Episode 26: Reflecting upon the finale

The pat week was a wild ride. After giving another practice presentation on Monday, submitting my final paper on Thursday, and delivering my final presentation on Friday, I completed AP Research, and the AP Capstone project. Here's a link to my slides. And here's a link to my paper. I can't thank my friends and family enough for showing up during the presentation. There was a lot pressure going into my presentation, but I managed to pull through. I crushed my presentation. Even the CEO of BASIS praised me for my presentation.

Me shortly after giving my presentation, greeting GG and Sergio

I'd like to shout out my 2 mentors, Mrs. Haag and Dr. Ozkan. Mrs. Haag guided me through the process and kept me on track when I'd get behind or encounter errors. Every week something went wrong, I'd be extremely anxious. And when I went in for my meetings, she'd find a way to fix the error or help me rearrange my schedule to ease that anxiety. My expert advisor, Dr. Ozkan, helped understand and grasp the concepts of protein folding, and conserved regions. Without her, completing the project would be impossible. Also a mini shout out to my grad student mentors, who helped me iron out the computational errors in my project.

Shout out to my mentors

The overall lesson I've learned from research is that planning is king. A theme common across AP Seminar and AP Research is the use of outlines. In other classes whenever a large paper was due, the responsibility to plan and outline the paper was on us. That's not a bad thing because in college the responsibility will lie with the student, but I never really grasped proper outlining techniques. After taking the AP Capstone program, I finally understand how to create a proper outline. We learned to integrate sources and structure our paper before actually writing it. The actual creation and writing of the paper is not as important as the argument and sources backing the paper.

As a debater and proficient public speaker, I thought communicating my research would be an easy task. But Mrs. Haag can tell you that the early drafts of my paper assumed too much knowledge and probably didn't make much sense to the average reader. I learned that providing background on topics as technical as protein folding is integral to the reader's understanding. Given my previous experience in communication, I purposely chose a highly technical topic to challenge myself. Now I have the groundwork laid down in case I have to pitch anything out of the box to someone in the future.

Anyone reading my first draft

But don't let the previous experience in debate fool you, my presentation skills may have been on par, but my slides and script were not. After 4 Seminar presentations and a giant Research presentation, I have finally managed to create decent presentations. With minimal words on the slides and lots of pictures I learned how to convey my message to the audience.

The most important take away for me is to be confident. If anyone told me that I'd be writing a 30 page paper in Research two years ago, I'd respond with I am not taking that class. But I realized that I can write academic papers and I am capable of pursuing my interests.

Peace out

Episode 25: Finalizing Perfection

Hi guys,
I'm back and the journey almost over. I took my last mock with the sole purpose of giving my AP Human Geography teacher more spending cash for his honeymoon this summer. If I get a 5 on the AP, I can say that his lunch in Barbados was on me. This past week I gave two practice presentations.

When Mrs. Haag saw my discussion slides

The first practice presentation was surprisingly good. I came in at 7am to practice my script for an hour or two (not because I had to drop my sister off at 7am). Personally, I felt the presentation was a bit shaky and I was not completely in control of my script. The slides were a bit rough (clip art of gears and word clouds were not bright decisions). But Mrs. Haag said I did a decent job of conveying the technicalities and intricacies of my complex work in an engaging way. In addition, my hypothesis was unclear as I did not properly explain that my paper was exploratory in nature. The big pitfall of my presentation was the discussion section, I needed to link it back to my hypothesis to properly finish the presentation. I needed to familiarize myself with the slides and overhaul the discussion section.

The second presentation that occurred on Saturday gave me more insight into the overall significance and following of my paper. I realized that I needed to frame the paper in terms of flexibility relating to function for the audience to understand the discussion section. Also there were still some dodgy slides in my second presentation. I still left the word clouds in there for some reason, and the centering on some slides were awful. I think I had poor eyesight when creating those slides.

Overall, I feel that I have fixed the problems associated with slides. All my slides are animated and simple to follow,  while also conveying a decent amount of information. On the other hand, I plan to introduce flexibility relating to function much earlier in the presentation to assist the audience. Additionally, my discussion section has been cleaned up. Unfortunately, I have quick turnaround and I give my final practice presentation to Mrs. Haag on Monday. I plan to continue practicing and give my presentation to a friend during the remainder of the week.

Till next week,
Ashwath V.

P.S. Don't beep beep like a sheep.

Episode 24: 1 man, 1 paper, 1 presentation

The college season is over and I have more time to stress out about AP Research now. The past few days were pretty rough, but bouncing back is a sign of resilience so here I go. Also I got on the front page of the BASIS August Gazette for April Fool's (ps Rick and Morty Season 3 Episode 1 was leaked April Fools (mini meme of the week))

Me heading into the final two weeks

Anyway the assignment for this week is to discuss ideal PowerPoints. The ideal PowerPoint will guide the listener and clarify abstract concepts with simple slides. The ideal presenter will interact with those slides and explain things concisely. The slides themselves should have a very few amount of words, clear diagrams, and should not distract the reader. In fact the presenter and presentation must be in sync to a T. If there is a slide that is not interacted with, it's useless. My slides have come a long way to the point they are now. Certain slides have reached their perfection, while others are clearly lacking. Currently, I'd say I have 2:1 ratio of perfect to not so perfect slides. I feel really confident about my graph slide because I professionally animated that one.

In comparison to my AP Seminar style presentations, the research presentation focuses on the primary research aspect a lot more than the lit review. As such, fewer sources are discussed in AP Research. The context and purpose of the AP Research style are centered around your primary research, rather than around your argument like AP Seminar. Students are forced to engage with their hands on research.

My rehearsal plan includes memorizing the topics of each slide, and developing transitions to memorize as well, but the rest will be conversational. My strat will be taking those points in my mind and discuss my research with the crowd. Practicing is something I do alone usually because I need to be comfortable with the presentation before I recite it to someone else. I'll do it daily (probably like 2 sessions) before I have it nailed down. Then my next step is to do it blindfolded, or something ridiculous like that to ease my nerves and solidify my knowledge on the topic. To top it all off I'll prob join a research gang prep session and practice my presentation with the boys before I ship it off to the April 14th deadline.

Till next week,
Ashwath

Episode 23: Scripting and Sliding

It's been an exciting week, of research. The editing got intense this week with revised papers. Everyone had to go the extra mile to give good feedback. Sad to see some teams NCAA bracket, Calais Campbell is gone from the Cardinals. Also the presentation is in 2 weeks, so that's creeping up on us.

The meme of the week is an old one, Supa Hot Fire. It is a character in a series of satrical YouTube videos, parodying battle rap. The videos consist of rapper Supa Hot Fire battling multiple rappers. The videos revolve around the crowd biasing around Supa Hot, overreacting to the extreme when he finishes his verse. Here's an example.

This week we were tasked with slides and scripts, and understanding the presentation rubric.

The first rubric row talks about the research question and the reasoning behind it. Being worth only 3, it is not a hard row to knock out of the park. I feel like my script adequately responded to this row. Row two is about the implications and limitations of my results. By conveying my results and discussing significance, implications, and limitations, I can attain the 6 points here. It is important to notice that the lit review has very little importance in this section, and that my focus should be on the methods and results.

The third row connects the hypothesis from the lit review to the conclusion arrived by the paper. I need to explain what I thought at first, what I arrived at in the conclusion, and what from my findings confirmed the hypothesis or not. Using Swint-Kruse as my hypothesis and initial thoughts will help me out in the presentation. I did a decent job of row 3 when arriving at my question and discussion. At a meager 3 points the row should not be difficult to achieve.

Now row four is my battle ground. The ability to present, speaking style, and presentation tools give this row a 6 point evaluation. As a veteran debater and public speaker, running my ideas past in a confident presentable way is not very difficult. My slides are simple and easy to understand.

I placed a lot of confidence in my ability to explain the graphs. It will be a lot easy to point and interact with tables and graphs as opposed to explaining things in a painstaking manner in my paper.

Till next week,

Ashwath V.

Episode 22: Revisiting a Paper

After my last MUN conference at ASU, I actually managed to win best delegate or first place on my committee PEMEX as the Undersecretary of Hydrocarbons for the Ministry of Energy. It was a lot of fun, we even took over the Mexican government. But I still don't know what college I'm going to, and that's not a fun reality to be living in.

The person I was representing

I am currently editing my paper, and the discussion section seems to be the thorn in my side (more like a gaping hole in my torso). The general feedback from my 2 peers was that my literature review provided significance and a decent background on my paper, but there needs to be a slight cleaning up of connections between using Lac1, folding mechanisms, and the actual research question. In addition I need to justify my gap more effectively. The methods section was relatively simple, there's only one real problem: technical terms. Looking back at it, I have defined only half the terms, and the terms I do define are often defined late. The results section was a worse version of this, as I basically hit the reader with a ton of technical jargon out of the gate. The visualization description was highly subjective, and I need to figure out how to phrase it in a more concrete way. The discussion interpreted the results, and completely forgot about the literature review, significance, and basically anything the reader would care about. I wrote it as if I was just publishing this for my peers in the biophysics field. I need to link the discussion to the lit review and tie the whole paper together.

As stated above, my strengths lie in the lit review and the results sections, and my weaknesses are technical terms, methods, and discussion. The main thing I'd like readers to search for is technical unclear terms, as I have lived in this paper for months and sometimes cannot convey terms simply.

The presentation for me should be interesting because I know everything about this paper, and frankly I explain things better while speaking over writing. My figures are exciting to discuss because I can physically point at them and identify regions etc... What I am nervous about is lapsing into technical jargon. My paper already uses a lot of diagrams, and it will be simpler to explain these in the presentation. 15 minutes will be a challenge, but I can always work around a time limit, and as technical as my project sounds, compared to other projects the amount of terms is smaller and more manageable.

The meme of this week is 322. 322 is term representing throwing a game. It originates from a Dota 2 match where professional player solo threw the game after making a bet against himself. The game score ended 3-22.

Episode 21: GRAPHS ARE IN

3D Models of the Chimera and 1efa

It's been a weird week, but I got the wheels back on the bus. I finally got my data back and my analysis back. The graphs are in and so are the structures. This week I was tasked with completing the paper! However, I only just got the results back this Sunday! I also have an extremely limited knowledge of what any of the DFI regions mean! Put those three things together and we now realize that I am very far behind. But if there's one thing I know about myself, the work will be done.

The comparison based on solely DFI values

The name of the game is finish the results and discussion section in time for peer editing this Wednesday. I am going to meet with Professor Ozkan this Monday. I will comprehend what the covariance matrix is, what it did, and how I got this graph (I have a general understanding, but if there was ever a time to clear up misunderstandings with the one person who knows it best, now would be that time). The second step is the discussion. I am not exactly a graduate student majoring in Physics, so identifying the specific interactions between amino acids will be difficult for me (I can generalize and explain them). Dr. Ozkan and I will go through the protein and basically identify the "hooks" and "nonconserved" structures. The other papers I have looked at are highly specific and very brief in their discussion. I will try to expand upon that style and interpret my results.

A brief look at my data shows that both the chimera is lower in DFI when compared with Lac1 at the DNA binding sequences (indicating less flexibility) and more flexible in the nonconserved regions of the body. In general it seems that the body of the protein is affected by the changing of nonconserved regions.

Overall, I feel rather good about the direction my paper is going in. Hopefully the paper is completed by the middle of this week for editing. The strengths of my paper lie in the literature review and my baby birding (editing). The biggest weakness on the other hand is my technical language and my unwritten sections.

The meme of the week is Scott Sterling, an unfortunate soccer player who gets pegged in the face multiple times. He does block all the penalties though. Check it out here.

Episode 20: Discussion and MUN

This week I attended a Model United Nations conference where I was Venezuela working with the Security Council on issues such as the South China Sea and Syria. It was a double team event, so I had a partner. His name was Amaan. I basically did all the talking, and Amaan did the writing.

When you hate the errors in CPUs holding you back

In terms of my research,  I am still waiting on my min12 results. The final step is just not coming together for whatever reason. Hopefully I can get it fixed in a timely manner. In preparation of a late arrival, I will write a results section based on the Lac1 data I have prepared. JUST KIDDING I JUST CHECKED IT AND I HAVE THE RESULTS BACK!!!!!!!!!!!!!!!

For the topic of this blog post, I was tasked with analyzing the discussion sections of my discipline. The three papers I decided to look at were 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 delved into the evidence by analyzing the flexibility of the linker region of Lac1. It talked about locking, binding affinity, and overall 3D descriptions. Then the writers moved into more theoretical extrapolations about reverse evolution. It seems to analyze the effects of their trials to each of the 3 regions of Lac1. It may be easier to explain if I walk through all 3 sections of a chimera in a similar fashion. But even after that it talks about future applications like Protein Engineering and in Vivo and in Vitro Functions. These really hook the reader, so it will be useful to add the analysis in.

The second paper was very focused on the use of DFI. The discussion was heavily linked to the DFI evaluations. I think I should try to combine the DFI analysis from the second paper with the extrapolations from the first.

Finally the third paper was extraordinarily technical in its discussions. Similarly to paper one, it did look into several different extrapolations. But the literature was so technical that the average reader would get lost in trying to understand the reading.

So my discussion section will focus on the DFI for each of the three protein regions first with 3D protein descriptions, then it will delve into the implications for the analysis.

And before I leave, let me hit you with the To Be Continued meme. It basically stops a situation right and the climax, leaving you wanting more. The origin is from the Jojo's Bizarre adventure cliffhangers. Check a compilation out here.

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.

Episode 15: DJ Khaled

Welcome back and enjoy the memes boys. Let's start off with an in depth analysis of DJ Khaled and his glorious sayings. The famous producer has been called out for his hip memes and in depth culture. One of his famous sayings is Anotha One. He reminds people that he is here to stay and he will always drop fire tracks as long as he is alive. Lion is another gem. It represents his commitment to being number 1 and being ferocious. Of course his famous saying Major Key is his most prominent saying. He refers to his most important things with Major Key alert. And if you have heard any song with DJ Khaled, you better believe he's screaming DJ KHALED.

When you want more trials.

Back to the research project. In continuation from last week, I have in fact created a few chimeras for the protein I plan to analyze in February. Basically I searched more databases in an attempt to fin proper alternative sequences to code like Galactose. have collected the Lac1 PDB files and trimmed them into usable sequences. I probably will still have to rely on Paul, buff dope grad student (did I mention he's cool?) to get me the other chimera sequences as I have only found the ones normally available online. Finding these sequences are a still difficult.

Also I have determined that there is a high possibility that I am able to run trials simultaneously. So my analysis should complete at the same time in the process. The only things holding me back are computer errors, and the trials should be completed relatively easily. The timeline is still on pace, and I will probably have the samples to fire off by February 6th. Since I won't really fall behind on the timeline, I need to hit the ground running so I don't get cocky.

In terms of the majority of my work this week, I have decided to reorganize the literature review and align it in a more understandable way. The reorganization effort was difficult, but necessary for the future success of the project. The conservation section was moved from the structure of proteins to the computer analysis section, allowing for a more fluid flow of information between topics.

The fun part of the analysis is learning how to perform DFI trials and extracting the data. So I can't wait to get cracking on that. The vision is clear and I am ready to wreck this project. As DJ Khaled said, We the Best. And I am in the best state for this project. I am truly a LIONNNNNNNNN.

Episode 14: Ready for take off

He is pretty hot

Hi guys welcome back to a more standard blog post. To start off we will take a look at the meme of the week: Salt Bae. Salt Bae has taken the internet by storm, as Nusret Gökçe uploaded a video of himself carving a steak and sprinkling salt onto the meat. The video from Instagram blew up within 2 days, and currently Salt Bae is definitely the meme of 2017 for now.

Now in terms of my research, I have only barely begun. I have collected the Lac1 PDB files and trimmed them into usable sequences. However, I am having trouble finding the PDB files of Galactose, Fructose and other proteins to compare the analysis off of. Dr. Ozkan does have a database for obtaining such sequences, but neither of us can work the terrible interface for now. My boy Paul should be able to help me with that. Finding these sequences are a little bit tougher than I anticipated, but my trials should be rather robust and efficient. Of course I haven't gotten into the meat of the research yet.

The measures I can take to ensure success in my methods is reliant upon my efficiency communicating with Dr. Ozkan and her graduate students and the computer's errors. In the past, there have been days where I have been unable to complete certain tasks due to a lack of communication between the lab team and myself. I will have to be on top of my game to ensure that my analysis proceeds in a timely manner. Hopefully I will have the samples ready for trial before I leave school. Ideally, they should be complete on February 6th.  After that point, I must learn how to run the trials and the DFI analysis, which will probably take up about half of my first week on site. Then running the trials and performing the analysis should conservatively take two to three weeks. Which means I will be finished with my trials before March begins.

If I ever fall behind on time, I can always limit the number of samples I decide to analyze. At the minimum I will do 2 new mutated samples, but the point of the analysis is to understand the dynamics changes within the protein. One sample is more than enough. But for validity checks and different changes more samples are necessary. I plan to pull off 4-6 samples for now, but I can cut back if I need to.

I am not able to run the trials remotely at this point in time because I need mentorship to learn about running the DFI trials. Luckily I have received advice on how to prepare my samples, and that is what I am to do for now.

Episode 13: We have the Number ONE Methods

When you see that extra long Ashwath Blog Post

Before I start my blog today, I want to explicate the slight change to my methods. Previously, the regions that I selected for analysis were chosen based on so called "proven mutations." I confused myself on the selection of the regions.

First of all here is here is the breakdown. When something evolves, normally you wouldn't expect the vestigial structures to matter much in everyday function. For example, if the genetic code of your tail bone was altered, you would not expect it to change the function of your overall body because your tail bone is not important to your structure (technical term: non-conserved). In a protein, a non conserved region is usually identified by a lack of change in structure. In general, these non conserved areas have very little effect on the structure of the molecule. If I had a red Lego brick tower, and I swapped one of the red bricks with a yellow one. You would expect that the tower would still stand because all I did was swap a brick with a similar one. That is what has been assumed in the protein research field. To put it in the context, Lac 1 is made of 3 regions (I'll name and explicate them in a revised version of my methods), 2 of these regions are conserved but the third region is non-conserved. If I swapped the third region with a code similar in structure, one would expect that the new region would not change the function of the protein because the structure is not changed. However, new research from Professor Swint-Kruse, has shown that these non-conserved regions actually matter in the function of the molecule, even if they do not affect the structure. But Professor Swint-Kruse only identified this discrepancy, she did not provide an analysis or explanation for her findings. That's where the gap is. I will use Lac1, the protein that she analyzed, and replicate her trials and protein models. But I will use the DFI analysis to explain the change in function by analyzing the dynamics of the protein. I will be looking at the interactions between each amino acid, looking further beyond the normal structural and functional analysis. The mutations I will use will maintain the conserved parts of Lac1, while changing the non-conserved structures to structurally similar structures from like Galactose1 and Fructose1 in order to see the differences in dynamic interactions.

Akash when he hears the instruction to close the door

Let me explain it again with another analogy. Mrs. Haag is telling me to close the door, so I get up and close the door. Now we swap me with Akash, who speaks a foreign language. Structurally, Akash and I are similar, so we would expect Akash to close the door. But Akash can't close the door because he can't understand English. He can't interact with Mrs. Haag properly, so the function of closing the door is impeded. In proteins, I want to find the why for the disfunction. Or in this case, find out that Akash, though structurally similar, cannot understand English.


The biggest weaknesses in my methods are 1. Explication, 2. Purpose of the Paper, and 3. DFI-analysis. As the large explanation above shows, I must ensure that all parts of my methods are understandable and justified. So far I have only talked about the side-benefits of my analysis, but I was finally able to put together the final picture shown above. Hopefully, I have explained it thoroughly enough. i will add it to my methods and lit review as necessary (not huge changes, but clarifies the project overall). Honestly, its almost like my excitement about my project has been renewed because I discovered a new purpose to my research, so I'm happy to delve into my project once again! The selection and preparation of my materials are solid. The biggest limiting factor is DFI-analysis. In the papers I have read, I have only been able to see the explanation of DFI and the results from DFI. I currently have not been able to interact with the DFI program to thoroughly understand and explain its inter-workings. This is the biggest unfixable problem that can only be solved by running the trials myself.

The main concern for me is my explication of the technical terms. I double-checked with Mrs. Haag and made sure that everything vague or assumed was explained in the methodology. But Mrs. Haag has been working with me on my project for a while now, so there might be assumed knowledge. This is one of the main weaknesses of my methods.

Overall, I am combining the DFI method from Dr. Ozkan, with an investigation of Lac1 first found by Professor Swint-Kruse. The strength of the scientific nature of the methods are certainly there, but I believe that my explanation is the key to success.

And of course I have not forgotten the meme of the week boys. It's We are Number One. This internet sensation has not only raised enough money to give a man cancer treatment, but is also light hearted and genuinely funny. The title of the videos found start with We are Number One BUT ... Then something is changed in the video.

Here is the Original:
https://www.youtube.com/watch?v=PfYnvDL0Qcw

Here is one of my favorite meme versions: We are number one but "we are number one" is replaced with Gordon Ramsay insults

https://www.youtube.com/watch?v=qEkH9BF0sKw