Engineering the Pattern of Protein Glycosylation Modulates the Thermostability of a GH11 Xylanase

Protein glycosylation is a common post-translational modification, the effect of which on protein conformational and stability is incompletely understood. Here we have investigated the effects of glycosylation on the thermostability of Bacillus subtilis xylanase A (XynA) expressed in Pichia pastoris. Intact mass analysis of the heterologous wild-type XynA revealed two, three, or four Hex_8–16GlcNAc₂ modifications involving asparagine residues at positions 20, 25, 141, and 181. Molecular dynamics (MD) simulations of the XynA modified with various combinations of branched Hex₉GlcNAc₂ at these positions indicated a significant contribution from protein-glycan interactions to the overall energy of the glycoproteins. The effect of glycan content and glycosylation position on protein stability was evaluated by combinatorial mutagenesis of all six potential N-glycosylation sites. The majority of glycosylated enzymes expressed in P. pastoris presented increased thermostability in comparison with their unglycosylated counterparts expressed in Escherichia coli. Steric effects of multiple glycosylation events were apparent, and glycosylation position rather than the number of glycosylation events determined increases in thermostability. The MD simulations also indicated that clustered glycan chains tended to favor less stabilizing glycan-glycan interactions, whereas more dispersed glycosylation patterns favored stabilizing protein-glycan interactions.     

Rule-based modeling and simulations of the inner kinetochore structure

Background

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins.

Results

Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts.

Conclusions

Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores.     

多措并举 激发兴趣 提高教学效果

针对高职招生文理兼收和学生学习基础实际,在细胞生物学与医学遗传学课程教学中,通过案例引导丰富感性认识,创设问题情境培养主动学习能力,运用网络优势培养获取信息和解读问题能力,设计趣味性开放实验提高实践能力,促进知识理解和技能提高,提高教学实效.     

一类人禽间传染病模型的动力学分析

讨论了一类人禽传染病模型,其中禽类被病毒感染后人们采取措施治疗病禽．治疗有助于禽类的存活,但人们可能通过接触病禽而被感染．禽间的疾病传播服从饱和接触率函数,人与禽的接触服从线性接触率．完成了稳定性和持久性研究,且进行了数值模拟以评估治疗的效果和风险．     

PBL联合CBL教学方法在胃肠外科临床见习教学中的应用

目的:探讨PBL联合CBL教学模式在医学生胃肠外科见习教学中的应用效果.方法:选取50名2008级胃肠外科见习医学生作为研究对象,将其随机分成两组:实验组采用PBL联合CBL教学模式,对照组则仅采用传统LBL教学模式.通过出科考核及问卷调查两种方式评价胃肠外科见习教学效果.结果:显示PBL+ CBL组的考试成绩要明显优于LBL组,差异有统计学意义(P＜ 0.05),并且见习后的问卷调查结果提示学生对PBL+ CBL的教学模式满意度较高.结论:我们的研究结果表明PBL+ CBL双轨教学模式受到学生欢迎,在提高学生理论知识水平方面比LBL模式更为有效.     

青年教师对医学临床课程教学能力现状调查及应对策略研究

如何提高我国临床课程青年教师团队的素质与教学能力,是近年来伴随国内医学教育发展扩大而日益突出的问题。作为当前医学临床课程的教学主力,青年教师的教学能力会对医学临床课程教学效果产生重大影响。但绝大部分临床课程青年教师都毕业于医学院校,未曾接受专业的师范类培训,导致尽管自身临床知识丰富,但教学水平明显受限的情况发生。本研究采取对我院各科室青年临床教师进行问卷调查的方法,深入分析青年教师的临床教学能力现状与问题,并提出改进方案,以使他们能够更快完成青年临床医师与青年临床教师之间的角色变换,提升自身教学能力,进而提高我院临床课程的教学质量。     

LBL结合PBL在物理诊断教学过程中的初步探索

目的:比较传统教学模式和问题教学法及二者结合教学法的不同优劣势,找出物理诊断学最佳教学方法。传统教学模式采用授课为主的教学法(lecture based learning,LBL),单单强调了教师的重要性,而忽视学生的主观能动性,不利于调动和培养学生自学和灵活运用所学知识的能力。问题教学法(Problem-based learning,PBL),其强调学生自身的主观能动性,弱化了教师在教学中的主体地位,学生有偏离教学主线的风险。因而如果将LBL与PBL有机结合在一起,将可能有利于提高学生的学习效率和学习效果。方法:选取97名全科医学本科学员,在物理诊断课程教学过程中,采用完全随机的方法分为2组,采用LBL教学方法组48人,采用LBL结合PBL教学方法组49人,通过分别对理论、实践分层打分,确定优秀、合格、不合格的比率,采用Mann-Whitney U检验最终评定2组教学方法的授课效果。结果:在理论考试中,2组学员在优秀、合格、不合格的分层评定上均无明显差异(P0.05),而在实践考核中,LBL+PBL组学员成绩在优秀这一分层评定中,优于LBL组,差异具有统计学意义(P0.05)。结论:LBL和PBL教学方法结合应用于物理诊断教学中,符合物理诊断教学的特点,更容易被学生接受,对于知识的识记和应用更有好处,从而更利于培养高素质医学人才,值得在物理诊断教学中进一步推广。     

由任务驱动的团队自主合作学习教学模式在微生物学课程中的探索和实践

为了提高学生的自主学习及合作学习能力,在微生物学教学中,采取由任务驱动的团队自主合作学习教学模式。该模式以任务为主线,把教学内容和能力培养目标隐含在任务之中;以教师为主导,引导学生主体利用学习资源,通过个人自主学习及团队合作学习来建构知识和提升能力。三轮教学实践表明,由任务驱动的团队自主合作学习教学模式,激发了学生的学习积极性,培养了学生的综合能力和创新意识,也促进了教师教学水平的提高。     

Genetic mappings in artificial genomes

This paper concerns processing of genomes of artificial (computer-simulated) organisms. Of special interest is the process of translation of genotypes into phenotypes, and utilizing the mapping information obtained during such translation. If there exists more than one genetic encoding in a single artificial life model, then the translation may also occur between different encodings. The obtained mapping information allows to present genes-phenes relationships visually and interactively to a person, in order to increase understanding of the genotype-tophenotype translation process and genetic encoding properties. As the mapping associates parts of the source sequence with the translated destination, it may be also used to trace genes, phenes, and their relationships during simulated evolution. A mappings composition procedure is formally described, and a simple method of visual mapping presentation is established. Finally, advanced visualizations of gene-phene relationships are demonstrated as practical examples of introduced techniques. These visualizations concern genotypes expressed in various encodings, including an encoding which exhibits polygenic and pleiotropic properties.