Pulses of Notch activation synchronise oscillating somite cells and entrain the zebrafish segmentation clock

Formation of somites, the rudiments of vertebrate body segments, is an oscillatory process governed by a gene-expression oscillator, the segmentation clock. This operates in each cell of the presomitic mesoderm (PSM), but the individual cells drift out of synchrony when Delta/Notch signalling fails, causing gross anatomical defects. We and others have suggested that this is because synchrony is maintained by pulses of Notch activation, delivered cyclically by each cell to its neighbours, that serve to adjust or reset the phase of the intracellular oscillator. This, however, has never been proved. Here, we provide direct experimental evidence, using zebrafish containing a heat-shock-driven transgene that lets us deliver artificial pulses of expression of the Notch ligand DeltaC. In DeltaC-defective embryos, in which endogenous Notch signalling fails, the artificial pulses restore synchrony, thereby rescuing somite formation. The spacing of segment boundaries produced by repetitive heat-shocking varies according to the time interval between one heat-shock and the next. The induced synchrony is manifest both morphologically and at the level of the oscillations of her1, a core component of the intracellular oscillator. Thus, entrainment of intracellular clocks by periodic activation of the Notch pathway is indeed the mechanism maintaining cell synchrony during somitogenesis

Modelling delta-notch perturbations during zebrafish somitogenesis

The discovery over the last 15 years of molecular clocks and gradients in the pre-somitic mesoderm of numerous vertebrate species has added significant weight to Cooke and Zeeman's ‘clock and wavefront’ model of somitogenesis, in which a travelling wavefront determines the spatial position of somite formation and the somitogenesis clock controls periodicity (Cooke and Zeeman, 1976). However, recent high-throughput measurements of spatiotemporal patterns of gene expression in different zebrafish mutant backgrounds allow further quantitative evaluation of the clock and wavefront hypothesis. In this study we describe how our recently proposed model, in which oscillator coupling drives the propagation of an emergent wavefront, can be used to provide mechanistic and testable explanations for the following observed phenomena in zebrafish embryos: (a) the variation in somite measurements across a number of zebrafish mutants; (b) the delayed formation of somites and the formation of ‘salt and pepper’ patterns of gene expression upon disruption of oscillator coupling; and (c) spatial correlations in the ‘salt and pepper’ patterns in Delta-Notch mutants. In light of our results, we propose a number of plausible experiments that could be used to further test the model

Test Procedures for Synchronized Oscillators Network CMOS VLSI Chip

The paper presents test procedures designed for application-specific integrated circuit (ASIC) CMOS VLSI chip that implements a synchronized oscillator neural network with a matrix size of 32×32 for object detecting in binary images. Networks of synchronized oscillators are recently developed tool for image segmentation and analysis. This paper briefly introduces synchronized oscillators network. Basic chip analog building blocks with their test procedures and measurements results are presented. In order to do measurements, special basic building blocks test structures have been implemented in the chip. It let compare Spectre simulations results to measurements results. Moreover, basic chip analog building blocks measurements give precious information about their imperfections caused by MOS transistor mismatch. This information is very usable during design and improvement of a special setup for chip functional tests. Improvement of the setup is a digitally assisted analog technique. It is an idea of oscillators tuning procedure. Such setup, oscillators tuning procedure and segmentation of a sample binary image are presented

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

Somitogenesis, the formation of the body's primary segmental structure common to all vertebrate development, requires coordination between biological mechanisms at several scales. Explaining how these mechanisms interact across scales and how events are coordinated in space and time is necessary for a complete understanding of somitogenesis and its evolutionary flexibility. So far, mechanisms of somitogenesis have been studied independently. To test the consistency, integrability and combined explanatory power of current prevailing hypotheses, we built an integrated clock-and-wavefront model including submodels of the intracellular segmentation clock, intercellular segmentation-clock coupling via Delta/Notch signaling, an FGF8 determination front, delayed differentiation, clock-wavefront readout, and differential-cell-cell-adhesion-driven cell sorting. We identify inconsistencies between existing submodels and gaps in the current understanding of somitogenesis mechanisms, and propose novel submodels and extensions of existing submodels where necessary. For reasonable initial conditions, 2D simulations of our model robustly generate spatially and temporally regular somites, realistic dynamic morphologies and spontaneous emergence of anterior-traveling stripes of Lfng. We show that these traveling stripes are pseudo-waves rather than true propagating waves. Our model is flexible enough to generate interspecies-like variation in somite size in response to changes in the PSM growth rate and segmentation-clock period, and in the number and width of Lfng stripes in response to changes in the PSM growth rate, segmentation-clock period and PSM length

Synchronicity from synchronized chaos

The synchronization of loosely-coupled chaotic oscillators, a phenomenon investigated intensively for the last two decades, may realize the philosophical concept of “synchronicity”—the commonplace notion that related eventsmysteriously occur at the same time. When extended to continuous media and/or large discrete arrays, and when general (non-identical) correspondences are considered between states, intermittent synchronous relationships indeed become ubiquitous. Meaningful synchronicity follows naturally if meaningful events are identified with coherent structures, defined by internal synchronization between remote degrees of freedom; a condition that has been posited as necessary for synchronizability with an external system. The important case of synchronization between mind and matter is realized if mind is analogized to a computer model, synchronizing with a sporadically observed system, as in meteorological data assimilation. Evidence for the ubiquity of synchronization is reviewed along with recent proposals that: (1) synchronization of different models of the same objective process may be an expeditious route to improved computational modeling and may also describe the functioning of conscious brains; and (2) the nonlocality in quantum phenomena implied by Bell’s theorem may be explained in a variety of deterministic (hidden variable) interpretations if the quantum world resides on a generalized synchronization “manifold”.publishedVersio

Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana.

Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark (LD) cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks can be set locally by organ-specific inputs but coordinated globally via spatial waves of clock gene expression

Temporal metabolic partitioning of the yeast and protist cellular networks:the cell is a global scale-invariant (fractal or self-similar) multioscillator

Britton Chance, electronics expert when a teenager, became an enthusiastic student of biological oscillations, passing on this enthusiasm to many students and colleagues, including one of us (DL). This historical essay traces BC’s influence through the accumulated work of DL to DL’s many collaborators. The overall temporal organization of mass-energy, information, and signaling networks in yeast in self-synchronized continuous cultures represents, until now, the most characterized example of in vivo elucidation of time structure. Continuous online monitoring of dissolved gases by direct measurement (membrane-inlet mass spectrometry, together with NAD(P)H and flavin fluorescence) gives strain-specific dynamic information from timescales of minutes to hours as does two-photon imaging. The predominantly oscillatory behavior of network components becomes evident, with spontaneously synchronized cellular respiration cycles between discrete periods of increased oxygen consumption (oxidative phase) and decreased oxygen consumption (reductive phase). This temperature-compensated ultradian clock provides coordination, linking temporally partitioned functions by direct feedback loops between the energetic and redox state of the cell and its growing ultrastructure. Multioscillatory outputs in dissolved gases with 13 h, 40 min, and 4 min periods gave statistical self-similarity in power spectral and relative dispersional analyses: i.e., complex nonlinear (chaotic) behavior and a functional scale-free (fractal) network operating simultaneously over several timescales

Synthetic Genetic Circuits: Plasticity and Robustness

Living organisms have evolved to survive in a multitude of environmental conditions. This plasticity, and the robustness to environmental fluctuations, is achieved by altering gene expression levels in response to perturbations while maintaining the basic processes essential for survival. Genetic circuits, which are networks of interacting genes, are responsible for carrying out both the basic processes to sustain life, such as counting time, as well as the specific processes that provide them with adaptability to various environmental conditions while maintaining homeostasis.Gene expression and its regulation are dynamic, stochastic processes. Namely, although gene expression was previously considered to be identical in cells arising from common ancestors, the observation of multiple, single cells expressing fluorescent proteins has shown that gene expression is noisy, which allows genetically identical cells in a homogeneous environment to behave differently, a phenomenon known as cell-to-cell phenotypic variability. Noise in gene expression arises from the fact that most of the underlying biochemical reactions involve small molecular numbers, which leads to infrequent, to some extent random in time, interactions and processes. While initially noise in gene expression was considered to be disadvantageous to the organisms, a number of recent studies suggest significant functional roles for noise in intracellular processes.The complexity and size of natural genetic circuits hampers their detailed study at present. One approach to overcome this problem is based on design of small, and thus more tractable, artificial circuits. Aside from its small size, in such circuits, all components are known and there is less chance that they interact with unknown cellular components. This strategy offers additional advantages, such as testability of whether a certain architecture is able to generate a desired trait or function without affecting natural cellular processes e.g., by inducing other downstream effectors that affect cell functioning. Moreover, it provides an opportunity to compare different circuit designs and determine which circuit architecture is preferable. Finally, due to detailed knowledge of their structure, the behavior of these circuits can be computationally simulated to assist, e.g., the study of their long-term behaviors, among other. Previous studies based on synthetic circuits have already provided key insights into the design principles and architecture of genetic circuits, such as how these organize genes so as to gain the ability to make decisions or track time. These circuits are also expected to become of great use in therapeutic and industrial applications.In this thesis, we focused on the study of the phenotypic plasticity and robustness of synthetic genetic clocks. We focused on the effects of temperature, copy number and the role of components; proteins and promoters, of the circuit. For this, we made use of the well-known genetic Repressilator, a synthetic genetic clock that is also one of the simplest genetic circuits known to be functional in a living system. To assist the studies, aside from techniques from cell and molecular biology, we made use of state of the art techniques in microscopy and image analysis. From the data, we characterized, first, the phenotypic plasticity of individual genes in Escherichia coli, as these are the main components of the Repressilator. Next, we performed a study of the effects of temperature on the dynamics of the genetic Repressilator. Subsequently, we studied the degree of synchrony between sister cells, each containing the Repressilator, in order to evaluate the extent to which cell division affects the dynamics of this circuit. Finally, we inserted the Repressilator genetic code into a single-copy vector so as to, by comparison with the original construct, study the effects of copy numbers on the dynamics of the circuit