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.     

How to be an anti-reductionist about developmental biology: Response to Laubichler and Wagner

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example.     

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.     

Reproductive biology of Trichocentrum pumilum: an orchid pollinated by oil-collecting bees

The reproductive biology, reward production and pollination mechanism of Trichocentrum pumilum were studied in a gallery forest in the interior of the State of São Paulo, southeast Brazil. The floral visitors and pollination mechanism were recorded, and experimental pollinations were carried out in order to determine the breeding system of this species. Trichocentrum pumilum blooms in spring. Each paniculate inflorescence bears an average of 85 flowers that present a central yellow callus and finger‐like trichomes on the lateral lobes of the lip. A lipoidal substance is produced and stored among these trichomes. In the studied population, T. pumilum is exclusively visited and pollinated by two bee species (Tetrapedia diversipes and Lophopedia nigrispinis). Pollinaria are deposited on mouthparts of bees during collection of the lipoidal substance from the lateral lobes of the labellum. Trichocentrum pumilum is self‐incompatible and pollinator‐limited. Natural fruit set was low (9%, compared to 45% in experimentally cross‐pollinated flowers). Potentially viable seed exceed 97% in fruits obtained through cross‐pollination and in natural conditions (open pollination).     

Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate ‘omic’ data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

冷冻电子显微学在结构生物学研究中的现状与展望

冷冻电子显微学近年来在电子显微镜的硬件设备及结构解析的软件算法等方面取得了多个重要的技术突破,正在成为结构生物学研究的重要技术手段,为越来越多的生物学研究者所重视.冷冻电子显微学的技术特点决定了它所具备的一些独特优势和发展方向,同时作为一个正在迅速发展的科学技术领域,需要多学科的交叉促进.本文主要介绍冷冻电子显微学的研究现状及面临的技术挑战,并提出未来可能实现结构生物学与细胞生物学不同尺度的研究在冷冻电子显微学技术上融合的新方法.     

进化细胞生物学的提出及其任务

作者提出应创建一门源于进化生物学与细胞生物学两者的交叉学科一进化细胞生物学(细胞的进化生物学)。其根本任务在于用进化的观点考察真核细胞的一切方面,从它们的起源和演化来认识它们的现在。文中列举了其具体的研究内容,并分析了其研究方法上的特点,指出在这里需要把进化生物学的综合性分析与细胞生物学的实验研究最紧密地结合起来。文中还论述了真核细胞的细胞器的“不进化”现象,指出其根本原因在于进化焦点的转移。     

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Large‐scale proteomic approaches have been used to study signaling pathways. However, identification of biologically relevant hits from a single screen remains challenging due to limitations inherent in each individual approach. To overcome these limitations, we implemented an integrated, multi‐dimensional approach and used it to identify Wnt pathway modulators. The LUMIER protein–protein interaction mapping method was used in conjunction with two functional screens that examined the effect of overexpression and siRNA‐mediated gene knockdown on Wnt signaling. Meta‐analysis of the three data sets yielded a combined pathway score (CPS) for each tested component, a value reflecting the likelihood that an individual protein is a Wnt pathway regulator. We characterized the role of two proteins with high CPSs, Ube2m and Nkd1. We show that Ube2m interacts with and modulates β‐catenin stability, and that the antagonistic effect of Nkd1 on Wnt signaling requires interaction with Axin, itself a negative pathway regulator. Thus, integrated physical and functional mapping in mammalian cells can identify signaling components with high confidence and provides unanticipated insights into pathway regulators.     

Multi-scale modeling in biology: how to bridge the gaps between scales?

Human physiological functions are regulated across many orders of magnitude in space and time. Integrating the information and dynamics from one scale to another is critical for the understanding of human physiology and the treatment of diseases. Multi-scale modeling, as a computational approach, has been widely adopted by researchers in computational and systems biology. A key unsolved issue is how to represent appropriately the dynamical behaviors of a high-dimensional model of a lower scale by a low-dimensional model of a higher scale, so that it can be used to investigate complex dynamical behaviors at even higher scales of integration. In the article, we first review the widely-used different modeling methodologies and their applications at different scales. We then discuss the gaps between different modeling methodologies and between scales, and discuss potential methods for bridging the gaps between scales.     

A computational framework for the design of optimal protein synthesis

Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework for the identification of a set of mutant codon sequences for optimized heterologous protein production, which uses a codon-sequence mechanistic model of protein synthesis. Through a sensitivity analysis on the optimal steady state configuration of protein synthesis we are able to identify the set of codons, that are the most rate limiting with respect to steady state protein synthesis rate, and we replace them with synonymous codons recognized by charged tRNAs more efficient for translation, so that the resulting codon-elongation rate is higher. Repeating this procedure, we iteratively optimize the codon sequence for higher protein synthesis rate taking into account multiple constraints of various types. We determine a small set of optimized synonymous codon sequences that are very close to each other in sequence space, but they have an impact on properties such as ribosomal utilization or secondary structure. This limited number of sequences can then be offered for further experimental study. Overall, the proposed method is very valuable in understanding the effects of the different properties of mRNA sequences on the final protein yield in heterologous protein production and it can find applications in synthetic biology and biotechnology.     

Construction,visualization, and analysis of biological network models in Dynetica

Mathematical modeling has become an increasingly important aspect of biological research. Computer simulations help to improve our understanding of complex systems by testing the validity of proposed mechanisms and generating experimentally testable hypotheses. However, significant overhead is generated by the creation, debugging, and perturbation of these computational models and their parameters, especially for researchers who are unfamiliar with programming or numerical methods. Dynetica 2.0 is a user-friendly dynamic network simulator designed to expedite this process. Models are created and visualized in an easy-to-use graphical interface, which displays all of the species and reactions involved in a graph layout. System inputs and outputs, indicators, and intermediate expressions may be incorporated into the model via the versatile “expression variable” entity. Models can also be modular, allowing for the quick construction of complex systems from simpler components. Dynetica 2.0 supports a number of deterministic and stochastic algorithms for performing time-course simulations. Additionally, Dynetica 2.0 provides built-in tools for performing sensitivity or dose response analysis for a number of different metrics. Its parameter searching tools can optimize specific objectives of the time course or dose response of the system. Systems can be translated from Dynetica 2.0 into MATLAB code or the Systems Biology Markup Language (SBML) format for further analysis or publication. Finally, since it is written in Java, Dynetica 2.0 is platform independent, allowing for easy sharing and collaboration between researchers.     

CelloSelect – A synthetic cellobiose metabolic pathway for selection of stable transgenic CHO cell lines

Current protocols for generating stable transgenic cell lines mostly rely on antibiotic selection or the use of specialized cell lines lacking an essential part of their metabolic machinery, but these approaches require working with either toxic chemicals or knockout cell lines, which can reduce productivity. Since most mammalian cells cannot utilize cellobiose, a disaccharide consisting of two β-1,4-linked glucose molecules, we designed an antibiotic-free selection system, CelloSelect, which consists of a selection cassette encoding Neurospora crassa cellodextrin transporter CDT1 and β-glucosidase GH1-1. When cultivated in glucose-free culture medium containing cellobiose, CelloSelect-transfected cells proliferate by metabolizing cellobiose as a primary energy source, and are protected from glucose starvation. We show that the combination of CelloSelect with a PiggyBac transposase-based integration strategy provides a platform for the swift and efficient generation of stable transgenic cell lines. Growth rate analysis of metabolically engineered cells in cellobiose medium confirmed the expansion of cells stably expressing high levels of a cargo fluorescent marker protein. We further validated this strategy by applying the CelloSelect system for stable integration of sequences encoding two biopharmaceutical proteins, erythropoietin and the monoclonal antibody rituximab, and confirmed that the proteins are efficiently produced in either cellobiose- or glucose-containing medium in suspension-adapted CHO cells cultured in chemically defined media. We believe coupling heterologous metabolic pathways additively to the endogenous metabolism of mammalian cells has the potential to complement or to replace current cell-line selection systems.     

Vaccinology in the era of high-throughput biology

Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced ‘experimental challenge models'' in humans.     

Vertical nontransovarial transmission of Bartonella in fleas

Pathogens use diverse pathways to infect host populations by vertical and/or horizontal routes. Horizontal transmission of bacteria belonging to the Bartonella genus via haematophagous vectors is well known. Vertical transmission of Bartonella species was also suggested to occur but its routes remain to be unveiled. In a previous study, we showed the absence of transovarial transmission of Bartonella species OE 1‐1 in Xenopsylla ramesis fleas, and that fleas feeding on Bartonella‐positive jirds produced Bartonella‐positive gut voids. This current study aimed to investigate whether vertical nontransovarial transmission of Bartonella occurs in fleas. For this aim, the X. ramesis–Bartonella sp. OE 1‐1 model was used. Four groups of fleas including Bartonella‐positive and Bartonella‐negative female fleas and larval offspring had access to either Bartonella‐negative or Bartonella‐positive gut voids and faeces. Sixteen per cent of flea offspring that had access to Bartonella‐positive faeces and gut voids became Bartonella positive. Our findings demonstrate that Bartonella‐positive flea faeces and gut voids are proper infection sources for flea larvae and indicate that vertical nontransovarial transmission of bartonellae occurs in fleas. This information broadens our understanding of Bartonella transmission routes in flea vectors and enlightens pathways of bartonellae transmission and maintenance in flea populations in nature.     

栽培红花山玉兰的传粉生物学

研究了栽培红花山玉兰（Ｍａｇｎｏｌｉａｄｅｌａｖａｙｉ）的开花生物学和传粉生物学特性,并探讨了红花山玉兰只开花而不结实的原因以及提高其结实率的技术措施。红花山玉兰的花被片为９,呈３轮排列。外轮花被片先张开,而内２轮花被片仍紧密地包裹着雌雄蕊群,约２４ｈ后,内２轮花被片才张开。在外轮花被片张开而内２轮花被片未张开时,柱头就有授粉能力,但雄蕊尚未成熟。因内２轮花被片紧密地包裹着雌雄蕊群而阻碍了传粉者进入花内传粉。当内２轮花被片张开时,雄蕊成熟,花药裂开而散发花粉;柱头外露,但此时的柱头已变棕红色,完全失去了授粉能力。若外轮花被片刚张开时,去掉全部花被片,蜜蜂可成为有效传粉者,其结果率可达到５３．３％;若去掉全部花被片,并施以人工异花授粉,其结果率可高达１００％。研究结果表明,红花山玉兰是雌雄异熟的,且异花授粉是亲和;其开花生物学特性适合甲壳虫携带花粉进入花内传粉。红花山玉兰只开花而不结实的原因可能是其开花生物学特性所要求的携带花粉进入花内传粉的甲壳虫无法进入花内传粉或者缺乏。     

Pollination biology in a palm swamp community in the Venezuelan Central Plains

RAMIREZ, N. & BRITO, Y., 1992. Pollination biology in a palm swamp community in the Venezuelan central plains. In a palm swamp community that differs strongly from the surrounding savanna in the Venezuelan central plains, the pollination and floral biology of 33 plant species were studied during three years: 1983, 1984 and 1989. The most frequent flower colours were white, pink, yellow, and in a lesser proportion green, brown, purple and red. Floral symmetry was found in roughly equal proportion for actinomorphic and zygomorphic flowers. Most flowers were short-lived (6–12 hours); in monoecious species the female flowers were longer-lived than the male flowers. The most frequent rewards were pollen and nectar (36.4%) and pollen (30.3%). At the community level, bee- and wasp-pollination prevailed in 57.1% of plant species studies, followed by wind- (14.3%), fly- (11.4%), butterfly- (8.6%), bird- (5.7%) and beetle-pollination (2.9%). Between one and five plant species were simultaneously visited by the visitor species. The vast majority of the pollinating species displayed a high degree of load specificity: 26 pollinator species (65.0%) carried pollen from only one plant species, eight (20.0%,) carried pollen from two plant species, three (7.5%) carried pollen from three plant species and one (2.5%) carried pollen from five plant species. Visitor specificity and pollen transportation were similar amongst the visiting agents. Plant pollination-system specificity and pollen transportation were statistically significant among plant species with different pollinator types, but plant pollination system and pollen transportation were not different among floral symmetry, floral longevity, reward type, plant sexuality, breeding system and plant life form. The visitor species/plant species ratio was 1.6, and the pollinator species/ plant species ratio was 1.3. Among different guilds, birds, Coleoptera and Lepidoptera showed the highest pollinator species/plant species ratio, and wind pollination exhibited the lowest.     

Will systems biology offer new holistic paradigms to life sciences?

A biological system, like any complex system, blends stochastic and deterministic features, displaying properties of both. In a certain sense, this blend is exactly what we perceive as the “essence of complexity” given we tend to consider as non-complex both an ideal gas (fully stochastic and understandable at the statistical level in the thermodynamic limit of a huge number of particles) and a frictionless pendulum (fully deterministic relative to its motion). In this commentary we make the statement that systems biology will have a relevant impact on nowadays biology if (and only if) will be able to capture the essential character of this blend that in our opinion is the generation of globally ordered collective modes supported by locally stochastic atomisms.     

系统生物学——生命科学的新领域

系统生物学是继基因组学、蛋白质组学之后一门新兴的生物学交叉学科,代表21世纪生物学的未来.最近,系统生物学研究机构纷纷成立.在研究上,了解一个复杂的生物系统需要整合实验和计算方法.基因组学和蛋白质组学中的高通量方法为系统生物学发展提供了大量的数据.计算生物学通过数据处理、模型构建和理论分析,成为系统生物学发展的一个必不可缺、强有力的工具.在应用上,系统生物学代表新一代医药开发和疾病防治的方向.