Transgenic animals in integrative biology: approaches and interpretations of outcome.

Technological innovations in methods for genetic manipulation of laboratory animals and in techniques for assessment of cardiovascular, respiratory, behavioral, and metabolic physiology in mouse models afford unprecedented opportunities for research in integrative biology. We provide here an overview of basic and advanced techniques for generation of transgenic mice and a discussion of how transgenic technology can be most advantageously applied to important physiological questions that can be addressed only within the intact organism.     

Putting proteins in context: Scientific illustrations bring together information from diverse sources to provide an integrative view of the molecular biology of cells

Scientific illustrations, such as this cross-section through part of an E. coli cell, can give an impression of the complexity of a cell's interior and of the way its macromolecules are arranged.     

Economic context and pigeons' risk-taking: an integrative approach

The present work tested pigeons' (Columba livia) risk sensitivity to changes in resource availability in the concurrent-chains choice procedure. Subjects were provided choices, generally between variable-ratio (VR) and fixed-ratio (FR) outcome schedules with equal or different mean values. Predictions from ecology's risk sensitivity, behavioral economic's rate maximization, and psychology's delay-reduction theory were contrasted under settings where budget was adversely affected by one of three manipulations in seven experiments: (1) session length was dramatically reduced; (2) choice-phase duration was substantially increased by increasing the response requirements in the choice phase, or (3) outcome duration was significantly increased by increasing the response requirements in the outcome phase while holding session length constant. Although preference measures were sensitive to every budget manipulation, the nature of the changes observed were dependent upon the manner in which resource availability was manipulated and the choice alternatives offered. For example, choice was affected in an opposite manner when budget was adversely altered by lengthening choice duration ("search time") as opposed to lengthening outcome duration ("handling time"). Findings revealed partial support for pigeons' sensitivity both to changes in budget and to changes in conditioned reinforcer value. The overall pattern of results thus favors an integrative approach to describing the effect of economic context on general risk sensitivity.     

Heavy metals in relation to the biology of the mummichog, Fundulus heteroclitus

Heavy metal levels of cadmium, copper, mercury, manganese, and zinc were examined in the mummichog, Fundulus heteroditus from industrialized and non-industrialized environments. With one exception, the environment with the highest trace metal in its waters, had the fishes with the highest metal concentration. Except for mercury, the concentration factor varied inversely with the metal concentrations of the fish and water, suggesting a possible regulatory mechanism for metals in the tissues of mummichogs from environments with high metal concentrations. There was an inverse relationship between standard length and concentrations of zinc, manganese, copper and cadmium in whole male and female fishes. The viscera contained significantly greater concentrations of these metals than somatic muscle tissue. There were also significant differences between males and females with respect to whole-body zinc and copper concentrations, but no sex differences for manganese and cadmium.     

Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics

In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space–time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space–time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential applications for the analysis, engineering and management of physical and biological systems and properties, and the consequences for the organization of transdisciplinary research and the scientific curriculum in the context of the SYSTEMOSCOPE Consortium research and development agenda.     

Theory structure,reduction, and disciplinary integration in biology

This paper examines the nature of theory structure in biology and considers the implications of those theoretical structures for theory reduction. An account of biological theories as interlevel prototypes embodying causal sequences, and related to each other by strong analogies, is presented, and examples from the neurosciences are provided to illustrate these middle-range theories. I then go on to discuss several modifications of Nagel's classical model of theory reduction, and indicate at what stages in the development of reductions these models might best apply. Finally I consider several implications of these analyses of theory structure and reduction for disciplinary integration in biology.     

History matters: ecometrics and integrative climate change biology

Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time-an approach we call 'ecometrics'. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.     

Forest structure,diversity, and primary production in relation to disturbance severity

1. Differential disturbance severity effects on forest vegetation structure, species diversity, and net primary production (NPP) have been long theorized and observed. Here, we examined these factors concurrently to explore the potential for a mechanistic pathway linking disturbance severity, changes in light environment, leaf functional response, and wood NPP in a temperate hardwood forest.
2. Using a suite of measurements spanning an experimental gradient of tree mortality, we evaluated the direction and magnitude of change in vegetation structural and diversity indexes in relation to wood NPP. Informed by prior observations, we hypothesized that forest structural and species diversity changes and wood NPP would exhibit either a linear, unimodal, or threshold response in relation to disturbance severity. We expected increasing disturbance severity would progressively shift subcanopy light availability and leaf traits, thereby coupling structural and species diversity changes with primary production.
3. Linear or unimodal changes in three of four vegetation structural indexes were observed across the gradient in disturbance severity. However, disturbance‐related changes in vegetation structure were not consistently correlated with shifts in light environment, leaf traits, and wood NPP. Species diversity indexes did not change in response to rising disturbance severity.
4. We conclude that, in our study system, the sensitivity of wood NPP to rising disturbance severity is generally tied to changing vegetation structure but not species diversity. Changes in vegetation structure are inconsistently coupled with light environment and leaf traits, resulting in mixed support for our hypothesized cascade linking disturbance severity to wood NPP.

     

Paramyosin in invertebrate muscles. II. Content in relation to structure and function

By quantitative sodium dodecyl sulfate-polyacrylamide gel electrophoresis, paramyosin:myosin heavy chain molecular ratios were calculated for three molluscan muscles:Aequipecten striated adductor, Mercenaria opaque adductor, and Mytilus anterior byssus retractor; and four arthropodan muscles:Limulus telson, Homarus slow claw. Balanus scutal depressor, and Lethocerus air tube retractor. These ratios correlate positively with both thick filament dimensions and maximum active tension development in these tissues. The role of paramyosin in these muscles is discussed with respect to the following characteristics: force development, "catch," and extreme reversible changes in length.