Noncoding RNAs in acute kidney injury

Acute kidney injury (AKI), caused by various stimuli including ischemia reperfusion, nephrotoxic insult, and sepsis, is characterized by abrupt decline of kidney function. Till now, the molecular mechanisms for AKI have not been fully explored and the effective therapies are still lacking. Noncoding RNAs (ncRNAs), a group of biomolecules function at RNA level, are involved in a wide range of physiopathological processes including AKI. MicroRNAs (miRNAs) are the most extensively studied ncRNAs in AKI. Evidence indicated that miRNAs are altered significantly in various types of AKI. Gain-and-loss-of-function studies demonstrated that miRNAs, such as miR-24, miR-126, miR-494, and miR-687, may bind to the 3′-untranslated region of their target genes to regulate inflammation, programmed cell death, and cell cycle in the injury and repair stages of AKI, indicating their therapeutic potential in AKI. In contrast, functions of long noncoding RNAs and circular RNAs in AKI are hot topics but still largely unknown. Additionally, ncRNAs packaged in exosome can be detected in circulation and urine, they may serve as specific biomarkers for AKI. This review summarized the alteration and functional role of ncRNAs and their therapeutic potential in AKI.     

花生根瘤菌Bradyrhizobium sp.MZ5 III型分泌系统调节基因ttsI突变体的功能分析

[目的]探究慢生型花生根瘤菌III型分泌系统在花生-根瘤菌互作的功能。[方法]本研究采用同源重组和三亲本接合转移的方法,构建Bradyrhizobium sp.MZ5的III型分泌系统调节基因ttsI突变体;荧光定量PCR检测添加大豆苷元（Daidzein）和染料木黄酮（Genistein）诱导物后野生型和突变株转录水平上ttsI的表达量变化及其差异;蛭石结瘤实验分析ttsI基因突变对花生结瘤能力的影响。[结果]在转录水平上,大豆苷元和染料木黄酮对MZ5的III型分泌系统调节基因ttsI的表达具有显著的抑制作用（P<0.05）。在MZ5△ttsI突变体中ttsI基因的表达量都明显下调,与野生型菌株的相比都达到极显著水平（P<0.001）。蛭石结瘤实验表明,与野生型菌株相比,MZ5△ttsI突变体在不同花生品种的结瘤数和地上部干重都显著性降低。根瘤石蜡切片表明,MZ5△ttsI突变体在根瘤内的含菌量少于野生型菌株。[结论]Bradyrhizobium sp.MZ5菌株中的III型分泌系统在花生-根瘤菌互作中对结瘤有积极的促进作用。     

基于高通量测序的乐安江冬季细菌群落特征分析

【目的】分析乐安江从上游至下游水体细菌群落结构组成变化,揭示细菌群落结构组成变化的影响因素。【方法】分析不同河段水体中C、N、P、Cu、Zn、As和Pb等化学指标。对水体DNA的16S rRNA基因进行高通量测序确定细菌群落特征。基于Bray-Curtis距离的采样点非度量多维尺度(NMDS)分析和聚类分析研究乐安江水体细菌群落结构差异,基于冗余分析(RDA)研究环境因子与细菌群落的关系。【结果】乐安江水体中C、N、P、Cu、Zn、As和Pb等化学指标含量中下游偏高。中游河水受德兴铜矿废水影响,细菌群落多样性降低,下游受农业、生活废水影响,细菌群落丰富度和多样性升高。水体中优势菌群为β-变形菌纲(Beta-proteobacteria,53.03%)、放线菌门(Actinobacteria,20.24%)和拟杆菌门(Bacteroidetes,14.75%)。中游受德兴铜矿废水影响,Beta-proteobacteria丰度增大,而Actinobacteria丰度减小;下游受微生物间捕食影响,Bacteroidetes丰度下降。在细菌群落与环境因子的关系中,DO是解释乐安江细菌群落结构变化的最佳环境因子。【结论】乐安江中游德兴铜矿废水和中下游农业、生活废水明显改变了水体细菌群落结构组成,使水体细菌群落特征从上游到下游发生显著变化。本研究为揭示人类活动对乐安江水生态环境的影响提供了参考性数据。     

Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data

Epigenetic modifications can extend over long genomic regions to form domain-level chromatin states that play critical roles in gene regulation. The molecular mechanism for the establishment and maintenance of these states is not fully understood and remains challenging to study with existing experimental techniques. Here, we took a data-driven approach and parameterized an information-theoretic model to infer the formation mechanism of domain-level chromatin states from genome-wide epigenetic modification profiles. This model reproduces statistical correlations among histone modifications and identifies well-known states. Importantly, it predicts drastically different mechanisms and kinetic pathways for the formation of euchromatin and heterochromatin. In particular, long, strong enhancer and promoter states grow gradually from short but stable regulatory elements via a multistep process. On the other hand, the formation of heterochromatin states is highly cooperative, and no intermediate states are found along the transition path. This cooperativity can arise from a chromatin looping-mediated spreading of histone methylation mark and supports collapsed, globular three-dimensional conformations rather than regular fibril structures for heterochromatin. We further validated these predictions using changes of epigenetic profiles along cell differentiation. Our study demonstrates that information-theoretic models can go beyond statistical analysis to derive insightful kinetic information that is otherwise difficult to access.     

Estrogen inhibits osteoclasts formation and bone resorption via microRNA-27a targeting PPARγ and APC

Inhibition of osteoclasts formation and bone resorption by estrogen is very important in the etiology of postmenopausal osteoporosis. The mechanisms of this process are still not fully understood. Recent studies implicated an important role of microRNAs in estrogen-mediated responses in various cellular processes, including cell differentiation and proliferation. Thus, we hypothesized that these regulatory molecules might be implicated in the process of estrogen-decreased osteoclasts formation and bone resorption. Western blot, quantitative real-time polymerase chain reaction, tartrate-resistant acid phosphatase staining, pit formation assay and luciferase assay were used to investigate the role of microRNAs in estrogen-inhibited osteoclast differentiation and bone resorption. We found that estrogen could directly suppress receptor activator of nuclear factor B ligand/macrophage colony-stimulating factor-induced differentiation of bone marrow-derived macrophages into osteoclasts in the absence of stromal cell. MicroRNA-27a was significantly increased during the process of estrogen-decreased osteoclast differentiation. Overexpressing of microRNA-27a remarkably enhanced the inhibitory effect of estrogen on osteoclast differentiation and bone resorption, whereas which were alleviated by microRNA-27a depletion. Mechanistic studies showed that microRNA-27a inhibited peroxisome proliferator-activated receptor gamma (PPARγ) and adenomatous polyposis coli (APC) expression in osteoclasts through a microRNA-27a binding site within the 3′-untranslational region of PPARγ and APC. PPARγ and APC respectively contributed to microRNA-27a-decreased osteoclast differentiation and bone resorption. Taken together, these results showed that microRNA-27a may play a significant role in the process of estrogen-inhibited osteoclast differentiation and function.     

Comprehensive metabolomic,proteomic and physiological analyses of grain yield reduction in rice under abrupt drought–flood alternation stress

Abrupt drought–flood alternation (T1) is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, the response mechanism of yield decline under abrupt drought–flood alternation stress at the panicle differentiation stage was analyzed by looking at the metabolome, proteome as well as yield and physiological and biochemical indexes. The results showed that drought and flood stress caused a decrease in the yield of rice at the panicle differentiation stage, and abrupt drought–flood alternation stress created a synergistic effect for the reduction of yield. The main reason for the decrease of yield per plant under abrupt drought–flood alternation was the decrease of seed setting rate. Compared with CK0 (no drought and no flood), the net photosynthetic rate and soluble sugar content of T1 decreased significantly and its hydrogen peroxidase, superoxide dismutase, peroxidase activity increased significantly. The identified differential metabolites and differentially expressed proteins indicated that photosynthesis metabolism, energy metabolism pathway and reactive oxygen species response have changed strongly under abrupt drought–flood alteration stress, which are factors that leads to the rice grain yield reduction.     

High-resolution imaging of rhizosphere oxygen (O2) dynamics in Potamogeton crispus: effects of light,temperature and O2 content in overlying water

Plant and Soil - Radial oxygen loss (ROL) for macrophytes is intimately involved in their survival and growth, thus detailed characterizations of ROL and its implication for geochemical processes...     

Cross‐taxon congruence of multiple diversity facets of freshwater assemblages is determined by large‐scale processes across China

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