Systems biology and metagenomics: a showcase of Chinese bioinformatics researchers and their work

<正>It is our great honor to guest-edit this Thematic Issue on Bioinformatics in Science China Life Sciences.In recent years,a strong cohort of Chinese scientists has emerged as leading scholars in the exciting fields of bioinformatics and computational biology.In this issue,we are pleased to present outstanding research work produced from 10 world renowned researchers.System biology and metagenomics are recently revitalized by the inception of next-generation sequencing technologies.The former seeks to understand the function and     

Evolutionary biology and practical conservation: bridging a widening gap

At the ecosystem, species and population level, available measures suggest that average rates of loss of populations and habitats are now around 1% per year and seem likely to increase in the future. Habitat conversion continues in most parts of the world, especially in areas of high species richness, and novel threats, especially climate change, will pose new challenges. With this pressure, maintaining evolutionary processes in natural populations will be critical to longer term persistence, and will often require specific planning relevant to the context. However, in many areas of policy and practice, urgent actions tend to focus on pattern-based analyses and considerations of evolutionary and ecological processes are neglected. At a variety of levels, from setting goals to implementing conservation management at the site or species level, there are simple adjustments that can be made. Improved methods for integrating the work of scientists and policymakers is recommended, from the beginning to end of the planning process.     

Genetics and conservation biology

Conservation genetics encompasses genetic management of small populations, resolution of taxonomic uncertainties and management units, and the use of molecular genetic analyses in forensics and to understanding species' biology. The role of genetic factors in extinctions of wild populations has been controversial, but evidence now shows that they make important contributions to extinction risk. Inbreeding has been shown to cause extinctions of wild populations, computer projections indicate that inbreeding depression has important effects on extinction risk, and most threatened species show signs of genetic deterioration. Inappropriate management is likely to result if genetic factors are ignored in threatened species management.     

Conservation biology: beyond marine protected areas

Socioeconomic and ecological analyses of eleven coral reef conservation efforts make clear that marine protected areas are not the answer, and that in fact support of local communities is far more important than some government mandated 'fishing closure'. Apparently there are marine 'paper parks' just as there are terrestrial 'paper parks'.     

Modularity: a new perspective in biology

Several decades of research in biochemistry and molecular biology have been devoted for studies on isolated enzymes and proteins. Recent high throughput technologies in genomics and proteomics have resulted in avalanche of information about several genes, proteins and enzymes in variety of living systems. Though these efforts have greatly contributed to the detailed understanding of a large number of individual genes and proteins, this explosion of information has simultaneously brought out the limitations of reductionism in understanding complex biological processes. The genes or gene products do not function in isolation in vivo. A delicate and dynamic molecular architecture is required for precision of the chemical reactions associated with "life". In future, a paradigm shift is, therefore, envisaged, in biology leading to exploration of molecular organizations in physical and genomic context, a subtle transition from conventional molecular biology to modular biology. A module can be defined as an organization of macromolecules performing a synchronous function in a given metabolic pathway. In modular biology, the biological processes of interest are explored as complex systems of functionally interacting macromolecules. The present article describes the perceptions of the concept of modularity, in terms of associations among genes and proteins, presenting a link between reductionist approach and system biology.     

Feeding biology of Calanus: a new perspective

Calanus has been, for a variety of reasons, one of the most popular subjects of copepod feeding studies, and much of what we have learned from studies of Calanus has been applied to other species of copepods. Nearly all the major factors controlling feeding rate and behavior in Calanus have been known for more than three decades. These forcing functions include light, body weight, temperature, the quantity, size and quality of food, and feeding history. The relationships between these variables are better understood than they were three decades ago, but the current knowledge of them still fails to explain extraordinary variance in observations of feeding rate.I suggest that the current understanding fails because our fundamental perception is incorrect. It is generally assumed that the feeding behavior we observe is the net response to instantaneous values of a suite of functions. Past values of forcing functions may be considered a factor, but subservient to those in the present. The critical change in perspective suggested here requires that we assume the integrals of forcing functions to be more significant than their present values in regulating feeding behavior.     

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities

A major research goal in microbial ecology is to understand the relationship between gene organization and function involved in environmental processes of potential interest. Given that more than an estimated 99% of microorganisms in most environments are not amenable to culturing, methods for culture-independent studies of genes of interest have been developed. The wealth of metagenomic approaches allows environmental microbiologists to directly explore the enormous genetic diversity of microbial communities. However, it is extremely difficult to obtain the appropriate sequencing depth of any particular gene that can entirely represent the complexity of microbial metagenomes and be able to draw meaningful conclusions about these communities. This review presents a summary of the metagenomic approaches that have been useful for collecting more information about specific genes. Specific subsets of metagenomes that focus on sequence analysis were selected in each metagenomic studies. This 'targeted metagenomics' approach will provide extensive insight into the functional, ecological and evolutionary patterns of important genes found in microorganisms from various ecosystems.     

Survey research in conservation biology

We present systematic arguments for the necessity of field survey in conservation biology. Preservation of biological diversity has become a major challenge in conservation biology, but to comprehend diversity, ecologists have to obtain information on what units the 'diversity' of different parts of the world consists of, where these units are, and how they respond to natural and human-induced environmental change. To reach this end, systematic survey procedures need to be developed that incorporate data collecting, data analysis and conclusions about distributional patterns as well as management recommendations into an iterative process that is corrected as experience accumulates. The appropriate survey design depends on the task and needs to be fixed separately in each case; developing long-term observational systems is no less challenging a task than developing experimental systems in laboratory research, or modeling systems in theoretical research. We conclude the paper with five principles of ecological survey. A common denominator of these principles is the need to make explicit decisions at each step so that errors and insufficiency can be corrected later.     

生物学的新军——合成生物学

合成生物学是一个新兴而极具研究前景的领域．旨在通过将多种天然或人工设计的生物学元件进行合理组合,创造出重构的或非天然的生物系统。综述了合成生物学这一新兴学科的核心理念、研究内容以及与相关学科的联系,详细介绍了J．CraigVenter研究小组所合成的“人造生命”,并展望了合成生物学广阔的发展前景和所面临的问题。     

Quantitative genetics in conservation biology

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.     

G-protein signaling: a new branch in an old pathway

A recent study provides evidence for a new branch of the yeast mating pathway in which a G-protein alpha subunit directly activates phosphatidylinositol 3-kinase at endosomes.     

Bioimage informatics: a new area of engineering biology

In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called 'bioimage informatics'. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources.     

Behavioural biology: an effective and relevant conservation tool

'Conservation behaviour' is a young discipline that investigates how proximate and ultimate aspects of the behaviour of an animal can be of value in preventing the loss of biodiversity. Rumours of its demise are unfounded. Conservation behaviour is quickly building a capacity to positively influence environmental decision making. The theoretical framework used by animal behaviourists is uniquely valuable to elucidating integrative solutions to human-wildlife conflicts, efforts to reintroduce endangered species and reducing the deleterious effects of ecotourism. Conservation behaviourists must join with other scientists under the multidisciplinary umbrella of conservation biology without giving up on their focus: the mechanisms, development, function and evolutionary history of individual differences in behaviour. Conservation behaviour is an increasingly relevant tool in the preservation of nature.     

Considering evolutionary processes in conservation biology

Conservation biologists assign population distinctiveness by classifying populations as evolutionarily significant units (ESUs). Historically, this classification has included ecological and genetic data. However, recent ESU concepts, coupled with increasing availability of data on neutral genetic variation, have led to criteria based exclusively on molecular phylogenies. We argue that the earlier definitions of ESUs, which incorporated ecological data and genetic variation of adaptive significance, are more relevant for conservation. Furthermore, this dichotomous summary (ESU or not) of a continuum of population differentiation is not adequate for determining appropriate management actions. We argue for a broader categorization of population distinctiveness based on concepts of ecological and genetic exchangeability (sensu Templeton).