Monday morning, February 8th, marked my first day back in the lab at TGen. I was welcomed by several exciting tasks and projects which I will begin to pursue in the next following months.
The day started off with me running a 1.8% agarose gel electrophoresis. Now, I know what you must be thinking, what exactly does this mean or what is the purpose of this gel? A gel electrophoresis separates DNA fragments based off of its size. An electric current then moves the DNA molecules across the gel.
The above image shows what a gel electrophoresis image looks like. The first column of bands is known as the DNA ladder. This is the set that all of the other bands will be compared to in order to genotype the DNA. Using the samples we have in the lab, I ran over 5 gels this week with only 2 being successful. Gels may not work for several reasons: the temperature may be too hot, the enzymes may be degraded, the gel may not have run for a long enough time, etc.
Using a 100 base pair DNA ladder, I was able to genotype several samples distinguishing if they were heterozygous, wild type, or mutant. If heterozygous, two bands will show up in the image. If wild type, there will only be one band on the bottom. And if mutant, there will only be one band on the top, which is exactly what we are searching for and are still yet to find.
Throughout the week, when I was not running a gel, I was running a PCR. Testing about 7-8 samples at a time, I followed the lab's new PCR protocol. After the PCR samples were done, I would upload them into a gel, completing the cycle.
In the next upcoming week, I will be furthering my research project by learning to conduct western blots, by working with mice models and even tissue samples. I will also begin to intern at the Center for Rare Childhood Diseases (C4RCD) where I will see the clinical aspect of the research in the lab. I am very excited to see where this research will take me and to eventually find out more about this severe disease.
Bye for now!
Pooja
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ReplyDeletePooja, It sounds like exciting work that you are doing at TGen. I can't wait to hear more about all that you will get to do during your project & the final presentation. Have fun!
ReplyDeleteThank you! I am excited to continue my research and see where this project will take me!
DeleteSounds very interesting! I'm wondering what DNA is the gel electrophoresis testing? (What type of DNA is being used for the procedure?)
ReplyDeleteThanks Sebastien! So the DNA I am testing is from the mice models. The gels will tell me what kind of DNA the sample is: mutant or wild type!
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ReplyDeleteGreat first post! Thanks for providing such helpful clarifications... every time that I had a question while reading your post, it was answered in the next sentence!
ReplyDeleteDoes a PCR provide helpful data/results even if the accompanying gel electrophoresis is not?
Thanks! Great question. The PCR is actually the step right before conducting the gel. I take my existing samples of DNA, follow the PCR protocol, upload the samples into the PCR machine, which will replicate the DNA, and only after the PCR is finished, I will cast and upload into the gel. So the only way to test if the PCR is successful is basically through the gel!
DeleteWhat does working with mice models change about your process? Loved your post!
ReplyDeleteThanks! The mice models allow me to analyze infected DNA as well as normal DNA. These models are the main source of research in the lab.
DeleteThat is so cool that you are using gel electrophoresis. I remember learning about that in class. Do you think you education at BASIS has helped you with your lab work?
ReplyDeleteHi Griffin! I do think that the knowledge I have gained from BASIS has helped me with my lab work. In AP Biology, we learned how to cast a gel and only a few months later did I actually do it successfully outside of the classroom setting. Even when it comes to genotyping or other conceptual ideas, what I have learned from my classes has definitely made my work at the lab easier. At the same time, however, what I have learned at BASIS is just the first step to my understanding. The lab has enabled me to learn so much more, beyond the scope of the class or what I even imagined!
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