Miniprep efficiency

Posted on by kmatreyek

The SARS CoV-2 pandemic -caused research ramp-down period was a weird time for me / the lab. I sent Sarah to work from home for 10 or so weeks, meaning I had to do the lab work myself if I wanted to make any progress on any of the existing grant-work, or for any of the SARS CoV-2 research I was trying to boot up. This has resulted in some VERY long weeks over the last few months, as I was really trying to do everything at that point. Cognizant of this, I even started timing myself doing some of the more routine / mundane tasks, to see if I could try to maximize my efficiency. Perhaps the most consistent / predictable of the tasks were minipreps. In particular, I was curious whether doing more minipreps simultaneously saved me time in the long run.

So short answer was yes. 24 is a very comfortable / logical number for me (I just fill up my mini-centrifuge, and the result is divisible by three so easy for processing as complete 8-strip PCR tubes for Sanger later on), and I consistently processed those in about an hour. Dong fewer would be somewhat less efficiency, though sometimes you have to do that if you’re in a rush to get some particular clone of recombinant DNA plasmid. Then again, doing more than 24 — while somewhat exhausting — does save me some time overall. Thus, I found out that was a worthwhile strategy to plan for during that period.

That said, I’m very glad to have Sarah back in the lab helping me with some of the wet-lab work again. Not only does it save me time, but also saves me focus; I’ve gotten pretty good at multi-tasking, but I still do hit a limit in terms of the number of DIFFERENT things I can do / think about at the same time.

Plasmid Lineages

Posted on by kmatreyek

Recombinant DNA work is integral to what we’re doing here, so I’ve become extremely organized with keeping track of the constructs we are building. This includes having a record of how sequences from two constructs were stitched together to create a new construct. Here’s a network map showing how one or more different plasmid sequences were combined to create each new construct.

[The series of letters and numbers prefixed with G (for Gibson) are unique identifiers I started giving new constructs when it became clear partway through my postdoc that I was going to need a better way of tracking everything I was building. Those prefixed with A are constructs obtained through addgene. Those prefixed with R are important constructs I had built before this tracking system, where I had to start giving them identifiers retroactively.]

Edit 9/1/2020: Even if some of my code / script-writing is kind of haggard, I figure I’ll still publicly post them in case it’s useful for trainees. Thus, you can find the script + data files to recreate the above plot at this page of the lab GitHub.

Directions to the office & lab

Posted on by kmatreyek

1) Enter Wolstein Research Building, and take an elevator from the lobby elevator bank up to the 5th floor. (or take the stairs if you want the exercise). Both the elevator bank and second floor of Wolstein requires keycard access. If you do not already have access to WRB, I suggest talking to the security desk right behind the elevator bank and they should be able to let you through.

2) Take a 45-degree right turn out of the elevator (or 90-degree left turn off of the stairs) through the double doors (see image below)

3A) My office is the second door on the left (Room 5133; see image below). If we are meeting, then this is where you want to go.

3B): If looking for the lab, turn right through the double doors next to the portrait of Mark A Smith PhD (see image below).

4) Go straight past the service elevator and turn left once you reach Jim Anderson’s office (see image below).


5) Our lab benches will be directly to your right after the turn. If looking for the TC room, keep going straight until you see room 5103 on the right (see image below).