Results

The second to the last week was surprisingly exciting. I was thrilled to see if we could find any associations using the lab data. Dr. Allison and Melanie assisted me in using statistical approaches to analyze my data. One of the interesting things that we found was that child IQ was predicted by genotype at one VDR SNP (RS7975128, p=0.01), and maternal smoking within the child’s first 7 years of life (p=0.03). However, the interaction between the VDR SNP and maternal smoking was not significant (p=0.40). The A/G and G/G genotypes of RS7975128 were associated with lower IQ, as was the occurrence of maternal smoking. I also attended a lab meeting and a clinical meeting.

BuSy Week With the ADHD samples!!!!

On Monday, I was able to plate my ADHD DNA using the Biomek robot. This made me extremely excited because I was finally able to start on my project. I left the plates to dry overnight at room temperature. The following day, I began working on my assays involving the ALAD gene and the VDR gene. I made 18 Taqman plates for 9 assays and ran 14 of those plates onto the PCR machine. I then scanned them on the 7900HT machine. Most of my TAqman went well except for two plates. Next, for Wednesday, I had to re-run the two plates that failed. I also ran 6 more plates on the PCR machine and made 2 plates for a single assay. I scanned those plates as well and they turned out great. For the rest of the day, I had to plate 20 extra plates using the Biomek robot. On Thursday, I made 5 Taqman plates in the morning. I ran them using the PCR machine and scanned them afterwards. I then added markers and detectors. Fortunately, they looked great. In the afternoon, I ran about 5 more plates and scanned them. In addition, the fire alarm went off again for the second time since I have been in CHG. On Friday, I really enjoyed the talk by Ms. Cleaver. It gave me many tips in applying for college. After that, I went to my lab and ran and scanned some plates that I had made prior. I also helped Kaia by making two agarose gels for her and running her PCR samples. Some looked good but the rest failed. Chris then helped me submit my data so that I could view them with a statistician next week. Unfortunately, two failed to submit but I’ll be able to do that on Monday. Overall, I had an exciting and this week was probably the busiest for me by far.

FAmily Visit

I was able to observe my first family visits on a Friday. So far, that was probably one of the highlights of my experience with the program. I watched as the entire family of four completed a series of behavioral and psychological tests as well as developmental histories to see if they could be diagnosed with ADHD. There are three rooms in the clinic area: a computer room, an interview room, and a blood room. One member of the family goes into the computer and interview room at a time. In the computer room, letters appear on the computer simultaneously at varying time intervals and every time a letter, other than “X”, appears, the participant has to push the space bar. This test takes place for exactly fourteen minutes. After a while, one of the young participants that I watched became bored of the test, so he continuously and randomly just began pushing the space bar, increasing his impulsitivity score. The interview room is where the psychologist assesses them and gives them an IQ test by asking several questions as well as by allowing them to complete spatial and hands-on tasks. Finally, after everyone in the family completes these tests, there blood is drawn and set to the DNA bank. Unfortunately, one of the children refused to get a blood draw. Overall, the entire family visit lasted for a period of three hours and thirty minutes.

ADHD

On Monday, I continued working on my methods section until Chris, my mentor, arrived. Surprisingly, one of my friends from school was assigned to the same lab as me and she had just begun working there. So, she had to observe Chris and I for that day. Prior to lunch, I worked on two PCR plates and four Taqman plates. Then after lunch, I had to make an agarose gel to test my PCR. My PCR worked; however, it was not that great since some of the wells looked as if they were missing DNA samples. I assisted my friend in practicing using the pipette. Then, I completed one more PCR plate and scanned my Taqman plates afterwards. Fortunately, all of my Taqman worked out well. For the rest of the time, I worked on my methods section again and completed my blog.

Tuesday, I worked on a Taqman plate and two PCR plates. After running them on the machine, I had to wait until they finished, so that they could be tested on an agarose gel. After lunch, I tested the samples on the gel. My results were better than my results on the previous day. So, I completed two more PCR plates using a different primer, and ran them on the PCR machine. Then Chris taught me a new method using Sephadex to filter the DNA from our PCR. It was fun being able to learn a new method. This was a gel like substance that allows the DNA to separate from the excess materials used during the PCR reaction. After that, I worked on my blog.

I had a wonderful Independence Day celebration with my friends on Wednesday and returned to work on Thursday. I felt so excited to receive my first paycheck. When I came to the lab, I made an agarose gel and ran my previous PCR samples on it. It actually worked out well. Afterwards, I made another PCR plate prior to lunch. I made another PCR plate after lunch and I also began labeling my ADHD plates. I then waited for my PCR plates to finish running so that they could be tested on an agarose gel.

Friday was a great day! I began my day by making a PCR plate. I then ran my PCR agarose gel that I made earlier in the week. Fortunately, all my samples worked. Next, I ate lunch early because I was invited to observe a family visit. This is when the proband as well as the entire family come into the clinic area to be tested for ADHD.

Taqman and PCR

Monday was quite interesting. A couple of minutes upon arriving at the Center for Human Genetics Building, the fire alarm went off and everyone had to be evacuated outside the building. When we came back in, I looked at the results for the last for Taqman plates. Sadly, two of the plates failed to amplify, which means that I have to re-do these plates. Then, Chris showed me how to do PCR. He explained the functions of the various ingredients in the master mix. For instance, the taq is an enzyme used for replication and amplification of a DNA fragment. He also showed me how to work the PCR machines. When I finished lunch, I had to re-do the plates that failed. Chris then allowed me to do PCR by myself, which was so exciting. For the remainder of the day, I analyzed the rest of the Taqman plates. In addition, I went into Pub Med and searched for the gene ALAD and lead and neurotoxicity.
Tuesday was a fun day also. I enjoyed the Primate Center tour. I have never seen lemurs in the past and it was amazing to see how closely they resembled humans. In the lab, Chris and I went to use the Biomek robot for transferring DNA into the 384 deep-well plates. At the same time, Robin came to my lab for a lab visit. We talked about various aspects of my project as well as the poster. After lunch, I had a meeting with Dr. Allison and Melanie. We looked at different data and statistics regarding smoking, genotypes, and polymorphisms in relation with ADHD. Amazingly, we found many significance in the data. We also discussed the status of the materials for my project. I then headed back to the lab and did two PCR plates. We actually had a small going away party for two members of the lab who are going to be relocating to Miami. We had some cake and everyone in my lab joined in. Overall, Tuesday went well.
On Wednesday, I was able to make an agarose gel. It was somewhat nerve wrecking to handle even just a small amount of ethidium bromide since it could possibly affect my future children’s DNA. It was, however, interesting how we made a gel with multiple rows of wells rather than just one. The purpose of the gel was to see if our PCRs worked. After running the gel, we took a picture of it and measured the band sizes. Fortunately my first PCRs were great. After lunch, I completed one more PCR plate, and then I proceeded to do two Taqman plates for different SNPs. I then started working on my blogs for thirty minutes. Afterwards, Chris and Dr. Allsion helped me out with my introduction.
On Thursday, I met with Dr. Allison in the morning. She informed me about the upcoming family visit for the ADHD research study patients, wherein they go through a series of tests and get their blood drawn. I am very thrilled to see that. After that, I went to my lab and finished two PCR plates. When lunch was over, I ran the samples from the plates onto the agarose gel to see if my PCR was successful. For the remainder of the day, I completed some more Taqman for patients enrolled in the hostility study.
Finally on Friday, I started planning out the methods section of my poster. Also, I searched about the various SNPs in the genes that I will be studying. I had to find its role and its functions. I made three PCR plates using different primers and ran them on the PCR machine. After that, I made an agarose gel to test my plates on. When lunch was over, I tested my samples from my PCR plates. As it turned out, my PCR turned out well. For the rest of the day, I worked on some more PCR plates and headed to the Schiciano Auditorium for the seminar speaker !! This week was a busy week, but it turned out great!

Second Week of ADHD Research

I had a wonderful day at the lab on Monday, June 18. First, I met with my principal investigator, Dr. Allison Ashley-Koch. We talked about an overview of my project. Unfortunately, the single nucleotide polymorphisms as well as the assays have not arrived yet. In addition, they were running low on ADHD DNA, so they have to wait until the DNA bank refills it before I could start on my project. As a result, I spent my day shadowing Chris, my mentor. This was a great introduction to me, attempting to learn more about the various instruments that they use in the lab. Moreover, with this practice, I will be more prepared when I start doing my own work on the ADHD DNA. Chris showed me how to use the Taqman recipe, which is used to figure out how much master mix, water, and assays should be added in accordance with the number of DNA samples. Next, I had to pipette the master mix onto the micro-well plates containing the DNA of patients enrolled in the Caregiver study. We then ran them on the PCR machine. After lunch, watched the Biomek robot transfer DNA into the micro-well plates. It was so fascinating to see how precise the machine worked. Lastly, we looked at the results from the Taqman plates earlier that day, and they were all quite successful.

Tuesday was another fun day in the lab. After speaking with Dr. Allison in the morning, I went to the third floor lab of the Center for Human Genetics Building. Chris asked me to pipette the Taqman recipe unto the micro-well plates containing DNA of patients enrolled in the Hostility study. However, before doing that I first had to make the recipe by adding water, master mix, and 20x assay. It was thrilling to do nearly the entire process by myself. After having to pipette two plates, I placed them in the centrifuge and took them upstairs to the PCR machine so that they can be ran for forty cycles. I was actually able to work the machine by myself (with instructions and Chris’ assistance of course =)). Then, I had to do the Taqman again, except this time, I used a different assay. This is because I was trying to find a different single nucleotide polymorphism (SNP) in the DNA. Upon returning from lunch, I created folders on the computer for my data to be stored in when we scan the plates. I also tried to find the gene and chromosome of the SNP that I was trying to observe. When I finished, it was time to take the plates out of the PCR machine so that they can be scanned using the 7900 machine. We then went to the computer to look at the data that we produced. None of the NTC controls were amplified, so we were able to submit the data to the clinical people for analysis. Finally, to end my day, we used the Biomek robot again. Overall, I was thrilled to be able to learn new techniques.

On Wednesday, June 20, I came to my lab and proceeded to the Post PCR refrigerator to get the plates that I prepared the day before. Chris allowed me to scan the plates by myself. Fortunately, I remembered most of the process that he showed me the prior. After scanning, he asked me to do the Taqman for the C-plates for Hostility. Since not all of the micro-wells contained DNA samples, I had to look at the chart to see where to pipette the Taqman recipe. I carefully completed that tedious process and centrifuged my resulting plates. Next, I ran the plates onto the PCR machine. When I returned after lunch, I did some more Taqman on DNA from patients enrolled in the Hostility study. Upon completion, I ended up with about fourteen plates. I went upstairs to store the plates in the cold room. This was a great day of practice and precision.

I had a rewarding day at the lab on Thursday. All of the plates that I ran on the PCR machine the prior were successful. I then looked at the results on the computer and none of the NTC controls amplified. After which, Chris showed me the DNA sequencing machine, wherein he uses a restriction enzyme to find a single nucleotide polymorphism in an insertion deletion. This is completed using micro satellites. He then asked me to do some more Taqman. I finished the list of assays needed to be run. Upon completion, I felt proud that I completed about twenty micro-well plates. Moreover, I am happy to say that my ID badge finally works, which means that I’ll be able to access most of the doors in the Center for Human genetics Building !!!

Finally Friday was more of an analyzing day. First, I scanned twelve plates unto the computer so that they can be run through on the 7900 machine. After a few minutes of waiting, I placed the plates in the cold room and analyzed the results to see if my PCR from the previous day was successful. To analyze the results, we used the program SDS 2.2.2. It generated graphs of the data, which is then submitted to a statistician for further evaluation. As it turned out, all of the plates that I completed were great. When I finished looking at the data that I produced, Chris showed me some useful tools in trying to find known mutations. There is a website called http://genome.ucsc.edu/ that is very helpful in doing so. We also used the Biomek robot to prepare for the PCR. Chris promised to show me how to use the PCR on Monday, so I’m very thrilled for that. Overall, this week was wonderful !!!!!