Collaborative Research: MODULUS: A Novel Spatiotemporal Multifractal Analysis to Evaluate Genome Dynamics

合作研究：MODULUS：一种评估基因组动力学的新型时空多重分形分析

• 批准号: 1936800
• 负责人: David Cook
• 金额: $ 54.8万
• 依托单位: Kansas State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-15 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1936800&HistoricalAwards=false
• 关键词: Collaborative; Research; MODULUS; Novel; Spatiotemporal

Currently there remains an incomplete understanding of how genomic information translates into organismal phenotypes, how environmental signals alter the flow of molecular information, and how biology's hierarchical organization of genomic information impacts information processing and genome dynamics over short and long-periods of time. This project integrates biological and mathematical methods to model and investigate mechanisms through which genomic information responds to change across multiple scales. Using statistical-physics and analytical methods typically applied to characterizing fractal-properties of non-biological systems, investigators explore the complex interdependency between chromosome organization, genome activity and genome evolution. Results of the work will further understanding of the genome-to-phenome relationship and spatiotemporal cross-dependencies governing the fungal genomic architecture. Through an immersive laboratory exchange program students participating in the project will receive a unique interdisciplinary training experience at the intersection of biology and mathematics. Investigators will also engage various cohorts of learners through the University of Southern California's Viterbi Summer Undergraduate Research Experience (SURE) and Kansas State University's Girls Researching Our World (GROW) programs. There is a great need to decode the complex interdependency between chromosome organization, genome activity and genome evolution and understand the genome-to-phenome relationships modulated by biological processes that span multiple spatial and temporal scales. The interdisciplinary team of investigators will use multi-fractal analysis, statistical physics and differential geometry to model and identify causal links in information processing across high-dimensional data describing chromatin dynamics. Key research objectives of the project include: 1) Development of a mathematical framework that integrates multidimensional genomic information in order to quantify the multi-scale nature of genome structure and predict the phenomenological consequences associated with temporally and environmentally driven genomic modulation; 2) Determination of the information processing machinery and multi-scale characterization of the flow of genetic information in concordance to changes in genome organization and environmental stress; 3) Using the mathematical framework developed, investigate whether DNA changes are purely random or if and to what extent physical, chemical and environmental stressors inform the formation of genomic regions of high evolvability. Outcomes of this project will provide insight into broader organizational principles of fungal and eukaryotic genomes. This award was co-funded by Systems and Synthetic Biology in the Division of Molecular and Cellular Biosciences and the Mathematical Biology Program of the Division of Mathematical Sciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

目前，对于基因组信息如何转化为生物体表型，环境信号如何改变分子信息的流动，以及生物学对基因组信息的分层组织如何在短期和长期内影响信息处理和基因组动态，仍然存在不完全的理解。该项目整合了生物学和数学方法来建模和研究基因组信息响应多尺度变化的机制。使用通常应用于表征非生物系统分形特性的物理学和分析方法，研究人员探索染色体组织，基因组活性和基因组进化之间复杂的相互依赖性。 研究结果将有助于进一步理解真菌基因组结构的基因组-表型关系和时空交叉依赖性。 通过沉浸式实验室交流计划，参与该项目的学生将在生物学和数学的交叉点获得独特的跨学科培训体验。 调查人员还将通过南加州大学的维特比夏季本科生研究经验（SURE）和堪萨斯州立大学的女孩研究我们的世界（GROW）计划吸引各种学习者。 有一个伟大的需要解码染色体组织，基因组活动和基因组进化之间的复杂的相互依赖性，并了解跨越多个空间和时间尺度的生物过程调制的基因组-表型组的关系。跨学科的研究团队将使用多重分形分析，统计物理和微分几何来建模和识别描述染色质动态的高维数据信息处理中的因果联系。该项目的主要研究目标包括：1）开发一个整合多维基因组信息的数学框架，以量化基因组结构的多尺度性质，并预测与时间和环境驱动的基因组调控相关的现象学后果; 2）确定信息处理机器和多个根据基因组组织和环境压力的变化，对遗传信息流进行规模表征; 3）使用开发的数学框架，调查DNA变化是否纯粹是随机的，或者是否以及在多大程度上是物理的，化学和环境应激源告知高度进化性的基因组区域的形成。 该项目的成果将提供深入了解真菌和真核生物基因组的更广泛的组织原则。该奖项由分子与细胞生物科学部的系统与合成生物学和数学科学部的数学生物学项目共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Dynamic Genomes - Mechanisms and consequences of genomic diversity impacting plant-fungal interactions

• DOI: 10.1016/j.pmpp.2023.102006
• 发表时间: 2023-03
• 期刊: Physiological and Molecular Plant Pathology
• 影响因子: 2.7
• 作者: Jun Huang;Sanzhen Liu;D. Cook

Controlling the Multifractal Generating Measures of Complex Networks

• DOI: 10.1038/s41598-020-62380-6
• 发表时间: 2020-03
• 期刊: Scientific Reports
• 影响因子: 4.6
• 作者: Ruochen Yang;P. Bogdan

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium

• DOI: 10.1128/mbio.01714-20
• 发表时间: 2020-09-01
• 期刊: MBIO
• 影响因子: 6.4
• 作者: Seidl, Michael F.;Kramer, H. Martin;Thomma, Bart P. H. J.
• 通讯作者: Thomma, Bart P. H. J.