Toward a stoichiometric framework for evolutionary biology

Ecological stoichiometry, the study of the balance of energy and materials in living systems, may serve as a useful synthetic framework for evolutionary biology. Here, we review recent work that illustrates the power of a stoichiometric approach to evolution across multiple scales, and then point to important open questions that may chart the way forward in this new field. At the molecular level, stoichiometry links hereditary changes in the molecular composition of organisms to key phenotypic functions. At the level of evolutionary ecology, a simultaneous focus on the energetic and material underpinnings of evolutionary tradeoffs and transactions highlights the relationship between the cost of resource acquisition and the functional consequences of biochemical composition. At the macroevolutionary level, a stoichiometric perspective can better operationalize models of adaptive radiation and escalation, and elucidate links between evolutionary innovation and the development of global biogeochemical cycles. Because ecological stoichiometry focuses on the interaction of energetic and multiple material currencies, it should provide new opportunities for coupling evolutionary dynamics across scales from genomes to the biosphere.     

A conceptual framework for impact assessment within SLCA

Purpose  

This paper aims at spelling out the area of protection (AoP), namely the general concept of human well-being and the impact categories in social life cycle assessment (SLCA). The applicability of the so-called capabilities approach—a concept frequently used for evaluating human lives—is explored. It is shown how the principles of the capabilities approach can be transferred to the impact assessment within SLCA.     

A conceptual framework for maize leaf development.

What is and is not known about the maize leaf is reviewed. Analysis of genetic mosaics and direct observation with the SEM have broken leaf development into three distinct phases: recruitment of cells within the meristem, cell division into the 0.6-mm tall primordium, and postprimordial division and differentiation into the mature leaf. New data are presented that imply that cell division rates in the leaf are coordinated by inductive signals from the internal cells. Leaf cells that tend to divide more are held in check by slower growing neighbors; this complicates the search for developmental compartments. Experiments with recessive mutants that remove the ligule and auricle have been important in identifying an inducer signal with the specific meaning "make ligule-auricle." We have studied many dominant mutant alleles at seven different genes. Each mutant alters the position of the ligule boundary. We conclude the following. First, the mutants act in particular domains of the primordium. Second, the dominant mutants all move the ligule boundary in the same direction. Third, the mutants all retard developmental stage transitions. Fourth, three and probably four of the seven genes for which dominant mutants have been studied specify homeodomain proteins in the wrong place. The concept of "maturation schedule" is used to explain these data. All of the dominant mutant phenotypes are seen as consequences of immature cells being in the wrong place when inductive signals pass through the leaf. Several specific questions of leaf development and especially questions as to source of inductive signals or homologies among juvenile and adult organ parts are recast in light of this "maturation schedule" hypothesis.     

A conceptual framework for selecting environmental indicator sets

In recent years, environmental indicators have become a vital component of environmental impact assessments and “state of the environment” reporting. This has increased the influence of environmental indicators on environmental management and policy making at all scales of decision making. However, the scientific basis of the selection process of the indicators used in environmental reporting can be significantly improved. In many studies no formal selection criteria are mentioned and when selection criteria are used they are typically applied to indicators individually. Often, no formal criteria are applied regarding an indicator's analytical utility within the total constellation of a selected set of indicators. As a result, the indicator selection process is subject to more or less arbitrary decisions, and reports dealing with a similar subject matter or similar geographical entities may use widely different indicators and consequently paint different pictures of the environment. In this paper, a conceptual framework for environmental indicator selection is proposed that puts the indicator set at the heart of the selection process and not the individual indicators. To achieve this objective, the framework applies the concept of the causal network that focuses on the inter-relation of indicators. The concept of causal networks can facilitate the identification of the most relevant indicators for a specific domain, problem and location, leading to an indicator set that is at once transparent, efficient and powerful in its ability to assess the state of the environment.     

A framework for evolutionary systems biology

Background  

Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.     

Toward computational systems biology

The development and successful application of high-throughput technologies are transforming biological research. The large quantities of data being generated by these technologies have led to the emergence of systems biology, which emphasizes large-scale, parallel characterization of biological systems and integration of fragmentary information into a coherent whole. Complementing the reductionist approach that has dominated biology for the last century, mathematical modeling is becoming a powerful tool to achieve an integrated understanding of complex biological systems and to guide experimental efforts of engineering biological systems for practical applications. Here I give an overview of current mainstream approaches in modeling biological systems, highlight specific applications of modeling in various settings, and point out future research opportunities and challenges.     

Toward a framework for the evaluation of feature binding in pigeons

Pigeons were trained in a new procedure to test for visual binding errors between the dimensions of color and shape. In Experiment 1, pigeons learned to discriminate a target compound from 15 non-target compounds (constructed from four colors and shapes) by choosing one of two hoppers in a two-hopper choice task. The similarity of the target to non-target stimuli influenced choice responding. In Experiment 2, pigeons learned to detect a target compound when presented with a non-target compound within the same trial under conditions of simultaneity and sequentiality. Non-target trials were arranged to allow for the testing of binding errors (i.e., false identifications of the target on certain non-target trials). Transient evidence for binding errors in two of the birds occurred at the start of two-item training, but decreased with training. The experiments represent an important step toward developing a framework for the evaluation of visual feature binding in nonhumans.     

A biomolecular isolation framework for eco-systems biology

Mixed microbial communities are complex, dynamic and heterogeneous. It is therefore essential that biomolecular fractions obtained for high-throughput omic analyses are representative of single samples to facilitate meaningful data integration, analysis and modeling. We have developed a new methodological framework for the reproducible isolation of high-quality genomic DNA, large and small RNA, proteins, and polar and non-polar metabolites from single unique mixed microbial community samples. The methodology is based around reproducible cryogenic sample preservation and cell lysis. Metabolites are extracted first using organic solvents, followed by the sequential isolation of nucleic acids and proteins using chromatographic spin columns. The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest. The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future.     

Toward a systems biology perspective on enzyme evolution

Large superfamilies of enzymes derived from a common progenitor have emerged by duplication and divergence of genes encoding metabolic enzymes. Division of the functions of early generalist enzymes enhanced catalytic power and control over metabolic fluxes. Later, novel enzymes evolved from inefficient secondary activities in specialized enzymes. Enzymes operate in the context of complex metabolic and regulatory networks. The potential for evolution of a new enzyme depends upon the collection of enzymes in a microbe, the topology of the metabolic network, the environmental conditions, and the net effect of trade-offs between the original and novel activities of the enzyme.     

Macroscopic electrical activity as a conceptual framework in cognitive neuroscience

This report has the aim to indicate relevant implications of the systems theory approach to the experiments in conscious brain. The reports related to comparative neurophysiology and to the understanding of brain as a “whole” are rare, an outstanding comparative approach report in biological sciences was that of Darwin, who performed a voyage in order to compare structures of species and the principle of natural selectivity.

In despite of the fruitful approach of Darwin, most of the brain scientists do prefer to analyze either one type of brain or even only one structure to interpret the brain function. The single neuron doctrine developed by Sherrington also did not consider these various aspects. The avenue opened by Hans Berger which introduced the analysis of the brain oscillations was an important step towards understanding of the “whole brain”.

In this report we aim to describe narratively, technical, strategical and philosophical steps to bridge “Sherrington Neuron Doctrine” with the “Neurons-Brain Theory” of the whole brain by means of the method developed by Hans Berger.     

Toward a framework for sulfoproteomics: Synthesis and characterization of sulfotyrosine-containing peptides

Tyrosine sulfation is one of the most common post-translational modifications in secreted and transmembrane proteins and a key modulator of extracellular protein-protein interactions. Several proteins known to be tyrosine sulfated play important roles in physiological processes, and in some cases a direct link between protein function and tyrosine sulfation has been established. In blood coagulation, tyrosine sulfation of factor VIII is required for efficient binding of von Willebrand factor; in leukocyte adhesion, tyrosine sulfation of the P-selectin glycoprotein ligand-1 mediates high-affinity binding to P-selectin; and in leukocyte chemotaxis, tyrosine sulfation of chemokine receptors is required for optimal interaction with chemokine ligands. Furthermore, tyrosine sulfation has been implicated in several infectious diseases. In particular, tyrosine sulfation of the HIV-1 co-receptor CCR5 is required for viral entry into host cells and tyrosine sulfation of the Duffy antigen/receptor for chemokines is crucial for erythrocyte invasion by the malaria parasite plasmodium vivax. Despite increasing interest in tyrosine sulfation in recent years, the sulfoproteome still remains largely unexplored. To date, only a relatively small number of sulfotyrosine-containing peptides and proteins have been identified, and a specific role for tyrosine sulfation has not been established for most of these. Here, we provide an overview of the biology and enzymology of tyrosine sulfation and discuss recent developments in preparative and analytical methods that are central to sulfoproteome research.     

A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence

Abstract In this article we propose a new framework for studying adaptive radiations in the context of diversity-dependent diversification. Diversity dependence causes diversification to decelerate at the end of an adaptive radiation but also plays a key role in the initial pulse of diversification. In particular, key innovations (which in our definition include novel traits as well as new environments) may cause decoupling of the diversity-dependent dynamics of the innovative clade from the diversity-dependent dynamics of its ancestral clade. We present a likelihood-based inference method to test for decoupling of diversity dependence using molecular phylogenies. The method, which can handle incomplete phylogenies, identifies when the decoupling took place and which diversification parameters are affected. We illustrate our approach by applying it to the molecular phylogeny of the North American clade of the legume tribe Psoraleeae (47 extant species, of which 4 are missing). Two diversification rate shifts were previously identified for this clade; our analysis shows that the first, positive shift can be associated with decoupling of two Pediomelum subgenera from the other Psoraleeae lineages, while we argue that the second, negative shift can be attributed to speciation being protracted. The latter explanation yields nonzero extinction rates, in contrast to previous findings. Our framework offers a new perspective on macroevolution: new environments and novel traits (ecological opportunity) and diversity dependence (ecological limits) cannot be considered separately.     

A conceptual framework for understanding arthropod predator and parasitoid invasions

Arthropods make up the largest group of invasive alien species (IAS) worldwide. Although invasion research has been biased towards alien plants and vertebrates, it has suggested potential mechanisms for the success of IAS and provided a theoretical framework for further investigation. Here we address key concepts from invasion biology that are essential to our understanding of the success of invasive alien arthropod predators and parasitoids including human intervention, environmental characteristics, propagule pressure, biological traits, and biological interactions. To gain a greater understanding of the factors most likely to influence the different stages of invasion (arrival, establishment, and spread) for alien arthropod predators and parasitoids, we use a comparative approach to compare and contrast the differential success of invasions by alien phytophagous and carnivorous arthropods. Insights gained from this comparison suggest that future research will require a multitrophic approach in order to enhance our understanding of invasions at higher trophic levels.     

A conceptual framework for ecosystem management based on tradeoff analysis

Three dimensions (natural, social and economic factors) in tradeoff analysis have not been focused in ecology. It is necessary to consider the multi-dimensions through a tradeoff analysis of disturbances to find their positive and negative effects (referred to as two-sidedness). We proposed an 11-step approach to integrate the concepts, methods and examples to understand ecological two-sidedness. We recommend that: (1) ecological complexity and large-scale systematic perspectives need to be integrated; (2) disparate disciplines should be integrated to classify the two-sidedness indicators; (3) models should be adopted to define the characteristic metrics of disturbed ecosystems; (4) researchers need to reconsider evaluation standards and for each indicator with marginal changes; and (5) initial decision-making should refer to the two-sidedness value and that final decision-making should be subject to debate. This approach has great significance for ecosystem management because decision-makers can obtain the superiority and inferiority of disturbance strategies and select optimal strategy.     

A semiotic framework for evolutionary and developmental biology

This work aims at constructing a semiotic framework for an expanded evolutionary synthesis grounded on Peirce's universal categories and the six space/time/function relations [Taborsky, E., 2004. The nature of the sign as a WFF--a well-formed formula, SEED J. (Semiosis Evol. Energy Dev.) 4 (4), 5-14] that integrate the Lamarckian (internal/external) and Darwinian (individual/population) cuts. According to these guide lines, it is proposed an attempt to formalize developmental systems theory by using the notion of evolving developing agents (EDA) that provides an internalist model of a general transformative tendency driven by organism's need to cope with environmental uncertainty. Development and evolution are conceived as non-programmed open-ended processes of information increase where EDA reach a functional compromise between: (a) increments of phenotype's uniqueness (stability and specificity) and (b) anticipation to environmental changes. Accordingly, changes in mutual information content between the phenotype/environment drag subsequent changes in mutual information content between genotype/phenotype and genotype/environment at two interwoven scales: individual life cycle (ontogeny) and species time (phylogeny), respectively. Developmental terminal additions along with increment minimization of developmental steps must be positively selected.