5/7/12
Today was sadly my last day at my internship with Dr. Kirchman and I had a fun time realizing how my skills have developed over this past year. First, Dr. Kirchman I quickly set up a PCR and poured a gel to run another test on the mysterious rail DNA. I made a master mix for the PCR and then put the DNA in the machine so it would begin to make copies of the DNA. Since a PCR takes about 2 hours before it is completed Dr. Kirchman and I headed over to the prep lab. I got to work labeling bones and rather than labeling tiny skeletons, I had to label the gigantic bird we had cleaned last week. After spending a good amount of time on the large bird, I realize I preferred putting minuscule numbers on tiny bones rather than the never-ending task of labeling every single toe bone on a larger skeleton.
After finishing the big bird, my time was almost up, but Dr. Kirchman had a surprise. Dr. Kirchman had written another article for the Auk and this one was about Carolina parakeets. These parakeets used to be found all over most of the east coast of the United States but went extinct in the early 1900s. Dr. Kirchman had me try to guess why they had gone extinct and I actually got part of it right! I asked Dr. Kirchman what their diet was and it turns out that they used to eat fruit. Farmers had been shooting the birds because they could strip a tree of its fruit and eat the farmers' crops. Today a reporter from a local newspaper was coming to ask Dr. Kirchman about the birds and his paper. I got to sit in on part of the interview and eat some cinnamon rolls Dr. Kirchman's wife had made for us. Sadly, my time ran out before the interview was finished, but I had a great last day in the lab and an overall amazing time this year at my internship.
Monday, May 14, 2012
Friday, April 27, 2012
Big birds and bitty bones
4/23/12
The bone I am holding which is the skull was one of the largest bones I had to write on. I think I wrote some of the tiniest numbers I ever had in my life, and luckily I wrote those numbers successfully. Dr. Kirchman even jokingly suggested that if I ever dropped out of school, I could get a job labeling bones :). I truly did not know that my handwriting could successfully be that small. After labeling all three skeletons, the big bird was finally all rinsed off. Dr. Kirchman and I cleaned up the skeleton which was much harder to clean that the smaller bird skeletons. We even needed scissors to cut the tendons and even then it was difficult. Dr. Kirchman and I removed as much of the tissue and tendons as we could and then put it back in the jar and added some fresh ammonia solution so that it could soak for a little longer. All over all, it was a pretty fun day in the lab.
Today Dr. Kirchman and I had another fun day in the lab. We decided that a few more bird skeletons were ready to emerge from the ammonia solution and be boxed and labeled. However, this time, I would have to do a little bit more of the work by myself. While one jar containing a bird skeleton was rinsing in the sink to wash out all of the stinky ammonia solution, Dr. Kirchman had me label some boxes and place bird skeletons we had done the previous week inside of them. While I was very nervous about the quality of my handwriting (which ironically gets much worse whenever I'm worried it is going to look messy) I successfully completed two boxes. Then we picked through the bird in the sink, making sure none of the bones were missing. Then we had to remove any remaining tissue or tendons from the bird. This, luckily, was not too difficult with the two smaller birds we did. However, after cleaning up those two birds and leaving them to dry on the blotting paper, Dr. Kirchman and I were only left with two humongous birds. I reluctantly dragged a giant bird skeleton into the sink, uncertain about the arduous task ahead and began to rinse it out. While the big bird :) was rinsing
Dr. Kirchman asked me to label the bones of the three smaller birds we had just put in the boxes. Each bird has an identification number and that identification number needs to be labeled on as many bones as possible so that in case the bones were dropped, one would still be able to identify which bones went with which bird. The problem: all three of the birds I worked on were minuscule.
The bone I am holding which is the skull was one of the largest bones I had to write on. I think I wrote some of the tiniest numbers I ever had in my life, and luckily I wrote those numbers successfully. Dr. Kirchman even jokingly suggested that if I ever dropped out of school, I could get a job labeling bones :). I truly did not know that my handwriting could successfully be that small. After labeling all three skeletons, the big bird was finally all rinsed off. Dr. Kirchman and I cleaned up the skeleton which was much harder to clean that the smaller bird skeletons. We even needed scissors to cut the tendons and even then it was difficult. Dr. Kirchman and I removed as much of the tissue and tendons as we could and then put it back in the jar and added some fresh ammonia solution so that it could soak for a little longer. All over all, it was a pretty fun day in the lab.Thursday, April 19, 2012
Perfecting PCRs
4/16/12
Today Dr. Kirchman and I got to do some lab work (luckily, I had even remembered to bring along a pair of closed-toe shoes to replace my flip-flops). Dr. Kirchman is also working on a project with spruce grouse so today I helped him run a gel. A previous PCR on the gel hadn't turned out so well so Dr. Kirchman decided to try and run a longer strand of the mitochondrial gene of the spruce grouse. To do this, we first needed to collect a bunch of primers so that they would be able to sequence the strip all the way from one section to the next. After going on a primer search through the freezers in the lab, we finally had enough and I started to make a gel. There were a lot of leftover gels from previous uses so I carefully (no explosions this time) melted down the gels in the microwave and then added the mutagen. Since we had 16 different DNA samples, I used two different combs for the same gel so that we would have enough slots to run all 16 samples at once. After the gel turned opaque and congealed, I was able to mix the ultraviolet sensitive dye with all 16 samples and squirt them into the gel with no mistakes and no desperate cry for assistance. I believe I am now worthy of the title of pipet master-in-training. When Dr. Kirchman and I went to run the gel however, there were some difficulties. The machine did not seem to want to send any electricity through the gel! However, after some fiddling around, we finally added more buffer which did the trick and the machine began to conduct electricity through the gel.
Since it takes 40 minutes for a gel to be successfully run, Dr. Kirchman and I went to the prep lab and after giving Joe a quick hello, I started cleaning my skeletons and putting them into boxes. Fist we put the skeletons on a metal container with holes in the bottom that let the ammonia fall through, but keep the bones from going down the drain of the sink. Next we put the bones on blotting paper and let them dry, sorting through the bones and extracting any remaining tissue or tendons from the skeleton. Once the skeleton was dry, it was put in a box corresponding with its size and then properly labeled with its scientific name, where it was found, when it was found, and other important details of the like.
When Dr. Kirchman and I went back to the lab to check on our PCR, it worked very well to our surprise. Every single one of our DNA samples was showing up and all of our negative controls were not showing anything. After marveling at our perfect PCR for a couple seconds, my time was up and Dr. Kirchman and I had to clean up. All over all it was a pretty good day in the lab with a minimum of technical difficulties and an abundance of success.
Today Dr. Kirchman and I got to do some lab work (luckily, I had even remembered to bring along a pair of closed-toe shoes to replace my flip-flops). Dr. Kirchman is also working on a project with spruce grouse so today I helped him run a gel. A previous PCR on the gel hadn't turned out so well so Dr. Kirchman decided to try and run a longer strand of the mitochondrial gene of the spruce grouse. To do this, we first needed to collect a bunch of primers so that they would be able to sequence the strip all the way from one section to the next. After going on a primer search through the freezers in the lab, we finally had enough and I started to make a gel. There were a lot of leftover gels from previous uses so I carefully (no explosions this time) melted down the gels in the microwave and then added the mutagen. Since we had 16 different DNA samples, I used two different combs for the same gel so that we would have enough slots to run all 16 samples at once. After the gel turned opaque and congealed, I was able to mix the ultraviolet sensitive dye with all 16 samples and squirt them into the gel with no mistakes and no desperate cry for assistance. I believe I am now worthy of the title of pipet master-in-training. When Dr. Kirchman and I went to run the gel however, there were some difficulties. The machine did not seem to want to send any electricity through the gel! However, after some fiddling around, we finally added more buffer which did the trick and the machine began to conduct electricity through the gel.
Since it takes 40 minutes for a gel to be successfully run, Dr. Kirchman and I went to the prep lab and after giving Joe a quick hello, I started cleaning my skeletons and putting them into boxes. Fist we put the skeletons on a metal container with holes in the bottom that let the ammonia fall through, but keep the bones from going down the drain of the sink. Next we put the bones on blotting paper and let them dry, sorting through the bones and extracting any remaining tissue or tendons from the skeleton. Once the skeleton was dry, it was put in a box corresponding with its size and then properly labeled with its scientific name, where it was found, when it was found, and other important details of the like.
 |
| Hello Joe! |
When Dr. Kirchman and I went back to the lab to check on our PCR, it worked very well to our surprise. Every single one of our DNA samples was showing up and all of our negative controls were not showing anything. After marveling at our perfect PCR for a couple seconds, my time was up and Dr. Kirchman and I had to clean up. All over all it was a pretty good day in the lab with a minimum of technical difficulties and an abundance of success.
Tuesday, April 10, 2012
Charming Charts
4/2/12
Today Dr. Kirchman and I spent another day working on graphs for the rail project. These were no mere data tables however, but complicated logarithm and other confusing number graphs. First, I'll show you the graphs just to give you an idea of what they look like:
Today Dr. Kirchman and I spent another day working on graphs for the rail project. These were no mere data tables however, but complicated logarithm and other confusing number graphs. First, I'll show you the graphs just to give you an idea of what they look like:
Unlike the data table I made last week, these graphs add a helpful visual component to seeing trends. Before I went to NYSM, Dr. Kirchman had already arranged the data I had put in my data table last week through some complicated mathematical process that was beyond me that basically summed up all the data and measurements we had for an individual bird into one number so that the data would be in the correct form to use a program. Then, we would try and use different measurements to show a trend in the graph. For example, in PC1 vs PC2 (physical characteristic one versus physical characteristic two), Dr. Kirchman and I successfully depicted a trend in flight that is easy on the eyes. As I talked about last week, one can often conclude that a bird is flightless if it has very long leg bones and a small sternum and arm bones. Therefore, for the first graph, the x axis (PC1) deals with the length of leg bones along with other measurements and the y axis (PC2) dealt with measurements of bones dealing with flight such as the sternum, radius etc. Therefore, G. philippensis can most likely fly (which Dr. Kirchman confirmed) and G. australis is most likely flightless (which Dr. Kirchman also confirmed, therefore our graphs were accurate and good to go). The second graph PC2 vs PC3 was also focused on size and the flying capabilities of birds, but since we could not get a distinct trend (since all of the groups are so close together and overlapping) the graph is rather unclear and we decided to move on. While the graphs may look simple, they actually took up most of my time during my internship, but I am quickly becoming an expert of graphing computer programs.
For the last couple minutes of my Monday morning at NYSM, Dr. Kirchman and I went to see how the skeletons we had placed in the diluted ammonia solution last week were coming along. Since the skeletons looked pretty clean, Dr. Kirchman began to show me how to pick the skeleton clean, removing any lingering traces of tissue or ligaments along with the talon sheaths that covered the bird's toes. Before I could have a chance to try it out, though, we ran out of time :(. Hopefully we will continue the rail project next week and I will be able to finish my skeletons.
Thursday, March 29, 2012
Ammonia Aromas
3/26/12
Whoops! I thought I had already posted about this so I'm sorry it's late D: This week Dr. Kirchman and I took a hiatus from computer work and did some work in the prep-lab. The prep-lab is where specimens are stuffed and bones are cleaned until they have been perfectly preserved. To get our specimens of choice (bird skeletons) Dr. Kirchman and I got to use the special elevators that went down to the basement to which your average Joe did not have access. In the big freezer (which was kept at a cool 4 degrees Celsius) I came face to face with a badger and a coyote carcass as Dr. Kirchman and I dragged out a plastic box and removed some bird skeletons. We brought the skeletons back to the prep-lab where we donned some gloves and got to work.
First, Dr. Kirchman explained to me how a bird became a skeleton in the lab. I had assumed that some type of liquid dissolved all the tissue on the bird, but I was pretty far off base. It turns out that a type of beetle picks the bones clean, and NYSM has a "bug box" where they put the specimens they want to turn into skeletons. If the temperature is not too cold, the bugs will hop right to work and can turn a bird into a pile of bones in about three days. What we had to do in the prep-lab was take these bones and remove all the bugs that had remained with the bird. The skeletons were placed in the freezer so that the bugs would freeze. Some of the bones were very small, so we had to sift through the bugs with tweezers and pick out the smaller bones. The toe bones were difficult to spot along with the little rings that were sections of the trachea of the bird. Unlike humans, birds' tracheas sometimes ossify which means that the tissue that makes up the trachea is replaced with bone. All the bird bones we sorted were placed in their own jars, each jar corresponding with the size of the bird. I then filled up the jar 80% of the way with water and the rest of the jar with an ammonia solution. In a couple weeks, the skeletons will be ready to go wherever their travels take them.
I had a lot of fun this week besides the smelliness of the bird skeletons and ammonia and got another lesson on keeping careful records in the lab. Each bird skeleton had a metal tag (so the bugs wouldn't eat it) with an identification number on it. The metal tag was taped to the jar the bird skeleton was placed in and there was a corresponding paper card with all the bird's information on it ready to be attached to the skeleton when it is removed from the jar. I am not quite sure what we are doing next week, but it is possibly more computer work as we dive back into the rail project.
Tuesday, March 20, 2012
Graphing Greatness
3/19/12
Today was more computer work, but not with DNA. Over break, Dr. Kirchman had gone to NYC (I think :D) where the rail bird samples are kept and took some measurements of skeletons. While in the lab, I took all the different measurements for four different species and found the averages of each measurement for males and females separately. Then I made a big table which may seem easy, but it took up the whole time at the internship. The tables included a bird we knew was flightless and a bird we knew could fly along with two other birds. From these measurements, we could make a pretty good guess that one of the other birds was flightless because its measurements were similar to those of the flightless bird. As you can see on the picture on the right, the bird on the left has very large leg bones in comparison to the other bird, but their wing bones are fairly similar in length. This implies that the bird on the left is used to using its legs more than the bird on the right. Another clue that implies the bird on the left does not often fly is that its sternum (the bone that looks like a triangle) is very skinny. The thickness of the sternum was one of the measurement I recorded for our table and it shows how many flight muscles the bird has. The bird on the right is smaller that the bird on the left, and yet its sternum is larger, implying it has more flight muscles than the bigger bird. Therefore, the bird on the left probably roamed the ground rather than the skies.
Today was more computer work, but not with DNA. Over break, Dr. Kirchman had gone to NYC (I think :D) where the rail bird samples are kept and took some measurements of skeletons. While in the lab, I took all the different measurements for four different species and found the averages of each measurement for males and females separately. Then I made a big table which may seem easy, but it took up the whole time at the internship. The tables included a bird we knew was flightless and a bird we knew could fly along with two other birds. From these measurements, we could make a pretty good guess that one of the other birds was flightless because its measurements were similar to those of the flightless bird. As you can see on the picture on the right, the bird on the left has very large leg bones in comparison to the other bird, but their wing bones are fairly similar in length. This implies that the bird on the left is used to using its legs more than the bird on the right. Another clue that implies the bird on the left does not often fly is that its sternum (the bone that looks like a triangle) is very skinny. The thickness of the sternum was one of the measurement I recorded for our table and it shows how many flight muscles the bird has. The bird on the right is smaller that the bird on the left, and yet its sternum is larger, implying it has more flight muscles than the bigger bird. Therefore, the bird on the left probably roamed the ground rather than the skies.
Monday, February 27, 2012
Confusing Computers
2/27/12
Today Dr. Kirchman did not work in the lab, but on his computer. The DNA we had sent off was back and sequenced so we spent the day cleaning up the data. To sequence DNA, a fluorescent dye is given to each nucleotide. A computer measures the wavelength each nucleotide produces, and using these wavelengths, can determine the nucleotide that goes with the corresponding color. Primers run in opposite directions that read the DNA sequence. Two primers are used because it takes a little while for a primer to get going so the wavelengths of the nucleotides are really unclear in the beginning. Therefore, if you have two primers that are unclear in the beginning, but are clear at the end and they run in opposite directions, you will hopefully be able to get a clear idea of what the nucleotides are. However, since our DNA samples of the rail birds were so small, the quality of our DNA wasn't too great, leading to the wavelengths of the nucleotides looking a bit like this:
when in a perfect world, they should look like this:
Basically, what I did today was edit the base pairs. When the computer cannot recognize whether the wavelength is a C or a G, there are other letters (for example R, K, and W) that represent a nucleotide that can be a C or a G or an A or a G. I went through the DNA and tried to make my best guess about what nucleotide matched the wavelength based on the prettier looking primer. Sometimes both wavelengths were messy and had double peaks really close to one another in which case, I would use one of the letters that represented that the exact nucleotide was unclear.
After going through all the base pairs, I then had to cut off the primers at the ends of the section of DNA. I did this by taking the sequenced primers and having the computer match them up at the ends of the sequence. I then simply removed the bases that overlapped with the primer. Lucky for me, the four DNA sequences I did were relatively clean and the section of DNA that Dr. Kirchman and I are using to examine the rail birds is relatively small. I am not going through the entire rail genome (which would take forever to do), but simply a small section of the DNA. Thankfully, I also did an okay job of my DNA cleaning up skills because when Dr. Kirchman and I quickly looked at the sequences, the nucleotides from the rail birds all pretty much matched up. Next week I will not be seeing Dr. Kirchman since it will be spring break, but he hopes to take a closer look at the rail DNA while I am gone and start analyzing it.
Today Dr. Kirchman did not work in the lab, but on his computer. The DNA we had sent off was back and sequenced so we spent the day cleaning up the data. To sequence DNA, a fluorescent dye is given to each nucleotide. A computer measures the wavelength each nucleotide produces, and using these wavelengths, can determine the nucleotide that goes with the corresponding color. Primers run in opposite directions that read the DNA sequence. Two primers are used because it takes a little while for a primer to get going so the wavelengths of the nucleotides are really unclear in the beginning. Therefore, if you have two primers that are unclear in the beginning, but are clear at the end and they run in opposite directions, you will hopefully be able to get a clear idea of what the nucleotides are. However, since our DNA samples of the rail birds were so small, the quality of our DNA wasn't too great, leading to the wavelengths of the nucleotides looking a bit like this:
when in a perfect world, they should look like this:
Basically, what I did today was edit the base pairs. When the computer cannot recognize whether the wavelength is a C or a G, there are other letters (for example R, K, and W) that represent a nucleotide that can be a C or a G or an A or a G. I went through the DNA and tried to make my best guess about what nucleotide matched the wavelength based on the prettier looking primer. Sometimes both wavelengths were messy and had double peaks really close to one another in which case, I would use one of the letters that represented that the exact nucleotide was unclear.
After going through all the base pairs, I then had to cut off the primers at the ends of the section of DNA. I did this by taking the sequenced primers and having the computer match them up at the ends of the sequence. I then simply removed the bases that overlapped with the primer. Lucky for me, the four DNA sequences I did were relatively clean and the section of DNA that Dr. Kirchman and I are using to examine the rail birds is relatively small. I am not going through the entire rail genome (which would take forever to do), but simply a small section of the DNA. Thankfully, I also did an okay job of my DNA cleaning up skills because when Dr. Kirchman and I quickly looked at the sequences, the nucleotides from the rail birds all pretty much matched up. Next week I will not be seeing Dr. Kirchman since it will be spring break, but he hopes to take a closer look at the rail DNA while I am gone and start analyzing it.
Wednesday, February 22, 2012
Tuesday, February 14, 2012
deceased downy ducks
2/13/12
Today, Dr. Kirchman and I spent a fun day in the range (where they keep the stuffed animals and skeletons... and where my emu friend is located) rather than the lab. Dr. Kirchman was going to lecture for a group of ornithology students from Bard College and show them some bird species requested by their professor. Dr. Kirchman took me to the range and showed me where they kept the birds for teaching lessons. Faced with 5 massive metal cabinets, a stepstool, and a piece of paper with about 25 different birds on it, I was off to the races as Dr. Kirchman went to go get passes for when the students came.
All I can say is thank goodness the cabinets were labeled! I slowly made my way down the list, straining to read little tags on the birds' feet and then trying to find the common name to match the one on the sheet rather than the scientific name. Luckily, some common sense came in handy while faced with a giant row of stuffed birds with an overwhelming number of tags in small print. Using my deductive reasoning skills, I was able to determine that when I was looking for a 'purple finch' I should look for a purple bird. I am proud to say that when Dr. Kirchman came back, I had found all the birds on the list but two, one of which was not in the collection, and the other, the ruddy duck, had been mounted on a platform right across from where I was working and had literally been staring me in the face. After moving my emu friend onto a table to create a little more space in the range, Dr. Kirchman showed me a hummingbird skeleton. It was amazing to see how tiny the bones were, and the only larger bones were the skull and the sternum.
While waiting for the students to arrive, Dr. Kirchman gave me two articles to read. I found one really interesting on climate change and how species were forced to adapt much more quickly, but the other article went over my head and before I could finish, the Bard students arrived. I was introduced to the professor, but while we were waiting in the lobby for some lollygagging students, I ran out of time and had to leave before I could hear Dr. Kirchman's lecture.
Next week is Presidents Day, so Dr. Kirchman and I will not meet, but Dr. Kirchman is going to send our rail DNA to be sequenced and I will have some computer work when I next see Dr. Kirchman as we approach our moment of truth in the rail project.
Today, Dr. Kirchman and I spent a fun day in the range (where they keep the stuffed animals and skeletons... and where my emu friend is located) rather than the lab. Dr. Kirchman was going to lecture for a group of ornithology students from Bard College and show them some bird species requested by their professor. Dr. Kirchman took me to the range and showed me where they kept the birds for teaching lessons. Faced with 5 massive metal cabinets, a stepstool, and a piece of paper with about 25 different birds on it, I was off to the races as Dr. Kirchman went to go get passes for when the students came.
All I can say is thank goodness the cabinets were labeled! I slowly made my way down the list, straining to read little tags on the birds' feet and then trying to find the common name to match the one on the sheet rather than the scientific name. Luckily, some common sense came in handy while faced with a giant row of stuffed birds with an overwhelming number of tags in small print. Using my deductive reasoning skills, I was able to determine that when I was looking for a 'purple finch' I should look for a purple bird. I am proud to say that when Dr. Kirchman came back, I had found all the birds on the list but two, one of which was not in the collection, and the other, the ruddy duck, had been mounted on a platform right across from where I was working and had literally been staring me in the face. After moving my emu friend onto a table to create a little more space in the range, Dr. Kirchman showed me a hummingbird skeleton. It was amazing to see how tiny the bones were, and the only larger bones were the skull and the sternum.
While waiting for the students to arrive, Dr. Kirchman gave me two articles to read. I found one really interesting on climate change and how species were forced to adapt much more quickly, but the other article went over my head and before I could finish, the Bard students arrived. I was introduced to the professor, but while we were waiting in the lobby for some lollygagging students, I ran out of time and had to leave before I could hear Dr. Kirchman's lecture.
Next week is Presidents Day, so Dr. Kirchman and I will not meet, but Dr. Kirchman is going to send our rail DNA to be sequenced and I will have some computer work when I next see Dr. Kirchman as we approach our moment of truth in the rail project.
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