The role of molecular modelling in biomedical research

The synergy between experimental and computational biology has greatly benefited both fields, providing invaluable information in many different areas of the life sciences. This minireview will focus on one specific aspect of computational biology, molecular modelling, and describe a few examples highlighting the effectiveness of protein structural analysis and modelling in providing relevant information about systems of biomedical interest.     

Rapid evolution as an ecological process

Rapid evolution of interspecific interactions (during a timespan of about 100 years) has the potential to be an important influence on the ecological dynamics of communities. However, despite the growing number of examples, rapid evolution is still not a standard working hypothesis for many ecological studies on the dynamics of population structure or the organization of communities. Analysis of rapid evolution as an ecological process has the potential to make evolutionary ecology one of the most central of applied biological sciences.     

Introducing "Frontiers in Zoology"

As a biological discipline, zoology has one of the longest histories. Today it occasionally appears as though, due to the rapid expansion of life sciences, zoology has been replaced by more or less independent sub-disciplines amongst which exchange is often sparse. However, the recent advance of molecular methodology into "classical" fields of biology, and the development of theories that can explain phenomena on different levels of organisation, has led to a re-integration of zoological disciplines promoting a broader than usual approach to zoological questions. Zoology has re-emerged as an integrative discipline encompassing the most diverse aspects of animal life, from the level of the gene to the level of the ecosystem.The new journal Frontiers in Zoology is the first Open Access journal focussing on zoology as a whole. It aims to represent and re-unite the various disciplines that look at animal life from different perspectives and at providing the basis for a comprehensive understanding of zoological phenomena on all levels of analysis. Frontiers in Zoology provides a unique opportunity to publish high quality research and reviews on zoological issues that will be internationally accessible to any reader at no cost.     

Reflections on the problem of "discreteness" and "steady state" in living processes

A survey is given over the different meaning of the dialectic pair of terms continuity and discontinuity in philosophy contrasting with sciences. In mathematics, the term continuum is defined by Cantor in set theory as the innumerable multitude of the real numbers especially in the interval [0, 1]. The discontinuum means in Cantor's definition the rational fractions in [0, 1] which in triadic development do not contain the figure 1 [written I). In a more general sense, continuum is used in the mechanics of continuous fluids and gases in physics as well as in physiology. Here, the use of this term neglects the reality of intermolecular spaces intentionally. To employ in the life sciences, the pair of terms steady state and discreteness is clearer. Processes of life mostly are steady in the sense of balanced proceedings but numbers of individuals, cells, molecules, sexes etc, are discrete only. For example, the difference or the dimorphism between males and females is a distinct one between two different conditions but cannot be projected on "discontinuity". Discreteness as a term comprehends Boole an variables as are male-female, living-dead, as well as crowds of measure points.     

Introduction

The edition of a special issue entitled “Neuroscience in China” provides a unique opportunity to introduce neuroscience research undertakings in China today. Among the biological sciences at large, neuroscience is one of the most advanced fields in China. To take two examples, more than 70% of the articles published in the Chinese Journal of Physiology were in the category of neuroscience; among the members of the Chinese Academy of Sciences (CAS), scientists in the field of neuroscience outnumber scientists in other disciplines of basic medical sciences. This assay tries to analyze the historical and contemporary background underlying the current status.     

New tools and new biology: Recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.     

生物过程化学机制的单分子荧光探测

单分子荧光检测越来越广泛地被应用于生命科学领域。这项技术可以对生物过程的化学机制进行定量、仔细的探究,与传统系综实验形成很好的互补。本文简介近几年单分子荧光检测研究的若干典型实例,以此展示这项技术的特点、优势及其可能的应用。它们涉及从简单的生化反应到复杂的蛋白表达调控等重要的生物过程。     

Physiology in the oeuvre of a prominent Hungarian medical scientist--Endre H"ogyes.

Endre Hógyes, one of the most prominent and internationally-renown leaders in the field of medical research, especially the treatment of rabies, was born one hundred and fifty years ago in Hungary. E. Hógyes had started his medical and research carrier in 1870. In 1889 he had become vice-president of the Royal Hungarian Society of Natural Sciences and was elected as a member of the Hungarian Academy of Sciences (MTA) and that member of the National Council of Public Health. Scientific carrier of E. Hógyes has always been closely linked to physiological sciences. E Hógyes made a significant contribution to different areas of physiological sciences; his most important scientific publications in this field deal with renal physiology, respitary mechanics, cerebellar function, and associated eye movement. Endre Hógyes was the first to organize Hungarian physiologists into a community. The "Special Physiological Conferences" were initiated within the Hungarian Royal Society of Natural Sciences in 1891. As a token of appretiation, Hungarian physiologists and other medical professionals have announced the year of 1997 as a memorial year of Dr. Endre Hógyes.     

Taverna: a tool for the composition and enactment of bioinformatics workflows

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.     

Competitive processes. II. Stability of random systems

In this work, by employing the concept of vector Lyapunov functions and the theory of random differential inequalities, the stability analysis of random competitive systems is initiated in a systematic and unified way. Furthermore, an attempt has been made to formulate and partially resolve the “deterministic vs. stochastic”, and the “complexity vs. stability” problems in stochastic competitive processes. Finally, the usefulness of the stability analysis of the competitive systems has been demonstrated by exhibiting several well-known examples of competitive processes in biological, medical, physical and social sciences in a coherent way.     

Models in biology: form and function

The relationships between physical and biological sciences are important in science education. This is shown in the links between the structure of biological science and the use of models. Although the physical sciences contain many principles of wide application, much of biology consists of very distinct examples. When these examples are used as models of organisms or processes, misunderstanding can occur if the characteristics of the model are used to make inaccurate generalizations. In biological education, stress on the importance of unique features must continually accompany the demonstration of similarities.

Theoretical models are constructed and reconstructed by students learning science, particularly in relation to broadly applicable principles. In biology a student may build a theoretical model of a subject which is itself a model used as an example. Distinct features of biological science may influence a variety of learning situations including problem solving.     

Aerodynamically assisted jetting and threading for processing concentrated suspensions containing advanced structural,functional and biological materials

In recent years material sciences have been interpreted right across the physical and the life sciences. Essentially this discipline broadly addresses the materials, processing, and/or fabrication right up to the structure. The materials and structures areas can range from the micro- to the nanometre scale and, in a materials sense, span from the structural, functional to the most complex, namely biological (living cells). It is generally recognised that the processing or fabrication is fundamental in bridging the materials with their structures. In a global perspective, processing has not only contributed to the materials sciences but its very nature has bridged the physical with the life sciences. In this review we discuss one such swiftly emerging fabrication approach having a plethora of applications spanning the physical and life sciences.     

系统发育研究中“长枝吸引”现象概述

系统发育研究(phylogeny)不仅有助于重建地球所有生物体的进化历史, 而且还可以揭示进化生物学领域中的一些基本问题。清晰了解各生物物种进化历程及不同物种之间的进化关系, 是进一步研究和探索生物学其他学科的基础。但是现今广泛应用的所有系统发育分析方法都存在一定的局限性, 在一定程度上不能有效消除各种误差, 从而不能客观地处理和分析数据, 也就不能成功重建生物进化历程, 真实反映物种进化关系。系统发育研究中, “长枝吸引” (Long-branch Attraction, LBA)假象是最为困扰研究者的问题。文章从“长枝吸引”问题的产生原由、检测方法以及消除策略等多个方面进行详尽概述, 并通过列举典型实例, 阐述了解决“长枝吸引”问题的途径。     

Crucial ignored parameters on nanotoxicology: the importance of toxicity assay modifications and "cell vision"

Until now, the results of nanotoxicology research have shown that the interactions between nanoparticles (NPs) and cells are remarkably complex. In order to get a deep understanding of the NP-cell interactions, scientists have focused on the physicochemical effects. However, there are still considerable debates about the regulation of nanomaterials and the reported results are usually in contradictions. Here, we are going to introduce the potential key reasons for these conflicts. In this case, modification of conventional in vitro toxicity assays, is one of the crucial ignored matter in nanotoxicological sciences. More specifically, the conventional methods neglect important factors such as the sedimentation of NPs and absorption of proteins and other essential biomolecules onto the surface of NPs. Another ignored matter in nanotoxicological sciences is the effect of cell "vision" (i.e., cell type). In order to show the effects of these ignored subjects, we probed the effect of superparamagnetic iron oxide NPs (SPIONs), with various surface chemistries, on various cell lines. We found thatthe modification of conventional toxicity assays and the consideration of the "cell vision" concept are crucial matters to obtain reliable, and reproducible nanotoxicology data. These new concepts offer a suitable way to obtain a deep understanding on the cell-NP interactions. In addition, by consideration of these ignored factors, the conflict of future toxicological reports would be significantly decreased.     

Molecular Graphics - Trends and Perspectives

The principles of molecular graphics are discussed in context with the optimization of man-machine communication in molecular sciences. The state of the art in this field is demonstrated with several examples. The paper is focussed on the discussion of a strategic basis of the information transfer between human activities and computational processes. It is demonstrated that enhancement of interactivity in the visualization process may lead to the generation of new insight on one side and the development of new computational algorithms based on the human visual pattern recognition strategy.Electronic Supplementary Material available.     

ON THE HISTORY AND CHARACTERISTICS OF SOME MULTIPLE DISCOVERIES IN BOTANY, 1648–1965

Historians and others have given attention to multiple independent discoveries because of their implications for the nature of scientific discovery in general. However, previously published lists of such discoveries include almost no examples from botany. That this has been a matter of oversight is shown by the presentation of 22 cases of multiple botanical discoveries, the circumstances of which are briefly described. These examples show a number of the same general characteristics as those in other fields of science. They range in importance from the broadly sweeping to the narrowly specific, and show various degrees of simultaneity. They illustrate the problems of interpretation involved in judging functional equivalence, identity of central message, and priority. The bearing of some of the examples on various theories of the cause of multiple discoveries is also discussed. It is concluded that multiple discoveries have probably occurred as frequently in botany as in other sciences, and they display the same characteristics and generate the same problems of interpretation.     

Use ofk 0-NAA in the life sciences

Biological Trace Element Research - The applicability and usefulness ofk 0-based reactor neutron activation analysis (NAA) in the life sciences is evaluated from the following examples: 1....     

The Spatial Turn: Geographical Approaches in the History of Science

Over the past decade or so a number of historians of science and historical geographers, alert to the situated nature of scientific knowledge production and reception and to the migratory patterns of science on the move, have called for more explicit treatment of the geographies of past scientific knowledge. Closely linked to work in the sociology of scientific knowledge and science studies and connected with a heightened interest in spatiality evident across the humanities and social sciences this ‹spatial turn’ has informed a wide-ranging body of work on the history of science. This discussion essay revisits some of the theoretical props supporting this turn to space and provides a number of worked examples from the history of the life sciences that demonstrate the different ways in which the spaces of science have been comprehended.     

The varied lives of organisms: variation in the historiography of the biological sciences

This paper emphasizes the crucial role of variation, at several different levels, for a detailed historical understanding of the development of the biomedical sciences. Going beyond valuable recent studies that focus on model organisms, experimental systems and instruments, we argue that all of these categories can be accommodated within our approach, which pays special attention to organismal and cultural variation. Our empirical examples are drawn in particular from recent historical studies of nineteenth- and early twentieth-century genetics and physiology. Based on the quasi-paradoxical conclusion that biological and cultural variation both constrains and enables innovation in the biomedical sciences, we argue that more attention should be paid to variation as an analytical category in the historiography of the life sciences.     

Revolutions in the earth sciences

The 20th century has been a century of scientific revolutions for many disciplines: quantum mechanics in physics, the atomic approach in chemistry, the nonlinear revolution in mathematics, the introduction of statistical physics. The major breakthroughs in these disciplines had all occurred by about 1930. In contrast, the revolutions in the so-called natural sciences, that is in the earth sciences and in biology, waited until the last half of the century. These revolutions were indeed late, but they were no less deep and drastic, and they occurred quite suddenly. Actually, one can say that not one but three revolutions occurred in the earth sciences: in plate tectonics, planetology and the environment. They occurred essentially independently from each other, but as time passed, their effects developed, amplified and started interacting. These effects continue strongly to this day.