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iGEM Thessaloniki 2018: Stable and constant protein production decoupled from gene and plasmid copy number

  iGEM Thessaloniki 2018 team

iGEM Thessaloniki 2018 team

Mankind was always interested in how life works, how life adapts, how life evolves, how life flourishes, and how life ends. Scientific and technological breakthroughs allowed organism manipulations and genetic material modification, creating “biological factories” and enabling the production of valuable biological products. Still, challenges are present, such as the sheer complexity of every living organism and the constantly changing cellular environment.

Biological systems are unpredictable, noisy, and difficult to stabilize, even under standardized conditions. Combined with the fickleness and stochasticity of gene expression, even on single cell level, the production rate of a desired protein inevitably fluctuates.

iGEM Thessaloniki aims to design a tunable synthetic biology circuit which guarantees a constant protein expression pattern. We apply control theory to design promoters which maintain constant levels of expression at any copy number. Furthermore, we introduce an element that makes our system tunable to make our system a dynamic and versatile tool with broader manufacturing and therapeutic application capabilities. Finally, we aim to apply machine learning to enable automatic tuning of gene expression depending on a case-by-case basis.

  Multiple levels of dynamic copy number control, as envisioned by iGEM Thessaloniki

Multiple levels of dynamic copy number control, as envisioned by iGEM Thessaloniki

This system will function as a foundational advance tool for both research and industry uses. Genetic engineers/synthetic biologists will have a wider choice of suitable  cloning vectors, while the conducted experiment’s accuracy will increase  significantly and inter-laboratory variations concerning experimental results will be eliminated. On industrial level, protein production will become more efficient, improving the product to cost ratio, thus maximizing profit and product quality.

Our team combines from different scientific backgrounds, such as Biology, Pharmacy, Engineering and Computer Science, our interdisciplinary team. As part of the iGEM 2018 Competition, we organize activities and workshops to communicate our project’s goals, while receiving valuable feedback from the public. Furthermore, we acknowledge the significance of bioethics and public engagement, so we recruited people specialized in fields such as anthropology and law. While we interacted with entrepreneurs, seeking funding and sponsorships, we came up with ways to integrate our project in business. We will tiresly continue our activities, talks, and other social events over the summer until late October and the Giant Jamboree. Till then, keep in touch with our team and ask us questions about the project on our social media pages!

You can read the original post on the PLOS Synbio Blog: http://blogs.plos.org/synbio/2018/07/16/igem-2018-two-synbio-teams-from-greece-are-here-to-leave-their-mark/

iGEM Marburg 2018: establishing Vibrio natriegens as a chassis for synthetic biology

Imagine a lab where you need twelve hours for a cloning cycle instead of three days. Imagine a lab where you start your culture in the morning and harvest your cells after lunch. Imagine a lab where the time lost waiting for cells to grow is reduced to the absolute minimum.

In the past years almost all processes (e.g. DNA synthesis or sequencing) have become faster, but one aspect is still unchanged: The organism that is used as chassis in the majority of Synbio projects remains Escherichia coli. The iGEM Team Marburg 2018 attempts to shake the fundaments of biological engineering by replacing E. coli with Vibrio natriegens, the fastest growing organism known to date, with a demonstrated doubling time of seven minutes.

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The iGEM Team Marburg and their project “Vibrigens - Accelerating Synbio“ aim for the establishment of V. natriegens as the new go-to organism for everyday lab work in both academic and industrial applications. This could improve production output of valuable chemicals and pharmaceuticals and pave the way for a brighter future of research. V. natriegens is very easy for labs to adapt to. It is a non-pathogenic S1 organism, which grows on salt rich standard LB-Medium.

The team is organized in three subgroups: First the strain engineering subgroup will adapt the genome to create the perfect chassis for molecular biology, as has been done with E. coli over the past decades. Strains without nucleases for ideal cloning, others with T7 expression systems and no proteases to express proteins as desired, and many more. These changes shall be done through genome engineering, recombineering and V. natrigens’s exceptional natural competence.

The part-collection subgroup will build the “Vibrigens MoClo toolbox” which will consist of a large number of precisely characterized parts. First experiments showed already, most parts commonly used in E. coli are also functional in V. natriegens. Still, plenty of work is required for the exact characterization of these parts in V. natriegens to achieve the same degree of predictability which is needed for the construction of synthetic regulatory networks or metabolic pathways.

Finally, the Metabolic Engineering subgroup will implement the first heterologous pathway into Vibrio natriegens, producing 3-Hydroxypropionic acid (3-HPA) one of the twelve most important bio-based chemicals needed to reduce dependence on fossil fuel. There is also another, theoretical pathway, which is the most efficient 3HPA-pathway. Because there is no known enzyme for the last reaction, it has never been tested in vivo, but that can be changed. The team will try to build multiple suitable enzymes by calculating the binding pocket for the substrate and subsequently expanding the protein structure until the whole enzyme is built. After testing these enzymes, the pathway can be perfected at a fast pace because biosensors will be established to translate product concentration into a measurable fluorescent output.

In their project “Vibrigens - Accelerating Synbio“ , Marburg's iGEM team is going to combine the fastest cloning methods available with the fastest growing organism Vibrio natriegens optimized for the needs of the community and to show its usefulness by producing 3-Hydroxypropionic acid.

In addition to their ambitious scientific project, iGEM Marburg will be hosting the German iGEM Meetup (22nd - 24th) in collaboration with iGEM Bielefeld and the GASB. This meetup will give all german iGEM teams a platform to reach out for collaborations and to present preliminary results of their projects.

 

You can join iGEM Marburg 2018 on social media to stay informed about their project:

Facebook      Twitter       Instagram

iGEM Montpellier 2018 : A New Non-Hormonal Contraception

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This year, and for the very first time, a Montpellier (France) iGEM team has been created, composed of nine passionate undergraduate students from different schools. iGEM is the world’s biggest competition of synthetic biology. They have decided to study the vaginal microbiome.

 

Microbiome. This word has been everywhere in the scientific community for the last decade. Although this is a very complex system, scientists are discovering new findings every day, and even if there are a lot of different microbiomes to study, one of the most represented is the gut microbiome. Did you know that another microbiome below is just as important and interesting than the gut microbiome for half of the population? The vaginal flora is part of every woman’s life, it is protecting every single one of them from a lot of inconveniences such as discomfort and even diseases. It is made from specific bacteria living together in balance to make the vagina a safe and healthy place. Unfortunately, this microbiome is sometimes damaged due to everyday life (for instance vaginal wash, bad hygiene or the membrane surfactant nonoxynol-9 (N-9) from vaginal contraceptive products). Once the balance is lost, the flora can be surrounded by pathogenic microorganisms. This can go from an itchy vagina to mycosis or increasing chances of having a sexually transmitted disease. Moreover, women have suffered from invasive and expensive methods for contraception, such as the pill and the IUDs (intrauterine devices). Based upon these facts, the Montpellier team wanted to tackle an iGEM project that would address those issues.

 

The team decided to focus on making a new kind of contraceptive using Lactobacillus jensenii, which is one of the most represented bacteria in the vaginal flora. This hormone-free contraception uses a designed Lactobacillus jensenii that has the ability to immobilize spermatozoa in the vagina. How does it really work? Their goal is to create bacteria capable of having a “light switch effect”. When a woman decides to turn it on, bacteria will have a spermicidal effect and will allow in situ contraception. Otherwise, bacteria will be in “off mode”, and spermatozoa will be able to pass. Several studies have demonstrated that Nisin - an antimicrobial peptide - has spermicidal activity. Nisin is a bacteriocin produced by Lactococcus lactis, which is nontoxic to humans. The idea is to introduce the gene that is coding for Nisin into Lactobacillus jensenii and then to apply a colony of these designed bacteria into the vagina for long-term contraception. When a woman wants to remove this contraceptive device, the team must find a way to stop the spermicidal effect of the bacteria.

 

Microbicide can allow a new way of contraception: safe and affordable, where women don’t have to negotiate with their partners.

Why is it crucial to find a new approach to contraception?

Hormonal contraception has a lot of side effects for women (such as weight gain or acne), a pill is easy to forget, and there is the environmental aspect of water contamination by hormones.

Moreover, it has been shown that it’s difficult for women to negotiate the use of condoms with their partners (which is the only method to prevent STD infections and another common method to avoid unwanted pregnancies). Microbicide can allow a new way of contraception: safe and affordable, where women don’t have to negotiate with their partners.

 

This project is generously supported by their university (Université de Montpellier), and the CBS research center (Center of Structural Biochemistry), which they are proud to represent on their visit to the USA. The team wants to take part in this science program by characterizing and sharing new parts of L. jensenii as well as to present their project to the scientific community.

 

You can join us on social media to follow our adventure:

Facebook     Twitter     Instagram  

Genome Engineering and Synthetic Biology (3rd edition)

A VIB TOOLS & TECHNOLOGIES CONFERENCE

Genome Engineering and Synthetic Biology are revolutionizing Life Sciences. Driven by advances in the CRISPR-toolbox for rapid, cheap, multiplex modification of genomes and breakthroughs in DNA synthesis technologies, the pace of progress enabled by these tools in the last years has been breathtaking.

The 1st and 2nd Genome Engineering and Synthetic Biology: Tools and Technologies meeting (GESB) in September 2013 and January 2016 were a roaring success and we are pleased to announce the 3rd edition of GESB in picturesque Bruges in January, 2018. 

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The conference will look at emerging tools & approaches in the field of: 

  • CRISPR and Synthetic Biology Tools
  • Gene and Genome assembly
  • Targeted Genome Engineering and Design
  • Genetic Circuits and Regulation
  • CRISPR Screens

The symposium will bring together some of the most highly regarded Academics and Companies in the world with novel technologies in several sessions. In addition to a great scientific and technology program, the conference will provide ample opportunities to network during the breaks, poster sessions, the conference dinner and our ‘Meet the Expert’ session!

Website link: https://vibconferences.be/event/genome-engineering-and-synthetic-biology-3rd-edition

Poster information: Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation

Deadlines:

  • Early Bird deadline: 14 December 2017
  • Abstract deadline: 30 November 2017
  • Final registration deadline: 11 January 2018

Speakers:

  1. Prashant Mali - University of California, US
  2. Michael Bassik - Stanford University, Department of Genetics, US
  3. Peter Cameron - Senior research scientist, Caribou Biosciences, US
  4. Emily LeProust - CEO, Twist Bioscience, US
  5. Tilmann Bürckstümmer - ‎Head Of Innovation, Horizon Discovery, US
  6. Paul Dabrowski - CEO, Synthego, US
  7. Benjamin P. Kleinstiver - Harvard Medical School, US
  8. Kevin Ness - CEO, Muse bio, US
  9. Philipp Holliger - MRC Laboratory of Molecular Biology, Cambridge, UK
  10. Linyi Gao - Zhang Lab - Broad Institute, US
  11. Helge Zieler - Founder/ President, Primordial Genetics, US
  12. Tom Ellis - Imperial College London, UK
  13. Paul Feldstein - CEO, Circularis, US
  14. Sunghwa Choe - School of Biological Sciences, Seoul National University, KR
  15. Tim Reddy - Duke University, US
  16. Daniel P. Dever - Stanford University, US
  17. Jason Moffat - University of Toronto, CA
  18. Tim Brears - CEO, Evonetix, UK
  19. Paul Diehl - COO, Cellecta Inc., US
  20. Akihiko Kondo - Kobe University, JP
  21. Mazhar Adli - University of Virginia, US
  22. Joseph Bondy-Denomy - UCSF, US
  23. Alan Davidson - University of Toronto, CA
  24. Theresa Tribble - Co-Founder, Business Development, Beacon Genomics, US
  25. Bing C. Wang - Co-Founder & CEO, Refuge, US
  26. Elaine Shapland - Head of Build, Ginkgo Bioworks, US
  27. Sven Panke - ETH Department of Biosystems Science and Engineering, CH
  28. Yvonne Chen - Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, US
  29. Kedar Patel - Director, Zymergen, US
  30. Steven Riedmuller - Synthetic Genomics Inc, US
  31. Farren Isaacs - Yale University, US
  32. Roy Bar-Ziv - The Weizmann Institute of Science, Rehovot, Israel

 

Address:

Site Oud Sint-Jan
Zonnekemeers (parking)
8000 Brugge
Belgium

More info


 

Introducing DOULIX: A Bio-Engineering Platform from Explora Biotech

Synthetic biology hinges on the ability to build biological systems from the bottom up using biological parts. Plasmid design is crucial and with so many parts to choose from, assembling compatible parts can be a bottleneck in Syn Bio workflows. To address this, Explora Biotech have recently launched Double Helix Technologies (DOULIXTM) – a toolkit to design, validate and synthesise custom constructs for synthetic biology.

This is a 3-step process:

1.      Design. Using their free online design platform, users can design a custom plasmid from their library of parts (‘biomodules’) or from your own custom sequence to assemble into a vector of choice.

2.      Validation. The software guides you through a design validation to avoid common design flaws.

3.      Synthesis. You can order ready-to-use full length constructs, or order individual Biomodules to assemble yourself.

It looks good on paper, so we got in touch with Davide De Lucrezia from DOULIX to find out more.

 

Q. What do you think are the current bottlenecks of synthetic biology projects?

We feel that the lack of in vivo standardization of standard biological parts is the main bottleneck. Without reliable in vivo data, any simulation will run on wobbling data and will inevitably be of little help to experimental synthetic biologists.

 

Q. How does DOULIX aim to circumvent these issues?

We started a challenging project to measure in vivo activity of most commonly used standard biological parts called DOULIX GrandChallenge. Together with the LIAR EU project (http://livingarchitecture-h2020.eu/) we aim to provide the SB community with rock-solid in vivo data to be used for simulation and model refinement. These data will be available through DOULIX’s database and used by our multiscale simulation platform to be released in 2018. Together with our synthesis platform, we hope to provide the SB community with a comprehensive toolkit that allows them to move seamlessly from design to fabrication.

 

Q. What is the average turn-around time for de novo constructs from DOULIX?

Individual dsDNA can be delivered in as little as 5 working days and full-length circular constructs of up to 10 kbp are usually delivered in 15 working days.

 

Q. Are the Biomodules all optimised for E. coli, or are other (and if so which?) expression systems catered for?

To date, most of our Biomodules are optimised for E.coli chassis. However, we are glad to announce to EUSynBioS a new partnership with Agilent that will tremendously expand our Biomodule collection to include parts optimised for Yeast and mammalian cells.

 

Q. What is the advantage of DOULIX over designing constructs ourselves?

With DOULIX you can finally use in vivo validated Biomodules so you can focus on construct/circuit design rather than part validation. I think that DOULIX is a substantial step ahead toward abstraction and decoupling in SB, something we really need if we want to unlock the full potential of SB.

 

Q. How do you see DOULIX expanding to serve the Synthetic Biology community in the future?

The next big thing is our DOULIX simulator, an integrated simulation platform for multiscale modelling using in vivo data. We expect it to have a big impact on the SB workflow. Yesterday we used the old genetic engineering approach of trial-and-error, today we are using the Synthetic Biology approach of design-build-test. But as for tomorrow we envision a time when we will confidently simulate before we built, saving time, money and delivering safer drugs, greener products and greater knowledge. Tomorrow, we envision the dawn of constructive biology.

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DOULIX are kind sponsors of EUSynBioS. For more information about Explora Biotech and DOULIX, visit https://www.explora-biotech.com/ and https://www.doulix.com/ or contact info@doulix.com.