Team Member Contributions

Nicola Zamboni

Primary PI

Tasks:

Other

Specific tasks:

Administrative support for our team

Emmanuel Matabaro

Instructor

Tasks:

Investigation, Safety, Conceptualization

Specific tasks:

(1) Safety - Introduction into protocols, lab equipment and safety. (2) Conceptualization - suggested the use of the BY4741 strain for yeast engineering (3) Investigation - Guidance on experimental debugging and material/instrument usage and choice, ordering (Lab manager), provided protocols for making competent yeast.

Michelle Scharte

Instructor

Tasks:

Investigation, Safety, Background Research

Specific tasks:

(1) Safety - Introduction into protocoling, lab equipment and safety. (2) Investigation, Background Research - Guidance for experiments and navigating the lab, guidance on Tecan usage and debugging Tecan measurement problems, providing media protocols.

Tsvetan K

Advisor

Tasks:

Analysis, Conceptualization, Fundraising, Other

Specific tasks:

(1) Analysis - Support and guidance for cloning-related parts of the project. Contributed the oxyR plasmid (2) Conceptualization - discussing project ideas, application and design (3) Fundraising - Sponsoring brochure review

Herta Elina Jansone

Student Leader

Tasks:

Conceptualization, Background Research, Investigation, Notebook/record keeping, Data Curation, Project Administration, Public Engagement, Fundraising, Entrepreneurship, Software, Wiki Coding, Writing, Visualization, Safety

Specific tasks:

(1) Conceptualization - Discussing ideas, researching biocontrol and biocontainment methods. (2) Investigation - Planning and conducting experiments in the lab until September (3) Fundraising - Contacting possible sponsors (4) Project administration - organizing advisors and lab space (4) Public Engagement - Wyss BioStars workshop participation and collaboration organizer, participation in expert/HP meetings (5) Entrepreneurship - Sponsoring brochure editor (6) Notebook, Wiki coding, Writing, Visualization - writing of the lab notebook, wiki coding, filmed footage for the promotional and presentation video, developed the initial concept of the promotional video. (6) Safety - writer of the check-in forms and safety forms; writing of the safety page; discussing GMO product and lab safety concerns with instructors and advisors; biocontainment / kill-switch method research for further applications

Tanaïs Moreau

Student Leader

Tasks:

Analysis, Background Research, Data Curation, Investigation, Conceptualization, Notebook/record keeping, Project Administration, Public Engagement, Fundraising, Visualization, Writing, Wiki Coding, Entrepreneurship

Specific tasks:

(1) Conceptualization - General project ideas and development (2) Background research - Research on fireblight and its prevention (also other ROS-linked blights), plant immunity, Reactive Oxygen Species (ROS), ROS-sensitive transcription factors in yeast plant and bacteria, quorum-sensing of infections, biocontrol strains, IBD etc (2) Investigation - Wet lab lead, design of all plasmids, new parts and primers, conducting experiments in the lab until September (3) Fundraising - Contacting possible sponsors (French and Swiss) (4) Project Administration - Wet lab lead, organizing advisors, Human Practices (5) Public Engagement - Wyss BioStars workshop participation, organizing and part of all expert meetings (6) Entrepreneurship - Main sponsoring brochure editor (7) Notebook, Wiki coding, Writing, Visualization - writing of the lab notebook, parts registry, coding and writing pages (home page, description, design, human practices, attributions)

Camille Membrez

Student

Tasks:

Analysis, Background Research, Conceptualization, Investigation, Notebook/record keeping, Data Curation, Writing, Visualization, Fundraising

Specific tasks:

(1) Conceptualization - Discussing ideas (2) Background research - Research on ROS-sensitive bacteria and yeasts transcription factors, biocontrol strains (3) Investigation - Planning and conducting experiments in the lab until September, helping with primers and parts design (4) Public Engagement - organizing and participating in meetings with experts (5) Notebook, Writing, Visualization - writing of the lab notebook, and parts registry, writing of wiki pages.

Elias Nehring

Student

Tasks:

Analysis, Data Curation, Fundraising, Software, Wiki Coding, Visualization, Writing, Conceptualization, Background Research, Project Administration

Specific tasks:

(1) Analysis - Analysis of experimental data, analysis of modeling results (2) Background research - Research on computational methods (3) Conceptualization - Developing dry lab plan, discussing ideas (4) Project Administration - Dry lab lead, team treasurer (5) Fundraising - Contacting possible sponsors (6) Software - Implementation of data analysis, modeling, and visualization (7) Entrepreneurship - Sponsoring brochure editor (8) Public Engagement - Participation in expert meetings (9) Wiki coding, Writing, Visualization - Wiki coding, writing of the dry lab page.

Tim Andermann

Student

Tasks:

Conceptualization, Investigation, Background Research, Notebook/record keeping, Public Engagement, Writing, Data Curation, Entrepreneurship, Fundraising, Project Administration, Analysis

Specific tasks:

(1)Conceptualisation - General project ideas and development (2) Background research - Research on fireblight, possible quorum-sensing approach, ROS-sensitive bacteria transcription factors, medical application (IBD, chronic inflammatory diseases), antioxidants (3) Investigation - Planning and conducting experiments in the lab (4) Public Engagement - Wyss BioStars workshop participation, bioengineering presentations and tutorials at schools, participation in expert meetings (5) Entrepreneurship - Sponsoring brochure editor (6) Notebook, Writing, Visualization - writing of the lab notebook, wiki and parts registry, filmed footage for the promotional video and presentation video, voiced the promotional and presentation video.

Tim Lennart Appel

Student

Tasks:

Background Research, Investigation, Notebook/record keeping, Data Curation, Writing, Public Engagement, Conceptualization, Visualization, Wiki Coding

Specific tasks:

(1) Conceptualization - Discussing ideas (2) Background research - Research on ROS-sensitive bacteria transcription factors (3) Investigation - Planning and conducting experiments in the lab until September (4) Fundraising - Contacting possible sponsors (5) Entrepreneurship - editor of the promotional video and main contents documenter (6) Public Engagement - Wyss BioStars workshop participation, bioengineering presentations and tutorials at gymnasiums, participation in expert meetings before labwork start (7) Notebook, Writing, Visualization - writing of the lab notebook, and parts registry, wiki coding, filmed footage for the promotional video and presentation video. Creation of logos and animations.

External Contributions

TWIST

Institution Type:

Industry

Relationship to Team:

Sponsor

Tasks:

Other

Specific tasks:

Synthesized DNA fragments for cloning; iGEM partner offer

Association Nationale Pommes-Poires

Institution Type:

Nonprofit

Relationship to Team:

Sponsor

Tasks:

Schweizer Früchte

Institution Type:

Nonprofit

Relationship to Team:

Sponsor

Tasks:

ETH Zürich

Institution Type:

Academic

Relationship to Team:

Sponsor

Tasks:

NCCR Molecular Systems Engineering

Institution Type:

Academic

Relationship to Team:

Sponsor

Tasks:

Cosima Pelludat

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization, Safety

Specific tasks:

(1) Conceptualization - discussion of our project idea and pertinent strains, mentionned using a short-lived Pantoea agglomerans strain for the safety aspect

Zhihui Li

Institution Type:

Other

Relationship to Team:

Other

Tasks:

Wiki Coding

Specific tasks:

Description page

Jenny Schmidt

Institution Type:

Other

Relationship to Team:

Other

Tasks:

Conceptualization, Project Administration

Specific tasks:

(1) Conceptualization - initial brainstorming (2) Project Administration - former project lead

Giovanni Broggini

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization, Safety

Specific tasks:

Conceptualization: Expert on fireblight with knowledge of the mechanisms of bacterial infection in plants, gave us leads about how to combine our sensor with relevant effector genes in our gene circuits. Safety: Discussed GMO regulations and how they affect bioengineered pesticide product development and testing, including ideas how to add a killswitch.

IDT

Institution Type:

Industry

Relationship to Team:

Other

Tasks:

Other

Specific tasks:

Synthesized DNA oligos for BS-x and OG-x sequences of the promotor used in latter stages of labwork; iGEM partner offer

Eric Allard

Institution Type:

Government

Relationship to Team:

External Advisor

Tasks:

Background Research

Specific tasks:

Sharing information on current approaches in fighting and monitoring fireblight in southern France, southern Germany and northern Italy.

Dr. Alexander Klotz

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Background Research

Specific tasks:

Guidance on measuring fluorescence and controlling for autofluorescence in bacteria and yeast; ideas for further ROS high-pass filter improvements

Xavier Leclanche

Institution Type:

Nonprofit

Relationship to Team:

External Advisor

Tasks:

Fundraising, Background Research, Other

Specific tasks:

Informed about economic aspects of fireblight, referred to further researchers of fireblight. Organized funding from the French Pear and Apple Association

Prof. Dr. Pablo Fuentes

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Background Research, Conceptualization

Specific tasks:

Guidance on selection of target for ROS sensing, current approaches for molecular ROS capture and signaling; directed evolution approaches discussion; optimal sensor and fluorophore considerations; suggestions to use the protein interaction modeling tool RosettaFold All-Atom

Prof. Dr. Randall Platt

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization, Background Research

Specific tasks:

(1) Conceptualization - discussion of mutagenesis methods including error-prone PCR, saturation mutagenesis and protocol optimization; (2) Brainstorming - calprotectin as potential target combinable with the sensor in the treatment of IBD

Prof. Dr. Theo Smits

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization

Specific tasks:

Brainstorming - enviromental factors influencing sensor activity and sensitivity for ROS in the case of fireblight; selection of optimal chassis for biocontrol product for fireblight

Prof. Dr. Gregory Velicer

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization

Specific tasks:

Potential plant disease targets for ROS sensing beyond fireblight - wheat blotch and other grain diseases caused by fungi as other potential targets. Fungal chassis selection for biocontrol: Aureobasidium pullulans as established engineerable organism and Myxococcus xanthus as a high-potential biocontrol agent which is currently difficult to engineer.

Dr. Clara Torres-Barcelo

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Background Research

Specific tasks:

Information on resistance development pace of E. amylovora against phages and other known biocontrol agents. Usage of bacterial biocontrol agents as hosts for developing and constantly producing Ea phages.

Dr. Lukas Roth

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization, Background Research

Specific tasks:

Advice on UAV (unmanned aerial vehicles) use for signal observation purposes. Current trends and applications of drone-based technologies; environmental, social and economic considerations for drone applications at a commune level.

Perrine Gravalon

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization

Specific tasks:

Information on known resistances and applications to improve resilience against fireblight that are used by farmers in Switzerland

Céline Gilli

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Background Research

Specific tasks:

Current economic situation in fireblight monitoring and R&D, cost-effective social and organic approaches for fireblight biocontrol, including commune-level private tree monitoring and trimming.

Dr. Aurélie Floch

Institution Type:

Industry

Relationship to Team:

External Advisor

Tasks:

Background Research, Entrepreneurship

Specific tasks:

Researcher at ANTI OXIDANT POWER, an industry lab investigating promising antioxidants for application in biopharmaceuticals and cosmetics. Described the market situation for over-the-counter antioxidant-containing treatments and cosmetics, as well as pros and cons of current approaches for IBD treatment.

Prof. Dr. med. Dr. phil. Gerhard Rogler

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Conceptualization

Specific tasks:

Director of the Department of Gastroenterology and Hepatology at the University Hospital Zurich. Information on the impact of ROS on IBD severity and how they could be targeted and neutralized. Currently used and developed probiotic approaches for IBD treatment and where our high-pass sensor could fit.

Prof. Dr. Markus Künzler

Institution Type:

Academic

Relationship to Team:

Collaborator

Tasks:

Other, Safety

Specific tasks:

Providing labspace for the Wyss BioStars camp workshop on 26.07.

Dr. Matthias Gstaiger

Institution Type:

Academic

Relationship to Team:

Collaborator

Tasks:

Safety

Specific tasks:

Providing consumables and instruments for the Wyss BioStars camp workshop.

Carolin Fleck

Institution Type:

Nonprofit

Relationship to Team:

Collaborator

Tasks:

Public Engagement, Other, Fundraising

Specific tasks:

Administration of the Wyss BioStars camp, early communication regarding the camp workshop timeline, covered workshop reagent and consumable costs

Dr. Ryan Separovich

Institution Type:

Academic

Relationship to Team:

External Advisor

Tasks:

Investigation, Conceptualization, Safety

Specific tasks:

Member of the Beltrao lab working on the same floor as us. Provided guidance on cloning, gel and PCR clean-ups, took out plates from the incubators and sent data from measured by the Tecan devices to us if the assays and incubations were running over the weekend.

Maria Zwyssig

Institution Type:

Academic

Relationship to Team:

Other

Tasks:

Safety, Other, Conceptualization

Specific tasks:

PhD Student at the Plant Pathology (Maurhofer) lab in the Department of Environmental Systems Science at ETH Zurich. Provided us with Pseudomonas fluorescens strain Pf-5. Gave us information about currently known autofluorescence issues and biocontrol successes from the research done in her lab, as well as informed us about innate antibiotic resistances of Pseudomonas, media for the selection of Pseudomonas, provided Pseudomonas-relevant protocols.

Louise Larsson

Institution Type:

Academic

Relationship to Team:

Other

Tasks:

Other

Specific tasks:

PhD student at the Slack lab in the department of Health Sciences and Technology at ETH Zurich. Provided us with the Nissle 1917 strain of E. coli.

Benjamin Danuser

Institution Type:

Academic

Relationship to Team:

Other

Tasks:

Other

Specific tasks:

PhD student in the Fussenegger lab in the department of Biosystems Science and Engineering. Participated in the iGEM competition as part of the ETH Zurich team in 2019, which was the last team that existed before ours. Benjamin gave tips on early team selection, task distribution and project ideation process for an iGEM team.

Cathy Marulli

Institution Type:

Academic

Relationship to Team:

Other

Tasks:

Other

Specific tasks:

PhD student in the Picotti lab in the Institute of Molecular Systems Biology of the Department of Biology at ETH Zurich. Participated in the 2019 ETH Zurich iGEM team and discussed sponsoring and fundraising strategies, from company contacts to brochure design, as well as team budget planning.

Erica Geneletti

Institution Type:

Other

Relationship to Team:

Other

Tasks:

Other

Specific tasks:

Currently Product Manager at Lunaphore in Lausanne. Participated in the 2019 ETH Zurich iGEM team and gave advice on sponsoring strategies and expected expenses.

Promega

Institution Type:

Industry

Relationship to Team:

Sponsor

Tasks:

Specific tasks:

Provided 1000 CHF of in-kind sponsoring to our team, which we used massively for minipreps and cloning.

Songyuan Zhang

Institution Type:

Academic

Relationship to Team:

Other

Tasks:

Conceptualization, Background Research

Specific tasks:

PhD student in the Zipfel lab at the University of Zurich. Forwarded us to the first experts in fireblight and general plant pathology, greatly helping us in kickstarting the plant application research.

Student Biolab Zurich

Institution Type:

Nonprofit

Relationship to Team:

Collaborator

Tasks:

Project Administration, Other

Specific tasks:

Formal parent organization to the ETH and UZurich iGEM teams. Helped in recruiting the team and setting up the bank account. Provided interim feedback on project progress.

Timeline

Building the Team Wiki

Start:

2024 June 1st

End:

2024 October 2nd

Total time:

18 weeks

Dry Laboratory Activities

Start:

2024 June 1st

End:

2024 September 6th

Total time:

14 weeks

Wet Laboratory Activities

Start:

2024 June 2nd

End:

2024 October 18th

Total time:

20 weeks

Recruit Team Members

Start:

2023 December 1st

End:

2024 April 30th

Total time:

22 weeks

Development of Project Plan

Start:

2024 January 1st

End:

2024 June 1st

Total time:

22 weeks