Noise control and utility: from regulatory network to spatial patterning

遗传调控网络中的出现阈值：果蝇形态发生中的蛋白质模式

Emergent thresholds in genetic regulatory networks: Protein patterning in Drosophila morphogenesis

我们提出了一个通用的方法，以建立遗传调控网络的数学模型。这种方法是基于质量作用定律和雅各布和莫诺操纵子模型。数学模型由\emph{Mathematica}软件包\emph{GeneticNetworks}符号化地建立。该软件包接受转录激活因子和阻遏因子的相互作用图作为输入，并以常微分方程系统的形式给出数学模型作为输出。所有相关的生物学参数由软件自动选择。在这个框架内，我们表明，在生物学中的阈值效应出现的基因和相关的守恒定律的催化性能。我们将这种方法应用于\emph{Drosophila}早期发育中的片段图案化，并校准和验证负责沿\emph{Drosophila}胚胎前后轴的间隙蛋白Hunchback和Knirps图案化的遗传转录网络。这表明，在缺口基因阶段的模式化是转录调节因子和它们沿胚胎的初始条件之间的关系的结果。

Core regulatory network motif underlies the ocellar complex patterning in Drosophila melanogaster

During organogenesis, developmental programs governed by Gene Regulatory Networks (GRN) define the functionality, size and shape of the different constituents of living organisms. Robustness, thus, is an essential characteristic that GRNs need to fulfill in order to maintain viability and reproducibility in a species. In the present work we analyze the robustness of the patterning for the ocellar complex formation in Drosophila melanogaster fly. We have systematically pruned the GRN that drives the development of this visual system to obtain the minimum pathway able to satisfy this pattern. We…

Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information

A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of W…

Cell density controls signal propagation waves in a multicellular synthetic gene circuit

During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical properties influence differentiation and cell fate decisions by modulating gene regulatory signaling networks. A major goal in synthetic development is to construct gene regulatory circuits that program the patterning and morphogenesis of synthetic multicellular structures. However, in the synthetic context, little is known regarding how the physical properties of t…

一种自发形成图案的反应扩散网络，包含整合的激活-抑制和底物耗尽机制，指定拟南芥根部的三基细胞命运

A spontaneously patterning reaction diffusion network, containing an integrated activator inhibitor and substrate depletion mechanism, specifies trichoblast cell fate in Arabidopsis roots

研究通过数学建模整合实验数据，揭示拟南芥根部表皮细胞命运由自发反应扩散网络调控，该网络整合激活-抑制和底物耗尽机制。

Optimizing information flow in small genetic networks. IV. Spatial coupling

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive co…