Mathematical models of H. pylori gastric colonization

描述（由申请人提供）：幽门螺杆菌是一种螺旋状、微嗜气细菌，持续定植于人体胃中，与上胃肠道疾病有关。越来越多的证据表明，幽门螺杆菌个体被克隆变异云定植，类似于RNA病毒的准物种。随着越来越多的证据表明，幽门螺杆菌的多样化能力对其体内持久性至关重要，涉及多个基因座的持续多样化。例如，涉及cagA和cagY的变异会影响宿主组织的相互作用。除了内源性的点突变外，幽门螺杆菌基因组还含有大量非随机分布的重复DNA，并且这些生物天生能够吸收来自其他幽门螺杆菌菌株的DNA；这些为多样化提供了重要的机制；大量证据表明，这发生在体内。这一提议的假设是幽门螺杆菌利用遗传变异作为适应（动态）宿主环境的主要机制。我们将研究重复DNA（目标1）和自然转化（目标2）之间的重组，以检查这些多样化方法的特点。这些研究将在体外进行，使用定量分析来探索所涉及的机制，并使用相关的幽门螺杆菌突变体的构建来验证所提出的特定假设。我们将使用计算机、实验和数学方法来表征这些机制，然后使用这些信息和方法来研究动物模型中的表型变异及其选择（目标3）。我们将继续关注在leb转基因小鼠模型中幽门螺杆菌细胞表面Lewis抗原变异的选择。这个实验系统的存在将允许分析导致基因型变化的遗传机制，产生改变的表型。实验结果将使基因型和表型变异与选择相关的确定性模型得以发展。

DESCRIPTION (provided by applicant): Helicobacter pylori are spiral, microaerophilic bacteria that persistently colonize the human stomach, and that are associated with diseases of the upper gastrointestinal tract. There is increasing evidence that H. pylori individuals are colonized by a cloud of clonal variants, analogous to the quasi-species of RNA viruses. The ability of H. pylori to diversify appears crucial to its in vivo persistence, with increasing evidence of ongoing diversification involving multiple loci. For example, variation involving cagA and cagY affect host tissue interactions. In addition to endogenous point mutations, the H. pylori genome contains extensive and non-randomly distributed repetitive DNA, and the organisms are naturally competent for uptake of DNA from other H. pylori strains; these provide important mechanisms for diversification; substantial evidence indicates that this occurs in vivo. The hypothesis of this proposal is that H. pylori uses genetic variation as a principal mechanism to adapt to (dynamic) host environments. We will study recombination between repetitive DNA (Aim 1) and natural transformation (Aim 2) to examine the characteristics of these diversification methods. These studies will be conducted in vitro using quantitative assays that explore the mechanisms involved, and using construction of relevant H. pylori mutants to test the specific hypotheses raised. We will use in silico, experimental, and mathematical approaches to characterize these mechanisms, and then use the information and approaches to study phenotypic variation and its selection in an animal model (Aim 3). We will continue to focus on the selection for H. pylori cell surface Lewis antigen variation in a Leb-transgenic mouse model. The existence of this experimental system will allow analysis of the genetic mechanisms leading to genotypic changes, producing altered phenotypes. The experimental results will enable development of deterministic models relating genotypic and phenotypic variation with selection.