位置：成果数据库 > 期刊 > 期刊详情页
夏威夷海洋微生物群落的功能基因组分析
  • ISSN号：1000-3282
  • 期刊名称：《生物化学与生物物理进展》
  • 时间：0
  • 分类：Q78[生物学—分子生物学] X55[环境科学与工程—环境工程]
  • 作者机构：[1]Department of Biomedical Engineering, College of Engineering,Peking University, Beijing 100871, China, [2]Center for Quantitative Biology, Peking University,Beijing 100871, China, [3]School of Life Sciences, Peking University, Beijing 100871,China
  • 相关基金：Acknowledgements This work was supported by the National ＂Twelfth Five-Year＂ Plan for Science and Technology of China （2012BAI06B02）, the National Natural Science Foundation of China （91231119, 30970667 and 11021463）, and the National Basic Research Program of China （2011CB707500）. We thank Prof. Zuhong Lu of Peking University for his interest to the project and valuable discussions. We also thank Dr. Yongchu Liu, Dr. Xiaobin Zheng, Longshu Yang, Feifei He, Qiuyue Wang, Fumeng Wang, and Peng Zhai for their helpful discussions.
作者： 王晓琦[1,2], 王琦[1,2], 郭潇[2], 刘璐瀛[1,2], 郭江涛[1,2], 姚锦仙[3], 朱怀球[1,2]
关键词： 功能基因组, 海洋环境, 宏基因组, 夏威夷, 微生物群落, 学分, 功能注释, 基因组分析, Marine microorganism , Metagenome Gene annotation , Codon usage bias , Metabolic pathway
中文摘要：

对宏基因组高通量测序数据的分析，是当前研究海洋微生物的重要方法．作者对夏威夷海域不同深度海水的微生物群落宏基因组进行功能基因组学分析．通过基因功能注释，发现了大量潜在的新基因，结果也表明极端环境加强了微生物密码子使用偏好．进一步根据光强、氧含量和低温高压等环境因素，进行代谢通路和基因序列分析，从分子水平上对海洋徽生物与环境的关联和适应性提出若干新的认识，探讨不同深度海洋环境中微生物特有的生存机制．

英文摘要：

Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.

同期刊论文项目
人肠道微生物组的基因预测与序列拼接方法研究
期刊论文 10
　视觉功能修复的基础理论与关键科学问题
期刊论文 22
生物网络研究
期刊论文 76
极端微生物宏基因组微进化的计算生物学研究
期刊论文 9 会议论文 1
同项目期刊论文
Salt-Induced Stabilization of EIN3/EIL1 Confers Salinity Tolerance by Deterring ROS Accumulation in
Functional genomic analysis of Hawaii marine metagenomes
Prediction of Translation Initiation Site in Bacterial and Archaeal Genomes
Horizontal gene transfer in an acid mine drainage microbial community
InteMAP: Integrated Metagenomic Assembly Pipeline for NGS Short Reads
大肠杆菌CFT073双拷贝pap操纵子动力学模型及致病机制研究
A mutation degree model for the identification of transcriptional regulatory elements
Understanding traditional Chinese medicine anti-inflammatory herbal formulae by simulating their reg
Inherent Relationships among Different Biophysical Prediction Methods for Intrinsically Disordered P
Evidences for the unfolding mechanism of three-dimensional domain swapping
Optimization of 5-hydroxytryptamines as dual function inhibitors targeting phospholipase A(2) and le
Computational Identification of a New Binding Site in Influenza Virus Hemagglutinin for Membrane Fus
Automatch: Target-binding protein design and enzyme design by automatic pinpointing potential active
Dynamic Modeling of Human 5-Lipoxygenase-Inhibitor Interactions Helps To Discover Novel Inhibitors
Sequence Preference of alpha-Helix N-Terminal Tetrapeptide
Dynamic eicosanoid responses upon different inhibitor and combination treatments on the arachidonic
Integrating Phosphorylation Network with Transcriptional Network Reveals Novel Functional Relationsh
Hybridization and amplification rate correction for affymetrix SNP arrays
Three-dimensional domain swapping in the protein structure space
Dynamical topology and statistical properties of spatiotemporal chaos
Experimental evidence of using a circularly polarized electric field to control spiral turbulence
Frequency-Dependent Escherichia coli Chemotaxis Behavior
Single Cell Analysis of Yeast Replicative Aging Using a New Generation of Microfluidic Device
Molecular phenotyping of aging in single yeast cells using a novel microfluidic device
Cell cycle synchronization by nutrient modulation
A parallel diffusion-based microfluidic device for bacterial chemotaxis analysis
Dynamic equilibrium between cancer stem cells and non-stem cancer cells in human SW620 and MCF-7 can
A novel density control device for the study of cancer cell autocrine effect
Decision making of the p53 network: Death by integration
Pathway-Based Mean-Field Model for Escherichia coli Chemotaxis
DNA damage strength modulates a bimodal switch of p53 dynamics for cell-fate control
A Reverse Engineering Approach to Optimize Experiments for the Construction of Biological Regulatory
A Formalized Design Process for Bacterial Consortia That Perform Logic Computing
Flux Balance Analysis of Ammonia Assimilation Network in E.coli Predicts Preferred Regulation Point
Discovery of novel chemoeffectors and rational design of Escherichia coli chemoreceptor specificity
Predicting kinetic constants of protein-protein interactions based on structural properties
Calumenin-15 facilitates filopodia formation by promoting TGF-beta superfamily cytokine GDF-15 trans
Molecular Docking and Competitive Binding Study Discovered Different Binding Modes of Microsomal Pro
Microsomal prostaglandin E synthase-1 exhibits one-third-of-the-sites reactivity
Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53
Do Intrinsically Disordered Proteins Possess High Specificity in ProteinProtein Interactions?
Microfluidic generation and dynamically switching of oxygen gradients applied to the observation of
Gene prediction in metagenomic fragments based on the SVM algorithm
Antibacterial properties of recombinant human non-pancreatic secretory phospholipase A(2)
Tailoring the pH Dependence of Human Non-pancreatic Secretory Phospholipase A(2) by Engineering Surf
Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers
Integrating multiple types of data to predict novel cell cycle-related genes
Statistical Analysis Reveals Co-Expression Patterns of Many Pairs of Genes in Yeast Are Jointly Regu
Operon Prediction Based On an Iterative Self-learning Algorithm
Dynamic behavior of small heat shock protein inhibition on amyloid fibrillization of a small peptide
LigBuilder 2: A Practical de Novo Drug Design Approach
Binding Site Detection and Druggability Prediction of Protein Targets for Structure-Based Drug Desig
Towards structure-based protein drug design
SDOCK: A Global Protein-Protein Docking Program Using Stepwise Force-Field Potentials
Engineering a zinc binding site into the de novo designed protein DS119 with a beta alpha beta struc
Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critica
Quinoline-4-methyl esters as human nonpancreatic secretory phospholipase A(2) inhibitors
Mass production of highly monodisperse polymeric nanoparticles by parallel flow focusing system
靛红类双功能抑制剂:调控SARS-3CL蛋白酶聚集状态与活性(英文)
Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo
Understanding molecular mechanisms of traditional Chinese medicine for the treatment of influenza vi
Slow and Bimolecular Folding of a De Novo Designed Monomeric Protein DS119
Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization
Scroll wave meandering induced by phase difference in a three-dimensional excitable medium
A microfluidic synchronizer for fission yeast cells
Evidence of negative-index refraction in nonlinear chemical waves
Automated Design of Genetic Toggle Switches with Predetermined Bistability
Adjustment method for microarray data generated using two-cycle RNA labeling protocol
蛋白质相互作用预测、设计与调控
Mechanism of 3D Domain Swapping for M-pro-C: Clues from Molecular Simulations
Differentiating stem cells on patterned substrates for neural network formation
大肠杆菌CFT073双拷贝pap操纵子动力学模型及致病机制研究
M~（pro）-C蛋白三维结构域交换的机理：来自分子模拟的线索
靛红类双功能抑制剂：调控SARS-3CL蛋白酶聚集状态与活性
基于迭代自学习的操纵子结构预测
Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryo
A de novo metagenomic assembly program for shotgun DNA reads
蛋白折叠中的暂态结构与表面水分子慢尺度动力学
大肠杆菌CFT073双拷贝pap操纵子动力学模型及致病机制研究
基于迭代自学习的操纵子结构预测
Characterization of Human Primary Chondrocytes of Osteoarthritic Cartilage at Varying Severity
金属与阿尔茨海默病的研究进展
沉默突触的激活机制及其功能意义
扇束等角型CT与等距型CT的比较研究
连续波核磁共振信号的解析
大黄酸对体外大鼠皮质神经元突起长度及微管相关蛋白2mRNA表达的影响
用于医学成像的碲锌镉单极型探测器研究进展
胰岛素对人RPE细胞增殖及转化生长因子-β2分泌的影响
数据插值对正电子发射断层成像设备的图像重建影响的研究
基于改进测地线模型的医学图像分割
高度近视患者玻璃体中MMP-2和TGF-β2水平与眼轴的相关性
基于支持向量机的肌电信号小波特征分类解码
高度近视黄斑裂孔性视网膜脱离手术后视网膜解剖结构及视功能变化
PI3K/Akt信号通路介导的胰岛素促RPE细胞增生及分泌转化生长因子β2作用
一种新型的小动物四模态分子医学影像系统
分子医学影像研究进展（上）
光声层析成像研究进展
分子影像探针-量子点在癌症成像和早期检测中的应用
PET/CT脑成像新药研究发展趋势及基于PET/CT设备的脑成像新药研发
分子医学影像设备研究进展（下）
期刊信息
  • 《生物化学与生物物理进展》
  • 中国科技核心期刊
  • 主管单位:中国科学院
  • 主办单位:中国科学院生物物理研究所 中国生物物理学会
  • 主编：王大成
  • 地址：北京市朝阳区大屯路15号
  • 邮编：100101
  • 邮箱：prog@sun5.ibp.ac.cn
  • 电话：010-64888459
  • 国际标准刊号：ISSN：1000-3282
  • 国内统一刊号：ISSN：11-2161/Q
  • 邮发代号:2-816
  • 获奖情况:
  • 1999年中国期刊奖提名奖,2000年中国科学院优秀期刊特别奖
  • 国内外数据库收录:
  • 美国化学文摘（网络版）,荷兰文摘与引文数据库,美国剑桥科学文摘,美国科学引文索引（扩展库）,美国生物科学数据库,日本日本科学技术振兴机构数据库,中国中国科技核心期刊,中国北大核心期刊（2004版）,中国北大核心期刊（2008版）,中国北大核心期刊（2011版）,中国北大核心期刊（2014版）,中国北大核心期刊（2000版）
  • 被引量:18821