After grueling 8.5 mile obstacle course fiasco, where my friend Akash cramped up on mile 4 and still dragged himself across the finish line. The Spartan Super was a lot of fun, but it appears that I am no longer able to move and there's a lot of pain. But my research is chugging along just fine.
 |
| Race Crew post Spartan Super |
There were a few setbacks, but nothing major. The computer errors took a bit of time to fix and the data should be back within in this week. Then we can get into the results and discussion section. This week I was tasked with analyzing the results and discussion sections of my discipline. Luckily, thanks to our methods assignment, I won't have to really search for new papers. The three papers I decided to look at are Subdividing Repressor Function: DNA Binding Affinity, Selectivity, and Allostery
Can Be Altered by Amino Acid Substitution of Nonconserved Residues in a
LacI/GalR Homologue,
The Role of Conformational Dynamics and Allostery in the Disease
Development of Human Ferritin, and Rheostats and Toggle Switches for Modulating Protein Function. The first paper is highly technical. The second is dealing with Lac1 and its chimeras (and is the paper that gives a gap for my lit review). The third is dealing with DFI analyses.
The biggest theme across all three papers is a lack of raw data. Obviously, a ton of raw numbers not only confuses the reader but also does not contribute to the significance of the paper in anyway. Instead, the papers focus on providing interpretations. The most common representations are graphs and 3D protein models. The combined representations clear up any confusion and the researcher can focus on explaining the graphs instead of getting bogged down by the statistics. The papers explain the important features of the graph and what they mean in context of the literature review. For example, the third paper explains the important regions of DFI analysis. They then use the context to analyze the region structures and understand why the mutations caused diseases in those locations.
 |
| DFI graph complete with 3D protein models |
My results section is basically going to mirror the third paper's graphs. I will use the same DFI graphs and protein structures. And I will overlay the two sets of data on the same graph to make it easier to compare between the original Lac1 and the chimera Lac1. I expect to then explain how the conserved and nonconserved regions are behaving in terms of their function and dynamic flexibility (what DFI measures). I imagine the results section will go relatively well.
And before I leave, I will give the shooting star meme. It is essentially a photoshop of someone falling being thrown into space with some pretty dank music. Check out a compilation here.
Hey Ashwath!
ReplyDeleteGood job on finishing the Spartan Race! I'm sure the wait for Akash was as excruciating as the race itself ... lol jk.
I'm glad that you have been working through the errors in your code (COMP BIO) and getting some really nice results. Having previous papers in your lab group (I assume the one you said you're modeling your results after is one of Ozkan's papers) is really nice because you have a kind of standard to go off of, especially for figures.
I understand that graphical comparisons are a great tool, and using models of protein folding helps explain your results and connect the "comp" with the "bio," but I would make sure to talk about and remember the data that underlies all of those. It is often a more rigorous way of showing comparisons, and the most understanding is conferred by explaining these measurements and results straight from your model, if you think it's possible.
My question to you is what does a DFI plot show? Make sure you explain what the axes mean, and connect them to the underlying data both in your paper and blog so we can follow along.
I'm so shook by that meme lol.
Good stuff,
Yash
(206)
Ashwath,
ReplyDeleteReally?!? Thanks for wasting 8 minutes of my life with that video (although I was at fault for clicking that link and then sitting through the whole video). In order to make this comment as effective as possible, I will be using the three things that you relate to the most: K-pop, anime, and memes.
Right now, you are kind of like Leeroy Jenkins. You are going into your the dungeon (results section) with only a faint idea of what you are going to do. I think this is because you know your research so well, that it is difficult for you to convey it to your reader, but you should be looking beyond just adding graphs.
It is definitely useful to have graphs in there, but graphs can not be your only option. Like Kagura and Shinpachi, your graphs should be supporting characters (supplements), or maybe even the Sadaharu—mascot— to your Gintoki/main character (results). What I am trying to say is that you should put all your data into words before you put it into your graphs.
Overall, I can you have come pretty far and your research is...drop the beat...FANTASTIC BABY. So don’t be a BAD BOY and keep up the good work so you can finish senior year with a BIG BANG (BANG BANG).
Ashwath,
ReplyDeleteI definitely should have drank more water, but oh well. At least you have the monkey bar scene of me screaming in your head now.
Anyways, I think it's great that you're working on rebuilding your results section right now from the Ozkan paper you have been using as a reference. It would definitely be a good idea to mimic the style of the results section that that paper uses in order to convey your own results to the reader. However, I think it's also really important to have a lot more visual aids in this research assignment than any others because a random person who doesn't know much about your project or field could be reading your research paper.
I think it's really important for you to create more graphical representations of your data, and as soon as you have that planned out, you should be good.
Other than than, I agree with Yash's comments. What does a DFI analysis show? Make sure you clarify that in your own results section because you definitely don't want the reader to be confused.
Peace,
Akash
Ashwath -- while you've conveyed that you'll rely primarily on graphs, I'm still not seeing how the results of all of the different pieces of your research are going to be represented, particularly in relation to each other. In other words, how are you going to order the different parts of your results and how will you show the relationship between those different parts?
ReplyDelete