This is my last post on this blog. I graduate high school in 5 days and I'm going on to bigger and better things. I'll be attending Dartmouth College this fall. I'm so thankful for all that this program has allowed me to learn. Because of my research experience in high school my love for science has only grown. My presentation went very well on grandparents and special friends day and I'd like to thank everyone who was able to attend. Below you'll find a link to my presentation:
docs.google.com/presentation/d/155mRJBRHeXIxv5BLAANrPqobcPN8oG2HWM6V3SMMpcY/edit?usp=sharing Once again thank you so much. Good bye:)
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The goal of trying to RT-PCR in a 96 well plate was to try and recreate results that have already been published by the lab and better by lab skills. I learned that lab work is really really hard. At every instance something managed to go wrong meaning that I had to not only redo the PCR but remake the cDNA that I had consequently ruined. Once I accidently put 1006 microliters of water when I mean to put 106. So I had to start over. Another time I got all the way through the process but mislabeled my control and non control tubes so that all of my results were the exact opposite of what they were supposed to be. That was a tad frustrating to say the least. Since my attempts with bench work weren't novel in the slightest and my last day in the lab was coming up on May 1st I decided to focus on what I worked on during the first half of the year when it comes to my final presentation.
Throughout March I mastered the art of making cDNA which is apart of RT-PCR. RT-PCR stands for Reverse Transcriptase Polymerase Chain Reaction. Making cDNA falls into the Reverse Transcriptase part of things. When making cDNA, a single stranded form of DNA, you put this thing called reverse transcriptase along with a bunch of other things in some tubes to ensure that you end up with a single strand of DNA. Apart from missing two weeks of lab because of spring break (I was in Italy touring with the Choir.) I worked on that process.
Throughout this month I got to observe Dr. R help a fellow lab researcher who was struggling to get results from a PCR due to trouble working with RNA. RNA is very unstable and easily broken down by the tiniest bit of contamination. I learned good lab behaviours which included spraying absolutely everything that you come into contact with RNAse spray to avoid contamination. You had to spray: the workbench, the pipette, even your gloves to avoid any possible contamination and still you might not get the results you're looking for due to contamination on quite literally the microscopic level. I first observed the protocol going from single stranded cDNA to RNA to primers to results until finally I thought I was ready to run my own PCR.
The head of the lab, Dr. D, jokingly asked me this when checking in on my progress and the short answer is no.
The long answer still ends in a resounding no but is a bit more intricate. After identifying the candidate genes by cross referencing the two lists of RNA binding factors and Nonsense Mediated Decay proteins I had 6 genes. My next step was to research those genes to see if they were at all involved with Cox - 2 a gene that's prevalence is heavily reduced whenever the integrin alpha 3 is knocked down. For most of them the answer was no but for a couple the answer was yes. I also researched their general function and was surprised to find out that some genes had functions as far reaching as embryonic development and when overexpressed leukimia. After doing that research the next steps would be to order primers for those 6 genes and run PCRs against alpha 3 to see if they really are down regulated as I predicted from cross referencing the two lists. Below is the schedule I figured out with my mentor. As of right now I'm right on track. I'll be missing most of December because Revels is next week (!!!) but I'll be reading up on the 6 candidate genes I've found and once I come back in January I'll get to do some PCR with the primers Rakshitha is ordering for me! I'm beyond psyched!
October Datamining UPF1 vs alpha 3 November Datamining RNA binding proteins that are known to have effects on splicing (splice factors) vs alpha 3 Finding which genes come out of both December Identify potential candidate that may be involved in alpha 3 dependent on Cox 2 Researching literature on those candidate genes Learning Blast Blasting those genes Research those genes and finding out if they effect Cox 2 January Do some qPCr with lead candidate genes February Continue validation of qPCR with lead candidate genes March Assimilate all findings from previous months April Preparation for final presentation May I had the awesome opportunity to sit and just talk with the PhD candidate with whom I work with closest.
M: Where are you from? R: I’m originally from India M: What did you want to be when you were little? R: I wanted to be a Medical Doctor M: Do you have any siblings? R: I have an older sister M: Did your parents want you to be anything? R: Not really, my mom didn’t want me to be a doctor, because in India, in order to be sucessful you have to have a relative in the medical field and we didn’t have any. She thought that if I became a medical doctor I would really suffer. M:What was your academic plan? M:What did you end up doing academically? I got my bachelors degree in Engineering with a major in biotechnology. I then went on to get my masters in biological science again with a major in biotechnology and now I’m working on getting my PhD. M: How long will it take you to get your PhD? R: For this department it takes an average of 5 years. M: How long have you been at this research institution? R: I’ve been here 3 years so I probably have around 2 more. M:What was your first job? R: I was a Quality Analyst at a Pharmaceutical company. However it was more of a volunteer position, I wasn’t actually paid. M:How many cities have you lived in? 3 M:Which ones? R: Banglore (India), Lowell over in Massachusetts,and Albany. M:What’s one fun fact about yourself? R: Hm, that’s a bit difficult I’m actually very good at hula hooping. M: If you were to give advice to someone who’s considering going into the biology whether as as a Medical Doctor or as a Researcher what would you tell them? R: I’d say do as you’re doing and experience all that you can about your field of interest ahead of time. I almost became a medical doctor but looking back I probably would have been miserable in medical school. M: Why don’t you think you would have enjoyed medical school? R: I think I’m just a better match for biological research I wouldn’t want to memorize tons of rote information. M: What’s your favorite part of research? R: It’s one of the few fields where you can have a genuine scientific question and you get to spend your days chasing after the answer. M: Is there anything else not covered that you’d say is important? R: I’d just say that one of the major driving factors to get into research was the loss of my father to cancer during undergrad. He passed away within 6 months after diagnosis and that left me with a “What the heck?” feeling. I though that we were so advanced when it came to medical science that even if we couldn’t cure cancer we could at least prolong a patients life. Finding out that wasn’t the case was a shock and motivated me to research cancer. M: Can I ask what kind of cancer he had? R: He had prostate cancer which is typically one of the cancers that you can have and still live with for a very long time but because he had a rare strain he died very quickly. M: I’m very sorry about that. That is an incredible motivator to come to work everyday. R: Absolutely M: Thanks so much for taking the time to sit down with me! I went to turn in my findings from Russ Carsten's file and Rakshitha informed me I'd make a tiny mistake that was going to cost me hours of work. When cross referencing this spreadsheet with the one for alpha 3 I used the Gene column (Red arrow). The problem with that is that column is just one name for any given gene and there's actually up to 5 or 6 names for the same gene! We're kind of in the dark ages when it comes to naming genes because we're discovering new ones everyday. Some genes are "discovered" more than once because they're important to one or more (or freakin 5) different functions.
So essentially I had to go back and make sure for each of the hundreds genes that I didn't look at the other names for that the name wasn't on the alpha 3 spread sheet... I had my work cut out for me. I've kind of spent the last 2 years of my life worshiping the Excel SpreadSheet. In my last project from my junior year, which you can find here, I used spreadsheets to statistically analyze the similarities and differences between patients with Hypertriglyceridemia and Pancreatitis and those without. The results of that work has been submitted to be published to a medical journal and I'll know by spring if it actually has been published.
This year I've been working with a lot of different spread sheets and this is the latest example. This is an image of part of the 200+ line spread sheet I've spent hours staring at. Sometimes science research is about as exciting as it sounds... |
Michaela BentonI'm lucky enough to go to this amazing school that has this amazing program that lets me learn amazing things. Archives
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