Role of integrin-linked kinase in regulating phosphorylation of Akt and fibroblast survival in type I collagen matrices through a beta1 integrin viability signaling pathway

A beta1 integrin phosphatidylinositol 3-kinase/Akt pathway regulates fibroblast survival in collagen matrices. When fibroblasts attach to collagen, Akt becomes phosphorylated, providing a survival signal. In contrast, in response to mechanical forces generated during collagen contraction, Akt is dephosphorylated and fibroblasts undergo apoptosis. The kinase(s) responsible for regulating Akt phosphorylation in response to matrix-derived mechanical signals are unclear. Integrin-linked kinase (ILK) is associated with the beta1 integrin in the focal adhesion complex and as such is a candidate kinase that may regulate Akt phosphorylation and fibroblast viability. Nevertheless, there is no direct evidence that matrix-derived mechanical forces regulate cell viability by modulating ILK activity. Here, we show that ILK activity decreased in response to collagen matrix contraction, which correlated with Akt dephosphorylation and induction of fibroblast apoptosis. In contrast, enforced activation of beta1 integrin by activating antibody preserved ILK and Akt activity during collagen matrix contraction, and this is associated with protection from collagen contraction-induced apoptosis. Knock-down of ILK by small, interfering RNA (siRNA) attenuated Akt phosphorylation in response to ligation of beta1 integrin by collagen or activating antibody and enhanced fibroblast apoptosis in response to collagen contraction. Kinase dead ILK attenuated Akt phosphorylation and enhanced fibroblast apoptosis, whereas hyperactive and wild type ILK augmented Akt phosphorylation and protected fibroblasts from apoptosis. Constitutively active Akt preserved Akt activity and rescued ILK siRNA-treated fibroblasts from collagen contraction-induced apoptosis. These data establish that matrix-derived mechanical forces sensed by beta1 integrin are capable of modulating ILK activity which regulates fibroblast viability via an Akt-dependent mechanism.     

Quantifying the biologically possible range of steady-state soil and surface climates with climate model simulations

The terrestrial biosphere shapes the exchange fluxes of energy and mass at the land surface. The diversity of plant form and functioning can potentially result in a wide variety of possible climatic conditions at the land surface and in the soil, which in turn feed back to more or less suitable conditions for terrestrial productivity. Here, I use sensitivity simulations to vegetation form and functioning with a global climate model to quantify this possible range of steady-states (“PROSS”) of the surface energy-and mass balances. The surface energy-and water balances over land are associated with substantial sensitivity to vegetation parameters, with precipitation varying by more than a factor of 2, and evapotranspiration by a factor of 5. This range in biologically possible climatic conditions is associated with drastically different levels of vegetation productivity. Optimum conditions for maximum productivity are close to the simulated climate of present-day conditions. These results suggest the conclusions that (a) climate does not determine vegetation form and function, but merely constrains it, and (b) the emergent climatic conditions at the land surface seem to be close to optimal for the functioning of the terrestrial biosphere.     

Golden bananas in the field: elevated fruit pro‐vitamin A from the expression of a single banana transgene

Vitamin A deficiency remains one of the world's major public health problems despite food fortification and supplements strategies. Biofortification of staple crops with enhanced levels of pro‐vitamin A (PVA) offers a sustainable alternative strategy to both food fortification and supplementation. As a proof of concept, PVA‐biofortified transgenic Cavendish bananas were generated and field trialed in Australia with the aim of achieving a target level of 20 μg/g of dry weight (dw) β‐carotene equivalent (β‐CE) in the fruit. Expression of a Fe'i banana‐derived phytoene synthase 2a (MtPsy2a) gene resulted in the generation of lines with PVA levels exceeding the target level with one line reaching 55 μg/g dw β‐CE . Expression of the maize phytoene synthase 1 (ZmPsy1) gene, used to develop ‘Golden Rice 2’, also resulted in increased fruit PVA levels although many lines displayed undesirable phenotypes. Constitutive expression of either transgene with the maize polyubiquitin promoter increased PVA accumulation from the earliest stage of fruit development. In contrast, PVA accumulation was restricted to the late stages of fruit development when either the banana 1‐aminocyclopropane‐1‐carboxylate oxidase or the expansin 1 promoters were used to drive the same transgenes. Wild‐type plants with the longest fruit development time had also the highest fruit PVA concentrations. The results from this study suggest that early activation of the rate‐limiting enzyme in the carotenoid biosynthetic pathway and extended fruit maturation time are essential factors to achieve optimal PVA concentrations in banana fruit.     

The Strengths of r- and K-Selection Shape Diversity-Disturbance Relationships

Disturbance is a key factor shaping species abundance and diversity in plant communities. Here, we use a mechanistic model of vegetation diversity to show that different strengths of r- and K-selection result in different disturbance-diversity relationships. R- and K-selection constrain the range of viable species through the colonization-competition tradeoff, with strong r-selection favoring colonizers and strong K-selection favoring competitors, but the level of disturbance also affects the success of species. This interplay among r- and K-selection and disturbance results in different shapes of disturbance-diversity relationships, with little variation of diversity with no r- and no K-selection, a decrease in diversity with r-selection with disturbance rate, an increase in diversity with K-selection, and a peak at intermediate values with strong r- and K-selection. We conclude that different disturbance-diversity relationships found in observations may reflect different intensities of r- and K-selection within communities, which should be inferable from broader observations of community composition and their ecophysiological trait ranges.     

A global distribution of biodiversity inferred from climatic constraints: results from a process‐based modelling study

We investigated the connection between plant species diversity and climate by using a process‐based, generic plant model. Different ‘species' were simulated by different values for certain growth‐related model parameters. Subsequently, a wide range of values were tested in the framework of a ‘Monte Carlo' simulation for success; that is, the capability of each plant with these parameter combinations to reproduce itself during its lifetime. The range of successful parameter combinations approximated species diversity. This method was applied to a global grid, using daily atmospheric forcing from a climate model simulation. The computed distribution of plant ‘species' diversity compares very well with the observed, global‐scale distribution of species diversity, reproducing the majority of ‘hot spot' areas of biodiversity. A sensitivity analysis revealed that the predicted pattern is very robust against changes of fixed model parameters. Analysis of the climatic forcing and of two additional sensitivity simulations demonstrated that the crucial factor leading to this distribution of diversity is the early stage of a plant's life when water availability is highly coupled to the variability in precipitation because in this stage root‐zone storage of water is small. We used cluster analysis in order to extract common sets of species parameters, mean plant properties and biogeographic regions (biomes) from the model output. The successful ‘species' cannot be grouped into typical parameter combinations, which define the plant's functioning. However, the mean simulated plant properties, such as lifetime and growth, can be grouped into a few characteristic plant ‘prototypes', ranging from short‐lived, fast growing plants, similar to grasses, to long‐lived, slow growing plants, similar to trees. The classification of regions with respect to similar combinations of successful ‘species' yields a distribution of biomes similar to the observed distribution. Each biome has typical levels of climatic constraints, expressed for instance by the number of ‘rainy days' and ‘warm days'. The less the number of days favourable for growth, the greater the level of constraints and the less the ‘species' diversity. These results suggest that climate as a fundamental constraint can explain much of the global scale, observed distribution of plant species diversity.     

A method of determining rooting depth from a terrestrial biosphere model and its impacts on the global water and carbon cycle

We outline a method of inferring rooting depth from a Terrestrial Biosphere Model by maximizing the benefit of the vegetation within the model. This corresponds to the evolutionary principle that vegetation has adapted to make best use of its local environment. We demonstrate this method with a simple coupled biosphere/soil hydrology model and find that deep rooted vegetation is predicted in most parts of the tropics. Even with a simple model like the one we use, it is possible to reproduce biome averages of observations fairly well. By using the optimized rooting depths global Annual Net Primary Production (and transpiration) increases substantially compared to a standard rooting depth of one meter, especially in tropical regions that have a dry season. The decreased river discharge due to the enhanced evaporation complies better with observations. We also found that the optimization process is primarily driven by the water deficit/surplus during the dry/wet season for humid and arid regions, respectively. Climate variability further enhances rooting depth estimates. In a sensitivity analysis where we simulate changes in the water use efficiency of the vegetation we find that vegetation with an optimized rooting depth is less vulnerable to variations in the forcing. We see the main application of this method in the modelling communities of land surface schemes of General Circulation Models and of global Terrestrial Biosphere Models. We conclude that in these models, the increased soil water storage is likely to have a significant impact on the simulated climate and the carbon budget, respectively. Also, effects of land use change like tropical deforestation are likely to be larger than previously thought.     

Thermodynamics of Random Reaction Networks

Reaction networks are useful for analyzing reaction systems occurring in chemistry, systems biology, or Earth system science. Despite the importance of thermodynamic disequilibrium for many of those systems, the general thermodynamic properties of reaction networks are poorly understood. To circumvent the problem of sparse thermodynamic data, we generate artificial reaction networks and investigate their non-equilibrium steady state for various boundary fluxes. We generate linear and nonlinear networks using four different complex network models (Erdős-Rényi, Barabási-Albert, Watts-Strogatz, Pan-Sinha) and compare their topological properties with real reaction networks. For similar boundary conditions the steady state flow through the linear networks is about one order of magnitude higher than the flow through comparable nonlinear networks. In all networks, the flow decreases with the distance between the inflow and outflow boundary species, with Watts-Strogatz networks showing a significantly smaller slope compared to the three other network types. The distribution of entropy production of the individual reactions inside the network follows a power law in the intermediate region with an exponent of circa −1.5 for linear and −1.66 for nonlinear networks. An elevated entropy production rate is found in reactions associated with weakly connected species. This effect is stronger in nonlinear networks than in the linear ones. Increasing the flow through the nonlinear networks also increases the number of cycles and leads to a narrower distribution of chemical potentials. We conclude that the relation between distribution of dissipation, network topology and strength of disequilibrium is nontrivial and can be studied systematically by artificial reaction networks.     

Modeling Free Energy Availability from Hadean Hydrothermal Systems to the First Metabolism

Off-axis Hydrothermal Systems (HSs) are seen as the possible setting for the emergence of life. As the availability of free energy is a general requirement to drive any form of metabolism, we ask here under which conditions free energy generation by geologic processes is greatest and relate these to the conditions found at off-axis HSs. To do so, we present a conceptual model in which we explicitly capture the energetics of fluid motion and its interaction with exothermic reactions to maintain a state of chemical disequilibrium. Central to the interaction is the temperature at which the exothermic reactions take place. This temperature not only sets the equilibrium constant of the chemical reactions and thereby the distance of the actual state to chemical equilibrium, but these reactions also shape the temperature gradient that drives convection and thereby the advection of reactants to the reaction sites and the removal of the products that relate to geochemical free energy generation. What this conceptual model shows is that the positive feedback between convection and the chemical kinetics that is found at HSs favors a greater rate of free energy generation than in the absence of convection. Because of the lower temperatures and because the temperature of reactions is determined more strongly by these dynamics rather than an external heat flux, the conditions found at off-axis HSs should result in the greatest rates of geochemical free energy generation. Hence, we hypothesize from these thermodynamic considerations that off-axis HSs seem most conducive for the emergence of protometabolic pathways as these provide the greatest, abiotic generation rates of chemical free energy.     

Focal adhesion kinase is upstream of phosphatidylinositol 3-kinase/Akt in regulating fibroblast survival in response to contraction of type I collagen matrices via a beta 1 integrin viability signaling pathway

The beta(1) integrin, functioning as a mechanoreceptor, senses a mechanical stimulus generated during collagen matrix contraction and down-regulates the phosphatidylinositol 3-kinase (PI3K)/Akt survival signal triggering apoptosis. The identities of integrin-associated signal molecules in the focal adhesion complex that are responsible for propagating beta(1) integrin viability signals in response to collagen matrix contraction are not known. Here we show that in response to collagen contraction focal adhesion kinase (FAK) is dephosphorylated. In contrast, enforced activation of beta(1) integrin by anti-beta(1) integrin antibody, which protects fibroblasts from apoptosis, preserves FAK phosphorylation. We demonstrate that ligation of beta(1) integrin by type I collagen or by enforced activation of beta(1) integrin by antibody promotes phosphorylation of FAK, p85 subunit of PI3K, and serine 473 of Akt. Wortmannin inhibited Akt but not FAK phosphorylation in response to enforced activation of beta(1) integrin by antibody. Blocking FAK by pharmacologic inhibition or by dominant negative FAK attenuated phosphorylation of p85 subunit of PI3K and Akt. Dominant negative FAK augmented fibroblast apoptosis during collagen contraction, and this was associated with diminished Akt activity. Constitutively active FAK augmented levels of p85 subunit of PI3K and Akt phosphorylation, and fibroblasts were protected from apoptosis. Our data identify a novel role for FAK, functioning upstream of PI3K/Akt, in transducing a beta(1) integrin viability signal in collagen matrices.