SynBio Newsreel, September

Lots of news this month. We’ll post a link to the video version of the newsreel later this week. Enjoy!

Synbio community news

Biosecurity

Industry news

Longreads

  • The snakebite crisis is escalating. Synbio could help—but it needs to avoid distracting from lower-tech initiatives, like scaling antivenom production in Africa and giving farmers boots.
  • A thought-provoking history of DNA data storage, which also outlines the challenges and opportunities ahead for the field.
  • In-depth analysis of the medical/pharmaceutical biotech investment ecosystem, from Brady Huggett.
  • Freeman Dyson writes an inspiring vision of biology’s place in space exploration.
  • The Summer 2016 edition of BioCoder is out (free PDF download if you register). Read it if you’re interested in DIYBio and synthetic biology from the perspective of hackers and makers.

Video

Non-synbio blog of the month

  • Genotopia is Professor Nathaniel Comfort’s blog about bio, genetics, medicine, history, and hype in biotech. His recent trilogy of posts about going to Yellowstone hot springs to study the origin of life is definitely worth reading.

Now, on to the research papers!

Biomolecule engineering

Genetic circuits

CRISPR/gene editing

Metabolic engineering

Building biology to understand it

  • Yizhi Cai and Roy Walker summarize the results from the Fifth Annual Sc2.0 meeting, providing updates on the Synthetic Yeast Genome Project, and renewed debates about the Human Genome Project-Write.
  • Review article argues that synbio could help to predict new biochemical innovations life may experience in the next few billion years. It’s an interesting perspective through which to view the field, and discusses cool work on improving photosynthesis and rewiring central carbon metabolism.

Autotrophs and agriculture

Therapeutic synbio

The strains, they are a changin’

    • A team led by Dan Gibson engineers Vibrio natriegens, which grows 2-3 times faster than E. coli, into a platform for plasmid cloning and protein expression. The design-build-test cycle in biology is about to get significantly faster.

SynBio Newsreel, August

We have more of a newsletter than a newsreel this month, since there’s no summary video. However, that was because we devoted our entire monthly meeting to a thought-provoking critique and discussion of the Human Genome Project-Write, led by Professor Laurie Zoloth. With that said, enjoy the newsreeletter!

Synbio community news:

Industry news:

Books and Longreads

  • I just discovered BioCoder, a quarterly newsletter about synthetic biology from technology media company O’Reilly Media, and I’m really enjoying it.
  • Carl Zimmer gets his genome sequenced and analyzed by some of the best researchers in the field. A Game of Genomes chronicles his adventure. A must-read.
  • Ed Yong’s fantastic book about the microbes that precede, surround, live on, and comprise us, I Contain Multitudes, came out. I cannot recommend enough that you get your hands (or ears, it’s on Audible!) on this book.

Now, onto the research papers!

Protein engineering:

Genetic circuits:

CRISPR/Gene Editing:

Metabolic Engineering

Building biology to understand it

SynBio Newsreel, July

There was a lot of news this month. Enjoy!

Northwestern News:

  • The Communicating Science Convention (ComSciCon) in Chicago is coming up! If you’re in Chicago on Saturday August 6, I highly recommend you attend the keynote, where Emily Graslie will talk about how she and her team at the Field Museum engage with the public about science online.

Protein engineering:

Genetic circuits:

CRISPR/Gene Editing:

Computational/Bioinformatics

  • BioPartsDB: software that helps you design and build your own large DNA sequences from overlapping oligos.
  • ATLAS of Biochemistry: an online map of all known and predicted metabolites, and all known and predicted enzymatic pathways to produce them.

Building biology to understand it

Industry news:

Synbio community news:

Cool iGEM projects

May Newsreel (a little late)

Here are all the links from the May meeting’s newsreel. Enjoy!

—Isaac

Non-research articles:

1. Gen9 and Arzeda sign DNA synthesis deal. In related news, Twist Bioscience partners with Microsoft on DNA data storage. But how big is the synthetic DNA market? Rob Carlson’s perspective.

2. Synthetic biology tackles the antivenin shortage.

3. DIY bio lab in Brooklyn gets a profile in The Guardian.

Research articles:

4. Modeling competition between genes for expression machinery.

5. De novo design of protein structures which associate via hydrogen bond networks (as opposed to hydrophobic effects).

6. DNA nanostructures encoded and self-assembled in living bacteria.

7. Computationally designed protein enables biomineralization of cadmium chloride nanocrystal.

8. Moss assembles DNA in vivo (like yeast!).

9. Targeted isolation and cloning of 100 kb microbe genome fragments through Cas9-assisted technique.

10. DNA-guided genome editing with Natronobacter gregoryi Argonaute (NgAgo)—comparable in vitro editing to Cas9, but uses guide DNA rather than RNA, and doesn’t require a PAM sequence!

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 google.com/alerts.
  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 google.com/alerts.

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.