Transcriptional Regulation of opaR, qrr2–4 and aphA by the Master Quorum-Sensing Regulator OpaR in Vibrio parahaemolyticus

Background: Vibrio parahaemolyticus is a leading cause of infectious diarrhea and enterogastritis via the fecal-oral route. V. harveyi is a pathogen of fishes and invertebrates, and has been used as a model for quorum sensing (QS) studies. LuxR is the master QS regulator (MQSR) of V. harveyi, and LuxR-dependent expression of its own gene, qrr2–4 and aphA have been established in V. harveyi. Molecular regulation of target genes by the V. parahaemolyticus MQSR OpaR is still poorly understood. Methodology/Principal Findings: The bioinformatics analysis indicated that V. parahaemolyticus OpaR, V. harveyi LuxR, V. vulnificu SmcR, and V. alginolyticus ValR were extremely conserved, and that these four MQSRs appeared to recognize the same conserved cis-acting signals, which was represented by the consensus constructs manifesting as a position frequency matrix and as a 20 bp box, within their target promoters. The MQSR box-like sequences were found within the upstream DNA regions of opaR, qrr2–4 and aphA in V. parahaemolyticus, and the direct transcriptional regulation of these target genes by OpaR were further confirmed by multiple biochemical experiments including primer extension assay, gel mobility shift assay, and DNase I footprinting analysis. Translation and transcription starts, core promoter elements for sigma factor recognition, Shine-Dalgarno sequences for ribosome recognition, and OpaR-binding sites were determined for the five target genes of OpaR, which gave a structural map of the OpaR-dependent promoters. Further computational promote

Numerical Study of Random Corrosion Characteristics of Metal Based On the Cellular Automata Method

In the production process of coal chemical companies, the corrosion of metal equipment and the resulting shortening of its service life can cause safety hazards. Simulation modeling of pit emergence and development during corrosion evolution provides a new approach to corrosion research. By analyzing the effect of different parameters on causing corrosion to occur, it is possible to reflect the influence of complex physico-chemical systems. In this paper, the simulation of a meta-cellular automaton model of pit growth under diffusion and the introduction of a passivation probability to correct the chemical reaction rate are developed; The effect of reaction passivation probability, chemical reaction rate and diffusion coefficient on the degree of corrosion was also analyzed by means of quantitative analysis. The results show that for metal corrosion loss processes, the degree of corrosion damage decreases with increasing probability of reactive passivation and increases with increasing chemical reaction rate, increasing electrolyte concentration and increasing time step. The CA model was applied to simulate the growth and change of pitting corrosion of metal materials with their corrosion protection layer under damaged conditions. The corrosion model can simulate the corrosion morphology change characteristics similar to the real metal to the corrosion pit evolution simulation related research has certain scientific, validity, reference

Numerical Study of Random Corrosion Characteristics of Metal Based On the Cellular Automata Method

In the production process of coal chemical companies, the corrosion of metal equipment and the resulting shortening of its service life can cause safety hazards. Simulation modeling of pit emergence and development during corrosion evolution provides a new approach to corrosion research. By analyzing the effect of different parameters on causing corrosion to occur, it is possible to reflect the influence of complex physico-chemical systems. In this paper, the simulation of a meta-cellular automaton model of pit growth under diffusion and the introduction of a passivation probability to correct the chemical reaction rate are developed; The effect of reaction passivation probability, chemical reaction rate and diffusion coefficient on the degree of corrosion was also analyzed by means of quantitative analysis. The results show that for metal corrosion loss processes, the degree of corrosion damage decreases with increasing probability of reactive passivation and increases with increasing chemical reaction rate, increasing electrolyte concentration and increasing time step. The CA model was applied to simulate the growth and change of pitting corrosion of metal materials with their corrosion protection layer under damaged conditions. The corrosion model can simulate the corrosion morphology change characteristics similar to the real metal to the corrosion pit evolution simulation related research has certain scientific, validity, reference

Local Climate Zone in Xi’an City: A Novel Classification Approach Employing Spatial Indicators and Supervised Classification

The Local Climate Zone (LCZ), as a foundational element of urban climate zone classification proposed by Oke and Stewart, categorizes urban surface types based on 10 influential parameters affecting the urban heat island effect, such as building density, surface reflectivity, sky view factor, and surface roughness length. This method divides cities into 17 different Local Climate Zones (LCZs) to standardize climate observations and promote global climate research exchange, offering valuable insights for heat island studies. In this study, we enhance the existing local climate zones spatial classification approach by focusing on Xi’an city’s urban layout and architectural features. By using urban spatial indicators and employing a supervised classification approach and a spatial clustering method with land parcels as statistical units, we investigate typical urban areas and classify Xi’an’s land parcels into 17 or 15 distinct local climate zones. Subsequently, through the evaluation of two distinct classification methods, the most suitable urban microclimate zoning method for Xi’an city was selected. This optimization of the local climate zoning representation introduces a spatial classification method tailored to urban climate planning and control, utilizing urban spatial indicators and remote sensing data. The resulting urban climate zoning map not only supports sample selection for urban heat environment parameter observation but also aids urban planners in identifying spatial distribution patterns for climate zoning

Interaction-free, single-pixel quantum imaging with undetected photons

A typical imaging scenario requires three basic ingredients: 1. a light source that emits light, which in turn interacts and scatters off the object of interest; 2. detection of the light being scattered from the object and 3. a detector with spatial resolution. These indispensable ingredients in typical imaging scenarios may limit their applicability in the imaging of biological or other sensitive specimens due to unavailable photon-starved detection capabilities and inevitable damage induced by interaction. Here, we propose and experimentally realize a quantum imaging protocol that alleviates all three requirements. By embedding a single-photon Michelson interferometer into a nonlinear interferometer based on induced coherence and harnessing single-pixel imaging technique, we demonstrate interaction-free, single-pixel quantum imaging of a structured object with undetected photons. Thereby, we push the capability of quantum imaging to the extreme point in which no interaction is required between object and photons and the detection requirement is greatly reduced. Our work paves the path for applications in characterizing delicate samples with single-pixel imaging at silicon-detectable wavelengths

Late Quaternary aggradation and incision in the headwaters of the Yangtze River, eastern Tibetan Plateau, China

River aggradation or incision at different spatial-temporal scales are governed by tectonics, climate change, and surface processes which all adjust the ratio of sediment load to transport capacity of a channel. But how the river responds to differential tectonic and extreme climate events in a catchment is still poorly understood. Here, we address this issue by reconstructing the distribution, ages, and sedimentary process of fluvial terraces in a tectonically active area and monsoonal environment in the headwaters of the Yangtze River in the eastern Tibetan Plateau, China. Field observations, topographic analyses, and optically stimulated luminescence dating reveal a remarkable fluvial aggradation, followed by terrace formations at elevations of 55-62 m (T7), 42-46 m (T6), 38 m (T5), 22-36 m (T4), 18 m (T3), 12-16 m (T2), and 2-6 m (T1) above the present floodplain. Gravelly fluvial accumulation more than 62 m thick has been dated prior to 24-19 ka. It is regarded as a response to cold climate during the last glacial maximum. Subsequently, the strong monsoon precipitation contributed to cycles of rapid incision and lateral erosion, expressed as cut-in-fill terraces. The correlation of terraces suggests that specific tectonic activity controls the spatial scale and geomorphic characteristics of the terraces, while climate fluctuations determine the valley filling, river incision and terrace formation. Debris and colluvial sediments are frequently interbedded in fluvial sediment sequences, illustrating the episodic, short-timescale blocking of the channel ca. 20 ka. This indicates the potential impact of extreme events on geomorphic evolution in rugged terrain

DiffTune: Auto-Tuning through Auto-Differentiation

The performance of robots in high-level tasks depends on the quality of their lower-level controller, which requires fine-tuning. However, the intrinsically nonlinear dynamics and controllers make tuning a challenging task when it is done by hand. In this paper, we present DiffTune, a novel, gradient-based automatic tuning framework. We formulate the controller tuning as a parameter optimization problem. Our method unrolls the dynamical system and controller as a computational graph and updates the controller parameters through gradient-based optimization. The gradient is obtained using sensitivity propagation, which is the only method for gradient computation when tuning for a physical system instead of its simulated counterpart. Furthermore, we use $\mathcal{L}_1$ adaptive control to compensate for the uncertainties (that unavoidably exist in a physical system) such that the gradient is not biased by the unmodelled uncertainties. We validate the DiffTune on a Dubin's car and a quadrotor in challenging simulation environments. In comparison with state-of-the-art auto-tuning methods, DiffTune achieves the best performance in a more efficient manner owing to its effective usage of the first-order information of the system. Experiments on tuning a nonlinear controller for quadrotor show promising results, where DiffTune achieves 3.5x tracking error reduction on an aggressive trajectory in only 10 trials over a 12-dimensional controller parameter space.Comment: Minkyung Kim and Lin Song contributed equally to this wor

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The osmotic regulator OmpR in <it>Escherichia coli </it>regulates differentially the expression of major porin proteins OmpF and OmpC. In <it>Yersinia enterocolitica </it>and <it>Y. pseudotuberculosis</it>, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in <it>Y. pestis </it>are not yet fully understood.</p> <p>Results</p> <p><it>Y. pestis </it>OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The <it>ompR </it>mutation likely did not affect the virulence of <it>Y. pestis </it>strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the <it>ompR </it>mutation, indicating the global regulatory role of OmpR in <it>Y. pestis</it>. Real-time RT-PCR or <it>lacZ </it>fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner.</p> <p>Conclusion</p> <p>OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. <it>Y. pestis </it>OmpR regulates <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and × at high osmolarity in <it>Y. pestis</it>, in contrast to the reciprocal regulation of them in <it>E. coli</it>. The main difference is that <it>ompF </it>expression is not repressed at high osmolarity in <it>Y. pestis</it>, which is likely due to the absence of a promoter-distal OmpR-binding site for <it>ompF</it>.</p

Regulatory effects of cAMP receptor protein (CRP) on porin genes and its own gene in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The cAMP receptor protein (CRP) is a global bacterial regulator that controls many target genes. The CRP-cAMP complex regulates the <it>ompR-envZ </it>operon in <it>E. coli </it>directly, involving both positive and negative regulations of multiple target promoters; further, it controls the production of porins indirectly through its direct action on <it>ompR-envZ</it>. Auto-regulation of CRP has also been established in <it>E. coli</it>. However, the regulation of porin genes and its own gene by CRP remains unclear in <it>Y. pestis</it>.</p> <p>Results</p> <p><it>Y. pestis </it>employs a distinct mechanism indicating that CRP has no regulatory effect on the <it>ompR-envZ </it>operon; however, it stimulates <it>ompC </it>and <it>ompF </it>directly, while repressing <it>ompX</it>. No transcriptional regulatory association between CRP and its own gene can be detected in <it>Y. pestis</it>, which is also in contrast to the fact that CRP acts as both repressor and activator for its own gene in <it>E. coli</it>. It is likely that <it>Y. pestis </it>OmpR and CRP respectively sense different signals (medium osmolarity, and cellular cAMP levels) to regulate porin genes independently.</p> <p>Conclusion</p> <p>Although the CRP of <it>Y. pestis </it>shows a very high homology to that of <it>E. coli</it>, and the consensus DNA sequence recognized by CRP is shared by the two bacteria, the <it>Y. pestis </it>CRP can recognize the promoters of <it>ompC</it>, <it>F</it>, and <it>X </it>directly rather than that of its own gene, which is different from the relevant regulatory circuit of <it>E. coli</it>. Data presented here indicate a remarkable remodeling of the CRP-mediated regulation of porin genes and of its own one between these two bacteria.</p