All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps

In this study, we have performed a comprehensive structural investigation of three major biochemical states of a kinesin complexed with microtubule under the constraint of high-quality cryo-electron-microscopy (EM) maps. In addition to the ADP and ATP state which were captured by X-ray crystallography, we have also modeled the nucleotide-free or APO state for which no crystal structure is available. We have combined flexible fitting of EM maps with regular molecular dynamics simulations, hydrogen-bond analysis, and free energy calculation. Our APO-state models feature a subdomain rotation involving loop L2 and α6 helix of kinesin, and local structural changes in active site similar to a related motor protein, myosin. We have identified a list of hydrogen bonds involving key residues in the active site and the binding interface between kinesin and microtubule. Some of these hydrogen bonds may play an important role in coupling microtubule binding to ATPase activities in kinesin. We have validated our models by calculating the binding free energy between kinesin and microtubule, which quantitatively accounts for the observation of strong binding in the APO and ATP state and weak binding in the ADP state. This study will offer promising targets for future mutational and functional studies to investigate the mechanism of kinesin motors.     

Development of a novel‐type transgenic cotton plant for control of cotton bollworm

The transgenic Bt cotton plant has been widely planted throughout the world for the control of cotton budworm Helicoverpa armigera (Hubner). However, a shift towards insect tolerance of Bt cotton is now apparent. In this study, the gene encoding neuropeptide F (NPF) was cloned from cotton budworm H. armigera, an important agricultural pest. The npf gene produces two splicing mRNA variants—npf1 and npf2 (with a 120‐bp segment inserted into the npf1 sequence). These are predicted to form the mature NPF1 and NPF2 peptides, and they were found to regulate feeding behaviour. Knock down of larval npf with dsNPF in vitro resulted in decreases of food consumption and body weight, and dsNPF also caused a decrease of glycogen and an increase of trehalose. Moreover, we produced transgenic tobacco plants transiently expressing dsNPF and transgenic cotton plants with stably expressed dsNPF. Results showed that H. armigera larvae fed on these transgenic plants or leaves had lower food consumption, body size and body weight compared to controls. These results indicate that NPF is important in the control of feeding of H. armigera and valuable for production of potential transgenic cotton.     

Mycobacterium tuberculosis ESAT-6 Exhibits a Unique Membrane-interacting Activity That Is Not Found in Its Ortholog from Non-pathogenic Mycobacterium smegmatis

Mycobacterium tuberculosis ESAT-6 (MtbESAT-6) reportedly shows membrane/cell-lysis activity, and recently its biological roles in pathogenesis have been implicated in rupture of the phagosomes for bacterial cytosolic translocation. However, molecular mechanism of MtbESAT-6-mediated membrane interaction, particularly in relation with its biological functions in pathogenesis, is poorly understood. In this study, we investigated the pH-dependent membrane interaction of MtbESAT-6, MtbCFP-10, and the MtbESAT-6/CFP-10 heterodimer, by using liposomal model membranes that mimic phagosomal compartments. MtbESAT-6, but neither MtbCFP-10 nor the heterodimer, interacted with the liposomal membranes at acidic conditions, which was evidenced by release of K⁺ ions from the liposomes. Most importantly, the orthologous ESAT-6 from non-pathogenic Mycobacterium smegmatis (MsESAT-6) was essentially inactive in release of K⁺. The differential membrane interactions between MtbESAT-6 and MsESAT-6 were further confirmed in an independent membrane leakage assay using the dye/quencher pair, 8-aminonapthalene-1,3,6 trisulfonic acid (ANTS)/p-xylene-bis-pyridinium bromide (DPX). Finally, using intrinsic and extrinsic fluorescence approaches, we probed the pH-dependent conformational changes of MtbESAT-6 and MsESAT-6. At acidic pH conditions, MtbESAT-6 underwent a significant conformational change, which was featured by an increased solvent-exposed hydrophobicity, while MsESAT-6 showed little conformational change in response to acidification. In conclusion, we have demonstrated that MtbESAT-6 possesses a unique membrane-interacting activity that is not found in MsESAT-6 and established the utility of rigorous biochemical approaches in dissecting the virulence of M. tuberculosis.     

Age- and Sex-Dependent Association between FTO rs9939609 and Obesity-Related Traits in Chinese Children and Adolescents

Background

The associations between common variants in the fat mass- and obesity-associated (FTO) gene and obesity-related traits may be age-dependent and may differ by sex. The present study aimed to assess the association of FTO rs9939609 with body mass index (BMI) and the risk of obesity from childhood to adolescence, and to determine the age at which the association becomes evident.

Methods

Totally 757 obese and 2,746 non-obese Chinese children aged 6–18 years were genotyped for FTO rs9939609. Of these, a young sub-cohort (n = 777) aged 6–11 years was reexamined 6 years later. Obesity was defined using the sex- and age-specific BMI cut-offs recommended by the International Obesity Task Force.

Results

The associations of FTO rs9939609 with BMI and obesity did not appear until children reached 12–14 years. The variant was associated with an increased BMI in boys (β = 1.50, P = 0.004) and girls (β = 0.97, P = 0.018), respectively. Thereafter, the magnitude of association increased in girls at ages 15–18 years (β = 2.02, P<0.001), but not boys (β = 0.10, P>0.05). Age was found to interact with the variant on BMI (P<0.001) and obesity (P = 0.042) only in girls. In the sub-cohort, the associations of FTO rs9939609 with BMI (β = 1.07, P = 0.008) and obesity (OR = 2.09, 95% CI: 1.12, 3.91) were only observed 6 years later (ages 12–18 years) in girls, even after adjusting for baseline BMI.

Conclusions

The association between FTO rs9939609 and obesity-related traits may change from childhood to adolescence in Chinese individuals, and the association may start as early as age 12 years, especially in girls.     

A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II

A combined STD-NMR/molecular modeling protocol to probe the binding modes of the glycosidase inhibitors kifunensine and salacinol to Drosophila melanogaster Golgi alpha-mannosidase II (dGMII) was tested. Saturation-transfer difference (STD) NMR experiments were carried out for the complexes of dGMII with these two inhibitors. The program AutoDock 3.0 was then used to optimize the interactions of the inhibitors with the residues in the active site of dGMII. Theoretical STD effects of the ligand protons in the complexes were calculated for the different binding modes with the recently developed CORCEMA-ST protocol. Comparison of experimental and theoretical effects then permitted selection of the likely binding modes of the ligands. The more rigid kifunensine was used initially to test the protocol. Excellent correlation between experimental and theoretical data was obtained for one of the binding modes that also corresponded to that observed in the crystal structure of the complex. The protocol was then extended to the more flexible salacinol. For the selected binding mode, good correlation of experimental and theoretical data for the five-membered ring was obtained; however, poor correlation for protons on the acyclic chain was obtained, suggesting flexibility in this portion of the molecule. Comparison of the selected binding mode with that from a crystal structure of salacinol with dGMII showed excellent superimposition of the five-membered ring but another orientation of the acyclic chain. The results suggest that reliable structural binding modes of a ligand to protein in aqueous solution can be provided with the combined use of STD-NMR spectroscopy, molecular modeling, and CORCEMA-ST calculations, although highly flexible portions of the ligand may be poorly defined.     

Caspase-3-dependent activation of calcium-independent phospholipase A2 enhances cell migration in non-apoptotic ovarian cancer cells

Calcium-independent phospholipase A(2) (iPLA(2)) plays a pivotal role in phospholipid remodeling and many other biological processes, including inflammation and cancer development. iPLA(2) can be activated by caspase-3 via a proteolytic process in apoptotic cells. In this study we identify novel signaling and functional loops of iPLA(2) activation leading to migration of non-apoptotic human ovarian cancer cells. The extracellular matrix protein, laminin-10/11, but not collagen I, induces integrin- and caspase-3-dependent cleavage and activation of overexpressed and endogenous iPLA(2). The truncated iPLA(2) (amino acids 514-806) generates lysophosphatidic acid and arachidonic acid. Arachidonic acid is important for enhancing cell migration toward laminin-10/11. Lysophosphatidic acid activates Akt that in turn acts in a feedback loop to block the cleavage of poly-(ADP-ribose) polymerase and DNA fragmentation factor as well as prevent apoptosis. By using pharmacological inhibitors, blocking antibodies, and genetic approaches (such as point mutations, dominant negative forms of genes, and siRNAs against specific targets), we show that beta(1), but not beta(4), integrin is involved in iPLA(2) activation and cell migration to laminin-10/11. The role of caspase-3 in iPLA(2) activation and cell migration are supported by several lines of evidence. 1) Point mutation of Asp(513) (a cleavage site of caspase-3 in iPLA(2)) to Ala blocks laminin-10/11-induced cleavage and activation of overexpressed iPLA(2), whereas mutation of Asp(733) to Ala has no such effect, 2) treatment of inhibitors or a small interfering RNA against caspase-3 results in decreased cell migration toward laminin-10/11, and 3) selective caspase-3 inhibitor blocks cleavage of endogenous iPLA(2) induced by laminin-10/11. Importantly, small interfering RNA-mediated down-regulation of endogenous iPLA(2) expression in ovarian carcinoma HEY cells results in decreased migration toward laminin, suggesting that our findings are pathophysiologically important.     

河南济源人工引水渠隧道蝙蝠冬眠生态学特征

2017-2020年期间,每年1月份对河南省济源市邵原镇布袋沟水库人工引水渠隧道内蝙蝠进行冬眠生态学特征调查,共发现2科5属7种蝙蝠在此冬眠,包括马铁菊头蝠（Rhinolophus ferrumequinum）、小菊头蝠（R.pusillus）、华南水鼠耳蝠（Myotis laniger）、白腹管鼻蝠（Murina leucogaster）、金管鼻蝠（Mu.aurata）、奥氏长耳蝠（Plecotus ognevi）和亚洲宽耳蝠（Barbastella leucomelas）。马铁菊头蝠是优势种（约52%-73%的冬眠个体）,其次是小菊头蝠（约19%-37%）、华南水鼠耳蝠（约5%-8%）,其余蝙蝠物种数量不足3%。2017-2020年冬眠蝙蝠个体总数呈增长趋势,但仍少于早期报道的数量。有42个隧道每年均有蝙蝠冬眠,而且不同年度冬眠数量也不尽相同。通过多元线性回归分析发现,隧道长度可能是影响蝙蝠冬眠栖息场所选择的主要影响因子（Adjusted R²=0.208,P=0.001）。每个隧道内,蝙蝠具有不同的冬眠栖点位置,约4/5的蝙蝠选择温暖且环境相对稳定的隧道深处（> 30 m）作为冬眠栖点,超过95%的个体选择长度> 60 m的隧道冬眠。蝙蝠具有不同的冬眠方式,绝大多数个体采用独栖方式进行冬眠（> 90%）,少数采用聚集方式。不同的冬眠栖点和冬眠方式可能有利于冬眠成本优化。此外,栖点温度与蝙蝠体温之间呈显著正相关（R²=0.98,P < 0.001）,而且蝙蝠冬眠期间的栖点温度具有种内和种间差异。研究结果为我国蝙蝠种群保护和冬眠场所管理提供科学依据。     

基于微波热声层析成像定量重建生物组织电导率的改进方法

目的 生物电磁学参数中的电导率与组织的功能性信息直接相关,精准重建生物组织电导率在医学成像技术和医学诊断领域中有着重要意义。本文改进定量微波热声层析成像（microwave-induced thermoacoustic tomography,MTAT）算法,使组织电导率的重建精度提高。方法 本文在利用有限元离散法求解热声波动方程和亥姆霍兹方程的基础之上,提出了一种基于正则化牛顿迭代法（regularized Newton iteration method,RNIM）定量重建组织电导率的改进方法。结果 通过数值模拟实验和含不同浓度NaCl溶液的仿体实验,验证了算法改进的有效性。组织仿体实验结果表明,目标在不同位置、不同大小、不同对比度情况下,相比于定量微波热声层析成像采用拟合（fitting）的方法,采用正则化牛顿法定量重建的仿体电导率相对误差明显降低,重建目标精度提高。在仿体实验中采用RNIM方法重建相同浓度的单目标在不同位置的电导率变化幅度更小,以及重建多目标电导率的相对比值与实际更接近,实验结果验证了改进方法的稳定性。结论 研究结果表明优化算法能更加准确地定量重建组织仿体的电导率,...     

Exosome-mediated miR-7-5p delivery enhances the anticancer effect of Everolimus via blocking MNK/eIF4E axis in non-small cell lung cancer

Everolimus is a kind of mammalian target of rapamycin (mTOR) inhibitors. Activated mitogen-activated protein kinase interacting kinases/eukaryotic translation initiation factor 4E (MNK/eIF4E) axis plays a crucial role in resistance to Everolimus in non-small cell lung cancer (NSCLC). The eIF4E phosphorylation increased by mTOR inhibitors is mainly mediated by MNKs. However, the mechanisms are poorly understood. Recently, extensive reprogramming of miRNA profiles has also been found after long-term mTOR inhibitor exposure. Our previous studies have confirmed that tumor suppressor miR-7-5p is decreased in A549 cells after treatment with Everolimus. Exactly, MNK1 is the target of miR-7-5p. In this study, we investigated the biological functions and potential molecular mechanisms of miR-7-5p in the NSCLC undergoing treatment with Everolimus. We confirmed that Everolimus targeted mTORC1 inducing NSCLC cells to secrete miR-7-5p-loaded exosomes in Rab27A and Rab27B-dependent manners. Loss of intracellular miR-7-5p induced phosphorylation of MNK/eIF4E axis, but a supplement of extra exosomal miR-7-5p could reverse it. Of note, both low expression of miR-7-5p and elevated MNK1 protein were associated with a poor prognosis of NSCLC. Both endogenous miR-7-5p and exo-miR-7-5p enhanced the therapeutic efficacy of Everolimus by inhibiting the proliferation, migration, and metastasis of NSCLC in vitro and in vivo. The combination of miR-7-5p with Everolimus induced apoptosis to exhibit a synergistic anticancer therapeutic efficacy through dual abrogation of MNK/eIF4E and mTOR in NSCLC. In conclusion, Everolimus decreases the intracellular miR-7-5p by releasing of miR-7-5p loaded exosomes from NSCLC cells in Rab27A and Rab27B dependent manners. Either endogenous miR-7-5p or exo-miR-7-5p combined with Everolimus can enhance the anticancer efficacy by targeting MNK/eIF4E axis and mTOR. Besides, both low levels of miR-7-5p and positive expression of MNK1 act as independent poor prognostic biomarkers for NSCLC. Therefore, restoring miR-7-5p carried by exosome may be a promising novel combined therapeutic strategy with Everolimus for NSCLC.Subject terms: Drug development, Growth factor signalling, Oncogenesis     

Pyroptosis by NLRP3/caspase-1/gasdermin-D pathway in synovial tissues of rheumatoid arthritis patients

We investigated the potential involvement of pyroptosis, a proinflammatory form of regulated cell death, in rheumatoid arthritis (RA). Synovial fluid, synovial tissues and/or serum were compared among 32 patients with RA, 46 patients with osteoarthritis (OA) and 30 healthy controls. Samples were assayed for interleukin (IL)-1β, IL-18 and lactate hydrogenase (LDH). Synovial expression of NLRP3, caspase-1 and cleaved gasdermin D (GSDMD) was assayed using immunohistochemistry and multiplex immunohistochemistry. Patients with RA showed significantly higher levels of IL-1β and IL-18 in synovial fluid than patients with OA, and significantly higher levels of both cytokines in serum than healthy controls. RA was associated with higher levels of LDH in synovial fluid than OA. Among patients with RA, levels of IL-1β, IL-18 and LDH were significantly higher in synovial fluid than in serum, and the levels in synovial fluid positively correlated with disease activity and inflammation. Synovial cells, particularly macrophages, showed upregulation of NLRP3, caspase-1 and cleaved GSDMD in RA compared to OA. Our results implicate pyroptosis in the pathogenesis of RA, perhaps as a driver of local inflammation in joints.