Episode 19: Finishing like a Spartan

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.

Episode 18: Out of the trenches but still fighting.

Alright folks, the plan went from "I'll be alright" to "OH MY GOD I MAY NOT FINISH" back to "I'll be alright". 

When you start the next step weeks earlier

I'm going to provide a quick crash course on what I've been doing. In order to write my paper I need a chimera of a protein to be 1) Refined by a computer 2) Refined manually 3) Simulated in MD and 4) DFI analyzed. Previously I expected the first step of my analysis to be complete around March 6th, which would have essentially screwed me over in timeline, but it turns out I don't need all 60,000 structures (which would have set me 2 weeks back). Instead I only need around 10,000 to carry on with my analysis.

So this week I focused on selecting the correct structures from step 1. I got the "scoring" of the structures back from the refinement and learned which structures were in the lowest energy state. The whole process of scoring took two days and a ton of troubleshooting, but I eventually got the data back. After selecting the data, I decided to create a fail safe incase the zam.py runs take too long. I will take the 10 or so structures to manual refinement to create the "ultimate chimera for steps 3 and 4, but just incase step 2 takes too long I will send minimized chimera 12 straight to step 3 to ensure that I have DFI data of chimeras. Friday was one crazy day. I came in at 10 to analyze the scoring data with Dr. Ozkan, we realized that the scoring algorithm was wrong. So John and I troubleshooted it and managed to get it to run. Then I manually extracted all the data from the terminals with the good old copy and paste. I had to listen to Kpop for about 2 and a half hours but I powered through it. Then at around 5pm, I started the GPU trials with the minimized chimera 12. And it ran smoothly until yesterday. I'll have to go back in and fix it on Monday.

Overall, I have step 1 complete and I will be able to secure chimeras in time for the final paper.

A protein model without conservation colors

My "data analysis" is essentially in step 4. I will take the structures and run them through DFI to learn about the interactions between non conserved and conserved positions within proteins. The timeline for this is one day, in fact I think it only takes around 2 hours. But the real issue is interpreting the results. I will obtain two different representations. The first is a graph with all 600 amino acids on the x axis and the DFI score on the y axis. By placing the chimera and the original side by side I will be able to pick out trends from the analysis. The second is a 3D model with blue and red highlights for conserved and non conserved regions. It will be easy compare between the original and the chimera.

So basically the raw numbers will give me the graphs to easily identify how the non conserved and conserved regions are moving within the original and chimera proteins.

The meme of the week on the other hand is Trash Doves, a notable set of Facebook stickers. It rose to fame with one of the birds thrashing their heads up and down.

Episode 17: The Hunger Games: A Search for Data

Hey Guys, welcome back to the meme blog. Let's start off with the classic "I used to ..., then I took an Arrow to the knee." It's a classic from Skyrim. Also download the app houseparty, It's lit.

But let's get right into the research. It was a rather exciting week, but there seems to be a wrench in my plans. Usually my ASU days start off with dropping my sister off at school at 7:30am. Then I start the half hour drive to Tempe, park in an Indian temple, then take a bus to PSF 3rd floor with Dr. Ozkan.

A great lecture with Ozkan

On Tuesday, I drove to the lab and attended a lecture 10:30am with Professor Ozkan. Then I met with her at 12pm. The professor who I talked about in my literature review from Kansas, actually sent the chimeras that I would analyze. It's super cool to know that you are actually contributing to the field and working with professors across the country. But a part of the trial that I had not anticipated occurred. I actually have to refine the chimera, before I can start running my computational analyses on protein folding. So I started pure Lac1 and Lac1 mutants in MD and started refining the Chimera.

Tushar on the left, Paul with the Fallout poster, and I usually work on the right

On Wednesday, I met my boi Paul, who was super sick with chest congestion, at 9:30am. He taught me how to run the computational simulations. Then I met with my other boi John at around 1, her taught me how to perform the chimera refinement. The file was broken, so we fixed it in Modloop. It was a relatively productive day, and I went home feeling pretty good. But then I checked the trials at home, and the problems started rolling in.

I came in Thursday to fix the error that occurred the previous night, after about 4 hours of surfing the Linux system, we found an error in my bash.rc directory, with some screwed up old commands. After fixing those pathways, I went home again. Only to realize that I had another error.

When the analysis fails on you 3 times

Then on Friday, I came to the lab to fix the new problem. Amber (one of the computer programs) was not recognizing atoms that were too far apart from each other. We fixed that problem, and finally it seems like the trials can start running smoothly.

My main concern so far is the timeline. If the trials drag out longer than I expect for the chimeras, I may have to switch to only analyzing Lac1 and its mutants. I can still look at conserved and non-conserved regions with the specific mutations, but I will miss out on the comparison to the chimera. In terms of other things, I have finally managed to see some official final DFI representations and models. I'll talk with Dr. Ozkan to better understand these representations.

Till next week,
Ashwath V.

Episode 16: Enter the darkness of Tri 3

Wassup my boys, the Superbowl just ended and Tom Brady won another trophy. So basically I hate the Patriots again this year. What really triggers me is that Michael Floyd was on that team, so he got the ring for basically doing nothing. Personally, the second trimester has just finished at BASIS. This means that I no longer go to school, but I will still have to complete my AP Research project in trimester 3. The blog will now pivot from mere topic discussions, and instead enter into a progress log, mirroring what a normal Senior Research Project would look like. A quick meme of the day for everyone. Cash Me Ousside / How Bow Dah is line spoken by a 13 year old girl with a heavy accent on Dr. Phil. The meme blew up on the Internet shortly afterwards.

Since I haven't had the opportunity to go to the lab yet (I will go to ASU on Monday), I'll talk about my progress on the lit review and methods this past week. I altered my literature review in a few ways. First, I cut out many of the repetitions and superfluous information present in the section. Often there was restatement of lines two or three times in the same paragraph. And I failed to link the purpose of each section to the paper's meaning. But one of the major flaws was separating the technicalities from their importance. I placed the two topics into separate paragraphs and broke the flow and understanding of the paper. Another flaw in my paper was my inability to focus on the static vs dynamic nature of proteins in techniques section of the paper. I had clouded my vision with the analysis techniques, losing sight of the more important goal. After my gap was thoroughly improved a few weeks ago, I have slowly made good progress on my paper.

In terms of my future plans, I need to hit the ground running this week. My greatest anxiety with my research is the availability of my advisors. If I cannot get a hold of them, my research will not be able to progress. Hopefully, I will be able to get in contact with Dr. Ozkan this week. The timeline will be on track if I manage to at least start the REMD trials this week. Since I can run these things simultaneously, I merely aiming to set up the trials for this week.

See you next week,
Ashwath V.