QSB: Modeling Predictive Biological Networks in Halobacterium sp.

盐杆菌属(Halbacterium sp.)是一种嗜盐(喜盐)生物，在高盐度(海水盐度的10倍)的自然环境中茁壮成长，如大盐湖、死海和太阳盐湖。该QSB(定量系统生物技术)项目旨在评估DNA损伤胁迫对盐生细菌的影响。由紫外线辐射、伽马辐射、氧化损伤和化学诱变造成的。在系统方法中，遗传和/或环境扰动的影响是在分子水平和全基因组范围内测量的。同时分析产生的大量数据集和不同的数据类型，以制定描述性和/或数学模型来描述整个生物体的行为。这最终将导致为重要和安全的生物技术应用设计复杂的生物过程。广泛的影响：这次合作将两个领先的实验室聚集在一起，在研究同一问题--DNA修复--方面具有不同的视角。这些研究将导致在UMD培训一名研究生和在ISB培训一名博士后研究员。虽然UMD将受益于全球视角、Brega实验室开发的新技术和软件，但ISB将受益于DiRuggiero实验室在DNA修复机制研究方面的专业知识。此外，ISB开发的所有软件都是开放源码的，所有项目的数据都可在ISB网站以及通过其他公共数据库免费获得。这项研究还将补充ISB正在进行的教育工作，因为Brega实验室最近加入了一个由NSF资助的补充性项目中的一个杰出的教育推广计划，将系统生物学的新概念带到高中课堂。该项目由分子和细胞生物科学部的分子生物化学计划和生物工程和环境系统部的生物技术计划共同资助。

Halobacterium sp. is a halophilic (salt loving) organism that thrives in naturally occurring environments of high salinity (10 times the salinity of sea water) such as the Great Salt Lake, the Dead Sea and solar salterns. This QSB (Quantitative Systems Biotechnology) project is designed to evaluate the effects of DNA damaging stress on Halobacterium sp. resulting from ultraviolet radiation, gamma radiation, oxidative damage and chemical mutagenesis using a systems approach. In a systems approach, the effects of genetic and/or environmental perturbations are measured at a molecular level and on a genome-wide scale. The resulting large data sets and diverse data types are analyzed simultaneously to formulate descriptive and/or mathematical models to describe the behavior of the whole organism. This will ultimately lead to engineering of complex biological processes for important and safe biotechnological applications.Broader impact: This collaboration brings together two leading laboratories with different perspectives regarding investigation of the same problem -DNA repair. These studies will result in training of one graduate student at UMD and one postdoctoral fellow at the ISB. Whereas UMD will benefit from global perspectives, new technologies and software developed in the Baliga laboratory, in return ISB will benefit from the DiRuggiero laboratory expertise in study of DNA repair mechanisms. Furthermore, all software developed at the ISB is open source and data from all projects is freely available on the ISB website as well as through other public databases. This study will also complement an ongoing education effort at ISB since the Baliga laboratory has recently joined an outstanding educational outreach program in a complementary NSF-funded project to bring new concepts of systems biology to high school classrooms. This project is co-funded by the Molecular Biochemistry Program in the Division of Molecular and Cellular Biosciences and by the Biotechnology Program in the Bioengineering and Environmental Systems Division.