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:

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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:

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3 Questions for Prof. Hyun Youk

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Our newest instalment of the "3 Questions for" interview series features Prof. Hyun Youk from Delft University of Technology in the Netherlands. His research makes use of quantitative methods as well as models and theory to understand the interactions between molecules and cells and discover common design principles. Here, he speaks about his transition from physics to biology and his view on the field of synthetic biology.

 

When and why did you move into the field of synthetic biology?

I never considered myself as a full-fledged synthetic biologist and I certainly haven't done any significant work in synthetic biology. But I have used and my group routinely uses tools of synthetic biology to modify and complement endogenous signalling pathways with engineered signalling circuits, with the goal of better understanding those endogenous pathways or what cells can do. On the other hand, my group doesn't build synthetic circuits to create logic gates, devices, desired dynamics, and practical applications. That’s why I hesitate to call myself a synthetic biologist in the conventional sense.

Instead, I can say when and why I moved into biology from physics.  At the core, I'm a physicist who’s been very interested in understanding how inanimate molecules - the same ones that make up many non-living systems - give rise to features that we associate with life in one scenario but not so in another scenario. This tells us that dynamics, not the molecular content, are what determines whether something is living or not and that we don’t really understand the principles that underlie these dynamics (keep in mind that even a dead cell can contain DNA so “ all living things contain DNA and non-living things don't” is not the answer). This question of what distinguishes the living from the non-living has stayed with me since 2006 when I started learning and doing biology. In 2006, I enrolled in MIT’s physics graduate program. As a beginning PhD student, my original intention was to join a cold-atomic physics group there. But I had a year of fellowship money to try other fields before formally committing to a lab. At first, I did an internship in a nanotechnology lab that studied how electrons moved through quantum dots. But that group’s PI let me go after a month - this is a gentrified way of saying “I was fired” -  because he thought that I wasn’t good and that I kept messing up a senior PhD student’s experiments. That was a low point for me because I had just started the PhD program and I had never been fired before. My options then were to just finish taking the required courses (in the American PhD programs, you had to take courses) and eventually join the atomic physics group after 9 months or try my hands at a different field.

In my daily commute to the nanotechnology lab, I passed by the biophysics lab of Alexander van Oudenaarden. I had no idea what he was working on, and I didn’t even understand the words in the title of his group's papers and posters that were posted outside his lab. My last course in biology was more than six years ago in high school, which was mostly about Mendelian genetics and ecology and almost nothing about molecular biology. At this point, as physics student, I also didn’t know what a pipette was, how RNA was different from DNA, and what the central dogma of molecular biology was. But what struck me about my morning commute through the hallway of Alexander’s group was how happy people seemed in his group. I routinely heard laughters coming out of the lab as I walked by. Before approaching Alexander for an unpaid internship, I first borrowed Alberts' book on molecular biology from a library. I found the book (and I still do) very difficult to read because biology textbooks were and still are written in styles that are very distinct from those of the physics and math textbooks that I was used to.  Even though I barely made through a page in any of the chapters in Alberts’ book, I found that I could pose for myself very simple questions about living systems while reading the book and that these questions, posed by someone without any biology background, were largely meaningful and still weren’t answered yet. That really hooked me on biology. So I asked Alexander for an internship and he generously gave me the chance. Since then I fell in love with biology, questions about life which could border on philosophy, and doing experiments with my own hands. I never looked back since then and I’m very grateful to Alexander to this day for giving me a chance and keeping me in his lab for the next 4 years.

Aside from the positive lab culture and the fact that I could pose “simple" questions, such as “how does a cell ’know’ this and not that", to which deep answers didn’t exist yet, the final clincher for me was the revelation that I could quantitatively address those simple questions about living systems with my own hands at the lab bench. Through my internship in Alexander’s lab, I found that I could resolve these questions about cells by designing “simple” experiments, doing them, and then having the results of those experiments tell me the next steps. I have found and still find this process to be similar to the process one uses in proving mathematical theorems through a series of logic, which I also enjoy doing, or how a detective would narrow down the list of suspects. I very much enjoy this hard-to-describe “funnelling” process that narrows down a complex biological system or a grand question about life into concrete conclusions. Aside from these grander points, I also found myself enjoying even the little things like pouring agarose gels, running PCR, aliquoting media, making master mixes, pasting gel pictures into my lab notebooks, etc.  In retrospect, I find that this aspect - enjoying even the seemingly little things in day-to-day bench activities - were indispensable for whatever success I’ve had in research.

So that’s my non-linear path to biology. I've revealed these details here to remind readers who are students that some small event - in my case, being fired from an internship - can literally have a life-changing consequence and that like in research, serendipity and seemingly devastating failures can actually lead to a very positive outcome in a scientist's career. I also think that my story is just one of many like it and that it shows one should not be afraid to enter a field that one knows nothing about. If you’re really fascinated by the question, then I say you should go for it.

 

What is the single most important piece of advice that you would give to a current PhD student or a post-doc?

My first advice is to take anyone’s advice, including mine, with a grain of salt. There’s no one shoe that fits everyone. With this caveat, my advice for PhD students is different from one that I’d give to postdocs.

If you’re a PhD student, keep in mind that your goal is to learn how to develop a story backed by data and then tell that story through writings and talks. In many countries, you have four years to develop and tell a story. Be very critical of your own work. Learning this is also an important part of a PhD. Once you know how to develop and tell a story, then you’ll find these are useful skills in any other field of science as well as outside of science (keeping in mind that you don’t have to stay in academia or in science after a PhD - leaving academia is not a “failure”). You can keep a text document and slides that you constantly update with new results. The idea is that the text will evolve into a manuscript and the slides evolve into slides for a talk that you can give to anyone about your work. When you first start a project, the text and slides will be empty, contain vague items, and a messy outline. But as you get new results, they will evolve. You’ll find that you’ll need to delete some paragraphs or slides because the story has changed. You’ll rearrange some slides because their order no longer makes sense according to the evolving story that you want to tell. The process of rearranging, deleting, and as a result, planning the next experiments is the process of learning how to do science. I think this is what every PhD training should be about.

If you're a postdoc who’s looking to run your group one day, I think you need to think about if there are questions that your own group will want to pursue that are unrelated to your current postdoc work while, at the same time, having the postdoc work being helpful in pursuing those questions (e.g., same organism with similar techniques). What you do in your own lab does not have to be a natural extension of your postdoc work. Don’t let a decision that you made years ago on where to do a postdoc dictate the next 10-20 years of your life. A luxury that we have in systems and synthetic biology, while not exclusive to these fields, is that we’re often driven by abstract concepts and are not tied to a particular pathway, mechanism, biological process, or an organism. So you can chart a course for your lab that really is distinct from what you did during your postdoc. But I think you can be strategic about doing this. For example, doing follow-up studies of your postdoc work may let you publish soon (1-3 years) after beginning your lab. In the meantime, you can explore a new area that really excites your group and if that new direction works out, then your lab can start publishing in that field after 4-5 years and start shifting into that new area, if you’d like. I think this strategy can let your group avoid the publication draught of the first few years that starting labs often experience while also having the time to develop a new line of research if that’s what you’d really like to do. On the other hand, there’s nothing wrong with more gradually extending your postdoc work and having that be the focus of your own lab. Again, no one shoe fits everyone. The most important thing is to dream big about what your lab will have contributed after 5- 10 years.

 

In which areas do you see the main challenges and opportunities for synthetic biology?

I think the biggest challenge for me is understanding biology well enough to build systems that mimic or extend natural systems. In my experience, no circuit that I or my group has built ever worked out the way that we thought that it would. These apparent “failures” yielded surprising findings and formed the bases of projects and publications in my PhD, postdoc, and now in my group. Think of how the repressilator led to, unsuspectingly, a vivid demonstration of noise in gene expression. That study helped in launching the burgeoning field of stochastic gene expression. For me, I think the challenges and opportunities are the same: Not understanding biological systems well enough and trying to perturb them has and will lead to discoveries about how cellular processes work, whether they be evolved or hand-made. I think this will be an ever-lasting challenge and opportunity that will outlive the technological limitations that we have now (e.g., cost-effectively writing DNA of an arbitrary length letter by letter and integrating it anywhere inside a cell of any type).

3 Questions for Prof. Sven Panke

This time the "3 Questions For" series features Prof. Sven Panke from ETH Zürich in Switzerland. Prof. Sven Panke currently holds a position as Professor at the Department of Biosystems Science and Engineering. His research focuses on the design of novel bioprocesses for the pharmaceutical and chemical industry.

 

When and why did you move into the field of synthetic biology?

I moved into Synthetic Biology in the early 2000s, when the topic was about to emerge in Europe. The engineering vision behind it displayed a very big attraction to me, even if it was clear from the very beginning that a simple transfer of engineering principles from classical engineering disciplines to biology would not work. However, the engineering narrative and the DNA synthesis methods seemed to promise a major improvement about earlier biological engineering methods. Another important factor was iGEM – a totally novel way of communicating a field to students and making them enthusiastic about it.

Since then, I stayed in Synthetic Biology because I think that it remains the most promising route to better strains in industrial biotechnology and in many neighboring fields, generating visionary projects that can capture the imagination of scientists from many different backgrounds.

 

What is the single most important piece of advice that you would give to a current PhD student or a post-doc?

Consider ignoring the advice of senior colleagues.

 

What do you think is presently the major limiting factor for progress in the field of synthetic biology?

I am not sure that I can name one factor that is more important than others. think that one major limiting factor is the time it takes to integrate of all the qualitative knowledge that we have accumulated over the years in computationally supported design platforms. We are making considerable advances there, but the process will, I fear, take another 10 years. I also think that we are becoming very good at certain aspects of synthetic biology, e.g. pathway optimization, but in the end this is only a certain aspect of the overall path from idea to real world impact – I think many projects still fail at an entirely different level, such as “this enzyme does not work in my chassis strain”, for whatever reason. And we should not forget that even if you have a good strain, you are still far away from having a good process. Finally, at some point we will return to the discussions that we had already once before, whether genetic engineering/synthetic biology is safe enough to be used outside contained facilities. The outcome of this discussion will have, I think, a strong impact on the future of synthetic biology outside of medicine.

 

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