The biological framework of environmental education

The need for environmental education is now widely recognized and a great variety of teaching programmes and projects exists at all levels of education. It is suggested, however, that particularly for secondary education there is still a need for a clearer definition of a conceptual framework, to give environmental education a more recognizable identity. Biological aspects of man's relationship with his environment are reviewed, and areas of stress identified, ecological, physiological, and behavioural, which environmental education may help to counteract. Environmental education is considered to be more concerned with observation, identification of relationships, evaluation, and appropriate forms of action, than with the assembly of theoretical knowledge from contributory subject areas.     

Contact guidance as a consequence of coupled morphological evolution and motility of adherent cells

Biomechanics and Modeling in Mechanobiology - Adherent cells seeded on substrates spread and evolve their morphology while simultaneously displaying motility. Phenomena such as contact guidance,...     

Formation of endonuclease III-sensitive sites as a consequence of oxygen radical attack on DNA

Exposure of the plasmid pBR 322 to the aerobic xanthine oxidase reaction introduced single strand scissions and endonuclease III-sensitive sites. The latter may be residues of thymine glycol. Both forms of DNA damage were completely prevented by superoxide dismutase or catalase, whereas bovine serum albumin was much less effective. Mannitol and benzoate, added as scavengers of HO., and desferrioxamine or diethylene triamine pentaacetate, added to sequester Fe(III), also protected. These results indicate a metal-catalyzed interaction of O2- with H2O2, which produces HO. which, in turn, causes DNA strand scission and oxidation of thymine residues to thymine glycol. Plasmid isolated from aerobically-incubated cells contained more strand scissions and endonuclease III-sensitive sites than did plasmid from anaerobically-incubated cells, and a low molecular weight scavenger of O2- prevented the damage seen with the aerobic cells. Genetic defects in AP endonucleases rendered E. coli more susceptible to the dioxygen-dependent lethality of plumbagin, which mediates O2- production. Similarly, plasmid DNA, within the endonuclease-deficient cells, exhibited more strand scissions and endonuclease III-sensitive sites upon aerobic exposure to plumbagin than did endonuclease-sufficient cells, and a low molecular weight scavenger of O2- was protective. These results are consistent with the conclusions that strand scissions and formation of endonuclease III-sensitive sites are among the consequences of exposure of DNA to O2- plus H2O2, both in vitro and in vivo.     

The formulation of a national strategy for biological control of possums and bovine Tb

Abstract

The Government has designated the control of possums and bovine Tb a National Science Strategy (NSS) research area. An NSS Committee has been appointed by the Ministry of Research Science and Technology, commissioned to “identify, coordinate and promote national priorities for possum and tuberculosis (Mycobacterium bovis) related research in order that threats both to New Zealand's export markets and to conservation values can be eliminated”.     

The sediment budget as conceptual framework and management tool

A review of the sediment budget concept, a brief history, cognate mass balances and the significance of the storage term. Questions of temporal and spatial scales, errors and uncertainties and the nature of system response. Management implications include natural hazards, climatic change and land use disturbance.     

Towards a lightweight generic computational grid framework for biological research

Background  

An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology.     

Evolutionary game theory as a framework for studying biological invasions

Although biological invasions pose serious threats to biodiversity, they also provide the opportunity to better understand interactions between the ecological and evolutionary processes structuring populations and communities. However, ecoevolutionary frameworks for studying species invasions are lacking. We propose using game theory and the concept of an evolutionarily stable strategy (ESS) as a conceptual framework for integrating the ecological and evolutionary dynamics of invasions. We suggest that the pathways by which a recipient community may have no ESS provide mechanistic hypotheses for how such communities may be vulnerable to invasion and how invaders can exploit these vulnerabilities. We distinguish among these pathways by formalizing the evolutionary contexts of the invader relative to the recipient community. We model both the ecological and the adaptive dynamics of the interacting species. We show how the ESS concept provides new mechanistic hypotheses for when invasions result in long- or short-term increases in biodiversity, species replacement, and subsequent evolutionary changes.     

Multi-node graphs: a framework for multiplexed biological assays.

Multiplex polymerase chain reaction (PCR) is an extension of the standard PCR protocol in which primers for multiple DNA loci are pooled together within a single reaction tube, enabling simultaneous sequence amplification, thus reducing costs and saving time. Potential cost saving and throughput improvements directly depend on the level of multiplexing achieved. Designing reliable and highly multiplexed assays is challenging because primers that are pooled together in a single reaction tube may cross-hybridize, though this can be addressed either by modifying the choice of primers for one or more amplicons, or by altering the way in which DNA loci are partitioned into separate reaction tubes. In this paper, we introduce a new graph formalism called a multi-node graph, and describe its application to the analysis of multiplex PCR scalability. We show, using random multi-node graphs that the scalability of multiplex PCR is constrained by a phase transition, suggesting fundamental limits on efforts to improve the cost-effectiveness and throughput of standard multiplex PCR assays. In particular, we show that when the multiplexing level of the reaction tubes is roughly theta(log (sn)) (where s is the number of primer pair candidates per locus and n is the number of loci to be amplified), then with very high probability we can 'cover' all loci with a valid assignment to one of the tubes in the assay. However, when the multiplexing level of the tube exceeds these bounds, there is no possible cover and moreover the size of the cover drops dramatically. Simulations using a simple greedy algorithm on real DNA data also confirm the presence of this phase transition. Our theoretical results suggest, however, that the resulting phase transition is a fundamental characteristic of the problem, implying intrinsic limits on the development of future assay design algorithms.     

Biana: a software framework for compiling biological interactions and analyzing networks

Background  

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.     

A framework to find the logic backbone of a biological network

Background

Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network.

Results

In this work, we propose a simple logic framework, based on categorizing causal relationships as sufficient or necessary, as a complement to Boolean networks. We identify and explore the properties of complex subnetworks that are distillable into a single logic relationship. We also identify cyclic subnetworks that ensure the stabilization of the state of participating nodes regardless of the rest of the network. We identify the logic backbone of biomolecular networks, consisting of external signals, self-sustaining cyclic subnetworks (stable motifs), and output nodes. Furthermore, we use the logic framework to identify crucial nodes whose override can drive the system from one steady state to another. We apply these techniques to two biological networks: the epithelial-to-mesenchymal transition network corresponding to a developmental process exploited in tumor invasion, and the network of abscisic acid induced stomatal closure in plants. We find interesting subnetworks with logical implications in these networks. Using these subgraphs and motifs, we efficiently reduce both networks to succinct backbone structures.

Conclusions

The logic representation identifies the causal relationships between distant nodes and subnetworks. This knowledge can form the basis of network control or used in the reverse engineering of networks.

     

Defining and detecting structural sensitivity in biological models: developing a new framework

When we construct mathematical models to represent biological systems, there is always uncertainty with regards to the model specification—whether with respect to the parameters or to the formulation of model functions. Sometimes choosing two different functions with close shapes in a model can result in substantially different model predictions: a phenomenon known in the literature as structural sensitivity, which is a significant obstacle to improving the predictive power of biological models. In this paper, we revisit the general definition of structural sensitivity, compare several more specific definitions and discuss their usefulness for the construction and analysis of biological models. Then we propose a general approach to reveal structural sensitivity with regards to certain system properties, which considers infinite-dimensional neighbourhoods of the model functions: a far more powerful technique than the conventional approach of varying parameters for a fixed functional form. In particular, we suggest a rigorous method to unearth sensitivity with respect to the local stability of systems’ equilibrium points. We present a method for specifying the neighbourhood of a general unknown function with \(n\) inflection points in terms of a finite number of local function properties, and provide a rigorous proof of its completeness. Using this powerful result, we implement our method to explore sensitivity in several well-known multicomponent ecological models and demonstrate the existence of structural sensitivity in these models. Finally, we argue that structural sensitivity is an important intrinsic property of biological models, and a direct consequence of the complexity of the underlying real systems.     

Microarray missing data imputation based on a set theoretic framework and biological knowledge

Gene expressions measured using microarrays usually suffer from the missing value problem. However, in many data analysis methods, a complete data matrix is required. Although existing missing value imputation algorithms have shown good performance to deal with missing values, they also have their limitations. For example, some algorithms have good performance only when strong local correlation exists in data while some provide the best estimate when data is dominated by global structure. In addition, these algorithms do not take into account any biological constraint in their imputation. In this paper, we propose a set theoretic framework based on projection onto convex sets (POCS) for missing data imputation. POCS allows us to incorporate different types of a priori knowledge about missing values into the estimation process. The main idea of POCS is to formulate every piece of prior knowledge into a corresponding convex set and then use a convergence-guaranteed iterative procedure to obtain a solution in the intersection of all these sets. In this work, we design several convex sets, taking into consideration the biological characteristic of the data: the first set mainly exploit the local correlation structure among genes in microarray data, while the second set captures the global correlation structure among arrays. The third set (actually a series of sets) exploits the biological phenomenon of synchronization loss in microarray experiments. In cyclic systems, synchronization loss is a common phenomenon and we construct a series of sets based on this phenomenon for our POCS imputation algorithm. Experiments show that our algorithm can achieve a significant reduction of error compared to the KNNimpute, SVDimpute and LSimpute methods.     

The challenge of determining the need for remediation following a wide-area biological release

Recovering from a biological attack is a complex process requiring the successful resolution of numerous challenges. The Interagency Biological Restoration Demonstration program is one of the first multiagency efforts to develop strategies and tools that could be effective following a wide-area release of B. anthracis spores. Nevertheless, several key policy issues and associated science and technology issues still need to be addressed. For example, more refined risk assessment and management approaches are needed to help evaluate "true" public health risk. Once the risk is understood, that information can be considered along with the types of characterization activities deemed necessary to determine whether the cost and time of decontamination are actually warranted. This commentary offers 5 recommendations associated with decision making regarding decontamination and clearance options that should accompany a comprehensive risk analysis leading to more effective risk management decisions. It summarizes some of the most important technological gaps that still need to be addressed to help decision makers in their objective of reducing health risks to an acceptable level. The risk management approach described should enable decision makers to improve credibility and gain public acceptance, especially when an adequate science and technology base is available to support the required decisions.     

Conflict resolution following aggression in gregarious animals: a predictive framework

Knowledge of how animals manage their conflicts is critical for understanding the dynamics of social systems. During the last two decades research on gregarious animals, especially primates, has focused on the mechanisms of conflict management, mainly on friendly postconflict reunions (also called ‘reconciliation’) in which former opponents exchange affiliative behaviour soon after an aggressive conflict. Our aim in this paper is to present a framework in which the costs and benefits of friendly postconflict reunions, both for each individual opponent and for their mutual relationship, are used to predict the patterning of postconflict resolution mechanisms in other gregarious animals. The framework predicts the occurrence of postconflict reunions in species that live in stable social units, have individualized relationships, and experience postconflict hostility, but especially in those in which intragroup aggression disrupts valuable relationships. The critical issue is whether aggressive conflicts occur between cooperative partners and whether the level of aggression is sufficient to jeopardize the benefits associated with such valuable relationships. We conclude by proposing four research priorities to evaluate the role of friendly reunions in negotiating relationships and the way they are themselves influenced by asymmetries in partner value and biological market effects. Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.