The days are still going by like minutes...
Since Monday, I've begun preparations for the next (albeit unofficial) stage of my project, but I'll get to that. On Tuesday, I was the only person in the lab, since Suzanne (the research specialist) was out, and none of the undergraduate workers or volunteers were available. ULTIMATE POWER...means nothing when you're the only one in the wasp lab. So, that went well, since all I had to was a little bit of culturing for about three hours. I actually had only about 80 minutes-worth of work to do, but I was able to find a secret Texas Encarsia pergandiella harvest that wasn't on the schedule. As it turns out, two weeks ago, that culture was accidentally infested, and we've just been rolling with it ever since. I'd just like to say right now that although this isn't a problem, the E. pergandiella wasps are not my favorites to harvest because their pupae are just so unappealing to look at. They're the scrawniest, palest pupae in the lab. Well, they're still easier to tell apart from whitefly pupae than are Eretmocerus pupae.
On Wednesday, the most important stuff occurred!!! I isolated about 200 pupae from 2 different Eretmocerus emiratus cultures that we're going to compare on Monday during our special mating experiments. The two different cultures we're going to be using are the Rickettsia-positive/Wolbachia-positive E. emiratus and the Rickettsia-positive/Wolbachia-negative E. emiratus. Unlike the wasps we used for my experiment, these ones are R+, instead of R- (this is a result of raising these wasps on R+ whiteflies; Rickettsia is horizontally transmitted), but this shouldn't really matter all that much, since Rickettsia hasn't been shown to do anything to E. emiratus. The experiment, of course, will determine whether a female wasp has a preference for a male wasp of a certain infection status. We will be using both W+ and W- females, and seeing whether they can tell that a male is W+ or W-, if at all. Of course, the W+ females act as more of a control, as do the W- males, since the interesting cross is between the W- females and the W+ males, because the W+ males can sabotage the reproduction of the W- females with their unusable, infected sperm. The W- female could still produce males from this cross, since they develop from unfertilized eggs, as is the case with many hymenopterans.
On Thursday, the most consequential thing that I did in the lab was assisting with another PCR to determine the effectiveness of various PCR primers. This time, we tried the primer CO1 (which worked kind of well before), but with twice the amount of magnesium chloride, and alongside this, we tried EF (elongation factor) made from Encarsia pergandiella proteins. We didn't use BSA (bovine serum albumin) on the CO1 PCR and one of the EF PCRs. In this case, the BSA, which we used on the other EF PCR, did not have a significant effect. The CO1 PCR with double magnesium chloride, worked very well.
Today was a relatively standard day... most of what I did was culturing, alongside the undergrads. There was a birthday, though, so there was lemon cake and mini chocolate muffins, but I didn't have any. Oh yeah, those pupae I isolated on Wednesday have begun to emerge, but the vast majority are still developing. The sex ratio doesn't look too biased...
Friday, April 9, 2010
Black and White Photography, A Return to the "Dark" Ages
I've been waiting all week to use that pun (okay, not really). As you might have gathered, this week I've done a lot with a photography in the form of a spectrograph. An instrument which takes light from a source and disperses it across a photo-reactive film.
Instead of the standard diffraction grating where light passes through the grating and is seperated into its constituent colors, the spectrograph uses a reflective grating. The difference is great, but the function is basically the same. Instead of allowing light to pass through, the reflective grating "reflects" the light while simultaneously dispersing it. The dispersed light will then shine on a photographic film (black-and-white, in this case) and produce a spectrum. Of course, the film needs to be developed, which is a large part of what I've been doing. The film must be first shielded from light, and then transported to the dark room. Once inside, all the lights have to be turned off, since any stray light will ruin your film. You must then remove the film from the holder - in the dark - roll it onto the holder, and place it in a light-tight container for developing. This process is no mean feat. If you drop your film, or any of the other several components in this delicate dance, you'll never be able to find it in the dark. Once the film is safely in the container, you can turn the lights on, and start developing. First, you must pour developer into the container, and let that sit for around eight to ten minutes. Once this is done, the container is filled with water and rinsed twice to remove any leftover developer. After the rinses are complete, fixer is poured into the container, and let sit for about twenty minutes. Finally, the fixer is flushed by a water rinse for another twenty minutes. At the end, you have a fully developed black and white film.
What do each of these steps accomplish, and why are they necessary?
The most important part, I guess, is why the film must be kept in the dark. The film itself is comprised of two sides, a side layered with a concoction of photo-reactive chemicals called the Immulsion, and a plastic side called-- the plastic side? Whenever a photon hits the immulsion something happens inside, and is released by the developer. Wherever a there's been light is darkened, so if you expose your film to light, all you end up with is a black film. Once the developer has soaked into the immulsion - this takes about eight to ten minutes, and can vary more or less based on the type of film you use - the areas which have 'seen' light, while darken, and you'll get your film. However, the fixer is necessary to neutralize the developer, so you can actually take your film out of the container and not ruin your image. Again, the water rinses are just to flush the chemicals off your film. Once this is done, you have a film which can be safely exposed to light.
I've also been taking color digital images.
Instead of the standard diffraction grating where light passes through the grating and is seperated into its constituent colors, the spectrograph uses a reflective grating. The difference is great, but the function is basically the same. Instead of allowing light to pass through, the reflective grating "reflects" the light while simultaneously dispersing it. The dispersed light will then shine on a photographic film (black-and-white, in this case) and produce a spectrum. Of course, the film needs to be developed, which is a large part of what I've been doing. The film must be first shielded from light, and then transported to the dark room. Once inside, all the lights have to be turned off, since any stray light will ruin your film. You must then remove the film from the holder - in the dark - roll it onto the holder, and place it in a light-tight container for developing. This process is no mean feat. If you drop your film, or any of the other several components in this delicate dance, you'll never be able to find it in the dark. Once the film is safely in the container, you can turn the lights on, and start developing. First, you must pour developer into the container, and let that sit for around eight to ten minutes. Once this is done, the container is filled with water and rinsed twice to remove any leftover developer. After the rinses are complete, fixer is poured into the container, and let sit for about twenty minutes. Finally, the fixer is flushed by a water rinse for another twenty minutes. At the end, you have a fully developed black and white film.
What do each of these steps accomplish, and why are they necessary?
The most important part, I guess, is why the film must be kept in the dark. The film itself is comprised of two sides, a side layered with a concoction of photo-reactive chemicals called the Immulsion, and a plastic side called-- the plastic side? Whenever a photon hits the immulsion something happens inside, and is released by the developer. Wherever a there's been light is darkened, so if you expose your film to light, all you end up with is a black film. Once the developer has soaked into the immulsion - this takes about eight to ten minutes, and can vary more or less based on the type of film you use - the areas which have 'seen' light, while darken, and you'll get your film. However, the fixer is necessary to neutralize the developer, so you can actually take your film out of the container and not ruin your image. Again, the water rinses are just to flush the chemicals off your film. Once this is done, you have a film which can be safely exposed to light.
I've also been taking color digital images.
Marana Project update
So far this week I've just been watering the remaining plants in the green house, as long as feeding the shrimp and fish everyday. I've noticed that the Lentiformis that I have been watering are finally starting to grow. However, the ones under the Vsep irrigation is not doing as well as the regular and RO irrigation. Also the Talapia in the green house are starting to stay more near the surface of the water more instead of all of them just hiding at the bottom the whole time, which shows that the fish are used to their new environment now.
For the irrigation experiment on the Lentiformis, we have decided to amp up the waterings to 1 full liter 3 times a week (as apposed to 500ml.) Also we had extra shrimp, so we are now running a long-term bio-assay on them using 10 gallon fish tanks in the lab (one with RO concentrate, one with 3 ppt artificial sea salt, one with Vsep brine, and one with 10 ppt artificial sea salt.)
Due to the lack of baby Talapia, we will probably not be doing experiments with the Talapia (apparently the babies were eaten by the bigger fish -how sad.) However, we did get some silver and black Mollies from the fish store, and set up a spawning tank within the green house. So later on we will have baby Mollies to work with (which are similar to Talapia, except that the Mollies are more popular for fish tanks rather than as food.)
I've also took some measurements using the light meter both inside and outside the greenhouse (to find the percentage of sunlight let into the greenhouse.) I also got to take some readings using a dissolved oxygen meter, which was easy.
Things seem to be going well so far, and I've also been offered a job as being a student assistant in some wet-land experiment. So if everything works out with that, that will be cool.
Thursday, April 8, 2010
CHAOS! and some non-computer analysis...
I would never have guessed that I would still be working on the repulsive charge trapping charge problem. It is so simple yet it has a surprising amount of depth. So, this week although I continued analyzing the problem using the computer (I've mostly fixed the programming issues :)), we (Dr. Manne/I) finally figured out (without a computer!) some bounding criteria for the problem for the 1/r^n force. This was done by looking at the problem from a rotating frame, writing out the forces (the Coriolis, centrifugal, and 1/r^2 force) and the energies associated with the problem, and then playing with the resulting equations.
So, switching reference frames is pretty helpful/interesting...
Besides that, I had Mathematica solve about a 100,000 differential equations and plot a few other quantities associated with the problem that I hadn't explored. I am trying to find patterns among these graphs, but most of them are so complicated (some are chaotic) it is useless (although under certain conditions sometimes these crazy graphs will start to morph into nice and simple cosine/sine/circular graphs which is cool).
That said, here are a few fun graphs:
Velocity is the velocity of the orbiting particle and the escape distance is the distance between the particles when the inner particle is 1 unit away from the origin.
These first 3 are for a repulsive 1/r^2 force between the two particles:
If you view the graph on the left from a rotating frame, it turns into the graph on the right.
Just a different orbiting velocity and you get the "Taco Bell" graph:
And this graph is if the force between the particle is 1/r^2:
And that is about it for this week.
So, switching reference frames is pretty helpful/interesting...
Besides that, I had Mathematica solve about a 100,000 differential equations and plot a few other quantities associated with the problem that I hadn't explored. I am trying to find patterns among these graphs, but most of them are so complicated (some are chaotic) it is useless (although under certain conditions sometimes these crazy graphs will start to morph into nice and simple cosine/sine/circular graphs which is cool).
That said, here are a few fun graphs:
Velocity is the velocity of the orbiting particle and the escape distance is the distance between the particles when the inner particle is 1 unit away from the origin.
These first 3 are for a repulsive 1/r^2 force between the two particles:
If you view the graph on the left from a rotating frame, it turns into the graph on the right.
Just a different orbiting velocity and you get the "Taco Bell" graph:
And this graph is if the force between the particle is 1/r^2:
And that is about it for this week.
Wednesday, April 7, 2010
This Week at NASA.........
So wind tunnel tests have began, last week, and they've already stopped. One of the dynamic actuators broke on the third test. I could go into what the dynamic actuators do and are but that would probably be pretty boring to those who aren't planning on studying engineering in college. Instead here's an overview: they move the rotor blades by very small amounts to fine tune certain coefficients that relate to various properties of the rotor. Since that part of my internship is on hold, I'm back to data analysis in the office.
What else has happened at NASA......Monday the interns took a field trip to NASA's Dryden Flight Research Center in scenic Mojave, California. Unfortunately it was pouring when we got down there so most of the test flights at the nearby Edwards Air Force Base were grounded. The only plane we got to see land was a KC-10 Extender. A few years ago the interns saw B-2's land as well as a few fly overs by F-22's. Decidedly cooler than a KC-10.......What we did see were the F-18 Hornets used by NASA as chase planes, the RQ-4 Global Hawks used by NASA for research, the 747 Shuttle Carrier, the F-15 ACTIVE, the F-16XL, the X-15, and the Ikhana Predator B that is also owned by NASA. But the best part of the tour, besides all of the amazing planes, was the F-18 simulator that we were allowed to fly for two minutes. AMAZING!
Oh yeah and I'm enrolling at Georgia Tech for the Fall of 2010.
What else has happened at NASA......Monday the interns took a field trip to NASA's Dryden Flight Research Center in scenic Mojave, California. Unfortunately it was pouring when we got down there so most of the test flights at the nearby Edwards Air Force Base were grounded. The only plane we got to see land was a KC-10 Extender. A few years ago the interns saw B-2's land as well as a few fly overs by F-22's. Decidedly cooler than a KC-10.......What we did see were the F-18 Hornets used by NASA as chase planes, the RQ-4 Global Hawks used by NASA for research, the 747 Shuttle Carrier, the F-15 ACTIVE, the F-16XL, the X-15, and the Ikhana Predator B that is also owned by NASA. But the best part of the tour, besides all of the amazing planes, was the F-18 simulator that we were allowed to fly for two minutes. AMAZING!
Oh yeah and I'm enrolling at Georgia Tech for the Fall of 2010.
Tuesday, April 6, 2010
Feast of Wire
Things have been busy down at KXCI and the Rialto these past two weeks, primarily because of the Festival en el Barrio Viejo. The festival was a benefit concert for KXCI Community Radio (91.3 FM) featuring some of the best musicians/bands in Tucson, with the local heroes Calexico headlining. During the lead up to the event I had a chance to interview/talk to Joey Burns of Calexico and while it was certainly interesting to discuss music and the festival, I will note that I discovered that Europe really has nothing comparable to the FCC or Clear Channel. This is important for many up and coming bands/artists because in the States they can't get any air play due to the monopoly on many media outlets, who focus on a small list of safe, established artists to cover. This is a major reason why many bands will go tour throughout Europe because DJs will go to their shows and then play the band's music on their shows later. Also, many countries in Europe really don't have many restrictions on what you can or can't play on air during a radio broadcast, so there's fewer restrictions on what DJs can play, ie songs with certain curse words. On a final note, I've also discovered that in Arizona, religious radio stations still have the highest priority over college, community and corporate radio stations. This comes in to play when a station like KXCI is trying to acquire a booster, a device that would pick up KXCI's signal and relay it so people in Oro Valley/Marana could listen in. That said, KXCI's low priority with Arizona is only a part of the booster issue, but still it's an interesting point.
Other than that, I'm reading these papers on Network Theory/Society by Manuel Castells, which will help me to explain the "everything is connected" phenomena I've noticed working at KXCI and the Rialto. It's really dense reading, but very informative and will certainly help with my presentation. I plan on making a network diagram to show how immense and connected the Tucson/Arizona/US music world really is.
Finally, I have decided to enroll at Reed College. They not only have a great Political Science department, but they also gave me a fantastic financial aid package. It looks like we're going to have a big BASIS contingency in the NW with all the BASIS kids going up there soon and all the ones already there.
Finally!
Good news: I finally got a PCR product to work! It seems that the annealing temperature was indeed the problem behind my previous failed PCRs.
However, I have found another oddity. It seems that only some of the primers worked. I had been using two different pairs of primers to cut the genomic DNA at different sites and obtain different fragments. Even though the one pair did not work, my results are consistient. Since all samples of the first primer pair worked, and none of the second pair worked, I can safely conclude that the problem has to do with the DNA-primer interaction, and is not a mistake made on my part.
I will be further investigating this anomaly prior to sending in the DNA fragments to be sequenced.
However, I have found another oddity. It seems that only some of the primers worked. I had been using two different pairs of primers to cut the genomic DNA at different sites and obtain different fragments. Even though the one pair did not work, my results are consistient. Since all samples of the first primer pair worked, and none of the second pair worked, I can safely conclude that the problem has to do with the DNA-primer interaction, and is not a mistake made on my part.
I will be further investigating this anomaly prior to sending in the DNA fragments to be sequenced.
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