生物信息学在免疫学上的应用

生物信息学的快速发展为免疫学的研究提供了新的手段,如果运用得当,能够大大加快研究进程,降低研究费用,缩短研究周期。兹从免疫学的常用数据库、免疫基因组以及MHC和多肽结合预测等3个方面,对生物信息学在免疫学中的应用进行了综述。国家自然科学基金资助项目(No.30400573

生物信息学在药物不良反应研究中的应用

目的介绍生物信息学在药物不良反应(ADRs)机制研究中的应用。方法通过对国内外相关文献的分析,并结合实际研究经验,对生物信息数据库及软件在ADR s事件监测,ADRs机制研究及新药的不良反应预测等方面的应用进行简明而系统论述。同时,对目前Internet上公众可获取的ADR s相关的生物信息学资源进行一定的汇总和归类。结果事实表明,将生物信息学应用于ADR s机制研究和预测,是一种可行、前瞻和先进的尝试。结论生物信息学在ADR s研究中的应用可以促进药物毒理学的发展,成为理性新药开发的重要组成,并标志着ADR s的研究进入了后基因组时代。国家自然科学基金资助项目(30400573

CytoSVM: an advanced server for identification of cytokine-receptor interactions

The interactions between cytokines and their complementary receptors are the gateways to properly understand a large variety of cytokine-specific cellular activities such as immunological responses and cell differentiation. To discover novel cytokine-receptor interactions, an advanced support vector machines (SVMs) model, CytoSVM, was constructed in this study. This model was iteratively trained using 449 mammal (except rat) cytokine-receptor interactions and about 1 million virtually generated positive and negative vectors in an enriched way. Final independent evaluation by rat's data received sensitivity of 97.4%, specificity of 99.2% and the Matthews correlation coefficient (MCC) of 0.89. This performance is better than normal SVM-based models. Upon this well-optimized model, a web-based server was created to accept primary protein sequence and present its probabilities to interact with one or several cytokines. Moreover, this model was applied to identify putative cytokine-receptor pairs in the whole genomes of human and mouse. Excluding currently known cytokine-receptor interactions, total 1609 novel cytokine-receptor pairs were discovered from human genome with probability ∼80% after further transmembrane analysis. These cover 220 novel receptors (excluding their isoforms) for 126 human cytokines. The screening results have been deposited in a database. Both the server and the database can be freely accessed at http://bioinf.xmu.edu.cn/software/cytosvm/cytosvm.php

GEPS: the Gene Expression Pattern Scanner

Gene Expression Pattern Scanner (GEPS) is a web-based server to provide interactive pattern analysis of user-submitted microarray data for facilitating their further interpretation. Putative gene expression patterns such as correlated expression, similar expression and specific expression are determined globally and systematically using geometric comparison and correlation analysis methods. These patterns can be visualized via linear plot with quantitative measures. User-defined threshold value is allowed to customize the format of the pattern search results. For better understanding of gene expression, patterns derived from 329 205 non-redundant gene expression records from the GNF SymAltas and the Gene Expression Omnibus are also provided. These profiles cover 24 277 human genes in 79 tissues, 32 905 mouse genes in 61 tissues and 4201 rat genes in 44 tissues. GEPS is available at

Frequency and distribution of AP-1 sites in the human genome

The AP-1-binding sequences are promoter/enhancer elements that play an essential role in the induction of many genes in mammalian cells; however, the number of genes containing AP-1 sites remains unknown. In order to better address the overall effect of AP-1 on expression of genes encoded by the entire genome, a genome-wide analysis of the frequency and distribution of AP-1 sites would be useful; yet to date, no such analysis of AP-1 sites or any other promoter/enhancer elements has been performed. We present here our study of the consensus AP-1 site and two single-bp variants showing that the frequency of AP-1 sites in promoter regions is significantly lower than their average rate of occurrence in the whole genomic sequence, as well as the frequency of a random heptanucleotide suggesting that nature has selected for a decrease in the frequency of AP-1 sites in the regulatory regions of genes. In addition, genes containing multiple AP-1 sites are more prevalent than those containing only one copy of an AP-1 site, which again may have evolved to allow for greater signal amplification or integration in the regulation of AP-1 target genes. However, the number of AP-1-regulated genes identified in various studies is far smaller than the number of genes containing potential AP-1 sites, indicating that not all AP-1 sites are activated in a given cell under a given condition, and is consistent with the prediction by others that cellular context determines which AP-1 sites are targeted by AP-1

中国海及邻近区域碳库与通量综合分析

中国海总面积约470万平方公里,纵跨热带、亚热带、温带、北温带等多个气候带.其中,南海北依\"世界第三极\"青藏高原、南邻\"全球气候引擎\"西太平洋暖池,东海拥有全球最宽的陆架之一,跨陆架物质运输显著,黄海是冷暖流交汇区域,渤海则是受人类活动高度影响的内湾浅海.中国海内有长江、黄河、珠江等大河输入,外邻全球两大西边界流之一的黑潮.这些鲜明的特色赋予了中国海碳储库和通量研究的典型代表意义.文章从不同海区（渤海、黄海、东海、南海）、不同界面（陆-海、海-气、水柱-沉积物、边缘海-大洋等）,以及不同生态系统（红树林、盐沼湿地、海草床、海藻养殖、珊瑚礁、水柱生态系统等）多层面对海洋碳库与通量进行了较系统地综合分析,初步估算了各个碳库的储量与不同碳库间的通量.就海气通量而言,渤海向大气中释放CO2约0.22Tg Ca-1,黄海吸收CO2约1.15Tg Ca-1,东海吸收CO2约6.92～23.30Tg Ca-1,南海释放CO2约13.86～33.60Tg Ca-1.如果仅考虑海-气界面的CO2交换,中国海总体上是大气CO2的\"源\",净释放量约6.01～9.33Tg Ca-1.这主要是由于河流输入以及邻近大洋输入所致.河流输入渤黄海、东海、南海的溶解无机碳（DIC）分别为5.04、14.60和40.14Tg Ca-1,而邻近大洋输入DIC更是高达144.81Tg Ca-1,远超中国海向大气释放的碳量.渤海、黄海、东海、南海的沉积有机碳通量分别为2.00、3.60、7.40、7.49Tg Ca-1.东海和南海向邻近大洋输送有机碳通量分别为15.25～36.70和43.39Tg Ca-1.就生态系统而言,中国沿海红树林、盐沼湿地、海草床有机碳埋藏通量为0.36Tg Ca-1,海草床溶解有机碳（DOC）输出通量为0.59Tg Ca-1;中国近海海藻养殖移出碳通量0.68Tg Ca-1,沉积和DOC释放通量分别为0.14和0.82Tg Ca-1.总计,中国海有机碳年输出通量为81.72～103.17Tg Ca-1.中国海的有机碳输出以DOC形式为主,东海向邻近大洋输出的DOC通量约15.00～35.00Tg Ca-1,南海输出约31.39Tg Ca-1.综上,尽管从海-气通量看中国海是大气CO2的\"源\",但考虑了河流、大洋输入、沉积输出以及微型生物碳泵（DOC转化输出）作用后,中国海是重要的储碳区.需要指出的是,文章数据是基于中国海各海区碳循环研究报道,鉴于不同研究方法上的差异,所得数据难免有一定的误差范围,亟待将来统一方法标准下的更多深入研究和分析.国家重点研发计划项目(编号:2016YFA0601400);;国家自然科学基金项目(批准号:91751207、91428308、41722603、41606153、41422603);;中央高校基础研究项目(编号:20720170107);;中海油项目(编号:CNOOC-KJ125FZDXM00TJ001-2014、CNOOCKJ125FZDXM00ZJ001-2014)资

The C-terminal region of envelope protein VP38 from white spot syndrome virus is indispensable for interaction with VP24

Natural Science Foundation of China [3077164035]; National "863'' Program of China [2006AA100312, 2006AA09Z445]; National "973'' Program of China [2006CB101801]White spot syndrome virus ( WSSV) is a large, rod-shaped, enveloped double-stranded DNA virus. In this study, VP38, a viral envelope protein, was expressed as a glutathione S-transferase (GST) fusion protein, and a polyclonal antibody against VP38 was obtained. Far-Western blotting and GST pull-down showed that VP38 interacted directly with VP24, a major WSSV envelope protein. In addition, to delineate the interaction region of VP38 with VP24, GST-VP38n (aa 1-142) and GST-VP38c ( aa 143-309) were expressed. The GST pull-down assay revealed that VP38 binds via its C-terminal region to VP24. The result implies that VP38 may participate in the formation of the WSSV envelope

Nuclear Transport Receptor,Importin β Family Proteins,and the Regulation Mechanisms in Nucleocytoplasmic Transport

核质转运是真核细胞的基本生命活动之一。Importinβ家族的蛋白质成员作为核质转运的受体,负责细胞内大部分蛋白质和核酸等生物大分子的跨核膜运输。同时,细胞通过多种方式对核质转运的过程进行精确调控,使底物能够在正确的时间与空间发挥功能,保证细胞增殖与分化的正常进行。核质转运的失调,则使得底物不能正常执行功能,导致个体发育的异常与疾病的发生。Nucleocytoplasmic transport of macromolecules is mediated by the soluble transport receptorscollectively named importin β super family proteins.RanGTP regulates the interactions between the receptors andcargos.In this review,we describe the structural features of importin β family proteins and possible regulationmechanisms in nucleocytoplasmic transport of large molecules,such as modulating the NLS/NES directly byphosphorylation,or covering the NLS/NES domain through polymerization.The precise regulation of nucleocyto-plasmic transport brings cargos to the correct subcellular locations,which is essential for the cargos’ cellularfunctions such as gene transcription regulation,cell cycle regulation,cell differentiation and proliferation.Disruptionof the nuclear import/export processes will result in the mislocation of cargoes,therefore causing developmentaldisorder and diseases.国家自然科学基金(No.3047085);; 福建省自然科学基金(No.C0510003)资助项目~

Regression methods for developing QSAR and QSPR models to predict compounds of specific pharmacodynamic, pharmacokinetic and toxicological properties

Mini-Reviews in Medicinal Chemistry7111097-1107MMCI

In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction

10.1016/j.toxlet.2005.11.017Toxicology Letters1642104-112TOLE