Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein

With the development of de novo binders for protein targets from non‐related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single‐chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking “disembodied” amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein‐antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen‐based detection agents for typhoid diagnostics.     

整治区植烟土壤养分空间变异及肥力适宜性等级评价

采用地理信息系统(GIS)技术和地统计学方法,研究了湖北省恩施市“清江源”现代烟草农业科技园区、恩施城郊和利川柏杨基地单元新整治区域的土壤属性和速效养分空间变异特征,并采用模糊数学法对其土壤肥力适宜性指数(SFI)进行评价.结果表明: 土地整治对土壤速效磷含量的变异和空间分布的影响较大,这种影响程度可能与地形地貌特征和整治程度有关;土地整治对土壤pH值的影响较小,但是柏杨土壤酸化严重(pH<5.5).77.6%的城郊土壤具有较低的SFI,而柏杨和清江源分别仅有17.1%和31.4%的土壤具有较低的SFI.柏杨需要重点解决土壤酸化问题,城郊需要重点解决整个区域土壤培肥和肥力均衡化问题,而清江源则需解决SFI较低区域的培肥问题.     

A Small Molecule Inhibitor of Polycomb Repressive Complex 1 Inhibits Ubiquitin Signaling at DNA Double-strand Breaks

Polycomb-repressive complex 1 (PRC1)-mediated histone ubiquitylation plays an important role in aberrant gene silencing in human cancers and is a potential target for cancer therapy. Here we show that 2-pyridine-3-yl-methylene-indan-1,3-dione (PRT4165) is a potent inhibitor of PRC1-mediated H2A ubiquitylation in vivo and in vitro. The drug also inhibits the accumulation of all detectable ubiquitin at sites of DNA double-strand breaks (DSBs), the retention of several DNA damage response proteins in foci that form around DSBs, and the repair of the DSBs. In vitro E3 ubiquitin ligase activity assays revealed that PRT4165 inhibits both RNF2 and RING 1A, which are partially redundant paralogues that together account for the E3 ubiquitin ligase activity found in PRC1 complexes, but not RNF8 nor RNF168. Because ubiquitylation is completely inhibited despite the efficient recruitment of RNF8 to DSBs, our results suggest that PRC1-mediated monoubiquitylation is required for subsequent RNF8- and/or RNF168-mediated polyubiquitylation. Our results demonstrate the unique feature of PRT4165 as a novel chromatin-remodeling compound and provide a new tool for the inhibition of ubiquitylation signaling at DNA double-strand breaks.     

我国森林脑炎病毒森张株编码区序列测定

为鉴定我国森林脑炎病毒亚型,了解基因组结构与生物功能的关系,同时为森林脑炎病毒新型疫苗研制打下基础,对森林脑炎病毒森张株编码区序列进行测定.根据已发表的Sofjin-HO、Oshima5-10株序列设计9对重叠引物,通过RT-PCR扩增不同的cDNA片段,分别克隆至pGEM(R)-T载体,转化DH5 α菌,挑阳性克隆PCR、酶切鉴定后测序.结果表明森张株编码区全长10 245nt,编码3 414个氨基酸.我国森林脑炎病毒森张株与Oshima5.10、Sofjin-HO、Sofjin同源性最近,属于远东亚型.     

DNA ligase III acts as a DNA strand break sensor in the cellular orchestration of DNA strand break repair

In the current model of DNA SSBR, PARP1 is regarded as the sensor of single-strand breaks (SSBs). However, biochemical studies have implicated LIG3 as another possible SSB sensor. Using a laser micro-irradiation protocol that predominantly generates SSBs, we were able to demonstrate that PARP1 is dispensable for the accumulation of different single-strand break repair (SSBR) proteins at sites of DNA damage in live cells. Furthermore, we show in live cells for the first time that LIG3 plays a role in mediating the accumulation of the SSBR proteins XRCC1 and PNKP at sites of DNA damage. Importantly, the accumulation of LIG3 at sites of DNA damage did not require the BRCT domain-mediated interaction with XRCC1. We were able to show that the N-terminal ZnF domain of LIG3 plays a key role in the enzyme''s SSB sensing function. Finally, we provide cellular evidence that LIG3 and not PARP1 acts as the sensor for DNA damage caused by the topoisomerase I inhibitor, irinotecan. Our results support the existence of a second damage-sensing mechanism in SSBR involving the detection of nicks in the genome by LIG3.     

两种群均具有常收获率或常投放率的Lotka-Volterra系统可以存在三个极限环

证明了两种群均具有常收获率或常投放率的Lotka-Volterra系统可以存在三个极限环。     

紫贻贝长期暴露于亚致死剂量的林丹和阿特拉津下的组织学反应

为开发快速、敏感的生物标记物以监测海洋贝类生物中是否存在农药,我们检测了双壳动物紫贻贝长期暴露在亚致死剂量的丙体六氯环乙烷(林丹,γ-HCH)和2-氯4-乙胺基-6异丙胺基-1,3,5-三氮苯(阿特拉津)下的组织学变化。紫贻贝容易积累环境中的杀虫剂,因此,本研究旨在阐明农药的生物积累与组织病理学效应之间的关系。利用GC/MSD分析法定期对贻贝和水样中的林丹与阿特拉津含量进行测定。将贻贝在实验室中培养21天,以使其代谢适应于带有水质控制的封闭式不间断流动系统。随后,30只贝暴露于亚致死剂量的林丹(0.9 mg/L)或阿特拉津(3.583 mg/L)溶液中56天。实验期间,控制重要的参数,比如温度和盐度分别控制在18℃和34‰。在处理28天和56天后取样,检测组织学损坏及吸收的农药量。暴露的紫贻贝每克干重分别能聚集约304.8-372.0μg/g林丹和83.3-137.4μg/g阿特拉津。组织学改变高度集中在鳃的上皮和外套膜组织;上皮与相邻的组织形成分离状态。组织病理学结果显示,抗性机制的激活使紫贻贝能在亚致死压力下存活。组织病理效应范围从浸润反应到以血淋巴细胞出现间质细胞反应为特征。因此,在农药聚集部位的组织学和超微结构的改变是敏感的,并与农药的生物积累具有正相关关系,说明这些改变可能作为农药暴露的生物标记物。     

胡杨叶片气孔导度特征及其对环境因子的响应

依据2005年对极端干旱区荒漠河岸林胡杨的观测资料,对胡杨气孔运动进行了分析研究以揭示胡杨的水分利用特征与抗旱机理。结果表明:(1)胡杨叶片气孔导度日变化呈现为周期波动曲线,其波动周期为2 h,傍晚(20:00)波动消失;净光合速率和蒸腾速率与气孔导度的波动相对应而呈现同步周期波动。(2)胡杨的阳生叶气孔导度高于阴生叶,且不同季节气孔导度值不同,阳生叶气孔导度的季节变幅大于阴生叶。(3)胡杨气孔导度与气温、相对湿度和叶水势有显著相关关系,当CO2浓度较小时,胡杨气孔导度随CO2浓度的增加而增加,当CO2浓度达到一定值后气孔导度不再增加,反而随CO2浓度的增加大幅度降低。(4)胡杨适应极端干旱区生境的气孔调节机制为反馈式反应,即由于叶水势降低导致气孔导度减小,从而减少蒸腾耗水,达到节约用水、适应干旱的目的,表明胡杨的水分利用效率随气孔限制值的增大而减小,二者呈显著负相关。     

GABAA受体在酒精依赖中作用的研究进展

酒精依赖的产生机制是由特定的GABAA受体亚单位介导的,并且能够影响其它GABAA受体亚单位,使其对一定剂量的酒精敏感.此外酒精还可以通过细胞内信号转导途径影响GABA在大脑不同区域及核团单元的表达.焦虑、抗惊厥、镇静催眠、认知功能障碍等由酒精依赖产生的现象或者机制,均与GABA受体的介导有关.这些机制包括酒精对GABAA受体的直接或间接的作用,以及GABA的合成和释放.因此对GABAA受体功能的研究,将有助于人们关注酒精依赖现象及其治疗手段,为寻找酒精依赖治疗药物和治疗酒精中毒的机制的提供新线索.