Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa

Posttranscriptional regulation plays an essential role in the quick adaptation of pathogenic bacteria to host environments, and RNases play key roles in this process by modifying small RNAs and mRNAs. We find that the Pseudomonas aeruginosa endonuclease YbeY is required for rRNA processing and the bacterial virulence in a murine acute pneumonia model. Transcriptomic analyses reveal that knocking out the ybeY gene results in downregulation of oxidative stress response genes, including the catalase genes katA and katB Consistently, the ybeY mutant is more susceptible to H2O2 and neutrophil-mediated killing. Overexpression of katA restores the bacterial tolerance to H2O2 and neutrophil killing as well as virulence. We further find that the downregulation of the oxidative stress response genes is due to defective expression of the stationary-phase sigma factor RpoS. We demonstrate an autoregulatory mechanism of RpoS and find that ybeY mutation increases the level of a small RNA, ReaL, which directly represses the translation of rpoS through the 5' UTR of its mRNA and subsequently reduces the expression of the oxidative stress response genes. In vitro assays demonstrate direct degradation of ReaL by YbeY. Deletion of reaL or overexpression of rpoS in the ybeY mutant restores the bacterial tolerance to oxidative stress and the virulence. We also demonstrate that YbeZ binds to YbeY and is involved in the 16S rRNA processing and regulation of reaL and rpoS as well as the bacterial virulence. Overall, our results reveal pleiotropic roles of YbeY and the YbeY-mediated regulation of rpoS through ReaL.IMPORTANCE The increasing bacterial antibiotic resistance imposes a severe threat to human health. For the development of effective treatment and prevention strategies, it is critical to understand the mechanisms employed by bacteria to grow in the human body. Posttranscriptional regulation plays an important role in bacterial adaptation to environmental changes. RNases and small RNAs are key players in this regulation. In this study, we demonstrate critical roles of the RNase YbeY in the virulence of the pathogenic bacterium Pseudomonas aeruginosa We further identify the small RNA ReaL as the direct target of YbeY and elucidate the YbeY-regulated pathway on the expression of bacterial virulence factors. Our results shed light on the complex regulatory network of P. aeruginosa and indicate that inference with the YbeY-mediated regulatory pathway might be a valid strategy for the development of a novel treatment strategy.</p

Predictive Modeling of Thermally Assisted Machining and Simulation Based on RSM after WAAM

The WAAM (Wire Arc Additive Manufacturing) process is well-respected because of its low cost and high deposition efficiency; nevertheless, the process has the limitations of high heat input and low forming accuracy. Hybrid manufacturing processes employing both additive and subtractive processes can effectively reduce shape error. The predictive modeling of surface roughness in thermally assisted machining is described in this paper on the basis of three important parameters: feed per tooth, spindle speed, and workpiece temperature. The predictive model indicates that temperature has a very significant influence on the surface quality. An experimental study on thermally assisted machining was performed to obtain the variation law of cutting surface quality with temperature in order to determine the optimal process interval of subtractive processes. Through finite element simulation of thermally assisted machining, the influence law of external main cutting force and the internal mean stress of the cutting material were determined

Influence of Anionic Surfactant on Saturated Hydraulic Conductivity of Loamy Sand and Sandy Loam Soils

Surfactants released into the terrestrial environment in large amounts can potentially alter the physical, chemical and biological properties of soils, particularly the saturated hydraulic conductivity (Ks). Unfortunately findings regarding this process are quite limited. In this study, column tests were used to analyze the effects of Aerosol 22, a widely used anionic surfactant, on Ks of loamy sand and sandy loam soils. Solutions were injected into columns from the bottom with controlled pressure heads. Both the overall Ks of columns and the Ks of 6 layers at distances of 0–1 cm, 1–3 cm, 3–5 cm, 5–7 cm, 7–9 cm, and 9–10 cm from the bottom, were continuously monitored before and after the surfactant injections. Results showed that the overall Ks of all columns decreased after 2–4 pore volumes of the surfactant injections. However, stabilization and even increase at the beginning of the surfactant injection was also observed due to the different Ks variations in different layers. Specifically, a surfactant injection of 2–4 pore volumes continuously decreased the Ks of the 0–1 cm layers which yielded a Ks reduction of two orders of magnitude and dominated the Ks variations of the column. In contrast, an increase in the Ks of the 1–3 cm and 3–5 cm layers was more likely, while Ks variation of the 5–10 cm layers was less likely. We hypothetically attributed the Ks variations to the swelling of clay, the collapse of soil aggregates and subsequent particle displacements from surfactant adsorption, which caused pore clogging in the bottom 0–1 cm layer and higher porosities in the layers above. The adsorption of the surfactant aggregates and crystallization were also possibly thought to cause a pore clogging in the bottom layer thus decrease the surfactant concentration from the inlet, the severity of which affects these layers less at greater distances from the inlet. In view of the uncertainty showed by the experimental results, we also suggest to include more replicate columns in future studies, so as to increase the repeatability of the measurements

Detecting the Critical States of Type 2 Diabetes Mellitus Based on Degree Matrix Network Entropy by Cross-Tissue Analysis

Type 2 diabetes mellitus (T2DM) is a metabolic disease caused by multiple etiologies, the development of which can be divided into three states: normal state, critical state/pre-disease state, and disease state. To avoid irreversible development, it is important to detect the early warning signals before the onset of T2DM. However, detecting critical states of complex diseases based on high-throughput and strongly noisy data remains a challenging task. In this study, we developed a new method, i.e., degree matrix network entropy (DMNE), to detect the critical states of T2DM based on a sample-specific network (SSN). By applying the method to the datasets of three different tissues for experiments involving T2DM in rats, the critical states were detected, and the dynamic network biomarkers (DNBs) were successfully identified. Specifically, for liver and muscle, the critical transitions occur at 4 and 16 weeks. For adipose, the critical transition is at 8 weeks. In addition, we found some “dark genes” that did not exhibit differential expression but displayed sensitivity in terms of their DMNE score, which is closely related to the progression of T2DM. The information uncovered in our study not only provides further evidence regarding the molecular mechanisms of T2DM but may also assist in the development of strategies to prevent this disease

Pnma-BN: Another Boron Nitride Polymorph with Interesting Physical Properties

Structural, mechanical, electronic properties, and stability of boron nitride (BN) in Pnma structure were studied using first-principles calculations by Cambridge Serial Total Energy Package (CASTEP) plane-wave code, and the calculations were performed with the local density approximation and generalized gradient approximation in the form of Perdew–Burke–Ernzerhof. This BN, called Pnma-BN, contains four boron atoms and four nitrogen atoms buckled through sp3-hybridized bonds in an orthorhombic symmetry unit cell with Space group of Pnma. Pnma-BN is energetically stable, mechanically stable, and dynamically stable at ambient pressure and high pressure. The calculated Pugh ratio and Poisson’s ratio revealed that Pnma-BN is brittle, and Pnma-BN is found to turn brittle to ductile (~94 GPa) in this pressure range. It shows a higher mechanical anisotropy in Poisson’s ratio, shear modulus, Young’s modulus, and the universal elastic anisotropy index AU. Band structure calculations indicate that Pnma-BN is an insulator with indirect band gap of 7.18 eV. The most extraordinary thing is that the band gap increases first and then decreases with the increase of pressure from 0 to 60 GPa, and from 60 to 100 GPa, the band gap increases first and then decreases again

Understanding of Storm Runoff Generation in a Weathered, Fractured Granitoid Headwater Catchment in Northern China

Few of the classical field studies of streamflow generation in headwater watersheds have been conducted in catchments with thin soils and deeply weathered crystalline silicate bedrock. As such, the role of the (potentially very large) storage capacity of weathered, fractured rock in baseflow and storm event discharge remains poorly characterized. Here we present a study of streamflow generation in an upland semi-humid watershed (Xitaizi Experimental Watershed, XEW, 4.22 km2) dominated by baseflow feeding one of the main water supply reservoirs for the city of Beijing, China. This catchment is relatively dry (625 mm/yr precipitation, 480 mm/yr Evapotranspiration), but has strongly seasonal precipitation that varies in phase with strongly seasonal potential evapotranspiration. The catchment was instrumented with four weather stations and precipitation collectors, 11 deep wells drilled into the bedrock along three hillslopes, and additional soil moisture sensors and water samplers along one hillslope. In six storm events over two years, samples of rainfall, soil water (10&ndash;80 cm depth), groundwater, and stream water were collected with high frequency and analyzed for stable water isotopes (&delta;18O and &delta;2H). Tracer-based hydrograph separation showed that event water (precipitation) makes up the majority of the hydrograph peak above baseflow, and pre-event water contributions (on average) simply represent the steady release of groundwater. The quantity of event water corresponded to a very small effective contributing area (&lt;0.2% of the catchment) that nevertheless showed a clear dependence on catchment wetness as measured by the streamflow. The streamflow itself was isotopically identical to the deep groundwater in wells. This suggests that the fractured, weathered, bedrock system dominates the production of streamflow in this catchment

Spatial Variability of Soil Moisture in a Forest Catchment: Temporal Trend and Contributors

Understanding the spatio-temporal dynamic of soil moisture is critical in hydrological and other land surface related studies. Until recently, however, there have been controversies about the relationship between spatial mean and spatial variance of soil moisture and the contributions of each of these factors to spatial variability. Therefore, in this study, spatial variability of soil moisture in a 7 km2 forest catchment is analyzed by time-series data on soil moisture obtained at a total of 12 observation sites. Results showed that soil moisture spatial mean and spatial variance varied almost synchronously and in three cyclic patterns during the monitoring period from 1 April 2015 to 31 October 2015. The spatial mean-variance relationship during the ascending and descending periods of spatial mean could be well-fitted by upward and downward convex quadratic curves, respectively, indicating possible clockwise hysteresis of this relationship. It was found that all through the monitoring period, contributions of time-invariant factors on total spatial variance increased from 68.9% to 88.2% with depth, and temporally stable ranking of sites was obtained. Because of the high spatial variation of soil moisture in our study area, it should be noted that a large number of sample plots would be needed to adequately estimate the spatial variability of soil moisture

Dihydrolipoamide Acetyltransferase AceF Influences the Type III Secretion System and Resistance to Oxidative Stresses through RsmY/Z in Pseudomonas aeruginosa

Carbon metabolism plays an important role in bacterial physiology and pathogenesis. The type III secretion system (T3SS) of Pseudomonas aeruginosa is a virulence factor that contributes to acute infections. It has been demonstrated that bacterial metabolism affects the T3SS. Meanwhile, expression of T3SS genes is negatively regulated by the small RNAs RsmY and RsmZ. In this study, we studied the relationship between the dihydrolipoamide acetyltransferase gene aceF and the T3SS. Our results reveal an upregulation of RsmY and RsmZ in the aceF mutant, which represses the expression of the T3SS genes. Meanwhile, the aceF mutant is more tolerant to hydrogen peroxide. We demonstrate that the expression levels of the catalase KatB and the alkyl hydroperoxide reductase AhpB are increased in the aceF mutant. The simultaneous deletion of rsmY and rsmZ in the aceF mutant restored the expression levels of katB and ahpB, as well as bacterial susceptibility to hydrogen peroxide. Thus, we identify a novel role of AceF in the virulence and oxidative response of P. aeruginosa

Thermosensitive black phosphorus hydrogel loaded with silver sulfadiazine promotes skin wound healing

Abstract Wounds can lead to skin and soft tissue damage and their improper management may lead to the growth of pathogenic bacteria at the site of injury. Identifying better ways to promote wound healing is a major unmet need and biomedical materials with the ability to promote wound healing are urgently needed. Here, we report a thermosensitive black phosphorus hydrogel composed of black phosphorus nano-loaded drug silver sulfadiazine (SSD) and chitosan thermosensitive hydrogel for wound healing. The hydrogel has temperature-sensitive properties and enables the continuous release of SSD under near-infrared irradiation to achieve synergistic photothermal and antibacterial treatment. Additionally, it exerts antibacterial effects on Staphylococcus aureus. In a rat skin injury model, it promotes collagen deposition, boosts neovascularization, and suppresses inflammatory markers. In summary, the excellent thermosensitivity, biocompatibility, and wound-healing-promoting qualities of the reported thermosensitive hydrogel make it suitable as an ideal wound dressing in the clinic

Strains used in this study.

<p>^a, American Type Culture Collection (ATCC), USA.</p><p>^b, Clinic isolate.</p><p>^c, Plasmid or genome.</p><p>^d, Microbe Test Center, Academy of Military Medical Sciences, China.</p><p>^e, Institute of Medical and Veterinary Science (IMVS), Australia.</p><p>^f, Institute of Microbiology, Chinese Academy of Sciences, China.</p><p>^g, Institute of Food Fermentation industry, Ministry of Light Industry, China.</p><p>^h, Czech Collection of Microorganisms (CCM), Czech Republic.</p><p>ⁱ, National Center for Medical Culture Collection (CMCC), China.</p><p>^j, National Center for Veterinary Culture Collection (CVCC), China.</p><p>^k, Culture Collection, University of Goteborg, Sweden.</p><p>Strains used in this study.</p