Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations.     

Quality by design approach for viral clearance by protein a chromatography

Protein A chromatography is widely used as a capture step in monoclonal antibody (mAb) purification processes. Antibodies and Fc fusion proteins can be efficiently purified from the majority of other complex components in harvested cell culture fluid (HCCF). Protein A chromatography is also capable of removing modest levels of viruses and is often validated for viral clearance. Historical data mining of Genentech and FDA/CDER databases systematically evaluated the removal of model viruses by Protein A chromatography. First, we found that for each model virus, removal by Protein A chromatography varies significantly across mAbs, while remains consistent within a specific mAb product, even across the acceptable ranges of the process parameters. In addition, our analysis revealed a correlation between retrovirus and parvovirus removal, with retrovirus data generally possessing a greater clearance factor. Finally, we describe a multivariate approach used to evaluate process parameter impacts on viral clearance, based on the levels of retrovirus‐like particles (RVLP) present among process characterization study samples. It was shown that RVLP removal by Protein A is robust, that is, parameter effects were not observed across the ranges tested. Robustness of RVLP removal by Protein A also correlates with that for other model viruses such as X‐MuLV, MMV, and SV40. The data supports that evaluating RVLP removal using process characterization study samples can establish multivariate acceptable ranges for virus removal by the protein A step for QbD. By measuring RVLP instead of a model retrovirus, it may alleviate some of the technical and economic challenges associated with performing large, design‐of‐experiment (DoE)—type virus spiking studies. This approach could also serve to provide useful insight when designing strategies to ensure viral safety in the manufacturing of a biopharmaceutical product. Biotechnol. Bioeng. 2014;111: 95–103. © 2013 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

The variation of the water deficit during the winter wheat growing season and its impact on crop yield in the North China Plain

The North China Plain (NCP) is one of the main agricultural areas in China. However, it is also widely known for its water shortages, especially during the winter wheat growing season. Recently, climate change has significantly affected the water environment for crop growth. Analyzing the changes in the water deficit, which is only affected by climate factor, will help to improve water management in the NCP. In this study, the Decision Support System for Agrotechnology Transfer (DSSAT) was used to investigate the variations in the water deficit during the winter wheat growing season from 1961 to 2010 in 12 selected stations in the NCP. To represent the changes in the water deficit without any artificial affection, the rainfed simulation was used. Over the past 50 years, the average temperature during the winter wheat growing season increased approximately 1.42 °C. The anthesis date moved forward approximately 7–10 days and to late April, which increased the water demand in April. Precipitation in March and May showed a positive trend, but there was a negative trend in April. The water deficit in late April and early May became more serious than before, with an increasing trend of more than 0.1 mm/year. In addition, because the heading stage, which is very important to crop yield of winter wheat, moved forward, the impact of water deficit in late April was more serious to crop yield.     

绿海龟稚龟性别鉴定及临界温度

通过组织形态学鉴定、羊水和血液中性激素测定等手段,对惠东港口海龟保护区不同恒温下孵化的绿海龟(Chelonia mydas)进行研究,寻求绿海龟稚龟性别鉴定的最佳方法。结果显示,(1)组织形态学,绿海龟性腺切片分皮层和髓质两部分,卵巢的皮层较厚、基质中有大小不一的未成熟卵细胞,髓质中空腔较少;睾丸的皮层较薄,髓质中空腔较多,呈现出显著的被基质包围的髓质索。(2)性激素测定,当雌二醇与睾酮含量之比E2∶T1.5时,孵出的稚龟为雄性(♂);当E2∶T1.5时,为雌性(♀)。(3)绿海龟性别决定的临界温度在29.4～29.5℃之间,此时孵出稚龟的性比约为1∶1。本文还讨论了各种不同性别鉴定方法的优劣和时期选择。     

鹤顶兰胚囊发育过程中Ca~（2＋）分布的超微细胞化学定位（英文）

用焦锑酸盐沉淀法对鹤顶兰（Phaius tankervilliae）胚囊发育过程中的Ca2＋状态进行超微细胞化学定位。观察结果发现：功能大孢子时期,珠孔端的胚囊壁上开始出现小颗粒的Ca2＋沉淀,但功能大孢子细胞内未见明显的Ca2＋标记;四核胚囊时期胚囊壁上的Ca2＋沉淀明显增多,液泡膜上有Ca2＋沉淀出现,珠孔处的Ca2＋沉淀颗粒较大;成熟胚囊时期,胚囊壁上的Ca2＋沉淀进一步增多,且胚囊内Ca2＋分布明显增多,且极性明显,珠孔端助细胞、卵细胞比合点端反足细胞有更多的Ca2＋沉淀。鹤顶兰成熟胚囊内Ca2＋积累的来源有：（1）在胚囊成熟前主要由珠被细胞、珠细胞通过胞间连丝向胚囊运输;（2）以沉淀有大量Ca2＋的小泡形式跨过胚囊壁进入胚囊。     

乳腺癌中雌激素受体α表达水平调节的分子机制

雌激素受体α(ERα)在乳腺癌的发生发展中扮演重要角色,因而ERα成为乳腺癌治疗的分子靶标。ERα的表达水平在乳腺癌患者中差异较大,即使同一患者,在乳腺癌的不同阶段也可能有很大的差别。乳腺癌内分泌治疗的疗效以及预后都与ERα表达水平密切相关。影响ERα表达水平的分子机制复杂,众多调节分子在染色质、转录、转录后、翻译和翻译后等水平参与ERα表达水平的调节。在染色质和转录水平,许多分子通过直接或间接地与ERα启动子的相互作用改变ERα的转录;在转录后/翻译水平,一些microRNA通过诱导ERαmRNA的降解和/或抑制其翻译降低ERα的水平;在翻译后水平,许多分子通过泛素-蛋白酶体途径调节ERα蛋白水平。文章从不同水平,对这些调节分子的调节机制进行简要综述。     

夏季舟山渔场及邻近海域浮游动物群落结构特征分析

2006年8月在舟山渔场及邻近海域（29°30′ ～31°30′ N,124°30′ E以西）开展海洋生态系统综合调查,用浅水Ⅰ型浮游生物网采集的浮游动物样本,对该海域浮游动物的种类组成、数量分布、生物多样性等群落结构特征进行了分析。结果得知,在调查海域共鉴定出浮游动物93种（不包含浮游幼虫）,其中以桡足类的种类数为最多,有50种,优势种主要有精致真刺水蚤（Euchaeta concinna）、软拟海樽（Dolioletta gegenbauri）、肥胖箭虫（Sagitta enflata）、百陶箭虫（Sagitta bedoti）、中华哲水蚤（Calanus sinicus）、普通波水蚤（Undinula vulgaris）、微刺哲水蚤（Canthocalanus paupe）、长尾类幼虫（Macruran larvae）、双生水母（Diphyes chamissonis）、背针胸刺水蚤（Centropages dorsispinatus）、肥胖三角溞（Evadne tergestina）、太平洋纺锤水蚤（Acartia pacifica）等12种。调查海域浮游动物丰度平面分布呈现南部高、北部低,近岸高、外海低的特征。生物多样性分析表明,调查海域浮游动物种类数较多,且具有较高的均匀度（0.70）,因此其生物多样性指数较高（4.98）。根据聚类分析结果,可将夏季调查海域的浮游动物在17.13%相似性水平上分为A、B、C三个组群。生物−环境匹配分析显示,浮游动物的丰度除了与表层盐度、硝酸氮和硅酸盐含量有关外,还与镉、铅的含量存在着一定相关性。     

三疣梭子蟹Profilin基因全长cDNA的克隆与表达分析

三疣梭子蟹（Portunus trituberculatus）是我国沿海重要养殖品种之一,近年来养殖病害呈逐年上升趋势,制约了三疣梭子蟹养殖产业的健康可持续发展。克隆三疣梭子蟹免疫相关基因,研究免疫基因的功能和作用机制,可为三疣梭子蟹养殖病害的防治奠定基础。本研究从三疣梭子蟹血细胞全长cDNA文库中克隆了742 bp 的profilin基因全长cDNA。Profilin全长cDNA中开放阅读框长375 bp,编码125 aa。推导的三疣梭子蟹profilin理论等电点pI 5.87,氨基酸序列与冈比亚按蚊（Anopheles gambiae）profilin同源性最高,序列一致性为42.9%。荧光定量RT-PCR分析结果显示在正常的三疣梭子蟹机体中,血细胞profilin表达水平最高,其次为肝胰脏;在致病菌副溶血弧菌（Vibrio parahaemolyticus）诱导后,血细胞中profilin表达量显著上升（P<0.01）,表明profilin可能参与了三疣梭子蟹的免疫防御反应,是一个免疫相关因子。     

A potent potassium channel blocker from Mesobuthus eupeus scorpion venom

Scorpion venom-derived peptidyl toxins are valuable pharmacological tools for investigating the structure–function relationship of ion channels. Here, we report the purification, sequencing and functional characterization of a new K⁺ channel blocker (MeuKTX) from the venom of the scorpion Mesobuthus eupeus. Effects of MeuKTX on ten cloned potassium channels in Xenopus oocytes were evaluated using two-electrode voltage-clamp recordings. MeuKTX is the orthologue of BmKTX (α-KTx3.6), a known Kv1.3 blocker from the scorpion Mesobuthus martensii, and classified as α-KTx3.13. MeuKTX potently blocks rKv1.1, rKv1.2 and hKv1.3 channels with 50% inhibitory concentration (IC₅₀) of 203.15 ± 4.06 pM, 8.92 ± 2.3 nM and 171 ± 8.56 pM, respectively, but does not affect rKv1.4, rKv1.5, hKv3.1, rKv4.3, and hERG channels even at 2 μM concentration. At this high concentration, MeuKTX is also active on rKv1.6 and Shaker IR. Our results also demonstrate that MeuKTX and BmKTX have the same channel spectrum and similar pharmacological potency. Analysis of the structure–function relationships of α-KTx3 subfamily toxins allows us to recognize several key sites which may be useful for designing toxins with improved activity on hKv1.3, an attractive target for T-cell mediated autoimmune diseases.