Data as Art Exhibit: Today through February

We invite you to join us for an opening reception Jan. 26 at 5:00 pm in the Ford Atrium to welcome the Data as Art Exhibit. This year’s projects include two projects that are synbio focused and make use of the Addgene database.

Data as Art is a fall-term course co-taught by faculty from the School of the Art Institute of Chicago (SAIC) and Northwestern Engineering. In this course, students from both institutions work across multiple disciplines to engage in a critical dialogue about information visualization and to conduct collaborative research using data sets. The final projects represent data on a platform of visual art.

Data as Art culminated in an exhibition of the projects at SAIC’s LeRoy Neiman Center where the students’ work was on display Dec. 5-17. Now it is our turn to welcome the exhibition, which will be on display in Ford’s atrium for the next month. Please join us for the installation viewing accompanied by light refreshments.

If you can’t make it to the reception, the exhibit will be on display in the Ford Atrium for the next month.

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.

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.

1/11/2016: Biomaterials

Recently in biomaterials:

• For highly repetitive biopolymers such as collagen and spider silk, DNA synthesis is extremely challenging using modern techniques. To address this problem, Tang and Chilkoti developed an algorithm to optimize synthesis of DNA sequences for highly repetitive proteins. They arrived at a codon scrambling method by applying a variation on the Traveling Salesman problem, in which the computer is asked to find an optimal route that only visits each target once. They demonstrated the efficacy of their method by optimizing the sequences for 19 challenging, repetitive-sequence proteins, including elastin, collagen, TALENs and spider silk. DNA sequences for these proteins were commercially ordered and successfully cloned. Their work is found here.

1/11/2016

Recently in research:

• Vasquez et al. added synthetic pauses in translation to improve protein solubility. They made use of the known fact that in nature, ribosomes exhibit strategic pauses in translation to allow protein domains to fold efficiently before continuing translation.  They edited the sequence of linkers between protein domains for varying ribosome affinity, to induce ribosome stalling. Their work demonstrates a 7-fold difference in expression level of soluble protein by changing only the linkers and not the protein’s primary sequence. Their work can be found here.

• Zhang et al. showed that, at the single cell level in culture, gene expression plateaus at two distinct levels: a dynamically active steady state, and a dynamically inactive but higher second plateau. Previous measurements of “steady state” gene expression have assayed expression at the second plateau, but Zhang et al. demonstrate that measurements at the first, dynamically active plateau are more predictive of a promoter’s behavior when assembled into a circuit. Their work is found here.

Gene Drives

On January 11th we learned about gene drives and explored their safety and regulation. This brought up key questions:

• Can we really know enough about our environment to make gene drives safe?
• Are there any issues with the currently advertised safety measures for gene drives?
• What would be the ideal characteristics of a gene drive regulatory strategy?
• How can gene drives be implemented responsibly?
• What regulatory body would be qualified to make a decision about the use of a gene drive?

What do you think? Please join the discussion in the comments below.