Analytical ultracentrifugation in a Gibbsian perspective

The analytical ultracentrifuge has come into new intensive use following complete instrumental redesign and the use of advanced computer technologies for the analysis and interpretation of experimental results. Major attention is now devoted to the evaluation of interactions between similar and dissimilar biological macromolecules in dilute and concentrated systems. Electrostatically charged biological solute systems additionally comprise low molecular weight charged and non-charged cosolvents. Solvent/cosolvent interactions, insufficiently considered in most current analytical ultracentrifugation analyses, may quantitatively affect solute/solute interactions. For comprehensive analysis the Svedberg derivation considering a buoyant molar mass (1 - rho0 partial specific volume)M2 and valid at vanishing solute concentration for strictly two component systems only, should be replaced, following classical thermodynamic analysis, by the ratio (delta rho/delta c2)(mu)/d pi/dc2 of the density increment at constant chemical potential of diffusible cosolvents, to the derivative of the osmotic pressure with solute concentration. Disregard of the solvent/cosolvent and solute/cosolvent interactions should be avoided.     

Analytical and numerical tools for diffusion-based movement models

I present a general diffusion-based modeling framework for the analysis of animal movements in heterogeneous landscapes, including terms representing advection, mortality, and edge-mediated behavior. I use adjoint operator theory to develop mathematical machinery for the assessment of a number of biologically relevant quantities, such as occupancy times, hitting probabilities, quasi-stationary distributions, the backwards equation, and conditional probability densities. I derive finite-element approximations, which can be used to obtain numerical solutions in domains which do not allow for an analytical treatment. As an example, I model the movements of the butterfly Melitaea cinxia in an island consisting of a set of habitat patches and the intervening matrix habitat. I illustrate the behavior of the model and the mathematical theory by examining the effects of a hypothetical movement barrier and advection caused by prevailing wind conditions.     

Analytical tools for characterizing heterogeneity in organelle content

Heterogeneity in the content and function of subcellular organelles on the intercellular and intracellular level plays an important role in determining cell fate. These variations extend to normal-state and disease-state cellular functions and responses to environmental stimuli, such as oxidative stress and therapeutic drugs. Analytical tools to characterize variation in all types of organelles are essential to provide insights that can lead to advances in medicine, such as therapies targeted to specific subcellular regions. In this review, we discuss analytical techniques for interrogating individual intact organelles (e.g. mitochondria and synaptic vesicles) and lysates in a high-throughput manner, including a recently developed nanoscale fluorescence-activated subcellular sorter and techniques based on capillary electrophoresis with laser-induced fluorescence detection. We then highlight the advantages that droplet microfluidics offers for probing subcellular heterogeneity.     

A comprehensive approach towards product and organisation related environmental management tools

The international standardisation of Environmental Management (EM) is documented by the ISO 14000 series. Within this series a number of Environmental Management tools are treated. Therefore, it can be seen as a “toolbox” which offers several options for sound Environmental Management practices in organisations. However, a number of questions remain because they are not treated by the standards themselves. Some examples are which of the tools should be applied to what kind of Environmental Management problem or what are the synergisms and antagonisms between these tools. To illustrate the importance of a comprehensive choice and a compatible approach towards EM-tools, Life Cycle Assessment (ISO 14040 series) is discussed in the context of Environmental Management Systems (ISO 14001). The focus of ISO 14001 are organisations, while LCA deals with products or processes. In principle, they are not compatible, since the life-cycle approach analyses one production chain from “cradle to grave” or even back to the cradle, while a management system according to ISO 14001 analyses organisations, i.e. a number of product chains, from “gate to gate”. LCAs, however, could be compiled by aggregating several “gate to gate” energy and material balances of companies. LCA can assist in prioritising and achieving the objectives of an EM-System. LCA can also help to understand the environmental impact of organisations and what share of their overall environmental burden is produced “inside the gates” or “outside the gates”, respectively.     

On the limitations of life cycle assessment and environmental systems analysis tools in general

The potential and limitations of life cycle assessment and environmental systems analysis tools in general are evaluated. More specifically this is done by exploring the limits of what can be shown by LCA and other tools. This is done from several perspectives. First, experiences from current LCAs and methodology discussions are used including a discussion on the type of impacts typically included, quality of inventory data, methodological choices in relation to time aspects, allocation, characterisation and weighting methods and uncertainties in describing the real world. Second, conclusions from the theory of science are practised. It is concluded that it can in general not be shown that one product is environmentally preferable to another one, even if this happens to be the case. This conclusion has important policy implications. If policy changes require that it must be shown that one product is more (or less) environmentally preferable before any action can be taken, then it is likely that no action is ever going to take place. If we want changes to be made, decisions must be taken on a less rigid basis. It is expected that in this decision making process, LCA can be a useful input. Since it is the only tool that can be used for product comparisons over the whole life cycle, it can not be replaced by any other tool and should be used. Increased harmonisation of LCA methodology may increase the acceptability of chosen methods and increase the usefulness of the tool.     

The value of applying molecular biology tools in environmental engineering: Academic and industry perspective in the USA

The integration of molecular biology tools in environmental engineering is a challenge. We discuss our views on the following four critical issues: (i) faculty career development, (ii) tool standardization, (iii) teaching, and (iv) the application of molecular biology tools in practice. For (i), we suggest that administrators and faculty need to understand the special challenges inherent to research and teaching within this highly interdisciplinary area. Furthermore, we suggest preparing two white papers aimed at educating administrators in universities and agencies. For (ii), we conclude that, because molecular biology tools are still in a state of rapid development, proposing standards at this time is premature. In the future, standards for widely applied tools should be in an on-line, peer-reviewed format. Concerning (iii), we believe that molecular biology should be taught only to the degree needed to achieve program goals. For example, environmental engineering practitioners only need to know the vocabulary and basic concepts of molecular biology tools, not be experts at doing them hands on. To help engineering students gain the right level and type of information, learning modules should be developed for them. Finally, although engineering successes applying molecular biology tools are available (iv), the biggest value will come when the tools are fully integrated with practice. Therefore, we encourage the creation of a demonstration project to document the value of applying molecular biology tools in environmental engineering. This revised version was published online in June 2006 with corrections to the Cover Date.     

Information management for proteomics: a perspective

Proteomics is a data-rich discipline that makes extensive use of separation tools, mass spectrometry and bioinformatics to analyze and interpret the features and dynamics of the proteome. A major challenge for the field is how proteomics data can be stored and managed, such that data become permanent and can be mined with current and future tools. This article details our experience in the development of a commercial proteomic information management system. We identify the challenges faced in data acquisition, workflow management, data permanence, security, data interpretation and analysis, as well as the solutions implemented to address these issues. We finally provide a perspective on data management in proteomics and the implications for academic and industry-based researchers working in this field.     

Information management for proteomics: a perspective

Proteomics is a data-rich discipline that makes extensive use of separation tools, mass spectrometry and bioinformatics to analyze and interpret the features and dynamics of the proteome. A major challenge for the field is how proteomics data can be stored and managed, such that data become permanent and can be mined with current and future tools. This article details our experience in the development of a commercial proteomic information management system. We identify the challenges faced in data acquisition, workflow management, data permanence, security, data interpretation and analysis, as well as the solutions implemented to address these issues. We finally provide a perspective on data management in proteomics and the implications for academic and industry-based researchers working in this field.     

A model management systems approach to manufacturing systems design

Manufacturing systems design involves the solution of a complex series of interrelated problems. This complexity will increase in the future as manufacturing practices change to meet increased global competition. Research within manufacturing systems design has mainly been focused on finding improved models for solving particular problems, or extending existing modeling techniques. This has resulted in numerous modeling tools being available to support manufacturing systems design. However, little research work has been carried out into consolidating the existing theories and models. As a result, a large body of this work has not been applied in industry. Model management has evolved as a research area which investigates methods for storing, modifying, and manipulating models. This article describes a prototype model management system for manufacturing systems design. The objective here is not to develop “another” decision support system for manufacturing design, but to illustrate, through the development of a prototype system, a number of key ideas of how concepts from the area of model management systems can be used to support manufacturing systems design. The prototype model management system utilizes the structured modeling framework and uses an extended version of the structured modeling language. An important aspect of the prototype model management system is the incorporation of the model development task, thus allowing the system to be easily updated and adapted. The prototype system was evaluated using a range of queueing network models for manufacturing systems design.     

Analytical tools for unravelling the metabolism of gas-fermenting Clostridia

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Emerging tools for synthetic genome design

Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives.     

Networks in cognitive systems and biomedicine: cerebral processes, models and mathematical tools design

Convergence of clinical, empirical, methodological and theoretical approaches aimed at understanding the relation between brain function and cognition, is by now standard in most if not all academic programs in the area of Cognitive Science. This confederation of disciplines is one of the liveliest domains of inquiry and discussion into some of the most fundamental--and historically resilient--questions human beings have posed themselves. The contributions gathered in this special issue of Biological Research, directly inspired by the ongoing work at the Instituto de Sistemas Complejos de Valparaiso and the December 2006 CONICYT-INSERM-SFI workshop "Networks in Cognitive Systems/Trends and Challenge in Biomedicine: From Cerebral Process to Mathematical Tools Design", Chile, represent an explicit invitation to the reader to dive deeper into this fascinating terrain.     

Environmental life cycle assessment (LCA) as a tool for identification and assessment of environmental aspects in environmental management systems (EMS)

Purpose  

The paper presents a discussion on the possibilities of using LCA in identification and assessment of environmental aspects in environmental management systems based on the requirements of the international ISO14001 standard and the European Union EMAS regulation. Some modifications of LCA methodology are proposed in Part 1 while the results of a review of environmental aspects for 36 organisations with implemented EMS are presented in Part 2 of the article.