A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area

Background

Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein structures, in this study, our aim was to design predictors for estimating relative solvent accessibility (RSA) of amino acid residues to discover protein folding characteristics from sequences.

Methods

The proposed 20 real-value RSA predictors were designed on the basis of the support vector regression method with a set of informative physicochemical properties (PCPs) obtained by means of an optimal feature selection algorithm. Then, molecular dynamics simulations were performed for validating the knowledge discovered by analysis of the selected PCPs.

Results

The RSA predictors had the mean absolute error of 14.11% and a correlation coefficient of 0.69, better than the existing predictors. The hydrophilic-residue predictors preferred PCPs of buried amino acid residues to PCPs of exposed ones as prediction features. A hydrophobic spine composed of exposed hydrophobic residues of an α-helix was discovered by analyzing the PCPs of RSA predictors corresponding to hydrophobic residues. For example, the results of a molecular dynamics simulation of wild-type sequences and their mutants showed that proteins 1MOF and 2WRP_H16I (Protein Data Bank IDs), which have a perfectly hydrophobic spine, have more stable structures than 1MOF_I54D and 2WRP do (which do not have a perfectly hydrophobic spine).

Conclusions

We identified informative PCPs to design high-performance RSA predictors and to analyze these PCPs for identification of novel protein folding characteristics. A hydrophobic spine in a protein can help to stabilize exposed α-helices.

     

Tissue tropism of swine influenza viruses and reassortants in ex vivo cultures of the human respiratory tract and conjunctiva

The 2009 pandemic influenza H1N1 (H1N1pdm) virus was generated by reassortment of swine influenza viruses of different lineages. This was the first influenza pandemic to emerge in over 4 decades and the first to occur after the realization that influenza pandemics arise from influenza viruses of animals. In order to understand the biological determinants of pandemic emergence, it is relevant to compare the tropism of different lineages of swine influenza viruses and reassortants derived from them with that of 2009 pandemic H1N1 (H1N1pdm) and seasonal influenza H1N1 viruses in ex vivo cultures of the human nasopharynx, bronchus, alveoli, and conjunctiva. We hypothesized that virus which can transmit efficiently between humans replicated well in the human upper airways. As previously reported, H1N1pdm and seasonal H1N1 viruses replicated efficiently in the nasopharyngeal, bronchial, and alveolar epithelium. In contrast, representative viruses from the classical swine (CS) (H1N1) lineage could not infect human respiratory epithelium; Eurasian avian-like swine (EA) (H1N1) viruses only infected alveolar epithelium and North American triple-reassortant (TRIG) viruses only infected the bronchial epithelium albeit inefficiently. Interestingly, a naturally occurring triple-reassortant swine virus, A/SW/HK/915/04 (H1N2), with a matrix gene segment of EA swine derivation (i.e., differing from H1N1pdm only in lacking a neuraminidase [NA] gene of EA derivation) readily infected and replicated in human nasopharyngeal and bronchial epithelia but not in the lung. A recombinant sw915 with the NA from H1N1pdm retained its tropism for the bronchus and acquired additional replication competence for alveolar epithelium. In contrast to H1N1pdm, none of the swine viruses tested nor seasonal H1N1 had tropism in human conjunctiva. Recombinant viruses generated by swapping the surface proteins (hemagglutinin and NA) of H1N1pdm and seasonal H1N1 virus demonstrated that these two gene segments together are key determinants of conjunctival tropism. Overall, these findings suggest that ex vivo cultures of the human respiratory tract provide a useful biological model for assessing the human health risk of swine influenza viruses.     

超级干扰素抑制A549增殖诱导其衰老

该研究利用MTT和结晶紫的方法证明sIFNα对肺癌细胞A549增殖有很强的抑制作用,而同样剂量的普通干扰素IFNα2b抑制作用要小很多。与对照组相比,sIFNα处理后,细胞形态发生改变,细胞体积变大,形态呈扁平状;Hoechst33258染色发现,细胞核形态无变化并且未检测到凋亡;SA-β-gal染色发现大多数细胞呈现阳性,同时,衰老相关蛋白p53和p21表达量明显上调。而IFNα2b处理组细胞形态基本没有变化,SA-β-gal染色也只有少部分的细胞呈现弱阳性。由此说明,sIFNα比IFNα2b能更好地抑制癌细胞增殖,其机制可能为诱导癌细胞发生衰老。     

3个X-STR基因座荧光标记复合扩增

为研究DXS6803、DXS981和DXS68093个基因座多态性及其在法医学中的应用,建立X染色体基因座（DXS6803、DXS981和DXS6809）的荧光复合扩增体系。用荧光标记引物PCR技术复合扩增3个基因座,并用ABI PRISM 3100毛细管电泳及其软件进行基因分型。结果在中国汉族340名无关男性个体及195名无关女性个体中,DXS6803、DXS981和DXS6809三个基因座分别发现了13、12、11个等位基因,男性个体共检出183种单倍型,单倍型多样性为0．9926。结果表明这3个基因座有较高的多态性信息,在个体识别和亲权鉴定（特别是在缺失双亲的特殊检案）中有重要的应用价值。     

管花秦艽的传粉生态学研究——兼与同域分布近缘种的比较

在青藏高原东北部连续两年观察了晚秋开花植物管花秦艽Gentiana siphonantha的传粉生态学特征,并在此基础上进一步比较分析了与该物种同域分布且亲缘关系较近、但开花较早的麻花艽G straminea之间的传粉生态学特征.管花秦艽的花发育过程表现出雌雄异熟和雌雄异位的特点,不存在花内的自花传粉,套袋隔离的花不结实也支持这一结论;株内自交的高结实率表明该物种是自交亲和的.盛花期每植株平均有15朵开放的花,雄性和雌性阶段的花比例为1.2:1;自然条件下产生种子必须依赖传粉媒介;苏氏熊蜂是最有效的传粉昆虫,且访花过程中埘雄性和雌性阶段花不具明显的偏向性;株内连续访花的频率高达87.8%,从而导致同株异花传粉自交的广泛存在.与同域分布的麻花艽相比,管花秦艽的单花花期、雄性和雌性期持续时间缩短.但盛花期开花数量明显增加.令人感兴趣的是尽管两个近缘种的花形态特征存在显著差异,但都是由同一种熊蜂传粉.这一特点与过去认为花颜色和花管长度是物种分化过程中与不同传粉昆虫协同进化导致牛殖隔离的假说不相符合.管花秦艽单花的访花频率和同株异花连续访花的比例都明显高于麻花艽.两个物种不同花序设计导致访花昆虫行为的改变可能是造成这一差异的主要原因.两个物种具有不同的开花时间,但仍然存在一定的花期重叠,表现出不完全的传粉生殖隔离状态.     

云南香格里拉葡萄酒产区酿酒相关酵母菌的生物多样性

【背景】云南香格里拉高原葡萄酒产区位于云南三江并流世界自然遗产保护区内,微生物资源丰富,其中与葡萄酒酿造相关的野生酵母种类也非常多样。【目的】研究香格里拉葡萄酒产区酿酒相关酵母菌的种类多样性和酿酒酵母的遗传多样性。【方法】从香格里拉金沙江和澜沧江两岸选取5个葡萄园进行成熟葡萄样品的采集,分别对葡萄果皮和自然发酵过程中的酵母菌进行分离,运用WL营养琼脂鉴定培养基(Wallerstein laboratory nutrient agar)和26S rDNA D1/D2区序列分析法对酵母的种类进行鉴定,用SSR分子标记的方法研究酿酒酵母的遗传多样性。【结果】从香格里拉葡萄酒产区成熟浆果上共分离到230株野生酵母,鉴定为13属18种,其中有10种酵母为香格里拉地区首次发现。用SSR分子标记的方法对香格里拉分离到的47株酿酒酵母进行遗传多样性分析,47株酿酒酵母被分为24种基因型,11个微卫星位点共检测到70个等位基因,平均多态信息含量(PIC)为0.640,平均观测杂合度(Ho)为0.166,平均期望杂合度(He)为0.693。【结论】香格里拉葡萄酒产区酵母菌资源丰富,表现出较高的物种多样性和中等程度的酿酒酵母遗传多样性。研究该产区酵母菌的多样性,为香格里拉酵母资源多样性的保护和利用奠定基础。     

浑善达克沙地无芒雀麦(Bromus inermis)空间分布格局

通过西北-东南和东北-西南方向两条宽5m×长3km的样带和一块4m×4m的样方调查,研究了浑善达克沙地无芒雀麦、植被、土壤水分及土壤盐分的空间变异特点及其相互关系。结果表明,样带内植被盖度、无芒雀麦盖度、土壤水分和土壤盐分的空间变化格局相似,然而,在不同的空间方向上,它们具有不同的空间变化;样方内无芒雀麦地上部生物量、分株数和土壤盐分具有相似的空间变化格局,但却不同于植被地上部总生物量和土壤水分的空间变化格局。相关分析表明,样带内植被盖度、无芒雀麦盖度与土壤水分和土壤盐分之间均具有显著的正相关关系。土壤水分和土壤盐分也具有显著的正相关。样方内无芒雀麦地上部生物量、分株数及植被地上部总生物量与土壤水分均具有显著的正相关关系,但与土壤盐分没有显著的相关关系。无芒雀麦地上部生物量、分株数和植被地上部总生物量三者之间,以及土壤水分和土壤盐分之间也均具有显著的正相关关系。研究结果表明了植被与土壤之间的相互关系依赖于空间尺度。     

针叶小爪螨板栗和杉木种群间的遗传分化和杂交试验

为明确针叶小爪螨Oligonychus ununguis（Jacobi）山东板栗种群和浙江杉木种群的遗传分化程度,本研究对其基因序列（线粒体COⅠ和核糖体ITS2）进行了比较,并通过杂交试验测定了两者间的杂交亲和性.采用PCR产物直接测序法获得410 bp的COⅠ片段及469 bp（板栗种群）和513 bp（杉木种群）的完整ITS2序列,COⅠ及ITS2序列在两种群间的差异分别为10.5%~10.8%和15.2%~15.7%.杂交试验表明两种群间存在完全的生殖隔离.根据两者间的序列差异和杂交结果,初步认为山东板栗和浙江杉木上的小爪螨可能是两个不同的种     

PATCHY CONTRAST OF HABITAT AFFECTS INTRACLONAL DIVISION OF LABOR OF POTENTILLA ANSERINA

 相互连接的克隆植物分株分别处于资源互补性的不同斑块时, 将可能发生形态结构的特化, 以更有效地吸收利用所处斑块中丰富的资源, 形成分株的功能分化, 即克隆内分工。生境的斑块对比度, 作为资源或环境异质性的主要素, 在一定程度上决定克隆内分工的发生状况。该文以鹅绒委陵菜(Potentilla anserina)为材料, 在自然条件下将多组分株对置于不同的斑块对比度处理下, 比较了它们克隆内分工的发生状态, 试图发现分工与斑块对比度的关系, 同时考察在克隆分工过程中分株的可塑性变化及其与分工的关系。该实验的理论假设是: 分株发生分工的程度与分株所处斑块的资源对比度成正相关。研究结果表明, 鹅绒委陵菜分株的高度和叶面积对局部光照环境产生强烈的可塑性反应, 反应的结果是增加了对匮乏的光资源的获取。从分株根冠比和我们提出的分工指数来看, 分工的程度在一定的斑块对比度范围内随斑块对比度的增强而增强, 但到达一个最大值后又迅速降低。鹅绒委陵菜分株之间的分工和结构特化往往滞后于分株对所处局部环境的适应性可塑性变化, 而后者往往在分株之间具有独立性和局部特征。克隆内分工主要依赖于生物量分配的调节而实现, 其发生状态都是分株系统在分工收益、分工代价与分工风险之间权衡的结果, 而这种结果在很大程度上取决于分株所处的斑块对比度。