Thursday, January 28, 2010
1-28-2010: Last day of the internship
Tomorrow I will be shadowing Dr. Harper, a general surgeon.
1-28-2010: Results Day
Tuesday, January 26, 2010
1-26-10: paper feedback
I am working on my paper some more tonight and tomorrow we will be finishing the last western blott I will be here for and getting our results.
Monday, January 25, 2010
1-25-2010: Western blott and dissections
Over the weekend I got my TB test and background check so that I can shadow in the OR on Friday and I will be shadowing a general surgeon, Dr. Harper. I also worked on my paper a bit over the weekend and Dr. Nuss said that he would read it tomorrow to make sure it's accurate and organized well.
Friday, January 22, 2010
1-22-2010: Shadowing Dr. Larrimore
Then we went to the hospital and saw three patients. One woman had just had twins and was in a hospital bed recovering. She was having a sharp pain near her right hip and Dr. Larrimore said that she may have an infection and had a nurse do a urine test to check for infection. The second woman we saw was having contractions and about to have a baby. We just went in to check on her and see if she needed any pain medication. The last woman we saw had just had a baby and was leaving the hospital that day. We also went to the area of the hospital where they keep the babies right after they are born. I talked with the nurses that work there and they told me all about their job and how peaceful it is unless they have a baby that is going through drug withdrawl because they are always irritable from being weened off of whatever drug their moms were on while they were pregnant. We also met and spoke with a radiologist who had done an X-ray on one of Dr. Larrimore's patients. Dr. Larrimore said that they usually only work halfdays on Fridays and I left during lunchtime around 11:30.
Now, I am about to write in my shadowing log about what I did today and I am going to write up a rough draft of the western blotting procedure we have been doing in the lab for my paper.
Thursday, January 21, 2010
1-21-2010: More dissections...
In the midst of doing dissections, I also prepared the western blott for the primary antibody wash. I put the antibodies on and the nitrocellulose paper is soaking in the antibodies overnight.
Tomorrow I will not be shadowing Dr. Harper because I found out that I have to have a background check and a TB test in order to shadow in the operating room. However, I will be shadowing an OBGYN, Dr. Larrimore, tomorrow.
Wednesday, January 20, 2010
1-20-10: Gel Day
Dr. Brown gave me some extra textbooks today on endocrinology that should help with the primary literature I have been reading. I have been reading one of the books during some of the down time today.
I also spoke to my dad last night and he said that he had arranged for me to shadow Dr. Harper, general surgeon on Friday.
Tomorrow we will label the paper and do the primary and secondary washes over our western blott.
Tuesday, January 19, 2010
1-19-10: Sample Preparation
Last week when we photographed our results, I saved the pictures of our results onto my flashdrive in order to post them onto the blog, but I was unable to do so I think because the images are saved as .tif files. So, Dr. Nuss said that I would be able to label each of the lanes with which sample it was and change the tif file to a jpeg file with photoshop. So I installed photoshop onto one of our lab computers and am going to try to modify and post a pictures of last week's results.
This image is a photograph of the results of our first western blott from last week. Before adding the antibodies to the proteins on the paper, we cut the paper into three different segments so that we could test 3 different types of antibodies on our samples. The middle piece of paper was washed with a purified primary antibody while the other two side pieces of paper were washed with a raw primary antibody. The piece of paper washed with purified antibody did not show on the first photograph (30 second exposure) because there is no binding going on in the background. Antibodies are made by injecting the target proteins into an animal (in this case a goat), and in response, the goat's immune system makes antibodies. The raw primary antibodies include antibodies for other things that the goat encountered and are not seperated from our target antibody for ILP3. For that reason, the background of the paper washed with the raw primary antibodies are darker due to binding from the other antibodies in the raw solution.
Before we ran the gel, we mixed our samples into two different types of buffer (NuSep and Reducing). The reducing buffer functions to break the disulfide bonds that connect the A chain and B chain of the ILP. The NuSep does not do that and it is harder to compare the sizes of the bigger peptide with the A chain and B chain together with the ILP3 A chain standard and ILP3 B chain standard. The size is marked by the ladders that are in the middle of the three sheets of paper.
The lefthand segment of the paper was ILP3 A chain and B chain standards as well as Aedes aegypti head extractions (done via dissection, grinding and mixing with protein extraction solutions). If you look at the bands on the paper, all of the ILP3 chain standards showed up, which is good because Dr. Nuss had done a previous experiment in which they did not show. However, we did not see any bands for the Ae. aegypti heads. For that reason, today we prepared Ae. aegypti heads in different extraction solutions to run on the gel in hopes that we will be able to detect this ILP3.On the segment of paper to the right we tested ILP134 standards and Anopholes stephensi heads. The ILP134 standard is made up of different segments of conserved ILP1, 3, and 4, and the antibodies should recognize any one of the three ILPs. Our lab has hypothosized that the function of ILPs 1, 3, and 4 is somewhat redundant and that is why we tested for all three of the ILPs. On this blott, we did get a band for the mosquito heads, but it was bigger than what was to be expected. If you compare the size to the standards, you can see the difference in the sizes.
Also, we tested the standards again by dotting the standards onto the nitrocellulose paper prior to the primary and secondary antibody washes. You can see this best on the segment of paper to the left in the bottom lefthand corner. We did this as a positive control because if there was anything wrong with the process before the antibody washes, then we would have seen the ILP3 dotted standards, but not the standards that went through electrophoresis on the gel and onto the paper. There is a small dot which is the B chain ILP3 standard. The different standards and bands look better or worse depending on the exposure time as well.
To finish the day, I am going to continue to help Animesh with ovary dissections.
Monday, January 18, 2010
1-18-10: MLK Day
Friday, January 15, 2010
1-15-10: Shadowing Dr. Michael Manning
One thing that I don't like about researching in a lab (at least the one lab that I have experienced) is that it's not a very social job. There aren't too many people in our lab, and the people that are there generally don't collaborate too much. Most of the people work on the same general theme but they all do their own projects and independent research. In comparison, Dr. Manning's office was much more of a social atmosphere. I really loved talking to all of the patients, nurses and doctors in his practice. Just that aspect of his job was a big improvement in the nature of the work and more suitable to my personality.
One reason I sought out Dr. Brown's lab to shadow is because I am very interested in malaria and research that could possibly improve the condition of people with malaria or prevent the transmission of malaria from the mosquito to people. One thing that I don't like about working on the research is that it is a very distant way of bringing relief to people. The mentality of the research is that we are doing this research because there is a correlation with insulin and mosquito lifespan and transmission of malaria which could help to decrease the number of people affected, but first, we need to learn more about ILPs and the insulin pathway in mosquitos which is a very indirect way of solving a problem (and I am so I glad that there are people who are willing to do all of the research and work for medical advancements, but I don't think that I want to do that). I really liked the patient/doctor relationship between Dr. Manning and his patients and the direct way that he was able to improve their conditions and help them to live better and healthier.
One thing that has kind of kept me from definitely wanting to go to medical school is the fear that I would go through a lot of school, have a specialty and then eventually have an incredibly repetetive job and not really learn anything new too often. Dr. Manning told me that because he has such a general practice, he has to know about so many different conditions and problems in every part of his patients' bodies. He also said that because of technology there are always advancements and new treatments that he has to continually read about and learn about in order to provide his patients with the best care. That is one aspect of his job that he likes and something that I really liked about his field as well.
Today I arrived at his office around 8:30 and saw patients with him until about 12 and we had lunch and then went to see a patient of his in the hospital until 2. Then we came back and saw patients for another hour or two. He stayed later but I left around 3:30. I really enjoyed the experience and it has made me much more excited and enthusiastic about potentially applying to medical school.
Thursday, January 14, 2010
01-14-10: Mosquito dissection day
Wednesday, January 13, 2010
1-13-10: Results today!
1. First, you prepare your protein samples (our samples are controls that definitely contain insulin like peptides and mosquito body parts that we don't know if they contain insulin like peptides or not).
2. Load the samples into a gel and electrophorese in order to seperate the proteins into different sizes. Proteins with a higher molecular weight appear higher on the gel and proteins with a lower molecular weight appear lower on the gel. We also load markers which indicate the size of the proteins that show up in our sample.
3. Transfer the proteins from the gel to nitrocellulose paper. This is done by placing the paper next to the gel and running another electric current through the gel in order to pull the negatively charged proteins from the gel to the positive pole and onto the nitrocellulose paper.
4. When the proteins are on the nitrocellulose paper, they are not visible. To make them visible, we add antibodies that are specific to bind with the ILPs.
5. We then add secondary antibodies to the proteins and the antibodies that is specific to bind to the antibodies. When the secondary antibodies bind to the antibodies, a reaction occurs, a color is produced, and you know whether or not ILPs are present in the mosquito heads.
Today, Dr. Nuss and I finished our first Western Blott. We left the protein samples on the nitrocellulose paper to soak in the primary anitbodies overnight last night. When we came in this morning, we did 3 washes for twenty minutes each with the TBS-T (tris saline buffer with tween 20). Then, we added the secondary antibody to our proteins and allowed that to soak for about four hours. And then we were able to photograph our samples and view our results. Before I started working this week, Dr. Nuss ran a Western Blott with chain A standard, chain B standard, mosquito heads, thoraxes and abdomins. The bioactive form of insulin is made up of an A chain and B chain connected by a disulfide bonds. The chain A and chain B standards are the segments of insulin, and should definitely show up on the Western Blott. One of the first times Dr. Nuss ran the procedure, he ran it with these standards, but for some reason the standards did not show up in the results when he ran it. The Western Blott we have been running the past three days included chain A standards, chain B standards, and mosquito heads. In our results, we were able to see the standards, so the procedure worked, but there were no bands for the mosquito heads. Dr. Nuss said that he thought it may have been a problem when making the mosquito extract.
We also started our second Western Blott by preparing our samples and running them on a gel. Then we transferred the proteins from the gel to the nitrocellulose paper and the paper is on the lab counter drying.
Tomorrow I am going to finish the second Western Blott that we started today and dissect some mosquitos because we are going to increase the number of mosquito heads in our next Western Blott to see if increasing the amount of mosquito juice will give us a band on our next Western Blott.
I also spoke with my dad (who is a gastroenterologist) and he has arranged for me to shadow one of his friends, Dr. Manning - a family practicioner, this Friday.
Tuesday, January 12, 2010
1-12-10: Mosquito feeding day...
In the immunoblot procedure, there are two main washes that need to be performed: an antibody wash and a wash that contains a catalyst such as an enzyme. The first wash is the antibody wash because the antibodies in the liquid bind to the proteins on the membrane of the nitrocellulose paper. The second wash contains the catalyst and this portion of the procedure is done because the enzyme binds to the antibody and then a reaction occurs which produces a color and allows for the protein to be visible. We performed the first of the two washes by preparing a block solution from ECL and TBS-T and drained the TBS-T from the paper and poured our newly made block solution onto the paper and put it in a rocker in the cold room. After about two hours we took our papers from the coldroom and injected antibodies into each of the dishes containing the block solution and paper. Now, the samples with the antibodies are on the rocker in the cold room and we will finally get our results tomorrow.
Then we made up some new TBS buffer by mixing NACL, HCL, Tris base and deionized water. It took a while to make the buffer because the HCL that we were using was highly concentrated and dangerous to handle. We only handled a small amount at a time (about 10 mL) and then safely disposed of the extra that we had left over.
Then I labeled 30 small tubes because tomorrow wer are going to alloquat a large amount of an antibody solution into the smaller tubes so we can put the solution into the -80 degree refrigerator so that bacteria does not begin to grow in the solution. Dr. Nuss explained that it is important to put the solution into small amounts because if you freeze and thaw a solution containing proteins several times then the proteins begin to degrade.
Before I went to lunch, I went into the mosquito room because another person working in our lab needed to bloodfeed the mosquitos so that they would mature and be able to produce eggs. He had anethesized a rat and put it on a screen for the mosquitos to feed on it and it was kind of neat to watch. He is doing an experiment that involves injecting different solutions into the mosquito that will hopefully stop the genes controlling insulin like peptides from being expressed. He let me inject one of the mosquitos using a small needle and syringe and it was really tedious, but it was kind of cool because first he froze them so they could pick them up and handle them, injected them and then put them in a container and right after the injection they would start flying around like nothing happened.
Tomorrow we will get our results and I think start a second western blot.
Monday, January 11, 2010
01-11-10: First stage of Western Blotting technique
One type of experiment that we will be doing to identify ILPs in the mosquito is a technique called Western Blotting. Last week, before we were able to start experimenting today, Dr. Nuss had to do some preparations to run the Western blot. One thing that he did before we could start the experiment today was to disect about 500 mosquitos by seperating the heads from the body, grinding them up, centrifuging them and collecting the supernatant to run for the Western Blot. We are doing this experiment in order to identify whether or not the ILPs are located in the head of the mosquito. Today, there were three main parts of the first stage that we ran: preparing the protein samples, running the samples on a gel, and then transferring the proteins from the gel to nitrocellulose paper. We had 16 samples to run on our gel, and they were all either samples of mosquito heads, chain A of insulin or chain B of insulin. Insulin is a hormone made of of chains B, C, and A, but chain C is cleaved out of the active form of insulin and chains B and A are connected by disulfide bonds. So the samples with chain A and chain B are just insulin. We mixed the chains B and A, and the mosquito heads with different buffers (sample buffer and reducing buffer - which serves to bind with proteins that may be "sticky"and bind with anything, such as the proteins we are trying to detect) in order to make our 16 samples. Once our samples were made, we loaded them into a gel and did electrophoresis for about 3 and 1/2 hours. During that time I went to part of a seminar on termites and how they could be a valuable energy source because they could be used as a high calorie food or to produce high amounts of methane gas. Then I went to lunch with the program director, Dr. Marianne Robinette. After that, Dr. Nuss showed me how to set up the next part of the Western blot. During the remainder of the time to wait for the gel, I read a primary literature article that relates to the research we are doing. Once the gel was ready, Dr. Nuss showed me how to prepare the Western Blot "sandwich". We prepared two pieces of nitrocellulose paper on two sponges and then put our gel in between the two pieces of paper and into a machine to transfer the proteins on our gel to the nitrocellulose paper. The transfer to the nitrocellulose paper took one hour and I read part of another literature article. Then we were able to look at the nitrocellulose paper and our markers were visible. Tomorrow we will need to do a couple of washes over the paper that will cause the proteins to change color and be visible in order to see if they transferred to the paper. That was all we did for today and tomorrow we will be finishing up the Western blot.
