210 research outputs found

    The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures

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    Non-coding RNAs (ncRNAs) are regulatory molecules encoded in the intergenic or intragenic regions of the genome. In prokaryotes, biocomputational identification of homologs of known ncRNAs in other species often fails due to weakly evolutionarily conserved sequences, structures, synteny and genome localization, except in the case of evolutionarily closely related species. To eliminate results from weak conservation, we focused on RNA structure, which is the most conserved ncRNA property. Analysis of the structure of one of the few well-studied bacterial ncRNAs, 6S RNA, demonstrated that unlike optimal and consensus structures, suboptimal structures are capable of capturing RNA homology even in divergent bacterial species. A computational procedure for the identification of homologous ncRNAs using suboptimal structures was created. The suggested procedure was applied to strongly divergent bacterial species and was capable of identifying homologous ncRNAs

    Influence of Excess Charge on Water Adsorption on the BiVO4 010 Surface

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    We present a combined computational and experimental study of the adsorption of water on the Mo doped BiVO4 010 surface, revealing how excess electrons influence the dissociation of water and lead to hydroxyl induced alterations of the surface electronic structure. By comparing ambient pressure resonant photoemission spectroscopy AP ResPES measurements with the results of first principles calculations, we show that the dissociation of water on the stoichiometric Mo doped BiVO4 010 surface stabilizes the formation of a small electron polaron on the VO4 tetrahedral site and leads to an enhanced concentration of localized electronic charge at the surface. Our calculations demonstrate that the dissociated water accounts for the enhanced V4 signal observed in ambient pressure X ray photoelectron spectroscopy and the enhanced signal of a small electron polaron inter band state observed in AP ResPES measurements. For ternary oxide surfaces, which may contain oxygen vacancies in addition to other electron donating dopants, our study reveals the importance of defects in altering the surface reactivity toward water and the concomitant water induced modifications to the electronic structur

    Cation insertion to break the activity/stability relationship for highly active oxygen evolution reaction catalyst

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    The production of hydrogen at a large scale by the environmentally-friendly electrolysis process is currently hampered by the slow kinetics of the oxygen evolution reaction (OER). We report a solid electrocatalyst α-Li2IrO3 which upon oxidation/delithiation chemically reacts with water to form a hydrated birnessite phase, the OER activity of which is five times greater than its non-reacted counterpart. This reaction enlists a bulk redox process during which hydrated potassium ions from the alkaline electrolyte are inserted into the structure while water is oxidized and oxygen evolved. This singular charge balance process for which the electrocatalyst is solid but the reaction is homogeneous in nature allows stabilizing the surface of the catalyst while ensuring stable OER performances, thus breaking the activity/stability tradeoff normally encountered for OER catalysts

    Mesoporous Ternary Nitrides of Earth-Abundant Metals as Oxygen Evolution Electrocatalyst

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    As sustainable energy becomes a major concern for modern society, renewable and clean energy systems need highly active, stable, and low-cost catalysts for the oxygen evolution reaction (OER). Mesoporous materials offer an attractive route for generating efficient electrocatalysts with high mass transport capabilities. Herein, we report an efficient hard templating pathway to design and synthesize three-dimensional (3-D) mesoporous ternary nickel iron nitride (Ni3FeN). The as-synthesized electrocatalyst shows good OER performance in an alkaline solution with low overpotential (259 mV) and a small Tafel slope (54 mV dec(−1)), giving superior performance to IrO(2) and RuO(2) catalysts. The highly active contact area, the hierarchical porosity, and the synergistic effect of bimetal atoms contributed to the improved electrocatalytic performance toward OER. In a practical rechargeable Zn–air battery, mesoporous Ni(3)FeN is also shown to deliver a lower charging voltage and longer lifetime than RuO(2). This work opens up a new promising approach to synthesize active OER electrocatalysts for energy-related devices. [Image: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40820-020-0412-8) contains supplementary material, which is available to authorized users

    The E. coli Anti-Sigma Factor Rsd: Studies on the Specificity and Regulation of Its Expression

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    Background: Among the seven different sigma factors in E. coli s 70 has the highest concentration and affinity for the core RNA polymerase. The E. coli protein Rsd is regarded as an anti-sigma factor, inhibiting s 70-dependent transcription at the onset of stationary growth. Although binding of Rsd to s 70 has been shown and numerous structural studies on Rsd have been performed the detailed mechanism of action is still unknown. Methodology/Principal Findings: We have performed studies to unravel the function and regulation of Rsd expression in vitro and in vivo. Cross-linking and affinity binding revealed that Rsd is able to interact with s 70, with the core enzyme of RNA polymerase and is able to form dimers in solution. Unexpectedly, we find that Rsd does also interact with s 38, the stationary phase-specific sigma factor. This interaction was further corroborated by gel retardation and footprinting studies with different promoter fragments and s 38-ors 70-containing RNA polymerase in presence of Rsd. Under competitive in vitro transcription conditions, in presence of both sigma factors, a selective inhibition of s 70-dependent transcription was prevailing, however. Analysis of rsd expression revealed that the nucleoid-associated proteins H-NS and FIS, StpA and LRP bind to the regulatory region of the rsd promoters. Furthermore, the major promoter P2 was shown to be down-regulated in vivo by RpoS, the stationary phase-specific sigma factor and the transcription factor DksA, while induction of the stringent control enhanced rsd promoter activity. Most notably, the dam-dependent methylation of a cluster of GATC sites turned ou

    Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis

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    RNA sequencing provides a new perspective on the genome of Mycobacterium tuberculosis by revealing an extensive presence of non-coding RNA, including long 5’ and 3’ untranslated regions, antisense transcripts, and intergenic small RNA (sRNA) molecules. More than a quarter of all sequence reads mapping outside of ribosomal RNA genes represent non-coding RNA, and the density of reads mapping to intergenic regions was more than two-fold higher than that mapping to annotated coding sequences. Selected sRNAs were found at increased abundance in stationary phase cultures and accumulated to remarkably high levels in the lungs of chronically infected mice, indicating a potential contribution to pathogenesis. The ability of tubercle bacilli to adapt to changing environments within the host is critical to their ability to cause disease and to persist during drug treatment; it is likely that novel post-transcriptional regulatory networks will play an important role in these adaptive responses

    Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element

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    Background: Small bacterial RNAs (sRNAs) have been shown to participate in the regulation of gene expression and have been identified in numerous prokaryotic species. Some of them are involved in the regulation of virulence in pathogenic bacteria. So far, little is known about sRNAs in Bordetella, and only very few sRNAs have been identified in the genome of Bordetella pertussis, the causative agent of whooping cough. Results: An in silico approach was used to predict sRNAs genes in intergenic regions of the B. pertussis genome. The genome sequences of B. pertussis, Bordetella parapertussis, Bordetella bronchiseptica and Bordetella avium were compared using a Blast, and significant hits were analyzed using RNAz. Twenty-three candidate regions were obtained, including regions encoding the already documented 6S RNA, and the GCVT and FMN riboswitches. The existence of sRNAs was verified by Northern blot analyses, and transcripts were detected for 13 out of the 20 additional candidates. These new sRNAs were named Bordetella pertussis RNAs, bpr. The expression of 4 of them differed between the early, exponential and late growth phases, and one of them, bprJ2, was found to be under the control of BvgA/BvgS two-component regulatory system of Bordetella virulence. A phylogenetic study of the bprJ sequence revealed a novel, so far undocumented repeat of ~90 bp, found in numerous copies in the Bordetella genomes and in that of other Betaproteobacteria. This repeat exhibits certain features of mobil

    High-performance and stable photoelectrochemical water splitting cell with organic-photoactive-layer-based photoanode

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    Considering their superior charge-transfer characteristics, easy tenability of energy levels, and low production cost, organic semiconductors are ideal for photoelectrochemical (PEC) hydrogen production. However, organic-semiconductor-based photoelectrodes have not been extensively explored for PEC water-splitting because of their low stability in water. Herein, we report high-performance and stable organic-semiconductors photoanodes consisting of p-type polymers and n-type non-fullerene materials, which is passivated using nickel foils, GaIn eutectic, and layered double hydroxides as model materials. We achieve a photocurrent density of 15.1 mA cm???2 at 1.23 V vs. reversible hydrogen electrode (RHE) with an onset potential of 0.55 V vs. RHE and a record high half-cell solar-to-hydrogen conversion efficiency of 4.33% under AM 1.5 G solar simulated light. After conducting the stability test at 1.3 V vs. RHE for 10 h, 90% of the initial photocurrent density are retained, whereas the photoactive layer without passivation lost its activity within a few minutes
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