Introducing spatial information into predictive NF-kappa B modelling - an agent-based approach

Nature is governed by local interactions among lower-level sub-units, whether at the cell, organ, organism, or colony level. Adaptive system behaviour emerges via these interactions, which integrate the activity of the sub-units. To understand the system level it is necessary to understand the underlying local interactions. Successful models of local interactions at different levels of biological organisation, including epithelial tissue and ant colonies, have demonstrated the benefits of such 'agent-based' modelling [1-4]. Here we present an agent-based approach to modelling a crucial biological system the intracellular NF-kappa B signalling pathway. The pathway is vital to immune response regulation, and is fundamental to basic survival in a range of species [5-7]. Alterations in pathway regulation underlie a variety of diseases, including atherosclerosis and arthritis. Our modelling of individual molecules, receptors and genes provides a more comprehensive outline of regulatory network mechanisms than previously possible with equation-based approaches [8]. The method also permits consideration of structural parameters in pathway regulation; here we predict that inhibition of NF-kappa B is directly affected by actin filaments of the cytoskeleton sequestering excess inhibitors, therefore regulating steady-state and feedback behaviour

Volumetric diffusers : pseudorandom cylinder arrays on a periodic lattice

Most conventional diffusers take the form of a surface based treatment, and as a result can only operate in hemispherical space. Placing a diffuser in the volume of a room might provide greater efficiency by allowing scattering into the whole space. A periodic cylinder array (or sonic crystal) produces periodicity lobes and uneven scattering. Introducing defects into an array, by removing or varying the size of some of the cylinders, can enhance their diffusing abilities. This paper applies number theoretic concepts to create cylinder arrays that have more even scattering. Predictions using a Boundary Element Method are compared to measurements to verify the model, and suitable metrics are adopted to evaluate performance. Arrangements with good aperiodic autocorrelation properties tend to produce the best results. At low frequency power is controlled by object size and at high frequency diffusion is dominated by lattice spacing and structural similarity. Consequently the operational bandwidth is rather small. By using sparse arrays and varying cylinder sizes, a wider bandwidth can be achieved

Space processing float zone thermal analysis

Thermal analysis (BETA) computer program adaptations were prepared to analyze phase change histories in crystal specimens. The first program (BETA-CYL) treats right circular cylinder configurations and the second, more general, program (BETA-BOR) treats a generalized body-of-revolution configuration. A series of computer runs were made for silicon material to determine boundary conditions which produce flat solidification interfaces while, at the same time, minimizing peak temperatures in the molten zone. Flat solidification interfaces are a goal believed by some investigators to be required to produce high quality semiconductor materials. The thermal effects of convection in a molten zone were examined and found to be negligible in comparison to the conduction heat transfer of the melt

Estimating the effect of nitrogen fertilizer on the greenhouse gas balance of soils in Wales under current and future climate

The Welsh Government is committed to reduce greenhouse gas (GHG) emissions from agricultural systems and combat the effects of future climate change. In this study, the ECOSSE model was applied spatially to estimate GHG and soil organic carbon (SOC) fluxes from three major land uses (grass, arable and forest) in Wales. The aims of the simulations were: (1) to estimate the annual net GHG balance for Wales; (2) to investigate the efficiency of the reduced nitrogen (N) fertilizer goal of the sustainable land management scheme (Glastir), through which the Welsh Government offers financial support to farmers and land managers on GHG flux reduction; and (3) to investigate the effects of future climate change on the emissions of GHG and plant net primary production (NPP). Three climate scenarios were studied: baseline (1961–1990) and low and high emission climate scenarios (2015–2050). Results reveal that grassland and cropland are the major nitrous oxide (N2O) emitters and consequently emit more GHG to the atmosphere than forests. The overall average simulated annual net GHG balance for Wales under baseline climate (1961–1990) is equivalent to 0.2 t CO2e ha-1 y-1 which gives an estimate of total annual net flux for Wales of 0.34 Mt CO2e y-1. Reducing N fertilizer by 20 and 40 % could reduce annual net GHG fluxes by 7 and 25 %, respectively. If the current N fertilizer application rate continues, predicted climate change by the year 2050 would not significantly affect GHG emissions or NPP from soils in Wales

Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast

Plant organelles produce retrograde signals to alter nuclear gene expression in order to coordinate their biogenesis, maintain homeostasis, or optimize their performance under adverse conditions. Many signals of different chemical nature have been described in the past decades, including chlorophyll intermediates, reactive oxygen species (ROS), and adenosine derivatives. While the effects of retrograde signaling on gene expression are well understood, the initiation and transport of the signals and their mode of action have either not been resolved, or are a matter of speculation. Moreover, retrograde signaling should be considered as part of a broader cellular network, instead of as separate pathways, required to adjust to changing physiologically relevant conditions. Here we summarize current plastid retrograde signaling models in plants, with a focus on new signaling pathways, SAL1-PAP, methylerythritol cyclodiphosphate (MEcPP), and β-cyclocitral (β-CC), and outline missing links or future areas of research that we believe need to be addressed to have a better understanding of plant intracellular signaling networks

Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast

Plant organelles produce retrograde signals to alter nuclear gene expression in order to coordinate their biogenesis, maintain homeostasis, or optimize their performance under adverse conditions. Many signals of different chemical nature have been described in the past decades, including chlorophyll intermediates, reactive oxygen species (ROS), and adenosine derivatives. While the effects of retrograde signaling on gene expression are well understood, the initiation and transport of the signals and their mode of action have either not been resolved, or are a matter of speculation. Moreover, retrograde signaling should be considered as part of a broader cellular network, instead of as separate pathways, required to adjust to changing physiologically relevant conditions. Here we summarize current plastid retrograde signaling models in plants, with a focus on new signaling pathways, SALl-PAP, methylerythritol cyclodiphosphate (MEcPP), and beta-cyclocitral (beta-CC), and outline missing links or future areas of research that we believe need to be addressed to have a better understanding of plant intracellular signaling networks

Sulfate and Phosphate Speleothems at Jenolan Caves, New South Wales, Australia

Sulfate and phosphate deposits at Jenolan Caves occur in a variety of forms and compositions including crusts, ‘flowers’ and fibrous masses of gypsum (selenite), and clusters of boss-like speleothems (potatoes) of ardealite (calcium sulphate, phosphate hydrate) with associated gypsum. This boss-like morphology of ardealite does not appear to have been previously described in the literature and this is the first report of ardealite in New South Wales. Gypsum var. selenite occurs in close association with pyrite-bearing palaeokarst, while the ardealite gypsum association appears to relate to deposits of mineralised bat guano. Isotope studies confirm that the two gypsum suites have separate sources of sulfur, one from the weathering of pyrite (-1.4 to +4.9 δ34S) for gypsum (selenite) and the other from alteration of bat guano (+11.4 to +12.9 δ34S) for the ardealite and gypsum crusts

Development of strategies for genetic manipulation and fine-tuning of a chloroplast retrograde signal 3′-phosphoadenosine 5′-phosphate

Homeostasis of metabolism and regulation of stress-signaling pathways are important for plant growth. The metabolite 3'-phosphoadenosine-5'-phosphate (PAP) plays dual roles as a chloroplast retrograde signal during drought and high light stress, as well as a toxic by-product of secondary sulfur metabolism, and thus, its levels are regulated by the chloroplastic phosphatase, SAL1. Constitutive PAP accumulation in sal1 mutants improves drought tolerance but can impair growth and alter rosette morphology. Therefore, it is of interest to derive strategies to enable controlled and targeted PAP manipulation that could enhance drought tolerance while minimizing the negative effects on plant growth. We systematically tested the potential and efficiency of multiple established transgenic manipulation tools in altering PAP levels in Arabidopsis. Dexamethasone (dex)-inducible silencing of SAL1 via hpRNAi [pOpOff:SAL1hpRNAi] yielded reduction in SAL1 transcript and protein levels, yet failed to significantly induce PAP accumulation. Surprisingly, this was not due to insufficient silencing of the inducible system, as constitutive silencing using a strong promoter to drive hpRNAi and amiRNA targeting the SAL1 transcript also failed to increase PAP content or induce a sal1-like plant morphology despite significantly reducing the SAL1 transcript levels. In contrast, using dex-inducible expression of SAL1 cDNA to complement an Arabidopsis sal1 mutant successfully modulated PAP levels and restored rosette growth in a dosage-dependent manner. Results from this inducible complementation system indicate that plants with intermediate PAP levels could have improved rosette growth without compromising its drought tolerance. Additionally, preliminary evidence suggests that SAL1 cDNA driven by promoters of genes expressed specifically during early developmental stages such as ABA-Insensitive 3 (ABI3) could be another potential strategy for studying and optimizing PAP levels and drought tolerance while alleviating the negative impact of PAP on plant growth in sal1. Thus, we have identified ways that can allow future dissection into multiple aspects of stress and developmental regulation mediated by this chloroplast signal