A conceptual framework for the study of modular responses to local environmental heterogeneity within the plant crown and a review of related concepts

Plants respond to local heterogeneity in abiotic and biotic conditions by changing module-level morphology, growth, and reproductive patterns. This paper presents a conceptual framework for the study of modular responses in plant crowns, clarifies the points that should be considered for scaling up from modular responses to the consequences at the whole-plant level, characterizes the interspecific differences in modular response patterns, and discusses their ecological significance. The modular response was defined as either autonomous or interactive, depending on whether the response of a module to its local condition is independent from the conditions of other modules. For evaluation of the autonomy of the modular response, the importance of considering positional relationships and organizational levels of modules was then proposed as these internally affect the modular response pattern, and their interspecific differences were characterized using several concepts. The identification of an autonomous modular unit is essential for scaling up module-level studies to the whole plant. For understanding the ecological significance of the modular response, further interspecific comparisons and assessments of the scale and the predictability of environmental heterogeneity are required. The conceptual framework will be useful for such purposes.     

A conceptual framework for the spatial analysis of landscape genetic data

Understanding how landscape heterogeneity constrains gene flow and the spread of adaptive genetic variation is important for biological conservation given current global change. However, the integration of population genetics, landscape ecology and spatial statistics remains an interdisciplinary challenge at the levels of concepts and methods. We present a conceptual framework to relate the spatial distribution of genetic variation to the processes of gene flow and adaptation as regulated by spatial heterogeneity of the environment, while explicitly considering the spatial and temporal dynamics of landscapes, organisms and their genes. When selecting the appropriate analytical methods, it is necessary to consider the effects of multiple processes and the nature of population genetic data. Our framework relates key landscape genetics questions to four levels of analysis: (i) node-based methods, which model the spatial distribution of alleles at sampling locations (nodes) from local site characteristics; these methods are suitable for modeling adaptive genetic variation while accounting for the presence of spatial autocorrelation. (ii) Link-based methods, which model the probability of gene flow between two patches (link) and relate neutral molecular marker data to landscape heterogeneity; these methods are suitable for modeling neutral genetic variation but are subject to inferential problems, which may be alleviated by reducing links based on a network model of the population. (iii) Neighborhood-based methods, which model the connectivity of a focal patch with all other patches in its local neighborhood; these methods provide a link to metapopulation theory and landscape connectivity modeling and may allow the integration of node- and link-based information, but applications in landscape genetics are still limited. (iv) Boundary-based methods, which delineate genetically homogeneous populations and infer the location of genetic boundaries; these methods are suitable for testing for barrier effects of landscape features in a hypothesis-testing framework. We conclude that the power to detect the effect of landscape heterogeneity on the spatial distribution of genetic variation can be increased by explicit consideration of underlying assumptions and choice of an appropriate analytical approach depending on the research question.     

Cross-cultural aspects of bereavement. I: A conceptual framework for comparative analysis

This paper reviews some key conceptual questions in the study of cross-cultural aspects of bereavement. Six questions are reviewed in cross-cultural perspective: whether individuals in all societies share the same private experience and public expression of grief; whether the stages of grief occur in the same sequence and at the same rate in all cultures; the nature of the relationship between the individual's private grief and his public mourning; the reactions of children to death, and the reactions of adults to the death of children; the role of religious belief; and the possibility that an ethnic group can experience collective grief in response to uprooting.     

A conceptual framework to assess the effects of environmental change on ecosystem services

A new conceptual framework is presented for the assessment of the impacts of environmental change drivers on ecosystem service provision and the policy and management responses that would derive from the valuation of these impacts. The Framework for Ecosystem Service Provision (FESP), is based on an interpretation of the widely-used Drivers-Pressures-State-Impact-Response (DPSIR) framework. FESP differs from the DPSIR by offering clarity in the definitions of the various DPSIR components as well as introducing novel elements of relevance to the ecosystem service approach. The value of a common framework lies in making the comparison across competing services accessible and clear as well as highlighting the conflicts and trade-offs between not only multiple ecosystem services, but also multiple service beneficiaries. The framework is explicit, for example, in recognising as state variables not only the attributes of the Ecosystem Service Providers (ESPs), but also the attributes of the Ecosystem Service Beneficiaries (ESBs). That a service depends as much on the attributes of the people whose well-being benefits from the service as on the attributes of the biology providing the service is an important step in integrated social-ecological thinking. FESP also identifies the mechanisms of either mitigation or adaptation to the environmental change problem through the effect of these response strategies on specific pressure or state variables. In this way, FESP can contribute to the policies and strategies that are used to support conservation management. This paper describes the principles of FESP and presents some indicative examples of its practical implementation.     

The coordination of azepine to transition-metal complexes: A DFT analysis

DFT calculations with full geometry optimizations have been carried out on a series of real and hypothetical compounds of the CpM(C₆NH₇) and (CO)₃M(C₆NH₇) (M = transition-metal) type. A rationalization of the bonding in all the known compounds and in hypothetical complexes is provided. Depending on the electron count and the nature of the metal, the azepine ligand can bind to the metal through the η¹, η², η⁴, η⁶, or η⁷ coordination mode.     

An essay on the evolution of cognition: Constructing a theoretical conceptual framework

In this essay we provide an interdisciplinary approach to the problem of the evolution of human cognition and suggest the theoretical framework of genetic system theory (GST) for organizing the relevant content of several disciplines. This bio-social-cultural theory is based on the assumption that organisms are dynamic systems which interact with one another and their environment and are themselves composed of dynamic internal relations at several levels. Special emphasis will be placed upon these internal cellular and molecular mechanisms underlying the physiological mechanisms of learning and memory. The human individual organism is emphasized because in its experiential activity over time it is the site of integration for social, and cultural stimuli and because of its unique properties among living things. The primary disciplines for our discussion are drawn from the biological, social, and humanistic sciences and several concrete examples are given from each science.     

Cooperativity in mechano-calcium feedbacks in the myocardium: Some conceptual discrepancies and overcoming inconsistency within the framework of a mathematical model

Mechano-calcium feedbacks that provide fine tuning of electrical and calcium activation of the heart muscle to mechanical conditions of contractions are an important element of electromechanical coupling as a key mechanism of the autoregulation of the contractile activity of the myocardium. A large quantity of experimental and theoretical evidence supports the cooperative dependence of the calcium-troponin complex kinetics on the cross-bridge concentration as a principal mechanism that underlies the mechano-calcium feedback in the intact myocardium. At the same time, experiments performed using skinned myocardial preparations have demonstrated that mechanical conditions significantly affected only the calcium sensitivity of the Ca²⁺–force relationship rather than its Hill coefficient of cooperativity. These data make some investigators doubt the contribution of cooperativity to the mechano-calcium feedbacks. To overcome these arising discrepancies, we propose an improved conception of cooperativity that reveals the extent of intensity differently in the steady state and in transitional processes. The proposed conception enables us to reproduce and explain both the mechanodependence of calcium activation in the intact myocardium and the results with skinned muscle within the framework of a mathematical model.     

A competitive fluorescence assay to measure the reactivity of compounds

A sensitive competitive method was developed for assessing the reactivity of compounds toward glutathione and toward thiols in general. The method employs the reaction of the fluorogenic reagent fluorescein-5-maleimide (FM) with glutathione (GSH) to generate a large increase in fluorescence emission. When the reaction is measured in the presence of a compound that competes with FM toward GSH, the rate constant for fluorescent product formation increases while the total amount of product formed at the end of the reaction decreases. These changes in the presence of a series of competitor concentrations allow one to calculate the rate constant of the reaction of the competitor with GSH. At 23 degrees C, pH 7.40 in PBS buffer the second-order rate constant of the FM-GSH reaction is k2 = (1.67 +/- 0.32) x 10(4) M(-1) x s(-1). Two GSH-reactive compounds were evaluated: the second-order rate constant for the reaction of PNU-27707 with GSH under our experimental conditions is k(i) = 5660 +/- 266 M(-1) x s(-1), while that of PNU-37802 is k(i) = 21,200 +/- 1600 M(-1) x s(-1). The method is easily adaptable to a high-throughput screening format.     

The dynamics of crop infraspecific diversity: A conceptual framework at the farmer level 1

There is an increasing concern over the loss of germplasm diversity in areas of crop domestication. Nevertheless in these areas many farmers continue to maintain a pool of varieties, many of them landraces, despite the fact that they have also incorporated improved varieties, and that some landraces have been eliminated. This paper provides a framework for analyzing the decision of a farmer to maintain, incorporate or discard a variety from his/her repertoire of varieties of one crop. It is based on an analysis of the roles that crop infraspecific diversity can play in a farmer’s well-being, how these roles change, the limits to these changes, and some predictions and suggestions derived from this framework.     

Molecular modeling approach to elucidate gas phase hydrodeoxygenation of guaiacol over a Pd(111) catalyst within DFT framework

Excessive amounts of oxy-functional groups in unprocessed bio-oil vitiate its quality as fuel; therefore, it has to be channelized to upgrading processes, and catalytic hydrodeoxygenation is one of the most suitable routes for the upgrading of crude bio-oil. In this computational work, catalytic hydrodeoxygenation (HDO) of guaiacol, which is an important phenolic compound of crude bio-oil, has been carried out using density functional theory (DFT) over a Pd(111) catalyst. The Pd(111) catalyst surface does not endorse direct eliminations of functional groups of guaiacol; however, it is found to perform excellently in stepwise dehydrogenation reactions of oxy-functionals of guaiacol according to present DFT results. The catechol product, formed through dehydrogenation of the methoxy group, followed by elimination of CH₂ and association of the hydrogen atom, has been identified as one of the major products. The overall reaction rate is controlled by scission of CH₂ from 2-methylene-oxy-phenol with an activation energy demand of 23.06 kcal mol^–1. Further, the kinetic analysis of each reaction step involved in HDO of guaiacol over the Pd(111) catalyst surface has also been carried out at atmospheric pressure and at a wide range of temperatures from 473 to 673 K, with temperature intervals of 50 K. In the kinetic analysis part, various kinetic parameters, such as forward and reverse reaction rate constants, Arrhenius constants, and equilibrium rate constants, are reported. The kinetic modeling of the dominating reaction steps has revealed that even a lower temperature of 473 K provides a favorable reaction environment; and the temperature increment further improves the reaction favorability.     

The Dashboard of Sustainability to measure the local urban sustainable development: The case study of Padua Municipality

The adoption of suitable indicators is fundamental to implement sustainable development at the local level. It helps in the analysis and evaluation; supports the decisional process and helps the communication between the citizens and the society, in general.Furthermore, the aggregated indexes – by representing the observed context in a simple way – may help the community in the definition of effective improvement goals and also serve as important tools to monitor the fulfillment of the planned objectives.The Dashboard of Sustainability (DS) is a mathematical and graphical tool designed to integrate the complex influences of sustainability and support the decision-making process by creating concise evaluations.The city of Padua, Italy, agreed to use the DS in its Local Agenda 21 project, financed by the Italian Ministry of Environment. The available data were sufficient to design 61 useful indicators of environmental protection, economic development, and social promotion.The results of the analysis were discussed in Padua's community forum on the Local Agenda 21 process. The graphical and numerical results helped Padua reach a consensus on the plan for future sustainability, one that was understood and accepted by all the stakeholders.In order to adapt this tool to a local context, two changes in the methodologies were necessary: to measure urban sustainability, for which “ad hoc” set indicators were used; and to allow a comparative evaluation, for which the performances of Padua were evaluated over time. These changes were possible, thanks to the flexibility of such tool.     

DFT study on the reactivity of iron porphyrins tuned by ring substitution

The effect of beta-substituents (-NO2, -Br, -OCH3) in the reactivity of Fe(II) and Fe(III) porphyrins is studied by means of density functional theory (DFT) calculations. The binding of nitric oxide, carbon monoxide and dioxygen (NO, CO, O2) was explored due to the relevance of their interactions in the chemistry of heme proteins and in biomimetic catalysis. The binding capability (BC) of the porphyrins was found to be strongly modulated both by the donor and attractor substituents used in the work. Unexpectedly, we found that the BC of Fe(II) porphyrins is mainly decreased for the diatomic ligands, when both donor or withdrawing substituents were considered. This effect was particularly significant when the ligand was oxygen. The correlation of Fe-X and X-O (X=N, C, O) bond distances is explained in terms of backdonation effects.     

Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies

The heme-AB binding energies (AB = CO, O₂) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O₂/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.     

The human genome project: Towards an analysis of the empirical,ethical, and conceptual issues involved

In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the project. The second section distinguishes among four kinds of issues relevant to an evaluation of the HGP: those economic and organizational issues related to the feasibility of the project; the ethical questions arising in the development of the project and the application of the data gathered; the empirical issues relevant to the scientific value of the project; and conceptual issues like reductionism and determinism relevant to understand the nature and scope of the project. In a third section, I analyze in detail whether the HGP and, more generally, molecular biology is reductionistic.     

A non-equilibrium thermodynamics analysis of active transport within the framework of the chemiosmotic theory

The proton circuit devised by Mitchell in the chemiosmotic theory was subjected to analysis using the formalism of irreversible thermodynamics. The phenomenological coefficients and the degree of coupling relating co-permeant flows were derived for anion/H⁺, substrate/H⁺, cation/H⁺ and anion/anion biporter models. Linearity and equality of the cross-coefficients in Onsager relations were always satisfied. Macroscopic flows leading to charges splitting, such as oxido-reduction, hydro-dehydratation and transhydrogenase, are driven by a composite thermodynamic force which includes the proton-motive component. Multiple coupling occurs in the circuit when it is assumed that the net inward flux of protons becomes zero, i.e. when the circulation of protons reaches a stationary state. Under these conditions, oxidative phosphorylation, ATPase- or respiration-linked transhydrogenase and uptake of anion or cation against their electrochemical gradient may be predicted, in agreement with known experimental evidence.