Hi
everyone!
I started working in the Bergsagel
lab at the Mayo Clinic this Monday, and I couldn't be more excited! I’ve
already been able to start analyzing cell line and patient DNA sequences, and I’ve
also had the opportunity to start practicing with the programs and protocols I’ll
be using.
This lab is the first one I've
worked in focusing on eukaryotic organisms and cell lines; in my previous lab
experience, I had only worked with E.
coli. So far, I've noticed a surprising amount of similarities between the
two. The overall concepts behind growing human cell cultures are very nearly
identical to those governing bacterial growth, even if the exact details of the
protocol might differ slightly. For example, E.
coli is usually incubated at
37°C in atmospheric air,
and mammalian cell lines are usually grown at 37°C
except in a slightly more controlled incubator, with 5% carbon dioxide in the
air to more closely match physiological conditions. And from what I've seen,
this pattern holds true for lots of the techniques I'd learned in the
microbiology lab compared to the techniques I'm learning right now. As a
result, most of the protocols I’ve practiced so far at Mayo are nearly
identical to how I had performed them before.
That being said, some of them differed
drastically from what I’d seen earlier, and some were entirely new. I’d never needed
to work under a laminar flow hood (which prevents contamination of the cell
cultures) or counted cells with a hemocytometer before. I’ll need to be careful
to remember exactly how the methods used in mammalian cell labs differ from
those in bacteria-focused labs so I don’t get the two mixed up.
Right now, the direction my project
will eventually take isn't set in stone, but it will begin with the same
initial steps regardless. The primary initial goal of my project is to
develop a qPCR assay that can detect different rearrangements of the genes that
encode antibodies. These rearrangements can occasionally make a mistake by swapping
with the wrong DNA sequence. And if certain oncogenes have their expression
increased by this inappropriate rearrangement, multiple myeloma can result. But
before we can easily identify these inappropriate rearrangements, we need to be
able to clearly analyze normal rearrangements. Creating this qPCR assay for
normal rearrangements will be the first step to developing another assay to
identify faulty rearrangements.
I’ll be posting again later this weekend to provide a short
summary of multiple myeloma and the IgL genes I am focusing on in my project,
so don’t forget to subscribe for email notifications if you’re interested!
Grady Day
I'm glad to see that you're past experience is applicable to your current project; it's great to not have to start from scratch. I'm excited to learn about how biologists actually get genetic data. (Shameless plug alert) If you're interested in seeing how that data is analyzed by bioinformaticians once collected, check out my SRP blog in the coming weeks!
ReplyDeleteHey Trey! I really like seeing how you go into more detail about the bioinformatic tools you're using like the TCGA database. I'm working with some similar databases and tools, and I hope to learn a little bit more about them through your project!
DeleteI think this is a super cool senior project since it deals with cancer, which is killing many people these days. How does the qPCR detect the rearrangements in the genes? Does it do a scan on a sample? Good Luck with your project!
ReplyDeleteHi Angela! The qPCR test I'll be designing will have pieces of DNA that correspond to each gene. The qPCR will amplify DNA only when those genes are adjacent after rearrangement.
DeleteHey Grady! I think its really interesting that you're finding similarities between your prior and current research. Is there a certain rearrangement in the genetic sequence that causes multiple myeloma or is it that any rearrangement can cause this? I'm just wondering what the possibility is for sequences rearrangements to induce separate diseases apart from multiple myeloma.
ReplyDeleteThe rearrangement I'm looking at is specific to developing B cells, so it applies both to multiple myeloma and a few other types of lymphomas. However, the general technique of the qPCR test to amplify rearrangements is pretty applicable to many other types of cancers.
DeleteHi Grady! It's great to see that your past experiences analyzing E. coli cells is similar to the methodology you're following now. Do you anticipate any other major differences in the next steps of the process? Also, I'm curious to know how the hemocytometer helped you count the cells. I look forward to learning more about multiple myeloma and seeing your progress every week!
ReplyDeleteHi Alicia! I think by now I know the general layout of my project pretty well, but that's not to say there won't be any setbacks. I expect I'll run into lots of issues with designing the specifics of my qPCR assay. The hemocytometer is basically a microscope slide with a bunch of tiny gridmarks on it, almost like graph paper. You just count the cells in each square and plug the resulting number into a formula that gives the number of cells per milliliter of the initial culture.
DeleteHey Grady, glad to see you are progressing on your project. It is interesting how a small genetic flaw can result in such a prevailing disease. I look forward to seeing your progression in your research and how your developments in bacteria turn out.
ReplyDeleteThanks for reading Ben! I'll keep you posted on the progress I make each week and the difficulties I will encounter.
DeleteHi Grady, I am excited by the enthusiasm in your writing, along with my general interest of CRISPR. However, I was wondering if you could explain how CRISPR is applied throughout the experiments, and how exactly the technology for this works. Have fun with the project!
ReplyDeleteHey Grady! It's interesting to see that the procedures for eukaryotic cells and E. Coli share some similarities in the protocols for analysis when they are in entirely different domains. I'm hoping to see more of these similarities and even differences that you'll find in the coming weeks, and how they affect the data you collect. Do you think there will be more differences as your research proceeds into its more complicated phases? I'm looking forward to how it turns out, and your progress in the near future!
ReplyDeleteThanks for your comment Syed! Right now, I feel pretty confident that I'll be at least somewhat familiar with most of what I encounter in the qPCR assay part of my project. That being said, it'll be very challenging to fully optimize and test the accuracy of my assay.
DeleteHi Grady! It's cool to see how your past experiences are helping you with your current research. I'm very interested with how your research will progress and change. I'm glad that you haven't set anything in stone yet because you don't want to lock into yet. Good luck in the rest of your research.
ReplyDeleteThanks Grayson! Keep reading for more updates!
DeleteHey Grady! Your research is fascinating and it's always a cool thing to see how what you've learned previously fits into the new things you do. I was just wondering if there have already been some faulty arrangements of the genes you mentioned identified. I can't wait to see what you find!
ReplyDeleteHey Tanmyaa! The rearrangements I'm studying are thought to sometimes affect a few of the many oncogenes the Bergsagel lab studies. Right now, I'm looking mostly to identify normal rearrangements, but once that's complete I'll hopefully be able to systematically characterize and identify faulty rearrangements of these genes.
DeleteHey bro! This project looks super interesting so far! How much of this are you able to do independent of the Bergsagels? Also, how do you think the work you are doing now compares in difficulty to projects you have worked on before? Good luck!
ReplyDeleteI really love how I get to work mostly semi-independently in the lab. Right now, I'm working very closely with Dr. Riggs and a few others to plan a general overview and strategy for my project. However, I'm able to mostly design and carry out the specific experiments (which are mostly PCR reactions) on my own.
DeleteThis comment has been removed by the author.
ReplyDeleteYour project so far sounds super intriguing. It's incredibly interesting that growing bacteria such as E. Coli is similar to human cells. Do you have an explanation for why these concepts are similar? Thanks, looking forward for whats to come!
ReplyDeleteI actually asked my on-site mentor about this (he's a microbiologist by training), and he described human cells as being a lot like big, slow-growing bacteria! One major difference, though, is that human cell cultures are actually pretty susceptible to contamination unlike bacterial cultures, which are relatively easy to keep sterile.
DeleteHi Grady! I can't claim to be super knowledgeable about all the biological research you are doing, but it sounds very interesting. I'm glad to see that some of your previous research carries over, but do you think you will be able to use any other things you've learned before in your new project?
ReplyDeleteHi Mimi! The stuff I've learned in the past is actually helping me very much. The work I've done before on PCR primer design and the experience I've had with sterile technique is extremely useful in my current project.
DeleteWow, Grady! Do the different types of organisms/cells differ in appearance? (Admittedly, it's been 10 years since I've taken a biology class!) If so, I'd love to see pictures!
ReplyDeleteThis comment has been removed by the author.
ReplyDeleteHi Grady! It is nice to see that your past experiences are coming into play in your current project. Also, I really like how you explain your studies thoroughly, so that everyone can understand. You mentioned that you have not fully decided on the direction of your project, but which way do you prefer it to go? Good luck on your research!
ReplyDeleteHi Divya! The direction my project takes will depend on how quickly I can finish my qPCR assay to detect normal rearrangements. If I can do that quickly enough, I will move towards adapting that assay to identify aberrant translocation that can activate oncogenes.
DeleteHi Grady,
ReplyDeleteYour research looks very interesting and I hope fruitful. My dad died of Multiple Myeloma, so this has particular relavance to me.
Good luck in your work!
Cindy Hammond (Sarah's mom)