棉铃虫剂量补偿相关基因Hamsl1的鉴定与功能分析

【目的】棉铃虫Helicoverpa armigera的剂量补偿(dosage compensation, DC)分子机制尚不清楚。本研究旨在通过克隆棉铃虫雄性特异性致死(male specific lethal, msl) 基因Hamsl1,利用RNA干扰技术明确其是否参与调控棉铃虫剂量补偿。【方法】利用RT-PCR同源克隆棉铃虫Hamsl1基因全长cDNA; 利用qPCR技术研究Hamsl1基因在棉铃虫不同发育时期的表达谱;通过显微注射Hamsl1 siRNA到棉铃虫3龄幼虫中对Hamsl1基因进行RNA干扰后,利用qPCR技术检测15个Z染色体基因的表达情况,分析Hamsl1是否调控Z染色体基因剂量。【结果】成功克隆了棉铃虫Hamsl1基因的cDNA序列,鉴定出Hamsl1基因mRNA存在2种剪接体,分别命名为Hamsl1a(GenBank登录号: MK564008)和Hamsl1b(GenBank登录号: MK564009)。功能域分析发现HaMSL1含有典型的PEHE和coiled-coil功能域,具有MSL1蛋白的特征。qPCR分析表明,Hamsl1基因位于棉铃虫Z染色体上;棉铃虫Hamsl1a与Hamsl1b基因表达均具有发育时期特异性,在成虫期表达量最高,且雌雄化蛹后基因表达量差异显著,具有性别特异性。通过同源比对和qPCR分析,在DNA水平鉴定了15个Z染色体候选基因。显微注射Hamsl1 siRNA于3龄幼虫体内72 h,干扰效率为36.01%~64.27%,并未发生雄性致死现象;与对照组相比,Hamsl1 RNAi处理组中棉铃虫15个Z染色体基因在雄性个体中整体呈现表达量上调趋势,而在雌性个体中平均表达水平差异不显著。【结论】本研究初步探明Hamsl1基因位于棉铃虫Z染色体上,且该基因可能通过抑制雄性棉铃虫Z染色体基因表达,调控棉铃虫Z染色体剂量补偿。本研究为深入研究棉铃虫剂量补偿分子机制和绿色防控棉铃虫提供了理论基础。     

MiR-26b-3p regulates osteoblast differentiation via targeting estrogen receptor α

BackgroundUnderstanding of the molecular mechanisms of miRNAs involved in osteoblast differentiation is important for the treatment of bone-related diseases.MethodsMC3T3-E1 cells were induced to osteogenic differentiation by culturing with bone morphogenetic protein 2 (BMP2). After transfected with miR-26b-3p mimics or inhibitors, the osteogenic differentiation of MC3T3-E1 cells was detected by ALP and ARS staining. Cell viability was analyzed by MTT. The expressions of miR-26b-3p and osteogenic related markers and signaling were examined by qPCR and western blot. Direct binding of miR-26b-3p and ER-α were determined by dual luciferase assay.ResultsmiR-26b-3p was significantly down-regulated during osteoblast differentiation. Overexpression of miR-26b-3p inhibited osteoblast differentiation, while inhibition of miR-26b-3p enhanced osteoblast differentiation. Further studies demonstrated miR-26b-3p inhibited the expression of estrogen receptor α (ER-α) by directly targeting to the CDS region of ER-α mRNA. Overexpression of ER-α rescued the suppression effects of miR-26b-3p on osteoblast differentiation, while knockdown of ER-α reversed the upregulation of osteoblast differentiation induced by knockdown of miR-26b-3p.ConclusionOur study demonstrates that miR-26b-3p suppresses osteoblast differentiation of MC3T3-E1 cells via directly targeting ER-α.     

pLoc_bal-mGpos: Predict subcellular localization of Gram-positive bacterial proteins by quasi-balancing training dataset and PseAAC

Knowledge of protein subcellular localization is vitally important for both basic research and drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization purely based on the sequence information alone. Recently, a predictor called “pLoc-mGpos” was developed for identifying the subcellular localization of Gram-positive bacterial proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems in which some proteins, called “multiplex proteins”, may simultaneously occur in two or more subcellular locations. Although it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mGpos was trained by an extremely skewed dataset in which some subset (subcellular location) was over 11 times the size of the other subsets. Accordingly, it cannot avoid the bias consequence caused by such an uneven training dataset. To alleviate such bias consequence, we have developed a new and bias-reducing predictor called pLoc_bal-mGpos by quasi-balancing the training dataset. Rigorous target jackknife tests on exactly the same experiment-confirmed dataset have indicated that the proposed new predictor is remarkably superior to pLoc-mGpos, the existing state-of-the-art predictor in identifying the subcellular localization of Gram-positive bacterial proteins. To maximize the convenience for most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mGpos/, by which users can easily get their desired results without the need to go through the detailed mathematics.     

Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associated single deletion of LYS9 in the light chain. By combining supervised and unsupervised machine learning methodologies and more traditional structural analyses on data from 10 μs molecular dynamics simulations, we show that the conformational ensemble of the ΔK9 mutant is significantly perturbed. Our analyses consistently indicate that LYS9 deletion destabilizes both the catalytic cleft and regulatory functional regions and result in some conformational changes that occur in tens to hundreds of nanosecond scaled motions. We also reveal that the two forms of thrombin each prefer a distinct binding mode of a Na⁺ ion. We expand our understanding of previous experimental observations and shed light on the mechanisms of the LYS9 deletion associated bleeding disorder by providing consistent but more quantitative and detailed structural analyses than early studies in literature. With a novel application of supervised learning, i.e. the decision tree learning on the hydrogen bonding features in the wild-type and ΔK9 mutant forms of thrombin, we predict that seven pairs of critical hydrogen bonding interactions are significant for establishing distinct behaviors of wild-type thrombin and its ΔK9 mutant form. Our calculations indicate the LYS9 in the light chain has both localized and long-range allosteric effects on thrombin, supporting the opinion that light chain has an important role as an allosteric effector.     

Bacterial reproductive manipulators in rice planthoppers

Rice planthoppers (Hemiptera: Delphacidae) are notorious pests for rice (Oryza sativa) in Asia, posing a serious threat to rice production and grain security. Rice planthoppers harbor diverse bacterial symbionts, including Wolbachia, Cardinium, Spiroplasma, and Arsenophonus, which are known to manipulate reproduction in arthropod hosts. This microreview is to introduce current knowledge of bacterial reproductive manipulators in rice planthoppers, including their diversity, population dynamics, localization, transmission, and biological functions.     

An evaluation of transferability of ecological niche models

Ecological niche modeling (ENM) is used widely to study species’ geographic distributions. ENM applications frequently involve transferring models calibrated with environmental data from one region to other regions or times that may include novel environmental conditions. When novel conditions are present, transferability implies extrapolation, whereas, in absence of such conditions, transferability is an interpolation step only. We evaluated transferability of models produced using 11 ENM algorithms from the perspective of interpolation and extrapolation in a virtual species framework. We defined fundamental niches and potential distributions of 16 virtual species distributed across Eurasia. To simulate real situations of incomplete understanding of species’ distribution or existing fundamental niche (environmental conditions suitable for the species contained in the study area; N* _F ), we divided Eurasia into six regions and used 1–5 regions for model calibration and the rest for model evaluation. The models produced with the 11 ENM algorithms were evaluated in environmental space, to complement the traditional geographic evaluation of models. None of the algorithms accurately estimated the existing fundamental niche (N* _F ) given one region in calibration, and model evaluation scores decreased as the novelty of the environments in the evaluation regions increased. Thus, we recommend quantifying environmental similarity between calibration and transfer regions prior to model transfer, providing an avenue for assessing uncertainty of model transferability. Different algorithms had different sensitivity to completeness of knowledge of N* _F , with implications for algorithm selection. If the goal is to reconstruct fundamental niches, users should choose algorithms with limited extrapolation when N* _F is well known, or choose algorithms with increased extrapolation when N* _F is poorly known. Our assessment can inform applications of ecological niche modeling transference to anticipate species invasions into novel areas, disease emergence in new regions, and forecasts of species distributions under future climate conditions.     

小菜蛾成虫下唇须感器的超微结构及其神经元中枢投射

【目的】明确小菜蛾Plutella xylostella成虫下唇须感器的形态结构及感器神经元的投射。【方法】利用光学显微镜观察和扫描电子显微镜观察下唇须结构和感器类型,利用神经回填技术和激光共聚焦显微镜观察下唇须感器神经元在脑部的投射。【结果】小菜蛾成虫下唇须共3节,其上存在Böhm氏鬃毛、钟形感器、鳞形感器、锥形感器、微毛形感器5种不同类型的感器和一个陷窝器结构。Böhm氏鬃毛短小尖细,钟形感器形如顶部凹陷的圆帽,两种感器均分布于下唇须第1节,且大小上均无雌雄二型差异;鳞形感器形同柳叶,锥形感器粗而直,均散生于下唇须的第2和3节,两种感器在大小上均存在雌雄二型差异,其中雌性的鳞形感器显著大于雄性的,根据其雌雄二型差异现象推测雌蛾的鳞形感器可能与感受寄主植物挥发物有关;下唇须第3节中上部具有一个圆形陷窝器结构,雄虫的陷窝器内径为5.68±0.33μm,雌虫的为6.03±0.23μm,雌雄间无显著性差异;凹坑内长有表面光滑的微毛形感器。小菜蛾下唇须感器神经元主要投射于脑部咽下神经节、每个触角叶的下唇须陷窝器神经纤维球和腹神经索3条通路。【结论】阐明了小菜蛾下唇须感器的类型、分布和形态特征及其感器神经元在脑部的投射形态,为深入了解小菜蛾下唇须感器的生理和功能奠定了基础。