Thank You

The PoPPY team would like to thank everyone who made this project possible, especially those described below. For the past five years, undergraduates at UCSC have participated in iGEM. This year, the team is composed of students studying Bioengineering (Biomolecular), Bioinformatics, Bioengineering (Assistive Technology: Motor), Molecular, Cellular, and Developmental Biology, Marine Biology, and Cognitive Science: Artificial Intelligence and Human Computer Interaction. Our diverse group of individuals is crucial for the creative process behind using synthetic biology to help others. Modern engineering demands collaboration between individuals and pushes them to think critically and work efficiently. Through synthetic biology, the 2018 UCSC iGEM team is solving worldwide issues and developing methods to expand their research in the future.

The Project Idea

After several journal club meetings, our team determined the PoPPY project was the most meaningful pursuit. The initial idea was proposed by captain Morgan Tardy and mentor McKenna Hicks.

Official Team

Advisors

David Bernick, Assistant Adjunct Professor, University of California Santa Cruz, Department of Biomolecular Engineering

Dr. Bernick for guided our team and offered valuable insight and advice through each stage of the project. He helped our team manage funding, finances and logistical tasks.

McKenna Hicks, Master's Student, University of California Santa Cruz, Department of Biomolecular Engineering

McKenna for provided advice on gene design and wet lab experiments.

Todd Lowe, Professor, University of California Santa Cruz, Department of Biomolecular Engineering

Todd Lowe acted as our assistant advisor and provided advice on coding for our website.

Research Support

Hal Alper, Professor, University of Texas at Austin, Department of Chemical Engineering

Professor Alper provided recommendations for Tsynth27/Tsynth8 terminators and confirmed which promoters would be necessary for our project. Through a Materials Transfer Agreement, Alper sent us plasmids carrying terminators and fluorescent markers to test for gene activity.

William Belden, Associate Professor, Rutgers University, Department of Animal Sciences

Professor Belden provided valuable information on yeast-mediated cloning. Professor Belden inspired our parallel experiment design and even offered to help design our flanking oligos.

Erin Bredeweg, Biosystems Dynamics & Simula Scientist, Pacific Northwest National Laboratory

Erin Bredeweg assisted us in finding sequence information on our Yarrowia lipolytica strain.

Tony Carr, Professor of Molecular Genetics, University of Sussex, Genome Damage and Stability, Genome Damage and Stability Centre

Professor Carr answered our questions regarding the size of genomic insert, directionality of Lox sites, and cre-lox recombination.

Catherine Duport, University of Avignon, Microbiotechnology, Ecotoxicology, and Bioremediation

Catherine Duport helped clarify pieces of her 1998 experiment such as why certain promoters and genes were chosen. Duport also attempted to find us a Yarrowia lipolytica strain.

Daniel Gallie, Professor, University of California Riverside, Biochemistry Department

Professor Gallie sent us an electroporation protocol with mRNA for reference.

Marc Gartenberg, Professor, Rutgers University, Department of Biochemistry and Molecular Biology

Professor Gartenberg provided information on parts of pXRU3/L2 plasmid including HOp region, CEN/ARS regions, pRS marker, and how to insert Lox sites into these particular plasmids.

Rohinton Kamakaka, Professor, University of California Santa Cruz, Department of Molecular Cellular and Developmental Biology

Professor Kamakaka sent us protocols on yeast-mediated cloning. He also answered questions on growing and maintaining yeast and even provided us a Saccharomyces Cerevisiae strain for yeast-mediated cloning. Professor Kamakaka has also provided general support and advice for all our experiments.

Oliver Konzock, PhD Student, Chalmers University, Life Science Engineering

Oliver Konzock answered questions on how to grow yeast (and care for Yarrowia lipolytica). He also answered questions on how to successfully perform yeast-mediated cloning.

Jah Nehlin, Copenhagen University Hospital Hvidovre

Mehlin gave insight into how the GAL1 promoter works.

Jean-Marc Nicaud, Directeur de Recherche INRA

Jean-Marc Nicaud introduced us to the Golden Gate Assembly method. He also answered questions about building plasmids and showed us M1G1 wouldn't be an issue in terms of our promoter/terminator design.

Saumya Ramarao, Senior Associate, Reproductive Health Supplies Coalition

Ramarao provided information regarding birth control production and needs.

Hans Ronne, Professor, Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology

Professor Ronne attempted to determine how to stop the binding of MIG1 to GALI promoter.

Cory Schwartz, PhD Student, University of California Riverside, Department of Civil and Environmental Engineering

Schwartz provided pHR_AO8_hrGFP plasmid sequence that includes homologous arm regions.

Wendy Sun, University of Maryland Baltimore County, Department of Chemical Biochemical and Environmental Engineering

Sun assisted Xu in proving that Yarrowia lipolytica could produce progesterone.

Stefan Tippmann, Visiting Researcher, Chalmers University, Life Science Engineering

Tippmann taught us about yeast in general and providing us with additional readings to learn about Yarrowia lipolytica.

Adam Watson, Research Fellow, University of Sussex, Genome Damage and Stability

Watson answered questions regarding the size of genomic inserts, directionality of Lox sites, and Cre-lox recombination.

Ian Wheeldon, Associate Professor, University of California Riverside, Department of Chemical and Environmental Engineering

Wheeldon provided the pHR_AO8_hrGFP plasmid sequence that includes homologous arm regions.

Peng Xu, University of Maryland Baltimore County, Department of Chemical Biochemical and Environmental Engineering

Xu proved that Yarrowia lipolytica could produce progesterone despite its NHEJ preference. He showed that it is possible to use homologous recombination with a KU70 knockout strain.

Lab Support

Dr. Hugh Olsen, Lab Manager, University of California, Santa Cruz, Biomolecular Engineering Teaching Labs

Dr. Olsen provided assistance with autoclave-training, general laboratory safety training, obtaining materials and maintaining lab equipment.

Wiki Support

Evan Pepper, Former Undergraduate Student, University of California Santa Cruz, Biomolecular Engineering

Evan provided advice on design choices and website organization.

UCSC iGEM 2017

UCSC iGEM 2017 provided us with inspiration for the UCSC 2018 wiki and, more specifically, a layout for the Attributions page.

Shayan Vahdani

Shayan provided feedback on our wiki design and offered alternatives to make our display better.

Human Practices Support

Sandra Dreisbach, Professor, University of California Santa Cruz

Professor Dreisbach introduced our team to the IRB and prompted us to look into IRB exemption for our questionnaire.

Emily Fisch, Research Compliance Analyst, Office of Research Compliance Administration, University of California Santa Cruz

Emily for assisted our team in gaining IRB exemption for the Human Practices Birth Control Questionnaire.

Hank Pellissier, Director, Brighter Brains Institute

Pellissier provided our Human Practices team several women's groups to contact in Uganda.

Bri Quinn, Compliance Assistant, Institutional Review Board, University of California Santa Cruz

Bri for encouraged our team to apply for IRB exemption rather than a full protocol review.

Funding Support

UCSC iGEM 2017

UCSC iGEM 2017 provided monetary support for our 2018 team.

George Spix

George Spix provided significant monetary support for the 2018 team and future iGEM teams.

Industry Support

Asana

Asana provided/sponsored our team with free premium accounts to organize and communicate work ideas with each other.

Fungal Genetics Stock Center

The FGSC provided our team with a Yarrowia lipolytica strain.

Non-Profit Partnerships

Hank Pellissier, Director, Brighter Brains Institute

Pellissier provided our Human Practices team several women's groups to contact in Uganda.

Martyn Smith, Managing Director, Family Planning 2020

Martyn provided us contacts to funding bodies that regulate drug production in several of our target countries. Martyn also passed on our team's message to his coworkers and partners, including the Bill and Melinda Gates Foundation.

John Townsend, Director, County Strategy, Population Council

John discussed possible pathways to further develop our contraceptive outside of the iGEM competition.

Presentation Support

Zia Isola, Director, Genomics Institute Office of Diversity Programs, University of California Santa Cruz

Zia helped us prepare our poster for the UCSC 9th Annual Physical and Biological Sciences Summer Research Symposium.

General Support

Russell Evans, Senior Development Engineer, University of California, Santa Cruz, Campus Facilities

Russell provided the 2018 UCSC iGEM Team with separate dry lab research training and wet lab rooms. He also provided technical and equipment support.

Logan Mulroney, PhD Student, University of California, Santa Cruz, Bioinformatics

Logan provided the 2018 UCSC iGEM Team with general advice on project design and lab techniques.