Fourth assembly attempt continues

I think I'm now on my fourth attempt at cloning and purifying DNA for my last five splice variants. Today I stopped by the lab to take yesterday's liquid cultures off the shaker and pellet them. We ran out of our normal culture tubes so I had to use small ones; those didn't yield as large pellets but it should be sufficient. Tomorrow I'll use a completely different, new purification kit to attempt the DNA harvest.

Harvest failed again

Today I did another DNA preparation from last Friday's frozen cell pellets. It started off well - the cells were easy to resuspend - but when I finished and measured DNA concentration I got the same poor results. I started liquid cultures (again!) from the last set of plates. I'll pellet them tomorrow and probably harvest them with a different miniprep kit on Wednesday.

The last week begins

Suddenly there are only three days of instruction left in the semester. Tomorrow is pretty regular, but then there's a deluge of meetings, presentations, events, then final exams.

CS registration might not be possible

Next semester I'm hoping to take CS 241, System Programming. Like many CS classes, it's restricted by major/college for a time, in this case becoming generally available this coming Monday. Unfortunately, the only one of its two lectures I can attend (due to time conflict from a one-lecture core MCB class) is now full. I'll keep an eye on it in case someone drops, but I might not be able to take it next semester. There may be other interesting, non-core, CS classes available to me, though - I'll look into that.

Reassembly continues

Today between class and the start of a lab meeting I quickly pelleted the liquid cultures I started yesterday evening. All fifteen had growth, so on Monday I can try harvesting DNA again.

Reassembly going smoothly so far

This afternoon I stopped by the lab to check the plates I started for redoing plasmid assembly. There were numerous colonies (more than was convenient to count) on each plate except the negative control, which is all as desired. I started some liquid cultures immediately - without refrigerating the plates like I did last time - and will turn those into cell pellets tomorrow.

Trying assembly again

Since my last attempt at assembling plasmids for my last batch of splice variants failed, I tried again today. Just in case my last Gibson assembly was bad, I redid that this time and transformed into freshly purchased competent cells. Tomorrow after class I'll go in and see if colonies grew.

Helping more in lab

Another person in my lab needs to do some moderately tricky data analysis, so I volunteered to help. The task is well-defined, so it will be easier to make progress than with my previous collaboration. (Which I should spent more time on after exams end, hmm.)

Yet more exams

In the less-than-two-weeks prior to the end of instruction, CS 233 is holding two non-final exams. One was tonight: its one and only paper exam, known for being very difficult, which it was indeed. The other is this coming weekend, covering similar material but in short answer and multiple choice format.

Walking again

After several hours fiddling with a CS project this morning, I decided to take advantage of the beautiful weather and go walking again on my quest to see all the bus stops. There was a run of stops out east remaining, so I went that way out to the Urbana Walmart, then back along a slightly different route to pick up a few straggling stops I didn't get to on my last venture that direction. Since no buses ran today due to the Easter holiday, I had to go the entire way back on foot, for a total of 9.6 miles, my longest venture so far. In all I've now visited ~520 stops (47.2% done).

Many projects

With the end of the semester approaching, I'm currently handling several different projects. CS 233 has a contest involving assembly programming, its honors section has the FPGA final project, and MCB 253 has a final paper and poster. There's also a couple projects I'd like to make progress on for CS 125 development before the summer. Lots of work!

Undergraduate Research Symposium

This morning I presented my poster at the Undergraduate Research Symposium. I was assigned to the earliest session, so there was only a modest amount of people there, but a few wandered by to talk to me. One was a bioinformatician who was considering using Pac-Bio sequencing - the sequencing method that produced that data I worked with - so we discussed considerations for its use. After my session ended, I rolled the poster back up and stored it in the lab, where we'll put it up tomorrow.

Further plasmid problems

My second attempt at plasmid purification for my last five splice variants again yielded very poor results. Today I did a PCR on the results to see if there's any relevant DNA in those tubes at all. This is somewhat confounded by using a different (cheaper) polymerase with which I have no experience - hopefully I picked a reasonable annealing temperature - so a previous high-concentration tube was used as a positive control. We'll find out Friday or Monday, depending on when I have time to run the gel.

Housing for the fall

I've decided to leave the dorms in favor of an apartment, starting this fall. My group of four guys has selected a place on the west side of campus, approximately the same distance to class as my current dorm. I'll have time over the summer to adapt to apartment life before classes begin again.

Poster printed

When I got up this morning, I saw an email informing me that the poster I submitted last night had been printed. So after class today, I stopped by the printing facility to pick it up. It looks very sharp. Conveniently, it came in a clear plastic roll so I can safely transport it even if there's rain.

Poster done!

Today I finalized by poster by improving one figure and finagling some tiny alignment details. After sending it to my grad student for another quick review, I submitted it to the printing service!

Poster feedback

Today I showed my poster draft in a lab meeting and practiced explaining it to people. I learned some details of the sequencing method involved, in case people ask about that. We also identified some adjustments which I will make tomorrow. Overall it's going very well!

Poster practice

Tomorrow in lab meeting I'll show a draft of my poster to the group for feedback. To facilitate this I've printed out handout-sized copies of it (for annotation) and created a slide deck with one figure per slide for easy visibility. I should probably submit the final poster for printing by Monday so it can be ready for the symposium Thursday.

Retrying transformation

This afternoon in lab I restarted the process of getting plasmids of my last five splice variants. Fortunately I had kept the Gibson assembly mixes, so I didn't have to go all the way back to that step. I transformed bacteria, plated them, and will check for growth tomorrow morning.

Exams over for now

Tonight I finished this run of three exams by taking an MCB 252 midterm. Tomorrow is going to be a long day from regular-ish work and events, but then I get to relax for a while.

Delay in getting plasmids

This afternoon I went into lab to harvest DNA for my last five assemblies. Everything went mostly as normal until I measured concentration afterward and found very little DNA. There's probably some there in four of the five cases, but not even enough to sequence. Fortunately I kept the Gibson assembly mixes so I can easily transform some more bacteria and try again on Wednesday.

Series of exams

This week I have three exams in a row: CS 233 earlier today, MCB 300 tomorrow morning, and MCB 252 Tuesday evening. CS was straightforward as expected. After the MCB exams, I have a lot of things going on Wednesday, but after that I get to relax for a while.

Further poster development

Yesterday I continued working on my poster by applying some layout suggestions from my grad student mentor. Whitespace is much more consistent now and I think it looks much better. I sent a draft to the PI for review.

Mostly registered for next semester

Fall registration opened Monday for me, so I went ahead and added all the classes in my plan. The MCB ones all went through, of course, but the CS one is still closed to non-majors. I'll have to wait until the end of the month for that one. So far I've been able to get the seats I need - hopefully that will continue.

Preparing the rest of the plasmids

Previously I assembled, grew, and purified a batch of five plasmids. The other batch of five has been assembled and I'm now working on growing it in bacteria. There was the hiccup of some plates producing no colonies earlier this week, but I redid those yesterday and now have a few colonies for each plasmid.

Sublease confirmed

Previously I found a good deal on an apartment sublease for the summer, since I'll be spending a lot of time in town for a job. I viewed the apartment and signed the lease.

More poster progress

Last night I put together all necessary information into my poster and sent the draft to my grad student mentor for review. I got feedback today, implemented as much of it as possible, and sent the revised draft back. The layout is now much more comprehensible, but there's still a ways to go.

Yet more walking

Yesterday it was nice out and I had finished all necessary work, so I went out walking on my quest to visit all bus stops in town. This time I went east almost until the edge of the town, past some residential areas. I then doubled back and went north to visit a few stops left behind by previous trips. When I was done, there was no nearby bus to take me back to campus - it being near the end of daytime service on Sunday - and I had to walk a ways more to encounter any active route.

 The entire southeast quadrant of the map is now clear of unvisited stops. I've visited 494 stops (44.5%) so far.