Epithelial Migration and Non-adhesive Periderm Are Required for Digit Separation during Mammalian Development.

The fusion of digits or toes, syndactyly, can be part of complex syndromes, including van der Woude syndrome. A subset of van der Woude cases is caused by dominant-negative mutations in the epithelial transcription factor Grainyhead like-3 (GRHL3), and Grhl3-/-mice have soft-tissue syndactyly. Although impaired interdigital cell death of mesenchymal cells causes syndactyly in multiple genetic mutants, Grhl3-/- embryos had normal interdigital cell death, suggesting alternative mechanisms for syndactyly. We found that in digit separation, the overlying epidermis forms a migrating interdigital epithelial tongue (IET) when the epithelium invaginates to separate the digits. Normally, the non-adhesive surface periderm allows the IET to bifurcate as the digits separate. In contrast, in Grhl3-/- embryos, the IET moves normally between the digits but fails to bifurcate because of abnormal adhesion of the periderm. Our study identifies epidermal developmental processes required for digit separation

Laminar Cortical Dynamics of Visual Form and Motion Interactions During Coherent Object Motion Perception

How do visual form and motion processes cooperate to compute object motion when each process separately is insufficient? A 3D FORMOTION model specifies how 3D boundary representations, which separate figures from backgrounds within cortical area V2, capture motion signals at the appropriate depths in MT; how motion signals in MT disambiguate boundaries in V2 via MT-to-Vl-to-V2 feedback; how sparse feature tracking signals are amplified; and how a spatially anisotropic motion grouping process propagates across perceptual space via MT-MST feedback to integrate feature-tracking and ambiguous motion signals to determine a global object motion percept. Simulated data include: the degree of motion coherence of rotating shapes observed through apertures, the coherent vs. element motion percepts separated in depth during the chopsticks illusion, and the rigid vs. non-rigid appearance of rotating ellipses.Air Force Office of Scientific Research (F49620-01-1-0397); National Geospatial-Intelligence Agency (NMA201-01-1-2016); National Science Foundation (BCS-02-35398, SBE-0354378); Office of Naval Research (N00014-95-1-0409, N00014-01-1-0624

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

The Epitheliome: agent-based modelling of the social behaviour of cells

We have developed a new computational modelling paradigm for predicting the emergent behaviour resulting from the interaction of cells in epithelial tissue. As proof-of-concept, an agent-based model, in which there is a one-to-one correspondence between biological cells and software agents, has been coupled to a simple physical model. Behaviour of the computational model is compared with the growth characteristics of epithelial cells in monolayer culture, using growth media with low and physiological calcium concentrations. Results show a qualitative fit between the growth characteristics produced by the simulation and the in vitro cell models

From segment to somite: segmentation to epithelialization analyzed within quantitative frameworks

One of the most visually striking patterns in the early developing embryo is somite segmentation. Somites form as repeated, periodic structures in pairs along nearly the entire caudal vertebrate axis. The morphological process involves short- and long-range signals that drive cell rearrangements and cell shaping to create discrete, epithelialized segments. Key to developing novel strategies to prevent somite birth defects that involve axial bone and skeletal muscle development is understanding how the molecular choreography is coordinated across multiple spatial scales and in a repeating temporal manner. Mathematical models have emerged as useful tools to integrate spatiotemporal data and simulate model mechanisms to provide unique insights into somite pattern formation. In this short review, we present two quantitative frameworks that address the morphogenesis from segment to somite and discuss recent data of segmentation and epithelialization

Differential segregation in a cell-cell contact interface: the dynamics of the immunological synapse

Receptor-ligand couples in the cell-cell contact interface between a T cell and an antigen-presenting cell form distinct geometric patterns and undergo spatial rearrangement within the contact interface. Spatial segregation of the antigen and adhesion receptors occurs within seconds of contact, central aggregation of the antigen receptor then occurring over 1-5 min. This structure, called the immunological synapse, is becoming a paradigm for localized signaling. However, the mechanisms driving its formation, in particular spatial segregation, are currently not understood. With a reaction diffusion model incorporating thermodynamics, elasticity, and reaction kinetics, we examine the hypothesis that differing bond lengths (extracellular domain size) is the driving force behind molecular segregation. We derive two key conditions necessary for segregation: a thermodynamic criterion on the effective bond elasticity and a requirement for the seeding/nucleation of domains. Domains have a minimum length scale and will only spontaneously coalesce/aggregate if the contact area is small or the membrane relaxation distance large. Otherwise, differential attachment of receptors to the cytoskeleton is required for central aggregation. Our analysis indicates that differential bond lengths have a significant effect on synapse dynamics, i.e., there is a significant contribution to the free energy of the interaction, suggesting that segregation by differential bond length is important in cell-cell contact interfaces and the immunological synapse

Analysis of the transcriptional program governing meiosis and gametogenesis in yeast and mammals

During meiosis a competent diploid cell replicates its DNA once and then undergoes two consecutive divisions followed by haploid gamete differentiation. Important aspects of meiotic development that distinguish it from mitotic growth include a highly increased rate of recombination, formation of the synaptonemal complex that aligns the homologous chromosomes, as well as separation of the homologues and sister chromatids during meiosis I and II without an intervening S-phase. Budding yeast is an excellent model organism to study meiosis and gametogenesis and accordingly, to date it belongs to the best studied eukaryotic systems in this context. Knowledge coming from these studies has provided important insights into meiotic development in higher eukaryotes. This was possible because sporulation in yeast and spermatogenesis in higher eukaryotes are analogous developmental pathways that involve conserved genes. For budding yeast a huge amount of data from numerous genome-scale studies on gene expression and deletion phenotypes of meiotic development and sporulation are available. In contrast, mammalian gametogenesis has not been studied on a large-scale until recently. It was unclear if an expression profiling study using germ cells and testicular somatic control cells that underwent lengthy purification procedures would yield interpretable results. We have therefore carried out a pioneering expression profiling study of male germ cells from Rattus norvegicus using Affymetrix U34A and B GeneChips. This work resulted in the first comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis. We have identified 1268 differentially expressed genes in germ cells at different developmental stages, which were organized into four distinct expression clusters that reflect somatic, mitotic, meiotic and post-meiotic cell types. This included 293 yet uncharacterized transcripts whose expression pattern suggests that they are involved in spermatogenesis and fertility. A group of 121 transcripts were only expressed in meiotic (spermatocytes) and postmeiotic germ cells (round spermatids) but not in dividing germ cells (spermatogonia), Sertoli cells or two somatic control tissues (brain and skeletal muscle). Functional analysis reveals that most of the known genes in this group fulfill essential functions during meiosis, spermiogenesis (the process of sperm maturation) and fertility. Therefore it is highly possible that some of the �30 uncharacterized transcripts in this group also contribute to these processes. A web-accessible database (called reXbase, which was later on integrated into GermOnline) has been developed for our expression profiling study of mammalian male meiosis, which summarizes annotation information and shows a graphical display of expression profiles of every gene covered in our study. In the budding yeast Saccharomyces cerevisiae entry into meiosis and subsequent progression through sporulation and gametogenesis are driven by a highly regulated transcriptional program activated by signal pathways responding to nutritional and cell-type cues. Abf1p, which is a general transcription factor, has previously been demonstrated to participate in the induction of numerous mitotic as well as early and middle meiotic genes. In the current study we have addressed the question how Abf1p transcriptionally coordinates mitotic growth and meiotic development on a genome-wide level. Because ABF1 is an essential gene we used the temperature-sensitive allele abf1-1. A phenotypical analysis of mutant cells revealed that ABF1 plays an important role in cell separation during mitosis, meiotic development, and spore formation. In order to identify genes whose expression depends on Abf1p in growing and sporulating cells we have performed expression profiling experiments using Affymetrix S98 GeneChips comparing wild-type and abf1-1 mutant cells at both permissive and restrictive temperature. We have identified 504 genes whose normal expression depends on functional ABF1. By combining the expression profiling data with data from genome-wide DNA binding assays (ChIPCHIP) and in silico predictions of potential Abf1p-binding sites in the yeast genome, we were able to define direct target genes. Expression of these genes decreases in the absence of functional ABF1 and whose promotors are bound by Abf1p and/or contain a predicted binding site. Among 352 such bona fide direct target genes we found many involved in ribosome biogenesis, translation, vegetative growth and meiotic developement and therefore could account for the observed growth and sporulation defects of abf1-1 mutant cells. Furthermore, the fact that two members of the septin family (CDC3 and CDC10 ) were found to be direct target genes suggests a novel role for Abf1p in cytokinesis. This was further substantiated by the observation that chitin localization and septin ring formation are perturbed in abf1-1 mutant cells

A Neural Model of How Horizontal and Interlaminar Connections of Visual Cortex Develop into Adult Circuits that Carry Out Perceptual Grouping and Learning

A neural model suggests how horizontal and interlaminar connections in visual cortical areas Vl and V2 develop within a laminar cortical architecture and give rise to adult visual percepts. The model suggests how mechanisms that control cortical development in the infant lead to properties of adult cortical anatomy, neurophysiology, and visual perception. The model clarifies how excitatory and inhibitory connections can develop stably by maintaining a balance between excitation and inhibition. The growth of long-range excitatory horizontal connections between layer 2/3 pyramidal cells is balanced against that of short-range disynaptic interneuronal connections. The growth of excitatory on-center connections from layer 6-to-4 is balanced against that of inhibitory interneuronal off-surround connections. These balanced connections interact via intracortical and intercortical feedback to realize properties of perceptual grouping, attention, and perceptual learning in the adult, and help to explain the observed variability in the number and temporal distribution of spikes emitted by cortical neurons. The model replicates cortical point spread functions and psychophysical data on the strength of real and illusory contours. The on-center off-surround layer 6-to-4 circuit enables top-clown attentional signals from area V2 to modulate, or attentionally prime, layer 4 cells in area Vl without fully activating them. This modulatory circuit also enables adult perceptual learning within cortical area Vl and V2 to proceed in a stable way.Defense Advanced Research Projects Agency and the Office of Naval Research (N00014-95-1-0409); National Science Foundation (IRI-97-20333); Office of Naval Research (N00014-95-1-0657