Well, it's the end of the 8th week, and almost all of the data has been collected. If all goes according to plan, then Dr. Hunter is going to help us analyze the results of the research and finally figure out whether bacterial symbionts in the genus Wolbachia cause cytoplasmic incompatibility (CI) in Eretmocerus emiratus wasps.
CI is a mating incompatibility between wasps of differing infection status; when a male wasp infected with Wolbachia mates with an uninfected female, he sabotages the her reproduction, since Wolbachia-infected sperm can't make offspring with uninfected eggs. Because the wasps have a haplo-diploid sex-determination system, the sabotaged female can still make males (they have the haploid number of chromosomes). Basically, to prove that CI occurred, we're comparing the amounts of eggs laid versus female wasps emerged for each leaf disk. If there were many eggs laid, but few or no females emerged in testcrosses between W+ males and W- females, then CI occurred.
Our experiment was carried out over four intense weeks (although there were a couple of weeks of planning beforehand), and 80 female wasps were examined. After the dead and unmated wasps in this group were discarded, we were left with approximately 16 wasps per block of experiments, and there were four blocks (A through D) in total. We recorded our results on a spreadsheet, and so far, have gotten some odd ones. We haven't taken a good, long look at the results, yet, but so far, some of the W+ male--W- female crosses have yielded unexpected results. Although CI was expected to occur in all of these matings, there were surprising amounts of female progeny produced. What does this mean? Well, I guess we'll see when we analyze the data and test the wasps' DNA through PCR.
Hopefully these odd results will lead to the discovery of something new that will rock the field of host-symbiont interactions for years to come. We're going to do some more mating experiments next week, and I'll definitely start putting our results into paper-form soon enough.
Friday, April 2, 2010
Every Silver Lining Has a Cloud
So, while I'm very happy with my new monochrometer, the strip chart which accompanies it is a royal pain. It's old and crotchety, and does things when it wants to and not before. I swear, I think it'll hit me over the head with a cane one of these days. This has dampened my enthusiasm for the monochrometer since to get tangible data, a strip chart is generally required.
Sean came down to the lab the other day, and I got to show him around. Hopefully I didn't bore him too much. I get a little verbose when I'm talking about the stuff I'm doing.
Dr. Bickel and I are progressing into the final stages of our work. I'm gearing up for producing my final product, a notebook describing my work. It will contain strip charts and data, along with descriptions of experiments and equipment which I hope will be illuminating.
Other than that, things are still basically the same. I'm taking data with light sources, learning about more and more equipment and the fundamental physics behind the science.
Sean came down to the lab the other day, and I got to show him around. Hopefully I didn't bore him too much. I get a little verbose when I'm talking about the stuff I'm doing.
Dr. Bickel and I are progressing into the final stages of our work. I'm gearing up for producing my final product, a notebook describing my work. It will contain strip charts and data, along with descriptions of experiments and equipment which I hope will be illuminating.
Other than that, things are still basically the same. I'm taking data with light sources, learning about more and more equipment and the fundamental physics behind the science.
Hey it works now, well kind of........
So the long anticipated wind tunnel tests have began. The first forward flight run was finished yesterday at about 15:00. Everything went according the plan........kind of. There were metal chips in the transmission of the UH-60 so the test was pushed back by a few hours while the mechanics removed the chips and found and fixed the source of the chips. But after that everything went according to plan, until they turned the tunnel on........ then they found that the hydraulic system for some of the actuators (the things that move the entire helicopter up and down during a test) was leaking, so they had to perform an emergency shutdown. Despite the name everyone remained eerily calm during the entire emergency....... Maybe everyone who works at NASA is a robot and can't feel terror? But that's just idle speculation that would probably appear on a conspiracy theory forum. During some of the high thrust conditions some of the channels approached their safety limits so I got to talk over the intercom system, that was fun, well more fun than just sitting there for two hours. I don't think I've posted any pictures of the test stand on the blog so here are some I took a while ago.
So this is the actual wind tunnel with the LRTA (Large Rotor Test Apparatus) in it, this picture was from when they were calibrating one of the laser systems that measures the blade displacment.
This is the control room that sits under the wind tunnel. My station is at the left most moniters (the bottom one is cut off). I'll be spending a lot of time in this room as the test continues in the coming weeks.
-David Stevens
So this is the actual wind tunnel with the LRTA (Large Rotor Test Apparatus) in it, this picture was from when they were calibrating one of the laser systems that measures the blade displacment.
This is the control room that sits under the wind tunnel. My station is at the left most moniters (the bottom one is cut off). I'll be spending a lot of time in this room as the test continues in the coming weeks.-David Stevens
Trial and Error
The gel I ran on Tuesday barely had any DNA in it, sadly. I was prepared for this minor setback (certainly not the first one.) I decided to start from ground zero and take yet another set of DNA directly from my plants. After extracting the DNA, I prepared a PCR reaction and let it run overnight. I had started with new DNA, recalculated the annealing temperature, and double-checked all my work. On top of that, we had a specialist come in and recalibrate our pipettes. What could possibly go wrong?
This morning, I was informed that someone had accidentally unplugged all of the PCR machines, interrupting my reactions. The responsible party had attempted to set the reaction to a point where the remaining steps would be completed, but I was warned not to get my hopes up.
Beautiful. Just beautiful.
Right now, a gel containing the sad remains of my PCR is running. I expect that there will be little or no DNA in my samples and I will have to run another PCR today.
On the upside, I believe that I have discovered the origin of my plants' dwarfism. They have refused to grow any taller despite frequent application of Brassinosteroids, strongly supporting my hypothesis that these mutants possess dysfunctional Brassinosteroid receptor proteins.
This morning, I was informed that someone had accidentally unplugged all of the PCR machines, interrupting my reactions. The responsible party had attempted to set the reaction to a point where the remaining steps would be completed, but I was warned not to get my hopes up.
Beautiful. Just beautiful.
Right now, a gel containing the sad remains of my PCR is running. I expect that there will be little or no DNA in my samples and I will have to run another PCR today.
On the upside, I believe that I have discovered the origin of my plants' dwarfism. They have refused to grow any taller despite frequent application of Brassinosteroids, strongly supporting my hypothesis that these mutants possess dysfunctional Brassinosteroid receptor proteins.
Thursday, April 1, 2010
The Attractin Gene
This week was very successful and productive. I completed the steps necessary to sequence intron four in all specimen from the panel that I am utilizing. I then returned to intron 17, preparing the remaining samples from the backcross (a cross of individuals with individuals genetically identical to the parents) for sequencing in order to further determine the relation between variation in intron 17 of the attractin gene and variation in coat color. The data I have collected for the back cross so far reveals a direct relation between coat color variation and variation in this intron, as is found in the agouti gene. However, if one sample shows imperfect association between variation in the attractin gene and variation in coat color, than the agouti gene has a stronger association and linkage disequilibrium (the non-random association of a version of alleles [versions of a gene] at two or more loci) has begun to break down. After submitting forty-one samples for sequencing, I will have a large volume of sequences to clean and analyze in the coming weeks.
At the laboratory meeting this week, a graduate student discussed his research involving the genetic basis of the coat color of three species of bats. Based on his calculations comparing the Mc1r gene (a gene highly involved in the coat color pathway) in chimpanzees and humans, there is an expected divergence of 10% within this single exon (coding region) gene in bats; however, his sequences reveal no difference in the gene among these species. Thus, the lab meeting consisted of working backwards through his experimental process in search of the cause of this result. The first consideration was that the results may be accurate; however, this is unlikely, as, based on probability calculations, there are sixteen expected differences among the Mc1r genes in these bat species. The conversion then turned to a search for sources of error, which are very useful for all researchers in the laboratory to consider, as research consists of a majority of problem solving prior to receiving actual data. Suspected sources of error included contaminated DNA samples, contaminated PCR reactions, accidental extraction of the same DNA three consecutive times, mislabeled DNA extractions, mislabeled tissue from the museum that delivered the bat tissue or mislabeled specimen at the museum, or a mistake during the sequencing process at the sequencing center. In a search for valid results, the graduate student will continue his experiment by first repeating the PCR reaction and attempting to use new primers if the mitochondrial DNA sent for sequencing does show differences in the nucleotide base pairs. If the mitochondrial DNA sequences among the bat species are identical, he will extract new samples of DNA from new museum specimen in order to create accurate primers for continued work on non-contaminated samples. The graduate student then concluded his allotted presentation time by discussing his rotation in a laboratory studying the genetic makeup of a toxic algae and the extent of expression of the toxin in various environments. Each laboratory meeting has concluded with an important moral to remember when performing research: for each step of progress in one’s research, there is always some setback; however, collaboration with one’s colleagues will lead to progress in one’s research.
At the laboratory meeting this week, a graduate student discussed his research involving the genetic basis of the coat color of three species of bats. Based on his calculations comparing the Mc1r gene (a gene highly involved in the coat color pathway) in chimpanzees and humans, there is an expected divergence of 10% within this single exon (coding region) gene in bats; however, his sequences reveal no difference in the gene among these species. Thus, the lab meeting consisted of working backwards through his experimental process in search of the cause of this result. The first consideration was that the results may be accurate; however, this is unlikely, as, based on probability calculations, there are sixteen expected differences among the Mc1r genes in these bat species. The conversion then turned to a search for sources of error, which are very useful for all researchers in the laboratory to consider, as research consists of a majority of problem solving prior to receiving actual data. Suspected sources of error included contaminated DNA samples, contaminated PCR reactions, accidental extraction of the same DNA three consecutive times, mislabeled DNA extractions, mislabeled tissue from the museum that delivered the bat tissue or mislabeled specimen at the museum, or a mistake during the sequencing process at the sequencing center. In a search for valid results, the graduate student will continue his experiment by first repeating the PCR reaction and attempting to use new primers if the mitochondrial DNA sent for sequencing does show differences in the nucleotide base pairs. If the mitochondrial DNA sequences among the bat species are identical, he will extract new samples of DNA from new museum specimen in order to create accurate primers for continued work on non-contaminated samples. The graduate student then concluded his allotted presentation time by discussing his rotation in a laboratory studying the genetic makeup of a toxic algae and the extent of expression of the toxin in various environments. Each laboratory meeting has concluded with an important moral to remember when performing research: for each step of progress in one’s research, there is always some setback; however, collaboration with one’s colleagues will lead to progress in one’s research.
May develop spurious wiggles...
I think that I've decided how legitimate programming should be defined. If you are coding in some language and what you have coded works on the first try, say, 90% of the time, you are either an expert programmer (definitely not me), or whatever language you are using doesn't count as a legitimate programming language. On the other hand, if nothing works on the first try, it definitely is legitimate.
That said, Mathematica coding actually can be legitimately called programming since this week was mostly spent fighting with the computer (I'm currently winning). The reason for this is that I had to use an "if" statement as well as several "while" loops. I tried to avoid the use of such low level constructions (I am so glad that I'm not doing assembly...), but alas Mathematica does not come with every possible function that I desire.
With that in mind, I simulated various types of forces (constant, inverse square, linear, imaginary, etc.) between two particles and plotted out various quantities associated with their interactions. Also, for fun, I decided to create a graph from which I could view the particles from a rotating frame which was amazingly cool.
Besides, achieving superluminal travel not much else occurred worth mentioning...
That said, Mathematica coding actually can be legitimately called programming since this week was mostly spent fighting with the computer (I'm currently winning). The reason for this is that I had to use an "if" statement as well as several "while" loops. I tried to avoid the use of such low level constructions (I am so glad that I'm not doing assembly...), but alas Mathematica does not come with every possible function that I desire.
With that in mind, I simulated various types of forces (constant, inverse square, linear, imaginary, etc.) between two particles and plotted out various quantities associated with their interactions. Also, for fun, I decided to create a graph from which I could view the particles from a rotating frame which was amazingly cool.
Besides, achieving superluminal travel not much else occurred worth mentioning...
Some Things Every Self-Respecting Citizen of the World Should Know
This list is the culmination of a week's worth of research.
1. Alpaca's spit when they feel threatened. However, they actually expel little saliva. Instead, they spit up the contents of their stomach which is usually an acidic grass mixture.
2. African dance is often polyrhythmic. Dancers must move different parts of their body to different rhythms.
3. The Skookum Cast (named after the Skookum people of the Pacific Northwest) is one of the most important pieces of evidence supporting the existence of Bigfoot. On September 22, 2000, several members of the Bigfoot Field Researchers Organization created a fruit-baited mud trap. A few hours later, they found an imprint of an unrecognizable animal's haunches. Since the print matched no living animal and resembled a big ape, it was hypothesized to have been left by Bigfoot.
4. According to Carl Jung, life is divided into two phases. The first half of life is characterized by a fascination with sexuality and materialism and destruction meant to bring about self realization. The second half of life is all about community and spirituality and returning to the collective unconscious of humanity.
5. The Student of Prague, The Golem, Destiny, Nosferatu, Phantom, and The Last Laugh are all examples of German Expressionist films.
6. India Pale Ale was the first ever beer designed for export. Officers of the British East India Company frequently brought it to India. The beer lasted a long time due to its high alcohol content and large concentration of hops.
7. Dung beetles don't actually eat the dung they nest in. Instead they suck nutrient rich juice from the dung and feast on that.
8. Bardo is the Tibetan word for the period between death and reincarnation.
9. When discussing time travel philosophically, there are two main differing beliefs. Eternalism treats time as a dimension; everything that has ever happened and will ever happen already exists somewhere. Therefore, time travel is a very possible phenomenon. Presentisim states that neither future nor past events exist and, as such, time travel can’t exist. I myself am definitely a Presentist.
10. T.W. Adorno's has two main questions about aesthetics and modern art.
In other news, it appears that I will not be going to Columbia or Yale. I have my fingers crossed for Bard.
Subscribe to:
Posts (Atom)