Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping

Molecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.     

Evaluation of oxygen adaptation and identification of functional bacteria composition for anammox consortium in non-woven biological rotating contactor

In this study, the anammox consortium was found to adapt to the wastewater containing dissolved oxygen (DO), as the DO was gradually increased. Batch tests indicated the maximum aerobic ammonium oxidizing activity of the consortium was 1.38mmolNH(4)(+)-N(gVSS)(-1)day(-1), which played key roles in the oxygen consumption process; the maximum anaerobic ammonium oxidizing activity was slightly decreased after long-term oxygen exposure, but only from 21.23mmolNH(4)(+)-N(gVSS)(-1)day(-1) to 20.23mmolNH(4)(+)-N(gVSS)(-1)day(-1). Microbiological community analysis identified two strains similar to Nitrosomonas eutropha were responsible for oxygen consumption, which were able to exist in the autotrophic anaerobic condition for long periods and protect anammox bacteria Planctomycetales from the influence of oxygen. Microbiological composition analysis showed Nitrosomonas and Planctomycetales approximately accounted for 10% and 70% of the bacteria, respectively. The possibility of cultivation anammox consortium in presence of DO will lead to substantial savings of energy and resource in the industrial application.     

微核技术研究进展

微核试验作为检测染色体损伤最常用而有效的细胞遗传学检测方法之一,经济、简便、快速,在敏感性、特异性和准确性方面,与经典的染色体畸变分析方法基本相当。主要综述国内外微核检测技术的最新研究进展,尤其是微核的自动化检测技术。其中流式细胞仪自动化检测和激光扫描细胞仪自动化检测,以及微核试验高内涵筛选方法由于其特有的优势,应用和发展前景广阔。     

滞育和非滞育棉铃虫前胸腺的形态解剖学比较研究

该文用解剖镜和电子显微镜对滞育和非滞育棉铃虫Helicoverpa armigera前胸腺的形态解剖结构进行了比较研究。结果发现滞育棉铃虫的前胸腺细胞及其细胞间隙相对较小,不易着色,细胞核规则,较小,细胞质中几乎见不到光滑内质网和粗面内质网,线粒体极少,这些观察到的现象充分说明滞育棉铃虫的前胸腺活性较低。     

微小RNA与肺癌耐药

肺癌细胞对化疗药物产生耐药性是目前肺癌化疗过程中遇到的主要问题。微小RNA（miRNA）是一类内源性非编码短链小分子RNA,它能调节细胞生长、凋亡和信号转导。miRNA的多态性与药物代谢和耐药形成密切相关,异常表达的miRNA对预测肺癌化疗药物敏感性有重要作用。调节特异miRNA的表达,将为克服肺癌耐药和选择个体化治疗开辟新的途径。     

农药对土壤微生物的生态效应

大量有关农药对土壤微生物生态效应的研究表明,虽然有些农药对土壤微生物及其活性会产生抑制或促进作用,但这种作用一般是短暂的;按推荐浓度正常使用农药通常不会影响土壤微生物的各种生化过程和活性,对土壤的物质循环和土壤肥力也没有不利影响;但大多数土壤薰蒸剂和杀真菌剂能改变土壤微生物平衡,它们对土壤微生物的作用强于杀虫剂和除草剂;长期使用农药不致使土壤微生物数量和活性发生明显变化,这应部分归功于土壤微生物对农药的降解或转化．     

禽多杀性巴氏杆菌C48-3株ompH基因敲除突变株的构建及其生物学功能

[目的]探讨ompH基因在禽多杀性巴氏杆菌致病过程中的作用.[方法]利用同源重组原理构建中间为四环素抗性基因,两侧为ompH基因上下游同源序列同源的敲除载体pWSK29△ompH,将敲除载体电击转入C48-3株感受态细胞中,通过四环素抗性和菌落PCR筛选ompH基因的敲除突变株,并通过组合PCR、逆转录PCR和DNA测序对突变株进行验证.用生物学功能实验比较野生株、互补株和突变株在生长速率、荚膜结构、粘着能力和致病性等方面的差异.[结果]组合PCR、逆转录PCR和DNA测序结果证实ompH基因的敲除突变株C48-3△ompH构建成功,电镜观察结果证实ompH基因的缺陷影响细菌的荚膜合成能力,粘附实验结果显示与野生株C48-3和互补株C48-3C相比突变株C48-3△ompH对CEF细胞的粘附能力显著降低(P＜0.01),而小鼠毒力实验结果表明突变株C48-3△ompH的致病性相对减弱.[结论]本实验构建的突变株C48-3△ompH,为进一步研究多杀性巴氏杆菌的致病机理奠定基础.     

皖南尖吻蝮蛇毒出血毒素Ⅳ的纯化与初步鉴定

从皖南尖吻蝮蛇（Ａｇｋｉｓｔｒｏｄｏｎａｃｕｔｕｓ）毒液中经ＤＥＡＥ－Ｓｅｐｈａｒｏｓｅ和ＳｅｐｈａｃｒｙｌＳ－２００两步凝胶柱层析首次纯化出一种中分子量出血毒素（简称ＡａＨⅣ）．经ＳＤＳ－ＰＡＧＥ和等电聚焦凝胶电泳测定其分子量为４４ｋＤ,等电点为ｐＨ５．０．从５００ｍｇ粗毒中可获得２０ｍｇＡａＨⅣ纯品．ＡａＨⅣ有较强的出血活性,最小出血剂量（ＭＨＤ）为０．４μｇ．     

甜菜碱对NaCl胁迫下小麦细胞保护酶活性的影响

本文以小麦为材料,研究甜菜碱对ＮａＣｌ胁迫下小麦幼苗细胞保护酶系统的影响。结果表明,外源甜菜碱能够提高ＮａＣｌ胁迫下小麦幼苗超氧化物歧化酶、过氧化物酶等细胞保护酶的活性,抑制过氧化作用产物丙二醛的积累,降低叶片质膜透性和盐害对细胞膜的伤害。所有这些变化都有利于提高ＮａＣｌ胁迫下小麦幼苗细胞膜的稳定性、完整性和对ＮａＣｌ胁迫的适应性