Participating in the Oak Ridge Institute for Science and Education fellowship program. Developing skills to select and employ advanced bioinformatics approaches on recurring, emerging, and persistent (REP) strains identified for additional characterization including multi-drug resistant (MDR) Salmonella species associated with poultry, beef, and Mexican soft cheese. Engaging in a variety of CDC trainings in genomics, data science, and bioinformatics in addition to training to present at scientific conferences.

Participated in the pilot, three-year, postdoctoral program which seeks to address the increased demand for faculty members equipped to teach students computational skills that are applicable within a wide variety of disciplines. Audited computer science courses to learn both the fundamental and advanced concepts of computation and computational biology. Developed software to detect and map horizontal gene transfer events in an effort to better resolve phylogenomic relationships between microbes. Developed software to improve the taxonomic placement of newly isolated microbes based on modern sequence analyses. Collaborated with other postdocs and faculty from a diverse set of academic disciplines and personal backgrounds. Taught courses with an emphasis on computation in the biological sciences to undergraduates including an upper-level course of my own design.

Designed and implemented a new upper-level course for Math/Comp Bio majors. Prepared and delivered lectures on various topics at the intersection of both microbiology and computational biology. Developed course material including assignments and exams. Graded all course content.

One of two instructors for the course. Prepared and delivered lectures on the underlying principles of several algorithms as well as how to code them for several biological problems including global alignments, local alignments, BLAST, and maximum parsimony phylogenetic tree construction. Held regular office hours and helped develop course materials such as exams and homework assignments.

Instructor for two of the six sections in the course. Helped develop course materials, give lectures, and write/grade exams. Helped implement coding assignments into the course. Coordinated activities and learning goals with two other co-instructors. Held regular office hours each week.

Investigated the roles of putative genes involved in virulence and oxidative stress in Campylobacter concisus and Campylobacter jejuni using molecular genetics and biochemical techniques. Developed an improved transformation method for C. concisus. Constructed gene deletion mutants in C. concisus to investigate genes putatively involved in oxidative stress.

Helped write and grade assignments and exams for the course. Prepared and delivered a 50 minute lecture on bacterial conjugation and transformation. Coordinated activities with the other instructors and taught laboratory sections when necessary.

Investigated the taxonomic placement of 108 strains in the ecologically relevant clade, the roseobacter group. Used the EDGAR 2.0 server and custom Unix, Perl, and R scripts to analyze whole-genome sequence data to delineate the boundary of the bacterial genera and build maximum likelihood phylogenetic trees (Wirth and Whitman 2018). Developed the chemical synthesis of isotopically labeled dimethylsulfonio-propionate (DMSP) from elemental 34S and used 1H-NMR, 13C-NMR, and GC-MS to verify the product (Wirth and Whitman 2018). Investigated the metabolism of DMSP with isotopically labeled substrate in chemostat cultures. Isolated and derivatized amino acids from Ruegeria pomeroyi and Ruegeria lacuscaerulensis and analyzed isotope labeling profiles using GC-MS (Wirth, Wang, and Whitman, in prep). Investigated S-methyl-L-methionine degradation in Ruegeria pomeroyi. Used gene replacement for constructing R. pomeroyi strains to test putative functions of various gene products. Performed assays to characterize the enzyme kinetics of the observed reactions.

Prepared and delivered 25 minute lectures each week. Collaborated with the other instructors to create quizzes, practice problems, and test questions. Designed a new activity for the class and implemented an IRB-approved research project to assess the effectiveness this activity.

Prepared and delivered a 50 minute lecture on anaerobic metabolism and phototrophy. Designed a group activity for the class. Helped the instructor find and use Plicker, a free response system analogous to “clickers.” Helped create, apply, and grade course material.

Investigated the anaerobic biosynthesis of 5,6-dimethylbenzimidazole (DMB), the lower, axial ligand of coenzyme B12, in the model organisms Salmonella enterica serovar Typhimurium LT2, Geobacter lovleyi SZ, Pyrococcus furiosus COM1, Eubacterium limosum, and Rhodobacter sphaeroides 2.4.1. Identified a putative gene involved in cytokinin production that likely plays a role in the regulation of anaerobic DMB activation in S. enterica. Used genetic approaches such as phage transduction, transposon mutagenesis, site-specific mutagenesis, and “Wanner” gene deletions. Purified various proteins and assayed enzymatic activity in vitro. Sequenced whole genomes and used bioinformatics to aid in gene identification.

Cultured Methanosarcina isolates from the Columbia River estuary using anaerobic techniques. Developed a purification protocol for disaggregatase with the help of the William Metcalf group. Extracted DNA from the environmental isolates, and used PCR and gel electrophoresis to screen the DNA for specific genes. Prepared the genomic DNA for HiSeq library sequencing using Nextera-XT and Nextera-V2 kits. Used software like MacClade, Sequencher, Mauve, Velvet, Artemis, and CLCGenomics to analyze the draft genomes of Methanosarcina isolates. Measured methane produced with gas chromatography to determine the growth rates of environmental isolates (Youngblut, et al. 2015). Used Bash, Perl, R, SQLite3, and the command line to help investigate the CRISPRs present. Characterized the CRISPR-Cas systems, and identified two novel CRISPR variants. Identified a novel, putative provirus in a Methanosarcina isolate.