2009
COLLABORATORS
Past and present extramural collaborators include:
Dr. Rachel Karchin (JHU)
Dr. Brandt Eichman (Vanderbilt) for our genetic adaptation studies
Dr. Miriam Barlow (UC Merced)
Dr. Rocha-Gracia (Universidad Benemérita de Puebla) for our genomics studies with clinical strains of E. coli
Dr. Luís Mota-Bravo (UC Irvine) for studies of conjugation
Dr. Diego Montenegro (Chilloa Foundation, Colombia)
ALUMNI
Technicians/ Researchers
Julia Morocco: oxidative demethylase protection against methylating agent toxicity using complementation in E. coli as a model system
Melissa Standley: ColE1 origin of replication determinants of plasmid stability, fluorescence mutagenesis reporters, cefotaxime resistance landscape of TEM-1 β-lactamase
David Alexander: evolution of ALKBH2 mutants with altered substrate specificity, ColE1 origin of replication determinants of plasmid stability, protocols of Pol I-driven mutagenesis
Josh Lilly: review on mechanisms of plasmid replication, evolution of ALKBH2 mutants with altered substrate specificity
Jennifer Allen: fluorescence mutagenesis reporters, Pol I mutation footprinting of ColE1 plasmid replication, epistasis modelling using TEM-1 β-lactamase evolution of cefotaxime resistance as a model
Postdoctoral Researchers
Gerardo Cortés Cortés: conjugation detection; impact of conjugation on the genomic distribution of antibiotic resistance genes in E. coli; nanopore sequencing of plasmids
Ph. D. Students
Amanda Carbajal: evolutionary trajectories of fluoroquinolone resistance
Jay Kim: distribution of plasmid-borne antibiotics resistance genes in E. coli by multidimensional scaling; topoisomerase II gene evolutionary pathways; gene cargo in food vs. clinical plasmids; resistance landscape of TEM-1 β-lactamase under cefotaxime selection; epistasis modelling of HIV reverse transcriptase under selection with antiretrovirals; thermodynamics modelling of TEM-1 β-lactamase mutagenesis; ascribing mutation signatures found in HIV and cancer genomics; methods for genome-wide association analysis (GWAS) adapted to bacterial genomes; review on mechanisms of plasmid replication and replicon genomic structure. In addition, he developed and taught a bioinformatics class (Crown 89)
Cherie Musgrove: book chapter on methods for mutagenesis detection; footprint of HIV reverse transcriptase mutagenesis using an E. coli co fluorescence mutagenesis reporters, mplementation system. Transferred to Michael Stone’s lab.
Christopher Troll: tradeoff between DNA repair activity and cytotoxicity in N3mA DNA glycosylases; PoI mutation footprinting of ColE1 plasmid replication; characterization of impact of MGMT polymorphisms on O6mG repair; Role of ALKBH1 variants mutants in protection from alkylation DNA damage
Master’s Students
Giselle Quevedo: determinants of plasmid stability in the ColE1 plasmid origin of replication; review on plasmid genomic structure
Audrey Lyman: thermodynamics modelling of TEM-1 β-lactamase mutants
Anna Lepore: determinants of methyl- vs. etheno-adduct discrimination of the oxidative demethylase ALKBH2
Undergraduate Students
Listed individually are the undergraduate students that produced independent or semi-independent work. Authorship in accepted peer-reviewed articles are highlighted with an asterisk. Jay Kim played a major role in the recruitment and training of undergraduate students. Caison Warner and Christina Egami started as undergraduate students and continued their work as graduate students.
Neo Peng: recombineering in E. coli, evolution of fluoroquinolone resistance
Robert Misirian: HIV mutation signatures; evolution of HIV within individual patients
Shefali Qamar: Higher-order epistatic interactions in HIV reverse transcriptase. Recipient of the prestigious Grace Hooper fellowship for Women in computing; Spoke at ICBRA 2022 Berlin conference
*Vega Bugata: Review on mechanisms of plasmid replication and replicon genomic structure; Spoke at the ISPB 2021: Plasmids around the Globe conference
Belinda Zhen: Differential gene expression of Temozolomide-resistant vs. sensitive tumor cell lines
Allan Stamm: Adaptation of ColE1 plasmid origin of replication to error-prone Pol I: effects on mutation sprectrum
Hannah Francis, Melissa Montejano Viveros, Effy Hernandez, and Philip Law: Adaptation of ColE1 plasmid origin of replication to error-prone Pol I: effects on plasmid copy number
Ethan Santos and Anne Courtney: Transfer of antibiotic resistance genes by conjugation
Lily Tran and Sarah Cligher: Topoisomerase II evolutionary pathways
Yuky Floyd and Lucy Guan: Cefotaxime resistance landscape of TEM-1 β-lactamase.
Baiwen Huang: HIV mutation signatures
Jimmy Chan: HIV mutation signatures (Senior Thesis); Recipient of a Koret award
Noah Dove: Ascribing mutation signatures found in cancer genomes; Hierarchical Research Systems Foundation research award; Presented at the BCATS conference at Stanford
Duncan McColl: Ascribing mutation signatures found in cancer genomes; Recipient of a Summer UR Award; Presented at Dynamic DNA and RNA Structures in DNA Damage Response & Cancer conference
Layla Cervantes: Continuous in vivo mutagenesis; RMI award recipient; Travel Scholarship to attend the SACNAS (Society for Advancement of Chicanos and Native Americans in Science) conference in Los Angeles; Undergraduate Research in the Sciences Award to attend the ERN (Emerging Researchers National) Conference in Washington DC
Cynthia Smith: Footprint of HIV reverse transcriptase mutagenesis using an E. coli complementation system; UC Leads and RMI award recipient
Ramsey Aweti: Expression, genomic and drug sensitivity profiling of oxidative demethylases in NCI60 cell lines (Senior Thesis)
Ileena Mitra: Directed evolution of N3mA DNA glycosylase; UC Leads Scholar
Jillian Romsdahl (Senior Thesis): Protocols of Pol I-driven mutagenesis
Holly Cagliero: Impact of ColE1 ori mutations on plasmid compatibility
Jaime Hernández: Evolution of ALKBH2 mutants with altered substrate specificity; ACCESS Summer Research Fellow; MARC student
Chelsey Stephenson: Fluorescence mutagenesis reporters
*Samuel Million-Weaver: ColE1 origin of replication determinants of plasmid and DNA damage
Other undergraduate students: Francim Aguilar, Sofiga Vijayan, David Winograd, Amy Moffett, Shadi Arjmand, Morgan Thompson, Tovia Bavly, Joel van de Sande, Mark Landon, Roxane Li, Torie Tsuei, Tina Hsu, Eric Espinosa, Jennifer Wen, Deirdra Angelucci, Joshua Sánchez, Joshua Sánchez, Amy Shipley, Cameron Wales, Ragunathan Seelam, Robert Petro, Julia Hernandez, Lauren Paule, Jacob Lugo, Keerthana Sivakumar