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A Comparison of Traditional and Next Generation DNA Sequencing Approaches to Characterize Avian Malarial Parasite Infections

Project: 13
Name: Jason Weckstein, PhD | jdw342@drexel.edu
Department: Biodiversity, Earth, and Environmental Sciences and Academy of Natural Sciences of Drexel University, Ornithology Department

Description

Parasites are known to influence the behavior, ecology and evolution of their avian hosts and many studies of avian parasites have aimed to assess the effects of parasite infection prevalence and intensity on these aspects of host biology. In particular, avian malarial parasites and their relatives, in the genera Leucocytozoon, Haemoproteus and Plasmodium, have been studied for two centuries and have served as models for testing hypotheses about disease and parasite ecology and evolution. Since the development of a standard molecular genetic assay using nested PCR to screen avian blood samples for avian malarial parasites and their relatives, numerous studies have been published on these extremely diverse and widespread avian parasites. However, the Sanger DNA sequencing technology that has and continues to be used for this screening approach are not ideal for detecting and characterizing mixed infections of multiple malarial parasites in the same host individuals, which turns out to be relatively common in nature.

For this project, the student will test a modified approach to the nested PCR screening method that employs a combination of a recently developed quantitative PCR detection assay to assess whether birds are infected and then a next generation DNA sequencing approach to characterizing the infections and diversity of parasites in each host. The student will apply these new methods to a large sample of DNA extract from resident and migrant bird blood samples collected at Rushton Woods Preserve bird banding station in Newtown Square, Pennsylvania and will compare the results with a large dataset already generated by my lab using the traditional screening and DNA sequencing approach. This comparison will help us to assess whether the new methods will improve our ability to detect mixed infections, which will ultimately help us to better characterize the diversity and prevalence of these widespread parasites.

Gained Experience

The student will gain experience in both the wet lab and computation methods required for the collection and analysis of next generation DNA sequencing. The student will learn how to analyze malaria diversity data, and will conduct analyses of parasite intensity, prevalence and diversity.

Outcome

The ultimate goal of this project will be one or more peer reviewed publications.

Tasks

The student will be involved in all aspects of the project ranging from wet lab molecular genetics work, computer based processing of data, analysis of data, and ultimately development of a paper for submission to a peer reviewed journal.

Location

The work on this project will take place in the Laboratory of Molecular Systematics and Ecology in the Academy of Natural Sciences of Drexel University.

Possibility to Work Post Fellowship

Yes.