Effect of ethoxyformic anhydride on the Rieske iron—sulfur protein of bovine heart ubiquinol: Cytochrome c oxidoreductase

AbstractTreatment of bovine heart ubiquinol-cytochrome c oxidoreductase (complex III, bc1 complex) with ethoxyformic anhydride (EFA) inhibits electron transfer between cytochromes b and c1 [Yagi et al., Biochemistry 21 (1982) 4777–4782]. This paper shows that EFA alters the EPR lineshape of the Rieske iron—sulfur cluster in complex III and in the isolated Rieske protein without a significant decrease of spin concentration. The effect of EFA on the Rieske iron—sulfur cluster is competitive with that of Qo site inhibitors, such as stigmatellin, and is completely reversed by hydroxylamine. These results are consistent with the possible ethoxyformylation by EFA of histidine ligands of the Rieske iron—sulfur cluster at the non-iron binding imidazole nitrogens

Morphogen Transport in Epithelia

We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the fruit fly Drosophila

Helical Turing patterns in the Lengyel-Epstein model in thin cylindrical layers

The formation of Turing patterns was investigated in thin cylindrical layers using the Lengyel-Epstein model of the chlorine dioxide-iodine-malonic acid reaction. The influence of the width of the layer W and the diameter D of the inner cylinder on the pattern with intrinsic wavelength l were determined in simulations with initial random noise perturbations to the uniform state for W< l/2 and D l or lower. We show that the geometric constraints of the reaction domain may result in the formation of helical Turing patterns with parameters that give stripes (b ¼ 0.2) or spots (b ¼ 0.37) in two dimensions. For b ¼ 0.2, the helices were composed of lamellae and defects were likely as the diameter of the cylinder increased. With b ¼ 0.37, the helices consisted of semi-cylinders and the orientation of stripes on the outer surface (and hence winding number) increased with increasing diameter until a new stripe appeared

Modelling cell motility and chemotaxis with evolving surface finite elements

We present a mathematical and a computational framework for the modelling of cell motility. The cell membrane is represented by an evolving surface, with the movement of the cell determined by the interaction of various forces that act normal to the surface. We consider external forces such as those that may arise owing to inhomogeneities in the medium and a pressure that constrains the enclosed volume, as well as internal forces that arise from the reaction of the cells' surface to stretching and bending. We also consider a protrusive force associated with a reaction-diffusion system (RDS) posed on the cell membrane, with cell polarization modelled by this surface RDS. The computational method is based on an evolving surface finite-element method. The general method can account for the large deformations that arise in cell motility and allows the simulation of cell migration in three dimensions. We illustrate applications of the proposed modelling framework and numerical method by reporting on numerical simulations of a model for eukaryotic chemotaxis and a model for the persistent movement of keratocytes in two and three space dimensions. Movies of the simulated cells can be obtained from http://homepages.warwick.ac.uk/maskae/CV_Warwick/Chemotaxis.html

Sewerage tunnel leakage detection using a fibre optic moisture-detecting sensor system

The design and development of a new fibre optic sensor system for the optical detection of leakages in sewerage tunnels is reported. The system developed overcomes the disadvantages of the usually employed camera based inspection systems which are relatively complex and, in addition, require cleaning of the structures to be monitored beforehand. The sensor concept created combines a Fibre Bragg Grating (FBG)-based humidity sensor and a swellable polymeric fibre optic sensor. Both sensors are located along the sewerage tunnel so that they can response immediately to any leakages that may occur. The swellable polymeric fibre optic sensor shows a response of 34.2 dB in the presence of water, a performance which is superior to that seen form other swellable polymeric fibre optic sensors reported so far. Furthermore, the resistance of both sensors to highly alkaline environments (pH 13.4), an important feature of such sensors was verified. Consequently, when compared to the use of conventional inspection techniques, the novel fibre optic sensor system provides a robust, relatively low-cost and continuous monitoring system well suited to use in sewerage tunnels

Periodic pattern formation in reaction-diffusion systems -an introduction for numerical simulation

The aim of the present review is to provide a comprehensive explanation of Turing reaction–diffusion systems in sufficient detail to allow readers to perform numerical calculations themselves. The reaction–diffusion model is widely studied in the field of mathematical biology, serves as a powerful paradigm model for self-organization and is beginning to be applied to actual experimental systems in developmental biology. Despite the increase in current interest, the model is not well understood among experimental biologists, partly because appropriate introductory texts are lacking. In the present review, we provide a detailed description of the definition of the Turing reaction–diffusion model that is comprehensible without a special mathematical background, then illustrate a method for reproducing numerical calculations with Microsoft Excel. We then show some examples of the patterns generated by the model. Finally, we discuss future prospects for the interdisciplinary field of research involving mathematical approaches in developmental biology

A model for selection of eyespots on butterfly wings

The development of eyespots on the wing surface of butterflies of the family Nympalidae is one of the most studied examples of biological pattern formation.However, little is known about the mechanism that determines the number and precise locations of eyespots on the wing. Eyespots develop around signaling centers, called foci, that are located equidistant from wing veins along the midline of a wing cell (an area bounded by veins). A fundamental question that remains unsolved is, why a certain wing cell develops an eyespot, while other wing cells do not. We illustrate that the key to understanding focus point selection may be in the venation system of the wing disc. Our main hypothesis is that changes in morphogen concentration along the proximal boundary veins of wing cells govern focus point selection. Based on previous studies, we focus on a spatially two-dimensional reaction-diffusion system model posed in the interior of each wing cell that describes the formation of focus points. Using finite element based numerical simulations, we demonstrate that variation in the proximal boundary condition is sufficient to robustly select whether an eyespot focus point forms in otherwise identical wing cells. We also illustrate that this behavior is robust to small perturbations in the parameters and geometry and moderate levels of noise. Hence, we suggest that an anterior-posterior pattern of morphogen concentration along the proximal vein may be the main determinant of the distribution of focus points on the wing surface. In order to complete our model, we propose a two stage reaction-diffusion system model, in which an one-dimensional surface reaction-diffusion system, posed on the proximal vein, generates the morphogen concentrations that act as non-homogeneous Dirichlet (i.e., fixed) boundary conditions for the two-dimensional reaction-diffusion model posed in the wing cells. The two-stage model appears capable of generating focus point distributions observed in nature. We therefore conclude that changes in the proximal boundary conditions are sufficient to explain the empirically observed distribution of eyespot focus points on the entire wing surface. The model predicts, subject to experimental verification, that the source strength of the activator at the proximal boundary should be lower in wing cells in which focus points form than in those that lack focus points. The model suggests that the number and locations of eyespot foci on the wing disc could be largely controlled by two kinds of gradients along two different directions, that is, the first one is the gradient in spatially varying parameters such as the reaction rate along the anterior-posterior direction on the proximal boundary of the wing cells, and the second one is the gradient in source values of the activator along the veins in the proximal-distal direction of the wing cell

HOLISMOKES -- IV. Efficient mass modeling of strong lenses through deep learning

Modelling the mass distributions of strong gravitational lenses is often necessary to use them as astrophysical and cosmological probes. With the high number of lens systems ($>10^5$) expected from upcoming surveys, it is timely to explore efficient modeling approaches beyond traditional MCMC techniques that are time consuming. We train a CNN on images of galaxy-scale lenses to predict the parameters of the SIE mass model ($x,y,e_x,e_y$, and $\theta_E$). To train the network, we simulate images based on real observations from the HSC Survey for the lens galaxies and from the HUDF as lensed galaxies. We tested different network architectures, the effect of different data sets, and using different input distributions of $\theta_E$. We find that the CNN performs well and obtain with the network trained with a uniform distribution of $\theta_E$ $>0.5"$ the following median values with $1\sigma$ scatter: $\Delta x=(0.00^{+0.30}_{-0.30})"$, $\Delta y=(0.00^{+0.30}_{-0.29})"$, $\Delta \theta_E=(0.07^{+0.29}_{-0.12})"$, $\Delta e_x = -0.01^{+0.08}_{-0.09}$ and $\Delta e_y = 0.00^{+0.08}_{-0.09}$. The bias in $\theta_E$ is driven by systems with small $\theta_E$. Therefore, when we further predict the multiple lensed image positions and time delays based on the network output, we apply the network to the sample limited to $\theta_E>0.8"$. In this case, the offset between the predicted and input lensed image positions is $(0.00_{-0.29}^{+0.29})"$ and $(0.00_{-0.31}^{+0.32})"$ for $x$ and $y$, respectively. For the fractional difference between the predicted and true time delay, we obtain $0.04_{-0.05}^{+0.27}$. Our CNN is able to predict the SIE parameters in fractions of a second on a single CPU and with the output we can predict the image positions and time delays in an automated way, such that we are able to process efficiently the huge amount of expected lens detections in the near future.Comment: 17 pages, 14 Figure

HOLISMOKES -- IX. Neural network inference of strong-lens parameters and uncertainties from ground-based images

Modeling of strong gravitational lenses is a necessity for further applications in astrophysics and cosmology. Especially with the large number of detections in current and upcoming surveys such as the Rubin Legacy Survey of Space and Time (LSST), it is timely to investigate in automated and fast analysis techniques beyond the traditional and time consuming Markov chain Monte Carlo sampling methods. Building upon our convolutional neural network (CNN) presented in Schuldt et al. (2021b), we present here another CNN, specifically a residual neural network (ResNet), that predicts the five mass parameters of a Singular Isothermal Ellipsoid (SIE) profile (lens center $x$ and $y$, ellipticity $e_x$ and $e_y$, Einstein radius $\theta_E$) and the external shear ($\gamma_{ext,1}$, $\gamma_{ext,2}$) from ground-based imaging data. In contrast to our CNN, this ResNet further predicts a 1$\sigma$ uncertainty for each parameter. To train our network, we use our improved pipeline from Schuldt et al. (2021b) to simulate lens images using real images of galaxies from the Hyper Suprime-Cam Survey (HSC) and from the Hubble Ultra Deep Field as lens galaxies and background sources, respectively. We find overall very good recoveries for the SIE parameters, while differences remain in predicting the external shear. From our tests, most likely the low image resolution is the limiting factor for predicting the external shear. Given the run time of milli-seconds per system, our network is perfectly suited to predict the next appearing image and time delays of lensed transients in time. Therefore, we also present the performance of the network on these quantities in comparison to our simulations. Our ResNet is able to predict the SIE and shear parameter values in fractions of a second on a single CPU such that we are able to process efficiently the huge amount of expected galaxy-scale lenses in the near future.Comment: 16 pages, including 11 figures, accepted for publication by A&