A day of systems and synthetic biology for non‐experts

From understanding ageing to the creation of artificial membrane‐bounded ‘organisms’, systems biology and synthetic biology are seen as the latest revolutions in the life sciences. They certainly represent a major change of gear, but paradigm shifts? This is open to debate, to say the least. For scientists they open up exciting ways of studying living systems, of formulating the ‘laws of life’, and the relationship between the origin of life, evolution and artificial biological systems. However, the ethical and societal considerations are probably indistinguishable from those of human genetics and genetically modified organisms. There are some tangible developments just around the corner for society, and as ever, our ability to understand the consequences of, and manage, our own progress lags far behind our technological abilities. Furthermore our educational systems are doing a bad job of preparing the next generation of scientists and non‐scientists.     

光学量,光子量和单位在激光生物学中的应用

激光生物学是光子学和生物学相结合的交叉边缘学科,根据《光及有关电磁辐射的量和单位》国际标准（ＩＳＯ／ＤＩＳ３１－６,１９９０）和我国国家标准（ＧＢ３１０２．６,１９９３）,本文讨论了在激光生物学中常用的光学量、光子量和单位。     

Hierarchical competition models with the Allee effect II: the case of immigration

ABSTRACT

This is part II of an earlier paper that dealt with hierarchical models with the Allee effect but with no immigration. In this paper, we greatly simplify the proofs in part I and provide a proof of the global dynamics of the non-hyperbolic cases that were previously conjectured. Then, we show how immigration to one of the species or to both would, drastically, change the dynamics of the system. It is shown that if the level of immigration to one or to both species is above a specified level, then there will be no extinction region where both species go to extinction.     

高等师范院校分子生物学课程教学改革与实践

分子生物学是一门从分子水平研究生命现象、生命本质及其规律的科学,是现代生命科学中最具活力的带头学科,掌握分子生物学的基本理论和基本技能已成为21世纪生物科学对人才发展的一个需求。确定科学、合理的教学改革方案,重组、优化教学内容,精心设计教学方法、教学手段及考核方式,对确保分子生物学课程教学质量具有重要意义。结合近年来的分子生物学教学经验,就教材建设、教学内容整合、教学方法改进、课程考核方式、网络课程建设以及开放实验室管理等方面阐述了一些观点和体会,以期为提高分子生物学教学质量及培养素质型人才提供有益参考。     

The institutionalization of biology in Mexico in the early 20th century: the conflict between Alfonso Luis Herrera (1865-1942) and Isaac Ochoterena (1885-1950)

The aim of this work is to evaluate the roleplayed by Alfonso Luis Herrera and IsaacOchoterena in the institutionalization ofacademic biology in Mexico in the early 20thcentury. As biology became institutionalized inMexico, Herrera's basic approach to biology wasdisplaced by Isaac Ochoterena's professionalgoals due to the prevailing politicalconditions at the end of 1929. Theconflict arose from two different conceptionsof biology, because Herrera and Ochoterena haddifferent discourses that were incommensurable,not only linguistically speaking, but alsosocioprofessionally. They had different linksto influential groups related to education,having distinct political and socioprofessionalinterests. The conflict between Herrreraand Ochoterena determined the way in whichprofessional biology education has developed inMexico, as well as the advancement in specificresearch subjects and the neglect of others.     

A Brief History of De Novo Protein Design: Minimal,Rational, and Computational

Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the primary motivation for de novo protein design was to test our understanding of the informational aspect of the protein-folding problem; i.e., how does protein sequence determine protein structure and function? This necessitated minimal and rational design approaches whereby the placement of each residue in a design was reasoned using chemical principles and/or biochemical knowledge. At that time, though with some notable exceptions, the use of computers to aid design was not widespread. Over the past two decades, the tables have turned and computational protein design is firmly established. Here, I illustrate this progress through a timeline of de novo protein structures that have been solved to atomic resolution and deposited in the Protein Data Bank. From this, it is clear that the impact of rational and computational design has been considerable: More-complex and more-sophisticated designs are being targeted with many being resolved to atomic resolution. Furthermore, our ability to generate and manipulate synthetic proteins has advanced to a point where they are providing realistic alternatives to natural protein functions for applications both in vitro and in cells. Also, and increasingly, computational protein design is becoming accessible to non-specialists. This all begs the questions: Is there still a place for minimal and rational design approaches? And, what challenges lie ahead for the burgeoning field of de novo protein design as a whole?     

The ATP binding cassette transporter A1 contributes to the secretion of interleukin 1beta from macrophages but not from monocytes

Deficiency of ABCA1 causes high density lipoprotein deficiency and macrophage foam cell formation in Tangier disease. ABCA1 was also postulated to mediate the secretion of IL-1beta from monocytes and macrophages. We investigated the contribution of ABCA1 to IL-1beta secretion from human monocytes and macrophages of normal donors and Tangier disease patients. Neither an anti-ABCA1 antisense oligonucleotide nor ABCA1 deficiency interfered with LPS-induced secretion of IL-1beta from full blood or freshly isolated monocytes. By contrast, anti-ABCA1 antisense oligonucleotides decreased the LPS-induced secretion of IL-beta from macrophages by 30-50%. The secretion of the precursor pro-IL-1beta and TNFalpha was not inhibited. Compared to normal macrophages, LPS-stimulated Tangier disease macrophages secreted less IL-1beta relative to TNFalpha. Also the spontaneous secretion of IL-1beta by Tangier macrophages was lower than by control cells. We conclude that IL-1beta is secreted from monocytes by an ABCA1-independent pathway and from macrophages by ABCA1-dependent and -independent pathways.     

中国地衣学现状综述

本文对中国地衣学在多样性、系统性及其物种与基因资源生物学研究方面进行了综述。文中强调了多样性和系统性研究在自然界地衣资源与研究开发之间的桥梁作用。论述了地衣结皮固沙、固碳及其基因资源在沙漠生物地毯工程中的意义。揭开了不产次生代谢产物的地衣秘密及其破解途径。     

Maps, books and other metaphors for systems biology

We briefly review the use of metaphors in science and progressively focus on fields from biology and molecular biology to genomics and bioinformatics. We discuss how metaphors are both a tool for scientific exploration and a medium for public communication of complex subjects, by various short examples. Finally, we propose a metaphor for systems biology that provides an illuminating perspective for the ambitious goals of this field and delimits its current agenda.     

真菌生物多样性及其系统生物学与三大存取系统——祝贺杰出的真菌学家Korf教授88华诞

讨论了菌物、真菌和地衣的概念,它们的生物多样性,地衣型真菌的系统生物学及其三大存取系统.同时,对地衣资源研究进行了展望.     

分子生物学技术在植物内生菌分类鉴定中的应用

植物内生菌作为微生物中的一个研究领域,近年来一直备受关注。不仅是因为内生菌在农牧业生产和环境净化方面应用的良好表现,而且还为新药研制提供了新的途径。与此同时,植物内生菌分类鉴定的研究也有一定的进展,特别是在分子生物学技术应用到其中后。基于这点,就最近10年来有关植物内生菌分类鉴定的文献所使用的技术进行了分析和讨论。     

真菌生物多样性及其系统生物学与三大存取系统——祝贺杰出的真菌学家Korf教授88华诞(英文)

讨论了菌物、真菌和地衣的概念,它们的生物多样性,地衣型真菌的系统生物学及其三大存取系统。同时,对地衣资源研究进行了展望。     

Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs)

Mathematical modeling of complex gene expression programs is an emerging tool for understanding disease mechanisms. However, identification of large models sometimes requires training using qualitative, conflicting or even contradictory data sets. One strategy to address this challenge is to estimate experimentally constrained model ensembles using multiobjective optimization. In this study, we used Pareto Optimal Ensemble Techniques (POETs) to identify a family of proof-of-concept signal transduction models. POETs integrate Simulated Annealing (SA) with Pareto optimality to identify models near the optimal tradeoff surface between competing training objectives. We modeled a prototypical-signaling network using mass-action kinetics within an ordinary differential equation (ODE) framework (64 ODEs in total). The true model was used to generate synthetic immunoblots from which the POET algorithm identified the 117 unknown model parameters. POET generated an ensemble of signaling models, which collectively exhibited population-like behavior. For example, scaled gene expression levels were approximately normally distributed over the ensemble following the addition of extracellular ligand. Also, the ensemble recovered robust and fragile features of the true model, despite significant parameter uncertainty. Taken together, these results suggest that experimentally constrained model ensembles could capture qualitatively important network features without exact parameter information.     

我国新入侵害虫长林小蠹研究进展

长林小蠹Hylurgus ligniperda Fabricius是国际重大林业检疫性害虫,危害多种针叶树。近期,我国山东省泰安市、威海市和烟台市相继发现该小蠹,其主要危害树种为日本黑松Pinus thunbergia Parl。为深入了解和掌握长林小蠹生物学、流行规律,以及潜在风险,进而为制定相应检疫管理和防治措施提供基础资料与新信息,本文对其外部形态、生物学特征、携带真菌和线虫种类、我国种群来源及潜在分布、现有检疫和防治措施等基本情况进行了较为系统地阐述,并对长林小蠹未来需开展的相关调查与研究工作进行了讨论。     

Wild mice provide insights into natural killer cell maturation and memory

The immune system has evolved, and continues to evolve, in response to the selection pressure that infections exert on animals in their natural environments, yet much of our understanding about how the immune system functions comes from studies of model species maintained in the almost complete absence of such environmental selection. The scientific discipline of immunology has among its aims the improvement of human and animal health by the application of immunological knowledge. As research on humans and domesticated animals is highly constrained-ethically, logistically and financially-experimental animal models have become an invaluable tool for dissecting the functioning of the immune system. The house mouse (Mus musculus) is by far the most widely used animal model in immunological research but laboratory-reared mice provide a very narrow view of the immune system-that of a well-fed and comfortably housed animal with minimal exposure to microbial pathogens. Indeed, so much of our immunological knowledge comes from studies of a very few highly inbred mouse strains that-to all intents and purposes-our immunological knowledge is based on enormously detailed studies of very small numbers of individual mice. The limitations of studies in inbred strains of laboratory mice are well-recognized (Pedersen & Babayan 2011), but serious attempts to address these limitations have been few and far between. However, the emerging field of 'ecological immunology' where free-living populations are studied in their natural habitat is beginning to redress this imbalance (Viney et al. 2005; Martin et al. 2006; Owen et al. 2010; Abolins et al. 2011). As demonstrated in the work by Boysen et al. (2011) in this issue of Molecular Ecology, studies in wild animal populations-especially free-living M. musculus-represent a valuable bridge between studies in humans and livestock and studies of captive animals.     

Resources, standards and tools for systems biology.

Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from the literature, databases or direct experimental investigation. In this review, we describe different data resources, standards and modelling and simulation tools that are relevant to integrative systems biology.     

Molecular biology in the Soviet Russia (An essay)

Stages of the evolvement and development of the major directions of molecular biology in the 1950–1980’s and its prehistory bracketing the 1920–1940’s are considered against the backgrounds of the history of the Soviet science. Short outlines of the lives and activities of the leading scientists who shaped the directions of and provided for success in studying supramolecular cell structures and molecular mechanisms of processes on a cellular level. This essay, which is far from exhaustive in describing the problems that the Soviet scientists have been dealing with, does not cover the studies of the last decade, nor does it evaluate the contributions of the living molecular biologists.     

Building momentum for systems and synthetic biology in India

Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computational and experimental strategy was formally proposed in mid 1990s leading to the re-emergence of Systems Biology. However, soon it became clear that natural systems were far more complex than expected. A new strategy to address biological complexity was proposed at MIT (Massachusetts Institute of Technology) in June 2004, when the first meeting of synthetic biology was held. Though the term ‘synthetic biology’ was proposed during 1970s (Szybalski in Control of gene expression, Plenum Press, New York, 1974), the usage of the original concept found an experimental proof in 2000 with the demonstration of a three-gene circuit called repressilator (Elowitz and Leibler in Nature, 403:335–338, 2000). This encouraged people to think of forward engineering biology from a set of well described parts.