QSB: Modeling Predictive Biological Networks in Halobacterium sp.

盐杆菌属（Halobacterium sp.）是一种嗜盐（嗜盐）生物体，在高盐度（海水盐度的10倍）的自然环境中生长，例如大盐湖、死海和太阳盐。 该QSB（定量系统生物技术）项目旨在评估DNA损伤应力对盐杆菌的影响。使用系统方法，由紫外线辐射，γ辐射，氧化损伤和化学诱变引起。 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。 同时分析所产生的大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。 这将最终导致复杂的生物过程工程的重要和安全的生物技术应用。更广泛的影响：这次合作汇集了两个领先的实验室，对同一个问题的研究有不同的观点-DNA修复。 这些研究将导致一名研究生在UMD和一名博士后研究员在ISB的培训。 UMD将受益于Baliga实验室开发的全球视角、新技术和软件，而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代码的，所有项目的数据都可以在ISB网站上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Baliga实验室最近加入了一个优秀的教育推广计划，该计划是一个由NSF资助的补充项目，旨在将系统生物学的新概念带入高中课堂。 该项目由分子和细胞生物科学部的分子生物化学计划以及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.