严重急性呼吸综合征冠状病毒2膜蛋白对宿主细胞pre-mRNA 3"UTR加工的影响

目的 研究严重急性呼吸综合征冠状病毒2（SARS-CoV-2）膜蛋白对宿主细胞mRNA前体（pre-mRNA）3"非翻译区（UTR）加工的影响。方法 本研究以人肺上皮细胞系A549为模型，利用瞬时转染在细胞内过表达SARS-CoV-2膜蛋白；利用RNA-Seq测序技术及生物信息学分析方法，系统性描绘宿主细胞选择性多聚腺苷酸化（alternative polyadenylation，APA）事件；Metascape数据库对发生显著APA变化的基因进行功能富集分析；RT-qPCR验证靶基因3"UTR长度变化；蛋白质免疫印迹（Western blot）检测目的蛋白表达水平。结果 SARS-CoV-2膜蛋白外源表达后宿主细胞内共813个基因发生显著APA变化。GO和KEGG分析显示，差异APA基因广泛参与有丝分裂细胞周期、调节细胞应激等生物过程，涉及病毒感染和蛋白质加工等。从中进一步筛选出AKT1基因，在IGV软件中显示3"UTR延长；RT-qPCR验证AKT1基因的3"UTR长度变化趋势；Western blot结果显示AKT1蛋白磷酸化水平增加。结论 SARS-CoV-2膜蛋白潜在影响宿主pre-mRNA的3"UTR加工，其中参与多种病毒性生物过程的AKT1基因 3"UTR延长，且其编码的蛋白质功能在细胞内被激活。     

Cryo-EM reveals a previously unrecognized structural protein of a dsRNA virus implicated in its extracellular transmission

Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like viruses, with features similar to those of the Totiviridae family. Most reported members of this family infect fungi or protozoans and lack an extracellular life cycle stage. Here, we identified a new strain of OmRV and determined high-resolution structures for this virus using single-particle cryo-electron microscopy. The structures feature an unexpected protrusion at the five-fold vertex of the capsid. Disassociation of the protrusion could result in several conformational changes in the major capsid. All these structures, together with some biological results, suggest the protrusions’ associations with the extracellular transmission of OmRV.     

Synthesis,Biological Evaluation,and Docking Study of Ring-Opening Amide Analogs of Matrine as Antitumor Agents

In this article, we designed and synthesized two series of matrine analogs with ring-opening in the lactam portion of the molecule. Our in vitro cytotoxicity study showed that analog N-(3-bromophenyl)-4-[(1R,3aS,10aR,10bS)-decahydro-1H,4H-pyrido[3,2,1-ij][1,6]naphthyridin-1-yl]butanamide ( B11 ) with a meta-bromide on the phenyl ring displayed the best antiproliferative activity. Moreover, B11 induced cell cycle arrest in G1 phase and cell apoptosis in a dose-dependent manner in A549 cells. Molecular modeling revealed that B11 achieved a higher docking score compared to its precursor tert-butyl (1R,3aS,10aR,10bS)-1-[4-(3-bromoanilino)-4-oxobutyl]octahydro-1H,4H-pyrido[3,2,1-ij][1,6]naphthyridine-2(3H)-carboxylate ( A11 , an analog of B11 with a Boc group) and parent compound matrine, possibly because B11 formed a hydrogen bond with SER91 and a halogen bond with GLN320 on the binding site of annexin A2. Overall, we discovered the potential anticancer lead compound B11 , which can be used for further study both in vitro and in vivo.     

U-Shape Suppressive Effect of Phenol Red on the Epileptiform Burst Activity via Activation of Estrogen Receptors in Primary Hippocampal Culture

Phenol red is widely used in cell culture as a pH indicator. Recently, it also has been reported to have estrogen-like bioactivity and be capable of promoting cell proliferation in different cell lines. However, the effect of phenol red on primary neuronal culture has never been investigated. By using patch clamp technique, we demonstrated that hippocampal pyramidal neurons cultured in neurobasal medium containing no phenol red had large depolarization-associated epileptiform bursting activities, which were rarely seen in neurons cultured in phenol red-containing medium. Further experiment data indicate that the suppressive effect of the phenol red on the abnormal epileptiform burst neuronal activities was U-shape dose related, with the most effective concentration at 28 µM. In addition, this concentration related inhibitory effect of phenol red on the epileptiform neuronal discharges was mimicked by 17-β-estradiol, an estrogen receptor agonist, and inhibited by ICI-182,780, an estrogen receptor antagonist. Our results suggest that estrogen receptor activation by phenol red in the culture medium prevents formation of abnormal, epileptiform burst activity. These studies highlight the importance of phenol red as estrogen receptor stimulator and cautions of careful use of phenol red in cell culture media.     

Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.     

Physical Constraint Finite Element Model for Medical Image Registration

Due to being derived from linear assumption, most elastic body based non-rigid image registration algorithms are facing challenges for soft tissues with complex nonlinear behavior and with large deformations. To take into account the geometric nonlinearity of soft tissues, we propose a registration algorithm on the basis of Newtonian differential equation. The material behavior of soft tissues is modeled as St. Venant-Kirchhoff elasticity, and the nonlinearity of the continuum represents the quadratic term of the deformation gradient under the Green- St.Venant strain. In our algorithm, the elastic force is formulated as the derivative of the deformation energy with respect to the nodal displacement vectors of the finite element; the external force is determined by the registration similarity gradient flow which drives the floating image deforming to the equilibrium condition. We compared our approach to three other models: 1) the conventional linear elastic finite element model (FEM); 2) the dynamic elastic FEM; 3) the robust block matching (RBM) method. The registration accuracy was measured using three similarities: MSD (Mean Square Difference), NC (Normalized Correlation) and NMI (Normalized Mutual Information), and was also measured using the mean and max distance between the ground seeds and corresponding ones after registration. We validated our method on 60 image pairs including 30 medical image pairs with artificial deformation and 30 clinical image pairs for both the chest chemotherapy treatment in different periods and brain MRI normalization. Our method achieved a distance error of 0.320±0.138 mm in x direction and 0.326±0.111 mm in y direction, MSD of 41.96±13.74, NC of 0.9958±0.0019, NMI of 1.2962±0.0114 for images with large artificial deformations; and average NC of 0.9622±0.008 and NMI of 1.2764±0.0089 for the real clinical cases. Student’s t-test demonstrated that our model statistically outperformed the other methods in comparison (p-values <0.05).     

基于长时间序列landsat数据的科尔沁沙地土地利用演变分析

以科尔沁沙地沙丘-草甸过渡带区域主要土地覆被类型为研究对象，以1987-2017年多时相Landsat TM/OLI遥感影像解译分类为基础，参考生态学植被演替研究方法，系统分析研究区30年来的土地利用/覆被动态演变规律，研究结果表明：（1）决策树法在复杂下垫面不同覆被类型的同步识别效果较好，所有影像分类精度均达到88%以上，分类效果较好，其中2017年分类精度最高为95.24%，达到了分类研究的要求；（2）研究区存在着"半灌丛-草甸地-灌丛"的植被结构特征，且整体表现为"南进北退"的变化趋势。结合土地利用动态度分析结果表明人类活动干涉下，研究区整体上遵循了半干旱区植被条件改善的一般规律，侧面反映该研究区域生态环境的持续不稳定性和脆弱性；（3）研究区覆被类型发生变化的总面积达到2623.59 hm²，总变化强度为63.76%。其中正向演替的比例为52.61%，以半灌丛面积的持续减小与沙地草甸面积的持续扩张为主要变化特征。但同时，半灌丛转为沙地的面积为184.95 hm²，表明以放牧为主的研究区同时发生着局部的逆行演变；（4）质心迁移结果反映了1987-2017年间，除人为影响较大的林地、草地以及耕地向北迁移外，其他植被类型的质心都有很明显的南迁，主要植被类型重心迁移距离依次由大到小为耕地 > 半灌丛 > 灌丛 > 沙地草甸 > 湿地草甸 > 林地。研究通过记录科尔沁沙地连续扩展的时空模式，展示了遥感-生态和时间序列影像在30 m分辨率下跟踪土地利用/覆被变化的潜力，为提高干旱半干旱区土地利用情况的动态监测效率，开展土地利用/覆被动态演变研究提供参考。     

Natural Conception May Be an Acceptable Option in HIV-Serodiscordant Couples in Resource Limited Settings

Many HIV serodiscordant couples have a strong desire to have their own biological children. Natural conception may be the only choice in some resource limited settings but data about natural conception is limited. Here, we reported our findings of natural conception in HIV serodiscordant couples. Between January 2008 and June 2014, we retrospectively collected data on 91 HIV serodiscordant couples presenting to Beijing Youan Hospital with childbearing desires. HIV counseling, effective ART on HIV infected partners, pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) in negative female partners and timed intercourse were used to maximally reduce the risk of HIV transmission. Of the 91 HIV serodiscordant couples, 43 were positive in male partners and 48 were positive in female partners. There were 196 unprotected vaginal intercourses, 100 natural conception and 97 newborns. There were no cases of HIV seroconversion in uninfected sexual partners. Natural conception may be an acceptable option in HIV-serodiscordant couples in resource limited settings if HIV-positive individuals have undetectable viremia on HAART, combined with HIV counseling, PrEP, PEP and timed intercourse.