Genetic & Molecular Mechanisms


Developmental genetics of the vertebrate retina
(BEACON related)

Deborah Stenkamp Ph.D., Peter Fuerst Ph.D., Barrie Robison Ph.D., and Diana Mitchell Ph.D.

The Stenkamp lab studies how the specific neuronal and glial types of the vertebrate retina are generated and differentiated during development, and how they are regenerated after retinal damage. We use the zebrafish as our primary animal model, because teleost fish such as zebrafish develop as many as nine spectrally distinct types of retinal photoreceptors, and have the capacity for functional retinal regeneration. Our experiments involve developmental and genetic manipulations and the use of live and static imaging, and molecular analyses including RNA-seq. Our BEACON-related work includes a collaborative project with the Fuerst lab in which we investigate retinal structure and regenerative capacity in the gar, a fish that did not experience the genome-wide gene duplication event of teleosts and has a genome structure more similar to mammals. In addition, we are investigating the differential expression and evolution of tandemly-replicated visual pigment genes in teleost fish and primates. In many cases these tandem replications are very recent evolutionary events.


Evolution of flexibility for intrinsically disordered proteins

Gary Daughdrill Ph.D. and F. Marty Ytreberg Ph.D.

Intrinsically disordered proteins are highly dynamic, do not form compact structures, and their dysfunction is associated with many human diseases.  We hypothesize that the conformational flexibility of these proteins exerts selection pressure and determines the evolution of their specific binding mechanisms.  To test this hypothesis we are determining the conformational flexibility and binding mechanisms for homologous intrinsically disordered proteins using a combination of experiment and computer simulation.


Evolution of plasmid host range
(supported by NIH and NSF BEACON)

Eva Top Ph.D.

Since rapid plasmid-mediated spread of multi-drug resistance (MDR) to human pathogens is threatening our fight against infectious diseases, we need novel therapies aimed at limiting the spread of new resistance genes. However, we still do not understand if and how the host-range of a plasmid can expand, contract or shift over time. Our project aims at discerning patterns of plasmid host range evolution in bacteria through (i) experimental evolution studies followed by (ii) molecular and biochemical analysis of evolved plasmids, and (iii) mathematical and statistical modeling of the evolutionary processes in collaboration with J. Ponciano Ph.D. (University of Florida).


Plasmid persistence in biofilms
(supported by NIH and NSF BEACON)

Eva Top Ph.D. and Larry J. Forney Ph.D.

Most bacteria live in microcolonies or biofilms and rarely in completely mixed liquids. For example, infections of combat wounds are commonly caused by MDR bacteria that form biofilms. However, our understanding of bacterial evolution in real time comes mostly from laboratory studies with liquid cultures. We hypothesize that the evolutionary trajectories of MDR plasmids are different in biofilms than in well-mixed liquids due to the spatially structured environment of biofilms. To test this hypothesis we evolve bacteria-plasmid pairs in liquid cultures and biofilm flow cells, and compare the molecular mechanisms of plasmid-host coevolution.


Adaptive evolution of viruses 

Paul Joyce Ph.D., Holly Wichman Ph.D. and Craig Miller Ph.D.

With growing awareness of how pathogen adaptation impacts the battle against infectious disease, mathematical models of adaptation have become central to this fight. However, most of the theoretical work focuses on general patterns of adaptation, while the empirical work provides rich details specific to the pathogen under study. The long term goal of this research is to develop a flexible framework for predicting evolution that is rich enough to accommodate empirical data from organisms that evolve in real time.


Adaptive Evolution of Bacteriophage in a Spatial Context

Steve Krone Ph.D. and Celeste Brown Ph.D.

We are using a phage-bacteria system to explore the effects of spatial structure on adaptive evolution following a change in environmental conditions. We employ a combination of experimental evolution and mathematical modeling to determine the types of substitutions that are selected during adaptation and their ability to spread.


Genomic approaches to weediness and crop domestication: rapid evolution of vernalization and rosette structure in the genus Raphanus (radish)

Jeffrey K. Conner Ph.D., Ian Dworkin Ph.D.David Tank Ph.D. and James Foster Ph.D.

Wild radish, Raphanus raphanistrum, is one of the world’s worst weeds and is also an emerging model system in ecology and evolution. The loss of two overwintering traits, a vernalization requirement for flowering and the production of a rosette, were critical in the adaptation of native wild radish to farmer’s fields. These phenotypic differences are also paralleled in the two major groups of crop radish. This project seeks to uncover the genetic mechanisms underlying the evolution of these traits in weedy and crop radish using three complementary approaches – phylogeographic, population genetic, and quantitative trait loci (QTL) analyses to determine genomic regions affecting vernalization and rosette production. A molecular genetic understanding of the loss of overwintering phenotypes would provide fundamental insights into crop domestication, weed evolution, and life-history evolution in plants in general.


Behavioral Genomics:  The genetic basis of behavioral adaptation to captivity.  

Barrie Robison Ph.D. and Matt Singer Ph.D.

We are currently using the zebrafish as a model system to study the genetic basis of variation in anxiety, aggression, and feeding related behaviors.  We are particularly interested in how these behaviors evolve during the transition from a wild environment to a captive environment.  We employ comparative approaches using existing wild and laboratory strains of zebrafish, and are also developing selection lines that are divergent in their baseline levels of anxiety.  We use a variety of transcriptomic and genomic approaches to identify candidate genes and physiological pathways that may underlie the transition from a “wild” to a “tame” behavioral phenotype.


Physiological Genomics:  Embryonic stress and its long-term behavioral effects.  

Barrie Robison Ph.D., John Godwin Ph.D., and Gordon Murdoch Ph.D.

One of the pathways we have implicated in our behavioral genomic work is the stress axis.  We are currently testing the hypothesis that embryonic cortisol exposure has permanent transcriptional and behavioral effects in the zebrafish.  The zebrafish model is particularly well suited to this research, because its external development facilitates precise dosing and exposure.  To date, we have shown that chronic exposure to embryonic cortisol produces behavioral effects reminiscent of those observed in human studies.  We are now working to identify critical developmental windows and elucidate the mechanism of action. 


Nutritional Genomics:  The effects of Selenium supplementation on brain and behavior.  

Barrie Robison Ph.D., Maia Benner, Ron Hardy Ph.D., and Gordon Murdoch Ph.D.

Selenium is a micronutrient critical for the proper function of many biological systems.  There is currently controversy in the literature as to whether Selenium supplementation can be used to treat mood disorders such as depression and anxiety.  We have shown that this controversy may be caused by three variables that are rarely considered (until recently) in human trials:  sex, dose response, and genotype.  Interactions of these variables produce dramatically different behavioral responses in the zebrafish, highlighting the potential for personalized approaches in nutritional genomics.