系统分子生物学

系统分子生物学是在基因组学、蛋白质组学、信息科学和数学等学科基础上发展起来的综合性科学。它在多层次的技术平台上,研究生物体内的分子及其功能和相互作用,从而揭示生命活动的本质。

Epitypification:should we epitypify?

Epitypification can solve many taxonomic problems and stabilize the understanding of species, genera, families or orders. The aim of this paper is to illustrate how to epitypify. A few examples where taxa have been epitypified are considered and the benefits and disadvantages of epitypification are discussed. We also outline some examples of taxa which need to be epitypifled with reasons.

A hybrid neural network system for prediction and recognition of promoter regions in human genome

This paper proposes a high specificity and sensitivity algorithm called PromPredictor for recognizing promoter regions in the human genome. PromPredictor extracts compositional features and CpG islands information from genomic sequence,feeding these features as input for a hybrid neural network system (HNN) and then applies the HNN for prediction. It combines a novel promoter recognition model, coding theory, feature selection and dimensionality reduction with machine learning algorithm.Evaluation on Human chromosome 22 was ～66% in sensitivity and ～48% in specificity. Comparison with two other systems revealed that our method had superior sensitivity and specificity in predicting promoter regions. PromPredictor is written in MATLAB and requires Matlab to run. PromPredictor is freely available at http://www.whtelecom.com/Prompredictor.htm.

Effects of Nutrients on Biofouling Formation and Preponderant Bacteria Diversity in Recirculating Cooling Water System

A series of orthogonal array experiments were conducted using carbon source, ammonia nitrogen and total phosphorus （TP） as major influencing factors to investigate the effects of nutrients on biofouling formation and preponderant bacteria diversity in the recirculatiug cooling water system. Carbon source was demonstrated to be the most significant determinant affecting the biofouling formation. A minimum biofouling outcome was obtained when BOD2, NHa＋-N and TP were 25, 10, and 1 mg/L, respectively. Then the preponderant bacteria strains in biofouling mass under two typical culture conditions （negative and favorable） were identified applying both traditional biochemical methods and further molecular biology technology with phylogenetic affiliation analysis, which indicated that Enterobacteriaceae Enterobacter, Micrococcaceae Staphylococcus, Bacillaceae Bacillus, Enterobacteriaceae Proteus, Neisseriaceae Neisseria and Pseudomonadaceae Pseudomonas were dominant under negative condition, while Enterobacteriaceae Klebsiella, Enterobacteriaceae Enterobacter and Microbacterium - under favorable one.

Poly-contextural Logic： New Resource for Transdisciplinary Research in Sociology

A couple of decades ago natural phenomena began to be approached from a comprehensive and transdisciplinary point of view, as it was understood that living beings and their environments are not linear but complex. There is no doubt that this perspective of visualizing complexity and working inter- and trans-disciplinarily has to be applied. The reflection on the theoretical observation （i.e., meta-observation） involved in the concept of poly-contexturality is the framework in which a theory of complex systems is possible, which in turn enables an observation that oscillates （a concept of chaos theory） between models structured in a hierarchical order （normally linked to a logical-deductive formalization） and models structured in hetero-hierarchy. And this would allow this reflection to be done in a formalized language that does not follow either the principles of the Aristotelian logic or the postulates of the Kantian transcendental reflection. It is precisely this liberation from the dictates of mono-contextural logic what paves the way to an observation of complexity, in which one or the other language is used to model the states of things, such as the epistemological problems of molecular biology or the social systems. And-what is gaining relevance-it also paves the way to a true transdisciplinary meta-observation, since each discipline chooses its own contexture and only the use of poly-contexturality makes it possible to formulate transdisciplinary relationships within the framework of such meta-logic.

关于我国生物医学科学中长期战略发展和生物医学战略平台建设的建议

根据我国生物医学科学发展的现状和问题,文中提议在制订国家中长期科学和技术发展规划时应考虑国外当前生物医学科学战略转移所带来的挑战和机遇;建议以系统分子生物学和多系统生物学为基础,把“DNA复制调控和人类疾病”的研究作为我国生物医学科学中长期战略发展的一个切入点和突破点。以此搭建我国生物医学科学的战略平台,建设系统的国家生物医学学科和完整的生物医学科学研发体系,并充分发挥基金激励机制。

Application of Systems Biology Technology in Research of Traditional Chinese Medicine

Systems biology is an emerging science of the 21st century and its method and design of study resemble those of traditional Chinese medicine (TCM). Adopting systems biology technology will help to understand TCM Syndromes and modernize Chinese herbal medicine. The technology platforms of systems biology, especially proteomics can provide useful tools for exploring essence of TCM syndromes and understanding principle of herbal formulation. Moreover, compared with methods of molecular biology, such as genomics and proteomics, metabolomics provide more direct, rapid, concise and effective methods for study of kidney disease especially in the case of prevention and treatment with TCM.

Invasion genetics： Lessons from a ubiquitous bird, the house sparrow Passer domesticus

Following an introduction, non-native species are exposed to environments that differ from those found in their native range; further, as these non-native species expand beyond the site of introduction, they must constantly adapt to novel environ- ments. Although introduced species are present across most ecosystems, few species have successfully established themselves on a truly global scale. One such species, the house sparrow Passer domesticus, is now one of the world＇s most broadly distributed vertebrate species and has been introduced to a great part of its current range. To date, work on four continents suggests both ge- netic and phenotypic variation exists between native and introduced ranges. As such, house sparrows represent an excellent op- portunity to study adaptations to novel environments and how these adaptations are derived. The global distribution of this spe- cies and the multiple independent introductions to geographically isolated sites allow researchers to ask questions regarding ge- netic variation and adaptation on a global scale. Here, we summarize the molecular studies of invasive house sparrows from the earliest work using allozymes through more recent work on epigenetics; using these studies, we discuss patterns of dispersal of this species. We then discuss future directions in techniques （e.g. next generation sequencing） and how they will provide new in- sight into questions that are fundamental to invasion biology. Finally, we discuss how continued research on the house sparrow in light of these genetic changes and adaptations will elucidate answers of adaptation, invasion biology, range expansion, and resi- lience in vertebrate systems generally

Phylogeny of the Labeoninae （Teleostei, Cypriniformes） based on nuclear DNA sequences and implications on character evolution and biogeography

Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals （representing 24 genera and 73 species） of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine, a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.

Phylogeny and evolutionary history of the silkworm

The silkworm,Bombyx mori,played an important role in the old Silk Road that connected ancient Asia and Europe.However,to date,there have been few studies of the origins and domestication of this species using molecular methods.In this study,DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives.All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm.Domestication was estimated to have occurred about 4100 years ago(ya),and the radiation of the different geographic strains of B.mori about 2000 ya.The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya.These estimates are in good agreement with the fossil evidence and historical records.In addition,we show that the domesticated silkworm experienced a population expansion around 1000 ya.The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics,in the genetic analysis of domestic animals,and for understanding the spread of human civilizations.

Visible light-curable polymers for biomedical applications

Photocurable systems, which offer advantages such as microfabrication and in situ fabrication, have been widely used as dental restorative materials. Because the visible light-curable(VLC) system causes no biological damage, it is popular as a dental material and is being investigated by many researchers for other medical applications. Here, the principle of the VLC system is explained and recent progress in key components including photoinitiators, monomers, macromers, and prepolymers is discussed. Finally, biomedical applications for drug delivery and soft tissue engineering are reviewed. Considering the recent development of VLC systems, its importance in the field of medical applications is expected to continue to increase in the future.

Denitrification Rates and Their Controlling Factors in Streams of the Han River Basin with Different Land-Use Patterns

Land-use patterns can affect various nutrient cycles in stream ecosystems, but little information is available about the effects of urban development on denitrification processes at the watershed scale. In the presented study, we investigated the controlling factors of denitrification rates within the streams of the Han River Basin, Korea, with different land-use patterns, in order to enhance the effectiveness of water resource management strategies. Ten watersheds were classified into three land-use patterns （forest, agriculture and urban） using satellite images and geographic information system techniques, and in-situ denitrification rates were determined using an acetylene blocking method. Additionally, sediment samples were collected from each stream to analyze denitrifier communities and abundance using molecular approaches. In-situ denitrification rates were found to be in the order of agricultural streams （289.6 mg N20-N m-2 d-1） 〉 urban streams （157.0 mg N20-N m-2 d-1） 〉 forested streams （41.9 mg N20-N m-2 d-l）. In contrast, the average quantity of denitrifying genes was the lowest in the urban streams. Genetic diversity of denitrifying genes was not affected by watershed land-use pattern, but exhibited stream-dependent pattern. More significance factors were involved in denitrification in the sites with higher denitrification rates. Multiple linear regression analysis revealed that clay, dissolved organic carbon and water contents were the main factors controlling denitrification rate in the agricultural streams, while dissolved organic carbon was the main controlling factor in the urban streams. In contrast, temperature appeared to be the main controlling factor in the forested streams.

Zebrafish:A Renewed Model System For Functional Genomics

In the post genome era, a major goal in molecular biology is to determine the function of the many thousands of genes present in the vertebrate genome. The zebrafish （ Danio redo） provides an almost ideal genetic model to identify the biological roles of these novel genes, in part because their embryos are transparent and develop rapidly, The zebrafish has many advantages over mouse for genome-wide mutagenesis studies, allowing for easier, cheaper and faster functional characterization of novel genes in the vertebrate genome. Many molecular research tools such as chemical mutagenesis, transgenesis , gene trapping, gene knockdown,