is rather poor, chemical processes that transform urea into ammonia/ammonium prior to the FO-step should be considered in future studies to improve rejection.
    Keywords: Forward Osmosis ; Aquaporin-Based Membrane ; Hollow Fiber Module ; Urea Removal ; Ammonium Retention
    ISSN: 2214-7144
    Source: ScienceDirect Journals (Elsevier)
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  • 7
    Language: English
    In: mBio, 04/30/2019, Vol.10(2)
    Description: Proteins comprised of 50 or fewer amino acids have been shown to interact with and modulate the functions of larger proteins in a range of organisms. Despite the possible importance of small proteins, the true prevalence and capabilities of these regulators remain unknown as the small size of the proteins places serious limitations on their identification, purification, and characterization. Here, we present a ribosome profiling approach with stalled initiation complexes that led to the identification of 38 new small proteins.Small proteins consisting of 50 or fewer amino acids have been identified as regulators of larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the total number of small proteins remains unknown because conventional annotation pipelines usually exclude small open reading frames (smORFs). We previously identified several dozen small proteins in the model organism Escherichia coli using theoretical bioinformatic approaches based on sequence conservation and matches to canonical ribosome binding sites. Here, we present an empirical approach for discovering new proteins, taking advantage of recent advances in ribosome profiling in which antibiotics are used to trap newly initiated 70S ribosomes at start codons. This approach led to the identification of many novel initiation sites in intergenic regions in E. coli. We tagged 41 smORFs on the chromosome and detected protein synthesis for all but three. Not only are the corresponding genes intergenic but they are also found antisense to other genes, in operons, and overlapping other open reading frames (ORFs), some impacting the translation of larger downstream genes. These results demonstrate the utility of this method for identifying new genes, regardless of their genomic context.
    Keywords: Ribo-Seq ; Small Protein ; Alternate Orfs ; Antisense ; Genome Annotation ; Leader Peptide ; Biology;
    ISSN: mBio
    ISSN: 21612129
    E-ISSN: 2150-7511
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  • 8
    Language: English
    In: Frontiers in Environmental Science, 01 October 2019, Vol.7
    Description: Soils play a key role for the functioning of terrestrial ecosystems. Thus, soils are essential for human society not only because they form the basis for the production of food. This has long been recognized, and during the last three decades...
    Keywords: Soil Functions ; Ecosystem Services ; Soil Indicators ; Modeling Soil Functions ; Soil Evaluation ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 9
    Language: English
    In: Journal of Neural Engineering, 2019, Vol.16(2), p.026039 (10pp)
    Description: Objective . Currently, there are some 95 000 people in Europe suffering from upper-limb impairment. Rehabilitation should be undertaken right after the impairment occurs and should be regularly performed thereafter. Moreover, the rehabilitation process should be tailored specifically to both patient and impairment. Approach . To address this, we have developed a low-cost solution that integrates an off-the-shelf virtual reality (VR) setup with our in-house developed arm/hand intent detection system. The resulting system, called VITA, enables an upper-limb disabled person to interact in a virtual world as if her impaired limb were still functional. VITA provides two specific features that we deem essential: proportionality of force control and interactivity between the user and the intent detection core. The usage of relatively cheap commercial components enables VITA to be used in rehabilitation centers, hospitals, or even at home. The applications of VITA range from rehabilitation of patients with musculodegenerative conditions (e.g. ALS), to treating phantom-limb pain of people with limb-loss and prosthetic training. Main results . We present a multifunctional system for upper-limb rehabilitation in VR. We tested the system using a VR implementation of a standard hand assessment tool, the Box and Block test and performed a user study on this standard test with both intact subjects and a prosthetic user. Furthermore, we present additional applications, showing the versatility of the system. Significance . The VITA system shows the applicability of a combination of our experience in intent detection with state-of-the art VR system for rehabilitation purposes. With VITA, we have an easily adaptable experimental tool available, which allows us to quickly and realistically simulate all kind of real-world problems and rehabilitation exercises for upper-limb impaired patients. Additionally, other scenarios such as prostheses simulations and control modes can be quickly implemented and tested.
    Keywords: Kraftregelung ; Rehabilitation ; Schelf ; Virtuelle Realität ; Detektorsystem ; Nachweiseinrichtung ; Multifunktionsgerät ; Europa ; Behinderter Mensch ; Proportionalität ; Standardisierter Test ; Prothesensteuerung ; Handwerkzeug ; Anatomy & Physiology;
    ISSN: 1741-2560
    E-ISSN: 1741-2552
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  • 10
    In: mBio, 2019, Vol.10(1)
    Description: The protein ProQ has recently been discovered as the centerpiece of a previously overlooked “third domain” of small RNA-mediated control of gene expression in bacteria. As in vitro work continues to reveal molecular mechanisms, it is also important to understand how ProQ affects the life cycle of bacterial pathogens as these pathogens infect eukaryotic cells. Here, we have determined how ProQ shapes Salmonella virulence and how the activities of this RNA-binding protein compare with those of Hfq, another central protein in RNA-based gene regulation in this and other bacteria. To this end, we apply global transcriptomics of pathogen and host cells during infection. In doing so, we reveal ProQ-dependent transcript changes in key virulence and host immune pathways. Moreover, we differentiate the roles of ProQ from those of Hfq during infection, for both coding and noncoding transcripts, and provide an important resource for those interested in ProQ-dependent small RNAs in enteric bacteria. ABSTRACT FinO domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts, including mRNAs from many virulence regions, but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis, and virulence genes which is accompanied by altered MAPK (mitogen-activated protein kinase) signaling in the host. Comparison with the other major RNA chaperone in Salmonella , Hfq, reinforces the notion that these two global RNA-binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs (sRNAs), we show that the 3′UTR-derived sRNA STnc540 is capable of repressing an infection-induced magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella pathogenesis and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs.
    Keywords: Research Article ; Molecular Biology And Physiology ; Editor'S Pick ; Hfq ; Noncoding Rna ; Proq ; Rna-Seq ; Bacterial Pathogen ; Posttranscriptional Control
    ISSN: 21612129
    E-ISSN: 2150-7511
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