The Attractin Gene

This week, I have been continuing my work from the previous week of analyzing data and running PCRs to amplify various regions of the attractin gene. Analyzing the data is very exciting because I have the opportunity to actually see the progress I am making in discovering more about the association of the attractin gene to coat color variation in rock pocket mice. The new DNA sequences I collected last week included two regions of the attractin gene, introns (unexpressed regions of the gene) 27 and 4. The sequence for intron 27 was low quality, as I could not determine which bases were present in each region from the condensed and overlapping chromatogram, which is a graph showing the presence of each base with peaks of various colors. Thus, I ordered internal primers and will perform nested PCR on this region by diluting the product of my original PCR and running a new PCR with the internal primers to obtain more specific sequences. I will also attempt varying the conditions of the PCR to obtain better results, such as using supplies meant for long sequences. I did, however, obtain a successful sequence for intron 4 in one specimen, which contained two regions of heterozygosity (the presence of different versions of the same gene). I will continue to sequence this region in additional specimen in order to determine if there is any association of this variation (if it is present in more than one individual) to variation in coat color in any of the populations of rock pocket mice. In order to try to amplify additional regions of the attractin gene that have not successfully amplified with the previously ordered primers, I ordered internal primers for introns 23 and 13, as well.

I have also continued running PCR reactions and performing gel electrophoresis (to test whether the PCR was successful by separating bands of DNA in a gel that allows DNA to move from the negative to positive end of the container) this week. I am currently working with exon 1 (an expressed region of the attractin gene), altering the conditions of the reaction in order to obtain a clean fragment of DNA. This process has become very familiar to me, as I have currently run 157 PCR tubes in the month I have been working here (after the second trimester), and I am now able to complete the process very rapidly and locate the DNA stocks in the crowded freezer and refrigerator when I need to dilute the DNA to an appropriate concentration for the reaction.

I also had the opportunity to speak to Professor Nachman for an extended period of time this week. He explained the research currently being conducted concerning the mechanism for regulating the X chromosome in various animals, as females have two X chromosomes and males only have one. It is very interesting how different types of organisms have dealt with this dilemma in differing ways; for instance, the male fly upregulates the X chromosome to produce the effect of having two of each gene on that chromosome, while many female mammals turn off one X chromosome to produce the effect of having only one of each gene on the chromosome. However, while many ideas for this occurrence have been proposed, there is still no definite explanation of the mechanism responsible for this incidence. Professor Nachman further described the reasons for why he chose to study coat color (a trait essential for survival) and what brought his focus to the agouti gene (a gene shown in mice bred in the laboratory to have mutations prior to Professor Nachman’s research of this gene in wild mice populations). Additionally, Professor Nachman explained a very interesting connection between dentistry and evolution, as various mammals have developed tooth number and growth patterns independently of one another. Speaking to Professor Nachman is always a wonderful experience, as I learn so much in a brief period of time and become even more enthused by scientific discovery.

I look forward to completing this week by amplifying additional regions of the attractin gene and again nearing the number of samples necessary to prepare a plate of DNA for sequencing.

Not Much To Report

Today, I ran a gel on my DNA samples. When I took a UV image, I had visible bands of DNA, meaning that my PCR went well and I have DNA. Unfortunately, the gel wasn't good due to an elementary mistake on my part. So, I'll be going into the lab bright and early tomorrow. Hopefully I'll be able to run a gel before I have to rush off to work.

I also got to attend an undergraduate student's practice talk on his research. It was very helpful to hear the comments and suggestions of the professors who also watched the talk. I learned that for short talks, data should be referenced but not necessarily in the presentation. ("Our data shows X, please refer to Y for a complete list of data.")

Black, Blue and Bruised All Over

Sorry for not posting last week, but it was a crazy one. I got to meet Arianna Huffington, Sean Penn, Seth MacFarlane and Andrew Sorkin. They were all on "Real Time with Bill Maher" last week and my uncle is the producer so I got to come back for the taping. They're all really nice although I didn't get much past introductions because we had to rush home. I'm especially looking forward to getting to talk to Arianna more and lucky for me she's good friends with my uncle so I'll have a chance. But back to my actual project.

No one warns you when you start this program the toll it takes on your body. But I suppose the bruises all over my legs are worth it. Just to clarify I've gotten these bruises because this week the kids asked if I would creep with them during our all creeping class. Normally we during class the kids go to stations with their parents but sometimes the parents having meetings during class the staff keeps the class entertained. Needless to say I am NOT going to ever try to race a bunch of 6 year olds again.

Other than that most of the kids are moving along really nicely. Except with some notable exceptions everyone is past regressions and most parents are able to see substantial change in their kids.

Last week was a lot about different ways to help kids in school which I found very interesting. Little things such as slanted desks really help the brain process information and move between different information centers in the brain. A couple parents were talking about how even having their kids do work on top of binders to get that angle has shown a change in their school work. The image below is called a "lazy eight" it's basically an infinity symbol, it's important to go up to the left and up to the right. It helps to cross the mid-line in the brain. It's really good to do before tests or if you have one of those "it's on the tip of my tongue" moments. I'm coming to the last couple weeks on the eight week program, and after that I'm going to work the week long intensive program, which will be exhausting but I'm looking forward to it. And then I'll be working for a show my uncle is producing with Larry David for a week before heading back to Tucson. I really can't believe how quickly this is all moving but I'm loving every minute.

More Coding! Yipee!

So, this week, I'm getting back into the swing of things, after last week's trip to New Mexico. Currently I'm reading up on the data that needs to be sent from the main processor in the stethoscope into the audio codec (chip that makes audio signals understandable to the processor). While this sounds simple, I would like to insert a quote from the Texas Instruments datasheet for the codec: "[the codec] contains 108 pages of 8-bit registers, each page can contain up to 128 registers" essentially, this means that there is a theoretical maximum of 13824 values that must be loaded in order to get the darned thing to export audio data! This will likely be culled down to a more manageable several hundred after further reading and coding, as I am not using all the features within the codec, but still seems to imply a difficulty curve akin to running headlong into a brick wall. While I could write (read: bore you) more about the minutiae of the I2C and I2S (Inter Integrated Circuit and Inter-IC Sound) serial bus timings and arbitration protocols, doing so would serve very little purpose and would interest no one. So, with that said, I return now to my code, which keeps me less warm at night than I would like to think.

"Needs More Soap"

So on the menu for this week is the tasty procedure RT-PCR, and apparently my advisor has not run one since I was last here in the summer! What this means for me is that I got to spend my time in the lab yesterday "doing the dishes". It's like I was the last one to leave the party and I got stuck with the mess, but in reality I made the mess, left, and then came back.

Anyway, these tubes contain a caustic cocktail of carcinogenic proportions so there is a strict protocol for their cleaning. The most time demanding section of this was the washing. The tubes were placed into a tub full of water that seemed to have certain properties that caused soap bubbles to degrade very quickly. It got to the point where I began to play around with the idea that I should now focus my project around this mystical foam annihilating substance instead of paramutation. It is in my best interest to go water the plants now though.

Until next time.

What Week Is This?

Really, I've lost count of how long I've been at NASA. Anyways......I've already explained my research in enough detail I think so now I'll delve into the other duties of a NASA intern. Whenever anyone needs help with something they usually have to ask an intern for help first. This accomplishes a few things: we gain competence in more than just our research field, we get opportunities to get out of the office, and the real NASA employees may not have to work as hard. This doesn't mean I get to fetch coffee for a bunch of lazy engineers. Thing's I've got to help with: calibration of a laser measurement system, help paint our new office (we have to vacate our current office to make room for a visitor, a test pilot if I'm not mistaken), attempt to fix an anemometer (measures the wind speed), and place silver dollar sized retro reflectors on the UH-60A blades that are being tested in the wind tunnel.

I also got the opportunity to go a metrology (not meteorology) seminar about uncertainty. I could go into how to determine the uncertainty that arises from multivariate measurements (the end result is determined by multiple measurements, for example the volume of a cylinder is dependant by the area of the base and the height), but I'm fairly certain no one wants me to type up the entire textbook I was given and expected to read through and to be able to apply.

-David

P.S. (sorry for all the parenthetical statments)

A Week of More Talk than Action

This recent week has gone a lot slower in terms of the production but tons of research, and camera, and editing practice are taking place of shooting. I've been under the weather this past week but I'm real sure that I'll be well enough to get back on schedule for this next week. It's funny how many people are interested or connected to the film industry at BASIS that I've been able to learn a lot from. The Film festival reacquainted me with many students who have plenty of useful advice for me to take and experiences for me to learn from. One student in particular who didn't even participate but came to watch was Jesse Gilmer, after the festival Jesse and I hung out and we started talking about film making to which he told me his dad is in the film making business. Although his dad is mainly making commercials at the moment, Jesse said that he'd mention me to his dad who is on a business trip right now but will come back in March. On Friday I received a call from Jesse's dad and had a nice conversation where he answered many of my questions and showed quite a bit of interest in my project, enough to tell me to call him anytime I have a question about something. Although not much recording has been finished this week, a lot of knowledge from experienced people and the vast amount of information available to me on the internet and at the library have alleviated some of the problems I pictured in the production process and provided a renewed confidence in the project.