things keep looking up

I largely anticipated the way this week played on Monday, with a few important exceptions. I did end up determining the regulation status of 11 transposable element families in all the mops and now have some very cool data showing the very surprising differences and similarities between these three mediators.

However, today I was working on combining all this data into one powerpoint slide for a lab meeting, and I was interrupted by a call in which Mario basically told me to go take his place at a seminar being held at the Mariott. The formal name of the meeting was IGERT which stands for Integrative Graduate Education and Research Traineeship, and it is a nationwide program. I unknowingly sat next to one of the presenters whose name is Noah Whiteman, and after a full day of chatting, powerpoints, and incredible free food, he said he would not mind putting in a good word for me for a selective summer program at the Rocky Mountain Biological Laboratory where he works during the summer before my sophomore year of college. Hurray for networking!

AGCT is for Ambiguity, Graphs, and Carpel Tunnel

The sequences came in yesterday, but I didn't get a chance to look at them until today. After three hours of clicking, dragging, and editing, I had a compilation of all the DNA fragments we have sequenced so far.

The changes that I previously believed to be mutations may turn out to be something else entirely. After I assembled the contig file, I found that the differences in the DNA sequences were too numerous and too consistent to be DNA mutations. It was suggested to me that the plants are heterozygous, meaning that several sites may regularly have one of two bases. If this is the case, the sequencing part of my project will conclude with a recommendation that further research be done in this area. It is of course possible that the mutations are in a different part of the gene. This is quite believable, given that the BRI-1 gene is about 2000 bases long, and we have only sequenced about 1200 bases.

That being said, I doubt that I will have many problems writing a full-sized paper for my project, but it just won't be as conclusive as it could be.

The Attractin Gene

In addition to working on my presentation, I examined my research and communicated with my post-doctorate mentor to obtain a greater understanding of the significance of my research. My research focused on sequencing the introns of the Attractin gene, rather than the coding exons, in order to determine if variation in any sites in Attractin are associated with coat color. Most introns do not code for proteins; in addition, there is more likely to be variation within the non-coding regions of a gene, the introns. However, the likely causative mutation for coat color variation in the Agouti gene in the Kenzin, New Mexico, population was found in an exon (an expressed, coding region of a gene). It is unknown whether a mutation in the Attractin gene altering coat color (if one exists) would be in a coding or non-coding region. As Attractin is very large, fully sequencing the gene is not a rapid process. However, linkage disequilibrium (a non-random association of alleles) in wild house mice extends across reasonable distances, meaning the association of one loci in a gene to coat color most likely corresponds to the association of that loci to another in that gene. Thus, it is not necessary to sequence the causative site of coat color variation (if such a site exits) to pick up the “signal” of the presence of linkage disequilibrium; rather, such a “signal” is identifiable by sequencing something in close proximity to the causative mutation. Therefore, I sequenced the Attractin gene in regular intervals across the genes in areas likely to contain polymorphic (variable) sites (introns). While my research does not definitively rule out some contribution of variation in Attractin to the melanic phenotype, it does serve as strong evidence that there is no relation between the two.

Now the Hard Part of Writing

So I am already done with all the labwork for my project. This week I've basically been focusing on writing my paper and reading scientific articles pertaining to Attriplex hortensis and water reuse. I've already went through all of my data and created graphs for them, so now I just have to write all the information about my project. The hardest part is probably that I have to follow the style of science articles (sounding really professional and staying focused.)

I've also been going into the ERL still just to check up on things and/or feed things; basically just to help out. This week we found some baby Tilapia in the fish greenhouse (which means the ERL can now do experiments with baby Tilapia -which will be cool.) Also in one of the Molly fish tanks in the lab, we found 2 baby Mollies. The baby Mollies are ridiculously small and hard to see, but are basically very miniature versions of the adult ones (very cute.)

This week I also went down to Marana to do some Neutron Probe testing on the soil (to determine soil moisture.) I also helped to take down some drainage data on the plots over in Marana. Then I helped clean up by pulling some weeds and cutting back some of the plants.

So yeah, everything is going good. =)

Playing With Fire, Dissecting Wasps, and the Hexapodium! It Is the End...

I don't have too much time, so I'll make this as concise as possible.

Today was the last day, and I'm dying on the inside... Even so, this was among the most fun days I've had in a while.

After doing one bit of culturing (harvesting Encarsia hispida, the one with wiggling pupae), I got to dissect some female E. emiratus wasps for their spermathecae. It's a really difficult process, actually. It involves taking two probes, using one to pin down the wasp's microscopic body, and the other to split it apart at the abdomen. The spermatheca is located in the back third of the abdomen, and is pretty delicate, so the preferred way to get it out is by removing that part of the abdomen from the whole wasp, and then ripping away the tissue surrounding the spermatheca. Once the organ is in the open, it's safe to take a closer look at the specimen under the compound microscope.

Next, I played with fire. That's right, they trust me with fire. Anyway, I used the fire in order to make some tools for the lab. As I mentioned before, dissections are done using probes, and the probes are just pipettor tips with tiny metal filaments inside/sticking out of them. To keep the filament inside, though, the tip of the pipettor tip needs to be melted, and the filament needs to be wedged inside that melted plastic before it hardens. Too often, the pipettor tip actually catches fire, so, yeah, the job isn't without its risks.

Ah, yes, at 5:30, there's an insect science-related event called the Hexapodium that's happening at the BIO5 building, and I get to go! One of the grad students from my lab (Joe Deas) is presenting his research on Mimosestes beetles and their adaptations against parasitism. I don't know what the other presentations are, but I know that the event consists of like, 6 presentations on insects by grad students exclusively. Afterward, there's a dinner, but I'm not gonna participate.

It's over.

Spectral lines can be stubborn.

The conference went well; I believe I gave a good account of myself.

This week I've been taking more photographic spectra, looking for the Stark/Zeeman effect. The spectrum that I took yesterday is promising, since it shows evidence of the effect, but not conclusive proof. For that we need to see separation of the spectral lines, or - at the very least - broadening. The Hg spectrum I took yesterday shows a much lower intensity in many of the lines, which is good, because we know that our magnet is strong enough (~9000 Gauss (G) or .9 Tesla (T). By comparison, the Earth's magnetic field ranges from .31-.58G.) to affect the atoms in the mercury gas. To further search for the broadening, we will narrow the slit and increase the exposure time.

MEETING @ UPPER SCHOOL, MAY 4

Hello Seniors,
I recently sent you all an email asking you to come to the Upper School on Tuesday, May 4 at 3:30 for a meeting about presentations. Many of you have not replied. If you are in town, I need you to be there. Not showing up will count against you when we are deciding which projects will win awards. It will also make me unhappy, and I KNOW you don't want that to happen.

Please read and respond to your email!!!

Toews