Umm...News?

First, I realize it's been a while since last I updated you on life in the lab.  I have been falling into a bit of routine.  I now have my very own laboratory notebook, in which I need to detail my experiments.  It's like I'm a real scientist.  I have also gotten pretty good at all aspects of PCR.  Yesterday, I loaded a gel after PCR, and it was a real beauty!  Even better, it showed that everything worked very nicely.

Hampshire's only molecular/cell biology class with lab is called Gene Cloning.  It is every January.  It is a three week, 8 hours a day, intense lab boot camp.  My thoughts: how could they possibly learn anything useful (read: do any experiments well) in such a short period!?  I have been at this now for 7 weeks, and I work eight hour days!  I am only starting to get good at some things.

Today and tomorrow are the Spring Research Festival.  I went and explored.  It was awesome (in the quite literal sense- I was filled with awe).  Think huge circus tent.  Or exhibit hall if that suits you.  Eight rows of tables.  Easily 50 tables long.  It was huge.  If you register, you get a free t-shirt upon entering.  It's a nice one too.  I thought the easiest way to approach this was to start on the right and work my way down the tent.  It seems that this is how it was organized, so it was a good choice.  

Most of the tables on the right were Department of Defense, National Cancer Institute, Fort Detrick related things.  This included this included childcare services, Fort Detrick's recycling program, NCI-F's library services, etc.  I got a very nice pen from USAMRIID.  I think that is the Army's bio-warfare science unit.  It is a very nice pen though.

The next section was posters.  This was mostly postdocs showing off their work.  I felt bad for them.  I walked down one row of posters, and it was enough.  I emerged on to something that my mind had a hard time coping with.

I've only been to one kind of trade show in the past.  Jewish.  I have been to lots of Jewish conferences, and they often have exhibit halls.  Publishers show off books, leatherers show off book-bindings, there are pretty things wrought in silver, and other pretty things woven of fabrics.  A science trade show is like walking onto a movie-set for some futuristic something-or-another.  There was a booth filled with really pretty tools for cutting, namely scalpels, scissors of various shapes and sizes, and tweezer-like objects.  There were incubators from cute to discreet to "huh, that looks like an incubator," with sales-people showing off all their interesting features.  There was a robotic pipetting booth.  Basically, you use a computer program to tell it origin and destination information (and it is all color-coded and click friendly), and the robotic arm pipettes just the right amounts of the right stuff into the correct destination.

Food was brought by ZiPani, a sandwich place in town.  I went there once with AK because a name like that might lead you (as it did us) to believe that it is a bread place.  I got a sandwich at the ZiPani stand (it was pretty cheap and there was no sales tax!), and sat down out side at one of the picnic tables.

One of the exhibitors joined me, and his business is based in Natick MA, so he was quite familiar with Amherst, and even knew about Hampshire.  He was a real pleasure to chat with.  It was fun.  Aside from the requisite business name and his own name, his name tag said, "Likes broccoli and is good with kids!"  He was a pretty cool guy.

I came back and had to do a nuclear extraction.

A few days ago, I put some cells on cell culture plates, and transfected these cells with some DNA.  This means that I inserted DNA into the cell, with the hopes that the cell would then express (manufacture) the protein that the DNA codes for.

After the cells have been expressing this protein for a couple days, I basically scrape the cells off of the plates, and put them in test tubes.  The cells then get put in a centrifuge, and I separate off the liquid.  I then add materials that will allow me to extract the nuclei of the cells after spinning them down again.  

Today, it did not work.  I noticed when scraping the cells that they were "gummy."  As in, they stuck together in long strands.  When I sucked them up in my pipette, they pulled like boogers.  I put them in the centrifuge, and when I took them out there was no pellet.  Normally when you run the centrifuge, all the heavy stuff sticks together and forms a "pellet" at the bottom of the tube.  You can then suck off the liquid, and you are left with the pellet.  Either you add something else at this point and re-centrifuge or you stick it in the freezer depending on what you are trying to get from the pellet.

No pellet formed.  We thought that maybe I didn't spin the centrifuge fast enough, and thus there was not enough force to separate the pellet from the liquid.  We spun it faster.  No good.  A few of the tubes looked like they might have a pellet, but when I tried to pull the liquid, the boogers came with it.  

So what does this mean?  It means that my cells died before I scraped them.  I admit that I did not check on them under a microscope since I transfected them (two days ago).  But they should have been healthy.  We were using a different serum this time.  Normally we put FBS (fetal bovine serum) in the media, and the cells grow very happily.  However, we were out of FBS, and we used a different company's FCS (fetal calf serum).  These really should be the same thing.  So naming conventions aside, the difference was that the FCS was heat-treated.  The going theory at the moment is that my cells were acclimated to our regular serum/media combo, and the shock of changing this was detrimental to them.  Who knows?  No use speculating.

So on Friday, I will start a new transfection process.

In other news, NIH has apparently censored signing in to a blogger blog.  I am able to read blogs, but theoretically not post or comment.  I happened to have set up a way to blog by email.  Unfortunately, I can't check formatting and whatnot.  Hopefully that works.

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-Tal