小檗碱通过抑制经典的NLRP3炎症小体活化通路来下调LPS诱导的HUVEC炎症反应*

目的:探讨小檗碱(Berberine, Ber)对脂多糖(Lipopolysaccharide, LPS)诱导的人脐静脉血管内皮细胞(Human Umbilical VeinEndothelial Cells, HUVEC)炎症反应的抑制作用及相关机制。方法:MTT法检测不同浓度的Ber对HUVEC存活率的影响。以0.05μg/mL LPS刺激HUVEC建立炎症反应模型,并分别给予1.25、2.5、5μM Ber干预,Elisa检测Ber对炎症因子TNF-α、IL-1β分泌的影响,免疫印迹法检测Ber对NLRP3炎症小体信号通路中NLRP3、My D88、IL-1β、TLR4、ASC和Caspase-1蛋白表达的影响。结果:不同浓度的Ber对HUVEC增殖均具有抑制作用,且基本呈现浓度梯度,IC50值接近5μM;与LPS组相比,不同浓度Ber(1.25、2.5、5μM)均可以显著下调HUVEC中TNF-α、IL-1β炎症因子的分泌(P0.005及P0.01),并可以显著抑制细胞中NLRP3、My D88、IL-1β、TLR4、ASC和Caspase-1蛋白的表达(P0.05),其抑制作用基本呈剂量关系,以5μM Ber的抑制效果最佳。结论:Ber可以通过抑制经典的NLRP3炎症小体活化通路来下调LPS诱导的HUVEC炎症反应。     

Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure

Cultivation of dedicated soil plots called ‘landfarms' is an effective technology for bioremediation of hydrocarbon waste generated by various industrial practices. To understand the influence of soil conditions on landfarm microbial communities, analysis of bacterial and fungal community structure using next-generation sequencing at different sections and depths was performed across a hydrocarbon-waste landfarm in Regina, Saskatchewan, Canada. While a core set of hydrocarbon-associated bacterial and fungal taxa are present throughout the landfarm, unique bacterial and fungal operational taxonomic units are differentially abundant at sections within the landfarm, which correlate with differences in soil physiochemical properties and management practices. Increased frequency of waste application resulted in strong positive correlations between bacterial community assemblages and elevated amounts of oil, grease and F3 – F4 hydrocarbon fractions. In areas of standing water and lower application of hydrocarbon, microbial community structure correlated with soil pH, trace nutrients and metals. Overall, diversity and structure of bacterial communities remain relatively stable across the landfarm, while in contrast, fungal community structure appears more responsive to soil oxygen conditions. Results are consistent with the hypothesis that years of bioremediation activity have shaped microbial communities; however, several management practices can be undertaken to increase efficiency of remediation, including the removal of standing water and soil tilling across the landfarm.     

The Urfold: Structural similarity just above the superfold level?

We suspect that there is a level of granularity of protein structure intermediate between the classical levels of “architecture” and “topology,” as reflected in such phenomena as extensive three‐dimensional structural similarity above the level of (super)folds. Here, we examine this notion of architectural identity despite topological variability, starting with a concept that we call the “Urfold.” We believe that this model could offer a new conceptual approach for protein structural analysis and classification: indeed, the Urfold concept may help reconcile various phenomena that have been frequently recognized or debated for years, such as the precise meaning of “significant” structural overlap and the degree of continuity of fold space. More broadly, the role of structural similarity in sequence?structure?function evolution has been studied via many models over the years; by addressing a conceptual gap that we believe exists between the architecture and topology levels of structural classification schemes, the Urfold eventually may help synthesize these models into a generalized, consistent framework. Here, we begin by qualitatively introducing the concept.     

A modest proposal for restoration ecology

Restoration ecology struggles to mitigate human‐caused ecological damage. Non‐native species are a particular challenge. This article describes two restoration attempts following introduced species in California and then makes a radical culling proposal. Environmental regulations, legal protections, and restoration projects are necessary to preserve ecosystem services, but such policies are often unpopular. Restorers often struggle when public opinion opposes evidence‐based practice, and this occurs particularly when the interventions involve killing mammals. Therefore, restoration efforts may benefit from more attention to how individuals perceive the acceptability of environmental policies and how to communicate policy options effectively for individuals to make informed decisions. Restoration ecology can follow the recent shift of medicine away from imperatives and toward informed patient choice. Restoration projects may benefit from recent advances in psychology and communication that help individuals make policy decisions that align with their personal values.     

Mismatches between breeding phenology and resource abundance of resident alpine ptarmigan negatively affect chick survival

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高油酸油菜遗传育种研究进展

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Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations

The Escherichia coli chaperonin GroEL is a complex of identical subunit proteins (57 kDa each) arranged in a back-to-back stacking of two heptameric rings. Its hallmarks include nested positive intra-ring and negative inter-ring cooperativity in adenosine trisphosphate (ATP) binding and the ability to mediate the folding of newly transcribed and/or denatured substrate proteins. We performed unbiased molecular dynamics simulations of the GroEL subunit protein in explicit water both with and without the nucleotide KMgATP to understand better the details of the structural transitions that enable these behaviors. Placing KMgATP in the equatorial domain binding pocket of a t state subunit, which corresponds to a low ATP-affinity state, produced a short-lived (6 ns) state that spontaneously transitioned to the high ATP-affinity r state. The important feature of this transition is a large-scale rotation of the intermediate domain's helix M to close the ATP binding pocket. Pivoting of helix M is accompanied by counterclockwise rotation and slight deformation of the apical domain, important for lowering the affinity for substrate protein. Aligning simulation conformations into model heptamer rings demonstrates that the t-->r transition in one subunit is not sterically hindered by t state neighbors, but requires breakage of Arg(197)-Glu(386) intersubunit salt bridges, which are important for inter-ring positive cooperativity. Lowest-frequency quasi-harmonic modes of vibration computed pre- and post-transition clearly show that natural vibrations facilitate the transition. Finally, we propose a novel mechanism for inter-ring cooperativity in ATP binding inspired by the observation of spontaneous insertion of the side chain of Ala(480) into the empty nucleotide pocket.     

Structure-function relationships of the viral RNA-dependent RNA polymerase: fidelity, replication speed, and initiation mechanism determined by a residue in the ribose-binding pocket

Studies of the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV), 3Dpol, have shown that Asn-297 permits this enzyme to distinguish ribose from 2'-deoxyribose. All animal RNA viruses have Asn at the structurally homologous position of their polymerases, suggesting a conserved function for this residue. However, all prokaryotic RNA viruses have Glu at this position. In the presence of Mg2+, the apparent affinity of Glu-297 3Dpol for 2'-deoxyribonucleotides was decreased by 6-fold relative to wild type without a substantial difference in the fidelity of 2'-dNMP incorporation. The fidelity of ribonucleotide misincorporation for Glu-297 3Dpol was reduced by 14-fold relative to wild type. A 4- to 11-fold reduction in the rate of ribonucleotide incorporation was observed. Glu-297 PV was unable to grow in HeLa cells due to a replication defect equivalent to that observed for a mutant PV encoding an inactive polymerase. Evaluation of the protein-(VPg)-primed initiation reaction showed that only half of the Glu-297 3Dpol initiation complexes were capable of producing VPg-pUpU product and that the overall yield of uridylylated VPg products was reduced by 20-fold relative to wild-type enzyme, a circumstance attributable to a reduced affinity for UTP. These studies identify the first RdRp derivative with a mutator phenotype and provide a mechanistic basis for the elevated mutation frequency of RNA phage relative to animal RNA viruses observed in culture. Although protein-primed initiation and RNA-primed elongation complexes employ the same polymerase active site, the functional differences reported here imply significant structural differences between these complexes.