Topics Today: "Dr. Zeldenrust", 31 out of 48, and writing papers

I have my results back! Now it will just be a whole mess of work trying to get the nucleotide sequences sorted out, haplogroup them, and write my paper. I received an e-mail today telling me that my my sequences were done, and also the heading to the e-mail was "Hi, Dr. Zeldenrust". It really was awesome! I can't wait to get my doctorate so more people people can call me that. Haha.
      Out of the 48 samples that I sent, 31 came back as a usable nucleotide sequence, and as Dr. Baker tells me, that's a pretty respectable number, and a number comparable to the results that she gets back. Dr. Baker tells me that she is impressed, and that it's a really good outcome for my first solo try at this lab procedure. It's been a really good day :)


But, now that I have my results back, I need to get cracking on them. And I also need to get cracking on this paper. The results need to get done in order to write this paper, and this paper needs to be written by Monday! AHHHH. Also I need to contact all of the subjects, and tell them that either their samples didn't work or tell them their haplogroup. I think I'm going to do this during that really long weekend between Interim and Spring semester.   ugh, so much to do.


But this is a copy of what my results are when they got back. In another blog post, I'll write about how i transformed these into my actual data...

Beads on a String.

Trying to work on my paper.
   My entire project is pretty much being funded by Dr. Moss, who in return asked for a painting. I've been working on the painting all day and it is finally finished.

Last Day in the Lab

       Last day in the lab today was spent processing all the rest of the 11 samples that were done, filling out on line forms to ship all of my samples, and actually shipping my samples. I made it to the post office a full 15 minutes before they were closed.
      Enclosed in my little cooler that I sent, were all of my samples, the pictures that I took, and a letter explaining what I did to the samples. Who knew that all of this work would fit into a small Styrofoam box?
     I'm really worried about getting everything done in time, the samples that I've send off my not be done for another 2 weeks at most! And I still need to haplogroup them, which could could take a while. Ughhhhhh. why is interim so short?

Last lab day for now, now it's just working in my room on my paper.

Pictures:

Nothing seems more pathetic than being in a lab on a Sunday night....

PCR is now officially finished on the Re-do's and I have to say, that 11 of the 13 worked! I must have messed up something really small on the first time. But the other two probably didn't have enough DNA in them to begin with. But a total of 48 out of 50 samples is pretty good!

      I'm really proud.

Today I basically condensed 3 days of work into about 5 hours. I made the gel, electrophoresed the samples and took the spiffy UV pictures.

Tomorrow is officially shipping day, and I think it might also be my last day in the lab!
But what this means is working on the actual data and my freaking paper. Ugh. This was a pretty ambitious project, I'm realizing now. I'm pretty sure I can do this though.

Pictures from today, including one of me in the headgear that I have to wear while I'm taking the UV pictures.

All my tubes and wires, And careful notes, And antiquated notions...

It seems through throughout most of this project I've been throwing out more things than I've been actually getting out of this experiment. All the pipette tips, the tubes, the gloves, the swabs, the gel, the paper, the tape... It's quite a lot. (Maybe another SI project of mine is to design and advocate for recyclable plastics for use in laboratories).
     But anyway, the agenda today was to prepare everything for shipping (on Monday now. Hopefully that's what will happen) and to start the PCR process on the last 13.

Label everything, put it in rediculously small tubes.
 Start the PCR process and I need to keep it in the thermal cycler until Sunday because tomorrow I have to go read trivia questions for a Dorman quiz bowl tournament. Sunday, I'll have to be on my game and prepare the electrophoresis gel and run everything.

Well, that's really all I did today. Here are today's pictures:

Exo- Sap-It!

It feels like I didn't really do much today, but I really did. I Treated all of my samples with Exo-Sap-It, which "cleans-up" the samples of all the junk that I had put into it.
 I then had to find the website to submit a form for my samples, and fill out only the samples that I have done. I still have to re-do and wait on the results of the 13 that didn't work this first time.
With my samples, which are about 5 microliters in a giant tube to be shipped and treated, I have to send the primers (200 microliters) of the DNA I just sequenced.
   This is all really cool and a little daunting.
 I also need to start working on the painting for Dr. Moss that I'm doing to fund this wonderful project, and I need to finish it before he gets back from Israel, which I think is any day now.

 Tomorrow And this weekend I'm going to re-do the 13 samples that didn't work and see if it was something that I did wrong to it, rather than there being no DNA.


Here's Today's pictures:

The future's so bright, I gotta wear shades...

I'm a peeping-tom techie with x-ray eyes
Things are going great, and they're only getting better
I'm doing all right, getting good grades
The future's so bright, I gotta wear shades

 So, I'm not exactly studying nuclear science, nor am I awaiting impending nuclear war, but today was a really good day.

    I came in today to finish my labwork from yesterday, which would be to run the electrophoresis on all of my samples. This step would check whether or not I did everything right and if all the samples are good enough to send off to USC to be sequenced.

    I set up the electrophoresis apparati and started slowly loading up all of the samples on the gels I made yesterday . Loading up all of the gels takes a very long time and is very precise. Trying to keep your hand still while squeezing out a minuscule amount of liquid into an even tinier hole is no easy feat. But I'm really proud of myself; I didn't make any mistakes. In each of the gels I also added a DNA ladder, which acts as a reference to the sizes that the bands of DNA should be when the gel is done being electrophoresed.

   The electrophoresis chambers are hooked up to a battery and a current is run through the liquid and through the gels containing DNA. This process takes a while, up to an hour and a half.

        Well, I had started everything and the little gels that I had made were nearly done, when I realized that the big gel that I had made, which had 40 samples on it wasn't 'moving'! The tank was busted, I then had to gently take out the gel and try to find a tank big enough that would work, and then wait for another hour for it to run.

 In the mean time, Dr. Baker taught me how to use the UV light to take pictures of the gels. The first gel I took a photo of didn't really yield good results. 3 out of the 6 samples were useable. The second gel was much better, 5 of the 6 samples were good!

     I was really nervous about the big gel, because I thought that the results could go either way.

 Once the big gel was done, I placed it on the UV light box, turned off the lights and turned it on (only after putting on a protective UV face shield, of course!). The results were beautiful! All but 6 of the forty samples are good.

    Needless to say, I'm really happy, and really proud of my self. Also, I'm really exhausted from work and I haven't been sleeping that well.

Tomorrow, I'll be preparing the samples to be sent to USC for processing. Exo-Sap-It, Here I come!

Today's pictures: