Systems Biology analysis of biological timers and inflammation

随着我们年龄的增长，我们的免疫系统往往会变得更弱，要摆脱疾病变得越来越困难。与此同时，我们往往会患上关节炎和其他自身免疫性疾病，这些疾病都是局部失控炎症的表现。在这项拨款申请中，我们由生理学家、生物学家、数学家和计算机科学家组成的多学科科学家团队致力于研究一个非常重要的信号系统NF-kappaB。这个系统在应激和免疫反应中发挥着重要作用，并决定着体内细胞的命运，这对一般的健康和福祉是必不可少的。我们将使用实验和数学相结合的方法来分析在正常细胞和组织中控制核因子-kappaB信号的集成系统。我们发现，核因子-kappaB携带信号信息的时间，其移动之间的细胞核和细胞质。这些运动的时机决定了哪些基因被激活。我们现在希望了解NFkappaB信号的这一关键过程是如何在正常生活中受到控制的。它是如何被细胞分裂周期控制的，以及它是如何被24小时生物钟的睡眠-觉醒周期控制的。最近，我们发现，在35到40摄氏度的生理和发热范围内，核因子-kappaB信号系统的振荡速度对温度非常敏感。这似乎也显著改变了哪些基因被开启或关闭的模式。到目前为止，我们的工作是在实验室培养的细胞系中进行的，现在我们希望研究从转基因小鼠中提取的正常细胞中的NF-kappaB信号，这些转基因小鼠已经荧光标记了NF-kappaB蛋白。我们将使用这些细胞来确定核因子-kappaB对温度的反应，包括糖皮质激素(通常用于炎症治疗)在内的一系列生理刺激，筛选小分子药物以找到调节反应的药物，并研究与细胞周期和生物钟的定量关系。这些实验和文献中发表的其他数据将被用来建立综合的数学模型，这些模型可以预测细胞、组织和动物生理学的重要方面，这些方面与理解健康有机体的维持以及这种情况可能如何随年龄变化有关。关键目标将是了解时钟和细胞周期如何共同影响核因子-kappaB信号的时间和水平，以及哪些目标基因被开启。核因子-kappaB家族中的一种，由NFkB1基因编码的p105，已被发现在该基因缺失时会导致小鼠更快的衰老(Mann和von Ziglicki，个人交流)。我们希望研究核因子-kappaB的动态变化是否与这种老化状态有关。因此，我们将为P105制作一个BAC记者，在蛋白质的两端都有荧光融合。我们是执行这项工作的理想团队，因为我们在细胞成像、图像分析、分子细胞生物学、生理学、基因组学、生物信息学和数学建模方面拥有互补的跨学科技能。该团队的一个核心部分在合作分析NF-kappaB信令系统方面有着良好的记录。此外，这个新项目引入了在动物生理学、生物钟和内分泌学方面具有相当专业知识的新团队成员。

As we get older our immune system tends to get weaker and it becomes increasingly difficult to shake off diseases. At the same time we tend to develop arthritis and other auto-immune diseases which are localised instances of uncontrolled inflammation. In this grant application our multidisciplinary team of scientists consisting of physiologists, biologists, mathematicians and computer scientists aim to look at a very important signalling system NF-kappaB. This system plays an important role in stress and the immune responses and determines the fate of cells in the body, which is essential for general health and wellbeing. We will use a combined experimental and mathematical approach to analyse integrated systems that control NF-kappaB signalling in normal cells and tissues. We found that NF-kappaB carries signal information in the timing of its movements between the nucleus and cytoplasm. The timing of these movements determines which genes are switched on. We now wish to understand how this key process of NFkappaB signalling is controlled through normal life. How is it controlled by the cell division cycle, and how is it controlled by the sleep-wake cycle of the 24 h circadian clock.Recently, we have found that the speed of the oscillations in the NF-kappaB signalling system are very temperature sensitive in the physiological and fever range between 35 and 40 degrees C. This also appears to markedly change the pattern of which genes are switched on or off. Our work so far has been in cell lines grown in the laboratory and we now wish to investigate NF-kappaB signalling in normal cells taken from transgenic mice that have fluorescently labelled NF-kappaB proteins. We will use these cells to determine the NF-kappaB response to temperature, a range of physiological stimuli including glucocorticoids (which are often used in inflammatory treatment), to screen small molecule drugs to find ones that modulate the response and to study the quantitative relationships with the cell cycle and the circadian clock. The data from these experiments and others published in the literature will be used to build integrated mathematical models that can predict important aspects of cell, tissue and animal physiology relevant to understanding the maintenance of a healthy organism and how this may change with age.Key aims will be to understand how the clock and cell cycle together affect the timing and level of NF-kappaB signalling and which target genes are switched on. One of the NF-kappaB family of proteins, p105 encoded by the NFkB1 gene, has been found to cause faster ageing in mice when this gene is missing (Mann and von Ziglnicki, personal communication). We wish to investigate whether changes in NF-kappaB dynamics are involved in this ageing condition. Therefore, we will make a BAC reporter for p105 with fluorescent fusions at either end of the protein.We are an ideal team to perform this work, because we have complementary interdisciplinary skills in cell imaging, image analysis, molecular cell biology, physiology, genomics, bioinformatics and mathematical modelling. A core part of the team has an excellent track record of working together to analyse the NF-kappaB signalling system. In addition, this new project brings in new team members with considerable expertise in animal physiology, circadian clocks and endocrinology.