Research & Scientists

Four Core CCSB Projects

CCSB projects are focused on the discovery of properties and mechanisms of biological systems that confer phenotypic robustness against stochastic noise, environmental challenges, and genetic variation. The systems represent different types and scales of biological organization and complexity.

Projects are unified through a shared approach involving systematic data collection, modeling and prediction, and hypothesis testing. Collaborating investigators work at the University of Chicago and Northwestern University.

The Center's Four Core Projects are:

4 Core Projects

Three CCSB Pilot Studies & Five Research Projects

Three CCSB Pilot Studies and Five Research Projects

Circos Plot linking CCSB investigators with institution, research project funding, and each other. UC: Maroon; NW: Purple. White connections link PI collaborations. Colored edges link projects to PIs.



Robust biological oscillators generated by interlocked transcriptional and posttranslational networks: A systems analysis

Organisms living on the surface of the Earth experience a regular 24-hour rhythm in their environment: the steady rotation of the planet turning day into night and back again. Accordingly, many behaviors are temporally scheduled throughout the day, including sleep, feeding and reproductive functions. Across diverse organisms, this organization is controlled by a circadian clock – an endogenous biological oscillator that cycles with a period close to 24 hours and that is synchronized to the external environment. We are interested in understanding the mechanistic origin of robustness in biological oscillators and its role in reproductive fitness using the simplest known model system that exhibits these properties—the circadian clock derived from the cyanobacterium S. elongatus. In this system, there are strong transcriptional feedback loops that generate rhythmic expression in core clock genes. However, this transcriptional network is not strictly required for rhythmic function. Indeed stable ~24-hour oscillations in protein phosphorylation can be reconstituted using the purified clock proteins, KaiA, KaiB and KaiC. This remarkable reconstitutable system offers enormous potential for uncovering the functional motifs that drive circadian behavior. It indicates that there is a posttranslational network crucial for driving the oscillator, but the features of this network that are important for the functional properties of the circadian clock and the importance of its integration with the transcriptional network are unknown. Here, we propose to combine mathematical modeling with the development of novel biophysical instrumentation to develop a comprehensive understanding of how the systems properties of circadian clocks arise from molecular components.


Probing the Molecular Mechanisms of the Robust EGF-Mediated Transcriptional Response in Cancer Cells

The purpose of this one-year career development proposal is to perform several proofof-concept experiments that demonstrate the feasibility in relating EGFR signaling networks (in terms of protein modification, and nuclear translocation) with dynamic changes in mRNA and miRNA expression. By leveraging information regarding cell signaling and transcription factor protein function we will can perform further targeted functional validation on those transcription factors that are important for mediating transcriptional response to EGF perturbation. When extended to all human transcription factors in the future (using a larger transcription factor antibody panel), we intend to model the protein modification data, the protein localization data, and the mRNA and miRNA expression data as covariates at each time point, and integrate all of the data types into a model that ascribes correlations that can be subseq


Transcriptional Regulatory Network Sensitivity, Stability and Robustness in Drosophila Circadian Clocks: Solving the Mystery of Temperature Compensation

Circadian clocks are remarkably timekeepers, displaying precise timing over a wide range of temperatures. Genetic analyses have revealed a multiple feedback loop network at the core of circadian pacemakers. Yet the function of these multiple feedback loops remains unclear. We propose that the multiplicity of loops is a requirement for robustness under natural environmental conditions, especially varying temperature. To test this model, we will systematically profile the expression of several clock components from each feedback loop under low and high temperature conditions. These results will provide the high resolution and comprehensive data required to develop quantitative models for circadian network function.


Transcriptional Robustness of Staphylococcus to Host and Environmental Stresses

Staphylococcus aureus, a bacterium that produces the highest mortality of any infectious disease in the United States, commonly causes bloodstream infection, pneumonia, skin and soft tissue infection, osteomyelitis, and septic arthritis. Despite high demand for novel bactericidal antibiotics, the limited number of available targets has put increasing pressure on drug company pipelines. We consider virulence suppression an important alternative to bactericidal antibiotic treatments. The goal of virulence suppression is to reduce pathogenic potential of bacterial species, rendering the pathogen harmless. Targeting virulence regulation for treating bacterial infection has been limited by our ignorance of the host and/or environmental signals that trigger bacterial virulence. A detailed understanding of the molecular mechanisms of virulence regulation in pathogens should present important new possibilities for mitigating our most virulent microbes. This research program was set up to understand the signals, mechanisms, and pathways of the virulence regulatory network in S. aureus.


Structure, and Physiological and Evolutionary Robustness of Stress Response Networks in Eukaryotes

This project investigates the structure as well as physiological and evolutionary robustness of the conserved heat-shock response in C. elegans and other species of nematodes. In addition to the heat-shock response, the group studies networks of genes involved in other environmental cues such as heavy metal, UV, nutrient deprivation, osmotic and oxidative stresses. These networks are expected to reveal previously unknown regulatory relationships, identify similarities and differences between networks responsive to different stressors, and uncover conserved and divergent elements of stress responses between distantly related eukaryotes. Finally, the group uses computational and functional comparisons of the cis-regulatory elements of stress response genes from distantly related species of eukaryotes to understand the basic principles of their transcriptional control as well as mechanisms that maintain sensitive and yet highly conserved patterns of gene expression over long periods of evolutionary time.


Dynamics of the Drosophila Segmentation Network, Decoding the Mechanistic Basis of Stability Under Stress and Evolution

This project combines a multi-level approach to investigate the functional basis for robustness in the Drosophila segmentation network genes. A comprehensive network model of transcription factors controlling the segmentation pathway in Drosophila embryogenesis is evaluated by combining genomics and evolutionary approaches. In addition, a mathematical modeling of pattern formation by key genes is used to gain a deeper understanding of mechanisms controlling the robustness of each step in the segmentation pattern formation process.


Drosophila Eye Differentiation: The Yan Network

One of the most well understood transcriptional regulatory networks that responds to cell-cell signaling is the "Yan" network that controls neuronal cell fate in the Drosophila eye. The goal of this core project is to incorporate single cell analysis with predictive mathematical modeling to determine how the Yan transcription factor network specifies distinct cell fates in the developing Drosophila eye. Importantly, the analysis will consider not only the structural scaffold of transcriptional hierarchies and protein-protein interactions on which the network is based, but will also incorporate the complex patterns of post-translational modifications which constitute an essential but poorly understand component of the networks.


Elucidation of Design Principles, Dynamics and Robustness of Gene Regulatory Networks Orchestrating Hematopoietic Cell Fates

Hematopoietic stem cells give rise to all of the mature blood cells in the body, including red blood cells, platelet producing megakaryocytes, macrophages, neutrophils, and B and T cells. The mechanisms by which stem cells undergo successive divisions with greater restriction to eventually give rise to a specific cell type are incompletely defined. Molecular biological analysis of cell type specific patterns of gene expression and gene targeting of transcription factors have enabled the elucidation of a large set of regulatory proteins which control the generation of one or more lineages of the hematopoietic system. These regulators define components of complex gene regulatory networks, which orchestrate cell fate specification, commitment and differentiation. However the architectures and developmental dynamics of these networks remain poorly defined. Elaborating the structure of signaling pathways and gene regulatory networks that control discrete mammalian differentiation states and understanding their robustness and dynamics requires extensive collaborations between experimentalists and theoreticians. This project will elucidate the complex hematopoietic stem cells regulatory networks that give rise to blood and immune cells and understand their dynamics and robustness at the systems level. Our collaboration will integrate a combination of approaches including microwestern arrays, in situ transcription factor activity monitoring, high-throughput analysis of cis-elements, and computational and mathematical modeling. This inter-disciplinary analysis is expected to yield generalizable design principles concerning the architectures, dynamics, and robust properties of hematopoietic developmental signaling and gene regulatory networks in normal and disease states. It may also facilitate the directed generation of specific blood cell types from stem cells for therapeutic purposes