Biomathematics | IRBM Research Projects
Saber Elaydi, Director
One Trinity Place
San Antonio, TX 78212-7200
The main objective of this program is to engage students in research projects all year-round. There are seven faculty teams consisting of faculty from mathematics, biology, and engineering science, each with a specific research project. An additional team will join the group in year two and a seventh project will commence in year three. The IRBM program will present students with a broad range of projects spanning biological disciplines and mathematical tools. Students will also be encouraged to develop projects in their area of interest, allowing each to find a project that fits their talents. Below is a list of the research projects that are already available.
The Effect of Modulating Neuronal Membrane Composition on Toxicity of ß-Amyloid
Drs. James Roberts (Biology/Neuroscience), Kelvin Cheng (Physics and Astronomy), Farzan Aminian (Engineering)
ß-amyloid is a breakdown product of the ß-amyloid precursor protein ubiquitously expressed in neurons. It is toxic to neurons causing apoptotic death and is believed to be the basic event that results in the loss of neurons and subsequently the memory disorder of Alzheimer’s disease. The mathematical element of this project deals with a computational modeling of how the ß-amyloid protein aggregates with itself and then “melts” into the surface of the neuron, in essence causing a “hole” in the neuronal membrane which results in a loss of membrane potential and initiates apoptosis and cell death. Neuronal membranes have a complex composition with different phospholipids, glyco-sphingolipids and cholesterol. By culturing the neurons in different media or treating them with different reagents, one can alter the membrane composition and possibly alter the interaction of the ß-amyloid with the membrane and alter its toxicity. The student will model the interactions and make predictions as to how the modification w ll affect neuronal toxicity. Then the student will test the predictions in the laboratory using cultured neurons and fluorescent based cell viability assays.
Modeling special distributions of mammals
Drs. David Ribble (Biology), Saber Elaydi (Mathematics) and Roberto Hasfura (Mathematics)
As global temperatures change, species distributions typically respond by shifting accordingly and many dire predictions have been made for biodiversity based on these shifts. In this project, we will study and analyze the changes that in distributions of small mammals in Bexar and surrounding counties over the past 100 years and model the distribution changes that could accompany global climate change.
Modeling competition as a determinant of invasion success
Drs. Kelly Lyons (Biology), and Eddy Kwessi (Mathematics)
To improve degraded rangelands, non-indigenous, invasive grasses have been introduced into an immeasurable area of grassland throughout the United States and have had detrimental effects on native species and ecosystem functioning. In this project, we will test and develop mathematical models of species competition to determine whether reintroduction of native species with resource use that overlaps with a focal invader is more effective in controlling the invader than reintroduction of native species with resource use that does not overlap with a focal invader.
Homology detection in large DNA sequence datasets
Drs. Kevin Livingstone (Biology) and Peter Olofsson (Mathematics)
As DNA sequence data available to researchers grows exponentially, there comes an increased need for tools that allow us to create datasets that can be used to answer research questions. One meaningful way to organize sequence data is into groups of orthologous genes. The project will develop and refine a network/graphic presentation program that allows for the creation of a scalable database of the relationships between genes that is visual, quantitative, and easily manipulated.
Modeling the heat shock response of barley aleurone layers
Drs. Mark Brodl (Biology) and Natasa Macura (Mathematics)
Heat-shocked barley aleurone layers exhibit the classic unfolded protein response (UPR) which is a universal response focused on helping the cell’s endoplasmic reticulum (ER) cope with an accumulation of proteins that are unable to attain functional conformations. The response includes targeted decay of mRNAs that encode the destabilized proteins, re-tailoring the ER membranes and synthesizing proteins responsible for eliminating misfolded proteins. We plan to model the dynamics of the heat shock-induced UPR using neural networks.
Chemostat propagation of mixed bacteriophage Lambda-Escherichia coli K12 populations as a model system of predator-prey co-evolution: populations to genes
Drs. Frank G. Healy (Biology) and Saber Elaydi (Mathematics)
Predator/prey interaction dynamics are an important problem in evolutionary and population biology. Despite their antagonistic relationship, predator/ prey populations coexist within shared spatiotemporal habitats. In this project, we will generate datasets using measurements of chemostats parameters and genetic analysis of individuals from cultures of Escherichia coli and the viral predator bacteriophage lambda and apply these data to test and validate our mathematical models.
Modeling energy use in lizards
Drs. Michele Johnson (Biology) and E. Cabral Balreira (Mathematics)
The goal of this project is to better understand energy consumption in lizards. We build mathematical models to explain how lizards budget energy for growth, maintenance, and defense against parasites. We will develop new models to expand on Kleiber’s Law, a general description of the relationship between animal mass and metabolism. Students involved in this project will participate in the capture and sampling of lizards in the field, quantification of lizard parasite loads in the laboratory, and/or development of the models using mathematical software programs.