Turing's model for biological pattern formation and the robustness problem

One of the fundamental questions in developmental biology is how the vast range of pattern and structure we observe in nature emerges from an almost uniformly homogeneous fertilized egg. In particular, the mechanisms by which biological systems maintain robustness, despite being subject to numerous sources of noise, are shrouded in mystery. Postulating plausible theoretical models of biological heterogeneity is not only difficult, but it is also further complicated by the problem of generating robustness, i.e. once we can generate a pattern, how do we ensure that this pattern is consistently reproducible in the face of perturbations to the domain, reaction time scale, boundary conditions and so forth. In this paper, not only do we review the basic properties of Turing's theory, we highlight the successes and pitfalls of using it as a model for biological systems, and discuss emerging developments in the area

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

Noise-induced inhibitory suppression of malfunction neural oscillators

Motivated by the aim to find new medical strategies to suppress undesirable neural synchronization we study the control of oscillations in a system of inhibitory coupled noisy oscillators. Using dynamical properties of inhibition, we find regimes when the malfunction oscillations can be suppressed but the information signal of a certain frequency can be transmitted through the system. The mechanism of this phenomenon is a resonant interplay of noise and the transmission signal provided by certain value of inhibitory coupling. Analyzing a system of three or four oscillators representing neural clusters, we show that this suppression can be effectively controlled by coupling and noise amplitudes.Comment: 10 pages, 14 figure

Time Distribution of Faculty Workload at Boise State University

This project’s first phase was to get a general idea of what the average work day looks like for a Boise State University faculty member; from this stage we developed activity definitions to use for the next phase. Thirty faculty members were interviewed by fourteen trained undergraduate research assistants over the course of two weeks on alternating days, April 9-21, 2013. These thirty faculty members represented all colleges of the Boise State University campus, including the Library, providing a total of 166 faculty days’ worth of data. The positions held by each participant ranged between an Assistant Professor and a Department Chair. The time diary method enabled students to document the type and duration of activities, functions, locations, and presence or absence of other types of individuals. Data on general work patterns and activities of BSU faculty are presented and broken out by day of week, type of activity, function, and location. These findings indicate that faculty work more than expected and in a wide range of activities and they work alone much of the time

Sierpinski signal generates 1/fα1/f^\alpha spectra

We investigate the row sum of the binary pattern generated by the Sierpinski automaton: Interpreted as a time series we calculate the power spectrum of this Sierpinski signal analytically and obtain a unique rugged fine structure with underlying power law decay with an exponent of approximately 1.15. Despite the simplicity of the model, it can serve as a model for $1/f^\alpha$ spectra in a certain class of experimental and natural systems like catalytic reactions and mollusc patterns.Comment: 4 pages (4 figs included). Accepted for publication in Physical Review

TransCom N2O model inter-comparison - Part 2:Atmospheric inversion estimates of N2O emissions

This study examines N2O emission estimates from five different atmospheric inversion frameworks based on chemistry transport models (CTMs). The five frameworks differ in the choice of CTM, meteorological data, prior uncertainties and inversion method but use the same prior emissions and observation data set. The posterior modelled atmospheric N2O mole fractions are compared to observations to assess the performance of the inversions and to help diagnose problems in the modelled transport. Additionally, the mean emissions for 2006 to 2008 are compared in terms of the spatial distribution and seasonality. Overall, there is a good agreement among the inversions for the mean global total emission, which ranges from 16.1 to 18.7 TgN yr(-1) and is consistent with previous estimates. Ocean emissions represent between 31 and 38% of the global total compared to widely varying previous estimates of 24 to 38%. Emissions from the northern mid- to high latitudes are likely to be more important, with a consistent shift in emissions from the tropics and subtropics to the mid- to high latitudes in the Northern Hemisphere; the emission ratio for 0-30A degrees N to 30-90A degrees N ranges from 1.5 to 1.9 compared with 2.9 to 3.0 in previous estimates. The largest discrepancies across inversions are seen for the regions of South and East Asia and for tropical and South America owing to the poor observational constraint for these areas and to considerable differences in the modelled transport, especially inter-hemispheric exchange rates and tropical convective mixing. Estimates of the seasonal cycle in N2O emissions are also sensitive to errors in modelled stratosphere-to-troposphere transport in the tropics and southern extratropics. Overall, the results show a convergence in the global and regional emissions compared to previous independent studies

Cell-cell contact mediated signalling — no fear of contact

Cancer research with sole focus on the cancer cell and possibly growth factors cannot faithfully reproduce the environmental interaction, such as adhesion of tumor cells to e.g. stromal cells, which may determine the response of these tumors to therapy. Methodologically cell adhesion studies are often difficult since complete but careful detachment is the prerequisite for most signal transduction assays. We describe for the first time an alternative method for the co-incubation of multiple myeloma cells on long term primary bone marrow stromal cultures using the bone marrow stromal cell line HS-5. The methods are precisely described, advantages and disadvantages are discussed, and troubleshooting advises are given.Исследования роста опухолевых клеток in vitro не отражают многих факторов (взаимодействие клеток с окружающей средой, их адгезию к клеткам стромы), которые в свою очередь могут определять чувствительность опухоли к терапии. Методологически изучение клеточной адгезии часто бывает затруднено, так как разделение клеток является основой большинства методик по изучению передачи сигнала. Впервые описан альтернативный метод ко-культивирования клеток множественной миеломы с клетками стромы линии HS-5, полученных из клеток костного мозга. Приведено подробное описание, преимущества и недостатки этого метода с детальными техническими рекомендациями

Spatial and spatio-temporal patterns in a cell-haptotaxis model

We investigate a cell-haptotaxis model for the generation of spatial and spatio-temporal patterns in one dimension. We analyse the steady state problem for specific boundary conditions and show the existence of spatially hetero-geneous steady states. A linear analysis shows that stability is lost through a Hopf bifurcation. We carry out a nonlinear multi-time scale perturbation procedure to study the evolution of the resulting spatio-temporal patterns. We also analyse the model in a parameter domain wherein it exhibits a singular dispersion relation

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