Summer Research Projects

Marine and Freshwater Ciliates in Alabama

  • Project semester: Summer 2011
  • Student Researcher: Kelsey Caffey, Class of 2012
  • Faculty Mentor: Dr. David JohnsonBiological and Environmental Science

Project Description

For my Clark Scholars summer research, I am working with biology professor, Dr. David Johnson, to analyze and characterize both marine and freshwater ciliates. Ciliates have not been widely characterized in the state of Alabama, thus our first project focuses on identifying and looking at the relative biodiversity among ciliates from Shades Creek, located across the street from Samford University. This project is very exciting for us because on our first day in the lab we found a potential new species of ciliate. For this project, I used bioinformatics techniques to generate phylogenetic trees that relate the species and coauthored an article, A Molecular Survey Of Ciliates Found In Shades Creek, Jefferson County, Al: Sampling Strategies, which has been submitted to the journal of the Alabama Academy of Science for publication.

The second project we are working on came about through a British Petroleum grant that Dr. Johnson received to study ciliates from the Gulf Oil Spill. Samples have been taken from oil-contaminated beaches and uncontained beaches at Dauphin Island. Once we receive the sequence data, we will identify the ciliates to determine if there are unique populations in each area. We are interested to see what types of ciliates inhabit the contaminated areas because they feed off of
bacteria, and we know that some bacteria have evolved to metabolize oil. We want to know what type of effect these oil-metabolizing bacteria might have on the ciliate population.

Defining, mapping, and visualizing the health of a community

Project Description

Josh Moore Conference

What is Community Health? How can the health of a community be defined, assessed, mapped, and visualized using the social media and Geographic Information System (GIS) tools available today? This project involved the construction of tools that allow community leaders, politicians, and outside philanthropic interests to effect positive community transformation through the accurate visualization of community health statistics and mobilization of resources. Our approach has been the development of three websites for visualizing statistics (, mobilizing volunteers (, and managing the allocation of resources ( Finally, perhaps our most significant accomplishment to date is the establishment of a solid collaboration of like-minded individuals and organizations in Central Alabama, who have contributed time, money, and ideas for this ongoing project.

Josh presented this project at the Fall, 2010 ACM Mid-Southeast Chapter Conference in Gatlinburg, TN. This project also grew  into a paper with Dr. Toone ("Building a Community Mapping and Resource Mobilization Framework") and presentation at the ACM Southeast Conference in Kennesaw, GA in March, 2011.

Supporting Documents

Exploration of PTEN-deficient Cell Sensitization to Poly (ADP-ribose) polymerase (PARP) inhibition via RNAi Screening

  • Project semester: Summer 2011
  • Student Researcher: Ashley Spann, Class of 2011
  • Faculty Mentors: Michele Cleary, Merck Research Laboratories, Department of Automated Biotechnology; Matthew Tudor, Merck Research Laboratories, Department of Automated Biotechnology

Project Description

I focused my undergraduate research around the field of cancer treatment and cell signaling. In 2009, I performed research at Vanderbilt University observing bioavailable compounds as inhibitors of the WNT pathway.  In 2010, I was an undergraduate research fellow at Merck in the prestigious and highly competitive UNCF-Merck Undergraduate Science Research program. Only 15 of these research scholarships were awarded, nationwide.  

My research at Merck investigated the use of Poly (ADP-ribose) polymerase (PARP) inhibitors to induce synthetic lethality in tumor cells.  The ultimate objective was to take a multicomponent therapeutic approach of genomic screening using the Merck compound library to identify possible drug combinations would disable cancer cells.  Currently, I am a research intern under the Cancer Research Experiences for Students (CaRES) Program at UAB where I am working with various small molecule inhibitors of Gli-mediated transcription in the Sonic Hedgehog Pathway as potential compounds for use against breast cancer.  All of my research experiences were exciting and very rewarding for me, and I hope to continue my investigation of cancer and potential treatments as I complete medical school at UAB.

Supporting Documents

Evolution of Neural Architectures

Project Description

This project explores the evolution of neural circuitry. In particular, we seek to obtain a better understanding of the evolutionary constraints that could lead to the development of certain cognitive capabilities while excluding others. Our studies are done via simulation where genomes representing neural architectures and belonging to a population of simulated entities are manipulated via genetic algorithm in which selection is performed on the phenotypic  neural networks encoded by the genomes. One of the major challenges of this work is to identify and specify an appropriate set of selection pressures and pre-existing building blocks that could conceivably give rise to any particular cognitive capability. In simulations this inevitably requires significant abstraction but it is precisely that which, we believe, may make it possible to identify and focus on the major factors guiding selection. Initial simulation has focused on evolving oscillatory circuits potentially capable of enabling motion in primitive organisms.

Jon presented the initial steps in this project at the Fall, 2010 ACM Mid-Southeast Chapter Conference in Gatlinburg, TN where he received 3rd place for his presentation. Chris will be presenting results of evolving oscillatory control circuits during the 2011-2012 academic year.