Biochemical and phylogenetic characterization of a monomeric isocitrate dehydrogenase from a marine methanogenic archaeon Methanococcoides methylutens

Extremophiles - Monomeric isocitrate dehydrogenase (IDH) stands for a separated subgroup among IDH protein family. Up to now, all reported monomeric IDHs are from prokaryotes. Here, a monomeric IDH...     

Crystal Structure of DNA Cytidine Deaminase ABOBEC3G Catalytic Deamination Domain Suggests a Binding Mode of Full-length Enzyme to Single-stranded DNA

APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A3G-CD1) and an actively catalytic C-terminal CD2 deamination domain (A3G-CD2). Although many studies on the structure of A3G-CD2 and enzymatic properties of full-length A3G have been reported, the mechanism of how A3G interacts with HIV-1 single-stranded DNA (ssDNA) is still not well characterized. Here, we reported a crystal structure of a novel A3G-CD2 head-to-tail dimer (in which the N terminus of the monomer H (head) interacts with the C terminus of monomer T (tail)), where a continuous DNA binding groove was observed. By constructing the A3G-CD1 structural model, we found that its overall fold was almost identical to that of A3G-CD2. We mutated the residues located in or along the groove in monomer H and the residues in A3G-CD1 that correspond to those seated in or along the groove in monomer T. Then, by performing enzymatic assays, we confirmed the reported key elements and the residues in A3G necessary to the catalytic deamination. Moreover, we identified more than 10 residues in A3G essential to DNA binding and deamination reaction. Therefore, this dimer structure may represent a structural model of full-length A3G, which indicates a possible binding mode of A3G to HIV-1 ssDNA.     

Photobiomodulation Drives MiR-136-5p Expression to Promote Injury Repair after Myocardial Infarction

Photobiomodulation (PBM) has emerged as an alternative therapy involved in modulating a variety of biological effects. In this study, we verified whether PBM can affect cardiac physiological activity in mice through noninvasive irradiation using light-emitting diodes at a wavelength of 630 nm (LED-Red). We found that the PBM involved in regulating the repair of injured myocardium is wavelength-limited. LED-Red caused cardiomyocytes (CMs) that had exited the cell cycle to divide and proliferate again, and the cell proliferation ratio increased significantly with the accumulation of intracellular photopower. In addition, LED-Red promoted myocardial revascularization and myocardial regeneration, reduced the area of fibrosis in mice with myocardial infarction (MI), and thus improved cardiac contractile function. In regard to the mechanism, miRNA sequencing analysis showed that low-power LED-Red irradiation could induce differential changes in miRNAs in CMs. Among them, miR-136-5p was identified as a cardiac photo-sensitive miRNA and was obviously inhibited after stimulation, which produced a proliferation-promoting effect on CMs. Subsequent luciferase reporter assays confirmed the involvement of Ino80 as a binding target of miR-136-5p in the regulatory process of CM proliferation. Similarly, LED-Red irradiation elevated intracellular Ino80 expression. After knockdown of Ino80, the proliferation-promoting effect of LED-Red on CMs was inhibited. Collectively, this study demonstrates that LED-Red can promote CM proliferation by inhibiting cardiac photo-sensitive miRNA- miR-136-5p expression through targeting Ino80. The findings provided a new potential strategy for the treatment of ischemic cardiomyopathy (ICD).     

Metabolic disorder in the progression of heart failure

Heart failure(HF) is a major clinical concern owing to its high prevalence and high mortality. Metabolomics, an effective approach to predict diagnostic biomarkers and to explore the altered metabolic pathways in pathogenesis, has been extensively applied in evaluating the course of diseases. In this study, we used this approach to analyse the abundance of metabolites, with liquid chromatograph-mass spectrometer, in plasma samples from rats with transverse aortic constriction(TAC) and patients at different stages of HF. We compared the metabolic parameters within and between TAC rats and patients. An apparent metabolic shift was observed in rats, from compensated hypertrophy stage to decompensated hypertrophy stage, and in patients with HF,from stage A to stage B and subsequently stage C. Diagnostic biomarkers were predicted by comparing the variable importance in the projection scores and fold change analysis within and between rats and patients. Enrichment pathway analysis and network analysis provided an overview of the largely disturbed metabolic pathways, and those interfered at different stages and across species were confirmed. The significantly changed metabolites and pathways revealed the underlying mechanisms of HF pathogenesis, hinted at novel potential biomarkers, and provided potential therapeutic intervention targets for HF.     

不同经营模式山核桃林地土壤pH值、养分与细菌多样性的差异

为探究土壤细菌多样性及其功能对山核桃(Carya cathayensis)经营模式的指导作用, 本文采用16S rRNA基因高通量测序技术检测并比较了生态经营和过度经营的山核桃林土壤中的细菌群落, 分析了山核桃干腐病发病期干腐病感病指数、土壤pH值、养分与细菌多样性的相关性。结果表明: (1)生态经营山核桃林的感病指数(3.3 ± 3.35)显著低于过度经营山核桃林(81.9 ± 1.27)。(2)生态经营山核桃林土壤pH (6.64 ± 0.06)显著高于过度经营山核桃林(5.80 ± 0.04)。(3)过度经营山核桃林土壤的速效磷、速效钾和速效氮含量分别为18.10 ± 0.58 mg/kg、698.63 ± 11.24 mg/kg和227.13 ± 3.81 mg/kg, 均分别显著高于三者在生态经营山核桃林土壤中的含量(14.94 ± 0.27 mg/kg、497.13 ± 6.19 mg/kg和195.28 ± 6.01 mg/kg)。(4)生态经营和过度经营山核桃林土壤分别有14和21个主要细菌属, 其中鞘氨醇单胞菌属(Sphingomonas)、Gaiella和溶杆菌属(Lysobacter)为生态经营山核桃林土壤的优势属, 其相对多度显著高于过度经营山核桃林; 而Bryobacter、Candidatus Solibacter和慢生根瘤菌属(Bradyrhizobium)为过度经营山核桃林土壤中的优势属, 其相对多度显著高于生态经营山核桃林。两种经营模式下山核桃林土壤的OTUs、Ace指数、Chao指数、Shannon指数和Simpson指数无显著差异。RDA分析与蒙特卡罗检验表明, pH值、速效磷和速效氮均对土壤细菌优势菌群群落结构有显著影响(P < 0.05)。     

Climate Warming Since the Holocene Accelerates West–East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum

Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.     

响应面法优化蕤核叶片总黄酮提取工艺

采用超声波辅助提取的方法从蕤核叶片中提取总黄酮.利用响应面法(RSM法)研究了超声提取时间、乙醇浓度、液固比、提取温度等因素对总黄酮得率的影响,确定了超声波辅助提取蕤核叶片总黄酮的最佳工艺参数.结果表明,超声波辅助提取蕤核叶片总黄酮的最佳工艺务件为:超声时间50.1 min,乙醇浓度59.5%,液料比24.9:1,提取...     

Integrative taxonomy uncovers hidden species diversity in the rheophilic genus Potamometra (Hemiptera: Gerridae)

The genus Potamometra Bianchi, 1896 represents big rheophilic semi-aquatic bugs that typically inhabit middle-altitude mountainous streams. Here, we integrated molecular and morphological data for delimiting species boundaries and understanding the evolutionary history of the genus Potamometra. Twenty-seven complete mitochondrial genomes of Potamometra were sequenced, with samples representing most of the known geographically distributed locations around the Sichuan Basin. The results of different species delimitation methods (ABGD, bPTP, GMYC and BPP) based on the monolocus or multilocus data strongly supported the existence of two cryptic new species (Potamometra anderseni Zheng, Ye & Bu, sp. nov. and Potamometra zhengi Zheng, Ye & Bu, sp. nov.) although more entities were found in the tree-based delimitation methods. The two new species were successfully validated using morphological characters within a detailed taxonomic framework. Phylogenetic analyses supported the reciprocal monophyly of the seven highly node-supported clades, which were matched with the five known species and two new taxa. A novel gene arrangement pattern that two trnF (trnF1 and trnF2) genes separated by an intergenic spacer (IGS) were found in all the species except the sister group of Potamometra berezowskii Bianchi, 1896 and Potamometra linnavuorii Chen, Nieser & Bu, 2016. This gene rearrangement event could be explained by the tandem duplication and random loss (TDRL) model. Our study emphasized that the combination of molecular sequence data, morphological characters and mitochondrial structural information could improve the accuracy of species delimitation.     

Functional assessment of hydrophilic domains of late embryogenesis abundant proteins from distant organisms

Late embryogenesis abundant (LEA) proteins play a protective role during desiccation and oxidation stresses. LEA3 proteins are a major group characterized by a hydrophilic domain (HD) with a highly conserved repeating 11-amino acid motif. We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into α-helical structures with the addition of glycerol or trifluoroethanol. Heterologous HD expression conferred enhanced desiccation and oxidation tolerance to Escherichia coli. These four HDs protected the enzymatic activities of lactate dehydrogenase (LDH) by preventing its aggregation under desiccation stress. The HDs also interacted with LDH, which was intensified by the addition of hydrogen peroxide (H₂O₂), suggesting a protective role in a chaperone-like manner. Based on these results, the HDs of LEA3 proteins show promise as protectants for desiccation and oxidation stresses, especially DrHD, which is a potential ideal stress-response element that can be applied in synthetic biology due to its extraordinary protection and stress resistance ability.