SynBio Newsreel, November

Hey look, we figured out how to embed video! Now you can watch a newsreel summary first, and then read any of the papers that sounded particularly interesting. There are fewer links this month because work in November+December was crazy, but rest assured the January newsreel will be just as exhaustive as usual!

Synbio community news

  • Who needs CRISPR gene drives when you have Wolbachia? Scientists have successfully engineered the microbe, which lives in insect cells and spreads to all female offspring (while killing males), to render mosquitos inhospitable to dengue virus.
  • The GP-Write white paper came out. STAT summarized it.
  • iGEM happened! Many cool things. Grand prize winner was Imperial College London’s team, which engineered different strains of E. coli to co-culture at different population ratios.
  • This year’s iGEM saw the launch of bionet, a P2P sharing platform for biological materials developed through the Biobricks foundation and a Drew Endy-led team.
  • The Wyss Institute’s work on replacing animal drug testing models with human organoids on chips gets a write-up in Wired.
  • UK researchers apply to perform field trials on wheat that has been modified to photosynthesize more efficiently, boosting yields 20% (in a greenhouse).

Industry news

  • The Guardian profiles BioAmber and Bolt Threads, two companies trying to develop yeast-based pipelines for succinic acid and spider silk fabrics, respectively.
  • PacBio sues Oxford Nanopore for infringing patents related to reading a single DNA molecule twice. OmicsOmics argues this lawsuit probably won’t damage Oxford Nanopore’s business, and is more an act of desperation from PacBio.

Now, on to the research papers!

Biomolecule engineering

CRISPR/gene editing

Synthetic Biology Sources: Where to Start

Just after the grand opening of Northwestern’s new Center for Synthetic Biology, I got an email from a research assistant professor with a background in physics who was excited about synbio and wanted to know how to get up to speed on the field. What follows is a modified version of the email I sent him, which comprises most of the resources I’ve found and have used online to learn about synthetic biology. This post is by no means comprehensive (the list of important labs is especially incomplete, and probably merits its own post), but hopefully this is a useful starting point for anyone interested in learning more about the field.

List of Synthetic Biology Resources

1. There are a lot of really excellent presentations on Youtube which provide broad overviews of synthetic biology and background about where the field came from. Here are a few of them, which I’ve tried to arrange from most accessible to most academic/wonky:

2. For more in-depth background training in cell/molecular biology:

3. There are a bunch of excellent review articles for the field that link out to lots of seminal synbio papers. Here are some of them:

4. This special issue of Nature on systems and synthetic biology, while ~5 years old, is filled with important papers and perspectives, both contemporary with its publishing (2010) and reviewing the highlights of the field from 2000-2010. I particularly recommend the News and Views articles in it for a quick summary of where the field has gone and is going.

5. There are several labs whose research I recommend searching for/keeping abreast of, as they are important for various areas of synthetic biology:

  • Michael Elowitz, Caltech
  • Jim Collins, MIT
  • Christopher Voigt, MIT
  • Drew Endy, Stanford
  • Pam Silver, Harvard
  • David Baker, UW Seattle
  • George Church, Harvard
  • Christina Smolke, Stanford
  • Jay Keasling, UC Berkeley
  • Jennifer Doudna, UC Berkeley
  • Feng Zhang, MIT
  • John Dueber, UC Berkeley
  • Martin Fussenegger, ETH Zurich
  • Tom Ellis, Imperial College London
  • Ron Weiss, MIT

Synthetic Biology professors at Northwestern:

6. If you’re interested in learning about the policy/industry/economic aspects of synthetic biology, I recommend Rob Carlson’s book Biology is Technology, a lot of which is available online through that link for free. Carlson is generally a good source of realistic predictions about the field’s future. I also recommend his blog, Synthesis.

7. Speaking of blogs, here are a few other blogs/news sources I’ve found that regularly feature news/commentary about synthetic biology: 

  • PLOS SynBio (a blog completely devoted to synthetic biology/the synbio community)
  • Genome Web (mostly genomics, but lots of stuff on the synthetic biology industry)
  • Holman’s Biotech IP Blog (all about biotech and the law; had an excellent series recently on why DNA should be protected by copyright, not patents)
  • Trade Secrets (Nature’s biotech blog)
  • GetSynBio (good source for companies that provide synthetic biology services)

8. Carlson’s not the only person writing policy pieces on the field. Synberc (the Synthetic Biology Engineering Research Center, one of the first/biggest synbio organizations) maintains a list of white papers which discuss and argue about how the research, commercialization and regulation of synthetic biology should proceed. They make for very interesting reading.

9.  Here are a few journals that regularly publish synthetic biology research:

10. Finally, to keep up with current developments in synthetic biology, I recommend setting an auto-search on PubMed and Google News for synthetic biology. I wrote an article recently about how to do this. I actually think this is a more efficient way to find new research/developments in synthetic biology than reading particular journals.

What did I miss?

I’m planning to update/revise this post as new and better resources come to my attention. If you think I left something obvious off, let me know in the comments!

Automating the Search for SynBio News

If you’re reading this, you’re probably quite interested in synthetic biology. The synbio community is diverse and widely distributed, and I have yet to find a single site which efficiently aggregates all the content that a synthetic biologist might want to read. We started GeneMods in part to pool our collective eyeballs and better keep abreast of developments in synbio research, policy and industry. In that spirit, here is the first post in a series about where to find synthetic biology content on the web.

Automated Search is Your Friend

If you’re lazy like me, the quickest and most powerful way to find articles on synthetic biology is to let your computer do the searching for you. Automated searches save you a bunch of googling, and bring news sources you might never have otherwise discovered right into your email inbox. I recommend using an automated PubMed search to find research articles, and a weekly Google Alert to find both synbio news and the sites that publish it.

Automated PubMed Search

This is a really easy and flexible way to get a ton of primary literature. It takes literally five steps:

  1. Register for a PubMed/NCBI account. All it takes is an email address, username and password.
  2. Go to PubMed, and search “synthetic biology” (include the quotes) while signed in on your account.
  3. Click the “Create alert” button right under the search bar.
  4. Adjust the number/frequency/date settings to your liking. I set mine to email me the abstracts and links to 10 synbio articles every Saturday morning. Yay weekend reading!
  5. Save your settings, and adjust them later by clicking the “My NCBI” button at top right and editing your Saved Searches.

If all goes well, you should start receiving emails from “My NCBI” which summarize recently published synthetic biology research.

Google Alerts

Google is pretty good at finding stuff, and Google Alerts are a simple way to have Google bring that stuff to your inbox. I particularly like Google Alerts because they show me articles from sites I wouldn’t have otherwise found, some of which have since become my favorite sources of synbio news and essays. Setting up a Google Alert also takes only five steps:

  1. Sign into your Google/Gmail account.
  2. Go to
  3. Type “synthetic biology” into the search bar.
  4. Click “Show options” and adjust the number/frequency/language settings to your liking. I set mine to receive the best results in English from any region once a week.
  5. Save your Alert, and adjust them later by going back to

You should start receiving emails from Google Alerts containing titles, links and the first few lines of synbio news articles from around the web.

There’s a Whole World Out There!

I’ve outlined two simple and useful automated searches, but these are by no means the only or the best ways to find synbio content online. I like to think of them as starting points: with these searches, you can start to figure out which journals and labs publish the papers you like, and which sites publish articles you enjoy reading. From there, you can subscribe to weekly newsletters or RSS feeds for the sites you really like, set up further PubMed searches to flag articles from your favorite lab or sub-field, and google your favorite authors to find their blogs. In future posts I’ll outline some of the best sources of synbio content I’ve found through these further searches. In the meantime, I hope I’ve made it a little easier to explore the world of synthetic biology.

Special thanks to Drew Endy for first showing me how to set these searches up.

Tools: antisense promoters

Brophy and Voigt report characterizing antisense promoters to tune the transcription and translation of a forward-facing gene, and to build a simple NOT circuit. They note that the effects of antisense promoters on repressing gene expression is largely context-independent, and that level of repression correlates well with the strength of the antisense promoter. According to their model, two mechanisms contribute equally to this phenomenon. Most obviously, antisense promoters create antisense RNA which base pair with mRNA to obstruct translation. Collisions between RNA polymerases heading opposite directions on the same gene also contribute. Their work can be found here.