The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study

Abstract

Huntington's disease is a neurodegenerative disorder caused by a polyglutamine (polyQ) expansion near the N-terminus of huntingtin. Previous studies have suggested that polyQ aggregation occurs only when the number of glutamine (Q) residues is more than 36-40, the disease threshold. However, the structural characteristics of polyQ nucleation in the very early stage of aggregation still remain elusive. In this study, we designed 18 simulation trials to determine the possible structural models for polyQ nucleation and aggregation with various shapes and sizes of initial β-helical structures, such as left-handed circular, right-handed rectangular, and left- and right-handed triangular. Our results show that the stability of these models significantly increases with increasing the number of rungs, while it is rather insensitive to the number of Qs in each rung. In particular, the 3-rung β-helical models are stable when they adopt the left-handed triangular and right-handed rectangular conformations due to the fact that they preserve high β-turn and β-sheet contents, respectively, during the simulation courses. Thus, we suggested that these two stable β-helical structures with at least 3 rungs might serve as the possible nucleation seeds for polyQ depending on how the structural elements of β-turn and β-sheet are sampled and preserved during the very early stage of aggregation.     

Structure of the Type VI Effector-Immunity Complex (Tae4-Tai4) Provides Novel Insights into the Inhibition Mechanism of the Effector by Its Immunity Protein

The type VI secretion system (T6SS), a multisubunit needle-like apparatus, has recently been found to play a role in interspecies interactions. The Gram-negative bacteria harboring T6SS (donor) deliver the effectors into their neighboring cells (recipient) to kill them. Meanwhile, the cognate immunity proteins were employed to protect the donor cells against the toxic effectors. Tae4 (type VI amidase effector 4) and Tai4 (type VI amidase immunity 4) are newly identified T6SS effector-immunity pairs. Here, we report the crystal structures of Tae4 from Enterobacter cloacae and Tae4-Tai4 complexes from both E. cloacae and Salmonella typhimurium. Tae4 acts as a dl-endopeptidase and displays a typical N1pC/P60 domain. Unlike Tsi1 (type VI secretion immunity 1), Tai4 is an all-helical protein and forms a dimer in solution. The small angle x-ray scattering study combined with the analytical ultracentrifugation reveal that the Tae4-Tai4 complex is a compact heterotetramer that consists of a Tai4 dimer and two Tae4 molecules in solution. Structure-based mutational analysis of the Tae4-Tai4 interface shows that a helix (α3) of one subunit in dimeric Tai4 plays a major role in binding of Tae4, whereas a protruding loop (L4) in the other subunit is mainly responsible for inhibiting Tae4 activity. The inhibition process requires collaboration between the Tai4 dimer. These results reveal a novel and unique inhibition mechanism in effector-immunity pairs and suggest a new strategy to develop antipathogen drugs.     

藏鹀的自然历史、威胁和保护

藏鹀(Emberiza koslowi)是我国青藏高原东部的特有珍稀鸟种,目前关于它的资料非常匮乏.为了解藏鹀的分布、数量和基本生活史特征,促进对于该物种的有效保护,自2005年起以青海省果洛州久治县白玉乡为中心对藏鹀进行了持续6年的观察,并针对其面临的威胁采取了相应的保护措施.结果显示,藏鹀主要分布在青海的玉树、果洛和四川的阿坝一带海拔3 500～4 700 m范围内的适宜栖息地,该分布区比原有认知更靠东北,更为狭小且海拔更高.用样线法开展的藏鹀数量监测,在7.4 km2的调查范围内记录到一个18 ～33只的稳定种群.此外,还对藏鹀的筑巢、育雏和争斗等行为进行了详细描述.食肉动物的捕食、冬季食物缺乏和牲畜踩踏鸟卵是藏鹀面临的最直接威胁.通过持续监测、与当地牧民协商、建立保护小区并开展有针对性的保护,藏鹀种群趋于稳定.     

Synthesis and antibacterial activity of 9-oxime ether non-ketolides,and novel binding mode of alkylides with bacterial rRNA

We report a series of new 9-oxime ether non-ketolides, including 3-hydroxyl, 3-O-acyl and 3-O-alkyl clarithromycin derivatives, and thiophene-containing ketolides 1b–1d. Unlike previously reported ketolide 1a, none of them is comparable to telithromycin. A molecular modeling study was performed to gain insight into the binding mode of alkylides 17–20 with bacterial rRNA and to rationalize the great disparity of their SAR. The 3-O-sidechains of 19 and 20 point to the so-called hydrophilic side of the macrolide ring, as seen in clarithromycin. In contrast, the 3-O-sidechains of 17 and 18 bend to the backside, the so-called hydrophobic side of the macrolide ring. The results clearly indicated the alkylides with improved antibacterial activity might possess a novel binding mode, which is different from clarithromycin and the alkylides with poor activity.     

农地保护的外部效益测算——选择实验法在武汉市的应用

农地保护的外部效益是农地保护补偿政策制定的依据.对外部效益进行了理论界定和实证测算,认为农地保护的外部效益是农村集体和农地使用者以外个体从农地保护中得到的收益,通常是非市场收益,对其测算应区分外部效益的内部(外部效益发出者)和外部(外部效益接受者),并确定外部区域的范围.实证利用选择实验模型对武汉市5个区域进行了支付意愿测算,在内外部划分的基础上估算了武汉市农地保护的外部效益并比较了不同方法下外部效益测算结果的差别.结果表明,武汉市耕地、园地、林地和农村水面的外部效益分别为30773.2,653860.0,119267.0和82472.7元/hm2;用行政区域直接代替外部性影响区域的做法会使耕地外部效益的测算结果偏高,也会造成园地、林地和农村水面测算的误差,为避免这类误差,外部性测算及相关补偿、税费政策应考虑内外部区域的划分.     

基于高分辨率遥感影像的森林地上生物量估算

以南京市紫金山林区为研究区,利用e-Cognition面向对象分类方法,基于光谱和空间信息融合后的IKONOS影像提取单木树冠阳性冠幅(PoCA, Positive crown area)信息,并结合野外实测的样方生物量数据,分别建立了针叶林和阔叶林地上生物量 (AGB, Aboveground Biomass)的遥感估算模型,并利用实测森林生物量数据对模型进行了验证。结果表明,基于遥感影像提取的PoCA与实测AGB存在较好的非线性相关关系,所建针叶林AGB估算模型的可靠性优于阔叶林模型。对建模样本而言,估算的针叶林和阔叶林AGB与观测数据比较的R2分别为0.62 (P<0.01,n=9) 和0.56(P<0.01,n=16)。验证表明,所建AGB估算模型的可靠性较好,估算的针叶林和阔叶林AGB与观测数据比较的R2分别为0.55(P<0.01,n=6) 和0.52(P<0.01,n=10),但当AGB较低时,模型结果偏高,AGB较低时,模型结果偏低。研究说明通过高分辨率遥感数据的融合、提取树冠信息进行生物量估算是可行性的。     

吐鲁番市胃食管反流病发生相关危险因素分析（附280例报道）

目的：探讨280例胃食管反流病（GERD）的分布特点及危险因素。方法：对临床诊断和胃镜确诊的280例GERD患者进行临床和风险因子相关性分析。结果：不论汉族还是维族,男性患者比例均明显高于女性;汉族患者高发年龄段早于维族患者（z=-2．939,P=0．003,）;汉族和维族患者占反流性食管炎和Barrett食管比例分别为42．4％、81_3％及56．5％、18．8％,其中汉族患者Barrett食管比例较高（X2=14．358,P=0．000）;肥胖、习惯性便秘、重体力活动者、饮食习惯不良在维族患者中的比例较高（P〈0．001）。结论：GERD与性别、年龄密切相关,男性多于女性,汉族患者发病年龄高峰旱于维族患者;汉族患者Barrett食管发生比例高于维族患者;肥胖、习惯性便秘、重体力活动、饮食习惯不良可能是GERD尤其是维族人群GERD的危险因素。     

Effect of propionic acid on citric acid fermentation in an integrated citric acid–methane fermentation process

In this study, an integrated citric acid-methane fermentation process was established to solve the problem of wastewater treatment in citric acid production. Citric acid wastewater was treated through anaerobic digestion and then the anaerobic digestion effluent (ADE) was further treated and recycled for the next batch citric acid fermentation. This process could eliminate wastewater discharge and reduce water resource consumption. Propionic acid was found in the ADE and its concentration continually increased in recycling. Effect of propionic acid on citric acid fermentation was investigated, and results indicated that influence of propionic acid on citric acid fermentation was contributed to the undissociated form. Citric acid fermentation was inhibited when the concentration of propionic acid was above 2, 4, and 6 mM in initial pH 4.0, 4.5 and, 5.0, respectively. However, low concentration of propionic acid could promote isomaltase activity which converted more isomaltose to available sugar, thereby increasing citric acid production. High concentration of propionic acid could influence the vitality of cell and prolong the lag phase, causing large amount of glucose still remaining in medium at the end of fermentation and decreasing citric acid production.     

耐低温荧光假单胞菌筛选体系建立及其植物促生作用评价

【目的】以前期研究小麦生境分离细菌为菌株库,从中筛选耐低温菌株,评价其植物促生效果。【方法】通过4°C低温培养筛选耐低温菌株。以产吲哚乙酸、1-氨基环丙烷羧酸(ACC)脱氨酶、嗜铁素以及无机、有机磷溶解能力为评价指标,测定15°C和28°C环境中耐低温菌株的植物促生作用潜力,利用赋分评估系统选定潜力菌株进行温室和田间试验验证其植物促生作用。【结果】筛选到34株耐低温菌株,从中选定的8株植物促生潜力细菌温室试验促生效果和评估分值之间的相关性在0.62以上,菌株1b YB22和3b JN2在28°C环境中对黄瓜的促生效果均在28%以上,二者在15°C环境中对青菜种子根长的促生效果分别为116.76%和46.82%,菌株1b YB22在15°C环境中对青菜的促生效果为25.11%。菌株1b YB22在田间应用对小麦生长同样具有促生作用,增产效果达0.58%。【结论】研究建立的筛选体系从小麦生境分离菌株中获得了耐低温荧光假单胞菌株1b YB22和3b JN2,两株细菌在15°C和28°C均具有植物促生作用,同时可以在田间促进小麦生长。