Quantitative and contextual modelling of transcriptional responses to auxin

生长素是一种植物激素，在植物生长发育的许多不同方面起着重要作用。例如，生长素一方面调节从生长的茎尖长出叶子的模式，而另一方面，它调节环境反应，如在向光源生长的芽中观察到的弯曲生长。由于生长素在植物发育过程中起着不可或缺的作用，因此了解生长素的工作原理对我们理解植物生长和改善重要作物性状都是至关重要的。生长素是一种小而简单的分子，虽然我们还不清楚生长素是如何调控如此多样化的过程的，但我们知道，基因表达的变化是重要的，数百个基因在生长素的作用下被打开或关闭。几个实验室的工作已经建立了一个信号蛋白网络，其复杂的相互作用将细胞内生长素水平的增加转化为基因表达的变化。然而，这种生长素信号传导的模型是通用的，并且包含一些空白，这意味着在大多数情况下，它只提供了理解生长素在整个植物中如何运作的理论基础。我们可以确定纠正这种情况所需的新信息，并且通过这项工作，我们打算使用新的可用技术来获取这些数据并纠正当前模型的缺陷。生长素反应系统中相互作用的复杂性意味着描述它的数据也同样复杂，因此我们需要采用一种新的方法来分析我们将收集的信息，在这些信息中我们建立描述系统功能的数学模型。然后，这些模型可以用来测试我们对生长素反应系统如何工作的预测，产生关于其功能的新假设，并最终告诉我们是否已经了解了其基本细节。这种对生长素作用的更高层次的理解将对许多群体有用，包括植物生物学家、作物科学家和研究其他生物中类似复杂信号机制的科学家。

Auxin is a plant hormone that plays an important role in many, very different aspects of plant growth and development. For example, on one hand auxin regulates the pattern in which leaves emerge from the growing shoot tip, while on the other it mediates environmental responses such as the bending growth observed in shoots growing towards a light source. Because auxin is integral to so much of plant development, a knowledge of how auxin works is absolutely fundamental to our ability both to understand how plants grow and to improve important crop traits. Although it is unclear how auxin, a small and simple molecule, is able to regulate such a diversity of processes, it is known that changes in gene expression are important and that several hundred genes are either turned on or off in response to auxin. Work from several labs has established a network of signalling proteins whose complex interactions translate increases in auxin levels within a cell into gene expression changes. However, this model of auxin signalling is generic and contains several gaps which mean that in most cases it offers only a theoretical basis for understanding how auxin operates throughout the plant. We can identify the new information required to remedy this situation and with this work we intend to use newly available techniques to obtain these data and correct the deficiencies of the current model. The complexity of the interactions in this auxin response system mean that the data that describe it are similarly complex, and therefore we need to adopt a new approach for analysing the information that we will gather in which we build mathematical models that describe the functioning of the system. These models can then be used to test our predictions of how the auxin response system works, generate new hypotheses about its functioning, and ultimately tell us if we have understood its essential details. This higher level of understanding of auxin action will be useful to a number of groups, including plant biologists, crop scientists, and scientists studying similarly complex signalling mechanisms in other organisms.