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Microbial DNA, Biobricks and Body Odor, My Post Grad Year with iGEM Paris Bettencourt

By Aakriti Jain

The iGEM, or International Genetically Engineered Machine, competition offers a platform for university students across the world interested in synthetic biology to work on creative projects centered around the foundation of synthetic biology: streamlining biology into an engineering science and building biological systems from standard parts that are operated in living cells.

To facilitate this, teams are provided with a kit of standardized biological parts (biobricks) at the beginning of the summer. The teams may modify and combine the biobricks or synthesize new parts of their own design to build novel biological systems. The competition was started in 2003 at the Massachusetts Institute of Technology, as an intersession project. Since then, the competition has grown to 245 teams participating from all over the world, showcasing a large variety of projects from dye-producing bacteria, to those engineered to help cure tuberculosis.

The Paris Bettencourt iGEM team, part of the Centre Recherches Interdisciplinaires (CRI), has been a participant since 2007. Last year, the team was the Grand Prize winner in the overgraduate category with the best Health and Medicine project. Their project, titled “Fight Tuberculosis with Modern Weapons,” used synthetic biology tools to fight tuberculosis with a four-part strategy: gene detection, drug targeting, infiltrating macrophages and, finally, the sabotage of the synthesis of proteins.

As a student from the University of California, Berkeley, with a keen interest in synthetic biology, I always knew about iGEM, but focused on working at different industrial summer internships instead of joining the Berkeley team. Last February, with graduation around the corner, I was presented with the chance to join the Paris Bettencourt iGEM team. For someone who is interested in science, engineering, and endeavors to experience different cultures and environments, this was the perfect unexpected opportunity that led me to take an unconventional post-graduation step for a chemical engineer and join the Paris Bettencourt iGEM team.

igem

A truly international & multidisciplinary perspective on applications for synthetic biology and “good” and “bad” odors 

What really captivated me about the Paris Bettencourt iGEM team is how international the team is; we have students from France, Spain, Poland, China, India, Mexico and the United States. Not only are we unique in our cultural backgrounds, but also in the skills we bring to the table. Our team is comprised of synthetic biologists, engineers, computer scientists, designers, and more. Our different educational and cultural backgrounds allow us to develop and nurture creative scientific ideas.

Finding creative applications of synthetic biology truly defines our team’s goals. This year, we are working on treating a problem that, while taboo to talk about, is omnipresent in our world: body odor. There are few synthetic biologists who have attempted to engineer bacteria to treat malodor; the main reason this area is lacking in study is the difficulty in quantifying an odor. We hope to use odor professionals and scientific tools in order to overcome this hurdle and intelligently investigate the links between our skin microbiota and body odor.

In order to combat common human body odor, we are targeting a gene called agaA in a bacterium commonly found in the skin microbiome: Corynebacterium striatum. C. striatum metabolizes sweat compounds into volatile sulfurous compounds which are what we perceive as body odor. The goal of this particular project is to isolate natural mutants of C. striatum that have nonfunctional agaA by using CRISPRs to target mutational hotspots in the gene.

Trying to find a cure to the common body odor we experience while taking the metro in Paris or the subway in NYC, is just one part, we are also trying to see if we can neutralize specialized cases of unpleasant body odor. One such case is the odor in seniors over the age of 40, who experience an increase in the amount of a greasy smelling unsaturated aldehyde called 2-nonenal on their skin surface. The other special case is a rare genetic disease called fish-odor syndrome, caused by the excretion of an unpleasant smelling compound called trimethylamine due to the lack of production of an enzyme known as Flavin-containing monooxygenase 3. For all these projects, we will be using synthetic biology techniques such as bioinformatics analyses, modeling, directed evolution to find mutants that reduce odor, and cloning genes found in other organisms into a C. striatum chassis in order to create a microbial therapeutic for body odor.

Apart from eliminating causes of malodor, we are also working on creating a library of pleasant odors in order to understand human perception of smell. Similar to how all colors can be created by a combination of the primary colors, the odors we perceive can be based on primary odor categories. We hope to create a database of gene sequences that can be assembled in E. coli correlating to these primary odors, thereby being able to produce a large range of odors.

Going local with citizen science and open science links

In order to improve our knowledge of the connection between human microbial flora and smell perception we are conducting an open citizen science project, titled “Gym Class Heroes.” We are designing a kit that will include sweat collection apparatus and a questionnaire about the individual and his or her lifestyle. We will extract and sequence individual microbial DNA samples and correlate the sequencing data to body odor.. Thus, we will be able to offer individuals the opportunity to learn about their microbiome, help us analyze the data we receive, and also discover how others perceive their body odor.

In conjunction with all the scientific projects, we are trying to create an environment of collaboration within the synthetic biology community. We have started a biweekly newsletter with fourteen iGEM teams from across the world, with more teams joining in every week. This newsletter highlights updates on projects each team is working on and questions they may have concerning their topic. This creates a forum for feedback among the participating teams, and raises awareness about the different projects teams are working on prior to the Jamboree itself.

Extending the idea of open science and collaboration even further gave rise to two other projects that the iGEM Paris Bettencourt team is working on. The first is to create a comprehensive guide on creating an iGEM team for high school students. While the iGEM foundation had the first High School Jamboree in 2011, only 54 teams registered last year, and awareness remains low. This guide, which will be hosted on Education Genius, will include videos on forming and fundraising for a successful iGEM team, brainstorming for feasible ideas, carrying out a synthetic biology project, and other logistical and administrative nuances that may not be obvious from simply reading the iGEM website. Our goal is to improve attendance to the High School iGEM jamboree across the world.

The second project is a mobile application called “Minder.” The goal of this application is to connect individuals with others in their vicinity with synthetic biology related ideas they are interested in. If an individual likes an idea, they can chat with the person who had the idea and potentially join the project. This mobile app will be structured similarly to the popular dating application called Tinder for its ease of use in swiping either left or right depending on whether to accept or reject an idea.

For someone who went to school and grew up in the Silicon Valley, the level of openness and entrepreneurial spirit that the Paris Bettencourt iGEM team manifests is encouraging. After being in the San Francisco area for so long, I began to become a little closed-minded to the fact that there are people with amazing ideas all over the world; it was refreshing to see that I was completely wrong.

I am more than excited for the rest of my time in Paris and on this wonderful team, and hope to see you at the iGEM Jamboree in Boston come November!

All views expressed in this post belong to the author, and are not necessarily those of PLOS.

apicAakriti Jain is a recent graduate of the University of California, Berkeley with a degree in Chemical and Biomolecular Engineering. She has an interest in novel scientific technologies, writing, and new experiences.  

Follow Aakriti on Twitter: @twitajain

Follow Paris Bettencourt iGEM: @iGEM_Paris

Discussion
  1. As a total nube -what is meant by “bio bricks”.Are these parts available off the shelf ? Who defines the specs ?are there international standards ?

  2. Hi! Thank you for your comment and question!

    BioBricks are building blocks or PARTS that are used to design and assemble into a DNA biological circuit that is useful in some pre-determined application. These different DNA parts can be things like promoters (which is where a protein called an RNA polymerase binds), or other sites on a DNA sequence that are important for creating RNA and proteins.

    These parts are available open access in the “Registry of Standard Biological Parts” which is a database that was designed by researchers from MIT, Harvard and UCSF and also in a public funded facility called “BIOFAB International Open Facility Advancing Biotechnology”.

    The specification for each part is defined by the user, and yes, there are international standards, but currently most parts are submitted by organizations like different iGEM teams and so there may not be a lot of information for every single part that is in the registry (and this is something that needs to be worked on in the synthetic biology community, since the streamlining of data in synbio is still a very new concept).

    If you’re interested, our MOOC videos will be covering some of these topics in greater details and we will also be providing links to more information on the MOOC. 🙂

    Aakriti

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