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

The end is closer than it was last time...

This week, I finalized my powerpoint presentation for the talk I will be giving on May 5 only to have Dr. Manne tell me that it was too long and that he had come up with a much better way of explaining a couple of aspects of the talk. So... I will be somewhat starting over...

Normally, this would be a bad thing, but it in this case it was fairly fantastic because it gave me something else to work on. Hopefully, this will all get worked out soon...

Besides the powerpoint, "Bistromath" is quite fun...

Almost there!

Only three weeks til graduation and only two weeks til presentations! I am really looking forward to both. Since I focused heavily on my paper last week, I've been working mostly on my powerpoint this week. Both are looking pretty good except for the gaps in the Wild Things section (I will conduct all three of the Wild Things interviews this Sunday, after which I will be able to fill in all of the holes). I'm sorry if these posts are getting shorter and more repetitive but I have little to say that is new or that I can say without ruining my presentation.

Well, I'm gonna go eat some ice cream. Talk to ya'll later!

Summer is Approaching

The title should come as no surprise to anyone, of course summer is approaching, it does the same thing every year. But what it means for NASA, is that the Spring Interns are leaving this Friday. But what it means for me, is that I will be only one of two interns still working here next week. Having an office that could fit six people comfortably with only two people will be interesting, I expect we'll have a lot of chair races around the room with all the extra space.

So the end of the spring intern session also means that many of the intern projects are drawing to a close. Mine is not though, I still have another two full weeks of research to complete (approximately), and that's a good thing because it has taken some interesting turns within the last day. What turns? Well if I told you now, you wouldn't have any reason to come to the presentations. So in lieu of describing my research, I'll talk about the Airloads test that I've been doing the safety monitoring for. The test hasn't been going as well as they planned, there are a lot of components that are breaking down. So what's broken so far?

1. Dynamic Actuators
2. The Chip Detector Warning Light went off
3. One of the M-G sets blew a fuse the size of a VW bug
4. Bolts holding the rotor blades together have sheared off
5. Bolts holding the transmission were sheared off
6. Many other things

Its beginning to seem like there is more downtime fixing the LRTA than time spent running. Hopefully this will change before the Navy kicks us out in order to test their super-secret project.

P.S. If I didn't do this, I would be breaking a promise to Cody. So to everyone who doubted Cody, Coachella was incredible and you should have been there.

Madness? This is SCIENCE!

I sent in our remaining samples for sequencing today, except for one little nonconformist rebel that stubbornly refused to amplify properly. No matter, we can do very well without him.

My project's wrapping up nicely, and I've made some good progress on my paper. I'm hoping that I'll be done with the lab work by the end of this week.

As was expected, I found a few base pair substitution mutations in my DNA sequences. More on that in my presentation.

The Attractin Gene

This week, I have completed my research paper, although, as I have been organizing my extensive research into the paper, I have thought of various questions that I will discuss with my lab mentors. I will also be working on my presentation more this week. I further completed statistical analysis of my data and am gaining an understanding of how to appropriately interpret and communicate my results. Thus, I am continuing to gain valuable skills to apply to any research.

In addition to the implications of my research in supporting the presence natural selection, the results of my research have numerous medical applications. Both the agouti and attractin gene, which are currently being studied regarding their involvement in the pigmentation pathway, have numerous pleiotropic effects throughout the body. Agouti effects numerous tissues, especially due to ectopic expression in the hypothalamus; for instance, production of eumelanin (dark pigment) may shield the skin from ultraviolet radiation, while the Agouti-induced production of pheomelanin may lead to the production of free radicals that cause carcinogenesis. Additionally, Agouti, especially when overexpressed in the wrong regions of the body (ectopically overexpressed) in the lethal yellow mouse, causes adult-onset obesity, insulin-resistant diabetes, hyperleptinemia (increased levels of serum leptin, a peptide [amino acid chain] hormone neurotransmitter produced by fat cells and involved in appetite), increased linear growth, higher tumor susceptibility, hyperphagia (increased appetite), hyperglycemia (high levels of blood glucose), and infertility. Dominant mutations in Agouti further result in neurological defects, hyperinsulinemia, coronary heart disease, and other fatal or debilitating ailments in many mammals, including humans. Agouti has also been implicated in controlling influx and efflux of Ca+2, which plays a significant role in signal-transduction, and thus influences hormone secretion, neurotransmitter release, enzyme and ion channel activity, gene expression, mitosis and meiosis, apoptosis, and possibly insulin-mediated glucose transport, resulting in obesity and diabetes. The mechanisms for these many pleiotropic effects of Agouti are uncertain; however, some research suggests that the receptor to which Agouti binds is expressed in nonpigmentated tissue or that Agouti can bind to a family of receptors (Miller et al. 1993).

The Attractin gene further has numerous pleiotropic effects beyond the pigmentation pathway. Attractin likely has an independent role in the brain. Attractin also influences the development and function of the central nervous system. The structure of Attractin suggests its involvement in cell adhesion or axon (a nerve fiber that conducts impulses away from the nerve cell) guidance. Homozygosity (two of the same allele [version of a gene]) for Atrnmg-3J results in vacuolation (becoming filled with cavities) of the brain and spinal cord; furthermore, an autosomal (non-sex cell) recessive loss-of-function mutation in Attractin (Atrnzi), which decreases the amount of Attractin mRNA in the brain, results in the phenotype of the zitter rat, which has spongy degeneration, increased oxidative stress (the release of free radicals, causing cellular degeneration), apoptosis leading to neuronal cell death, and hypomyelination (defective formation of myelin, a fatty lipid that encloses axons and nerve fibers, in the spinal cord and brain)in the central nervous system that causes tremor, abnormal auditory brainstem responses (to sound), and flaccid paresis (loss of muscle tone due to injury of the nerves) of the hind limbs. A major function of Attractin is likely to maintain cell-cell interactions, and, when this function is not performed, vacuolation of the central nervous system takes place. The Attractin gene likely has a significant role in body weight regulation both influenced by and independent of Agouti and likely plays a role in regulating cellular response to neurotoxins, even protecting against certain toxins through mitochondrial functions. The soluble Attractin found in humans and rats may be involved in immune cell interactions. Thus, Attractin mutations cause pleiotropic effects of dark coat, juvenile-onset neurodegeration, hypomyelination, split myelin sheaths (lipid and lipoprotein structures, which surround a nerve fiber or axon and aid in the transmission of nerve impulses), axonal swelling, hyperactivity, and progressive vacuolation and tremor, causing increased energy expenditure, and altered immune response. Additionally, neurodegeneration in Attractin mutant mice is likely the cause of abnormal behavior, increased movement, and decreased lean body mass. Still, the mechanisms for these pleiotropic effects, as well as for Attractin’s interaction with Agouti, are unclear. Therefore, my research studying the Attractin gene and its relation to the Agouti gene, beyond adding to a growing understanding of the process of evolution, has a potential role for therapeutic and preventative intervention in human disease.

Some Weird Stuff with Wasp DNA, and CAKE!!!

Today was a busy day. So busy, in fact, that all the work could not be contained within one building. Also, I didn't even have time to do any culturing (fortunately, the army of undergrad workers was there to help out, but tomorrow, I won't have that luxury).

So, as the title of this post suggests, we did some advanced stuff with wasp DNA that was entirely new to me. Using the QIAquick brand kits, we did a gel extraction of wasp DNA, and then messed around with it in a NanoDrop machine to determine the concentration of DNA within, in nanograms per microliter. But why did we have to jump through all of these hoops to get usable DNA when we already started with usable DNA, and had a lot of it? The answer: preparation for sequencing. Apparently, there's some sort of controversy or uncertainty with the DNA of the various Encarsia inaron wasps, and so we're painstakingly working towards sequencing the DNA of the Italian population of E. inaron and 8-times intergressed local E. inaron. If I remember correctly, we did a series of chelex DNA extractions a while back, and used those samples today.

First, we mixed all of the similar samples (same DNA, same primer pair) into their own large samples, and ran those for about 40 minutes on a small agarose gel. Once that was completed, we took the gel over to the neighboring Riehle (pronounced "really") Lab and cut out the DNA bands. To see the DNA bands, the we placed the gel on a UV light source. Since in this gel we used SYBR safe instead of SYBR green, the bands were nice and uniform, instead of "all over the place." After cutting out the bands, we had to add a series of buffers to their tubes, and incubate them at 50 degrees Celsius until the mixture all melted together, at which point a process similar to the kit extraction took place (for more info on that, refer to a previous post, or remember that stuff we did earlier this year with E. coli, those of you who were in Capstone Biochemistry).

As I mentioned, we had to go to another lab/building in order to figure out how concentrated our DNA product was, so we headed over to Life Sciences South and used their NanoDrop machine. It's quite a cool piece of technology! All we had to do was put a 1-microliter drop of our DNA product onto the sensor, and within 30 seconds, the machine told us what the concentration of DNA was. It determines this by comparing its absorbency to the absorbency of the solvent in which it is dissolved (in this case, PCR water). We needed to know the concentration in order to determine the extent to which our DNA needs to be diluted before it is ready to be sequenced. Yes, certain lengths of DNA need to be at a certain concentration in order to be properly and precisely sequenced. The formula is quite simple, all we needed to do was multiply the length (in base pairs) of the region of DNA specified by our primers by 0.02. The resulting number is the concentration (in nanograms per microliter) that the DNA must be at. Of course, determining the length of the DNA fragments is not always easy. Although some of this information is lying around in the lab, and some of it is available on the internet, some isn't, and so we had to make educated guesses. We used 5 types of primers: 28S, CO1, EF, gyrB, and Cardinium. They all have more specific names, but those are the general families of primers. I know that 28S is a eukaryotic gene, and EF is made from Encarsia pergandiella, and "Cardinium" refers to a gene in the bacterial symbiont, Cardinium.

Oh yeah, we're having cake on Thursday. I'm hoping for red velvet!!!

More power than I'll ever need

So, I haven't posted an update to the blog in two weeks. Why, you ask? Well, I was out of town visiting colleges week one, and sick for the better part of week two. Unfortunately, this means I'm also having to cram a lot of work into a short-ish amount of time, since I would very much like to have a demonstrable product to show off during my presentation.

Anyhow, since recovering I've been working flat-out to get a series of designs worked up for the beta version of the stethoscope, which will be much different than the final version I will be working on over the summer. The beta version consists of three modules: 1, the microphone and pre-amp board (brings in sound, turns it to voltage, makes the voltage easily measurable) 2, the codec (takes the changing voltage from the microphone and turns it to digital values for processing, and visa-versa for headphones) and 3, the processor board, which does the actual data manipulation necessary for what I'm doing.

(technical jargon follows, not for the faint of heart)

If you remember from a while back, I ran into an issue with processing overhead in the chips I was planning to use. The code I made required too long to process, meaning audio data would be lost and generally bad things would happen. Well, while drifting off to sleep one night, I suddenly had the idea of linking three such chips together, and overclocking them to increase their speed 25%. So, my beta version uses three chips, each dedicated to a single task (I'm devoting one chip just for use as a division engine, which repeatedly divides a number sent to it, another will add things together, and the last chip will handle the audio data to and from the codec).

(you're safe now)

So, with good coding and some luck, I can do pretty much anything with the board. Once I look over it a little more to make sure everything is shipshape in the design, I'll send the files over to my friends at Prototron and have them build up the boards for me. To give you some idea of what they'll look like, I've attached 3D renderings of the circuit boards below.

First is the Codec board. The big grey thing is the connector that runs back to the processor board. Next is the processor board itself, the three big rectangles are for the aforementioned processors.

Anyhow, besides my project, I've pretty well decided I'm going to be going to Rice University in Houston.

Cheers,

Alex Davis

I get to what??!

As it turns out, the work that I have been doing does actually fit into some larger scheme of things. I'm not saying I'm surprised, but it's always nice to know that you weren't just assigned a menial task to get you out of the way. All last week I was validating upregulated segments of DNA in mop3, and that is what the focus of my project was. However, this week I will be expanding the technique that has become so second nature to me (ya right) to the other two mops: mop1, and mop2. Apparently if this all works out I get to have my name on the paper that they publish with MY results. Since I am not very experienced I don't think I fully appreciate the gravity of this news, but that doesn't mean I'm not excited.

Working in a research lab is like having Christmas everyday!

I would like to tactfully point out that the statement above is not an accurate reflection of the general atmosphere in a lab. However, Friday was a perfect example of this situation.

Before getting into the lab I made a few job search stops that I knew were on my way (more or less). This involved dropping in to my alma mater of 14 years ago, the second street preschool. I was warmed to the core on that somewhat chilly day by my reception. They even recognized me without the tap dancing shoes I felt were so necessary to wear every day back then! After the brief rendezvous, I made my way to the lab.

For the past couple weeks I have been working one a single experiment that is the focus of my project. Unfortunately, each repeat seemed to expose errors that hadn't been there in the previous attempt. Because it is a longish process and our total sample reservoir has a finite limit, I was worried about the fate of my entire senior project. In a last ditch effort to yield results, I doubled my experiment. The benefit I saw behind this was that any small mistake that had a snowballing effect for each ensuing step would not be repeated in both of the tubes I was using for a reaction. The draw back is that the time required to go from start to finish is also doubled. In order to minimize the draw backs, I attempted to multitask whenever possible. This also had a catch: my attention was noticeably beginning to break down. Luckily I held it together until 5pm on Friday when this pretty little picture came up on the computer screen after I took the picture of my gel in UV light.

Results.... Feels good....

All my lab work is now finished. So this week I've just been going in to feed the fish and shrimp and helping out around the Lab when I can. Also this week, I've been reading a lot of articles and papers about hortensis and aquaculture irrigation. A lot of the papers have a lot of biology and chemistry jargon, but I understand them for the most part. I've also been working on my paper: graphing my data, and writing up my methods section. I've also been gathering pictures for my slideshow presentation. I can't believe there are only a couple weeks of our projects left. It's been fun.

Editing and Learning

I've been spending quite a bit of time trying to edit footage again and going through it a second time is teaching me a lot of things. One of my lessons from Mr. Van Ballenberghe was to make mistakes so I could learn from them. I'm not saying I purposely made mistakes but I should expect mistakes to happen. I'm also taking notes on how to fix little clips that can't be fixed through editing as well as getting an idea on the mindsets that cinematographers have when looking through a camera lens. I didn't expect to have a great mastery of filming when I started but did I hoped the things I would be filming were simple enough to get a high production value or high quality look; nevertheless, the work that I have now is not completely close to that quality but it does show progress I suppose. I guess I'm going to visit the UofA sometime soon to grab some advice from my advisors again.

I guess time is coming up and we are at the polishing stage of all of our work and I hope for the best for everyone. I'm pretty happy that I got to see most of you on spare time even when we were busy with projects. Maybe this is a sort of equivalent to the APs that are coming up for the other grades in the school so this may be super serious time. Let's get a practicin' on this presentation that will make up for any loss points on other parts of this project.

Family Free Day

Today I went to the museum to make up some hours after taking a few days off to visit Tufts. Every month, the museum hosts a Family Free Day, which is essentially exactly what it sounds like. For the majority of the day, I was in the Idea Box, helping kids with the craft I created (the paper houses). It was great to see kids actually working on the craft I designed and it was really popular. I also helped out with the teen craft, which was an awesome graffiti workshop.The museum was filled with kids and everyone seemed to be having a really great time.

This week, I also visited Tufts. It was amazing and I'm pretty positive that I'm going there. When I got to campus and checked in, Becky, the admissions rep for Arizona, immediately jumped up and said, "I'm so glad to see you!" and then, to her colleagues, "She's from Basis; Basis girls will bust you on some stuff." Only she didn't say stuff. Juniors, you now have a reputation in the Tufts admission office. While visiting, I went to a discussion hosted by the founder of DC based advocacy group GOProud. He was really quite interesting and very well spoken. However, I think the clincher was that there is ginger ale in the cafeteria soda machines. Go Jumbos!

The Attractin Gene

I have spent much of this week further examining my data and reviewing my extensive research concerning the pigmentation pathway. One of the many interesting aspects of my research is how applicable the experimentation I am currently conducting is towards the further portrayal of evolution and natural selection. My work sequencing the Attractin gene in the Kenzin and Carrizozo populations of rock pocket mice is aiding immensely in the natural representation of convergent evolution.

Rock pocket mice serve as the first demonstration of the genetic basis of adaptive melanism (dark coloration) in mammals. Most rock pocket mice live on light rocks and have light, sandy-colored coats; however, when found on dark lava flows, these mice often have dark dorsal coats and white underbellies. The distinction between the phenotypes is identifiable by visually comparing mice. The lava flows from which the specimen were collected are geographically isolated by light rocks on which C. intermedius can reside or sand on which C. intermedius cannot reside. The sites range in area from a few km2 to 1500 km2. These sites further vary in age from under 1000 years old to almost two million years old. By camouflaging with its surroundings, a rock pocket mouse is less susceptible to attack by the owl predator, proving that coloration is essential to the mice’s fitness and is an adaptive tool against predation. For instance, Dice conducted an experiment in 1947, finding that Barn owls and Long-eared owls captured twice as many conspicuously colored mice as concealingly colored mice in the darkness. In 1937, Dice and Blossom noted variation in vertebrate coloration in the Tularosa Basin of New Mexico, where, within 25km, the substrate altered from nearly black basaltic lava to white gypsum (a nearly colorless mineral used to manufacture plaster and fertilizer) dunes. Specifically, the pocket mice from the genus Chaetodipus and Perognathus, range from nearly pure black to nearly pure white to match the substrate on which they live. The same findings have been noted on Florida’s Gulf and Atlantic coasts; however, these findings relate more to pattern differences of beach mice from the genus Peromyscus. Experimental studies of the adaptive importance of color variation show the strong effect of substrate matching on predation rates by visual avian hunters in many vertebrates (Hoekstra 2006). Additionally, while the Mc1r gene causes melanism in one mouse population, other genes, such as Agouti, have caused different pigmentations in other populations of both mice and other vertebrates; such melanic morphs, for instance, within Chaetodipus intermedius are present on geographically distant lava flows with little evidence of historical gene flow among them (Hoekstra 2006). Additionally, pocket gophers (Thomomys bottae) express variation in color to match its substrate that is not due to the mutation in Mc1r that is the source of pigmentation variation in the rock pocket mice of the Pinacate lava flow. Thus, the ongoing research concerning the coloration of Chaetodipus intermediusis clearly exemplifies convergent evolution, as multiple “genetic solutions” have led to the same result regarding coloration among species (Hoekstra and Nachman 2003, Kingsley et al. 2009; Nachman 2005, Wlasiuk and Nachman 2007).

Practice Makes Perfect

Not a lot of different things happening this week. My presentation is very different from any of the ones I've given at Basis since I'm not using powerpoint. Instead, I've created hand-drawn viewgraphs which I've then xeroxed onto transparencies. The transparencies will be shown through an overhead, and I'll talk about the different slides. My presentation focuses on what I've done so far, including describing the equipment I've used, displaying examples of data, and commenting on which spectrograph is ideal for finding the Stark and Zeeman effects.

I've been practicing for awhile, and I'm feeling confident in my presentation; I believe it will go very well.

Wish me luck!

A Week of Wasp DNA Extraction, Plus Matings

Well, I'd say it's really winding down, but my days are still full of excitement and work...

So, on Tuesday we did some more matings, but this time, our little test subjects decided to cooperate! Seriously, they didn't desiccate, drown, or fly away into the abyss, and so we were able to get some mating results that weren't flukes or frustratingly difficult to obtain. After two sessions of matings in the last two weeks, we've got data for about 40 wasp trios, and hopefully we'll analyze it before I leave, but I don't believe that I'll be writing about it. That reminds me, I've got to get on that before long. I've got all of the data, and ideas for graphs were suggested to me by my generous adviser, Dr. Hunter, who has a whole series of topic planned for me to cover. Unfortunately, since my research is on such an obscure subject, I'll probably have to spend half of the presentation explaining the background, but I guess that'll be a test of my grasp of the subject, as well.

Ah yes, I can't forget to mention the other big thing we did this week: DNA extraction, the HARD way. Up until Wednesday, all of my DNA extractions were chelex extractions, which involved grinding up my wasps in a drop of proteinase K on parafilm using a beveled tip on a pipettor, which was very easy. But alas, my days of easy DNA extraction ended abruptly on the morning of April 21, when I experienced my first extraction using a kit. Well, technically it wasn't my first, since that's the type we did in class with Johnston earlier this year, but it had been a while. Anyway, that was an arduous process involving 56-degree Celsius incubation, max-force centrifuging, and containers with holes in the bottom. Using that specially prepared DNA, which is more valuable than the one from chelex extractions (it lasts much longer in storage and doesn't have those annoying beads in it), we did some valuable PCRs and gel electrophoresis reactions. The story doesn't stop there, because even the gel electrophoresis was different this time around. Since we're planning on sending this DNA in for sequencing, we can't mix loading dye and SYBR green into it, so we have to place drops of dye/SYBR mix onto parafilm, and then mix that with some of the DNA, and then load it into super-tiny gel wells.

We did one PCR/gel yesterday with that method, and FOUR PCRs/gels today. Fortunately, I didn't have to do any culturing, since that was taken care of by the undergrads, but it was still a challenging day. Oh yeah, I got to see a practice talk by a grad student, and witnessed the feedback/critique of that talk by a university professor, so that's good experience for me when I practice my talk.

Sunburns, Soggy Mangoes, and A Boundless Buildup of Boulders

“On each side rose the canyon walls, roughly perpendicular. There was no way to continue except by dropping into the pool. I hesitated. Beyond this point there could hardly be any returning, yet the main canyon was still not visible below. Obviously the only sensible thing to do was to turn back. I edged over the lip of stone and dropped feet first into the water.” -Edward Abby

Inspired by our new friend Edward Abbey, Sean Campbell and I set out on a trip we had been planning for several weeks. Our plan was to conquer the Upper Salome Canyon, just north of Roosevelt Lake. Despite the unique characteristics that make this canyon very beautiful, few have ever seen it due to it's isolation and inherent ruggedness.

Day one was spent driving to globe. We took separate cars, since the hike was one way, and we would need a vehicle at the end as well as a vehicle to get us to the trail head. We didn't arrive to the trail head until about 9:30 pm. We made a fire, ate dinner, and slept under the stars.

Day two we woke up bright and early thanks to the mega-church group that occupied the entire campground. By 8:30 we were packed up and on the trail making our way to “Hell's Hole.” After hiking for three hours, we got there and took a break for lunch. From here, we followed a game trail along Workman's Creek, a tributary, to the Workman's Creek- Salome Creek confluence. On a side note, I've been hiking for a long time, and this was by far the worst trail I've ever been on. “Game trail” would be an over statement in describing the condition of the trail. Once we reached the confluence, we were forced to hike down an extremely steep runoff ditch, in order to get down to the river. Though we were never able to pinpoint the source, we believe the water gave us stomach problems not long after arriving at the confluence. For this reason, we only hiked another quarter mile or so before setting up camp on the side of a cliff, just above the river.

Day three we woke up much later, and started off strong. Due to our position, the only way to advance further down the river, was to swim. Now normally I don't have a problem with swimming. But at 10:30 in the morning, at 6000 ft, swimming in a sub-60 degree river is about the last thing I want to do. Nevertheless, there weren't any other options so feet first we went.. After almost an hour of wading and swimming, we took a break on a sand bar to ensure that our gear was staying dry. A quick check revealed that nearly half of our food supply was ruined, all spare clothes were sopping wet, and the worst of all, all of our toilet paper had disintegrated into a soggy lump. I guess now would be a good time to write, NEVER TRUST A ZIPLOCK BAG. No matter how many you use or how they seal, there is no substitution for a dry sack. We salvaged what we could of the food supply, and made a quick attempt to dry some of our gear. After an hour or so, we decided we had to keep going so we threw everything back in our packs, and continued on down the river. From here on we took whatever route we could, in order to avoid swimming. At certain points this included down-climbing 20-30 foot walls above the water- a little nerve wrecking, but worth it in our minds at the time. After a very long day of hiking, we finally pitched camp on a nice little sandbar, had a huge fire, and slept just like little babies.

After getting satellite reception and pinpointing our spot on the map, we realized we needed to make incredible time on day four in order to make up for the delays we encountered on days two and three. Luckily this section of the river was rather dry which allowed us to boulder hop for hours on end, only crossing the river when we had to. We made excellent time, and by lunch we were nearing the head of what is known as, “The Jug.” Now, this gorge known as The Jug would be a pretty amazing place to look at regardless of it's rock type. The Jug however, is extra special due to it's pink-hued polished granite that forms the marble smooth canyon walls. A little while later, we found ourselves in the midst of it, stunned by the waterfalls, the rock, and of course it's sheer size. Though we were originally planning on descending through the canyon down The Jug itself (we had lugged a 60 meter rope along to rappel down into it), it quickly became evident that such a decision could easily become fatal at this water level. As a result we were forced to scramble back up the canyon walls and bypass The Jug, cutting back in at the very end of it. A quick two mile hike up an abandoned jeep trail took us back to our second vehicle and ended our first "Canyoneering" trip.

Enjoy the pictures!

presentation schedule

Hello Seniors (soon to be alumni!)

Presentations are scheduled for the nights of May 12, 13, 17 and 18. They will all be in the black box theatre, and run from 6-8ish.

Advisors have asked that all of their advisees be grouped on the same night, and several of you have requested specific days. In grouping by advisor, I'd like to have theme nights -- a biology night, an arts night, a physics night, etc. I think this will actually help us to bring in audiences that are are interested in your topics.

Here is the schedule I'm looking at. Please tell me if you HAVE to switch nights.

Wed, May12:
Business and Economics Night, plus Q, who doesn't fit easily into a category.
Christina, Victoria, Sean S., and Q

Thurs., May 13:
Arts Night:
Cody, Grainne, Brian, Rita

Mon., May 17:
Physics Night:
Sean C., Charlie, Alex D., David

Tues., May 18:
Biology Night:
Mirissa, Devin, X, Josh, Collin (this night may run a little bit later than others)

Ms. Toews

The End is Near!

Like many of my fellow members of the class of 2010, I've begun work upon my powerpoint for my presentation at the U of A with Derek (the other student working with me). Besides that, not much worth mentioning has occurred. Mainly this week I've learned a few new computer tricks, played around with 3D plots/contour plots, and continued taking an online multivariable calculus course through MIT opencourseware in an attempt to better understand some of the more mysterious (sorta) math that is commonly used in physics.

Oh... Alex Harris... I came across this interesting article concerning the usefulness of research into Wolbachia. You probably are familiar with the information in it, but I thought it was neat.

Mechanics, Engineers, and Heating

These two creatures work in perfect harmony at NASA's 40x80 foot Wind Tunnel, most of the time. Deny an engineer its lunch, ho-hum they'll keep working without too much of a fit. Deny a mechanic a 10-minute break every hour or a 1-hour lunch break, all hell will break loose. The lesson to learn here is that mechanics need to eat constantly or they might throw a temper tantrum.

So the wind tunnel tests. They are progressing, albeit very slowly but they are progressing. Yesterday during one of the warm up runs one of the screws on the tips of the rotor blades sheared off. There wasn't any damage done to anything else, but they had to stop testing for the day and inspect the model and replace the screw. So I had the afternoon off. Saying it was off might be slightly misleading I had the afternoon off from sitting in the control room to sitting in meetings and at my desk doing my other work. The other work is going well and its become more focused. Instead of looking entire population of the reference points, I am now just looking at the power readings from the test stand. What changed one might ask? Well as I was looking at the housekeeping points, something strange began to appear. The mean values for the backup sensor started to read a lower value at the end of the run than they were reading at the beginning of the run. They should have been reading the same, or rather within a reasonable percentage difference, but instead they were reading almost 5% lower than they were reading at the beginning of the run. So this raised the question of what the hell the sensor was up to. So without going into how a rotor balance is constructed just know that heat can cause thermal expansion which can then change the measurement of the sensors in the test stand. So now I have to find evidence of these "thermal effects" in other points besides the housekeeping points. My research may have been narrowed but this is the first time these effects have been observed so figuring the thermal effects is more important than checking if the mechanics can set up on the correct test conditions.

Seeing a Human Brain? Yes Please!

So I am striking out on getting into any surgeries. The trolls (that's a nice description) in human resources at NW will not budge on letting me into the hospital. Angry, why yes I am. But that's ok my time will come.

On a happier note I am LOVING working with Dr Chua. It turns out he is the chief of surgery at the hospital so he sees a lot of cases. He also assists on a lot of surgeries, which I am forced to miss, but he is kind enough to share all the details with me later. Today the P.A. (physicians assistant) in the office brought in a knot board (photo below) and they taught me how to tie different kinds of surgical knots. The different parts of the board are for different situations. I am awful at it but as the drawstring on my PJs can attest I am practicing. I'm really hoping to get a suture board in the future, there's one that mimics differnet kinds of tissue which I really want for my birthday (just an idea if you can't think of something), if you're feeling really giving you can get ones with a full suture board as well.


I have learned a lot of interesting things, but if I listed them all no one would read this so I'll sum it up. First: most neurosurgery work is on the spine not the brain (bummer I know), and secondly: most of the patients you meet with don't actually need surgery.

Dr. Chua is great about walking me through things, so I am learning a lot. He keeps worrying that it's boring me but I have to admit I am loving every minute, nothing has ever interested me this much. I love looking at some one's MRI figuring out what their spine says and then getting into the room and realizing that as awful as their spine looks it's not the cause of their pain. It's amazing to me every day how the body works.

Even medical journals are interesting, when you understand what the jargon means you realize that they are full of interesting, complicated patients. Unfortunately those journals are the reason I am still up at midnight. So because I do have work early tomorrow I will say goodnight.

=D
PS next week I'll write about actual cases but those are REALLY long so I'll spare you all for now.

Long Un-Punctuated Statements Appear To Be Appropriate Titles For Scientific Papers

Today I ran a gel on the PCR reaction that I set up on Tuesday. Nothing, again... I went back to ground zero and prepared more DNA samples from plant tissue. I suspect that DNA samples can only be frozen and unfrozen so many times before becoming unusable.

I started working on my paper today, had quite a time trying to come up with a reasonable title. Well, I guess "reasonable" is a bit of a stretch, even though my title does sound very science-y: "Three Brassica Oleracea Dwarf Mutants Are Brassinosteroid-Insensitive."

I almost wish that I was working with seven dwarf mutants instead of three, that way I could throw a cheap pun into my PowerPoint.

Boston!

So my new strategy is just to name my new blog posts after whatever is going through my head. I'm going to Boston tomorrow for Admitted Students Day at Tufts. Hopefully this visit will help me finally make up my mind.

This past week I have been busy working on my proposal. I finally finished my first draft on Friday. Here is a rough breakdown of what it looks like. The proposal is composed of three parts: Summary, Plan and Impact. Each is pretty self-explanatory. The summary is a brief rundown of what the proposal covers. In the plan, I discuss the objective of my program, the layout (where & when), the cost both to the museum and of tickets and some possible performers. Then, in the impact section, I talk about who the target audience of the program is. I'm meeting with Ama later today to discuss it, and I hope I didn't do too much wrong.

I also talked with Beth Harris, who is in charge of the dance program at the Kemper Museum of Contemporary Art in Kansas City. She was very busy and could only talk for a few minutes, so I didn't learn much.

So far, I have spent today on the phone with various companies asking to be removed from their mailing lists and updating the museum's Teen Program's facebook page.

The Attractin Gene

This week, my focus will be primarily on performing the statistical analysis of the data and conducting extensive research on the pigmentation mechanism. The statistical analysis will include the Hardy-Weinberg test to determine if the populations studied contain the expected number of alleles of each type. The Hardy Weinberg principle states that allele and genotype frequencies remain constant unless influenced by non-random mating, mutations, selection, limited population size, overlapping generations, random genetic drift (the change in the frequency in which a gene occurs in a population) and gene flow; these circumstances, however, should be present in natural populations. The extent to which the population obeys Hardy-Weinberg equilibrium will be determined with Fisher’s exact test to determine whether the expected number of heterozygotes that are present in the studied populations of rock pocket mice. Additionally, I will conduct a test to determine the extent of linkage disequilibrium (non-random association of alleles at two or more loci) among the loci expressing variation within the attractin gene and the variation in pigmentation.

With regards to the research I have been conducting, an article by H.E. Hoekstra in 2006 describes a clear description of the pigmentation production pathway. In mammals, there are two pigments: eumelanin, which creates black to brown color, and phaeomelanin, which creates red to yellow color. In melanocytes, numerous genes cause a shift between the production of these two pigments. The pigment type-switching is controlled by the interaction of the melanocortin-1 receptor (Mc1r), which encodes a seven-transmembrane receptor expressed in melanocytes, and its ligand (a molecular group that binds to another chemical entity to form a larger complex), agouti, whose protein product is secreted from dermal papilla (projections of the dermis) cells and inhibits Mc1r signaling. Without the Agouti protein, standard levels of Mc1r activity maintain levels of intracellular cyclic AMP (cAMP) to activate eumelanin synthesis. α-MSH (melanocyte-stimulating hormone) activates Mc1r and signals via cAMP. Intracellularly, the enzymes tyrosinase, tyrosinase-related protein 1 (Tyrp1), and dopachrome tautomerase (Dct), catalyze the oxidation (the removal of electrons and addition of oxygen)of tyrosine (CHNO) to dopaquinone. When all three enzymes function properly, eumelanin is deposited in melanosomes. However, in the presence of the Agouti protein, Mc1r activity is inhibited, cAMP levels are reduced, and melanocytes stop producing eumelanin and begin producing phaeomelanin. Agouti, the inverse agonist (binds to the same receptor as Mc1r but has an inverse effect) of Mc1r, binds to Mc1r with the aid of the extracellular protein Attractin (Atrn) to repress intracellular cAMP levels and switch pigment production. To produce phaeomelanin, xCT partially regulates the uptake of cystine (a white crystalline amino acid, CHNOS) (Hoekstra 2006). Thus, the interaction of the Mc1r and Agouti proteins is critical in developing pigment to be deposited in developing hairs. The full influence of surrounding genes in this pigmentation process is largely undetermined.

I am eager to continue reviewing my research that I have conducted over the past year and to determine the extent of statistical significance of the data I have obtained.

There is a wait so long

Between editing and filming there is time that needs to be spent productively even though sometimes the wait seems to drag for quite a while. This time has been spent on ways varying from writing notes on current progress, drawing diagrams for future filming, and getting advice from my adviser. There is lots of time spent to put as much effort into my project as I can but there are times where it seems like all I can do is wait until I film some more. I would be lying if I said I didn't play guitar or read something other than film making on some of my free time but that doesn't mean I'm abusing the time given to me by the school to work on this project. There haven been plenty of ups and downs since I have begun working on this project but overall I do believe that I have gained a lot by it even if the evidence to show it is slowly disappearing.

For the wait at hand I am trying to gather as much as possible to use in presentation and refer to in my paper. A portion of my time spent at home during my project has also been taking notes to use when speaking and getting used to presenting. I know presentations are what we've been doing throughout the school year with the power points but I still believe I've got a bit to work on with those. I can't access photos right now but maybe I will update this post later to add in something for y'all.

Mating Stacks! Wasp Competitive Mating, Part 2!!

Well, today was a Monday, and as of last week, that means MATING OBSERVATIONS!!! The boldness and redness of that text should illustrate how frustrating it all is. Similarly to last week, our precious little wasps had a hard time getting on to the leaf dish, and this time, that problem was compounded by the threat of drowning...

So, if you'll recall, the mating observations we're doing this week involve two males and one female in something we like to call "competitive mating." Ideally, we place the female wasp on first, and then we add the two males onto the dish, and hope that something interesting happens. Often enough, something interesting does happen, namely, the mating stack, where the two males wrestle each other for access to the female, while actually on the female's back. Frequently, the stack falls over and the female leaves the two warring males alone to fight it out, but not uncommonly, one male will mate with the female, then be interrupted and replaced by the second male, who will also mate, but actually perform postcopulatory behavior, uninterrupted. The postcopulatory behavior, as it turns out, is quite an important part of the Eretmocerus emiratus mating process, since it allows the male to "mark" the female with his scent, thereby telling the other males that she's taken and can't be mated with anymore. When postcopulatory behavior is interrupted, other males can, and will try to mate with the already mated female.

More mating observations will happen tomorrow. Later in the week, we should be doing DNA extractions on some of our unexamined males from last week, and we should also be sequencing the genome of Encarsia inaron wasps (unrelated to my experiment), in order to be sure that the cultures at the lab are indeed accurately labeled. Shouldn't be a difficult week, but it should be a fun one!!!

Find a job you love, and you'll never work a day in your life

Hello you.

So last week was one of the best for me.
Wednesday I spent the day driving around town to every Gadabout with Megan and Jana to deliver Mother's Day promotions. From now till Mother's Day, if you go into any one of the salons, you'll see the front desk ladies wearing pink scarves for the occasion, and those scarves will be recycled and used for later months (i.e. breast cancer awareness month) just as another step in "going green."
Thursday I spent the day at the River/Campbell location with Frank, because thursdays are the one day a week that he cuts hair, so you can imagine how hard it is to get an appointment with him. I wasn't actually allowed to touch any hair, because I'm not certified in any way to, but he walked me through some of the steps and kept me informed on what he was doing. The hair interns showed me how to mix colors in the dispensary (the color room), and I did end up working a tad bit up at the front desk checking guests in. At the end of the day Frank asked me what the most important thing was that I had learned that day, and I was like "umm to have fun?" He said the most important thing was to love what you do. He loves, and I mean absolutely LOVES what he does, and he doesnt consider it to be work, because it really isn't for him. Even just by watching him work, you could see that this truly is his passion. How do you find that? Like how can you be so sure that you'll end up choosing a career that you were meant to be in?

Anyways, I am at the resource center. We have three studio C's to attend this week: One eskimo, The Avett Brothers and Local Natives, so it should be fun.

You know, after having spent 3 months here at Gadabout (yes, 3 because I just had my 90 day review), I am going to really very honestly miss these people. They have changed my life and my outlooks on it so much, and I don't know if I can really thank them enough for it. I think I know what I want for the future, or atleast Im still trying to mold the idea, and that's owning something of my own, and I want to cut hair.

Frank just gave me my first comb kit, with 9 different styling combs for when I get started, and I think I'm gonna cry

-Me

Exactly one month til graduation!!!

Hey kids. Nothing much is new. I started my powerpoint this week and am still slaving away at the old paper. I think I pretty much have all the information I need now except for three Wild Things interviews (one with Deborah, one with an actor, one with an audience member) which will all hopefully be conducted within the next two weeks. I still am enjoying all the work that I am doing at the theater and will probably continue to work with LTW (and possibly Borderlands too) after school gets out.

"Re"search

My guess is for this next week I will be conducting RT-PCR in the same fashion as last week, but just on different locations in the maize genome. To make things interesting I will be attempting to do the steps that took me most of last week all in one day. This will make it possible for me to spend the rest of the week interpreting my results. I may have everything I need to finish my presentation at the end of this week!

One Week

I have officially been home one week! I did in fact go and see Christina first, mainly because my parents were off in Mexico, but there was a lot of screaming and jumping: which made for quite the reunion. Reunions aside though Tucson is not much different from the city I left. And as nice as it is to not have to pack, or drive between LA and SD twice a week, I REALLY miss California. I knew that the weather was different, but I've gotten very use to a nice 78 with a light ocean breeze. But the good thing about Tucson is I have finally been able to catch up on my sleep and no longer feel like the walking dead.

I don't start working with Dr Chua, the neurosurgeon, until tomorrow so I've had a week to kick back and work on writing my paper without distractions. That turned out to be a blessing, upon reading my rough draft I realized I needed to start over because it was awful. The new version is better but still needs work.

Otherwise not a whole lot has been happening. But I'm sure next weeks post will be much more exciting since I will hopefully have seen people's brains! But we will have to see how that goes since Dr Chua isn't sure about me shadowing him in surgery (which makes sense since he barely knows me). But pray I get to see a brain on something more than a scan!

Sailfin Mollies

Much progress has been made this week. As usual, I have been regularly feeding the fish and shrimp, and watering the plants in the greenhouse. This week we decided to terminate the shrimp bio-assay in the lab, and the whole main shrimp experiment within the lab. So we took all the shrimp out of their tanks and weighed, measured, and counted them. Data wise, we will be concentrating on the growth of the shrimps and survival rates of the shrimp within the tank treatments. The data has yet to be analyzed, but just from eye-balling it, the shrimp grew the most and survived the most in the 20 ppt artificial sea salt water, followed by the 3 ppt artificial sea salt water, and then the RO concentrate water (in which a lot less survived.)

In place of the Pacific White Shrimp, we did a short term bio-assay with Sailfin Mollies in 10 ppt artificial sea salt water, 3 ppt artificial sea salt water, RO concentrate, and Vsep brine. After 94 hours, none of the Mollies died in the tanks. So we got 47 more Sailfin Mollies and set them up in the old shrimp tanks (and replacing the 20 ppt artificial sea salt water with freshwater.) We also took note of the weight, full length (as apposed to standard), and sex of the Mollies for a growth comparison between treatments, and possibly a reproduction comparison. Due to the projects almost being over, the Molly data will most likely not be within my paper, but it will be interesting data.

In addition to setting up the Molly experiment, this week we've also grinded up the dry samples of the Attriplex hortensis which will be sent to a lab and analyzed to see if it is safe to eat. If everything turns out to be ok, then the water plant at Marana can start using their RO waste water to grow both fish and halophytes; which would give them two crops to raise using the waste water, as opposed to just dumping it and wasting it.

The Attractin Gene

This week, I spent a majority of my time analyzing DNA sequences. I further learned about numerous statistical tests to apply to my data. In addition, I attended the laboratory meeting on Tuesday. This laboratory meeting focused on the research being conducted by the laboratory technician who is sequencing genes surrounding the agouti gene in search of a break-down of linkage disequilibrium (the non-random association of alleles at two or more loci [regions of the gene]) around agouti; if found, this would indicate that variation in agouti is the probable source of coat color variation. Upstream of agouti and even within agouti on that region of the chromosome, linkage disequilibrium decays. The laboratory technician is now sequencing genes downstream of agouti in order to study linkage disequilibrium. In her effort to sequence additional genes, she has applied the twelve buffer system, a new addition to the laboratory; this system is meant to optimize PCR by utilizing twelve buffers of varying MgCl2 and KCl concentration and pH to identify the optimum conditions for the amplification reactions of the DNA fragments. This system will be very useful in future attempts to sequence a region of any gene with new primers and will hopefully make the sequencing process more rapid to allow for greater accumulation of data. Furthermore, as many of her PCR reactions have resulted in numerous nonspecific DNA fragments of undesired length, we discussed further options at her stage in the research for troubleshooting such results. For instance, she may consider nested primers, which are primers designed to splice the DNA within the initial sequence obtained from the first set of primers. She may also consider applying a gel stab, in which she extracts the distinct possible bands of desired DNA sequence from the gel and cleans them for sequencing; she would then align these sequences to her primers to determine the accurate sequence. Once again, the most important aspect of the laboratory meetings is the amount of applicable knowledge one obtains from cooperation and communication.

We Have Cytoplasmic Incompatibility! Wasp Research Results!!

It. Has. Happened.

On Wednesday, Dr. Hunter, Suzanne, and I took a close look at our data sheet that contained all of the information from those four hardcore weeks of experiments, and determined--once and for all--that the bacterial symbiont, Wolbachia, causes cytoplasmic incompatibility (CI) in Eretmocerus emiratus wasps. CI is the term that describes the process where sperm from an infected male can't fertilize an uninfected female's egg because the cytoplasm from the male's cells is incompatible with the cytoplasm from the female's cells. An uninfected male can still successfully reproduce with an infected female, and wasps with the same infection status can, of course, reproduce with each other. In crosses between infected males and uninfected females, male wasps can still be produced, since they develop from unfertilized eggs.

We determined that CI was indeed occurring between W+ males and W- females by comparing the amount of wasp eggs that developed on whitefly host as compared to the amount of eggs laid. In matings between W- males and females, most of the eggs that were laid (approximately 64%), developed successfully into adult wasps, whereas in matings between W+ males and W- females, less than half of all eggs laid (approximately 39%) developed into adult wasps. The fun part about all of this is that even though there was a pattern when the data was examined overall, both testcrosses contained interesting variations. For example, although most of the results from the individual W+/W- dishes did suggest CI, there were a few dishes in which 70% or more of the wasps developed, with significant amounts of females in them. Similarly, there were W-/W- dishes in which less than 20% of wasps made it to adulthood. How odd!

Oh, but I should mention that since we're all good scientists over at the Hunter Lab, we do have to confirm our results through DNA extraction and PCR/gel electrophoresis, so that's what we're doing now. Today, we started on this by doing two DNA extractions sets of our wasps (which we had kept frozen in a -80 degree Celsius freezer) to determine their infection statuses. Hopefully we didn't screw up too badly in the experiment, since these are significant results. I guess I should mention that my experiment was not the first of its kind. A few years back, a foreign exchange student from Israel named Elad Chiel, tried to determine whether Wolbachia caused CI in E. emiratus, but he got contradictory results from multiple experiments. Our experiment was more thorough than his, and involved a few more reliable techniques (such as mating observations in leaf dishes rather than in vials, so that wasps could mate in a more natural environment).

Sequences in!

So, the sequences came in today. I loaded them up on the Vector NTI program and did some "trimming" to get rid of some of the garbled, ambiguous sections. Frans says that the sequences look fine, but we will have to have more information in order to come to a conclusion about where the individual mutations are. (I am looking for one base-pair changes in sequences that will end up being 500-2000 bases long.)

I started running some more PCR reactions. I was initially keeping track of all the PCRs I did, but I stopped somewhere around 30. Once these PCRs are finished, we will hopefully be able to purify them and send them in for sequencing.

Conferencing

For the past week or so, Dr. Bickel and I have mainly been focusing on preparing for the "International Physics Conference," when Dr. Bickel and a Professor from PCC gather some of their students and hold a conference where each student presents on a topic of interest. The conference is catered by "expert chef" - which fills me with fear.

Culinary pitfalls aside, the conference is a great opportunity and a sort of "first run" for my final presentation to the basis community. My presentation focuses on the work I've done so far in the project, and the equipment I've used. It will sum up with a description of my final research goal, and how I intend to achieve it.

The Stark/Zeeman Effects are difficult to discover, and my results will probably be unspectacular - if we see any at all. Dr. Bickel assures me, however, that finding any noticeable change in the spectral lines is an achievement in and of itself.

Still Standing...

This week has been insane. My prediction on Tuesday that I would be conducting RT-PCR work for most of the week was correct. I am now a RT-PCR God. I have paid dearly for this title I'll have you know however. I was responsible for working on both my project and Adele's project and the result was my non-stop use of the PCR machine. The timing of this fast paced week could have been better. At the moment I under the weather, and have been somewhat sleep deprived, so my normal problems with staying focused have only gotten worse.

Yesterday I got to hear two presentations given at our lab meeting from two of the other students who also work in the lab. My only confusion comes from the fact yesterday was the first time I had even laid eyes on the two of them, and its difficult to believe that we just have differing schedules because mine is practically non-existant. Bewilderment aside, the presentations were fantastic! These two youngbloods really got the older members of my lab excited, and even though I was only with the flow of understanding part of the time, the energy was infectious. Apparently in the near future, the gene that is the subject of my work may be finally mapped, and there is a possibility that its identity and position is already known.

Earlier today I went to a house warming party for someone in my lab, and had a great time talking with all the people I barely see from day to day. It's always a nice reminder that these towering intellectuals can still find time to laugh at a Sean Connery joke (if the accent is right).

"Nash, I'm not staying up all night just so you can be a wizard"...

So this week got off to a bit of a slow start (project wise) due to the fact that I was in California for Harvey Mudd's admitted students weekend and only got back on Tuesday. In other words, my weekend/Monday was spent meeting extremely nerdy people (a good thing mostly), learning some awesome math tricks/facts (I won a free DVD!), and playing a complicated version of tag/RPG in the tunnels underneath the campus... So luckily HMC is probably one of the most incredible places on Earth (I'm not sure that is hyperbole) seeing as I applied ED there.

As for my project, this week the charge trapping problem (applied math problem) that I have been working on is coming to a close as there isn't whole lot left to explore or program. I have compared my results to Derek's (a student at the U of A who is using Matlab to explore the same problem) and they match up. Also, we've figured out some analytic stuff as well (most of the work has involved numerically solving differential equations).

So basically, I'm more or less done with making pretty graphs for now. That's a good thing since Dr. Manne wants us (Derek and I) to present our problem/analysis during the undergraduate research symposium on May 5 which will give me some practice for my BASIS presentation.

So that's about it for now.

Sean Campbell

Riots Avoided

I can't be sure of how much coverage has been given to the President's FY2011 Budget on the regular news, but its gotten a lot of coverage at NASA. Why would a bunch of scientists and engineers care about a budget that usually draws more concern from economists and pundits? Because there are big changes to NASA in the budget. NASA will overall see a budget increase, especially for research and development (most of what Ames does), but the manned spaceflight (what a lot of NASA Centers do) program is being effectively killed. Thats not to say Ames Research Center doesn't interact with the manned program, Ames just provides all the research side of it, like supercomputing, arc jet testing, etc. A lot of people could potentially lose their jobs because the Constellation Program was cancelled. So why was a riot avoided? Details were few and far between about what cancelling Constellation meant. The first metnion we heard of it was that all manned flight would be stopped and private corporations would take over. That was not a good day at Ames, even for those who do not work on the manned spaceflight program. Why would they care? Well the average age of the employees here is around 40-50, so that means they saw the moon landings, after that a lot of them decided to work for NASA. It was that manned spaceflight program that inspired a large number of people to work for NASA and in the private sector. Heck I was inspired by that, and I was not even alive to see the landings live.
I keep digressing, the riot, so today The President announced his new space policy. If the president had announced something that was radically different from what he did announce, there might have been a riot at Ames. I can see it now, test tube moltovs, the arc jet turned into a weapon, the UH-60s being commandered by the distraught engineers. But it was avoided, thanks to the smooth talking of el Presidente. If you don't know what his proposal is, here's a summary. Short term: scrap Ares I and IV, Shuttle is scrapped, hitch ride with the Russkies, finish orion for a lifeboat, hitch cheap rides on SpaceX's rockets, develop a new heavy lifter by 2015. Long Term: launch the heavy launcher, skip the moon, go to an asteroid, orbit Mars, have humans land on Mars by 2030s. Thats the plan at the moment but we'll see what happens, if new presidents keep cancelling the former's programs in favor of their own, we're never going to go anywhere.

Photo Shoots and Badly Sung "Happy Birthdays"

I decided I don't like carrot cake. Just thought I'd let you know.

Anyways, this week is going surprisingly well. Last Thursday and Friday I was working at the front desk of the Gadabout on Grant, checking people in/out, answering phones, etc. This week however, I am back at the resource center, doing little things here and there really. So Gadabout does modeling adds...or just stuff like that for marketing, and yesterday they had a photo shoot at Oracle, which I got to go to. Megan and I arrived there a bit late, but it was still cool watching everybody work. Today, Frank, Jana, Megan, Pam(who is like the very top of Gadabout) and I all sat around the computer and looked through all of the pictures taken, and selected ones that will possibly be used in future adds for the company.

Thursday I'll be at River working alongside Frank, which I am so so excited for. I'll be able to focus more on what the owner of Gadabout has to take care of in the day, as well as observing him double as a stylist.

I've started working on parts of my presentation, which I can already tell you is going to be quite fabulous. I can't really tell you what's being planned though because I want it to be a surprise...atleast for the most part.

Oh and today was Jana's birthday. I was invited to join in the Gadabout custom of singing happy birthday in the worst possible way you could manage, as a group of course. At first I didnt get it and was like" What the hell is going on?!" But apparently they do that for everyone. Her cake was carrot cake, which I'm not a fan of, but I ate it anyway.

Why is advice so cheap?
Because supply always exceeds demand.

With Sincerity.

Wrapping Up

So, I finally got enough DNA purified to use for sequencing. I put it in the secret chamber where we put DNA samples (well okay, it's not too secret.) The results should arrive by e-mail in 3-4 days. In the meantime, I will be preparing more samples to be sequenced (which means running more PCR.) I will be doing some pre-research on the computer for Frans and his team that probably won't be in my project, but will be similar to what I have been doing and undoubtedly helpful for their research over the summer.

Chick-Fil-A was nice enough to let me have all next week off from work. I will use that time to do some more research and hopefully write my paper. After that, I have probably two more weeks before the research portion of my project is finally over.

Whirlwind College Tour

I unfortunately don't have anything to post as an update to my project from last week, however, I felt I should post an update on what I have been up to.

I went on a long tour through Rochester Institute of Technology, Rensselaer, and Rice to try to narrow down my college list to a final decision. So far, it's looking like a choice between Rensselaer and Rice, which should be a very tough choice to make.

Regarding my project, I'll be back to work coding again tomorrow.

'till next time,

Alex

Moving Forward

So this is the week in which I should be getting my results. It's actually really exciting! I am working somewhere close to over time. Yesterday Mario told me it would be great to have my help finishing the work left by my undergrad friend, but he would be too busy until after 4, so I worked from 4-9 pm. It was a basic PCR run, but we needed to have the gel running by the time we called it quits. I have to admit it was strange for it to be sunny when I went in, and then full-on night when I got out.

My prediction for my week is that I will be running RT-PCR on samples of Heterozygous Mop3 and Homozygous Mop3 from which I will be able to compare gels and determine the differences in regulation. This process will take a few days because we must extract RNA and then carry out the Reverse Transcriptase part of the RT-PCR.

The Attractin Gene

This week, I am focusing intensely on analyzing the data I have obtained throughout experimentation. I returned to the laboratory this morning to find numerous sequences for me to clean and analyze. Thus, I spent most of my day on the computer, searching for polymorphisms (regions of variation) in introns 4, 17, and 23of the attractin gene. I worked with so many sequences that I could remember the order of some bases within the introns and the IUPAC codes (codes for multiple bases occurring simultaneously in a gene) by the end of the day. I further entered all regions of variance into an excel spreadsheet to ease the analysis process. I am looking forward to the final step of the experiment, as I will finally analyze the association of variation in the studied regions of the attractin gene to variation in coat color using statistical analysis.

Interviews and things

This week I've finished up everything that has to do with the Borderlands aspect of my project. I conducted two interviews (one from someone who saw Pancho Villa and one from one of the actresses) and am pretty satisfied with the way the answers fit into my paper (which I have also been working on). Apart from that, Saturday was the first day I visited Deborah while she was teaching one of her classes at Live Theatre (this play is the first one she has directed for LTW but she does a lot of teaching there) and her directing and teaching styles seem to be pretty much the same to me. The performances have also been going well although things usually feel a little hectic during the play (I set up the backdrop, Christmas tree lights, and sparkly background, do the makeup for some of the actors, do the puppets, control the music for all the songs, change the sets in between scenes, help actors with costumes, and clean everything up), although I prefer this to not having very many duties and having to watch the people who do. Overall things are going well and I have no complaints. My paper is coming along nicely and I absolutely love what I'm doing.

Ta ta for now!

It'll Be a Brutal Tuesday for the Wasps and for Me...

Well, another week, but this time, not an easy one!!! Don't let the fact that I got out at 2:30 fool you, today was one of the most frustrating days I've had in a while with those little wasps.

So, the "secret" part of my experiment over at the Hunter lab has now begun. Today, we did competitive mating experiments on my population of Eretmocerus emiratus wasps that I isolated last week. They've had a while to develop, and today, they were ready to get some action...or so we hoped. Suzanne had an easier time with it than I did, but it was still very difficult to get these things to behave. The process goes like this: take a Wolbachia-negative female wasp and place her on a leaf dish; then take two males, one W+, and one W-, and put them in the same small glass vial; once they're comfortably settled in, tap them into the leaf dish and spy on them as they try to mate with the female. In an ideal world, each male would get his chance with the female, and after being rejected or accepted, would go away so that he can be safely aspirated into a pipette and stored for DNA extraction later.

Unfortunately, that's not how it goes...the males don't like to be transferred from one vial to another, or transferred at all, so as soon as they get the chance, they'll escape, especially if they land on the leaf dish and don't notice the female, so, yeah, they're jerks. Assuming both males make it onto the leaf dish and see the female and aren't injured from the transfer (which happened to me maybe like, 4 times out of 9), they'll try to mate with her. Since this is competitive, the male that isn't currently in the process of mating with the female will go over and break it up, typically resulting in a hilarious 3-way wrestling match that ends when the female has had enough. This is assuming they even notice the female. When they don't, they will aimlessly wander in the dish for 10 minutes at a time before trying to approach the female, who can still effectively kick unwanted suitors away for another five minutes. That's still not the worst scenario, though. Wasps like it humid, and if they're left out for too long, they'll get thirsty, and spend 10 minutes just drinking agar once they arrive in the dish, which keeps them from noticing the female, and when they do notice her, she's typically cranky from being so thirsty. This must not sound like a fun thing, right? WRONG! If the results we want are the results we get, this will be quite an important discovery.

Oh, but onto the stuff I mentioned in the title...tomorrow, there are no undergrad workers coming in to help us with culturing, so in addition to that stuff, we'll be doing another primer-testing PCR and more matings. We're gonna do so much stuff tomorrow that we'll deserve medals if we survive...

Happy trails, y'all.

Decisions, Decisions

     This week, I spoke with Surinder Martignetti, the head of the performing arts department at MCA Chicago. Our conversation was a major breakthrough in my research, as Surinder gave me a lot of very good ideas and suggestions for MCA Denver's own soon-to-be performing arts program. She stressed the importance of developing long-term relationships with both performers and audiences. It is important for the museum to seek out new and upcoming performers and give them a space/chance that they wouldn't have otherwise. In addition, it is also extremely important for the museum to establish the trust of audiences coming to dance performances. As with contemporary art, modern dance can sometimes be difficult to approach and comprehend. It is the museum's job to educate the audience about modern dance and make them comfortable each and every performance.
     I also finished up the Mixed Kids project I was working on last week. Every summer, the museum hosts a series of lectures called Mixed Taste. Once a week, two experts on very different topics (Absinthe and Arctic Ice Caps or The Stigmata and The Black Panthers, for example) come and give lectures on their specialties and the audience draws parallels between the two topics. Along with these lectures, the museum hosts crafts for kids on the topics covered. Ama wanted me to come up with names for these kids events combining both lecture topics. After spending a few days researching, I came up with the perfect names. Bigfoot and Carl Jung → Dreaming of Mythical Monsters. Bananas and the Tibetan Book of the Dead → Reincarnated as Bananas. However, Ama then informed me that the titles needed to be very simple: ______ and ______. So, Dreaming of Mythical Monsters was changed to Dreams and Monsters and Reincarnated as Bananas changed to Zombies and Bananas.
     I also went to Admitted Students Day at Colorado College last week. I love that place so much! The block program seems to me to be the perfect way to organize classes. Also, every single student that I talked too had only positive things to say. I plan on visiting Tufts next week and hopefully that will help make up my mind.

The Good, the Bad, and the Actiony

These past plenty of weeks have put me through quite a bit of the twists and turns on independent film making. There are your downsides where you have to learn to adapt and try to take whatever you can from a situation and there are your upsides where you once again have to take whatever you can because they are limited. Things have been a little difficult lately with all of the filming but there have been some pretty lucky things as well.

Over the course of the project so far I've received a lot of help from many friends and new acquaintances which have saved me on some of my personal deadlines and goals. Most recently I've spoken to my UofA advisor and her assistant about the edited footage I've taken so far and help on the rest of the project. Although I made my doubts aware to them about my work, they've reassured me that I am making good progress for such an ambitious project. Other really convenient help from this past week has been from Dany Joumaa in helping me with some background music in edited scenes. Not only has Dany provided me with music he's created but he has also helped me learn a bit of the scorer's job and how they work. I'm happy to be learning a lot from some experiences and people rather than trying to get everything from books. It's great to have so many people willing to help out and I can't wait to thank them in the end of all of the saves.

Other news involves compiling all a ton of notes I've written over the course of working on this project to make a working presentation and paper. Places that I've been visiting for use of their location have been quite helpful and nice as well. Hope to show y'all a bit of the actiony after I finish gathering some clips.

Oh No.

So what I expected to complete this week is very different from what I set out to do. Originally I was going to attempt to uncover families of Transposable Elements inside the mop3 mutant genome. What I actually ended up doing was reading my weight in research papers, drafting refresher slides for my final presentation, and running into Johnston at Subway (I am keeping my word here).

Recent events in the lab are the source of this change of direction in my week. The undergraduate student with whom I work with did something that made my advisor furious. Some plants that were the focus of future research are dead or dying. It is unclear whether I will be inheriting some of this workload or if I will be unaffected if she leaves. Even in a sterile environment, drama is found...

The Attractin Gene

This week, I completed the steps necessary to sequence intron 23 of the attractin gene in the final specimen. If a majority of the sequences are sequenced successfully, I will have performed my last PCR, gel electrophoresis, PCR clean-up, and nanodropping for my senior research project. These are all processes that I have performed so frequently (completing these processes for nearly five hundred PCR tubes) that I have become well acquainted with both the timing and protocol involved; however, as I have realized throughout my experimentation in this laboratory, there are always new challenges and obstacles in research that one must work through before obtaining desired results, and, thus, I am well prepared to have to repeat certain portions of the experiment as necessary. Yet, completing the procedure necessary to sequence the three introns in the attractin gene in the samples was a very rewarding accomplishment, as I will now devote all of my time in the laboratory to cleaning and analyzing the data. I am eager to further experience and learn the next stages in this research project.

I further attended the laboratory meeting on Tuesday, where we discussed numerous statistical tests that Megan, the postdoctorate who is mentoring me in the laboratory, is applying to published data concerning genetic variance in house mice. She hopes to uncover patterns of natural selection in house mice by examining this data; however, she commonly found that the amount of data was insufficient for a complete portrayal of such patterns.