Biomedical Engineering Group

The Biomedical Engineering Group at Villanova focuses on developing new mathematical modeling and systems analysis techniques for biological systems. The developed theoretical methods will be applied not only to medical applications, but also to the development of biofuel technology. The medical side of the research conducted at the lab is centered around investigating strategies to manipulate metabolism of disease-associated pathogens in biofilms. The biofuel research conducted at the lab deals with engineering microorganisms to produce biofuels such as higher alcohols and hydrogen.

A more in-depth explanation of Systems Biology is below.

A Brief Introduction to Systems Biology
 

Three Types of Cellular Networks

In biological systems, cellular networks can be categorized into the following three groups: signal transduction pathways, metabolic networks, and gene regulatory networks. This classification is based on the different hierarchical and organizational levels of networks. Specifically, signal transduction pathways mainly deal with how the extracellular stimulus is conveyed from the membrane of the cell into the cell nucleus for target gene expression through sequential biochemical reactions. Metabolic networks specify conversions between small biochemical molecules (e.g., metabolites) to produce biomass and energy that are critical for the cell growth, whereas gene regulatory networks govern expression of genes on the basis of the interaction between proteins and DNA.

 

Three Types of Cellular Networks

How Microorganisms Grow

Although the three types of networks have different components and biological functions, they couple with each other to maintain the functions and metabolism of the cell. Signal transduction pathways activate specific proteins in response to extracellular signals (e.g. available nutrients or extracellular stimuli like stress), some of which are transcription factors that can trigger the synthesis of other functional proteins. Some of these proteins are metabolic enzymes that catalyze specific metabolic reactions to convert nutrients into energy and biomass. All of these processes can affect the growth of microorganisms.

 

How Microorganisms Grow

 

The growth of microorganisms is regulated by signal transduction pathways, gene regulatory networks, and metabolic networks. Transcription factors are activated via signal transduction pathways and they in turn regulate genes that interact with other genes via gene regulatory networks. This results in the activation of metabolic enzymes that catalyze metabolic reactions, which convert nutrients into energy and biomass for the growth of microorganisms.

 

Why Systems-Biology Matters

Biological reaction networks consist of hundreds of highly-interacted components. It is the interactions between these components that determine the function and behavior of a biological system. Systems Biology is a research field that takes a systems-level approach to characterize the interactions between molecules involved in a biological system and thus investigate strategies for manipulating the behavior of that system. It lies at the intersection of Chemical Engineering, Computer Science, Biomedical Engineering, Physics, and Biology, and has recently generated significant interest. Specifically, mathematical models are developed and thus validated by experimental data, which can then be used as an in-silico platform for predicting the behavior of the system. Based on the developed models, systems analysis techniques are used to investigate interactions of components in the system and determine the components/reactions that play an important role in determining the response of the biological system to specific stimuli. This information can be used for drug development, for experiment design, and for control strategy development.