People

Dave Kennedy (PI)

Dave’s primary interest is in understanding the effects of disease ecology on pathogen evolution. Pathogen evolution can have important consequences in a variety of settings, including public health, food production, and wildlife conservation. Moreover, infectious diseases offer great opportunities to study evolution in biological systems, because both the ecological and evolutionary dynamics of disease occur on short timescales. In his research, Dave uses variation in host-pathogen systems to address fundamental questions about infectious disease dynamics and the evolution of infectious diseases. This leads him to ask: Why does pathogen resistance evolve more readily against one public health intervention than another? Why does one pathogen strain cause more harm to hosts than another? Why is a pathogen population diverse in one host, and clonal in another? His approach to studying these questions combines data collection and empirical approaches with mathematical modeling and quantitative approaches. His goal is to develop a deeper understanding of how host-pathogen ecology affects pathogen evolution, with the aim of improving pathogen management.

 

Amrita Bhattacharya (Postdoctoral scholar;  link to personal website)

Amrita is investigating why resistance to vaccines evolves less commonly among pathogens than resistance to antimicrobial drugs.  She is performing this work using experimental approaches in the nematode host C. elegans and  its natural viral pathogen, Orsay virus.  Vaccines are increasingly being recognized as an important tool in efforts to delay the crisis of antibiotic resistance.  Her work demonstrates an additional way in which vaccines may be useful in delaying the evolution of antibiotic resistance — by teaching us the features of interventions that delay the evolution of resistance.

Prior to joining the Kennedy lab, Amrita earned undergraduate and Masters degrees in India.  She moved to Bloomington, Indiana to pursue a Ph.D. in evolutionary biology at Indiana University with Dr. Farrah Bashey and Prof. Curt Lively to explore how the evolution of social interactions among pathogenic bacteria can affect disease and disease management strategies.  The bulk of her dissertation focused on the spiteful trait, bacteriocin production, in the natural insect-pathogen, Xenorhabdus spp. Additionally, she led projects investigating the genetic basis of disease resistance in a natural snail-host and trematode-parasite system. Besides her research, Amrita is passionate about traveling and hiking, and she occasionally paints. 

 

Clara Shaw (Postdoctoral scholar)

Clara is interested in determining the ecological and evolutionary factors that influence pathogen adaptation and spread in new hosts. In particular, she is working to identify the factors that govern pathogen host range and the factors that promote pathogen spillover between host species. She is conducting this work using experimental approaches in the nematode-virus system. Although this system is still being developed as a model for studying disease ecology and evolution, it has tremendous promise for answering fundamental questions that have so far been difficult to answer. She is thus simultaneously working to further develop the system as a model for experimental disease ecology, by developing assays to empirically quantify parameters of key importance to the dynamics of infectious disease, such as single-host assays to directly measure transmission rates from individual hosts. 

Before joining the Kennedy lab, Clara received her BA in biochemistry from Oberlin College, she taught high school biology and coached track and field in Meridian, Mississippi with the Mississippi Teachers Corps, and she earned her PhD from the University of Michigan in 2019. In her dissertation work, Clara studied the dynamics of bacterial and fungal parasites that can become epidemic in Daphnia populations in midwestern lakes. Her work focused on how the abiotic factors light and lake clarity impacted epidemic size and timing. In addition, she studied how the parasites moved between different host species within lake communities.

 

Aniruddha Deka (Postdoctoral scholar)

Aniruddha is interested in understanding the benefits and costs of using transmissible vaccines in animal populations. Transmissible or self-disseminating vaccines that can transmit between hosts can reduce disease burden in the wild population in a fast and cost-effective manner. However, they have substantial evolutionary risks, as they may evolve rapidly and revert to wild-type virulence or recombine with pathogen virus to become highly pathogenic thereby undermining the utility of vaccines. Through mathematical modeling and numerical analysis, he is trying to understand the key knowledge gaps of using a transmissible vaccin

Prior to joining the Kennedy lab, Aniruddha earned his Ph.D. in mathematical biology at Shiv Nadar University, India with Dr. Samit Bhattacharyya. The aim of his thesis was to study the complex non-linear interactions between human vaccinating behavior and disease dynamics, and how to optimally design management of public perceptions including budget allocations during a disease outbreak. His work focused on social learning and human choice with respect to vaccination strategies under different perceived risks of vaccine and disease prevalence. Incorporating these social interactions on vaccination, he tried to optimize the allocation of a limited budget for control and prevention of disease outbreak.

 

Beth Tuschhoff (Graduate student)

Beth is interested in evolutionary dynamics of pathogens and transmissible vaccines and enjoys modeling infectious diseases and vaccination campaigns in general. She is currently working on a project to quantify heterogeneity in a population’s susceptibility to an emerging pathogen to better predict final epidemic size in conjunction with R0. She is conducting this work using a mixture of mathematical modeling and data collection techniques.

Before joining the Kennedy lab,  Beth earned a B.S. in mathematical biology with a minor in computer science from the University of Idaho. At the University of Idaho, she investigated the optimization of recombinant transmissible vaccine design as a balance between transmission, efficacy, and evolutionary stability. She also worked on projects to determine the effectiveness of swamping to prevent unwanted evolution in transmissible vaccines and to develop the coalescent structure of a neutral Wright-Fisher model with replication-dependent and replication-independent mutations. Outside of research, Beth enjoys swimming and playing piano.

 

Anton Aluquin (Undergraduate student)

Anton is a current sophomore in the Schreyer Honors College majoring in Health Policy and Administration and Immunology and Infectious Diseases. His current research interests include infectious disease, public health, health policy, and antibiotic resistance and its mechanisms. He is currently working on a project in the lab investigating antibiotic resistance patterns across drug classes. Besides his work in the lab, Anton is passionate about swimming, acting, and singing and is a part of the show choir The Singing Lions on campus.

 

 

 

Shannon Sager (Undergraduate student) — Picture and interests forthcoming.