Team:Amsterdam/Team

Forbidden FRUITS

Team
Team Members
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Research
Description
Design
Notebook
Experiments
Results
Engineering Success
Hardware
Proof Of Concept
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Overview
Parts
Human practices
Human Practices
Proposed Implementation
Education & Engagement
Survey
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Acknowledgements
Attributions
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Dennis Dekker

Dennis is a graduate student Biomedical Sciences as well as Bioinformatics & Systems Biology. He sees iGEM as an opportunity to contribute to society and the environment. He feels that we can change the way we look at and work with microbes to change the way we produce..In the iGEM project, he is working on making a growth-coupled production of mannitol in Synechocystis PCC6803. Outside the lab, he is working on making the Forbidden Fruits algorithm use different databases in order to have a wider selection of compounds and reactions. He is also responsible for making the Wiki together with Mingdong. As the founding father and team leader of the iGEM Amsterdam 2020 team, he is also taking charge of payments and forms.

Samira van den Bogaard

Samira is a graduate student at the VU/UvA in Bioinformatics and Systems Biology with a background in biotech and life sciences. She is passionate about everything which is mathematical and computational and has the superbold aspiration to save the planet from being polluted using microbes. Samira is responsible for optimizing the so-called ‘plumber’. The plumber is the part of forbidden fruits which tries to predict the minimal modifications which need to be made to be able to couple a specific compound to the growth of the organism. In the lab she is responsible for making Synechocystis PCC6803 produce salicylic acid. To do so, she still has to knockout a specific gene, pyk2, which is involved in the pyruvate metabolism of Synechocystis PCC6803.

But besides the ‘real’ science, Samira is involved in multiple projects to make science available for the general public. With her enthusiasm she is discussing, surveying and teaching about real life applications of bacteria. She hopes to make more people aware of what microorganisms can do for people and the planet and that bugs are no longer considered to just make people sick.

Kelly Klomp

Kelly is an ambitious student studying Bioinformatics and Systems Biology at the VU/UvA. During her bachelor Forensic Science she got fascinated about analysing data. This passion brought her to her current study. Kelly works on optimizing the product yield. She is designing an algorithm which creates a path between essential metabolites and downstream of the production reaction. Her goal is to find a strategy where flux (energy) needed for this growth essential reaction is used at a downstream position in the network, leaving more energy for the production reaction. In the lab she is responsible for lactate production in Synechocystis PCC6803. Lactate can be used to make bioplastics.She needs to knock-in the reaction producing lactate and knock-out the ppc gene.

Kelly is also writing a blog about her iGEM journey to inform the general public about our project. She is excited to contribute to a greener world. A world we all make use of. Kelly is also involved in a survey about genetic modification and she will guide some small experiments with the public about our project at a museum of bacteria.

Robin Laird

Robin is a lover of all things microbiome. She’s obsessed with exploring the points where human physiology and behavior meet. The iGEM Amsterdam 2020 project, Forbidden FRUITS, is exciting to her since it is fundamental. She believes that having a better understanding of how we can produce any compound in any microorganism can lead to radical advancements in human health and disease prevention. Specifically, Robin is excited by the potential of Forbidden FRUITS to help us study and perturb the human microbiome. Though her original project in lactic acid bacteria proved to be too complex to execute in the time frame of the iGEM competition, she is now excitedly working on producing the medically-relevant compound salicylate in the cyanobacterium strain Synechococcus UTEX 2973.

Robin is a graduate student at the University of Amsterdam, studying Biochemistry and Biotechnology. Outside of her studies, she is a health coach and entrepreneur pursuing tech solutions that empower people to better understand their bodies and health behaviors. She is the co-founder of the mobile app Health Curious, which aims to do just that. She is the person to get in touch with when it comes to the outreach and graphic design part of this iGEM project. With her experience in filming, graphics and communication greatly supports the team in many ways.

Mingdong Liu

Mingdong is a master student studying Bioinformatics and Systems Biology at the VU&UvA with a background in Neuroscience. This iGEM project is fascinating for him because of its huge potential to enable sustainable production of metabolites with cell factories. He is in charge of developing critical features to Forbidden FRUITS: he is responsible for building a method that reads out Gene-Protein-Reaction Associations (GPRA) information from SBML models and a method that will generate a network based on gene products instead of based on merely reactions. Once the methods are established, he is to incorporate them into the program, extending the database with GPRA information and building up new interfaces to perform network transformation.

Beside his project, he is also responsible for making the iGEM wiki pages, which requires him to learn HTML language. He enjoys the valuable experience in this iGEM project of learning so much including programming, software development and web page development.

Joris Visser

Joris is currently a Master student Biomolecular Sciences with a specialization into Molecular Bioinformatics. He thinks that the combination of biology and computational techniques can lead to innovative sustainable products that can make positive changes to the world. That’s also his motivation for joining this year's iGEM Amsterdam project.In the lab, he is working on genetically engineering E.coli for the production of salicylic acid. Besides, he has been helping out his colleagues inside and outside the lab, not only with the experiments, but also by using his talent to organize and communicate.Additionally, he will be working on making the Forbidden FRUITS algorithm more advanced with gene optimization software to improve heterologous expression. He is also responsible for market research & funding and likes to contribute to the valorisation of the overall project.

Vicky Ramírez López

Vicky is a masters student of Bioinformatics and Systems Biology. She has a bit of a different background from the rest of the team members. A mechatronic engineer who got captivated by the complexity of cells as the fundamental units of life after working with tissue 3D-bioprinting. Why biology then? She loves knowing that we are working on something that can take some weight off the shoulders of our planet.As an engineer, Vicky feels more comfortable programming than playing with the microbes in the lab. She will be working on making the Forbidden FRUITS algorithm capable of finding strategies for an even wider range of non-native compounds by implementing what we call “cheap lunch” strategies. To put Vicky’s experience with electronics and technology to work, she is also in charge of the calibration of a 24-well cultivator for photoautotrophs, which is a device that has been under development in the MMP lab at the University of Amsterdam but that still needs some fine tuning before it can be used to test our experiments under the best conditions.

Other than that, she has been the one behind our crowdfunding campaign in Indiegogo and is in charge of giving Dennis and Mingdong a hard time with making the webpage look good as, together with Joris, she has been in charge of the aesthetics of it. And amongst all of these, she will always have time to meditate and enjoy a good workout or yoga session to keep her feeling her best.

Forbidden FRUITS

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igem.amsterdam.2020@gmail.com

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Forbidden FRUITS

Team:Amsterdam/Team

Dennis

Dennis Dekker

Samira

Samira van den Bogaard

Kelly

Kelly Klomp

Robin

Robin Laird

Mingdong

Mingdong Liu

Joris

Joris Visser

Vicky

Vicky Ramírez López

Our supervisors

Filipe

Dr. Filipe Branco dos Santos

Max

Max Guillaume

Joeri

Joeri Jongbloets

Wei

Dr. Wei Du

Wenyang

Wenyang Wu

Hugo

Hugo Pineda Hernandez