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蛋白质解折叠的拉伸分子动力学模拟效率优化

高分子学报 2024年第11期55卷 1608-1616页

作者：许超郑斌李森淼郑鹏南京大学化学与化工学院化学与生物医学创新中心、配位化学国家重点实验室南京210023

拉伸分子动力学(SMD)模拟是揭示生物大分子在机械力作用下行为的一种重要计算方法,与蛋白质展开的单分子力谱实验技术相似.尽管SMD模拟已经广泛应用,但由于模拟大分子系统的计算需求,研究范围受到限制.最近计算机硬件的技术进步使得更... 详细信息

拉伸分子动力学(SMD)模拟是揭示生物大分子在机械力作用下行为的一种重要计算方法,与蛋白质展开的单分子力谱实验技术相似.尽管SMD模拟已经广泛应用,但由于模拟大分子系统的计算需求,研究范围受到限制.最近计算机硬件的技术进步使得更广泛且经济的模拟成为可能.本研究基于白细胞介素-6(IL-6)的解折叠过程,寻找使用GROMACS进行SMD模拟的最佳硬件配置.研究表明,目前八核中央处理器(CPU)与一块图形处理器(GPU)的配置能提供最高效的性能.此外,具有更高频率的CPU和更强FP32计算能力的GPU可以显著提升模拟效果.此外,模拟体系原子数与模拟效率呈负相关,体系原子数小于1.2×10^(7)时这种相关性较为明显.本研究不仅明确了进行蛋白质展开的SMD模拟的最佳硬件设置,还将这种详细分子研究的可行性扩展到更广泛的研究中,为分子水平理解力学机制提供了一条更高效的途径,也为未来理解和研究更复杂的高分子在力学作用下的行为提供了重要基础.

关键词：分子动力学模拟蛋白质解折叠效率优化

Neurosyphilis complicated by anti-γ-aminobutyric acid-B receptor encephalitis: A case report

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World Journal of Clinical Cases 2024年第11期12卷 1960-1966页

作者： Ya-Xiu Fang Xiao-Ming Zhou Dong zheng Guang-Hui Liu peng-Bo Gao Xiao-Zhen Huang Zhi-Cheng Chen Hui Zhang Lin Chen Ya-Fang Hu Department of Neurology The Affiliated Brain Hospital of Guangzhou Medical UniversityGuangzhou 510000Guangdong ProvinceChina Department of Neurology Nanfang HospitalSouthern Medical UniversityGuangzhou 510000Guangdong ProvinceChina

BACKGROUND Syphilis is an infectious disease caused by Treponema pallidum that can invade the central nervous system,causing *** cases of anti-N-methyl-Daspartate receptor autoimmune encephalitis(AE)secondary to neurosyphilis have been *** report a neurosyphilis patient with anti-γ-aminobutyric acid-B receptor(GABABR)*** SUMMARY A young man in his 30s who presented with acute epileptic status was admitted to a local *** was diagnosed with neurosyphilis,according to serum and cerebrospinal fluid(CSF)tests for *** 14 d of antiepileptic treatment and anti-Treponema pallidum therapy with penicillin,epilepsy was controlled but serious cognitive impairment,behavioral,and serious psychiatric symptoms were *** was then transferred to our *** Mini-Mental State Examination(MMSE)crude test results showed only 2 *** magnetic resonance imaging revealed significant cerebral atrophy and multiple fluidattenuated inversion recovery high signals in the white matter surrounding both lateral ventricles,left amygdala and bilateral ***-GABABR antibodies were discovered in CSF(1:3.2)and serum(1:100).The patient was diagnosed with neurosyphilis complicated by anti-GABABR AE,and received methylprednisolone and *** treatment,his mental symptoms were *** impairment was significantly improved,with a MMSE of 8 *** anti-GABABR antibody titer decreased to 1:*** patient received methylprednisolone and penicillin after *** months later,the patient’s condition was stable,but the serum anti-GABABR antibody titer was 1:*** This patient with neurosyphilis combined with anti-GABABR encephalitis benefited from immunotherapy.

关键词： Anti-γ-aminobutyric acid-B receptor GABABR Neurosyphilis Tissue-based assay Magnetic resonance imaging Mini-mental state examination Case report

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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Molecular Plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu peng zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State Key Laboratory of Rice Biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan Institute of Zhejiang University Sanya 572025China National Key Laboratory of Plant Molecular Genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China Department of Molecular Biology and Center for Computational and Integrative Biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

Efficient DIPA-CRISPR-mediated knockout of an eye pigment gene in the white-backed planthopper,Sogatella furcifera

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Insect Science 2024年第4期31卷 1015-1025页

作者： Meng-Qi Zhang Lang-Lang Gong Ya-Qin Zhao Yun-Feng Ma Gui-Jun Long Huan Guo Xuan-zheng Liu J.Joe Hull Youssef Dewer Chao Yang Ning-Ning Zhang Ming He peng He National Key Laboratory of Green Pesticides Key Laboratory of Green Pesticide and Agricultural BioengineeringMinistry of EducationCenter for R&D of Fine Chemicals of Guizhou UniversityGuiyangChina Pest Management and Biocontrol Research Unit US Arid Land Agricultural Research CenterUSDA Agricultural Research ServicesMaricopaArizonaUSA Phytotoxicity Research Department Central Agricultural Pesticide LaboratoryAgricultural Research CenterDokkiGizaEgypt Guizhou Jifeng Seed Industry Limited Liability Company XingyiGuizhou ProvinceChina Shandong Facility Horticulture Bioengineering Research Center Weifang University of Science and TechnologyWeifangShandong ProvinceChina

Although CRISPR/Cas9 has been widely used in insect gene editing,the need for the microinjection of preblastoderm embryos can preclude the technique being used in insect species with eggs that are small,have hard shells,and/or are difficult to collect and maintain outside of their normal *** is the case with Sogatella furcifera,the white-backed planthopper(WBPH),a significant pest of Oryza sativa(rice)that oviposits inside rice *** extraction from the stem runs the risk of mechanical damage and hatching is heavily influenced by the micro-environment of the rice *** bypass these issues,we targeted embryos prior to oviposition via direct parental(DIPA)-CRISPR,in which Cas9 and single-guide RNAs(sgRNAs)for the WBPH eye pigment gene tryptophan 2,3-dioxygenase were injected into the hemocoel of adult *** at varying numbers of days posteclosion were evaluated to determine at what stage their oocyte might be most capable of taking up the gene-editing *** evaluation of the offspring indicated that the highest G0 gene-edited efficacy(56.7%)occurred in females injected 2 d posteclosion,and that those mutations were heritably transmitted to the G1 *** study demonstrates the potential utility of DIPA-CRISPR for future gene-editing studies in non-model insect species and can facilitate the development of novel pest management applications.

关键词： CRISPR/Cas9 DIPA-CRISPR gene editing tryptophan 2,3-dioxygenase WBPH

Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

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Frontiers of Medicine 2024年第1期18卷 109-127页

作者： Guoqiang Li peng Pu Mengqiao Pan Xiaoling Weng Shimei Qiu Yiming Li Sk Jahir Abbas Lu Zou Ke Liu zheng Wang Ziyu Shao Lin Jiang Wenguang Wu Yun Liu Rong Shao Fatao Liu Yingbin Liu Department of Biliary-Pancreatic Surgery Renji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer InstituteShanghai200127China Shanghai Key Laboratory of Biliary Tract Disease Shanghai200082China Department of Health Science and Engineering University of Shanghai for Science and TechnologyShanghai200082China Shanghai Tenth People’s Hospital of Tongji University Shanghai200072China Department of General Surgery Xinhua HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200082China Department of Pharmacology Shanghai Jiao Tong University School of MedicineShanghai200025China

Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human ***,knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely ***,by taking advantage of in situ Hi-C,RNA-sequencing,and chromatin immunoprecipitation sequencing(ChIP-seq),we investigated structural reorganization and functional changes in chromosomal compartments,topologically associated domains(TADs),and CCCTC binding factor(CTCF)-mediated loops in gallbladder cancer(GBC)tissues and cell *** observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression *** inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal ***,the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control ***-specific enhancer–promoter loops,which contain multiple transcription factor binding motifs,acted as a central element to regulate aberrant gene *** of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene ***,our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.

关键词： 3D genome cancer TADs loop gene regulation

Six types of spin solitons in three-component Bose-Einstein condensates

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Communications in Theoretical Physics 2024年第6期76卷 57-65页

作者： Yu-Hao Wang Ling-zheng Meng Li-Chen Zhao School of Physics Northwest UniversityXi'an 710127China School of Science Xi'an Technological UniversityXi'an 710032China peng Huanwu Center for Fundamental Theory Xi'an 710127China

Exact analytical solutions are good candidates for studying and explaining the dynamics of solitons in nonlinear *** further extend the region of existence of spin solitons in the nonlinearity coefficient space for the spin-1 Bose-Einstein *** types of spin soliton solutions can be obtained,and they exist in different *** analysis and numerical simulation results indicate that three types of spin solitons are stable against weak *** non-integrable properties of the model can induce shape oscillation and increase in speed after the collision between two spin *** results further enrich the soliton family for non-integrable models and can provide theoretical references for experimental studies.

关键词： Bose-Einstein condensate non-integrable spin soliton exact analytical solution

Consensus statement on research and application of Chinese herbal medicine derived extracellular vesicles-like particles(2023 edition)

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Chinese Herbal Medicines 2024年第1期16卷 3-12页

作者： Qing Zhao Tong Wang Hongbin Wang peng Cao Chengyu Jiang Hongzhi Qiao Lihua peng Xingdong Lin Yunyao Jiang Honglei Jin Huantian Zhang Shengpeng Wang Yang Wang Ying Wang Xi Chen Junbing Fan Bo Li Geng Li Bifeng Liu Zhiyang Li Suhua Qi Mingzhen Zhang Jianjian zheng Jiuyao Zhou Lei zheng Kewei Zhao Guangdong Engineering Research Center of Chinese Herbal Vesicles The Third Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhou 510378China Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis The Third Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhou 510378China Institute of Life and Health Engineering the First Affiliated HospitalJinan UniversityGuangzhou 510630China School of Pharmaceutical Sciences Guangzhou University of Chinese MedicineGuangzhou 510006China College of Pharmacy Nanjing University of Chinese MedicineNanjing 210046China Institute of Basic Medicine Chinese Academy of Medical SciencesBeijing 100005China College of Pharmaceutical Sciences Zhejiang UniversityHangzhou 310030China School of Pharmaceutical Sciences Tsinghua UniversityBeijing 100084China Department of Bone and Joint Surgery The First Affiliated Hospital of Jinan UniversityGuangzhou 510630China State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoAomen 999078China Shanghai Jiao Tong University Affiliated Sixth People’s Hospital Shanghai 200233China School of Basic Medical Sciences Southern Medical UniversityGuangzhou 510515China School of Life Sciences Nanjing UniversityNanjing 210008China Nanfang Hospital Southern Medical UniversityGuangzhou 510515China Laboratory Animal Center Guangzhou University of Chinese MedicineGuangzhou 510405China College of Life Science and Technology Huazhong University of Science and TechnologyWuhan 430074China Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital Nanjing 210008China School of Medical and Technology Xuzhou Medical UniversityXuzhou 221004China School of Basic Medical Sciences Xi’an Jiaotong UniversityXi’an 710065China The First Affiliated Hospital of Wenzhou Medical University WenZhou 325035China

To promote the development of extracellular vesicles of herbal medicine especially the establishment of standardization,led by the National Expert Committee on Research and Application of Chinese Herbal Vesicles,research experts in the field of herbal medicine and extracellular vesicles were invited nationwide with the support of the Expert Committee on Research and Application of Chinese Herbal Vesicles,Professional Committee on Extracellular Vesicle Research and Application,Chinese Society of Research Hospitals and the Guangdong Engineering Research Center of Chinese Herbal *** on the collation of relevant literature,we have adopted the Delphi method,the consensus meeting method combined with the nominal group method to form a discussion draft of“Consensus statement on research and application of Chinese herbal medicine derived extracellular vesicles-like particles(2023)”.The first draft was discussed in online and offline meetings on October 12,14,November 2,2022 and April and May 2023 on the current status of research,nomenclature,isolation methods,quality standards and research applications of extracellular vesicles of Chinese herbal medicines,and 13 consensus opinions were finally *** the Third Academic Conference on Research and Application of Chinese Herbal Vesicles,held on May 26,2023,Kewei Zhao,convenor of the consensus,presented and read the consensus to the experts of the Expert Committee on Research and Application of Chinese Herbal *** consensus highlights the characteristics and advantages of Chinese medicine,inherits the essence,and keeps the righteousness and innovation,aiming to provide a reference for colleagues engaged in research and application of Chinese herbal vesicles at home and abroad,decode the mystery behind Chinese herbal vesicles together,establish a safe,effective and controllable accurate Chinese herbal vesicle prevention and treatment system,and build a bridge for Chinese medicine to the world.

关键词： Chinese herbal medicine extracellular vesicles research application consensus

Cinobufotalin prevents bone loss induced by ovariectomy in mice through the BMPs/SMAD and Wnt/β-catenin signaling pathways

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Animal Models and Experimental Medicine 2024年第3期7卷 208-221页

作者： Da-zhuang Lu Li-jun Zeng Yang Li Ran-li Gu Meng-long Hu Ping Zhang peng Yu Xiao Zhang zheng-wei Xie Hao Liu Yong-sheng Zhou Department of Prosthodontics Peking University School and Hospital of StomatologyBeijingChina National Center of Stomatology BeijingChina National Clinical Research Center for Oral Diseases BeijingChina Beijing Key Laboratory of Digital Stomatology BeijingChina Department of Cariology and Endodontology Peking University School and Hospital of StomatologyBeijingChina Peking University International Cancer Institute Peking University Health Science CenterPeking UniversityBeijingChina Central Laboratory Peking University School and Hospital of StomatologyBeijingChina National Engineering Research Center of Oral Biomaterials and Digital Medical Devices BeijingChina

Background:Osteoporosis is a chronic bone disease characterized by bone loss and decreased bone ***,current anti-resorptive drugs carry a risk of various *** deep learning-based efficacy prediction system(DLEPS)is a forecasting tool that can effectively compete in drug screening and prediction based on gene expression *** study aimed to explore the protective effect and potential mechanisms of cinobufotalin(CB),a traditional Chinese medicine(TCM),on bone ***:DLEPS was employed for screening anti-osteoporotic agents according to gene profile changes in primary ***-CT,histological and morphological analysis were applied for the bone protective detection of CB,and the osteogenic differentiation/function in human bone marrow mesenchymal stem cells(hBMMSCs)were also *** underlying mechanism was verified using qRT-PCR,Western blot(WB),immunofluorescence(IF),***:A safe concentration(0.25mg/kg in vivo,0.05μM in vitro)of CB could effectively preserve bone mass in estrogen deficiency-induced bone loss and promote osteogenic differentiation/function of *** BMPs/SMAD and Wnt/β-catenin signaling pathways participated in CB-induced osteogenic differentiation,further regulating the expression of osteogenesis-associated factors,and ultimately promoting ***:Our study demonstrated that CB could significantly reverse estrogen deficiency-induced bone loss,further promoting osteogenic differentiation/function of hBMMSCs,with BMPs/SMAD and Wnt/β-catenin signaling pathways involved.

关键词： BMPs/SMAD bone loss cinobufotalin hBMMSCs osteogenesis osteoporosis Wnt/β-catenin signaling pathways

恒流充电有限柱体电极浓度分布及扩散诱导应力解析分析

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物理学报 2024年第15期73卷 225-234页

作者：彭颖吒张锴郑百林同济大学航空航天与力学学院上海200092

常见的柱状电极模型中,在轴向方向一般采用无限长假设广义平面应变分析方法,本文考虑恒流充电下有限柱形电极模型,基于力-化耦合一般方程,推导出位移与扩散诱导应力解析解.有限柱体电极中浓度分布由仅考虑径向扩散和仅考虑轴向扩散两部... 详细信息

常见的柱状电极模型中,在轴向方向一般采用无限长假设广义平面应变分析方法,本文考虑恒流充电下有限柱形电极模型,基于力-化耦合一般方程,推导出位移与扩散诱导应力解析解.有限柱体电极中浓度分布由仅考虑径向扩散和仅考虑轴向扩散两部分叠加求解.将浓度函数代入力学方程,使用Boussinesq-Papkovich函数得到应力分量解析解.计算了表面自由柱状电极中浓度和应力场,并将其结果与有限元软件计算的结果进行对比计算.结果表明,理论解和数值解中浓度分布一致,应力分量趋势一致数值相差较小,在荷电状态为17.9%时径向应力在中心处相对误差最大约为4%.本文分析了不同长径比柱状电极中径向和轴向单向扩散对应力场的影响,结果表明,随着长径比的增大,轴向扩散对浓度分布影响下降,径向扩散对应力场影响上升.

关键词：锂离子电池有限柱体电极扩散诱导应力 Boussinesq-Papkovich 函数