Ski what?

Anyone interested in a ski trip over the winter break? New Mexico? Colorado? Utah? They're all somewhat close and I know there was interest in doing something together over the break.

Coming to a Mailbox Near You

If you posted your address to the Facebook group expect a letter in the mail shortly, (or now depending). =D

I've spent several hours in the last week procrastinating and writing letters to everyone because it seemed like such a great idea and few of us have followed through with it. Also because I've realized the immense joy one gets in getting mail that is not another coupon book.

Otherwise life has been lovely. The temperature is finally cooling down, although we are still decidedly in short and flip-flop weather. And life is moving along. With just four weeks until winter break (and the end of our first semester of college) I can't believe how quickly time is flying by.

I hope you all had wonderful Halloweens! I dressed up with a bunch of girls from my hall as the Disney Princesses, not very original but still very fun. The quote when we showed up at one party was "The whole fucking Disney Channel just showed up". Priceless. Other than that the rest of the weekend was unremarkable. ASU won the football game, drunk people stormed the campus, same old same old.

Here's hoping everyone did great on their midterms! Can't wait to see you all over Christmas break!

Skyping shenanigans and Winter plans.

Like 10 minutes to set up on the computer and get chattin' away with people if ya got a mic. and camera thing on your computer. Had a wicked 4 and a half hour conversation with Cody and Rita yesterday night that was a lot more fun than I thought it was going to be, especially compared to typing things in Facebook group chat(not that there is anything wrong about it). Glad to see some forms of communication rolling around between us but it gives me less and less to write about in letters since "How is college?" has already been thrown in. I really hope to get as much done as possible so I can have things to show and tell when we chat or reunion in the next few months. We are going to do something and unfortunately it will require planning. That's all for now, still countin' the days until winter reunion.

Just Follow the Sound of the Drum

It's been awhile since I've heard from anybody, except Cody really, and that upsets me (nothing against Cody). How is everyone doing? I will be getting some stationary in the next few days, so you should start expecting letters from me if you gave me your address. Hope all is well wherever you may be, we really all should talk more...

-Andy

All of a Sudden I Miss Everyone

Cody, I expect you to get the reference in the title. But while I was mourning all of our departures I started thinking something like "hey class of '10 we should start planning something when we're all back in Tucson over winter break." My thinking is that if we actually start planning it now it may not end up being in some tiny hotel room! Hell most of us even have an entire month off what if we went somewhere exciting? But yeah, let's start planning now so it actually happens.

Missing Everyone Dearly,

David "Plastic Sword" Stevens

For a sec, I forgot we grew up

So Im definitely waiting to hear how everyone's first few weeks of school went.

It's weird, because I know that BASIS already started like 2 weeks ago, but I feel like we just start at a later time, but we're still supposed to go back at some point, and that college is just kind of a side thing to do in the mean time.

A couple of my classes are in the auditoriums that we had language fair in, and everytime I'm there, I remember stupid little lines from our spanish skits, and it makes me wish that we still did language fair with Senora. I'd agree to doing spanish again at BASIS if it meant spending a good half of the yr working on a 5 minute skit.

I miss you guys already, and it's still only my first week of non-basis school. But if I had to choose between my english 101 and english with Mrs. Toews and Ethan Frome's pickle dish, I'd choose the pickle dish.....and the "stuff."

With complete adoration for the '10 class
Tini

Hey all

How many of us love getting mail? I would bet that's everybody. So, here's my idea - BASIS Postcard Exchange! Postcard stamps are cheap and you have so many different postcard options.  I'll create a google document that everyone can add their addresses to and we can begin! It can be as organized (aka, some sort of rotation) or as unorganized as we like. 

Are you guys interested??

Life is what happens when you're busy making other plans....

So. I'm back. Not exactly the way I wanted, but I'm back.

Three weeks ago - the Friday of my fourth week of Beast - after suffering severe leg pain, I was ordered to report to Keller Army Community Hospital Orthopedics, where they x-rayed my feet and legs, and informed me that I had tibial stress fractures in each leg and another fracture in my left foot. I was then told that I would not be able to complete Beast and would be sent home. Here I am. At this point in time, I am still technically a cadet, and am on a payed Medical Leave of Absence for the year. I am looking at various options to keep myself busy and will likely take classes at the U of A. I'm still on crutches at the moment, and will be for a while, so first semester seems unlikely, though if I want to take advantage of my scholarship, I may have no choice. Anyway, I'm glad to see that everyone's doing okay and getting off to college successfully.

Thanks to those who wrote while I was away, it meant a lot.

Everyone come to the party please!

that is all.

Grainne in Denver

Hello everyone! I miss you all heaps.

Denver is beautiful, but I am not really doing anything very exciting. I was interning for Q's aunt, but she just hired me so now I am a full time editorial assistant, which basically means I get paid and have a fancy title. Basically, I'm writing activities for both gifted and talented and at-risk middle schoolers; while this isn't terribly exciting, it's definitely interesting.

I also just got back from spending a week in New York City! Somehow, I managed to pick the week that New York was ravaged by a record breaking heat wave. After living through that, I'm not sure that I'll be able to survive east coast humidity. Tucson's dry heat is infinitely superior. Apart from the heat, New York was amazing! So many awesome museums, one beach plus amusement park, a few bicycle rides, great food, and, most importantly, a fantastic roller derby game, not to mention some excellent thrift shopping--can you say cashmere J Crew sweater for $6?

I hope the all of your summer's are full of excitement and relaxation!

From Germany with Love

It feels so weird to be writing one of these again, but since I've been having adventures I feel like now I can finally contribute.

So as you all probably know I got to spend the last month in wonderful Deutschland and if you're friends with me on facebook, you'll also know that I've been having quite a bit of fun.

I started my trip in Erlangen with my dad (he stayed for the first 9 days so he could attend my great aunt's 80th birthday party). We stayed in Herzogenaurach (a tiny little town in the country side, mostly known for its enormous Adidas and Puma outlets) with my three beautiful friends Kerstin (my age), Berit (the one who came to America three years ago) and Meike (the awesome rock climber and slackliner). Kerstin is my age and the other two have already moved out so I mostly spent all my time with Kerstin. We only stayed for a few days before we went to Mannheim for a week (but my dad left half way through). In Mannheim I stayed with some very close friends Tim (my age), Sonja (Gordon's age) and Katrin (older and living in Freiburg). I had a ton of fun with Tim and Sonja (I only got to visit Katrin once), we played a lot of soccer and volleyball, I did some yoga with Sonja, I went to school with Tim twice (the first time happened to be on the day of their senior prank), and Tim and I watched the World Cup with 5,000 other people in a hot little tent and then jumped in a fountain with a few hundred other people afterward. Then I took a four and a half hour train ride back to Erlangen for another week. Other than getting kicked out of first class and almost missing my train connection, I think I did pretty well.

Being with Kerstin and her sisters again was so much fun! We cooked, went to bars, slacklined, went to festivals, shopped, watched I Love You, Man, and went swimming and tanned (well some of us got really REALLY bad sunburns). I met so many fun people that I am now friends with on facebook and talk to all the time, and getting to experience the nightlife of the town was pretty cool. About a week ago I took another train to Augsburg, this time I came insanely close to ending up in the completely wrong city but I managed to figure out I was on the wrong train and get on the right one just in the nick of time.

I am now staying with my aunt and uncle who live very near the center of the city so every time they have to work I can wander into downtown which is awesome. My aunt and uncle felt bad that I didn't have anyone my own age to hang out with so my uncle asked his college with a daughter my age if she could spend some time with me on Friday night. I admit I was a little bit reluctant to agree to being set up with a stranger for the night (after all my aunt and uncle are pretty cool so I was content to stay with them). However, the night turned Julia and I (and her friend that came with us) into very good friends and was probably one of the greatest adventures I had on the entire trip (if you want me to elaborate, see me in person) and I was ultimately very glad I agreed to go. Today Julia and I hung out and went shopping for her graduation dress and her friend told me that when I come to Germany again I should stay with her for a while. It's such a great feeling to make these international connections!

Anyway, now I'm supposed to be packing my bags because tomorrow I leave for Frankfurt to stay with my dad's cousin for one night, then I'll be on my way home! I can't wait to see you guys, I really have been thinking a lot about you all (in fact, I've seen German doppelgangers for many of you) and maybe someday I'll cook you guys some German food! See you soon! XOXOXO

Rita

We celebrated Christina's 18th birthday

At Club Congress after Second Saturdays downtown. Bigger room this time and it was a lot of fun.

Bicycles, Backpacks, Thumbs, Mountains and Canyons

Summer is great. I feel like I am taking a gap year given that I haven't been in school for five months, and I won't return for another two and a half...
As Brian mentioned in his previous post, I took a large group of people camping up in the Pineleno mountains a few weeks ago which was a lot of fun. We played horseshoes, sat around campfires, and had some awesome jam sessions.

When it was time to go, I got dropped off in Safford where I started my next journey: hitchhiking to Canyon de Chelly just below the four corners. I had my bicycle, but it was more of a secondary form of transportation given that I had three days to get to the canyon (I was meeting some friends from California there). The first day was really hard, which was my fault. I decided I wanted to take route 191 all the way north to canyon, which proved to be a poor decision, given that I only saw maybe 8 cars on my first day. This made getting a ride really tough, and I only made 30 of the 370 miles I had to go. Luckily, the next two days, my luck turned around and I made some awesome time. On top of that I got to ride up the part of hwy 191 that I was supposed to come down on my last bicycle journey. This was an exceptionally beautiful area packed so tightly with aspen you could hardly see the sky. Day three I made it to the canyon by 10 in the morning. I met up with my friends that afternoon and through a series of really lucky events I ended up backpacking into the canyon that night. A few days later my friends left and I headed home, taking a different route, that took me through Flagstaff. It took me two days to get home.

Over the 4th of July Sean C., Sean S., and myself decided to climb Mount Wrightson where we could watch the fireworks from the summit. Being the tallest mountain in southern Arizona, it was awesome. We watched fireworks from Tucson, Sierra Vista, Nogalas, Saughrita, and Sonoita (among others) at the same time. We then spent the night on the mountain drinking coco around the fire before we passed out like little babies.

Thats all I got for now, I'll be camping this weekend, and next week I leave for Colorado. The fun never stops....
Enjoy the pictures!

Brief Update

Been biking a bunch, bothering a bunch of people by calling and randomly stopping by their houses on my bike, swimming, bits o' ping pong, and making sandwiches. Honestly my sleep schedule is slowly going to hell lately because I end up staying up till around 3am and then just trying to fall asleep because I don't want to try when the sun starts shining through my window blinds. I've been waking up at times ranging from 11:30am to 2pm. Recently I went on a weird biking trip with Devin, Sam, and David Gifford on the 24th and I did type a long post about it but I do feel that it needs shortening or else it will just drag on too long. Andy also hosted a pretty cool camping trip and has a bunch of pictures and stuff that he should edit and post. I've gone climbing with Devin and his climbing buds up in mt. Lemon to do boulder climbing which is pretty fun. Oh yeah and since this is crazy World Cup soccer season I've been getting my ass handed to me in soccer when a bunch of us meet at Himmel. If ya'll are interested I could try typing more detailed stories but I just wasn't sure if you would really want to sit through long paragraphs without cool pictures showing it.

Hope the rest of everyone's summer is going great, I'm going to be in California for a while with mah folks and bro so hopefully nobody else leaves for college yet while I'm away. I'm trying to stop by peoples places before they leave but that's only worked for Grainne and Rita so far, I missed Charlie because I was still camping with Andy... my bad. Oh yeah I've also been shooting hoops with Collin, Cody, and Jendy quite a bit; would like to throw in some time at the golf driving range as well. I do feel bad that I do not have a job like most of you who are probably sick of hearing about all of the free time I have but I do feel I am using it quite productively at the least. Will work on updating you guys more often if ya don't mind all of this.

-Brian

mmmmm.... goat milk.

The last weekend me and Grainne went up to a little "community" called Wind Spirit. It's about 16 miles north of Winkelman (if any of you know where that is) off a dirt road in the middle of nowhere. The time we spent their was awesome. There are 15-20 people who are currently living there, all of whom are very interesting..... I think the coolest person I met while I was there was The Goat Dude. He was an older guy, who after getting 5 degrees (including his doctorate) decided life was too short and became a goat herder. I tried some of his goat milk (there's only so many opportunities in life) and I must say it is quite tasty and refreshing. They also had ducks, chickens, an awesome vegetable garden, and an abundance of fruit & citrus trees.

The days were really hot, so we would wake up at four or five in the morning in order to get some awesome hiking done while it was still cool. When the sun would come around, we'd read, sleep & widdle. We also got to help out, and make a giant makeshift ramada out of bamboo, to shade one of the buses that a really nice Israeli woman and her daughter were living in.

I was originally hoping to road trip up to Yellowstone and The Gran Tetons this month but it looks like those plans have fallen through. Instead I think I will be trying to hitchhike up to Canyon De Chelly at the end of the month. Thats life in a nut shell, I look forward to hearing from the rest of you soon!

Caliiiiforniaaaaaaaa here we comeeeeee

Ok, so again no one is really posting. But I'm pretty sure from facebook we're having some crazy adventures, so I've decided to share mine. Although disclaimer they are really that crazy.

So I'm back in LA, no offense to Tucson but I wish I had been raised here. They have summers you can actually spend time outdoors during, crazy idea but rather enjoyable. So I got here Friday and mostly hung out this weekend since I didn't start work until today! I'm spending a week working for my aunt's interior design business after which I will go back to being a PA on Curb and then end my trip with one more week in the design office. All in all it should be a rather fun and easy month for me.

On other notes, I'm sorry I didn't get to see a lot of you before I left. I wasn't planning on coming out here until about a week before I did. But hopefully I will get to see everyone before we all head off to college in the fall. BBQ at some one's house maybe? Who knows. Anyway, miss you all start writing so I don't feel so removed from everything.
xoxo
Q

Summer Life

So it's the 28th and nobody has kept up with Andy's idea of the posting after grad.
Well I just thought I'd share my current events:

Gadabout gave me a job, so i've been working at the front desk every day. Saw Ms. Misha when she came in for her hair appt. Thanks Mrs. K for recommending Gadabout!!

Hope you guys are having fun. Sorry I missed skate country

Miss you,
Tini

No End In Sight

Can we keep this going forever? I feel like it'd be a cool way for everyone to keep in touch and know where everyone else is at in life.

Not entirely sure if we still have to post but...

Unfortunately, the people at Prototron Circuits forgot to send me the quote for the boards, so by the time I received them to sign off on the cost, it had pushed the delivery date back too far to be ready by presentation time. Basically, the boards will be finished sometime during the day I present. While that ticks me off and depresses me in equal measure, I think I'll have more than enough to talk about staying in theoryland without showing off an actual demonstration. In other news, I've almost finished my paper to turn in in lieu of a purty stethoscope. It currently weighs in at around 10 pages, and does not include circuit schematics, board layouts, code, or pictures.

'till next time,

Alex Davis

GRADUATION

Patty needs to talk to all of you at once, so we need a senior meeting. I also need to talk to you about the ceremony.

How about we all arrive early for the Thursday presentations, at 5:00?
Ms Toews

Yep, It's Almost All Done!

So this week I have finally finished up my paper. It is nice to not have to worry about writing it anymore. (Of course there will probably be some minor revisions needed, but the hard part is over.) Not that my paper is finished, I have been focusing on creating a power-point about my project for the presentation.

Like Brian said, there is so much to be said on our 20 minute presentations, so hopefully I will have time to finish it, practice it, and refine it. The rest of my time for the week has been filled with birthday parties, practice for an upcoming 3v3 soccer tournament, and practicing bass.

Diagnosing my first patient!

So not too much has been happening this week beside working on my paper and putting the final touches on my presentation. Since that's pretty much what everyone is doing I won't bore everyone with such things.

Luckily for all of us exciting things are happening at Dr. Chua's office. There were quite a few trauma emergency patients this week, which although I'm not allowed to see them in the hospital I still get to hear everything about. On Monday Dr. Chua got called in at 2a.m. to do emergency surgery on a lady who had a brain hemorrhage, he got it out and then she started squirting blood! He got it all under control even though she coded three times and 24hours after surgery she was beginning to wake up.

We're also starting to see patients who I recognize. Most people don't just sign up for surgery, they like to think about it more tests are generally done and then they come back to further discuss their options. On Friday an 82 year old woman with a pituitary tumor came back. Her vision in her left eye is being affected because the tumor is pushing on her optical nerve, but with the vision test they also had a much more focused MRI scan.

Dr. Chua, his P.A. Lisa and Dr. Scully all looked over her scan because she has quite the tumor. Your pituitary gland is roughly the size of a pea and this tumor is the size of a strawberry. Dr. Scully turned to me and asked how I would treat her. Needless to say I was very taken aback at first, but then I just answered which shocked him. I thought she shouldn't have surgery because of her age, other health problems, and medication list. Also pituitary tumors are very slow growing, so at her age it most likely won't change her life that much. And I was right!!! I correctly diagnosed my first patient. Dr. Chua was very proud and Scully and Lisa were impressed.

All in all it was a GREAT week!

Muttering imprecations all the while.

This has been an interesting week. The spectrographic spectrometer failed to produce conclusive evidence of the Zeeman effect, so we had to use an interferometer, a very high resolution imager. We took some photos, got our pattern, and figured that this would be a piece of cake since all we have to do is put it in the computer, let it do its thing, and it'll spit out an analysis of the ring system created by the interferometer... oh. The computer's broken. So, we had to find images which can easily show the effect. And this all has to be done with analog film, so you don't know until you develop the film. Or - like I did one time - you failed to secure the new film properly, and find out that all those photos you took didn't expose onto new film...

I honestly don't want to think about it.

I have pictures. I am happy.

Thank you and good night.

*Gasp* You are a high school student?

So today, Derek and I gave a presentation at the U of A undergraduate research symposium. Afterward, we received numerous compliments on how well our presentation went which made us feel pretty smart.

Initially, before we gave our presentation near the end of the symposium we had been feeling pretty nervous since a) everyone else presenting was at least a junior b) every other presentation title contained huge amounts of jargon c) about half of the other presentations were concerned with extremely complicated looking quantum mechanics equations whereas our presentation dealt solely with lowly, lowly classical mechanics. In other words, our presentation didn't fit in with the others (i.e. it was probably understandable by everyone).

By the time, the symposium ended there was only one other presentation that I fully understood and that concerned the efficiency of windmills with different numbers of blades (2 blade turbines produce the most power at high speeds and 5 blade turbines are better for low wind speeds). Despite the many complicated presentations, the fact that after 4 years of study one gains this awesome power to understand slide after slide of quantum mechanics equations is both amazing and motivating.

Anyway, afterward, we got free food, compliments, and a lecture on how awesome physicists are.
And now I must get back to my paper...

Seis de Mayo Monster Mash

As I type this, there is a Bigfoot expert recounting his tales of Bigfoot tracking to the museum's programming director. "Picture a gorilla about 8 feet tall...They're very crafty...The best sound recordings come from the Sierra Nevadas...This redneck woman kept feeding him blueberry pancaked with syrup!" It's my last day at the museum and I am going to miss this place.

As of today, I have finished up both my presentation and my proposal. I'm due to present my proposal to Ama in a few hours. This week at the museum has been extremely busy. Everyone is preparing for the spring fundraising gala, which is happening this evening. The point of the event, titled Seis de Mayo Monster Mash, is to release the topics of the museum's Sunday lecture series, Mixed Taste. It's going to be insane! There will be Bollywood dancers, King Kong, Godzilla and several strong men lifting up a smart car, along with several volunteers representing topics handcuffed together. Tickets cost upwards of one hundred dollars, but I get to go for free and don't even have to do any work (because it's my last day).

I can't wait to come back to Tucson and see all of you soon! By the way, if any of you are looking for a good summer read, I would highly recommend Daniel Dennett's Conscioisness Explained. It's absolutely mind-blowing. And what's even more mind-blowing is the fact that I might be taking a class from him sometime in the next four years!

The Attractin Gene

This week, I am continuing to focus on my presentation. I also hope to meet with Mr. Johnston and make any necessary revisions to my research paper. After communicating with my post-doctorate mentor at Professor Nachman’s laboratory, I further obtained additional, valuable information concerning my experiment. During my experiment, I combined the Armendaris and Carrizozo, New Mexico, specimen. This was possible because, not only are the two populations in close proximity to one another on their respective lava flows, a previous study demonstrates that the two populations are actually one population of interbreeding animals; thus, the geographic separation between the two locations has not led to speciation with respect to the rock pocket mice located in these regions. There is always more to learn regarding an experiment and I am eager to continue to gain knowledge to better analyze my data.

The Pace Quickens

Last week I felt pretty good about how quickly I could run through a batch of RT-PCR. That was nothing. Instead of running each genotype on separate days, I had to run all the different mops in one day, because this is my last week, and Mario needs these results for his presentation at the lab meeting this Friday. These genotypes are color coded in the picture with mop1 as black, mop2 as blue, and mop3 as red. 84 tubes full of PCR product, and 12 tubes full of cDNA are what I have to show for my 10 hour day at the lab

I will be running the gels of these tubes tomorrow, but after that the only thing that is certain is that I will be writing.

So Much to Say and So Much to Write

With revisions and possibly more paragraphs to add into the paper as well as all of the things I want to mention during the presentation I've still got some work to do. It is nice that the paper is not as limited as the presentation but I also wouldn't want to go on for too long in the paper. 20 minutes is quite the short amount of time to speak about all of the things I've learned and experienced during the project but I guess I'll have to get lucky on how I present. Hopefully I can practice enough so that I don't make the same mistakes that were in previous presentations throughout the school year. It's the last push and I've got to be ready to give it my all.

They changed my life, one hair color at a time...

So last Friday was officially my last day at the Resource Center. Dear god it broke my heart to walk out of that office, away from the group who i'd spent every week with for the past 3 months. Of course I couldnt just end our relationship there, so I agreed to help Megan with the Gadagirl Model search May 1st and 8th. (By the way, any of you 18yr + girls out there want to audition to be a cover model for Tucson Lifestyle Magazine and be used in a Gadabout ad, as well as help out some local charities, feel free to come to the Oracle Salon next Saturday from 10am-2pm).

I guess it's time to start crackin' the whip and get a move on with my presentation. It's coming along, slowly but surely. I can't believe graduation is less than 3 weeks away!

Is it sad to say that I already miss my desk in Megan's office? I do.

Birthday Wishes

So much of my work this week was on my paper since Dr. Chua was in the OR most of the week. I did work with him on Wednesday which was fun. He is now having me read the scans before him and tell him what I see. Thankfully we didn't have as many patients with herniated disks (it gets old after awhile), we had a woman with a tethered spinal cord. Your spinal cord should descend from your brain stem and nerve endings should filter down your spine, but it isn't connected to the bottom it just hangs. Hers because of a birth defect was fused, this can cause kidney and bladder problems, and although there is a surgery that can fix it it is so risky (because of the specific complication she had as a baby) that no doctor specialises in that surgery.

Wednesday we also got to have cake because Dr. Chua and I both had birthdays on Friday. April 30th is clearly a good day to be born =).

Next week should be very interesting (for me at least) because he is in the office every day except Tuesday. He says my suture knots are looking really good and my speed with them is picking up, although my suturing itself needs improvement. He looked over the parts of my PowerPoint that talk about my time with him to check my work and said he was very impressed. If any BASIS kids want to work with a a neurosurgeon in the coming years I highly recommend him, not only is he a great teacher but he really likes BASIS now.

Dessert Week at the MCA

     As I reflect back on this week's work at the museum, what instantly comes to mind is dessert. On Wednesday, a new baker in town brought a huge sample platter to the cafe in hopes of becoming a supplier. Since there were so many pastries (which were all vegan), the whole museum staff was invited to taste the pastries and give their input. My personal favorites included a cherry almond muffin and a chai cupcake with ginger icing. Continuing with the desert theme, Thursday was the birthday of the museum's cafe manager, so we all gathered in the cafe and had Boston creme pie and champagne (well, everyone but me) in celebration.

    As far as my project goes, I am finalizing my proposal and working on my power point presentation. I'm a little worried about how I will manage to condense my experience at the museum into twenty minutes. There is so much to talk about! 

    On Thursday evening, I went to an amazing performance at the museum. The piece, performed by local artist Michelle Ellsworth, was essentially a response to recent scientific research indicating that the Y chromosome is becoming increasingly obsolete. Did you know that the Y chromosome is loosing genes at the rate of 4 every 1 million years? Pretty intense. Anyways, in her performance, Ellsworth presented some of the archival work she's doing to preserve the memory of men when they no longer exist. She also displayed some apparatuses she'd invented to represent men, my favorite being a large, unblinking eye representing the male gaze. Overall, it was hilarious and an excellent performance.

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.