SysMO LAB (Hugenholtz)-Westerhoff

分子和基因组学方法极大地促进了我们对细菌的理解。它们也导致了一些意外。其中之一是，看似高度不同的生物体在分子方面相当相似。人类的许多分子组成与细菌的组成相似。在与人类相互作用的方式高度不同的细菌之间发现了更接近的相似性。科学的最新发展，称为系统生物学，认识到生物体的功能不仅仅是由它们的组成部分决定的，而且还由这些组成部分之间相互作用产生的特性决定，就像足球运动员的得分不仅仅是由球员自己决定的一样。在这里，我们建议测试我们的假设，生物体之间的差异来自于它们的组件之间的相互作用的差异。三个相关的生物体将进行比较，一个是生产我们的奶酪，一个是食物的粪便污染物，一个是引起喉咙痛的。这三种细菌的网络将被解开，碳和能量通过这些网络的流动将被确定，细菌能够在多大程度上调整其网络以适应改变的环境将被测量。这些结果将被组装到计算机模型中，然后再现细菌的行为。将研究这些计算机版本的生物体是否以及如何解释它们引起疾病或作为帮助生产我们食物的生物体发挥作用的程度的差异。这些解释将通过实验进行检验。

Molecular and genomics approaches have contributed greatly to our understanding of bacteria. They have also led to a number of surprises. One is the fact that organisms that appear to be highly different are rather similar in terms of their molecules. Many of the molecular components of humans are similar to components of bacteria. Even closer similarities have been found between bacteria that are highly different in the way they interact with human beings. A recent development in the sciences, called Systems Biology, recognizes that the functioning of living organisms is not merely determined by their components, but also by properties that emerge from the interactions between those components, just like the scoring by a football player is not just determined by that player himself. Here we propose to test our hypothesis that much of the differences between organisms derives from differences in the interactions between their components. Three related organisms will be compared, one that produces our cheese, one that is a fecal contaminant of food, and one that causes sore throats. The networks of the three bacteria will be unraveled, the flow of carbon and energy through those networks will be determined, and the extent to which the bacteria are able to adjust their networks to altered environments will be measured. The results will be assembled into computer models that should then reproduce the behavior of the bacteria. It will be examined whether and how these computer versions of the organisms explain the differences in the extent to which they cause disease or function as organisms that help produce our food. These explanations will then be tested experimentally.