蛋白质纯化虚拟仿真课程的教学设计

目的 蛋白质纯化是医学与生物学实验教学课程中的一个重要内容，本文通过设计新的蛋白质纯化虚拟仿真教学内容，开发虚拟仿真教学系统，希望学生能够更有效率地掌握蛋白质纯化技术的要点，提升教学质量。方法 利用3D虚拟仿真技术，构建虚拟仿真实验室。结合线下教学经验，确定虚拟仿真教学中需要体现的教学内容、教学重点、核心仪器的特色、评分指标、考核方式、操作体验等。结果 本文基于3D虚拟仿真技术构建了蛋白质纯化虚拟仿真实验室，和传统教学相比，虚拟仿真教学可以提高教学效率，节省教学成本和场地占用；教学设计和虚拟仿真教学系统融合了教学、练习和考核模块，根据以往的教学经验优化了评分体系，保证学生更加有效、严谨地掌握技术细节；涵盖了全新的教学内容——荧光检测联用的分子排阻层析，添加了蛋白质层析的常用案例，保证了内容的新颖与实用；完全再现了现实实验室中仪器设备的搭建模式，实现虚拟学习与实际操作的无缝衔接。结论 蛋白质纯化虚拟仿真教学系统由虚及实，由点及面，把控细节，保证学生动手能力和探索能力的提高，学以致用，并且拥有传统教学模式不可比拟的优势。     

Four-dimensional imaging with virtual reality to quantitatively explore jigsaw puzzle-like morphogenesis of Arabidopsis cotyledon pavement cells

In most dicotyledonous plants, leaf pavement cells exhibit complex jigsaw puzzle-like cell morphogenesis during leaf expansion. Although detailed molecular biological information and mathematical modeling of this jigsaw puzzle-like cell morphogenesis are now available, a full understanding of this process remains elusive. Recent reports have highlighted the importance of three-dimensional (3D) structures (i.e., anticlinal and periclinal cell wall) in understanding the mechanical models that describe this morphogenetic process. We believe that it is important to acquire 3D shapes of pavement cells over time, i.e., acquire and analyze four-dimensional (4D) information when studying the relationship between mechanical modeling and simulations and the actual cell shape. In this report, we have developed a framework to capture and analyze 4D morphological information of Arabidopsis thaliana cotyledon pavement cells by using both direct water immersion observations and computational image analyses, including segmentation, surface modeling, virtual reality and morphometry. The 4D cell models allowed us to perform time-lapse 3D morphometrical analysis, providing detailed quantitative information about changes in cell growth rate and shape, with cellular complexity observed to increase during cell growth. The framework should enable analysis of various phenotypes (e.g., mutants) in greater detail, especially in the 3D deformation of the cotyledon surface, and evaluation of theoretical models that describe pavement cell morphogenesis using computational simulations. Additionally, our accurate and high-throughput acquisition of growing cell structures should be suitable for use in generating in silico model cell structures.     

探索以“霍乱弧菌检测虚拟仿真实验”为载体的混合式实验教学模式

虚拟仿真实验是一种现代信息化和智慧教学的重要方法,对高等医学院校教学质量的发展起到重要的推进作用。我们自主开发建设的“霍乱弧菌检测与防控虚拟仿真实验”,既弥补了因生物安全问题不能开展的实验教学,也解决了微生物学检验实验教学中存在的操作标准化问题。采用“三步进阶”混合教学模式,实现以“学生为中心”的师生互动模式,创建“设计性实验报告”,与育人元素有机结合,培育医学生的职业使命感。细化考核标准,实现过程性评价。探索课前启发铺垫、课中内化升华、课后巩固拓展混合式实验教学模式,有效提高学生的实验技能,实现知行合一、素能共育的教学目标。     

Outlier detection methods are still effective even using virtual species created with the probabilistic approach

Liu et al. (Journal of Biogeography, 2018, 45 :164–176) presented an approach to detect outliers in species distribution data by developing virtual species created using the threshold approach. Meynard et al. (Journal of biogeography, 2019, 46 :2141–2144) raised concerns about this approach stating that ‘using a probabilistic approach … may significantly change results’. Here we provide a new series of simulations using the two approaches and demonstrate that the outlier detection approach based on pseudo species distribution models was still effective when using the probabilistic approach, although the detection rate was lower than when using the threshold approach.     

Minimizing false positives in kinase virtual screens

In spite of recent improvements in docking and scoring methods, high false-positive rates remain a common issue in structure-based virtual screening. In this study, the distinctive features of false positives in kinase virtual screens were investigated. A series of retrospective virtual screens on kinase targets was performed on specifically designed test sets, each combining true ligands and experimentally confirmed inactive compounds. A systematic analysis of the docking poses generated for the top-ranking compounds highlighted key aspects differentiating true hits from false positives. The most recurring feature in the poses of false positives was the absence of certain key interactions known to be required for kinase binding. A systematic analysis of 444 crystal structures of ligand-bound kinases showed that at least two hydrogen bonds between the ligand and the backbone protein atoms in the kinase hinge region are present in 90% of the complexes, with very little variability across targets. Closer inspection showed that when the two hydrogen bonds are present, one of three preferred hinge-binding motifs is involved in 96.5% of the cases. Less than 10% of the false positives satisfied these two criteria in the minimized docking poses generated by our standard protocol. Ligand conformational artifacts were also shown to contribute to the occurrence of false positives in a number of cases. Application of this knowledge in the form of docking constraints and post-processing filters provided consistent improvements in virtual screening performance on all systems. The false-positive rates were significantly reduced and the enrichment factors increased by an average of twofold. On the basis of these results, a generalized two-step protocol for virtual screening on kinase targets is suggested.     

新工科背景下生物反应工程课程的多元化教学模式改革与探索

生物反应工程作为一门理论性与应用性都很强的专业课程,在生物工程等相关专业的课程设置中处于桥梁和纽带地位,对新型应用型工科人才的培养发挥着重要的作用.但由于该课程中公式等抽象理论知识过多,导致学生学习效率十分低下.因此,为了适应新工科教育背景下对创新型人才培养的需求,提高学生的学习兴趣和积极性,并培养学生的自主学习等创新...     

Inhibitor binding studies of Mycobacterium tuberculosis MraY (Rv2156c): Insights from molecular modeling,docking, and simulation studies

Abstract

Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis (M.tb) or tubercule bacillus, and H37Rv is the most studied clinical strain. The recent development of resistance to existing drugs is a global health-care challenge to control and cure TB. Hence, there is a critical need to discover new drug targets in M.tb. The members of peptidoglycan biosynthesis pathway are attractive target proteins for antibacterial drug development. We have performed in silico analysis of M.tb MraY (Rv2156c) integral membrane protein and constructed the three-dimensional (3D) structure model of M.tb MraY based on homology modeling method. The validated model was complexed with antibiotic muraymycin D2 (MD2) and was used to generate structure-based pharmacophore model (e-pharmacophore). High-throughput virtual screening (HTVS) of Asinex database and molecular docking of hits was performed to identify the potential inhibitors based on their mode of interactions with the key residues involved in M.tb MraY–MD2 binding. The validation of these molecules was performed using molecular dynamics (MD) simulations for two best identified hit molecules complexed with M.tb MraY in the lipid bilayer, dipalmitoylphosphatidyl-choline (DPPC) membrane. The results indicated the stability of the complexes formed and retained non-bonding interactions similar to MD2. These findings may help in the design of new inhibitors to M.tb MraY involved in peptidoglycan biosynthesis.     

Design,synthesis and biological evaluation of novel 1H-1,2,4-triazole,benzothiazole and indazole-based derivatives as potent FGFR1 inhibitors viafragment-based virtual screening

Abstract

Fibroblast growth-factor receptor (FGFR) is a potential target for cancer therapy. We designed three novel series of FGFR1 inhibitors bearing indazole, benzothiazole, and 1H-1,2,4-triazole scaffold via fragment-based virtual screening. All the newly synthesised compounds were evaluated in vitro for their inhibitory activities against FGFR1. Compound 9d bearing an indazole scaffold was first identified as a hit compound, with excellent kinase inhibitory activity (IC₅₀ = 15.0?nM) and modest anti-proliferative activity (IC₅₀ = 785.8?nM). Through two rounds of optimisation, the indazole derivative 9?u stood out as the most potent FGFR1 inhibitors with the best enzyme inhibitory activity (IC₅₀ = 3.3?nM) and cellular activity (IC₅₀ = 468.2?nM). Moreover, 9?u also exhibited good kinase selectivity. In addition, molecular docking study was performed to investigate the binding mode between target compounds and FGFR1.