Professor Charles F. Aquadro ("Chip")
My primary interests are in molecular population genetics, molecular evolution, and comparative genomics. Our current research focuses on the molecular population genetics and evolution of genes that regulate Drosophila germline stem cell (GSC) maintenance and differentiation. Our goal is to understand the types of natural selection shaping variation within and between species that is observed in GSC genes, to understand the functional consequences of this variation and diversification, and to test hypotheses as to the evolutionary forces driving the strong positive selection for protein diversification that we have observed at the key “switch” genes bag of marbles (bam) and benign gonial cell neoplasm (bgcn). Of particular interest are the roles that bacterial endosymbionts (e.g., Wolbachia) and other germline “parasites” (including transposable elements and viruses) play in driving the rapid evolution of these and other GSC genes. As part of this work, we are also continuing our computational analyses of the evolutionary rate covariation (“ERC”) statistics developed with Nathan Clark when he was a postdoc in our group (he is now on the faculty at the University of Pittsburg School of Medicine). Current work includes an extensive reanalysis of evolutionary rate correlations of all orthologous protein coding loci across 20 species of Drosophila. I also have a productive and enjoyable collaboration with my colleague Eric Alani analyzing the mutational and population genetic consequences of variants in mismatch repair genes in the yeast Saccharomyces cerevisiae.
Faculty web page including recent publication list: https://mbg.cornell.edu/people/charles-aquadro
Jaclyn E. “Jackie” Bubnell
I am interested in understanding the functional consequences of evolution in Drosophila using population genetic and functional approaches. Our lab and others have identified a set of germline stem cell genes that have been undergoing rapid, adaptive evolution in the sister species Drosophila melanogaster and Drosophila simulans. In D. melanogaster, these genes play key roles in the maintenance and differentiation of the germline, but their functions have not been defined in other Drosophila species. Have these genes been rapidly evolving due to changes in germline function, or is there an evolutionary conflict resulting in an “arms race,” thereby driving sequence diversification?
I’m currently working to functionally characterize these genes in D. simulans and other divergent Drosophila species to determine if core germline function has diverged. I plan to define both the expression patterns of these genes as well as protein function. I’m also exploring the possibility that the maternally inherited germline parasite Wolbachia pipientis has introduced an evolutionary conflict with the host germline and is thereby driving the positive selection of a subset of the rapidly evolving germline stem cell genes, especially bag of marbles which our lab has shown to be genetically interacting with Wolbachia.
- Choi, J.Y., J.E. Bubnell, and C.F. Aquadro. 2015. Population genomic analysis of the infectious and integrated Wolbachia pipientis genomes in Drosophila ananassae. Genome Biology and Evolution 7(8):236-82.
- Flores, H.A.F., J.E. Bubnell, C.F. Aquadro, and D.A. Barbash. 2015. The Drosophila bag of marbles gene interacts genetically with Wolbachia and shows female-specific effects of divergence. PLoS_Genetics 11(8):e1005453.
- Jamet S, Bubnell J, Pfister P, Tomoiaga D, Rogers ME, Feinstein P (2015) In Vitro Mutational Analysis of the β2 Adrenergic Receptor, an In Vivo Surrogate Odorant Receptor. PLoS ONE 10(10): e0141696.
- Bubnell J, Jamet S, Tomoiaga D, D’Hulst C, Krampis K, Feinstein P (2015) In Vitro Mutational and Bioinformatics Analysis of the M71 Odorant Receptor and Its Superfamily. PLoS ONE 10(10): e0141712.
- Bubnell J, Pfister P, Sapar ML, Rogers ME, Feinstein P. 2013. β2 Adrenergic Receptor Fluorescent Protein Fusions Traffic to the Plasma Membrane and Retain Functionality. PLoS ONE 8(9): e74941.
I am exploring the evolutionary and functional relationship between Drosophila and the endosymbiont bacteria Wolbachia. My main project focuses on searching for evidence of historic Wolbachia infections in Drosophila. Recent Wolbachia infections have been well documented, with Wolbachia presence reported in both reproductive and somatic tissues of Drosophila, as well as a myriad other arthropods and nematodes. Additionally, entire Wolbachia genomes or segments of them have been found integrated into Drosophila genomes. These Wolbachia insertions are often intact and easily recognizable, suggesting a more recent infection of Wolbachia in the population. On the other hand, evidence of historic infections remains unexplored. By employing a k-mer sequence matching program found useful to detect evidence of past viral and transposable element infections in mammals, I am testing for evidence of older Wolbachia insertions to help shed light on various questions, such as, have multiple Wolbachia strains infected the same lineage of Drosophila? And what is the earliest Wolbachia infection that we can detect? With answers to questions such as these, we can better understand the manipulative properties of Wolbachia as a parasite, specifically its interaction with the rapidly evolving bag of marbles germline stem cell gene.
Kristen Rose Baxter
Undergrad Research Student
I’m an undergraduate working closely alongside Chip and Jackie to assist with their research. At Cornell, I’m studying Biology with a concentration in Genetics, Genomics, and Development. When I’m not in the lab, you can probably find me at Schoellkopf Stadium or Lynah Rink playing with the Big Red Marching Band and Big Red Pep Band.
Undergrad Research Student
I have designed and created constructs that contain a hypomorphic mutation in the bam gene of Drosophila simulans. The overall goal was to use CRSPR/cas9 to insert a sequence including the hypomorphic mutation, 3xp3 promoter, and dsRED marker between two pBac transposons into the bam gene in D. simulans. The next step after injection is to screen for mutants with the DsRed marker and backcross those flies to a pBac transposase line to remove the marker. This will create D. simulans bam hypomorphs whose phenotypes can be assessed. I am a Biology major concentrating in Molecular and Cell Biology, am on the club tennis and soccer teams, as well as a member of Step Up, and am a CALS tutor and a Biology Student Advisor. For fun, I like to explore Ithaca, especially its gorges and farmer’s market.