Nanami Kubota

PhD student in the Cooper Lab at the University of Pittsburgh. Research on bacteria and phage coevolution.

EDUCATION
Ph.D. in Microbiology and Immunology
August 2020 – Present
University of Pittsburgh, School of Medicine, Program in Microbiology and Immunology
Advisor: Dr. Vaughn S. Cooper
B.A. in Biology
August 2016 – June 2020
Macaulay Honors College at Queens College, City University of New York (CUNY)
Advisor: Dr. John J. Dennehy (Queens College, CUNY)
Thesis: Mutations and Selection in Erwinia amylovora Phages Adapting to Host's Codon Usage Patterns
High School Diploma
September 2012 – June 2016
The Bronx High School of Science
Advisor: Dr. José D. Anadón (Queens College, CUNY)
Thesis: Global Drivers of Beta Diversity in Birds
RESEARCH EXPERIENCE
Ph.D. Student
August 2020 – Present
Program in Microbiology and Immunology, School of Medicine, University of Pittsburgh
(Supervised by Dr. Vaughn S. Cooper)
  • Applying evolutionary game theory to understand fitness dynamics of Pseudomonas aeruginosa that carry Pf prophage.
  • Investigating role of defective interfering Pf phages in Pseudomonas aeruginosa population composition.
Research Technician
June 2020 – July 2020
Biology Department, Queens College, CUNY
(Supervised by Dr. John J. Dennehy)
  • Aided in deactivating and extracting RNA from sewage samples for SARS-CoV-2 detection.
  • Generated maps of sewage drainage areas in R.
Undergraduate Researcher
February 2017 – June 2020
Biology Department, Queens College, CUNY
(Supervised by Dr. John J. Dennehy)
  • Conducted independent research on the drivers of Erwinia amylovora phages adapting to their host’s codon usage bias via experimental evolution.
  • Trained new lab recruits on basic lab skills such as aseptic techniques, bacteria and phage propagation, and other maintenance skills (i.e. autoclaving, preparation of media, etc.).
Undergraduate Researcher
August 2016 – June 2020
Biology Department, Queens College, CUNY
(Supervised by Dr. José D. Anadón)
  • Writing a manuscript for publication on an independent research project regarding the global drivers of taxonomic and phylogenetic beta diversity in approximately 10,000 bird species.
  • Assisted undergraduate student in the research on global patterns of evolutionary endemism in birds by generating raster maps and phylogenetic trees.
High School Researcher
September 2014 – June 2016
Biology Department, Queens College, CUNY
(Supervised by Dr. José D. Anadón)
  • Conducted independent research on global drivers of taxonomic beta diversity in approximately 10,000 bird species.
  • Competed in Intel Science Talent Search (Intel STS), Junior Science and Humanities Symposium (JSHS), and New York City Science and Engineering Fair (NYCSEF).
HONORS AND AWARDS
2020
Colwin Award (awarded to a graduating senior for outstanding research in biology), Biology Department at Queens College, CUNY

Provost’s Award (awarded to 2 graduating seniors selected by the Chief Academic Officer for remarkable academic achievement and postgraduate potential), Macaulay Honors College, CUNY

Honors in Mathematics and Natural Sciences, Queens College, CUNY
2019
Student Travel Award, 38th Annual Meeting of the American Society for Virology at the University of Minnesota, Twin Cities.
2018
Second Place Poster Award, NYC Regional SEA-PHAGES Symposium at Mount Saint Mary College
2016
University Scholar (full tuition merit scholarship for undergraduate studies), Macaulay Honors College at Queens College, CUNY
PUBLICATIONS
  1. Smyth DS, Trujillo M, Gregory DA, Cheung K, Gao A, Graham M, Guan Y, Guldenpfennig C, Hoxie I, Kannoly S, Kubota N, Lyddon TD, Markman M, Rushford C, San KM, Sompanya G, Spagnolo F, Suarez R, Teixeiro E, Daniels M, Johnson MC, & Dennehy JJ. (2022). Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nature Communications, 13(1), 635.
  2. Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, San KM, Smyth DS, Dennehy JJ. (2021) Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV- 2 RNA from wastewater. PLoS One 16, e0257454.
  3. Smyth DS, Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, Markman M, San KM, Sompanya G, & Dennehy JJ. (2021) Detection of Mutations Associated with Variants of Concern Via High Throughput Sequencing of SARS-CoV-2 Isolated from NYC Wastewater. medRxiv.
PRESENTATIONS
(*presenting author)
2022
*Kubota N, Scribner MR, & Cooper VS. Impact of Pf prophage on the evolution of Pseudomonas aeruginosa. Pittsburgh Phage Project (P3) Symposium at the University of Pittsburgh.

*Kubota N, Scribner MR, & Cooper VS. Impact of Pf prophage on the evolution of Pseudomonas aeruginosa. Meetings in Microbial Ecology & Evolution at the Max Planck Institute for Evolutionary Biology in Plön, Germany.
2021
*Scribner MR, Kubota N, Stephens AC, Huong JL, Richardson AR, & Cooper VS. Adaptation to the Nutritional Environment of the Cystic Fibrosis Airway Promotes Rapid Ecological Diversification and Prophage Induction. World Microbe Forum. Remote.

*Dennehy JJ, Smyth D, Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, Markman M, & San K; Isolating and Sequencing SARS-CoV-2 from Wastewater to Monitor Variants of Concern. World Microbe Forum. Remote.

*Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, San K, Smyth D, & Dennehy JJ. Protocol for Safe, Affordable, and Reproducible Isolation and Quantitation of SARS-CoV-2 RNA from Wastewater. World Microbe Forum. Remote.

*Smyth D, M. Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, Markman M, San K, Sompanya G, & Dennehy JJ. Detection of Mutations Associated with Variants of Concern via Targeted High Throughput Sequencing of SARS-CoV-2 Isolated from Wastewater. World Microbe Forum. Remote.
2019
*Kubota N, Rosario E, Stoyanova G, & Dennehy JJ. Mutations and Selection in Erwinia amylovora Phages Adapting to Host's Codon Usage Patterns. American Society for Virology 38th Annual Meeting at the University of Minnesota, Minneapolis.

Rodriguez DA, *Abellán P, Kubota N, & Anadón JD. Global-scale spatial patterns of phylogenetic endemism in birds. 9th Biennial Conference International Biogeography Society in Málaga, Spain.
2018
*Kubota N, Rosario E, & Dennehy JJ. Mutations and Selection in Erwinia amylovora Phages Adapting to Host's Codon Usage Patterns. NYC Regional SEA-PHAGES Symposium at Mount Saint Mary College (Second Place Poster Award)
2017
*San KM, Kubota N, Anadón JD, Bird J, Joyner J, Muth T, & Dennehy J. The Impact of Urbanization on Soil Microbiome in Long Island, New York. 31st Annual Sigma Xi Research Day at Queens College, City University of New York.
2016
*Kubota N, Abellán P, & Anadón JD. Global Drivers of Beta Diversity in Birds. Senior Research Students Poster Presentation at The Bronx High School of Science.
2015
*Kubota N, Abellán P, & Anadón JD. Global Drivers of Beta Diversity in Birds. Science Expo at The Bronx High School of Science.
TEACHING, MENTORING, AND LEADERSHIP
Vice President of Finance
July 2022 – Present
University of Pittsburgh, School of Medicine, Biomedical Graduate Student Association
  • Manages financial accounts for the Biomedical Graduate Student Association (BGSA).
  • Organizes and operates the BGSA Travel Awards and Travel Awards Committee.
Big Buddy
April 2022 – Present
University of Pittsburgh, School of Medicine, Biomedical Graduate Student Association
  • Mentors incoming first year PhD students on adjusting to and navigating through graduate school.
  • Coordinates with other older students to create events that will allow first year students to get to know other members of their cohort and program.
Lab Mentor
February 2022 – April 2022
University of Pittsburgh, School of Medicine, Cooper Lab
  • Taught rotation student and visiting researchers on how to script in R and Bash to do analyses and data visualization of DNA sequencing data.
  • Built dry lab tutorials for bench scientists who are beginners in R and Bash.