I am currently working in Dr. Nathaniel K. Jue’s functional bacterial genomics lab where we are investigating the genomes of pesticide remediating bacteria. I develop protocols for solubilizing pesticides, conduct large scale growth assays to phenotype the bacterial strains, sequence the 16s rRNA of our samples, construct genetic libraries, and am currently in the process of devising a transposon sequencing methodology. I am also studying the evolutionary history of hermaphroditism in Perciformes fish via transcriptomic analysis.
In the Corbett-Detig lab at the University of California, Santa Cruz, I am conducting phylogenetic and evolutionary analyses on metazoan orthologs of the highly conserved CTCF gene and investigating the evolution of CTCF binding site locations and motifs in primates.
EVOLUTIONARY ANALYSIS OF THE CTCF GENE
University of California, Santa Cruz | NIH Big Data to Knowledge Program | JUN-AUG 2020
Mentors: Dr. Russ Corbett-Detig and Jakob McBroome
CTCF, or CCCTC-binding factor, is a protein encoding gene that is highly conserved across metazoa. The CTCF protein is an eleven-zinc-finger protein that regulates transcription as a repressor and activator, functions as an enhancer-blocking insulator, and contributes to genomic organization by establishing and maintaining chromatin loops. While CTCF is a core regulatory gene that exercises crucial control over genome-wide transcriptional activity, its evolutionary history remains poorly understood. To elucidate the functional importance of evolutionarily conserved regions of the CTCF gene, we collected transcripts of CTCF orthologs from 65 bilaterian species with publicly accessible Hi-C sequencing data. We aligned the transcripts and generated a maximum likelihood phylogenetic tree based upon the alignment. The tree displayed four distinct clades of mammals, insects, fish, and aviators and reptiles. Within the alignment, we identified a range that consists of 932 nucleotide bases conserved across all species of analysis with frequent synonymous mutations in wobble base positions. We observed a 44-base deletion of otherwise conserved sequence specific to the insect clade. By constructing predicted protein structures, we determined that the deletion encodes the third C2H2 zinc finger protein domain in species in which the sequence is still present. These findings will be used to inform a study investigating nuclear spatial structural data for the species included in our analysis that will identify correlation between systematic changes in the spatial dataset with changes in our sequence alignment.
University of California, Santa Cruz | NIH Big Data to Knowledge Program | JUN-AUG 2020
Mentors: Dr. Russ Corbett-Detig and Jakob McBroome
CTCF, or CCCTC-binding factor, is a protein encoding gene that is highly conserved across metazoa. The CTCF protein is an eleven-zinc-finger protein that regulates transcription as a repressor and activator, functions as an enhancer-blocking insulator, and contributes to genomic organization by establishing and maintaining chromatin loops. While CTCF is a core regulatory gene that exercises crucial control over genome-wide transcriptional activity, its evolutionary history remains poorly understood. To elucidate the functional importance of evolutionarily conserved regions of the CTCF gene, we collected transcripts of CTCF orthologs from 65 bilaterian species with publicly accessible Hi-C sequencing data. We aligned the transcripts and generated a maximum likelihood phylogenetic tree based upon the alignment. The tree displayed four distinct clades of mammals, insects, fish, and aviators and reptiles. Within the alignment, we identified a range that consists of 932 nucleotide bases conserved across all species of analysis with frequent synonymous mutations in wobble base positions. We observed a 44-base deletion of otherwise conserved sequence specific to the insect clade. By constructing predicted protein structures, we determined that the deletion encodes the third C2H2 zinc finger protein domain in species in which the sequence is still present. These findings will be used to inform a study investigating nuclear spatial structural data for the species included in our analysis that will identify correlation between systematic changes in the spatial dataset with changes in our sequence alignment.
During the summer of 2019, I conducted research at the American Museum of Natural History under Dr. Mark Siddall. Using metagenomics, we acquired gene sequences from myxozoan parasites infecting fish found in three different aquatic ecosystems of the Amazon Rainforest. Bioinformatic techniques were applied to separate host from parasite reads, determine the identity of the myxozoans, compare the myxozoan diversity across the three habitats. I also identified the physiological location of antimicrobial peptide (AMPs) secretion in Dermatobia hominis larvae and characterized the AMPs through transcriptome sequencing and analysis. With Dr. Evon Hekkala, of the AMNH and Fordham University, I collected samples from archaic Crocodilian specimens and extracted their DNA for identification and potential reclassification.
METAGENOMIC ANALYSIS OF MYXOZOAN PARASITES FROM THE AMAZON RAINFOREST
American Museum of Natural History | MAY-AUG 2019
Mentors: Dr. Mark Siddall and Kalani Williams
Myxozoans are highly diverse, global, microscopic, obligate parasites that cause infections that can yield detrimental symptoms in many economically important fish species and some amphibian species. We isolated DNA from over 500 gill samples from fish found at the confluence of the Rio Amazona, the Rio Tapajós, and the Rio Arapiuns. Pooled isolates were subject to amplification of SSU rDNA both for myxozoan parasites and for ciliates. Ciliate sequences recovered were predominantly species in the genus Trichodina. Twenty-two of 44 pools revealed gill infections of 12 species of myxozoans (esp.species of Ellipsomyxa, Henneguya and Myxobolus) across all of the samples analyzed from all three rivers. There were 35 occurrences of myxozoan infections in samples from the Rio Tapajós, 12 in samples from the Rio Arapiuns, and 7 in samples from the Rio Amazona. Infections were more common in knifefish, catfish, cichlids, and characins. Tiger fish, piranhas, and anchovies were not infected regardless of location. Interestingly, species of fish found to be infected in the Tapajós were invariably uninfected in the less acidic Rio Arapiuns and Rio Amazona. Similarly, some species only amplified for myxozoans if the fish was from the Rio Amazona. Because the three rivers have drastically different water types, the presence or absence of parasites in the fish present can be used as an indication of water chemistry and of the ecological impact of invasive freshwater aquaculture.
American Museum of Natural History | MAY-AUG 2019
Mentors: Dr. Mark Siddall and Kalani Williams
Myxozoans are highly diverse, global, microscopic, obligate parasites that cause infections that can yield detrimental symptoms in many economically important fish species and some amphibian species. We isolated DNA from over 500 gill samples from fish found at the confluence of the Rio Amazona, the Rio Tapajós, and the Rio Arapiuns. Pooled isolates were subject to amplification of SSU rDNA both for myxozoan parasites and for ciliates. Ciliate sequences recovered were predominantly species in the genus Trichodina. Twenty-two of 44 pools revealed gill infections of 12 species of myxozoans (esp.species of Ellipsomyxa, Henneguya and Myxobolus) across all of the samples analyzed from all three rivers. There were 35 occurrences of myxozoan infections in samples from the Rio Tapajós, 12 in samples from the Rio Arapiuns, and 7 in samples from the Rio Amazona. Infections were more common in knifefish, catfish, cichlids, and characins. Tiger fish, piranhas, and anchovies were not infected regardless of location. Interestingly, species of fish found to be infected in the Tapajós were invariably uninfected in the less acidic Rio Arapiuns and Rio Amazona. Similarly, some species only amplified for myxozoans if the fish was from the Rio Amazona. Because the three rivers have drastically different water types, the presence or absence of parasites in the fish present can be used as an indication of water chemistry and of the ecological impact of invasive freshwater aquaculture.
Research InterestsMy personal research interests lie within the domain of archaeogenetics, specifically hominin evolution and omics.
Outside of academia, I have passions for music, literature, art, and nature. After graduate school, I plan to become a curator and principal investigator at a natural history museum. I will connect my research interests with my everyday interests in an anthropological context, working with cultural anthropologists to connect human evolution with the fundamental historical eras. Furthermore, I have adopted the personal mission of applying archaeogenetic findings to the betterment of the planet, as I am a strong believer that we, as stewards of the Earth, are obligated to leave our environment better than we found it. |