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Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

Biophysics Reports 2017年第Z2期3卷 100-108页

作者： Zhou Gong Zhu Liu Xu Dong Yue-He Ding meng-qiu Dong Chun Tang CAS Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic Molecular Physicsand National Center for Magnetic Resonance at WuhanWuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences RNA Therapeutics Institute University of Massachusetts Medical School National Center for Magnetic Resonance at Wuhan Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences Department of Pharmacology Institute of NeuroscienceKey Laboratory of Medical Neurobiology of the Ministry of Health of ChinaZhejiang University School of Medicine National Institute of Biological Sciences

Chemical cross-linking coupled with mass spectroscopy(CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigidbody refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein–protein complexes, and is freely available at ***/resources.

关键词： Chemical cross-linking DynaXL Ensemble refinement Multi-domain protein Protein–protein complex Solvent accessible surface distance

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Combined hybrid energy storage system and transmission grid model for peak shaving based on time series operation simulation

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Global Energy Interconnection 2023年第2期6卷 154-165页

作者： Mingkui Wei Yiyu Wen qiu meng Shunwei Zheng Yuyang Luo Kai Liao Southwest Branch of State Grid Corporation of China No.299 Shuxiu West RoadChengdu 610000P.R.China School of Electrical Engineering Southwest Jiaotong UniversityNo.999 Xi’an RoadChengdu 610000P.R.China

This study proposes a combined hybrid energy storage system(HESS) and transmission grid(TG) model, and a corresponding time series operation simulation(TSOS) model is established to relieve the peak-shaving pressure of power systems under the integration of renewable energy. First, a linear model for the optimal operation of the HESS is established, which considers the different power-efficiency characteristics of the pumped storage system, electrochemical storage system, and a new type of liquid compressed air energy storage. Second, a TSOS simulation model for peak shaving is built to maximize the power entering the grid from the wind farms and HESS. Based on the proposed model, this study considers the transmission capacity of a TG. By adding the power-flow constraints of the TG, a TSOS-based HESS and TG combination model for peak shaving is established. Finally, the improved IEEE-39 and IEEE-118 bus systems were considered as examples to verify the effectiveness and feasibility of the proposed model.

关键词： Peak shaving Hybrid energy storage system Combined energy storage and transmission grid model Time series operation simulation

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太赫兹光谱结合特征谱区筛选算法在发动机润滑油含水量定量分析中应用研究

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光谱学与光谱分析 2021年第5期41卷 1393-1397页

作者：陈孟秋何明霞李萌曲秋红天津大学测试计量技术及仪器国家重点实验室天津300072 莱仪特太赫兹(天津)科技有限公司天津300019

发动机润滑油是保障汽车发动机持久且稳定运转的基石,准确评定发动机润滑油各项性能指标是其在生产到使用全过程必不可少的步骤。发动机润滑油在一段时间的使用后会因为多种原因引起油品变质,发动机润滑油变质的指标可以用其中非磁性颗... 详细信息

发动机润滑油是保障汽车发动机持久且稳定运转的基石,准确评定发动机润滑油各项性能指标是其在生产到使用全过程必不可少的步骤。发动机润滑油在一段时间的使用后会因为多种原因引起油品变质,发动机润滑油变质的指标可以用其中非磁性颗粒物浓度、金属屑含量、pH值、粘稠度、含水率等表述。关于发动机润滑油含水量的检测,传统的检测方法存在操作复杂,及时性差等缺点。太赫兹对水吸收强烈,适合用于对样品中微水含量的分析。通过透射式太赫兹时域光谱系统获得1.0~3.5THz下的六种不同水含量的发动机润滑油的吸收系数谱线,对谱线进行Savitzky-Golay(SG)平滑去噪,剔除奇异样本后,采用Kennard-Stone算法划分样品集,尝试常规区间偏最小二乘法(iPLS)、向后区间偏最小二乘法(BiPLS)和联合区间偏最小二乘法(SiPLS)对其太赫兹时域光谱特征谱区间进行筛选,着重研究区间间隔数、PLS组件数、最佳主因子数和区间选择等因素对PLS模型属性的影响,并且对不同含水量的润滑油建模分析,对不同模型比较选优,建立最优定量分析模型。建模结果表示特征谱区筛选可以提高建模性能、降低模型复杂性,特征谱区筛选算法通过剔除发动机润滑油太赫兹吸收系数谱线中非线性或者无关变量的方式,使建模结果更好的表达吸收系数谱线与其含水量的关系。结果表明:采用BiPLS模型用于发电机润滑油中微量水含量的定量分析时建模效果最佳,模型区间数为26,入选区间为[18 10 4 3 8 12 5 11 24 13 16 21 2],主因子数为10,最优模型的交互验证均方根误差RMSECV为0.003 5,预测均方根误差RMSEP为0.004 6,校正集相关系数r为0.919 3,预测集相关系数r为0.865 7。由此可见,可以采用反向区间偏最小二乘法(BiPLS)用于发动机润滑油水含量的测定,且实验过程简单,建模计算速度快,效果理想,可以适用于非接触式油品含水量的定量分析。

关键词：太赫兹时域光谱技术特征谱区筛选算法发动机润滑油水含量检测

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Establishment and preliminery use of hepatitis Bvirus preS1/2 antigen assay

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World Journal of Gastroenterology 1999年第6期5卷 550-552页

作者： CHEN Kun, HAN Bao Guang, MA Xian Kai, ZHANG He qiu, meng Li, WANG Guo Hua, XIA Fang, SONG Xiao Guo and LING Shi Gan 解放军军事医学科学院基础医学所北京

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Active compounds in RenShenJian decoction ameliorate insulin resistance in vitro

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Traditional Medicine Research 2022年第4期7卷 8-16页

作者： Zhen-Hua Lan Lan-Fang Tan Guo-En Wang meng-qiu Tang Ruo-Hong Wang Shu-Mei Wang Guangdong Pharmaceutical University Guangzhou 510006China Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of Traditional Chinese Medicine and Engineering&Technology Research Center for Chinese Materia Medica Quality of Guangdong Province Guangdong Pharmaceutical UniversityGuangzhou 510006China.

Background:RenShenJian decoction,a combination of Pueraria lobata(Willd.)Ohwi and Panax ginseng ***,has been used in China since the Song Dynasty(960-1279 C.E.)to relieve symptoms of diabetes ***,the key compounds in RenShenJian that ameliorate insulin resistance remain *** study identified the anti-diabetic compounds in RenShenJian by rescuing the decreased function of adenosine 5’-monophosphate-activated protein kinase(AMPK),sirtuin 3(SIRT3),or glucose transporter isoform 4(GLUT4).Methods:After streptozotocin-induced diabetic mice were treated with RenShenJian,fasting blood glucose levels and protein expression of SIRT3,p-AMPK,and AMPK were *** from RenShenJian in plasma were monitored using multiple responses by liquid chromatography-mass ***,two insulin-resistant cell models were incubated with compounds identified in RenShenJian in the *** uptake was determined using the fluorescent analog 2-(N-(7-nitrobenz-2-oxa-1,3-dia-xol-4-yl)amino)-*** expression levels of p-AMPK,AMPK,SIRT3,and GLUT4 were detected by western ***:RenShenJian decreased FBG levels and upregulated SIRT3 expression and AMPK phosphorylation in diabetic *** RenShenJian extracts were identified in the blood,11 of which increased the ratios of 2-(N-(7-nitrobenz-2-oxa-1,3-dia-xol 4-yl)amino)-2-deoxyglucose uptake in two insulin-resistant cell *** extracts increased AMPK phosphorylation,nine increased SIRT3 expression,and six elevated GLUT4 expression in palmitate-induced HepG2 *** extracts-puerarin,puerarin 6″-O-xyloside,genistein,ginsenoside Rb1,and ginsenoside Rd-simultaneously activated AMPK,SIRT3 and ***:A series of compounds in RenShenJian that target AMPK,SIRT3,and/or GLUT4 was confirmed and indicate the chemical material basis of amelioration of insulin resistance by RenShenJian.

关键词： SIRT3 AMPK GLUT4 diabetes Pueraria lobata(Willd.)Ohwi Panax ginseng C.A.Mey

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利用黏弹性有限元模型研究挪威北海北部地区末次冰期以来的冰后回弹和应力演化

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地球物理学报 2020年第10期63卷 3751-3763页

作者：孟秋胡才博石耀霖中国科学院大学地球与行星科学学院中国科学院计算地球动力学重点实验室北京100049

挪威北海北部在末次冰期存在较大范围的冰盖,其冰盖的加载和卸载会对地表变形和内部应力调整产生重要影响.本文基于Maxwell黏弹性本构关系,根据初应力法自主开发了一套Maxwell黏弹性体有限元程序,它可以考虑重力和构造加载、地球介质弹... 详细信息

挪威北海北部在末次冰期存在较大范围的冰盖,其冰盖的加载和卸载会对地表变形和内部应力调整产生重要影响.本文基于Maxwell黏弹性本构关系,根据初应力法自主开发了一套Maxwell黏弹性体有限元程序,它可以考虑重力和构造加载、地球介质弹性的纵向和横向不均匀性以及黏性的分层性,可以计算冰川载荷变化引起的地球表面变形及内部应力状态的变化.利用它研究了挪威北海北部1.1 Ma以来的冰川载荷变化、特别是两万多年以来冰盖的消退引起的地表冰后回弹.结果表明,自2万年以来,冰后回弹效应在冰盖载荷变化的不同阶段呈现明显的时空变化,现今地表垂直变化速率为几个毫米/年,与观测结果一致.下地壳和上地幔的黏弹性松弛效应明显,上地壳的应力状态在现今海岸线两侧存在差异性,水平和垂直正应力变化可达几十兆帕,剪应力变化有一个先增加后迅速减小至零的过程,与古地震、现今地震时空分布及应力测量结果也比较符合,研究结果有助于加深对冰后回弹的动力学过程的认识.

关键词：黏弹性有限元冰后回弹流变性冰川

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论贵州毛南族地区基础教育改革与发展的思路

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贵州民族研究 2006年第4期26卷 167-172页

作者：蒙秋明黔南民族师范学院贵州都匀558000

教育脱贫,是解决贵州毛南族地区贫困问题的治本之举,因此,加快当地基础教育的改革与发展步伐显得尤为重要。在贵州毛南族地区基础教育改革与发展中,要注意转变观念,充分认识教育的战略重要性;要树立合理的基础教育发展战略指导思想;要... 详细信息

教育脱贫,是解决贵州毛南族地区贫困问题的治本之举,因此,加快当地基础教育的改革与发展步伐显得尤为重要。在贵州毛南族地区基础教育改革与发展中,要注意转变观念,充分认识教育的战略重要性;要树立合理的基础教育发展战略指导思想;要优化资源配置,提高基础教育资源的使用效率;要实现教育与经济的协调发展;要促进教师专业化发展和规范基础教育财政转移支付制度。

关键词：毛南族基础教育改革与发展

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Individualized elective irradiation of the clinically node-negative neck in definitive radiotherapy for head and neck squamous cell carcinoma

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Cancer Communications 2021年第4期41卷 303-315页

作者： Jia Kou Li Lin Cheng-Yang Jiao meng-qiu Tian Guan-Qun Zhou Xue Jiang Jun Ma Zhen-Yu Qi Yao Lu Ying Sun Department of Radiation Oncology Sun Yat-sen University Cancer Center/State Key Laboratory of Oncology in South China/Collaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhouGuangdong 510060P.R.China Perception vision medical technology co.LTD GuangzhouGuangdong 510275P.R.China School of Data and Computer Science Sun Yat-sen UniversityGuangdong Province Key Laboratory of Computational ScienceGuangzhouGuangdong 510275P.R.China

Background:Oral cavity(OC),oropharyngeal(OP),hypopharyngeal(HP),and laryngeal(LA)squamous cell carcinoma(SCC)have a high incidence of regional lymph node metastasis(LNM).Elective irradiation for clinically node-negative neck is routinely administered to treat lymph nodes harboring occult ***,the optimal elective irradiation schemes are still *** this study,we aimed to establish individualized elective irradiation schemes for the ipsilateral and contralateral node-negative neck of these four types of ***:From July 2005 to December 2018,793 patients with OC-SCC,464 with OP-SCC,413 with HP-SCC,and 645 with LA-SCC were recruited *** on the actual incidence of LNM and the tumor characteristics,risk factors for contralateral LNM,as well as node level coverage schemes for elective irradiation,were determined using logistic regression ***,we developed a publicly available online tool to facilitate the widespread clinical use of these ***:For the ipsilateral node-negative neck,elective irradiation at levels Ⅰ-Ⅲ for OC-SCC and levels Ⅱ-Ⅳa for OP-,HP-and LA-SCC are generally *** addition,level Ⅶa should be included in patients with *** analyses revealed that posterior hypopharyngeal wall and post-cricoid region involvement were independently associated with level Ⅶa metastasis in HP-SCC(all P<0.05).For the contralateral node-negative neck,multivariate analyses revealed that ipsilateral N2b2-N3,tumors with body midline involvement,and degree of tumor invasion were the independent factors for contralateral LNM(all P<0.05).In patients who require contralateral neck irradiation,levels Ⅰ-Ⅱ are recommended for OC-SCC,and additional level Ⅲ is recommended for patients with ipsilateral N3 *** Ⅱ-Ⅲ are recommended for OP-,HP-,and LA-SCC,and additional level Ⅳa is recommended for patients with advanced T or ***,additional level Ⅶa

关键词： clinically node-negative neck elective irradiation head and neck squamous cell carcinoma individualization neck node level

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Genome-wide detection of selective signatures in a Jinhua pig population

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Journal of Integrative Agriculture 2020年第5期19卷 1314-1322页

作者： XU Zhong SUN Hao ZHANG Zhe Zhao Qing-bo Babatunde Shittu Olasege Li qiu-meng Yue Yang Ma Pei-pei Zhang Xiang-zhe Wang Qi-shan Pan Yu-chun Department of Animal Science School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240P.R.China Shanghai Key Laboratory of Veterinary Bio-technology Shanghai 200240P.R.China

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig *** results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production *** the present study,we performed extended haplotype homozygosity(EHH)tests to identify significant core regions in 202 Jinhua pigs.A total of 26161 core regions spanning 636.42 Mb were identified,which occupied approximately 28%of the genome across all autosomes,and 1158 significant(P<0.01)core haplotypes were *** in these regions were related to several economically important traits,including meat quality,reproduction,immune responses and exterior traits.A panel of genes including ssc-mir-365-2,KDM8,RABEP2,GSG1L,RHEB,RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme *** findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome,and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.

关键词： pig genome selection signatures extended haplotype homozygosity(EHH) candidate genes

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4.4 A Resolution Cryo-EM structure of human mTOR Complex 1

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Protein & Cell 2016年第12期7卷 878-887页

作者： Huirong Yang Jia Wang mengjie Liu Xizi Chen Min Huang Dan Tan meng-qiu Dong Catherine C. L, Wong Jiawei Wang Yanhui Xu Hong-Wei Wang Fudan University Shanghai Cancer Center Institute of Biomedical Sciences Shanghai Medical College of Fudan University Shanghai 200032 China Key Laboratory of Molecular Medicine Ministry of Education Department of Systems Biology for Medicine School of Basic Medical Sciences Shanghai Medical College of Fudan University Shanghai 200032 China State Key Laboratory of Genetic Engineering Collaborative Innovation Center of Genetics and Development School of Life Sciences Fudan University Shanghai 200433 China Ministry of Education Key Laboratory of Protein Sciences Tsinghua-Peking Joint Center for Life Sciences Beijing Advanced Innovation Center for Structural Biology School of Life Sciences Tsinghua University Beijing 100084 China National Center for Protein Science Shanghai Institute of Biochemistry and Cell Biology Shanghai Institutes of Biological Sciences Chinese Academy of Sciences Shanghai 200031 China National Institute of Biological Sciences Beijing 102206 China

Mechanistic target of rapamycin （mTOR） complex 1 （mTORC1） integrates signals from growth factors, cel- lular energy levels, stress and amino acids to control cell growth and proliferation through regulating trans- lation, autophagy and metabolism. Here we determined the cryo-electron microscopy structure of human mTORC1 at 4.4 A resolution. The mTORCI comprises a dimer of heterotrimer （mTOR-Raptor-mLST8） mediated by the mTOR protein. The complex adopts a hollow rhomboid shape with 2-fold symmetry. Notably, mTORC1 shows intrinsic conformational dynamics. Within the complex, the conserved N-terminal caspase- like domain of Raptor faces toward the catalytic cavity of the kinase domain of mTOR. Raptor shows no caspase activity and therefore may bind to TOS motif for sub- strate recognition. Structural analysis indicates that FKBP12-Rapamycin may generate steric hindrance forsubstrate entry to the catalytic cavity of mTORCI. The structure provides a basis to understand the assembly of mTORC1 and a framework to characterize the regu- latory mechanism of mTORC1 pathway.

关键词： mTORC1 structure cryo-electronmicroscopy

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