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.     

Effects of S-Abscisic Acid (S-ABA) on Seed Germination,Seedling Growth,and Asr1 Gene Expression Under Drought Stress in Maize

The objective of this study was to evaluate the ability of the phytohormone S-abscisic acid (S-ABA) to protect maize seedlings grown under drought stress and to measure their increased drought tolerance. The maize hybrids ‘Zhengdan 958’ (ZD958; drought tolerant) and ‘Xundan 20’ (XD20; drought sensitive) were treated with nutrient solutions of different concentrations (1, 2, 4, 8, and 10 mg/kg) of S-ABA under polyethylene glycol (PEG, 15% w/v, MW 6000) simulated drought stress. Optimal concentrations of S-ABA were designed to be sprayed onto the leaves of seedlings, and their effect on endogenous ABA, malondialdehyde (MDA), osmotic substances, antioxidant enzyme activities, and Asr1 gene expression in seedlings were studied. Results indicated that, under drought stress, S-ABA treatment significantly improved maize seed germination rate (GR), germination energy (GE), and seedling biomass (p < 0.05). After spraying 4 mg/kg S-ABA onto leaves, the endogenous hormone ABA, osmotic substances, antioxidant enzyme activities, and expressive quantity of the Asr1 gene were extended and MDA content dropped significantly (p < 0.05). Moreover, ZD 958 endogenous ABA content, osmotic substances content, antioxidant enzyme activity and Asr1 gene expressive quantity were higher than that of XD 20 (p < 0.05). In conclusion, S-ABA treatment increased the content of endogenous ABA, induced an increase in antioxidant enzyme activity and Asr1 gene expression level, reduced the oxidative damage caused by drought to maize leaves, and improved the adaptability of maize seedlings to withstand drought stress. The promoting effect of S-ABA on the drought-tolerant variety ZD 958 was more obvious (p < 0.05). These results serve as a reference for the use of S-ABA in mitigating drought stress in maize.

     

Effects of calpain inhibitor on the apoptosis of hepatic stellate cells induced by calcium ionophore A23187

We previously showed that changes in calcium concentrations were related to cell apoptosis in vitro. The endoplasmic reticulum (ER) is the main component of calcium storage and signal transduction, and disrupting the balance of intracellular Ca²⁺ can cause endoplasmic reticulum stress (ERS). In this process, the ER releases stored Ca ²⁺ into the cytoplasm and activates calpain-2. To further investigate the effect of calpain in hepatic stellate cells (HSCs), in the current study, we examine the effect of N-acetyl-leu-leu-norleucinal (ALLN) on apoptosis resulting from calcium ionophore A23187–induced ERS. Our findings indicate that calpain inhibition reduces calcium ionophore A23187–induced apoptosis of HSCs and decreases the expression of ER stress proteins that may be related to the calpain/caspase signaling pathway.