Monthly Archives: September 2015

Yesterday I went on the Church Lab Retreat!

Up in the New Hampshire woods, everyone crowded around a tiny projector to listen to silly 5 minute talks.

george church

George talked about terraforming Venus.

Some quotes from the talks:

“The paper was so dense, not even light could escape.” ~ Paul

“I’ve been offered more than 5 minutes, but I won’t take them. I have 1000 slides.” ~ George

“Puzzle boxes can be NP hard” ~ Kevin

One of the talks was about natto. A sample platter was passed around.


Let’s say it’s very much an acquired taste.

There were also other notable moments, like when Joe taught everyone how to throw a giant net, me eating the best veggie burger I’ve had in my life, people’s horror encountering a clivus toliet for the first time.

I got to share a ride with my new favorite grad students Johnny and Su and unexpectedly hung out with Veronica before she left for NYC.

It was a super fun time!

This list was inspired by Robert’s Cryobiology and Electron Microscopy reading list.

When I started doing research again, Alex was super great and sent me a slew of papers to catch me up to the latest developments in synthetic biology relating to Cas9.

A while ago, I made a post with some links introducing Cas9, but after seeing Robert’s list, I feel I should post the entire list of Alex’s recommendations.

So here it is!

Introduction to Cas9:

Development and Applications of CRISPR-Cas9 for Genome Engineering
DOI: 10.1016/j.cell.2014.05.010
This is a very well written and easily digestible summary covering events from the discovery of Cas9 to recent applications in biological engineering.

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
The key paper that uncovered Cas9’s behavior and opened the door for engineering with Cas9. It’s a little dense for those not in the field.

Applications to mammals and humans:

Multiplex Genome Engineering Using CRISPR/Cas Systems
DOI: 10.1126/science.1231143
Native Cas9 cleaves DNA in bacterial cells. This paper shows that Cas9 can be used for target cleaving in human and mouse cells using a split Cas9 system.

RNA-Guided Human Genome Engineering via Cas9
DOI: 10.1126/science.1232033
Native Cas9 uses two guide RNAs to recognize what target to cleave.  This paper shows that the two guide RNAs can be combined into one for easier engineering.

Related to my research:

A Split-Cas9 Architecture for Inducible Genome Editing and Transcription Modulation
The paper describes how Cas9 can be split and and modified to reassemble in the cell in the presence a specific molecule.

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA
This is one of a few papers describing the structure of Cas9. The structural data from this paper is submitted to the Protein Data Bank as ID:4OO8.

Small Molecule–Triggered Cas9 Protein with Improved Genome-Editing Specificity
Cas9 can be fused with other domains that it only activates in the present of particular molecule

Highly Efficient Cas9-Mediated Transcriptional Programming
DOI: 10.1038/nmeth.3312
Cas9 can be fused to transcription activators to create a custom genetic ON switch

Check these papers out if you want a better understand of why Cas9 is so hot in synthetic biology right now. They’re a good read and present some really interesting possibilities.