145 research outputs found
Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo
Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryonic development, is an area of debate. We have developed a computational modeling framework for studying this process, by which the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. At a purely mechanical level, we demonstrate that the perpendicular alignment of the animal-vegetal (a-v) and embryonic-abembryonic (eb-ab) axes is a result of minimizing the total elastic conformational energy of the entire collection of cells, which are constrained by the zona pellucida. The coupling of gene expression with the mechanics of cell movement is important for formation of both the trophectoderm and the endoderm. In studying the formation of the trophectoderm, we contrast and compare quantitatively two hypotheses: (1) The position determines gene expression, and (2) the gene expression determines the position. Our model, which couples gene expression with mechanics, suggests that differential adhesion between different cell types is a critical determinant in the robust endoderm formation. In addition to differential adhesion, two different testable hypotheses emerge when considering endoderm formation: (1) A directional force acts on certain cells and moves them into forming the endoderm layer, which separates the blastocoel and the cells of the inner cell mass (ICM). In this case the blastocoel simply acts as a static boundary. (2) The blastocoel dynamically applies pressure upon the cells in contact with it, such that cell segregation in the presence of differential adhesion leads to the endoderm formation. To our knowledge, this is the first attempt to combine cell-based spatial mechanical simulations with genetic networks to explain mammalian embryogenesis. Such a framework provides the means to test hypotheses in a controlled in silico environment
Squeezed Light for the Interferometric Detection of High Frequency Gravitational Waves
The quantum noise of the light field is a fundamental noise source in
interferometric gravitational wave detectors. Injected squeezed light is
capable of reducing the quantum noise contribution to the detector noise floor
to values that surpass the so-called Standard-Quantum-Limit (SQL). In
particular, squeezed light is useful for the detection of gravitational waves
at high frequencies where interferometers are typically shot-noise limited,
although the SQL might not be beaten in this case. We theoretically analyze the
quantum noise of the signal-recycled laser interferometric gravitational-wave
detector GEO600 with additional input and output optics, namely
frequency-dependent squeezing of the vacuum state of light entering the dark
port and frequency-dependent homodyne detection. We focus on the frequency
range between 1 kHz and 10 kHz, where, although signal recycled, the detector
is still shot-noise limited. It is found that the GEO600 detector with present
design parameters will benefit from frequency dependent squeezed light.
Assuming a squeezing strength of -6 dB in quantum noise variance, the
interferometer will become thermal noise limited up to 4 kHz without further
reduction of bandwidth. At higher frequencies the linear noise spectral density
of GEO600 will still be dominated by shot-noise and improved by a factor of
10^{6dB/20dB}~2 according to the squeezing strength assumed. The interferometer
might reach a strain sensitivity of 6x10^{-23} above 1 kHz (tunable) with a
bandwidth of around 350 Hz. We propose a scheme to implement the desired
frequency dependent squeezing by introducing an additional optical component to
GEO600s signal-recycling cavity.Comment: Presentation at AMALDI Conference 2003 in Pis
The ACIGA Data Analysis programme
The Data Analysis programme of the Australian Consortium for Interferometric
Gravitational Astronomy (ACIGA) was set up in 1998 by the first author to
complement the then existing ACIGA programmes working on suspension systems,
lasers and optics, and detector configurations. The ACIGA Data Analysis
programme continues to contribute significantly in the field; we present an
overview of our activities.Comment: 10 pages, 0 figures, accepted, Classical and Quantum Gravity,
(Proceedings of the 5th Edoardo Amaldi Conference on Gravitational Waves,
Tirrenia, Pisa, Italy, 6-11 July 2003
Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem
A central unanswered question in stem cell biology, both in plants and in animals, is how the spatial organization of stem cell niches are maintained as cells move through them. We address this question for the shoot apical meristem (SAM) which harbors pluripotent stem cells responsible for growth of above-ground tissues in flowering plants. We find that localized perception of the plant hormone cytokinin establishes a spatial domain in which cell fate is respecified through induction of the master regulator WUSCHEL as cells are displaced during growth. Cytokinin-induced WUSCHEL expression occurs through both CLAVATA-dependent and CLAVATA-independent pathways. Computational analysis shows that feedback between cytokinin response and genetic regulators predicts their relative patterning, which we confirm experimentally. Our results also may explain how increasing cytokinin concentration leads to the first steps in reestablishing the shoot stem cell niche in vitro
Computational modelling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence
Bone-marrow-derived progenitors must continually enter the thymus of an adult mouse to sustain T-cell homeostasis, yet only a few input cells per day are sufficient to support a yield of 5 Ă 10^7 immature T-cells per day and an eventual output of 1â2 Ă 10^6 mature cells per day. While substantial progress has been made to delineate the developmental pathway of T-cell lineage commitment, still little is known about the relationship between differentiation competence and the remarkable expansion of the earliest (DN1 stage) T-cell progenitors. To address this question, we developed computational models where the probability to progress to the next stage (DN2) is related to division number. To satisfy differentiation kinetics and overall cell yield data, our models require that adult DN1 cells divide multiple times before becoming competent to progress into DN2 stage. Our findings were subsequently tested by in vitro experiments, where putative early and later-stage DN1 progenitors from the thymus were purified and their progression into DN2 was measured. These experiments showed that the two DN1 sub-populations divided with similar rates, but progressed to the DN2 stage with different rates, thus providing experimental evidence that DN1 cells increase their commitment probability in a cell-intrinsic manner as they undergo cell division. Proliferation-linked shifts in eligibility of DN1 cells to undergo specification thus control kinetics of T-cell generation
Squeezed light in a frontal-phase-modulated signal-recycled interferometer
The application of squeezed Light to a frontal-phase-modulated signal-recycled interferometer is considered. We present a simple model to understand the required spectrum of squeezing so as to make the interferometer more sensitive. In particular we analyze the broad-and narrow-band cases for signal recycling and fmd that the sensitivity of the detector can be enhanced provided an appropriate input squeezed spectrum is used. We also discuss the effect of using squeezed light on the bandwidth of the detector
Predicting Pancreas Cell Fate Decisions and Reprogramming with a Hierarchical Multi-Attractor Model
Cell fate reprogramming, such as the generation of insulin-producing ÎČ cells from other pancreas cells, can be achieved by external modulation of key transcription factors. However, the known gene regulatory interactions that form a complex network with multiple feedback loops make it increasingly difficult to design the cell reprogramming scheme because the linear regulatory pathways as schemes of causal influences upon cell lineages are inadequate for predicting the effect of transcriptional perturbation. However, sufficient information on regulatory networks is usually not available for detailed formal models. Here we demonstrate that by using the qualitatively described regulatory interactions as the basis for a coarse-grained dynamical ODE (ordinary differential equation) based model, it is possible to recapitulate the observed attractors of the exocrine and ÎČ, ÎŽ, α endocrine cells and to predict which gene perturbation can result in desired lineage reprogramming. Our model indicates that the constraints imposed by the incompletely elucidated regulatory network architecture suffice to build a predictive model for making informed decisions in choosing the set of transcription factors that need to be modulated for fate reprogramming
Purity of Gaussian states: measurement schemes and time-evolution in noisy channels
We present a systematic study of the purity for Gaussian states of
single-mode continuous variable systems. We prove the connection of purity to
observable quantities for these states, and show that the joint measurement of
two conjugate quadratures is necessary and sufficient to determine the purity
at any time. The statistical reliability and the range of applicability of the
proposed measurement scheme is tested by means of Monte Carlo simulated
experiments. We then consider the dynamics of purity in noisy channels. We
derive an evolution equation for the purity of general Gaussian states both in
thermal and squeezed thermal baths. We show that purity is maximized at any
given time for an initial coherent state evolving in a thermal bath, or for an
initial squeezed state evolving in a squeezed thermal bath whose asymptotic
squeezing is orthogonal to that of the input state.Comment: 9 Pages, 6 Figures; minor errors correcte
Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch
Cellular transformations which involve a significant phenotypical change of
the cell's state use bistable biochemical switches as underlying decision
systems. In this work, we aim at linking cellular decisions taking place on a
time scale of years to decades with the biochemical dynamics in signal
transduction and gene regulation, occuring on a time scale of minutes to hours.
We show that a stochastic bistable switch forms a viable biochemical mechanism
to implement decision processes on long time scales. As a case study, the
mechanism is applied to model the initiation of follicle growth in mammalian
ovaries, where the physiological time scale of follicle pool depletion is on
the order of the organism's lifespan. We construct a simple mathematical model
for this process based on experimental evidence for the involved genetic
mechanisms. Despite the underlying stochasticity, the proposed mechanism turns
out to yield reliable behavior in large populations of cells subject to the
considered decision process. Our model explains how the physiological time
constant may emerge from the intrinsic stochasticity of the underlying gene
regulatory network. Apart from ovarian follicles, the proposed mechanism may
also be of relevance for other physiological systems where cells take binary
decisions over a long time scale.Comment: 14 pages, 4 figure
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