# positions[].organizations[].parent[].label
College of Agriculture and Life Sciences

# overview
Living systems make decisions by integrating information from their environments in order to optimize their own fitness. This decision-making process has many intricacies, with a dual nature characterized by stochasticity and determinism, and considerable effort has been dedicated to characterizing the factors contributing to cell-fate heterogeneity. Our primary goal is to determine how multiple environmental and genetic factors, some deterministic and some stochastic, impact developmental outcomes. We choose to study paradigms of cellular decision-making such as bacteriophage lambda lytic-lysogenic development to simplify the complicated nature of cell-fate selection. By distilling the study of a ubiquitous and vital process into basic questions, we hope to generate new insights into how decision-making affects cellular development and differentiation in higher organisms.

We utilize high-resolution live-cell fluorescence microscopy, single-molecule fluorescence microscopy, quantitative data analysis, and simple mathematical modeling to mechanistically dissect the decision-making processes at single-cell/molecule levels. Our favorite biological models are the lysis-lysogeny systems of bacteria and their viruses, like E. coli being infected by paradigm phages lambda and P1. By revisiting established systems with a new, technologically advanced perspective, we are able to reveal previously hidden complexities to better understand the nature of living cells.

# keywords[]
4012 Fluid Mechanics And Thermal Engineering

# keywords[]
4012 Fluid Mechanics And Thermal Engineering

# educationAndTraining[].organization.label
University of Illinois at Urbana Champaign - (Urbana, Illinois, United States)

# educationAndTraining[].field
Theoretical and Applied Mechanics, minor in Computer Science and Engineering

# educationAndTraining[].organization.label
University of Illinois at Urbana Champaign - (Urbana, Illinois, United States)

# publications[].label
Decision making at a subcellular level determines the outcome of bacteriophage infection.

# publications[].label
INTERACTION OF A FINITE-SIZED PARTICLE WITH WALL TURBULENCE

# publications[].label
Phage DNA dynamics in cells with different fates.

# publications[].label
Virus interactions: cooperation or competition?

# publications[].label
Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection.

# publications[].label
Contributions of F-specific subunits to the F plasmid-encoded type IV secretion system and F pilus.

# publications[].label
Type IV secretion systems: Advances in structure, function, and activation.

# publications[].label
Spatial propagation of temperate phages within and among biofilms.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Genomic and proteomic features of mycobacteriophage SWU1 isolated from China soil.

# publications[].label
Co-infecting phages impede each other's entry into the cell.

# publications[].label
Cell fate decisions emerge as phages cooperate or compete inside their host.

# publications[].label
Interactions of a stationary finite-sized particle with wall turbulence

# publications[].label
Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
ssRNA phage penetration triggers detachment of the F-pilus.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Following cell-fate in E. coli after infection by phage lambda.

# publications[].label
Following Cell-fate in E-coli After Infection by Phage Lambda

# publications[].label
Wall-induced forces on a rigid sphere at finite Reynolds number

# publications[].label
The Global Reciprocal Reprogramming between Mycobacteriophage SWU1 and Mycobacterium Reveals the Molecular Strategy of Subversion and Promotion of Phage Infection.

# publications[].label
Coupling of DNA Replication and Negative Feedback Controls Gene Expression for Cell-Fate Decisions.

# publications[].label
Late-Arriving Signals Contribute Less to Cell-Fate Decisions.

# publications[].label
New Insights into the Structure and Assembly of Bacteriophage P1.

# publications[].label
The role of side tail fibers during the infection cycle of phage lambda.

# publications[].label
Forces on a finite-sized particle located close to a wall in a linear shear flow

# publications[].label
Structural basis of Acinetobacter type IV pili targeting by an RNA virus.

# publications[].label
Wake response of a stationary finite-sized particle in a turbulent channel flow

# publications[].label
Single-virus tracking reveals a spatial receptor-dependent search mechanism.

# publications[].label
Visualization of phage DNA degradation by a type I CRISPR-Cas system at the single-cell level.

# publications[].label
Interactions between Viral Regulatory Proteins Ensure an MOI-Independent Probability of Lysogeny during Infection by Bacteriophage P1.

# publications[].label
Bacteriophage P1 does not show spatial preference when infecting Escherichia coli.

# publications[].label
Emerging heterogeneous compartments by viruses in single bacterial cells.

# publications[].label
Cells with Stochastically Increased Methyltransferase to Restriction Endonuclease Ratio Provide an Entry for Bacteriophage into Protected Cell Population

# publications[].label
BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site.

# publications[].label
High-resolution studies of lysis-lysogeny decision-making in bacteriophage lambda.

# publications[].label
From Bench to Keyboard and Back Again: A Brief History of Lambda Phage Modeling.

# publications[].label
Removal of Pseudomonas type IV pili by a small RNA virus.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# researcherOn[].label
Integration of Diverse Inputs Determines Developmental Outcomes

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].awardedBy.preferredLabel
DHHS-NIH-National Institute of General Medical Science

# researcherOn[].label
Role of Spatial Structure in Decision Making

# researcherOn[].awardedBy.label
Directorate for Biological Sciences - (Arlington, Virginia, United States)

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Molecular Mechanism for Genomic RNA Delivery in ssRNA Phages

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
Reducing Virulence Through the Suppression of Retractile Pili

# researcherOn[].awardedBy.label
National Institute of Allergy and Infectious Diseases - (Bethesda, Maryland, United States)

# streetAddress
Texas A&M University; Biochemistry & Biophysics; 2128 TAMU

# organizations[]
College of Agriculture and Life Sciences

# schools[]
College of Agriculture and Life Sciences

# inTheNews[].label
A New Lead For Disarming Antibiotic-Resistant Bacteria

# inTheNews[].label
New research lead disarms antibiotic resistance in bacteria

# etdChairOf[].label
Shao, Qiuyan (2017-12). Single-Cell and Single-Molecule Studies of Bacteriophage Lambda Post-Infection Decision-Making. Doctoral Dissertation.