ICNP与SeqCode：组学时代原核生物命名面临的机遇与挑战

自1936年细菌学家Buchanan负责起草专门的细菌命名法规以来,国际原核生物命名法规(International Code of Nomenclature of Prokaryotes, ICNP)在不断发展和完善过程中,积极促进了原核生物分类学及相关学科的发展。随着组学技术在原核生物多样性研究中的应用,越来越多未培养的细菌和古菌新类群被发现,却因为ICNP要求活的生物材料作为命名模式(nomenclatural type),而无法获得生效名称(validly published name)。2022年,原核生物命名法规从序列数据描述原核生物命名法(Code of Nomenclature of Prokaryotes Described from Sequence Data, SeqCode)正式发布,以补充ICNP在未培养微生物类群命名方面的不足。SeqCode不希望和ICNP产生较大分歧,并尽可能保留在将来和ICNP合并的可能性。然而,作为两种独立运行的命名法规,尚不明确SeqCode和ICNP并存会对学术界产生怎样的影响。本文系统介绍了ICNP和SeqCode各自的发展历程和主要内容,分析了二者的优势和局限性,并呼吁微生物学相关领域的学者共同关注原核生物命名法规并应用于实践,以期构建更加合理、有效的原核生物名称系统。     

Cassava breeding: opportunities and challenges

Although cassava is a major food crop, its scientific breeding began only recently compared with other crops. Significant progress has been achieved, particularly in Asia where cassava is used mainly for industrial processes and no major biotic constraints affect its productivity. Cassava breeding faces several limitations that need to be addressed. The heterozygous nature of the crop and parental lines used to generate new segregating progenies makes it difficult to identify parents with good breeding values. Breeding so far has been mainly based on a mass phenotypic recurrent selection. There is very little knowledge on the inheritance of traits of agronomic relevance. Several approaches have been taken to overcome the constraints in the current methodologies for the genetic improvement of cassava. Evaluations at early stages of selection allow for estimates of general combining ability effect or breeding values of parental lines. Inbreeding by sequential self-pollination facilitates the identification of useful recessive traits, either already present in the Manihot gene pool or induced by mutagenesis.     

Sex in the postgenomic era

The possible existence of ancient asexual lineages has long puzzled evolutionary biologists because a lack of recombination should, in theory, cause such lineages to be short lived. Recent research on what was considered to be a classic example of a such a lineage, an all-female polyploid hybrid complex of Ambystoma salamanders, not only refutes previous allegations of sexual abstinence in this complex, but also provides insights into unprecedented flexibility in interactions between genomes residing within individuals. These studies have important implications for understanding mechanisms for maintaining a functional balance between hybridizing genomes. They also demonstrate how combining genomic tools with older techniques can change current views on the rules governing genetic exchange.     

Data integration in the era of omics: current and future challenges

To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.     

基因组学时代的真菌分类学:机遇与挑战

真菌物种的形态特征有限,加之形态滞后和形态可塑性,仅靠外部形态、内部结构及生理生化指标,很难把握真菌的系统亲缘。应用DNA测序、基因组测序、比较基因组学及生物信息学等技术,研究人员可以快速识别真菌演化中出现的数量众多的单系支系,为建立各分类等级的新分类单元提供有力证据,为真菌分类学研究带来了新的希望和活力。自2000年以来,在真菌界至少发表了1新亚界、4新门、7新亚门、19新纲、9新亚纲、40余新目等高级分类单元。近3年来,我国发表了20余个真菌新属,其中绝大多数属的建立都有分子证据支持。可以预见,大量的新种、新属、新科乃至更高级分类单元将会在今后10年内持续发现和建立。这必将大大促进真菌分类学的发展,完善现有的真菌分类系统。我们应该顺势而上,利用我国丰富的真菌资源,为真菌分类学的发展做出应有贡献。与此同时,真菌分类学也面临着十分严峻的挑战。挑战主要来自3个方面,一是研究变得越来越综合,不但需要有相应的研究经费支持,而且要求从事该领域的研究人员技术更全面、知识更广博及知识更新速度更快捷;二是新物种描述进度偏慢,远远不能满足人们对物种认识和利用的日益增长的需要;三是研究人员亟需创新研究模式,以新技术、新思路、新机制来构建新的真菌分类学,加速新物种的发现和描述进度,最终为社会进步和科学发展服务。     

Plasmodium research in the postgenomic era

The complete genomic sequence of Plasmodium falciparum strain 3D7 was published in October 2002. At the Next Steps in Malaria Research meeting in April 2005, the next practical steps were considered and the priorities ranked for postgenomic research in Plasmodium. The high-throughput approaches that will help to answer the major biological questions regarding Plasmodium should, like the genome project itself, build community-shared resources, and efforts must be made to help researchers ready themselves to use the tools that will become available.     

Protein structure prediction in the postgenomic era

As the number of completely sequenced genomes rapidly increases, the postgenomic problem of gene function identification becomes ever more pressing. Predicting the structures of proteins encoded by genes of interest is one possible means to glean subtle clues as to the functions of these proteins. There are limitations to this approach to gene identification and a survey of the expected reliability of different protein structure prediction techniques has been undertaken.     

后基因组时代的代谢工程:机遇与挑战

代谢工程的研究目的是要改进细胞性质,增加工业生物产品的收率及生产能力。现在越来越多的生物基因测序的完成及功能基因组学研究的进展正把代谢工程研究引入一个新时代。代谢工程正面临一个极好的机遇,同时也遇到一些严重的挑战。这是由于细胞内存在着复杂的,非线性的,在酶、调控子及代谢物之间未知的相互作用．从而使代谢途径的优化极为困难。为了促进后基因组时代代谢工程的研究,综述了过去13年基于功能基因组学的代谢工程原理与方法的国内外研究进展,功能基因组学与代谢工程之间的关系以及后基因组时代代谢工程面临的机遇与挑战。     

Functional screening revisited in the postgenomic era

Functional screening can reveal a hidden function of a gene. cDNA library-based functional screening has flourished in various fields of biology so far, such as cancer biology, developmental biology and neuroscience. In the postgenomic era, however, various sequence database and public full-length cDNA resources are available, which now allow us to perform more straightforward, gene-oriented screening. Furthermore, the advent of RNA interference techniques has made it possible to perform effective loss-of-function screening. Gene-based functional screening is able to bridge the gap between genes and biological phenomena and raise important biological questions which should be tackled by integration of 'omic' datasets. These possible roles of functional screening will become more and more important in modern molecular biology moving toward the system level understanding of living organisms.     

Strain improvement in actinomycetes in the postgenomic era

With the recent advances in DNA sequencing technologies, it is now feasible to sequence multiple actinomycete genomes rapidly and inexpensively. An important observation that emerged from early Streptomyces genome sequencing projects was that each strain contains genes that encode 20 or more potential secondary metabolites, only a fraction of which are expressed during fermentation. More recently, this observation has been extended to many other actinomycetes with large genomes. The discovery of a wealth of orphan or cryptic secondary metabolite biosynthetic gene clusters has suggested that sequencing large numbers of actinomycete genomes may provide the starting materials for a productive new approach to discover novel secondary metabolites. The key issue for this approach to be successful is to find ways to turn on or turn up the expression of cryptic or poorly expressed pathways to provide material for structure elucidation and biological testing. In this review, I discuss several genetic approaches that are potentially applicable to many actinomycetes for this application.     

Assignment of protein function in the postgenomic era

Genome sequencing projects have provided researchers with an unprecedented boon of molecular information that promises to revolutionize our understanding of life and lead to new treatments of its disorders. However, genome sequences alone offer only limited insights into the biochemical pathways that determine cell and tissue function. These complex metabolic and signaling networks are largely mediated by proteins. The vast number of uncharacterized proteins found in prokaryotic and eukaryotic systems suggests that our knowledge of cellular biochemistry is far from complete. Here, we highlight a new breed of 'postgenomic' methods that aim to assign functions to proteins through the integrated application of chemical and biological techniques.     

Human nutrition and food research: opportunities and challenges in the post-genomic era

Sequencing of the human genome has opened the door to the most exciting new era for nutritional science. It is now possible to study the underlying mechanisms for diet-health relationships, and in the near future dietary advice (and possibly tailored food products) for promoting optimal health could be provided on an individual basis, in relation to genotype and lifestyle. The role of food in human evolution is briefly reviewed, from palaeolithic times to modern-day hunter-gatherer societies. The aetiology of 'diseases of modern civilization', such as diabetes, heart disease and cancer, and the effect of changes in dietary patterns are discussed. The risk of disease is often associated with common single nucleotide polymorphisms, but the effect is dependent on dietary intake and nutritional status, and is often more apparent in intervention studies employing a metabolic challenge. To understand the link between diet and health, nutritional research must cover a broad range of areas, from molecular to whole body studies, and is an excellent example of integrative biology, requiring a systems biology approach. The annual cost to the National Health Service of diet-related diseases is estimated to be in excess of 15 billion, and although diet is a key component of any preventative strategy, it is not given the prominence it deserves. For example, less than 1% of the pound 1.6 billion budget for coronary heart disease is spent on prevention. The polygenic and multifactorial nature of chronic diseases requires substantial resources but the potential rewards, in terms of quality of life and economics, are enormous. It is timely therefore to consider investing in a long-term coordinated national programme for nutrition research, combining nutritional genomics with established approaches, to improve the health of individuals and of the nation.     

Advances on Vibrio parahaemolyticus research in the postgenomic era

Vibrio parahaemolyticus is a leading cause of seafood-borne bacterial gastroenteritis in humans. Since its discovery in 1950, this bacterium has been isolated in widespread outbreaks and in sporadic cases of gastroenteritis worldwide. Although the exotoxin, thermostable direct hemolysin, had been the focus of extensive research on the pathogenicity of V. parahaemolyticus, the whole-genome sequencing of a clinical isolate, RIMD2210633 strain, was a breakthrough in this field. The possession of two sets of gene clusters for type III secretion systems (T3SS1 and T3SS2) was unveiled by that genome project. T3SS is a protein export apparatus that delivers bacterial proteins, called effectors, directly into the host's cytosol, to disrupt host cell function. The subsequent studies have established that T3SS2, which is encoded in an 80 kb pathogenicity island called V. parahaemolyticus pathogenicity island (Vp-PAI), is closely related to enteropathogenicity. Recent functional analyses of Vp-PAI-encoded genes revealed the sophisticated mechanisms in V. parahaemolyticus for sensing the intestinal environment and host cell contact, and a dozen T3SS2-exported proteins encoded in Vp-PAI. In this review, we summarize recent advances in V. parahaemolyticus research regarding the control of the expression of Vp-PAI-encoded genes, structural components and the secretory regulation of T3SS2, and the biological activities of T3SS2-exported effectors. Thus, Vp-PAI-encoded T3SS2 becomes an important key in the postgenomic era to shed light on the enteropathogenic mechanism of V. parahaemolyticus.     

Polyhydroxyalkanoates,challenges and opportunities

Open and continuous production of PHA by the constructed super PHA producer.

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