Multiscale modelling of plant hormone signalling: auxin regulated lateral root emergence

The formation of lateral roots is an important post-embryonic developmental process that allows plants to adapt to their environment via exploitation of soil mineral resources. New lateral roots initiate as lateral root primordia (LRP) in the pericycle cell layer adjacent to the central vascular tissue in the primary root, and must pass through the outer cell layers of endodermis, cortex and epidermis to emerge as mature roots. A key regulator of emergence is the plant hormone auxin and it has been shown previously that in Arabidopsis the auxin induced expression of the auxin influx carrier LAX3 in specific cortical cells over LRP is required for emergence to occur, as this leads to the expression of cell wall remodelling enzymes such as polygalacturonase (PG). By developing mathematical models of auxin transport and LAX3 expression the work in the thesis aims to test the existing conceptual models for lateral root emergence, and provide testable hypotheses for the existence of additional gene regulatory components. An initial single cell model demonstrates that hysteresis and bistability may explain the experimentally observed `all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. By fitting model parameters against experimental data, the model is then used to show that some auxin homeostasis mechanism is present, with both endogenous and exogenous sources of homeostasis investigated. The single cell model also investigates the validity of several alternative gene regulatory networks for LAX3, and its apparent repression by a key mediator of the auxin response, ARF19. Finally, the model is extended to a multicellular context, in which the auxin distribution from a simulated LRP source cell is used as a basis for the expression of LAX3, leading to the expression of PG in specific cells between which the LRP must pass

Multiscale modelling of plant hormone signalling: auxin regulated lateral root emergence

The formation of lateral roots is an important post-embryonic developmental process that allows plants to adapt to their environment via exploitation of soil mineral resources. New lateral roots initiate as lateral root primordia (LRP) in the pericycle cell layer adjacent to the central vascular tissue in the primary root, and must pass through the outer cell layers of endodermis, cortex and epidermis to emerge as mature roots. A key regulator of emergence is the plant hormone auxin and it has been shown previously that in Arabidopsis the auxin induced expression of the auxin influx carrier LAX3 in specific cortical cells over LRP is required for emergence to occur, as this leads to the expression of cell wall remodelling enzymes such as polygalacturonase (PG). By developing mathematical models of auxin transport and LAX3 expression the work in the thesis aims to test the existing conceptual models for lateral root emergence, and provide testable hypotheses for the existence of additional gene regulatory components. An initial single cell model demonstrates that hysteresis and bistability may explain the experimentally observed `all-or-nothing' LAX3 spatial expression pattern in cortical cells containing a gradient of auxin concentrations. By fitting model parameters against experimental data, the model is then used to show that some auxin homeostasis mechanism is present, with both endogenous and exogenous sources of homeostasis investigated. The single cell model also investigates the validity of several alternative gene regulatory networks for LAX3, and its apparent repression by a key mediator of the auxin response, ARF19. Finally, the model is extended to a multicellular context, in which the auxin distribution from a simulated LRP source cell is used as a basis for the expression of LAX3, leading to the expression of PG in specific cells between which the LRP must pass

Controls on soil carbon sequestration and dynamics: lessons from land-use change

Includes bibliographical references (pages 82-83).Soil carbon (C) dynamics and sequestration are controlled by interactions of chemical, physical and biological factors. These factors include biomass quantity and quality, physical environment and the biota. Management can alter these factors in ways that alter C dynamics. We have focused on a range of managed sites with documented land use change from agriculture or grassland to forest. Our results suggest that interactions of soil type, plant and environment impact soil C sequestration. Above and below ground C storage varied widely across sites. Results were related to plant type and calcium on sandy soils in our Northern sites. Predictors of sequestration were more difficult to detect over the temperature range of 12.4°C in the present study. Accrual of litter under pines in the moist Mississippi site limited C storage in a similar manner to our dry Nebraska site. Pre-planting heterogeneity of agricultural fields such as found in Illinois influences C contents. Manipulation of controls on C sequestration such as species planted or amelioration of soil quality before planting within managed sites could increase soil C to provide gains in terrestrial C storage. Cost effective management would also improve soil C pools positively affecting soil fertility and site productivity.Publisher version: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3380508

Evaluation of dietary and lifestyle changes as modifiers of S100β levels in Alzheimer's disease

There is a significant body of research undertaken in order to elucidate the mechanisms underlying the pathology of Alzheimer's disease (AD), as well as to discover early detection biomarkers and potential therapeutic strategies. One such proposed biomarker is the calcium binding protein S100β, which, depending on its local concentration, is known to exhibit both neurotrophic and neuroinflammatory properties in the central nervous system. At present, relatively little is known regarding the effect of chronic S100β disruption in AD. Dietary intake has been identified as a modifiable risk factor for AD. Preliminary in vitro and animal studies have demonstrated an association between S100β expression and dietary intake which links to AD pathophysiology. This review describes the association of S100β to fatty acids, ketone bodies, insulin, and botanicals as well as the potential impact of physical activity as a lifestyle factor. We also discuss the prospective implications of these findings, including support of the use of a Mediterranean dietary pattern and/or the ketogenic diet as an approach to modify AD risk. Publisher Statement: This is an Accepted Manuscript of an article published by Taylor & Francis in Nutritional Neuroscience on 11th July 2017, available online: http://www.tandfonline.com/10.1080/1028415X.2017.134903

Auxin fluxes through plasmodesmata modify root-tip auxin distribution

© 2020. Published by The Company of Biologists Ltd. Auxin is a key signal regulating plant growth and development. It is well established that auxin dynamics depend on the spatial distribution of efflux and influx carriers on the cell membranes. In this study, we employ a systems approach to characterise an alternative symplastic pathway for auxin mobilisation via plasmodesmata, which function as intercellular pores linking the cytoplasm of adjacent cells. To investigate the role of plasmodesmata in auxin patterning, we developed a multicellular model of the Arabidopsis root tip. We tested the model predictions using the DII-VENUS auxin response reporter, comparing the predicted and observed DII-VENUS distributions using genetic and chemical perturbations designed to affect both carrier-mediated and plasmodesmatal auxin fluxes. The model revealed that carrier-mediated transport alone cannot explain the experimentally determined auxin distribution in the root tip. In contrast, a composite model that incorporates both carrier-mediated and plasmodesmatal auxin fluxes re-capitulates the root-tip auxin distribution. We found that auxin fluxes through plasmodesmata enable auxin reflux and increase total root-tip auxin. We conclude that auxin fluxes through plasmodesmata modify the auxin distribution created by efflux and influx carriers

Scalable Identification of Load Imbalance in Parallel Executions Using Call Path Profiles

Abstract—Applications must scale well to make efficient use of today’s class of petascale computers, which contain hundreds of thousands of processor cores. Inefficiencies that do not even appear in modest-scale executions can become major bottlenecks in large-scale executions. Because scaling problems are often difficult to diagnose, there is a critical need for scalable tools that guide scientists to the root causes of scaling problems. Load imbalance is one of the most common scaling problems. To provide actionable insight into load imbalance, we present post-mortem parallel analysis techniques for pinpointing and quantifying load imbalance in the context of call path profiles of parallel programs. We show how to identify load imbalance in its static and dynamic context by using only low-overhead asyn-chronous call path profiling to locate regions of code responsible for communication wait time in SPMD executions. We describe the implementation of these techniques within HPCTOOLKIT. I

The Effect of L-Theanine Incorporated in a Functional Food Product (Mango Sorbet) on Physiological Responses in Healthy Males: A Pilot Randomised Controlled Trial

Consumption of L-Theanine (L-THE) has been associated with a sensation of relaxation, as well as a reduction of stress. However, these physiological responses have yet to be elucidated in humans where L-THE is compared alongside food or as a functional ingredient within the food matrix. The aim of this study was to determine the physiological responses of a single intake of a potential functional food product (mango sorbet) containing L-THE (ms-L-THE; 200 mgw/w) in comparison to a flavour and colour-matched placebo (ms). Eighteen healthy male participants were recruited in this randomised, double-blind, placebo-controlled trial. The participants were required to consume ms-L-THE or placebo and their blood pressure (BP) (systolic and diastolic), heart rate (HR), and heart rate variability (HRV) were monitored continuously over 90 minutes. Eleven males (age 27.7 ± 10.8 years) completed the study. Changes in area under the curve for systolic and diastolic blood pressure and HRV over the 90 minute observation period indicated no differences between the three conditions (all p > 0.05) or within individual groups (all p > 0.05). The values for heart rate were also not different in the placebo group (p = 0.996) and treatment group (p = 0.066), while there was a difference seen at the baseline (p = 0.003). Based on the findings of this study, L-THE incorporated in a food matrix (mango sorbet) demonstrated no reduction in BP or HR and showed no significant parasympathetic interaction as determined by HRV high-frequency band and low-frequency/high-frequency ratio. Further studies should be focussed towards the comparison of pure L-THE and incorporation within the food matrix to warrant recommendations of L-THE alongside food consumption

A core mechanism for specifying root vascular patterning can replicate the anatomical variation seen in diverse plant species

Pattern formation is typically controlled through the interaction between molecular signals within a given tissue. During early embryonic development, roots of the model plant Arabidopsis thatiana have a radially symmetric pattern, but a heterogeneous input of the hormone auxin from the two cotyledons forces the vascular cylinder to develop a diarch pattern with two xylem poles. Molecular analyses and mathematical approaches have uncovered the regulatory circuit that propagates this initial auxin signal into a stable cellular pattern. The diarch pattern seen in Arabidopsis is relatively uncommon among flowering plants, with most species having between three and eight xylem poles. Here, we have used multiscale mathematical modelling to demonstrate that this regulatory module does not require a heterogeneous auxin input to specify the vascular pattern. Instead, the pattern can emerge dynamically, with its final form dependent upon spatial constraints and growth. The predictions of our simulations compare to experimental observations of xylem pole number across a range of species, as well as in transgenic systems in Arabidopsis in which we manipulate the size of the vascular cylinder. By considering the spatial constraints, our model is able to explain much of the diversity seen in different flowering plant species.Peer reviewe