Dynamic Image-Based Modelling of Kidney Branching Morphogenesis

Kidney branching morphogenesis has been studied extensively, but the mechanism that defines the branch points is still elusive. Here we obtained a 2D movie of kidney branching morphogenesis in culture to test different models of branching morphogenesis with physiological growth dynamics. We carried out image segmentation and calculated the displacement fields between the frames. The models were subsequently solved on the 2D domain, that was extracted from the movie. We find that Turing patterns are sensitive to the initial conditions when solved on the epithelial shapes. A previously proposed diffusion-dependent geometry effect allowed us to reproduce the growth fields reasonably well, both for an inhibitor of branching that was produced in the epithelium, and for an inducer of branching that was produced in the mesenchyme. The latter could be represented by Glial-derived neurotrophic factor (GDNF), which is expressed in the mesenchyme and induces outgrowth of ureteric branches. Considering that the Turing model represents the interaction between the GDNF and its receptor RET very well and that the model reproduces the relevant expression patterns in developing wildtype and mutant kidneys, it is well possible that a combination of the Turing mechanism and the geometry effect control branching morphogenesis

Growth of High Quality CdZnTe Films by Close-Spaced Sublimation Method

AbstractThe effects of substrate temperature, source temperature and separation distance between the source and substrate on the growth rate of CdZnTe (CZT) films by Closed Space Sublimation (CSS) were systematically investigated. A maximum deposition rate of above 5μm/min was achieved with a source temperature of 650°C. The CZT films were heat treated by CdCl2 vapour in CSS system. The CdCl2 treatment on the structural and optical properties of CZT films was studied

Growth of High Quality ZnMgO Films on Diamond Substrates

AbstractZnMgO films were prepared at room temperature on freestanding diamond (FSD) substrates by co-sputtering. The Mg content was controlled by varying RF sputtering power of MgO and the effects of Mg contents on the properties of ZnMgO films were investigated. The results showed that the (0002) peak of ZnMgO shifted from 34.5° to 35.6° with the increasing sputtering power of MgO target. The UV-visible and PL spetra of ZnMgO films revealed that the bandgap of ZnMgO was approximately linear related to the sputtering power of MgO target

Soft-core baryon-baryon potentials for the complete baryon octet

SU(3) symmetry relations on the recently constructed hyperon-nucleon potentials are used to develop potential models for all possible baryon-baryon interaction channels. The main focus is on the interaction channels with total strangeness S=-2, -3, and -4, for which no experimental data exist yet. The potential models for these channels are based on SU(3) extensions of potential models for the S=0 and S=-1 sectors, which are fitted to experimental data. Although the SU(3) symmetry is not taken to be exact, the S=0 and S=-1 sectors still provide the necessary constraints to fix all free parameters. The potentials for the S=-2, -3, and -4 sectors, therefore, do not contain any additional free parameters, which makes them the first models of this kind. Various properties of the potentials are illustrated by giving results for scattering lengths, bound states, and total cross sections.Comment: 22 pages RevTex, 6 postscript figure

Interface Depinning in the Absence of External Driving Force

We study the pinning-depinning phase transition of interfaces in the quenched Kardar-Parisi-Zhang model as the external driving force $F$ goes towards zero. For a fixed value of the driving force we induce depinning by increasing the nonlinear term coefficient $\lambda$, which is related to lateral growth, up to a critical threshold. We focus on the case in which there is no external force applied (F=0) and find that, contrary to a simple scaling prediction, there is a finite value of $\lambda$ that makes the interface to become depinned. The critical exponents at the transition are consistent with directed percolation depinning. Our results are relevant for paper wetting experiments, in which an interface gets moving with no external driving force.Comment: 4 pages, 3 figures included, uses epsf. Submitted to PR

BayFlux: A Bayesian Method to Quantify Metabolic Fluxes and their Uncertainty at the Genome Scale.

Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13C Metabolic Flux Analysis (13C MFA) is considered to be the gold standard for measuring metabolic fluxes. 13C MFA typically works by leveraging extracellular exchange fluxes as well as data from 13C labeling experiments to calculate the flux profile which best fit the data for a small, central carbon, metabolic model. However, the nonlinear nature of the 13C MFA fitting procedure means that several flux profiles fit the experimental data within the experimental error, and traditional optimization methods offer only a partial or skewed picture, especially in “non-gaussian” situations where multiple very distinct flux regions fit the data equally well. Here, we present a method for flux space sampling through Bayesian inference (BayFlux), that identifies the full distribution of fluxes compatible with experimental data for a comprehensive genome-scale model. This Bayesian approach allows us to accurately quantify uncertainty in calculated fluxes. We also find that, surprisingly, the genome-scale model of metabolism produces narrower flux distributions (reduced uncertainty) than the small core metabolic models traditionally used in 13C MFA. The different results for some reactions when using genome-scale models vs core metabolic models advise caution in assuming strong inferences from 13C MFA since the results may depend significantly on the completeness of the model used. Based on BayFlux, we developed and evaluated novel methods (P-13C MOMA and P-13C ROOM) to predict the biological results of a gene knockout, that improve on the traditional MOMA and ROOM methods by quantifying prediction uncertainty

Functional architecture of the rat parasubiculum

The parasubiculum is a major input structure of layer 2 of medial entorhinal cortex, where most grid cells are found. Here we investigated parasubicular circuits of the rat by anatomical analysis combined with juxtacellular recording/labeling and tetrode recordings during spatial exploration. In tangential sections, the parasubiculum appears as a linear structure flanking the medial entorhinal cortex mediodorsally. With a length of ∼5.2 mm and a width of only ∼0.3 mm (approximately one dendritic tree diameter), the parasubiculum is both one of the longest and narrowest cortical structures. Parasubicular neurons span the height of cortical layers 2 and 3, and we observed no obvious association of deep layers to this structure. The "superficial parasubiculum" (layers 2 and 1) divides into ∼15 patches, whereas deeper parasubicular sections (layer 3) form a continuous band of neurons. Anterograde tracing experiments show that parasubicular neurons extend long "circumcurrent" axons establishing a "global" internal connectivity. The parasubiculum is a prime target of GABAergic and cholinergic medial septal inputs. Other input structures include the subiculum, presubiculum, and anterior thalamus. Functional analysis of identified and unidentified parasubicular neurons shows strong theta rhythmicity of spiking, a large fraction of head-direction selectivity (50%, 34 of 68), and spatial responses (grid, border and irregular spatial cells, 57%, 39 of 68). Parasubicular output preferentially targets patches of calbindin-positive pyramidal neurons in layer 2 of medial entorhinal cortex, which might be relevant for grid cell function. These findings suggest the parasubiculum might shape entorhinal theta rhythmicity and the (dorsoventral) integration of information across grid scales

A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization

A simple chemical approach to regenerating the strength of thermally damaged glass fibre

Process-induced strength loss is a major technical barrier to the effective reuse of thermally recycled glass fibres in composite applications. We have developed a novel approach to effectively restore strength in glass fibres through treatment in alkaline solutions. Glass fibres were treated at elevated temperature and experienced significant strength loss found typically after thermal recycling processes. Different alkaline treatments were then applied to the thermally damaged fibres in an attempt to restore strength which had been lost as a result of the heat conditioning procedure. Results indicated that these treatments were able to generate considerable fibre strength recovery. The degree of strength regeneration was found to be highly dependent on reaction conditions, which were investigated and optimised. The positive effect of these simple chemical treatments demonstrated great potential for facilitating the reuse of thermally recycled glass fibres in composite applications