宏蛋白质组学信息分析的基本策略及其挑战

宏蛋白质组学是一门新型科学,它运用质谱技术规模化地采集自然界微生物种群的蛋白质信息,并结合多种组学数据,开展微生物种群的遗传特征及其生物功能的研究.宏蛋白质组学的信息分析与传统蛋白质组学方法有较大的不同,亟需拓展新的分析思路.由于宏蛋白质组的研究对象是复杂度极高的微生物样品,因此,需要构建尽可能囊括样本中所含微生物的基因组信息的物种数据库.面对庞大的数据库,必须考虑到分析过程中所消耗的计算资源和鉴定结果的质控标准,因此,需要高度优化库容量、搜库、假阳性控制等参数.鉴于宏蛋白质组数据中广泛存在复杂的同源蛋白质序列,因此,需要充分利用NCBI数据库中的分类信息进行匹配,并运用LCA算法过滤处理才能将蛋白质有效地归组到物种.本文立足于宏蛋白质组学信息分析,从宏蛋白质组的数据库建立、蛋白质归并、生物学意义发掘等几个方面着手,对该领域的发展现状、面临挑战以及未来研究方向进行了评述.     

Hope, Arkansas to Hope, Albania: naivete and idealism to reality and tragedy

The wars in Croatia, Bosnia and Kosovo were perpretrated by a radical nationalist Serbian cultural political consciousness that the American cultural political consciousness and leadership had difficulty responding to and understanding. There is a great cultural divide between a 'pathology' in Serbian culture, Milosevi?'s radical nationalism, and a humane 'naivete' in American cultural consciousness. I discuss why, finally, American political leadership, Bill Clinton from Hope, Arkansas, responded to the tragedy of these wars. However, we are still left with the question of good vs evil: What is the course of human history; psychotic political leadership causing repetitive human tragedy or can there be a higher humane and moral order to human cultural events?     

Translational Bioinformatics:Past,Present, and Future

Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex-tualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field.     

Trust,Identity, and Civic Hope

This article concerns the phenomenon of trust-in others who are familiar and in humanity in general. I make a case that the foundations of both forms of trust are rooted in formative experiences. Trust springs from the sense of security we develop in early nurturing relationships. In friendships and peer relationships we learn about loyalty, accountability, and the reciprocity between trust and trustworthiness. However, trust among friends is an insufficient basis for social trust. To nurture a faith in humanity, children need to interact and cooperate with people who are different from them and values of equality, tolerance, and empathy have to be high priorities in their families.     

Bioinformatics for glycomics: status, methods, requirements and perspectives

The term 'glycomics' describes the scientific attempt to identify and study all the glycan molecules - the glycome - synthesised by an organism. The aim is to create a cell-by-cell catalogue of glycosyltransferase expression and detected glycan structures. The current status of databases and bioinformatics tools, which are still in their infancy, is reviewed. The structures of glycans as secondary gene products cannot be easily predicted from the DNA sequence. Glycan sequences cannot be described by a simple linear one-letter code as each pair of monosaccharides can be linked in several ways and branched structures can be formed. Few of the bioinformatics algorithms developed for genomics/proteomics can be directly adapted for glycomics. The development of algorithms, which allow a rapid, automatic interpretation of mass spectra to identify glycan structures is currently the most active field of research. The lack of generally accepted ways to normalise glycan structures and exchange glycan formats hampers an efficient cross-linking and the automatic exchange of distributed data. The upcoming glycomics should accept that unrestricted dissemination of scientific data accelerates scientific findings and initiates a number of new initiatives to explore the data.     

Hope and Sorrow: Uncivil Religion,Tibetan Music Videos,and YouTube

Tibetan activists and their supporters are interpreting the lyrical and visual symbolism of contemporary Tibetan music videos from China as a call for Tibetans to return to a shared Tibetan identity, centered around religious piety and implied civil disobedience, in order to counter fears of cultural assimilation. As the popularity of some videos on social-networking sites dovetailed with the 2008 protests in Tibet, viewers employed a progressive hermeneutical strategy which demanded a sectarian political interpretation of the lyrics and imagery of the most popular videos out of Tibet. Within China, Tibetans have begun to add these videos to the growing canon of an emerging uncivil religion, which emphasizes Tibetan cultural, linguistic, and religious autonomy within China. Through comparing online and offline ethnography, this article explores the relationship between offline and online worlds and the connections between Tibetans in China and their supporters.     

Antibody fragments: Hope and hype

The antibody molecule is modular and separate domains can be extracted through biochemical or genetic means. It is clear from review of the literature that a wave of novel, antigen-specific molecular forms may soon enter clinical evaluation. This report examines the developmental histories of therapeutics derived from antigen-specific fragments of antibodies produced by recombinant processes. Three general types of fragments were observed, antigen-binding fragments (Fab), single chain variable fragments (scFv) and “third generation” (3G), each representing a successive wave of antibody fragment technology. In parallel, drug developers have explored multi-specificity and conjugation with exogenous functional moieties in all three fragment types. Despite high hopes and an active pipeline, enthusiasm for differentiating performance of fragments should, perhaps, be tempered as there are yet few data that suggest these molecules have distinct clinical properties due only to their size.Key words: antibody fragments, scFv, Fab, technology development, antibody-drug conjugate     

Bioinformatics: alive and kicking

Bioinformatics has become too central to biology to be left to specialist bioinformaticians. Biologists are all bioinformaticians now.     

Bioinformatics: alive and kicking

Bioinformatics has become too central to biology to be left to specialist bioinformaticians. Biologists are all bioinformaticians now.