Quantitative morphogen analysis of periodic ruga patterning

在人类基因组计划之后，我们知道了创造和维持人体所需的基因总数。目前尚不清楚的是，哪些基因在何时何地都是活跃的，以及它们如何正确地发挥作用。将这类信息集成到大型电路图或类似计算机程序的描述中被称为系统生物学方法（类比于化工厂设计等领域的系统分析）。这是非常困难的，因为涉及到大量的数据，基因运作的地方有非常复杂的解剖结构，而将数据整合在一起的计算方法仍在发展中。这个问题的一个特别被忽视的方面是，不同细胞中的基因如何通过分泌的化学物质（形态因子）在一定距离内相互关闭，从而使胚胎在子宫内发育过程中在正确的位置形成正确的结构。到目前为止，这主要是在果蝇身上进行的分析，因为它们是一个比哺乳动物简单得多的系统，而且它们的早期发育特别简单。这个项目提案是研究我们已经发现的哺乳动物解剖学中类似的简单部分的基因调控：口腔顶部的横向脊，或“rugae”。人类有四个，老鼠有八个。每条条纹开始于一个特定基因的条带表达，每条条带都是相似和平行的。它们的特征间距和顺序外观构成了一维的“周期性”（即重复）模式问题。为了解决这个图案问题，我们将非常详细地分析小鼠上颚的基因表达和形态因子的作用，重点关注我们已经确定的在形成这些条纹中起重要作用的四种形态因子。这包括对特定基因产物（rna）进行染色，并使用工程小鼠品系，其细胞在特定基因开启的时间和地点精确地发出荧光。数字成像将允许这些基因信号被精确地量化。当把数据放在一起——如果足够详细和定量的话——可以通过所谓的“逆向工程”计算算法来解释，以找出哪些基因控制哪些其他基因和形态因子（包括诸如时滞、放大器和逻辑开关等特征），这样我们就能理解电路图和程序，从而使正确的解剖发展成为可能。这个简单的系统可以作为对这类过程的一般理解的范例。最终，这不仅为生物过程提供了丰富的见解，而且为调整这些电路以增强医疗目的的修复和再生提供了一条途径。

Following the Human Genome Project, we know the sum total of genes available to create and maintain the human body. What is still unknown is which genes are active where and when and how they all operate correctly to do their jobs. The integration of that kind of information into a large circuit diagram or computer programme-like description is referred to as a systems biology approach (by analogy to systems analysis in fields like chemical factory design). This is very difficult to do because huge amounts of data are involved, the places where genes operate have very complicated anatomical structures and the computational methods for putting the data together are still being developed. A particularly neglected aspect of this problem is how genes in different cells switch one another off at a distance via secreted chemicals (morphogens) so that in the embryo during development in the womb the right structures are made in the right places. So far, this has been analysed primarily in fruit flies because they are a much simpler system than mammals and their very early development is particularly simple. This project proposal is to study gene regulation in what we have discovered to be a similarly simple part of mammalian anatomy: the transverse ridges, or "rugae", in the roof of the mouth. Humans have four, mice have eight. Each ruga starts as a stripe of expression of one particular gene and each stripe is alike and parallel. Their characteristic spacing and sequential appearance constitute a one-dimensional "periodic" (i.e. repeating) patterning problem. To solve this patterning problem, we will analyze gene expression and morphogen action in the mouse palate in great detail, focusing on four morphogens that we have already identified as important in making these stripes. This involves staining for specific gene products (RNAs) and using engineered mouse strains whose cells light up fluorescently exactly when and where a particular gene is switched on. Digital imaging will allow these gene signals to be quantified accurately. When put together the data - if sufficiently detailed and quantitative - can be interpreted by so-called "reverse engineering" computational algorithms to work out which genes control which other genes and morphogens (including features such as time-lags, amplifiers and logic switches) so that we understand the circuit diagram and programme that makes development of correct anatomy possible. This simple system then serves as a paradigm for a general understanding of this kind of process. Ultimately, this provides not only rich insight into biological processes but also a route towards tweaking these circuits to enhance repair and regeneration for medical ends.