Student Research at Duke

Since Stephanie is going to Australia for a few days, I am helping my PI with his project on Ashbya Gossypii. I am doing a DNA extraction on different strains of Ashbya, and one of the major differences between Ashbya and E. coli is that you can’t pellet Ashbya, because it is a long filament and doesn’t form a pellet. What you do instead is you vacuum filter it and collect it off the filter paper. Vacuum filtration is a pretty basic technique–practically every single lab back in Organic Chemistry has some step that requires you to vacuum filter, so I didn’t think I would have any problems with it, until I had to look for the equipment to set up the fitration. And, as it turns out, we don’t really have the equipment (or it’s somewhere in the lab and we can’t find it). I was somewhat bewildered, since I remember back in the chemistry labs, each of us had our own filtration flask, and if you break your Buchner Funnel by accident you could easily get another one from the supply room, and rubber-stoppers-with-a-hole-in-the-middle were everywhere, heck, even General Chemistry kids probably have their own everything, and now that I’m working in a real lab, I… don’t have any of it.

So I had to empty and clean the only vacuum filtration flask we had, which contained probably the nastiest, worst smelling compounds in this entire lab, file a hole through a rubber stopper large enough for the funnel, which took at least an hour, and cut my own filter paper to fit the funnel. Well, that’s done with now so it’s all good… But I have to say that l find the whole process to be highly amusing…

For some reason or another my PCRs keep failing, so for as long as I can remember, PCR and gel electrophoresis are the only things I have been doing at work. (Well, I actually ran out of plasmid DNA yesterday, so I had to make more for the PCRs, but those failed too… twice. In fact, I am using someone else’s plasmids to run my PCR since I don’t have any more.) Progress has been pretty much halted (except for, I guess, more pipetting experience for me). Hopefully this PCR will work and I can go on with the yeast transformation.

I have been getting a lot of downtime with all the gels and PCRs (which require 30 minute and 3 hour waits, respectively), so I think I have ran out of things to entertain myself with. So feel free to suggest me things to do that would be appropriate at work aside from reading about yeast genetics (which, Stephanie, I can assure you I have been doing very diligenly).

7:50 AM: Wake up

8:10 AM: Eat breakfast

8:30 AM: Catch bus for work

9:00 AM: Arrive at lab

9:30 AM: Streak plates

10:30 AM: Prepare YPD solution

12:00 AM: Eat lunch

1:00 PM: Pour YPD plates

2:30 PM: Read about the history of yeast genetics

3:30 PM: Inoculate E. coli

4:30 PM: Go home

Now that work has settled down into a sort of routine, that’s what it looks like above. Obviously, I am not happy about waking up that early, the routine does get boring. But let’s not lose sight of the fact that it’s the overarching meaning of these actions that count. Speaking of which, so far, plasmids that are to be inserted into yeast are in the process of being created. They should be done by tomorrow, and we shall see if they were successful.

On a completely tangential sidenote, “if you don’t feel for Federer right now, consult your cardiologist immediately.” -Jon Wertheim, Sports Illustrated in “Au revoir, Roland Garros”

**Note to the admins** The text editor has issues–it inserts “rn” wherever a hard return is entered. Also, “this form must be submitted within 24 hours of when it was loaded” is misleading considering any more than about ten minutes results a “permission denied” page (which has caused to me lose this entry the first time I typed it).

The first week back to Duke has been incredibly busy with moving in, dealing with jet lag, and working every day. Having never worked in any biology lab before, I was completely unfamiliar with any of the techniques used; it was not dissimilar to learning how to write the first Hello World program in Java, in which one learns the syntax of how to set up the program–I had to learn how to work under sterile conditions, autoclaving the bottles of solutions and always putting them through flames before using, which is something that is not usually required in other sorts of labs. The first few days were quite tedious, as I had to ask people for help on nearly everything I did, including even seemingly simple things such as preparing solutions. Thankfully, I have become more familiar with the lab and I can do more things now without bothering everyone with questions. But it’s good to be settled down now, and I am eager to proceed with my experiment (which will remain undisclosed for now).  As a side note, on Friday when I had a little free time, I took some extra YPD plates and rubbed my fingers on them and put them into the thirty degrees incubator. We shall see what has grown from that over the weekend when I get back on Monday.