Classic limb patterning models and the work of Dennis Summerbell

Dennis Summerbell was a leading contributor to our understanding of limb patterning prior to the advent of molecular biology. He published several groundbreaking papers, including one that developed a key model for patterning the limb from the shoulder to the fingertips and another that presented the co-discovery of the effect of retinoids on limb morphogenesis. He brought detailed quantitative analyses to bear on these studies, as highlighted in two of his insightful papers published in the Journal of Embryology and Experimental Morphology, in which he provided elegant models that, today, remain relevant to limb patterning, as well as to many disciplines of developmental biology.     

Emergent insights from the synthesis of conceptual frameworks for biological invasions

A general understanding of biological invasions will provide insights into fundamental ecological and evolutionary problems and contribute to more efficient and effective prediction, prevention and control of invasions. We review recent papers that have proposed conceptual frameworks for invasion biology. These papers offer important advances and signal a maturation of the field, but a broad synthesis is still lacking. Conceptual frameworks for invasion do not require invocation of unique concepts, but rather should reflect the unifying principles of ecology and evolutionary biology. A conceptual framework should incorporate multicausality, include interactions between causal factors and account for lags between various stages. We emphasize the centrality of demography in invasions, and distinguish between explaining three of the most important characteristics by which we recognize invasions: rapid local population increase, monocultures or community dominance, and range expansion. As a contribution towards developing a conceptual synthesis of invasions based on these criteria, we outline a framework that explicitly incorporates consideration of the fundamental ecological and evolutionary processes involved. The development of a more inclusive and mechanistic conceptual framework for invasion should facilitate quantitative and testable evaluation of causal factors, and can potentially lead to a better understanding of the biology of invasions.     

Revised h index for biomedical research

Proposed by Hirsch as a quantitative measure of the total output of a researcher, the h index does not work well in the field of life sciences, where an author’s position on a paper typically depends on the author’s contribution. We revise the h index by weighing first and last authorship papers four times heavier than middle authorship papers. The revised index (r) signifies a shift in how we evaluate the research output in biology and medicine: it places more value on conducting and directing original, independent investigations as compared with contributing to projects conducted and directed by others.     

Thermoregulation and endurance running in extinct hominins: Wheeler's models revisited

Thermoregulation is often cited as a potentially important influence on the evolution of hominins, thanks to a highly influential series of papers in the Journal of Human Evolution in the 1980s and 1990s by Peter Wheeler. These papers developed quantitative modeling of heat balance between different potential hominins and their environment. Here, we return to these models, update them in line with new developments and measurements in animal thermal biology, and modify them to represent a running hominin rather than the stationary form considered previously. In particular, we use our modified Wheeler model to investigate thermoregulatory aspects of the evolution of endurance running ability. Our model suggests that for endurance running to be possible, a hominin would need locomotive efficiency, sweating rates, and areas of hairless skin similar to modern humans. We argue that these restrictions suggest that endurance running may have been possible (from a thermoregulatory viewpoint) for Homo erectus, but is unlikely for any earlier hominins.     

Revised h index for biomedical research

Proposed by Hirsch as a quantitative measure of the total output of a researcher, the h index does not work well in the field of life sciences, where an author’s position on a paper typically depends on the author’s contribution. We revise the h index by weighing first and last authorship papers four times heavier than middle authorship papers. The revised index (r) signifies a shift in how we evaluate the research output in biology and medicine: it places more value on conducting and directing original, independent investigations as compared with contributing to projects conducted and directed by others.     

Statistical considerations for in vitro research: II — Data to presentation

Summary The paper is the second of two papers about statistical considerations that researchers should make while doing in vitro plant biology research. The first paper focused on aspects from developing a plan to do research through the collection of data. This paper continues with information about editing data, handling outliers, analyzing quantitative and qualitative data, comparing treatment means, preparing graphs and tables, and presenting results.     

代谢组学：一个迅速发展的新兴学科

对代谢组学的含义,中心任务,研究方法,样品要求,应用及其发展方向进行了简要综述. 系统生物学概念的诞生标志着研究哲学由“还原论”向“整体论”的变化. 系统生物学的中心任务就是要针对生物系统整体 (无论它是生物细胞,多细胞组织,器官还是生物整体),建立定量,普适,整体和可预测 (QUIP) 的认知. 具体而言,系统生物学研究就是要将给定生物系统的基因,转录,蛋白质和代谢水平所发生的事件,相关性及其对所涉及生物过程的意义进行整体性认识. 从而出现了许多的“组”和“组学”的新概念. 但是现已提出的一百多个“组”和“组学”,可以大体归纳为“基因组”/“基因组学”,“转录组”/“转录组学”,“蛋白质组”/“蛋白质组学”和“代谢组”/“代谢组学”四个方面. 显而易见,DNA,mRNA 以及蛋白质的存在为生物过程的发生提供了物质基础 (但这个过程有可能不发生!),而代谢物质所反映的是已经发生了的生物学事件. 因此代谢组学是对一个生物系统进行全面认识的不可缺少的一部分,是全局系统生物学 (global systems biology) 的重要基础,也是系统生物学的一个重要组成部分. 在现有的英文表述中,代谢组学同时存在两个不同的词汇和概念,即metabonomics 和 metabolomics. 尽管前者多用在动物系统而后者多用于植物和微生物系统,但这些概念的本质从他们的定义中能够得到较细致的了解. Metabonomics 的最初定义是就生物系统对生理和病理刺激以及基因改变的代谢应答的定量测定(“the quantitative measurement of the multi-parametric metabolic response of living systems to pathophysiological stimuli or geneticmodifications”). 我们认为这个定义现在可以更广泛地表述为:代谢组学是关于定量描述生物内源性代谢物质的整体及其对内因和外因变化应答规律的科学 (“Metabonomics is the branch of science concerned with the quantitative understandings of themetabolite complement of integrated living systems and its dynamic responses to the changes of both endogenous factors (such asphysiology and development) and exogenous factors (such as environmental factors and xenobiotics).”). 其中心任务包括 (1) 对内源性代谢物质的整体及其动态变化规律进行检测,量化和编录,(2) 确定此变化规律和生物过程的有机联系. Metabolomics 存在多个定义,但其精髓是:对一个生物系统的细胞在给定时间和给定条件下所有小分子代谢物质的定量分析(the quantitativemeasurement of all low molecular weight metabolites in an organism's cells at a specified time under specific environmentalconditions). 因此,metabolomics 可以译作“代谢物组学”. 不难看出,前者是对生物系统进行的整体和动态的认识 (不仅关心代谢物质的整体也关注其动态变化规律),而后者强调分析而且是个静态的认识概念. 因此可以认为,metabolomics 是metabonomics 的一个组成部分 (参看定义). 近年又有人提出了“dynamic metabolomics”的概念,这个概念所表达的含义十分接近“metabonomics”本身的含义. 所以,可以预见,随着这门新兴学科的发展和更深入讨论,这两个概念必将趋向一致. 因此我们建议,在中文表述中将“代谢组学”一词和英文中的 metabonomics 相对应,以避免不必要的混淆和争议. 就细胞系统而言,不仅存在细胞自身的代谢物质组成问题,存在细胞之间代谢物质交换的问题,也存在代谢过程所发生的位点问题. 因此,简单地分析代谢物质的总组成 (即代谢组) 缺乏“整体论”所要求的全面性,其意义有一定局限. 代谢组学属于全局系统生物学 (Global systems biology) 研究方法,便于对复杂体系的整体进行认识. 譬如,一个正常工作的人体包括“人体”本身和与之共同进化而来且共生的消化道微生物群体 (或称菌群),孤立地研究“人体”本身的基因,转录子以及蛋白质当然可以为人们认识人体生物学提供重要信息,但无法提供使人体正常工作不可缺少的菌群的信息. 人体血液和尿液的代谢组却携带着包括菌群在内的每一个细胞的信息,因此代谢组学方法对研究如人体这样复杂的进化杂合体十分有效. 正因如此,代谢组学已经广泛地应用到了包括药物研发,分子生理学,分子病理学,基因功能组学,营养学,环境科学等重要领域. 在代谢组学诞生的过去 6 年里,有关代谢组学的研究论文和专利以指数的形式逐年增长. 可以预见,这门新兴学科将应用到更为广泛的领域.     

Quantitative cell biology: the essential role of theory

Quantitative biology is a hot area, as evidenced by the recent establishment of institutes, graduate programs, and conferences with that name. But what is quantitative biology? What should it be? And how can it contribute to solving the big questions in biology? The past decade has seen very rapid development of quantitative experimental techniques, especially at the single-molecule and single-cell levels. In this essay, I argue that quantitative biology is much more than just the quantitation of these experimental results. Instead, it should be the application of the scientific method by which measurement is directed toward testing theories. In this view, quantitative biology is the recognition that theory and models play critical roles in biology, as they do in physics and engineering. By tying together experiment and theory, quantitative biology promises a deeper understanding of underlying mechanisms, when the theory works, or to new discoveries, when it does not.     

The PLOS ONE Synthetic Biology Collection: Six Years and Counting

Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community.     

Parallelism-based approaches in computational biology: a view from diverse case studies

Computational biology allows and encourages the application of many different parallelism-based approaches. This special issue brings together high-quality state-of-the-art contributions about parallelism-based approaches in computational biology, from different points of view or perspectives, that is, from diverse case studies. The special issue collects considerably extended and improved versions of the best papers, accepted and presented in PBio 2016 (4th International Workshop on Parallelism in Bioinformatics, and part of Euro-Par 2016). The domains and topics covered in these 6 papers are timely and important, and the authors have done an excellent job of presenting the material.     

Molecular biology in biorheology

This presentation is aimed at giving some background information on molecular biology, thus serving as an introduction to the Symposium on Molecular Biorheology held during the Sixth International Congress of Biorheology in Vancouver. The papers presented at this Symposium indicate that the use of molecular biological techniques allows the understanding of normal and abnormal rheological properties of cells and organs at the molecular level. It is hoped that these examples will provide an impetus for us to open new frontiers of research in biorheology by taking advantage of the powerful tools developed from recent advances in molecular biology.     

How wide is the “knowing-doing” gap in invasion biology?

Invasion biology is a growing discipline with clear ecological, social and economic implications. A wide range of research effort is thus required to address the invasion problem, and literature on the topic is extensive. However, the extent to which the invasion biology research is addressing the challenges associated with management and mitigation of the impacts of invasions has been questioned. Using bibliometric analysis, we investigated the extent to which the literature on the subject contributes to implementation of knowledge generated, by addressing aspects of management, policy, and/or implementation; the impact of these papers as indicated by the number of citations they attract; and the geopolitical scale of focus of invasion ecology papers, particularly those that attempt to bridge the knowing-doing gap. We then compared these findings with the information needs of conservation practitioners. We first looked globally at popular search engines and then narrowed our focus to South Africa—one of three regions outside USA where researchers producing highly cited papers in invasion ecology are well represented. At this level, we conducted a content analysis of invasion ecology-related papers, of which at least one author was affiliated to a South African institution. The knowledge base in the field of invasion biology is comprised largely of research oriented towards “knowing”, while research aimed at strategically applying or implementing that knowledge is poorly represented in the scientific literature, and the scale of its emphasis is not local. Conservation practitioners clearly indicate a need for basic knowledge. However, invasion science must develop channels for effective engagement to ensure that the research is contextualised, and will deal with the complex ecological, social and economic challenges posed by invasions.     

Molecular biology in physiology

The aim of this symposium on molecular biology in physiology was to introduce molecular biology to physiologists who had relatively little exposure to the new developments in this field, so that they can become conversant on this topic and contribute to the advancement of physiology by incorporating molecular biological approaches as a part of their research arsenal. After the discussion of the basic concepts, terminology, and methodology used in molecular biology, it was shown how these basic principles have been applied to the study of the genes encoding two membrane proteins that have important transport functions (band 3 and ATPase). The second half of the symposium consisted of papers on the state-of-the-art developments in the application of molecular biology to the studies of the atrial natriuretic factor and renin genes, adenylate cyclase-coupled adrenergic receptors, acetylcholine receptors and sodium channel, and long-term and short-term memories. The ultimate goal is that these examples will provide an impetus for the opening of new frontiers of research in physiology by taking advantage of the tools developed from recent advances in molecular biology.     

从文献计量角度分析中国生物多样性研究现状

以汤森路透科技集团的WEB OF KNOWLEDGE信息平台提供的Science Citation Index Expanded数据库为数据源,检索到从1997年至2009年期间国际生物多样性研究论文文献219773篇,其中11182篇来自于中国学者。利用NoteExpress软件,对这13a间生物多样性研究论文发表的国家分布、年度分布、研究机构、引用情况、期刊分布和学科分类等做的分析与比较表明:1)全球生物多样性研究的论文数量一直呈增长趋势,中国13年间每年发文量占当年全球生物多样性论文总量的百分率逐年增加;2)从论文总被引频次、篇均引用次数和h-index三项论文影响力特征参数分析,中国与国际其他国家相比有一定差距;3)从学科分类来看,与国际相比,中国在生物多样性保护领域、进化生物学和海洋与淡水生物学领域研究略显不足,昆虫学和真菌学研究领域活跃。     

Combining Experiments and Simulations Using the Maximum Entropy Principle

A key component of computational biology is to compare the results of computer modelling with experimental measurements. Despite substantial progress in the models and algorithms used in many areas of computational biology, such comparisons sometimes reveal that the computations are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy applications in our field has grown steadily in recent years, in areas as diverse as sequence analysis, structural modelling, and neurobiology. In this Perspectives article, we give a broad introduction to the method, in an attempt to encourage its further adoption. The general procedure is explained in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results that are at not in complete and quantitative accordance with experiments. A common solution to this problem is to explicitly ensure agreement between the two by perturbing the potential energy function towards the experimental data. So far, a general consensus for how such perturbations should be implemented has been lacking. Three very recent papers have explored this problem using the maximum entropy approach, providing both new theoretical and practical insights to the problem. We highlight each of these contributions in turn and conclude with a discussion on remaining challenges.     

基于Web of Science的合成生物学文献计量分析

合成生物学是一个新兴的交叉学科,近年来得到了广泛关注。本文以1992-2012年期间Web of Science数据库收录的5012篇与合成生物学相关的论文为研究对象,进行年代分布、地域分布、机构分布、研究热点等方面的计量分析,以探究合成生物领域的研究实力分布、研究热点与发展动态。通过文献计量分析发现合成生物学领域近十年来发展迅猛,美国等发达国家占据主动。我国在该领域的论文产出数量可观,但学术影响力有待提高。研究的热点主要集中在基因调控网络构建、基因基因组合成、功能回路设计等方面。     

Preface: Biology of skates

Synopsis Skates have become a concern in recent years due to the preponderance of these elasmobranchs that are caught as bycatch or as a directed fishery. This has raised concern because skates have life history characteristics that may make them vulnerable to over-exploitation. It was due to this increasing awareness and concern about these batoids that prompted us to organize an international symposium on the “Biology of Skates”. The aims and goals of the symposium were to bring together an international group of researchers to meet, discuss, perhaps develop collaborations, and present their most recent findings. The symposium was held over two days, on 13–14 July, 2006, in conjunction with the 22nd annual meeting of the American Elasmobranch Society in New Orleans, LA. A total of 31 authors from four countries contributed 16 papers that appear in this special issue. The papers are broadly arranged into four separate categories: systematics and biogeography, diet and feeding ecology, reproductive biology, and age and growth. To the best of our knowledge this is the first dedicated book on the biology of skates. We hope that readers will find this issue of interest and that it helps encourage and stimulate future research into these fascinating fishes.     

中国园林生态学发展综述

运用文献计量等方法对已有科研成果进行统计分析,结果表明:中国近50年园林生态学科领域科研发展经过了起步探索(1962-1981)、缓慢发展(1982-2001)、快速发展(2002-2011)3个时期,园林生态学作为生态学一个新的分支学科,于20世纪90年代末初见端倪,作为一门新兴独立的应用生态学分支学科于21世纪初已基本形成.中国园林生态学领域的研究包括园林生态系统中生物与环境相互作用关系问题、人与环境相互作用关系问题以及园林生态系统与其他生态系统之间相互作用关系问题.当代园林生态研究主要有生态效益研究、生物与环境研究、人的需求与行为研究、生态规划与生态管理研究4个方面,目前园林生态学研究主要侧重生物与环境研究和生态效益研究,两方面的研究成果占总体研究成果的76.3％.不同研究方面也有各自的侧重点,如生物与环境研究侧重对植物的研究,生态效益研究侧重净化环境、水土保持和防灾减灾,生态规划与生态管理研究则侧重生态规划与设计.对四个研究方面的论文主题词检索和高频主题关键词的分布进行统计,结果显示,研究的热点有多样性、群落、水土保持、防灾避险、净化环境、生态规划与设计等.对CNKI中4个研究方面成果中获基金资助项目论文进行统计(不排重),总体成果中基金项目论文所占比重为10.8％,国家和地方基金是园林生态学科研基金资助的主要来源,基金论文比例之和达到85.4％,且国家和地方基金资助论文较多的是“生态与环境研究”和“生态效益研究”,合计占基金论文79.1％.SCI-E中收录的文献基金论文率为47.1％,是CNKI数据库收录的文献基金论文率的4.3倍,且国际基金是基金论文的主要资助来源之一,说明中国园林生态学领域部分科研成果得到国际学界关注.基于CNKI相关主题词统计,“园林生态学”的研究成果只有“景观生态学”的1％,“城市生态学”的8.3％,“园林生态学”学科系统理论研究在相关生态学科研究中所占比重很低,其理论和方法研究还较薄弱.今后在进一步完善学科理论体系、持续开展生态效益和园林植物研究的同时,为更好地研究和解决人-自然复合生态系统问题,提供更多的科学理论支撑,还需拓展交叉生态心理学或环境心理学等其他相关理论,更多地关注人与环境互相作用关系以及生态规划与生态管理等方面的研究,既使环境更好地满足人的行为需求,也使人认识到改变一些行为能更好地保护环境.     

Quantitative methods for analysing cumulative effects on fish migration success: a review

It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival.