Vertex-element models for anisotropic growth of elongated plant organs

New tools are required to address the challenge of relating plant hormone levels, hormone responses, wall biochemistry and wall mechanical properties to organ-scale growth. Current vertex-based models (applied in other contexts) can be unsuitable for simulating the growth of elongated organs such as roots because of the large aspect ratio of the cells, and these models fail to capture the mechanical properties of cell walls in sufficient detail. We describe a vertex-element model which resolves individual cells and includes anisotropic non-linear viscoelastic mechanical properties of cell walls and cell division whilst still being computationally efficient. We show that detailed consideration of the cell walls in the plane of a 2D simulation is necessary when cells have large aspect ratio, such as those in the root elongation zone of Arabidopsis thaliana, in order to avoid anomalous transverse swelling. We explore how differences in the mechanical properties of cells across an organ can result in bending and how cellulose microfibril orientation affects macroscale growth. We also demonstrate that the model can be used to simulate growth on realistic geometries, for example that of the primary root apex, using moderate computational resources. The model shows how macroscopic root shape can be sensitive to fine-scale cellular geometries

Hybrid vertex-midline modelling of elongated plant organs

We describe a method for the simulation of the growth of elongated plant organs, such as seedling roots. By combining a midline representation of the organ on a tissue scale and a vertex-based representation on the cell scale, we obtain a multiscale method, which is able to both simulate organ growth and incorporate cell-scale processes. Equations for the evolution of the midline are obtained, which depend on the cell-wall properties of individual cells through appropriate averages over the vertex-based representation. The evolution of the organ midline is used to deform the cellular-scale representation. This permits the investigation of the regulation of organ growth through the cell-scale transport of the plant hormone auxin. The utility of this method is demonstrated in simulating the early stages of the response of a root to gravity, using a vertex-based template acquired from confocal imaging. Asymmetries in the concentrations of auxin between the upper and lower sides of the root lead to bending of the root midline, reflecting a gravitropic response

Techniques for analysing pattern formation in populations of stem cells and their progeny

<p>Abstract</p> <p>Background</p> <p>To investigate how patterns of cell differentiation are related to underlying intra- and inter-cellular signalling pathways, we use a stochastic individual-based model to simulate pattern formation when stem cells and their progeny are cultured as a monolayer. We assume that the fate of an individual cell is regulated by the signals it receives from neighbouring cells via either diffusive or juxtacrine signalling. We analyse simulated patterns using two different spatial statistical measures that are suited to planar multicellular systems: pair correlation functions (PCFs) and quadrat histograms (QHs).</p> <p>Results</p> <p>With a diffusive signalling mechanism, pattern size (revealed by PCFs) is determined by both morphogen decay rate and a sensitivity parameter that determines the degree to which morphogen biases differentiation; high sensitivity and slow decay give rise to large-scale patterns. In contrast, with juxtacrine signalling, high sensitivity produces well-defined patterns over shorter lengthscales. QHs are simpler to compute than PCFs and allow us to distinguish between random differentiation at low sensitivities and patterned states generated at higher sensitivities.</p> <p>Conclusions</p> <p>PCFs and QHs together provide an effective means of characterising emergent patterns of differentiation in planar multicellular aggregates.</p

Diffusion-mediated HEI10 coarsening can explain meiotic crossover positioning in Arabidopsis.

In most organisms, the number and distribution of crossovers that occur during meiosis are tightly controlled. All chromosomes must receive at least one 'obligatory crossover' and crossovers are prevented from occurring near one another by 'crossover interference'. However, the mechanistic basis of this phenomenon of crossover interference has remained mostly mysterious. Using quantitative super-resolution cytogenetics and mathematical modelling, we investigate crossover positioning in the Arabidopsis thaliana wild-type, an over-expressor of the conserved E3 ligase HEI10, and a hei10 heterozygous line. We show that crossover positions can be explained by a predictive, diffusion-mediated coarsening model, in which large, approximately evenly-spaced HEI10 foci grow at the expense of smaller, closely-spaced clusters. We propose this coarsening process explains many aspects of Arabidopsis crossover positioning, including crossover interference. Consistent with this model, we also demonstrate that crossover positioning can be predictably modified in vivo simply by altering HEI10 dosage, with higher and lower dosage leading to weaker and stronger crossover interference, respectively. As HEI10 is a conserved member of the RING finger protein family that functions in the interference-sensitive pathway for crossover formation, we anticipate that similar mechanisms may regulate crossover positioning in diverse eukaryotes

Systems analysis of auxin transport in the Arabidopsis root apex

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin’s shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability

The receptor mechanism mediating the contractile response to adenosine on lung parenchymal strips from actively sensitised, allergen-challenged Brown Norway rats.

Parenchymal strips prepared from lungs removed from actively sensitised Brown Norway rats challenged with allergen show hyperresponsiveness to adenosine. The response is mast cell mediated and a preliminary pharmacological analysis suggested the involvement of a receptor (or receptors) that could not be classified as any of the known adenosine receptor subtypes. We present a further analysis of the response. Male Brown Norway (BN) rats, actively sensitised to ovalbumin (OA), were challenged intratracheally with OA and killed 3 h later to provide parenchymal strip preparations. The augmented contractile responses to adenosine were partially blocked by the 5-HT receptor antagonist, methysergide, or the A(1) receptor antagonist, DPCPX, and abolished in the presence of both antagonists. Responses to high concentrations of the A(1) receptor agonist, CPA were, like those to adenosine, augmented on tissues from allergen-challenged animals and blocked by a combination of methysergide and DPCPX. The A(3) receptor agonist, Cl-IB-MECA, did not contract the tissue, but partially blocked the response to adenosine. A combination of Cl-IB-MECA and methysergide induced a similar degree of blockade to that seen with either drug given alone. Combination of Cl-IB-MECA and/or methysergide with DPCPX abolished the response to adenosine. The effects of the A(3) receptor agonist, inosine, were augmented on tissues from allergen-challenged animals and markedly inhibited by disodium cromoglycate, methysergide or Cl-IB-MECA. Responses to adenosine were abolished when parenchymal strips were taken from rats pretreated 48 h previously with pertussis toxin. 8-SPT, CGS 15943, XAC, MRS 1754, DPCPX and theophylline, at concentrations which inhibit the A(1) A(2A) and/or A(2B) receptors but have negligible affinity for the rat A(3) receptor, inhibited responses to adenosine, but high concentrations were required and blockade was incomplete. MRS 1523 and MRS 1191, which are antagonists at the rat A(3) receptor, had no effect on the response to adenosine. The present results support and clarify our earlier conclusion that an atypical receptor mechanism mediates contraction of the parenchymal strip prepared from the lungs of actively sensitised BN rats challenged with allergen to adenosine. The response arises from a combined effect of adenosine on the A(1) receptor and a receptor with similarities to the A(3) receptor, but where Cl-IB-MECA behaves as an antagonist and MRS 1523 and MRS 1191 are inactive at concentrations that substantially exceed their affinities for the rat A(3) receptor

Progress Towards Novel Adenosine Receptor Therapeutics Gleaned From The Recent Patent Literature

Importance of the field: The principle of treating disease with selective adenosine receptor ligands has been demonstrated with drugs on the market, while the lesser understood receptor subtypes are still being probed with new and druglike pharmaceutical tools. The field of adenosine receptor research is therefore highly important as an emerging and proven point of intervention in disease. Areas covered in this review: From 2008-2009, over 120 primary patent applications claimed adenosine receptor ligands, which we analyse by applicant and target. Particularly significant disclosures are described in detail, paying particular attention to the biological data marshalled to support the case. What the reader will gain: The first published disclosure of new compounds, compound uses or drug targets is often in the patent literature, which can be difficult to trawl, interpret and verify since it is not subject to peer review. We have critically reviewed this area and share our conclusions regarding progress, trends and identification of early tool compounds or compounds of potential clinical significance, ahead of peer-reviewed publication. Take home message: Adenosine receptor research is a thriving field, with continuing claims of exciting new compounds with high specificity, and intriguing examples of new uses for such ligands

Vertex-element models for anisotropic growth of elongated plant organs

New tools are required to address the challenge of relating plant hormone levels, hormone responses, wall biochemistry and wall mechanical properties to organ-scale growth. Current vertex-based models (applied in other contexts) can be unsuitable for simulating the growth of elongated organs such as roots because of the large aspect ratio of the cells, and these models fail to capture the mechanical properties of cell walls in sufficient detail. We describe a vertex-element model which resolves individual cells and includes anisotropic non-linear viscoelastic mechanical properties of cell walls and cell division whilst still being computationally efficient. We show that detailed consideration of the cell walls in the plane of a 2D simulation is necessary when cells have large aspect ratio, such as those in the root elongation zone of Arabidopsis thaliana, in order to avoid anomalous transverse swelling. We explore how differences in the mechanical properties of cells across an organ can result in bending and how cellulose microfibril orientation affects macroscale growth. We also demonstrate that the model can be used to simulate growth on realistic geometries, for example that of the primary root apex, using moderate computational resources. The model shows how macroscopic root shape can be sensitive to fine-scale cellular geometries