12/12/11
Today I was not only given another chance to 'perfect' ('form' may be a better word) my pipet skills, but also to do some aliquoting. An aliquot is basically a fraction of a whole, which in the research lab means taking a test tube of DNA and then sucking up a small amounts and plopping it in another test tube to give to another scientist for their research. I am embarrassed to admit that this seemingly simple act took up the full time of my internship. The task seemed simple: transfer 30 microliters of 30 different samples of spruce grouse DNA into 30 little plastic test tubes. Obviously, I still need to work on pipeting efficiently, but more importantly, I need a little practice writing in size 3 font legibly. My handwriting may be small, but small AND neat is a different story :). However, it was nice to get some more pipet practice in, and, from a big picture point of view, the whole process of extracting DNA is basically just moving liquids which I will hopefully be a master at by the end of the year. While before I determined being a pipet 'master' to simply understanding how to use a pipet, that definition has evolved to not only being able to use a pipet, but do so perhaps a little faster than a snail's pace. Besides my aliquoting experience, there is also some exciting news. Dr. Kirchman was able to run the filtered DNA through the gel I made last week, and while there were not the nice blocks of DNA that are found in good samples of DNA, there were stripy bands of DNA running through the gel. Dr. Kirchman cut these stripy bands out of the gel and ran the DNA contained in those bands again and to our delight, there were nice blocks of DNA in a couple of the test tubes. This means that we can continue the rail project in full force once the Winter Break is over.
Monday, December 12, 2011
Monday, December 5, 2011
oops. Day 3 and Day 4
11/28/11
Well I just noticed that I didn't make a post for my trip to the NYSM over break. On Monday over break, I headed up to the NYSM and Dr. Kirchman and I quickly got to work. We went to the ancient DNA lab where we got some Taq gold. Taq gold is a high quality solution used in PCR. Now, what is PCR? Well, since the pieces of rail tissue we used were so small, there was not a lot of DNA in them. What PCR does is it splits the chain of DNA in half using heat(I think I am going to try to draw a picture on paint and post it). DNA is made up of G's, C's, T's, and A's. The PCR adds ends to the DNA, and then since we know that G goes with C and T goes with A, during the PCR, G's C's T's and A's are taken from a 'soup' mixture of monomers and matched accordingly with each half strand of the DNA, forming two separate, yet identical strands of DNA. The DNA is then cooled again so that the newly added strands can attach to each previous strand. This process the repeats as the DNA is heated again, and the amount of DNA doubles each time. We completed the long PCR with our rail DNA and then made a gel so that we would be able to see the DNA. The gel is basically what it sounds like. After mixing a few chemicals whose names escape me and adding a mutagen (I believe it is ethidium bromide) which allows the DNA to be seen under an ultraviolet light. After making the gel and allowing it to harder, we put the results of the PCR in the wells in the gel along with some dye. We then ran electricity through the gel. Since DNA has a slight negative charge, it moves from the negative side of the gel toward the positive. The gel works as a sieve, however, allowing smaller sized particles to move through the gel more easily than the larger. However, when we viewed our rail DNA through the camera on top of an enclosed box that shone ultraviolet on our gel, we didn't see any DNA. It appeared that our rail DNA extraction had been a failure.
12/5/11
The next week, Dr. Kirchman had some exciting news. He had tried the PCR on the thrush DNA we had extracted our first week and had found that after running the PCR on the thrush DNA, the DNA was not visible under the ultra-violet light. He had also noticed some 'snowflakey' stuff in the tubes containing the DNA. This means that the PCR had done something to the extracted DNA or reacted strangely to something in our quick start DNA kit we used to extract the DNA from both the thrushes and the rails. Dr. Kirchman ran the rail DNA through a filter, but the 'snowflakey' stuff remained in the tube. However, the 'snowflakey' stuff may not even be the cause of our problems and some other chemical causing the problems may have been successfully filtered, leaving DNA that would be visible under our ultraviolet light. We spent today doing PCR with the filtered rail DNA along with other bird DNA simply to test how the PCR affect other bird DNA samples. I even got the chance to make a gel (almost) all by myself :). While hopefully the filter solved our DNA difficulties, I will not know until next week to see if the new PCR results were successful!
Well I just noticed that I didn't make a post for my trip to the NYSM over break. On Monday over break, I headed up to the NYSM and Dr. Kirchman and I quickly got to work. We went to the ancient DNA lab where we got some Taq gold. Taq gold is a high quality solution used in PCR. Now, what is PCR? Well, since the pieces of rail tissue we used were so small, there was not a lot of DNA in them. What PCR does is it splits the chain of DNA in half using heat(I think I am going to try to draw a picture on paint and post it). DNA is made up of G's, C's, T's, and A's. The PCR adds ends to the DNA, and then since we know that G goes with C and T goes with A, during the PCR, G's C's T's and A's are taken from a 'soup' mixture of monomers and matched accordingly with each half strand of the DNA, forming two separate, yet identical strands of DNA. The DNA is then cooled again so that the newly added strands can attach to each previous strand. This process the repeats as the DNA is heated again, and the amount of DNA doubles each time. We completed the long PCR with our rail DNA and then made a gel so that we would be able to see the DNA. The gel is basically what it sounds like. After mixing a few chemicals whose names escape me and adding a mutagen (I believe it is ethidium bromide) which allows the DNA to be seen under an ultraviolet light. After making the gel and allowing it to harder, we put the results of the PCR in the wells in the gel along with some dye. We then ran electricity through the gel. Since DNA has a slight negative charge, it moves from the negative side of the gel toward the positive. The gel works as a sieve, however, allowing smaller sized particles to move through the gel more easily than the larger. However, when we viewed our rail DNA through the camera on top of an enclosed box that shone ultraviolet on our gel, we didn't see any DNA. It appeared that our rail DNA extraction had been a failure.
12/5/11
The next week, Dr. Kirchman had some exciting news. He had tried the PCR on the thrush DNA we had extracted our first week and had found that after running the PCR on the thrush DNA, the DNA was not visible under the ultra-violet light. He had also noticed some 'snowflakey' stuff in the tubes containing the DNA. This means that the PCR had done something to the extracted DNA or reacted strangely to something in our quick start DNA kit we used to extract the DNA from both the thrushes and the rails. Dr. Kirchman ran the rail DNA through a filter, but the 'snowflakey' stuff remained in the tube. However, the 'snowflakey' stuff may not even be the cause of our problems and some other chemical causing the problems may have been successfully filtered, leaving DNA that would be visible under our ultraviolet light. We spent today doing PCR with the filtered rail DNA along with other bird DNA simply to test how the PCR affect other bird DNA samples. I even got the chance to make a gel (almost) all by myself :). While hopefully the filter solved our DNA difficulties, I will not know until next week to see if the new PCR results were successful!
Thursday, December 1, 2011
my improving pipet skills :)
Solutions used in the process of extracting DNA are added in very small amounts. Pipets are used to carefully take very small amounts of liquid and put it into very small test tubes. They also have disposable caps so that you can use the same pipet with a different plastic attachment each time so that the DNA in one test tube will not contaminate the DNA in another.
Monday, November 14, 2011
Second Day :D
11/14/11
Today was another information packed day at NYSM. Of course, the day could not be started without problems, including stand-still traffic on 787. However, I made it to NYSM relatively on time (scaling the escalators at an astonishing speed, and even having to make a quick retreat off a rapidly ascending escalator after going up one floor to many), and quickly got to work. With my new-found pipet-wielding skills, I was able to help Dr. Kirchman to begin extracting the DNA from rail birds from the Solomon Islands. I was a little nervous about working with the rail bird tissue, because unlike the ample amount of thrush tissue on hand at NYSM, the Solomon Islands were pretty far away and so was more rail tissue. Before the actual lab work began, Dr. Kirchman was able to show me a picture of the DNA we had extracted from the thrush birds the previous week. Using a type of gel whose most likely long and complicated name escapes me, the DNA was able to glow when exposed to ultraviolet light. The picture Dr. Kirchman had taken showed a brightly glowing strip at the top of the test tube. This was good, because not only did it prove that the test had worked, but also that we were able to extract DNA from the very small tissue samples of the thrush birds, similar in size to the tissue samples of the rail birds we would be using. The DNA was located near the top of the test tube, because over time, the long strands of DNA get chopped into smaller and smaller strands. These smaller strands are able to quickly move through the liquid with the DNA in the test tube and sink to the bottom, so thick glowing blocks at the top of test tubes are indicative to high quality DNA. Since the tissue samples from the thrush birds had been collected fairly recently, the DNA strands were still long and had not sunk to the bottom of the test tube. After examining the picture, it was off to work, and I was able to get some more time with my favorite pipets. However, there were a few technical difficulties as the machine I solely know as the 'milkshake machine' (thank you Dr. Kirchman for giving me names I can remember :D) which breaks open the cells inside the tissue and basically just shakes the test tube all over the place so as to expose the DNA, had not been fastened down tight enough and one of our test tubes cracked. We tried to salvage most of the DNA mixture out by transferring the liquid to another test tube with a pipet, but we will not know how successful we were until we use the gel to see if we saved a large enough portion of DNA from the cracked tube. On the bright side, my DNA extraction expertise has reached a new level (if you can consider two days of experience a new level) and I am excited to see how the results of our lab work turned out the next time I see Dr. Kirchman.
Today was another information packed day at NYSM. Of course, the day could not be started without problems, including stand-still traffic on 787. However, I made it to NYSM relatively on time (scaling the escalators at an astonishing speed, and even having to make a quick retreat off a rapidly ascending escalator after going up one floor to many), and quickly got to work. With my new-found pipet-wielding skills, I was able to help Dr. Kirchman to begin extracting the DNA from rail birds from the Solomon Islands. I was a little nervous about working with the rail bird tissue, because unlike the ample amount of thrush tissue on hand at NYSM, the Solomon Islands were pretty far away and so was more rail tissue. Before the actual lab work began, Dr. Kirchman was able to show me a picture of the DNA we had extracted from the thrush birds the previous week. Using a type of gel whose most likely long and complicated name escapes me, the DNA was able to glow when exposed to ultraviolet light. The picture Dr. Kirchman had taken showed a brightly glowing strip at the top of the test tube. This was good, because not only did it prove that the test had worked, but also that we were able to extract DNA from the very small tissue samples of the thrush birds, similar in size to the tissue samples of the rail birds we would be using. The DNA was located near the top of the test tube, because over time, the long strands of DNA get chopped into smaller and smaller strands. These smaller strands are able to quickly move through the liquid with the DNA in the test tube and sink to the bottom, so thick glowing blocks at the top of test tubes are indicative to high quality DNA. Since the tissue samples from the thrush birds had been collected fairly recently, the DNA strands were still long and had not sunk to the bottom of the test tube. After examining the picture, it was off to work, and I was able to get some more time with my favorite pipets. However, there were a few technical difficulties as the machine I solely know as the 'milkshake machine' (thank you Dr. Kirchman for giving me names I can remember :D) which breaks open the cells inside the tissue and basically just shakes the test tube all over the place so as to expose the DNA, had not been fastened down tight enough and one of our test tubes cracked. We tried to salvage most of the DNA mixture out by transferring the liquid to another test tube with a pipet, but we will not know how successful we were until we use the gel to see if we saved a large enough portion of DNA from the cracked tube. On the bright side, my DNA extraction expertise has reached a new level (if you can consider two days of experience a new level) and I am excited to see how the results of our lab work turned out the next time I see Dr. Kirchman.
Monday, November 7, 2011
First Day!!!
11/7/11
Today was my first day working with Dr. Jeremy Kirchman at the New York State Museum. The day was filled with new experiences, between my first ride on a shuttle (which presented some initial difficulty and worry at first between being afraid of missing the shuttle, not knowing what it would look like etc. but it was luckily a problem easily overcome), my first time on the third floor of the museum (an area of the museum off-limits to your run-of-the-mill visitor), and yes, surprisingly my first time attempting to extract DNA from bird tissue and blood samples. Dr. Kirchman told me that our project for the year would concern a type of birds called rails. Though some species of rail can fly a little, many of the birds located upon islands off the coast of Australia in the Pacific Ocean are flightless. This is mainly because these island-dwellers have the ability to be ground nesting birds since they have no predators on these islands along with rails having very thick strong legs built for carrying them along the floors of their biomes in search of food. Dr. Kirchman had spent a considerable period of time developing a phylogenetic tree, tracing back the common ancestors of the rail birds. However, he discovered that while many of the rails of the same genus were located right next to one another on the phylogenetic tree, a genus of birds located in the Solomon Islands were not grouped closely together. Our project for the year is to retest DNA samples of these rail birds and determine if this puzzling piece of information is simply the result of an error, or the some other abnormality that occurred in these creatures' history such as inbreeding. However, since this is my first time working with DNA in a lab, Dr. Kirchman and I worked on extracting DNA from the tissue and blood of thrushes today. While the time flew by pretty quickly, I was still able to get a general idea of the process of extracting the DNA from cells along with getting a chance at using a pipet. I am nowhere close to becoming a pipet expert, but luckily I was able to yield my pipet without completely destroying our samples or simply wreaking havoc. Next week, we are planning on continuing our exploration of DNA and hopefully the time will not go by as quickly.
Today was my first day working with Dr. Jeremy Kirchman at the New York State Museum. The day was filled with new experiences, between my first ride on a shuttle (which presented some initial difficulty and worry at first between being afraid of missing the shuttle, not knowing what it would look like etc. but it was luckily a problem easily overcome), my first time on the third floor of the museum (an area of the museum off-limits to your run-of-the-mill visitor), and yes, surprisingly my first time attempting to extract DNA from bird tissue and blood samples. Dr. Kirchman told me that our project for the year would concern a type of birds called rails. Though some species of rail can fly a little, many of the birds located upon islands off the coast of Australia in the Pacific Ocean are flightless. This is mainly because these island-dwellers have the ability to be ground nesting birds since they have no predators on these islands along with rails having very thick strong legs built for carrying them along the floors of their biomes in search of food. Dr. Kirchman had spent a considerable period of time developing a phylogenetic tree, tracing back the common ancestors of the rail birds. However, he discovered that while many of the rails of the same genus were located right next to one another on the phylogenetic tree, a genus of birds located in the Solomon Islands were not grouped closely together. Our project for the year is to retest DNA samples of these rail birds and determine if this puzzling piece of information is simply the result of an error, or the some other abnormality that occurred in these creatures' history such as inbreeding. However, since this is my first time working with DNA in a lab, Dr. Kirchman and I worked on extracting DNA from the tissue and blood of thrushes today. While the time flew by pretty quickly, I was still able to get a general idea of the process of extracting the DNA from cells along with getting a chance at using a pipet. I am nowhere close to becoming a pipet expert, but luckily I was able to yield my pipet without completely destroying our samples or simply wreaking havoc. Next week, we are planning on continuing our exploration of DNA and hopefully the time will not go by as quickly.
Wednesday, October 12, 2011
Internship Goals
My goals for the internship this year!
1. I would really like this internship to give me a better idea of what a career in science truly entails. I am still undecided on what I would like to pursue as a major in college, and I hope this internship will give an experience bringing me closer to this important decision.
2. I really just want to have fun. I love science class and would really like to have this opportunity to interact with real scientists and have fun exploring the subject I like so much.
Characteristics a good intern should have!
I'm not going to lie; I am very nervous for this internship. I can picture already the task I am assigned being too difficult, the topic way over my head, or me simply being confused. However, a good intern should be a good listener, try their best, and not be afraid to ask questions, and I believe if I simply listen to my instructor, I shouldn't have too much difficulty. As long as I try my best, I will feel accomplished and achieve at least a basic understanding of the concept. If I am not afraid to ask questions, I will be able to comprehend the task I am assigned and be able to get straight to work!
... no matter how many times I tell myself this, I am still nervous, but still excited for an exciting experience ahead of me :D
1. I would really like this internship to give me a better idea of what a career in science truly entails. I am still undecided on what I would like to pursue as a major in college, and I hope this internship will give an experience bringing me closer to this important decision.
2. I really just want to have fun. I love science class and would really like to have this opportunity to interact with real scientists and have fun exploring the subject I like so much.
Characteristics a good intern should have!
I'm not going to lie; I am very nervous for this internship. I can picture already the task I am assigned being too difficult, the topic way over my head, or me simply being confused. However, a good intern should be a good listener, try their best, and not be afraid to ask questions, and I believe if I simply listen to my instructor, I shouldn't have too much difficulty. As long as I try my best, I will feel accomplished and achieve at least a basic understanding of the concept. If I am not afraid to ask questions, I will be able to comprehend the task I am assigned and be able to get straight to work!
... no matter how many times I tell myself this, I am still nervous, but still excited for an exciting experience ahead of me :D
Subscribe to:
Posts (Atom)