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
DOI:10.1126/science.1225829
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
DOI:10.1038/nbt.3149
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
DOI:10.1016/j.cell.2014.02.001
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
DOI:10.1038/NCHEMBIO.1793
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.

A couple months ago, I started using washi tape in lab (’cause they’re purty). I wrote about how well they held up from -4C to 37C environments.

agarose

Here’s an update of the tape in 60C ovens. The label was created around mid July. There’s a little bit of feathering, but still mostly legible. It still has good hold on the bottle and is still residue free when peeling.

Here’s a picture of the tape living in -20C conditions. It’s mostly unchanged from the day the label was created (except for the ice).

ice box

Since the tape survives most of my working temperature ranges, I use it for everything.

Seriously consider washi tape for your lab. It’s just too fun.😀

Oh man, maybe ’cause I’m newer to Flask but this was a feature that I wrestled with for hours.

Turns out if you run the Flask app from not within the application directory, it won’t serve up your static assets (JS, CSS, etc.).

python app_directory/app.py

I guess you must always run it from the app directory???

cd app_directory
python app.py

Bananas

@______@

My recent trip to China has definitely been an interesting cultural experience. While I’m no ethnographer on young people in China like my friend Christina, I want to capture little snippets of a subculture I am familiar with: Magic the Gathering.

Magic has a healthy following in China. Wizards prints a lot of Chinese Magic cards and brands Magic as 万智牌 (wànzhìpái). Even my favorite online Chinese annotator will translate 万智牌 as Magic. 万 means “ten thousand” or “many”, 智 is a combination of “knoweldge”, “widsom” and “intellect”, and 牌 here is “cards”. So Magic is literally a card game of many wits. How cute.

Since I play quite a bit of Magic locally, I wanted spectate a Magic event in China, to see what’s different and what’s cross cultural.

First stop was to find a friendly local game store. Game stores are the heart of local Magic communities, supplying cards and hosting Wizards sanctioned events.

While I’m impressed to find games stores in China listed on Wizard’s official store locator, the website didn’t load for me while I was there, because they use Google Maps. Google services are generally heavily throttled in China, slowed to the point that they’re unusable. (I made the decision to visit a game store last minute while I was in China, so I didn’t have the luxury of researching before my trip).

I found forum posts about game stores on Baidu and listings on a site that hasn’t been updated since 2013, but they didn’t seem reliable. I ended up going on Reddit and meeting an American Magic player living in the local area.

He took me to SGM 桌游俱乐部 (SGM board game club).

SGM

SGM sign up close

SGM is seclusively tucked away behind a shopping center. It is one the third floor of a mixed-use building, where residential apartments neighbor commercial offices, with little transition in between. One door could lead to a doctor’s office while the next could be someone’s home. I don’t think I’ve ever been in a mixed-used building before, but I hear they’re not uncommon in China.

inside

The inside of SGM feels a little like being inside a large apartment that’s chalked full of Magic decor. It’s definitely a smaller game store that can probably seat a maximum of 30 players at a time. My favorite part of the store was the table on the balcony, for those who prefer the outdoors.

balcony

SGM is pretty update in terms of the latest Magic products. They give out the latest promo cards at Friday Night Magic events and has all the latest sets. Since Magic is becoming more popular, they’re getting more Chinese cards instead of English ones. Previously, the first Modern Masters sets they got were in English, but the second Modern Masters were all in Chinese.

Unfortunately, due to my crazy schedule (and poor planning), I visited SGM on a quiet night where only a couple of friends were playing. I was a little sad that I didn’t get to talk to the Friday Night Magic crowd, but I had fun playing a couple rounds of EDH Magic. From what I hear, local Magic is highly competitive. I’m not too surprised since, for the young people, they’re brought up in a highly competitive environment focused on the 高考 (gāokǎo), the college entrance exam that’s the sole determinator of which college they’ll attend.

EDH

Probably because we were playing with a German expat and a Chinese student, each of the decks we played with had a mix of German, English, and Chinese cards. While it felt natural to have multilingual decks there, I remembered I’ve never seen any non-English cards in a deck here. I was a little sad how monolingual we are in the States.

Overall, it was a really neat trip. Definitely not what I expected, though I’m not sure what I expected. I’m really happy I got to see a local game store in China and of course, always happy to play some Magic. I was really excited to finally play with Olivia Voldaren, which is an absurdly strong card. I sculpted a little token of her a while ago, for exactly EHD games.

Yay Magic!

Congratulations Ray and Shu!

Last weekend, I attended Ray and Shu’s wedding in China. It was a beautiful event and an awesome cultural experience.

On the morning of the wedding, there was 抢妻 (qiǎngqī), where Ray and his groomsmen push their way into Shu’s room, guarded by her bridesmaids and friends.

push
After answering trivia about Shu and doling out 红包(hóngbāo, red envelopes filled with money) to the bridal party, Ray is finally allowed to see Shu.

He proceeds to put golden slippers on her and link the heels together with golden chains.

goldenslippers

Next, the parents of the bride and groom offer well wishes through a tea ceremony and Ray and Shu share some 汤圆 (tāngyuán, soupy glutinous rice balls).

riceballs

Ray and Shu are then whisked away to a park for photographs. There’s even a drone taking aerial shots!

drone
When they return, the ceremony begins. Friends and relatives fill a banquet hall and give 红包 (hóngbāo) to the couple.

hongbao

The ceremony was lovely and I’ll post pictures when I get them.
I was the ring bearer!

After the ceremony, there was a feast with all sorts of amazing dishes like roasted duck and various fish. I got to try some 白酒 (báijiǔ, fire water), something I’m been meaning to do ever since I read the Serious Eats article. It was fiercely aromatic and alcoholic. I only tried a thimble-full, but man was it strong.

firewater

When the feast concluded, everyone retreated to a gaming room to play mahjong.

Overall it was a really fun event. While there were Western influences (such as Ray’s tuxedo and Shu’s white dress and the exchange of vows and rings), it was also very Chinese (抢妻, 红包, banquet, and mahjong). I found it interesting that while there were cake for dessert, it lacked any ceremonial significance. Even more interesting was the fact Ray and Shu consider their entire event a Western affair, and “not traditional at all”.

Anyhoo, Ray and Shu, I wish you the best in your new life together and 白头偕老!