Chaperone Spy Protects Outer Membrane Proteins from Folding Stress via Dynamic Complex Formation

Gram-negative bacteria have a multicomponent and constitutively active periplasmic chaperone system to ensure the quality control of their outer membrane proteins (OMPs). Recently, OMPs have been identified as a new class of vulnerable targets for antibiotic development, and therefore a comprehensive understanding of OMP quality control network components will be critical for discovering antimicrobials. Here, we demonstrate that the periplasmic chaperone Spy protects certain OMPs against protein-unfolding stress and can functionally compensate for other periplasmic chaperones, namely Skp and FkpA, in the Escherichia coli K-12 MG1655 strain. After extensive; in vivo; genetic experiments for functional characterization of Spy, we use nuclear magnetic resonance and circular dichroism spectroscopy to elucidate the mechanism by which Spy binds and folds two different OMPs. Along with holding OMP substrates in a dynamic conformational ensemble, Spy binding enables OmpX to form a partially folded β-strand secondary structure. The bound OMP experiences temperature-dependent conformational exchange within the chaperone, pointing to a multitude of local dynamics. Our findings thus deepen the understanding of functional compensation among periplasmic chaperones during OMP biogenesis and will promote the development of innovative antimicrobials against pathogenic Gram-negative bacteria.; IMPORTANCE; Outer membrane proteins (OMPs) play critical roles in bacterial pathogenicity and provide a new niche for antibiotic development. A comprehensive understanding of the OMP quality control network will strongly impact antimicrobial discovery. Here, we systematically demonstrate that the periplasmic chaperone Spy has a role in maintaining the homeostasis of certain OMPs. Remarkably, Spy utilizes a unique chaperone mechanism to bind OmpX and allows it to form a partially folded β-strand secondary structure in a dynamic exchange of conformations. This mechanism differs from that of other E. coli periplasmic chaperones such as Skp and SurA, both of which maintain OMPs in disordered conformations. Our study thus deepens the understanding of the complex OMP quality control system and highlights the differences in the mechanisms of ATP-independent chaperones

Flood-driven jet flow and sedimentary regime in a river-dominated estuary

Sediment dynamics under floods are critical for estuarine morphological evolution. A two-dimensional coupled hydrodynamic/sediment transport numerical modeling was adapted to investigate the flood-driven jet structure and the resultant sedimentary regime in a river-dominated estuary, Modaomen Estuary, Pearl River Delta, China. The results show that the flow velocity of flood jet exhibits a Gaussian distribution in the transverse direction and shows a linear decreasing trend in the longitudinal direction. Moreover, a distinct zonation, including a zone of flow establishment (ZOFE) and a zone of established flow (ZOEF), was detected. The ZOFE was the core area of high turbidity and strong erosion and provided sufficient sediments to the ZOEF, where sediment diffused and settled. Due to the settling lag, the sediment diffusion and deposition areas were larger than those of the jet. Estuarine geomorphology regulates the shape of flood jet, which shows an asymmetry configuration with the main body located at the west side of the bifurcated estuary. Tidal dynamics play a crucial role in altering the range of jet diffusion, especially in the longitudinal direction. Increased flood intensity has little effect on the jet structure and erosion/deposition pattern, but significantly increases the magnitude of seaward current velocities and bed level changes, as well as the transverse diffusion range of jet and sedimentation

Zero-shot stance detection via contrastive learning

Zero-shot stance detection (ZSSD) is challenging as it requires detecting the stance of previously unseen targets during the inference stage. Being able to detect the target-related transferable stance features from the training data is arguably an important step in ZSSD. Generally speaking, stance features can be grouped into targetinvariant and target-specific categories. Target-invariant stance features carry the same stance regardless of the targets they are associated with. On the contrary, target-specific stance features only co-occur with certain targets. As such, it is important to distinguish these two types of stance features when learning stance features of unseen targets. To this end, in this paper, we revisit ZSSD from a novel perspective by developing an effective approach to distinguish the types (target-invariant/-specific) of stance features, so as to better learn transferable stance features. To be specific, inspired by self-supervised learning, we frame the stance-feature-type identification as a pretext task in ZSSD. Furthermore, we devise a novel hierarchical contrastive learning strategy to capture the correlation and difference between target-invariant and -specific features and further among different stance labels. This essentially allows the model to exploit transferable stance features more effectively for representing the stance of previously unseen targets. Extensive experiments on three benchmark datasets show that the proposed framework achieves the state-of-the-art performance in ZSSD

Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, <i>Scaevola taccada</i> and <i>S. hainanensis</i>—Insight into Adaptation Outside of the Common Range

While most of the species in Goodeniaceae family, excluding the Scaevola genus, are endemic to Australasia, S. taccada and S. hainanensis have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. S. taccada appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. S. hainanensis is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for S. taccada and S. hainanensis, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in S. hainanensis and contracted in S. taccada might have facilitated adaptation to high salinity in S. hainanensis. Moreover, the genes under positive selection in S. hainanensis have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with S. hainanensis, the more drastic copy number expansion of FAR1 genes in S. taccada might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of S. taccada and S. hainanensis provides novel insights into their genomic evolution after leaving Australasia

Imbibition characteristics and influencing factors of reservoirs with ultra-low permeability of Ordos Basin: a case study of third member of Triassic Yanchang Formation in Weibei Oil Field

The Weibei Oil Field of the Ordos Basin has reservoirs of ultra-low permeability with small pores and complex pore throat structures. Imbibition is obvious at the early stage of water injection, which improved the effect of oilfield development. However, the characteristics of imbibition and the extent of EOR by imbibition are not clear. By collecting core samples from the third member of the Triassic Yanchang Formation in the Weibei Oil Field, physical property test, cast thin section observation, scanning electron microscope test, high pressure mercury injection and various imbibition experiments were carried out to study the reservoir physical properties and pore throat structure characteristics of the study samples, and to make imbibition experiments under different media types and different oil saturation. Three types of pores were discovered in the study area, namely, dissolution pore, intergranular pore and intergranular pore. The pore throat structure corresponding to different pore types are largely different. Pore throat structures of the reservoirs dominated by dissolution pores and intergranular pores gradually deteriorates. The oil displacement efficiency of fractured reservoir is higher than that of matrix reservoir with the values of 34.8% and 23.2%, respectively. The imbibition experiment under residual oil saturation shows that imbibition can improve the displacement efficiency of reservoir, but the increase is limited (5.3%-6.7%). The main factors affecting oil displacement efficiency are physical property, pore throat structure, medium type and oil saturation. When the reservoir physical property is higher, the pore throat structure is better and the oil saturation is relatively lower, the reservoir imbibition is relatively weak and the imbibition displacement efficiency is relatively low

Numerical Analysis of Viscous Dissipation in Microchannel Sensor Based on Phononic Crystal

Phononic crystals with phononic band gaps varying in different parameters represent a promising structure for sensing. Equipping microchannel sensors with phononic crystals has also become a great area of interest in research. For building a microchannels system compatible with conventional micro-electro-mechanical system (MEMS) technology, SU-8 is an optimal choice, because it has been used in both fields for a long time. However, its mechanical properties are greatly affected by temperature, as this affects the phononic bands of the phononic crystal. With this in mind, the viscous dissipation in microchannels of flowing liquid is required for application. To solve the problem of viscous dissipation, this article proposes a simulation model that considers the heat transfer between fluid and microchannel and analyzes the frequency domain properties of phononic crystals. The results show that when the channel length reaches 1 mm, the frequency shift caused by viscous dissipation will significantly affect detecting accuracy. Furthermore, the temperature gradient also introduces some weak passbands into the band gap. This article proves that viscous dissipation does influence the band gap of phononic crystal chemical sensors and highlights the necessity of temperature compensation in calibration. This work may promote the application of microchannel chemical sensors in the future

Pulse Electrodeposited Super-Hydrophobic Ni-Co/WS2 Nanocomposite Coatings with Enhanced Corrosion-Resistance

The hydrophobicity and corrosion resistance of composite coatings can be effectively improved by changing the electrodeposition method and adding inorganic nanoparticles. In this work, the incorporation of WS2 nanoparticles significantly increased the surface roughness of Ni-Co coatings. The best hydrophobicity and corrosion resistance of the Ni-Co/WS2 nanocomposite coatings (water contact angle of 144.7&deg;) were obtained in the direct current electrodeposition mode when the current density was 3 A/dm2 and the electrodeposition time was 50 min. Compared with direct current electrodeposition, the pulsed current electrodeposition method was more conducive to improving the electrodeposition performance of the nanocomposite coatings. Under the conditions of a current density of 3 A/dm2, pulse duty cycle of 70%, and pulse frequency of 1000 Hz, the nanocomposite coatings reached a superhydrophobic state (water contact angle of 153.8&deg;). The nanocomposite coatings had a slower corrosion rate and larger impedance modulus in this state, and thus the corrosion resistance was superior. The wetting state of the Ni-Co/WS2 nanocomposite coating surface was closer to the Cassie&ndash;Baxter model. The protective air layer formed by the layered rough microstructures significantly reduced the actual contact area between the liquid and the substrate, achieving excellent hydrophobic and corrosion resistance properties