Browsing by Author "Igoshin, Oleg A"

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    Design Principles of Cellular Differentiation Regulatory Networks
    (2015-12-01) Narula, Jatin; Igoshin, Oleg A; Tabor, Jeffrey J; Bennett, Matthew R
    To understand cellular differentiation programs is to understand the often large and complex gene regulatory networks (GRNs) that control and orchestrate these programs. The work presented here aims to exploit the wealth of newly available experimental information and methods to identify design principles that relate how GRN structures relate to the functional requirements in three model differentiation/stress-response programs: embryonic hematopoiesis, sporulation and σB general stress response. First we used a statistical thermodynamic approach to characterize the biophysical mechanisms of combinatorial regulation by distant enhancers in eukaryotes and demonstrate how the GRN controlling embryonic hematopoiesis acts as an irreversible bistable switch with low-pass noise filtering properties. We further used our model of the hematopoiesis network to reconcile discrepant experimental observations about the regulator Runx1 and explained how it limits HSC emergence in vitro. In the second project we investigated the Bacillus subtilis sporulation network and showed how a cascade of feed-forward loops downstream of the master regulatory Spo0A~P control cell-fate during starvation. We also identified a rate-responsive network module in the Spo0A regulon to explain why accelerated accumulation of Spo0A~P leads to a dramatic reduction in sporulation efficiency. Further we found that the arrangement of two sporulation network genes on opposite ends of the chromosome ties Spo0A~P activation to the DNA replication status. We were also able to show that the slowdown of cell growth is the primary starvation signal that determines sporulation cell-fates by controlling Spo0A~P activation. For the third project we built a detailed model of the σB network in Bacillus subtilis to mechanistically explain the experimentally observed pulsatile response of this network under stress. We further showed that the same network architecture that enables this pulsatile response insulates the σB network from the effects of competition for cellular resources like RNA polymerase. The design principles identified in the studies of these networks are related to their topological structure and function rather than the specific genes and proteins that comprise them. As a result, we expect them to be widely applicable to and help in the study of a diverse array of other differentiation GRNs.
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    Role of mechanical interactions in self-organization behaviors of Myxococcus xanthus bacteria
    (2017-03-14) Balagam, Rajesh; Igoshin, Oleg A
    Coordinated cell movement and intercellular interactions are crucial for bacterial multicellularity and self-organization, and the mechanisms governing these processes are of active scientific interest. Individual cells interact with neighbors through various biochemical and mechanical interactions, but the role of mechanical interactions in coordination and selforganization of bacteria remains unclear. This work investigates the mechanisms underlying various multicellular patterns in Myxococcus xanthus bacteria, a model organism to study self-organization in bacteria, and the role of mechanical interactions in these self-organization behaviors using biophysical models of cell motility in an agent-based-simulation framework. Using this framework, first I studied the mechanism of gliding cell motility in M. xanthus by discriminating motility behavior of biophysical model cells during physical cell collisions from two alternative cell motility models proposed in the literature. Comparing the model cell motility behavior with experimental cell collision behavior showed that gliding cell motility in M. xanthus requires strong cell-substrate interactions supporting one of the proposed models. New predictions from this model are independently verified in direct experimentation. Next, I investigated the mechanisms responsible for formation and alignment of M. xanthus cells in groups and their collective movement in circular and spiral patterns under starvation, by simulating intercellular interactions among a large number of model cells. Results from the simulations show that these collective cell behaviors in M. xanthus can be explained through mechanical and biochemical interactions among cells and with the substrate. Finally, I investigated the mechanism for non-monotonic colony expansion behavior observed in M. xanthus motility mutants using the agent-based-simulation framework and analyzed individual cell motility behavior from experiments under similar conditions. Results from this work provide evidence that cell-stalling, a crucial assumption made by previous models to explain non-monotonic colony expansion, does not occur due to physical interactions and is not observed in experimental M. xanthus swarms. Results from this thesis work show that many self-organization behaviors in M. xanthus can be explained by a combination of mechanical interactions among cells, between the cells and the substrate and contact based biochemical signaling. This work improves our understanding of mechanisms governing various self-organization behaviors displayed by M. xanthus bacteria and provides a general framework to study self-organization behaviors in other surface motile bacteria.
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    The physics of cell-fate choice
    (2022-07-26) Tripathi, Shubham; Levine, Herbert; Igoshin, Oleg A
    Multicellular organisms are composed of many different cell types. All such cells arise from a single cell--- the zygote--- and acquire the various cell fates seen in adult organisms. The different cell types are characterized by distinct, cell-fate-specific gene expression patterns. Cells of different types can also exhibit varying metabolic states depending on their intrinsic needs and the nutrient microenvironment. Both during development and in adult organisms, cell-fate choice is tightly controlled, and its dysregulation is known to contribute to many pathologies, including cancer. In this thesis, I describe our simulations-based efforts to identify certain general principles underlying cell-fate choice. Throughout, I discuss how such regulation can go awry in a disease like cancer, leading to the emergence of aberrant cell fates. First, I describe a spin glass-based theory of minimal frustration in regulatory networks implicated in cell-fate choice, and show that the minimal frustration property is key to the robust establishment and maintenance of biological cell-fates. The minimal frustration property is also crucial to the success of various systems biology models of cell-fate choice. Next, I present two models concerning noise in cell-fate choice--- a mechanical model of DNA supercoiling-mediated transcriptional noise and a coarse-grained model of noise in partitioning during cell division that can create and maintain a phenotypically heterogeneous population. Finally, I describe a mechanistic model of the key metabolic pathways active in tumors and other fast-proliferating cells. Our model recapitulates tumor cell behavior across contexts and makes useful predictions concerning the ways tumor cells can evade metabolic therapies. Overall, this thesis describes multiple examples of how physical and systems biology-based approaches can be leveraged to understand the key principles underlying cell-fate choice across biological contexts.