Solution structure and dynamics of the I214V mutant of the rabbit prion protein

Background

The conformational conversion of the host-derived cellular prion protein (PrP^C) into the disease-associated scrapie isoform (PrP^Sc) is responsible for the pathogenesis of transmissible spongiform encephalopathies (TSEs). Various single-point mutations in PrP^Cs could cause structural changes and thereby distinctly influence the conformational conversion. Elucidation of the differences between the wild-type rabbit PrP^C (RaPrP^C) and various mutants would be of great help to understand the ability of RaPrP^C to be resistant to TSE agents.

Methodology/Principal Findings

We determined the solution structure of the I214V mutant of RaPrP^C(91–228) and detected the backbone dynamics of its structured C-terminal domain (121–228). The I214V mutant displays a visible shift of surface charge distribution that may have a potential effect on the binding specificity and affinity with other chaperones. The number of hydrogen bonds declines dramatically. Urea-induced transition experiments reveal an obvious decrease in the conformational stability. Furthermore, the NMR dynamics analysis discloses a significant increase in the backbone flexibility on the pico- to nanosecond time scale, indicative of lower energy barrier for structural rearrangement.

Conclusions/Significance

Our results suggest that both the surface charge distribution and the intrinsic backbone flexibility greatly contribute to species barriers for the transmission of TSEs, and thereby provide valuable hints for understanding the inability of the conformational conversion for RaPrP^C.     

大亚湾表层水中溶解无机碳的时空分布

于2010 年12 月～2011 年11 月分4 个季度,对大亚湾海域进行了采样调查,分析了大亚湾表层水体中溶解无机碳(Dissolved inorganic carbon, DIC)含量的时空分布特征,并讨论了大亚湾表层水DIC 与pH、盐度、水温和叶绿素a 等环境因子之间的关系。大亚湾海域表层水DIC 含量的变化范围为19.49～23.20 mg·L^-1,均值为21.13±1.07 mg·L^-1,较黄海及东海水域的DIC 含量低。DIC 的水平分布大致呈现出西部及西北部海域高于东部及湾口海域的趋势。大亚湾表层水DIC 含量呈现出冬季>夏季>秋季>春季的季节变化趋势,但春、夏及秋季差异不大。大亚湾海域表层水的DIC 含量除与盐度呈现了显著的正相关关系外,与pH 值、水温及叶绿素a 显示出负相关,但不显著。大亚湾海域DIC 的时空分布特征是多种因素综合作用的结果,其同时受季风、水温、盐度、水动力、生物地球化学和生物等因子的影响。     

不同覆盖方式对底泥内源营养盐释放的控制效果

通过底泥内源营养盐释放控制室内模拟试验,考察了塑料包被、斜发沸石、方解石、石英砂和硝酸钙5种覆盖材料对底泥氮磷释放效率的影响,系统分析了各自优劣程度,为实际环境中不同污染背景水体选择适宜的控制技术提供科学依据.结果表明: 不同覆盖材料对底泥总磷释放的控制效果依次为:塑料包被>硝酸钙>斜发沸石>方解石>石英砂;不同覆盖材料对底泥总氮释放的控制效果依次为:斜发沸石>塑料包被>方解石>石英砂>硝酸钙;不同覆盖材料对底泥硝态氮释放的控制效果依次为:塑料包被>斜发沸石>方解石>石英砂>硝酸钙;不同覆盖材料对底泥铵态氮释放的控制效果依次为:硝酸钙>石英砂>斜发沸石>方解石>塑料包被;温度和底泥内源营养盐释放有对应关系,水样中总磷、总氮和硝态氮浓度会随着温度上升而增加,而铵态氮浓度呈下降趋势.     

禾谷缢管蚜ABC转运蛋白基因的克隆、分子特性及表达分析

【目的】ABC（ATP-binding cassette）转运蛋白是一类重要的跨膜蛋白超家族,某些ABC转运蛋白基因在一些害虫的抗药性品系中表达显著提高。本研究旨在克隆禾谷缢管蚜 Rhopalosiphum padi ABC转运蛋白基因RhpaABCG9,RhpaABCG20和RhpaABCG23 cDNA全序列,分析这3个基因在该虫不同发育阶段和不同抗药性品系中的表达模式,为阐明ABC转运蛋白在禾谷缢管蚜抗药性中的作用和其他生理功能,以及深入分析该虫抗药性机理奠定基础。【方法】采用RT-PCR与RACE技术,克隆了基因cDNA全序列;利用实时荧光定量PCR技术,研究这3个基因在禾谷缢管蚜不同生长发育阶段和不同抗药性品系中的表达变化。【结果】获得了RhpaABCG9,RhpaABCG20和RhpaABCG23 3个基因cDNA全序列,其开放阅读框长度分别为2 103,2 436 和2 082 bp,分别编码700, 811和693个氨基酸。结构分析表明,3个蛋白均具有ABC转运蛋白家族典型的结构特征;系统进化分析结果显示,3个蛋白氨基酸序列分别与豌豆蚜Acyrthosiphon pisum各对应氨基酸的序列一致性最高。实时荧光定量PCR分析结果表明,这3个基因在禾谷缢管蚜不同发育时期均不同程度表达。RhpaABCG20在各个发育时期的表达变化差异不显著;RhpaABCG9表达量在4龄若蚜最高,在1龄若蚜最低;RhpaABCG23 表达量在3龄若蚜最高,1龄若蚜最低,其他阶段差异不显著。禾谷缢管蚜异丙威抗性品系中,RhpaABCG20表达量显著高于敏感品系,而RhpaABCG9和RhpaABCG23表达量均低于敏感品系,但差异不显著;禾谷缢管蚜吡虫啉抗性品系中,RhpaABCG20和RhpaABCG23表达量显著高于敏感品系,而RhpaABCG9表达上调不显著。【结论】RhpaABCG9,RhpaABCG20和RhpaABCG23基因可能参与禾谷缢管蚜体内农药的运输,并与禾谷缢管蚜的抗药性具有一定的关系。本研究结果为进一步深入分析禾谷缢管蚜的抗药性机制,以及该虫的抗药性治理与综合防治奠定了基础。     

土壤原生动物对川滇高山栎恢复时间的响应及生长季动态

青藏高原东缘生态环境脆弱, 森林频繁遭到砍伐, 生物多样性受到严重威胁, 森林砍伐后的生态恢复成为研究热点。原生动物在生态恢复中作为指示生物起着重要作用。本文就未砍伐、砍伐后不同恢复时期(20年、10年和1年)生的川滇高山栎(Quercus aquifolioides)林的土壤理化性质和原生动物在生长季的变化进行比较研究, 以探讨生长季不同月份、不同恢复期的原生动物数量变化规律, 分析土壤理化性质与其相关性。结果表明: (1)恢复10年和1年的林地的鞭毛虫数量(193个/g干土, 164个/g干土)显著高于原始林地(22个/g干土), 肉足虫在恢复1年的林地中数量最多(600个/g干土), 纤毛虫数量则随次生演替进程逐渐增多。(2)在生长季不同月份原生动物的数量呈先增加后减少的趋势。鞭毛虫和肉足虫的峰值分别出现在7月和8月, 而纤毛虫的数量在7、8、9月明显高于6月。(3)原生动物数量与土壤理化性质密切相关。鞭毛虫数量与pH值呈显著正相关(P = 0.019), 纤毛虫数量与铵态氮(P = 0.002)和碳氮比呈显著正相关(P = 0.022), 肉足虫数量与硝态氮(P = 0.008)和碳氮比(P = 0.016)呈显著负相关。结果显示, 三种原生动物数量在生长季不同月份表现出较大的波动性, 其数量变化受土壤理化性质等多种因素调控。纤毛虫数量对川滇高山栎林砍伐恢复有正响应, 而鞭毛虫、肉足虫数量有负响应。     

Lumping kinetics of ABE fermentation wastewater treatment by oleaginous yeast Trichosporon cutaneum

Lumping kinetics models were built for the biological treatment of acetone–butanol–ethanol (ABE) fermentation wastewater by oleaginous yeast Trichosporon cutaneum with different fermentation temperatures. Compared with high temperature (33°C, 306?K) and low temperature (23°C, 296?K), medium temperature (28°C, 301?K) was beneficial for the cell growth and chemical oxygen demand (COD) degradation during the early stage of fermentation but the final yeast biomass and COD removal were influenced little. By lumping method, the materials in the bioconversion network were divided into five lumps (COD, lipid, polysaccharide, other intracellular products, other extracellular products), and the nine rate constants (k₁–k₉) for the models can well explain the bioconversion laws. The Gibbs free energy (G) for this bioconversion was positive, showing that it cannot happen spontaneous, but the existence of yeast can after the chemical equilibrium and make the bioconversion to be possible. Overall, the possibility of using lumping kinetics for elucidating the laws of materials conversion in the biological treatment of ABE fermentation wastewater by T. cutaneum has been initially proved and this method has great potential for further application.     

Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes

The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous–Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India–Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.     

Silencing of SlPL,which encodes a pectate lyase in tomato,confers enhanced fruit firmness,prolonged shelf‐life and reduced susceptibility to grey mould

Pectate lyase genes have been documented as excellent candidates for improvement of fruit firmness. However, implementation of pectate lyase in regulating fruit postharvest deterioration has not been fully explored. In this report, 22 individual pectate lyase genes in tomato were identified, and one pectate lyase gene SlPL (Solyc03g111690) showed dominant expression during fruit maturation. RNA interference of SlPL resulted in enhanced fruit firmness and changes in pericarp cells. More importantly, the SlPL‐RNAi fruit demonstrated greater antirotting and pathogen‐resisting ability. Compared to wild‐type, SlPL‐RNAi fruit had higher levels of cellulose and hemicellulose, whereas the level of water‐soluble pectin was lower. Consistent with this, the activities of peroxidase, superoxide dismutase and catalase were higher in SlPL‐RNAi fruit, and the malondialdehyde concentration was lower. RNA‐Seq results showed large amounts of differentially expressed genes involved in hormone signalling, cell wall modification, oxidative stress and pathogen resistance. Collectively, these data demonstrate that pectate lyase plays an important role in both fruit softening and pathogen resistance. This may advance knowledge of postharvest fruit preservation in tomato and other fleshy fruit.