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Molecular dynamics simulation studies on some topics of water molecules on hydrophobic surfaces

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Nuclear Science and Techniques 2006年第2期17卷 71-77页

作者： FANG Hai-Ping HU Jun Shanghai Institute of applied Physics the Chinese Academy of Sciences Shanghai 201800 China Bio-X life Sciences Research center College of Life Science and Technology Shanghai Jiaotong University Shanghai 200030 China

Molecular dynamics simulations have been used to study two topics of water molecules on hydrophobic surfaces. Some properties of the nanobubbles with different ingredients and behavior of single water chains in sin- gle-walled carbon nanochannels are exploited. Molecular simulations show that the density of the N2 and H2 are quite high, which is critical for the stability of the nanobubbles and may have potential applications, such as hydrogen storage, incorporated with recent experimental method to controllably produce hydrogen nanobubbles. The water molecules inside the nanochannel show an unexpected directed motion with long time period, which is indispensable in the future study of the dynamics of biological channels.

关键词：分子动力学模拟纳米通道水分子防水薄膜

MosaicBase:A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals

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Genomics, Proteomics & bioinformatics 2020年第2期18卷 140-149页

作者： Xiaoxu Yang Changhong Yang Xianing Zheng Luoxing Xiong Yutian Tao Meng Wang Adam Yongxin Ye Qixi Wu Yanmei Dou Junyu Luo Liping Wei August Yue Huang center for bioinformatics State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijing 100871China Department of bioinformatics Chongqing Medical UniversityChongqing 400016China College of life Sciences Beijing Normal UniversityBeijing 100875China National Institute of Biological Sciences Beijing 102206China Peking-Tsinghua center for life Sciences(CLS) Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 100730China School of life Sciences Peking UniversityBeijing 100871China

Mosaic variants resulting from postzygotic mutations are prevalent in the human genome and play important roles in human ***,except for cancer-related variants,there is no collection of postzygotic mosaic variants in noncancer disease-related and healthy ***,we present MosaicBase,a comprehensive database that includes 6698 mosaic variants related to 266 noncancer diseases and 27,991 mosaic variants identified in 422 healthy *** and phenotypic information of each variant was manually extracted and curated from 383 *** supports the query of variants with Online Mendelian Inheritance in Man(OMIM)entries,genomic coordinates,gene symbols,or Entrez *** also provide an integrated genome browser for users to easily access mosaic variants and their related annotations for any genomic *** analyzing the variants collected in MosaicBase,we find that mosaic variants that directly contribute to disease phenotype show features distinct from those of variants in individuals with mild or no phenotypes,in terms of their genomic distribution,mutation signatures,and fraction of mutant *** will not only assist clinicians in genetic counseling and diagnosis but also provide a useful resource to understand the genomic baseline of postzygotic mutations in the general human *** is publicly available at http://***/or http://49.***.21.8:8000.

关键词： Postzygotic Mosaicism Noncancer Mutation MosaicBase

Mitochondrion-processed TERC regulates senescence without affecting telomerase activities

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Protein & Cell 2019年第9期10卷 631-648页

作者： Qian Zheng Peipei Liu Ge Gao Jiapei Yuan Pengfeng Wang Jinliang Huang Leiming Xie Xinping Lu Fan Di Tanjun Tong Jun Chen Zhi Lu Jisong Guan Geng Wang MOE Key laboratory of bioinformatics Cell Biology and Development CenterSchool of Life SciencesTsinghua University Beijing 100084China Peking University Research center on Aging Beijing 100191China Department of Biochemistry and Molecular Biology Peking University Health Science CenterBeijing 100191China

Mitochondrial dysfunctions play major roles in *** mitochondrial stresses invoke downstream responses and how specificity of the signaling is achieved, however, remains unclear. We have previously discovered that the RNA component of Telomerase TERC is imported into mitochondria, processed to a shorter form TERC-53, and then exported back to the cytosol. Cytosolic TERC-53 levels respond to mitochondrial functions, but have no direct effect on these functions, suggesting that cytosolic TERC-53 functions downstream of mitochondria as a signal of mitochondrial functions. Here, we show that cytosolic TERC-53 plays a regulatory role on cellular senescence and is involved in cognition decline in 10 months old mice, independent of its telomerase function. Manipulation of cytosolic TERC-53 levels affects cellular senescence and cognition decline in 10 months old mouse hippocampi without affecting telomerase activity, and most importantly, affects cellular senescence in terc^-/- cells. These findings uncover a senescence-related regulatory pathway with a non-coding RNA as the signal in mammals.

关键词： mitochondria retrograde signal nucleus transcription regulation non-coding RNA telomerase

Successive Picket Drive for Mitigating the Ablative Richtmyer–Meshkov Instability

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Chinese Physics Letters 2019年第2期36卷 28-31页

作者： Meng Li Wen-Hua Ye Institute of applied Physics and Computational Mathematics center for applied Physics and Technology HEDPS Peking University

The ablative Richtmyer–Meshkov instability(ARMI) is crucial to the successful ignition implosion of the inertial confinement fusion(ICF) because of its action as the seed of the Rayleigh–Taylor instability. In usual ICF implosions, the first shock driven by various foots of the pulses plays a central role in the ARMI growth. We propose a new scheme for refraining from ARMI with a pulse of successive pickets. With the successive-picket pulse design, a rippled capsule surface is compressed by three successive shocks with sequentially strengthening intensities and ablated stabilization, and the ablative Richtmyer–Meshkov growth is mitigated quite *** numerical simulations and theoretical analyses identify the validity of this scheme.

关键词： RMI ICF Successive Picket Drive for Mitigating the Ablative Richtmyer Meshkov Instability

Next-generation sequencing technologies for personalized medicine:promising but challenging

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Science China(life Sciences) 2013年第2期56卷 101-103页

作者： CHEN Geng SHI TieLiu center for bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal University

In the past several years, next-generation sequencing （NGS） technologies have greatly revolutionized our approaches to explore and depict the characteristics and functions of the genomes for various species. The NGS technologies have been broadly used in diverse fields including genomics （genome sequencing and exome sequencing） ,

关键词：测序技术个性化挑战性基因组测序医药基因组学物种

Review of the current status of fast ignition research atthe IAPCM

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High Power Laser Science and Engineering 2014年第1期2卷 4-12页

作者： Hong-bo Cai Si-zhong Wu Jun-feng Wu Mo Chen Hua Zhang Min-qing He Li-hua Cao Cang-tao Zhou Shao-ping Zhu Xian-tu He Institute of applied Physics and Computational Mathematics center for applied Physics and Technology Peking University

We review the present status and future prospects of fast ignition(FI) research of the theoretical group at the IAPCM(Institute of applied Physics and Computational Mathematics, Beijing) as a part of the inertial confinement fusion project. Since the approval of the FI project at the IAPCM, we have devoted our efforts to improving the integrated codes for FI and designing advanced targets together with the experimental group. Recent FI experiments [K. U. Akli et al., Phys. Rev. E 86, 065402(2012)] showed that the petawatt laser beam energy was not efficiently converted into the compressed core because of the beam divergence of relativistic electron beams. The coupling efficiency can be improved in three ways:(1) using a cone–wire-in-shell advanced target to enhance the transport efficiency,(2) using external magnetic fields to collimate fast electrons, and(3) reducing the prepulse level of the petawatt laser beam. The integrated codes for FI, named ICFI, including a radiation hydrodynamic code, a particle-in-cell(PIC) simulation code,and a hybrid fluid–PIC code, have been developed to design this advanced target at the IAPCM. The Shenguang-II upgraded laser facility has been constructed for FI research; it consists of eight beams(in total 24 kJ/3ω, 3 ns) for implosion compression, and a heating laser beam(0.5–1 kJ, 3–5 ps) for generating the relativistic electron beam. A fully integrated FI experiment is scheduled for the 2014 project.

关键词： fast ignition integrated simulation codes

Comparative population genomics dissects the genetic basis of seven domestication traits in jujube

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Horticulture Research 2020年第1期7卷 1769-1782页

作者： Mingxin Guo Zhongren Zhang Yanwei Cheng Sunan Li Peiyin Shao Qiang Yu Junjie Wang Gan Xu Xiaotian Zhang Jiajia Liu Linlin Hou Hanxiao Liu Xusheng Zhao College of life Sciences Luoyang Normal UniversityLuoyang 471934China Jujube Research center Luoyang Normal UniversityLuoyang 471934China Novogene bioinformatics Institute Beijing 100083China

Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural *** was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly ***,we report a comprehensive genome variation map based on the resequencing of 350 accessions,including wild,semi-wild and cultivated jujube plants,at a>15×*** the combination of a genome-wide association study(GWAS)and selective sweep analysis,we identified several candidate genes potentially involved in regulating seven domestication traits in *** fruit shape and kernel shape,we integrated the GWAS approach with transcriptome profiling data,expression analysis and the transgenic validation of a candidate gene to identify a causal gene,ZjFS3,which encodes an ethyleneresponsive transcription ***,we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using *** the selective sweep analysis,we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy *** study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.

关键词： jujube traits mining

EDdb:A web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder

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Science China(life Sciences) 2013年第11期56卷 1086-1096页

作者： ZHAO Min LI XiaoMo QU Hong center for bioinformatics State Key Laboratory of Protein and Plant Gene ResearchCollege of Life SciencesPeking University

Eating disorder is a group of physiological and psychological disorders affecting approximately 1% of the female population worldwide. Although the genetic epidemiology of eating disorder is becoming increasingly clear with accumulated studies, the underlying molecular mechanisms are still unclear. Recently, integration of various high-throughput data expanded the range of candidate genes and started to generate hypotheses for understanding potential pathogenesis in complex diseases. This article presents EDdb （Eating Disorder database）, the first evidence-based gene resource for eating disorder. Fifty-nine experimentally validated genes from the literature in relation to eating disorder were collected as the core dataset. Another four datasets with 2824 candidate genes across 601 genome regions were expanded based on the core dataset using different criteria （e.g., protein-protein interactions, shared cytobands, and related complex diseases）. Based on human protein-protein interaction data, we reconstructed a potential molecular sub-network related to eating disorder. Furthermore, with an integrative pathway enrichment analysis of genes in EDdb, we identified an extended adipocytokine signaling pathway in eating disorder. Three genes in EDdb （AD1PO （adiponectin）, TNF （tumor necrosis factor） and NR3C1 （nuclear receptor subfamily 3, group C, mem- ber 1）） link the KEGG （Kyoto Encyclopedia of Genes and Genomes）＂adipocytokine signaling pathway＂ with the BioCarta ＂visceral fat deposits and the metabolic syndrome＂ pathway to form a joint pathway. In total, the joint pathway contains 43 genes, among which 39 genes are related to eating disorder. As the first comprehensive gene resource for eating disorder, EDdb （http：//***） enables the exploration of gene-disease relationships and cross-talk mechanisms between related disorders. Through pathway statistical studies, we revealed that abnormal body weight caused by eating disorder and obesity may both be rela

关键词： eating disorder database adipocytokine signaling pathway pathway analysis

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Dynamic Perception of Jasmonates by the F-Box Protein C0l1

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Molecular Plant 2018年第10期11卷 1237-1247页

作者： Jianbin Yan Ruifeng Yao Li Chen Suhua Lit Min Gut Fajun Nan Daoxin Xie MOE Key Laboratory of bioinformatics Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China State Key Laboratory of Drug Research the National Center for Drug Screening Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai201203 China These authors contributed equally to this article.

Jasmonates （JAs） are cyclic fatty acid-derived phytohormones that regulate diverse aspects of plant defense and development. The endogenous active JA molecule （＋）-7-iso-JA-L-Ile （JA-Ile） and its analog coronatine trigger formation of a complex with the F-box protein C011 and JAZ repressors to induce degra- dation of the JAZs through the 26S proteasome pathway in a COil-dependent manner. To reveal the forma-tion process of COI1-JA-JAZ ternary complex, we employed several biochemical approaches to examine how JA is dynamically perceived. These analyses showed that the COI1 proteins of Arabidopsis and rice bind JA with appreciable binding affinity and revealed the kinetics and thermodynamics of the COI1-JA-JAZ ternary complex. Our results suggest that COI1 is the primary receptor perceiving the active JA molecule to initially form a COI1-JA complex that subsequently recruits JAZs for further signal transduction.

关键词： phytohormone receptor jasmonate C011