Episode 3: I don't know how to change the title of this blog.

So today on the meme enlightenment blog with some research on the side, we got a real classic here, Gnome Child, or Slayer. From the old Runescape days, the slayer arises into the Dank Meme mascot we all love and know today. Andy Salad has a terrible song with this Gnome Child. But on the topic of subtopics, dividing my area of inquiry is a difficult task.

This week I explored why LAC1 repressor, what does that even mean? Should I even care about it? That was basically this weekend. So LAC1 is just a protein that binds to DNA to prevent the coding of 3 proteins. Beta-galactosidase, which is the enzyme that performs the first step in lactose metabolism, making glucose and galactose. Galactoside acetyltransferase, which actually doesn't really do much in lactose metabolism (its unclear). And lactose permease transports lactose through membranes. LAC1 is called a repressor, because if it binds correctly lactose breakdown is stopped. But if the binding is off, the proteins are created and lactose is digested. The genes used for lactose utilization are negatively regulated. LAC1 binds and prevents the transcription of the genes that are used for lactose utilization. Also the protein is made of 4 subunits, and one side of the protein is a mirror of the other.

In terms of the subtopics, I don't really have a guided opinion of where to break the subtopics. In the papers, its written in english but you know its kinda not written in english with all the scientific terms so it takes forever to read through the literature. But I have vague idea. One subtopic would be the function of LAC1 and why its important. Another would be protein structure prediction models. Another would be the methods associated with testing. But I am not sure about the subtopics in my particular field. I need help here the most. For know I just looked into LAC1. I choose these topics because they are the most pertinent to the paper, why am I using this protein? what will this project be using? why look into protein structures?

I think my paper will be based around the history of folding proteins, and the significance of determining whether folding is altered by certain residue positions in LAC1. To end the blog I'll bring back the classic Gnome child in this beautiful track by Andy Salad.

https://www.youtube.com/watch?v=ldN9fNhZcsQ

Episode 2: Hopefully I'll get a meeting

 

This week on the meme team, 2EZ4RTZ is the meme of the day. But in all seriousness this week has kinda been awkward for me. On one hand I read deep into the literature of my topic and realized the real world implications of it. On the other hand I really wish I could arrange a meeting with my professor to help me confirm my research and hopefully give me some guidance. I’ll talk about the first topic first.

So I read the literature I had available to me, and I figured out the real world implications of my research. Protein folding is not an easy process and nature has created all of the most efficient working proteins. All man made proteins have only been done on a small scale and these proteins are significantly less efficient then the wild types (originals). Eventually scientists were like wtf we can’t create any proteins we gotta find a cheat for this process. Then probably some genius in the protein lab was like dude lets just take a natural protein and guide its evolution to serve a purpose that we want it too, its just 2EZ4RTZ. That genius was definitely Artour Babaev. Jokes aside they actually did that and it worked on large-scale proteins unlike the smaller scale ones from before. However Mother Nature was one step ahead of them, and the manufactured proteins were no where near as efficient as the wild types. The way they guide these proteins is by introducing mutations to change the proteins function. This is my angle, I one up the Artours and figure out whether these mutations actually significantly affect certain areas over others. However this is where topic two is gutting me.

My professor, greatest person in the world btw (I mean what professor is kind enough to let a 15 year old join her lab), has been sick all week. This means she definitely isn’t in the office taking care of her grad students. So she’s coordinating emails with them and me. We tried to set up this Saturday morning but it didn’t work out, so I sent her an email about her second available time this Monday afternoon. She is usually godspeed with anything I do, so this illness is pretty serious. I know the general area of research, hell I even know how to do my primary research with the ASU Supercomputer, but I really need the help with my research topic and why LAC1 and other questions. Also I kind of need her original research paper, the paper closest to my topic. It’s kinda like not free online. But maybe she even has an entirely different topic of research ready for me to dive into (in the protein folding field of course).

So to recap, I figured out real world applications and the surrounding field, but I really need to organize this meeting with my professor. My plan moving forward is look into the research on my own and organize the meeting. In terms of struggling, the field is pretty specific with some studies in academic conversation with each other, so I plan to expand my search area into protein folding in general to set up the significance of my future research. So like fingers crossed this meeting happens SOON.

Episode 1: Starting in the middle of nowhere and R.I.P. Harambe

Unlike AP Seminar from last year, this year in AP Research I intend to research something that truly interests me. So my goal for the class is pretty simple: Leave with a paper and presentation in a field that I like and be happy when I'm inevitably grinding out the literature review or presentation at 1am. Being happy is a pretty vague goal, but I want the class to feel like it’s a part time job as a writer. So it still feels like work, but I enjoy it at the same time.

My starting point in this class is paying respects to Harambe, and then finding a suitable topic. A suitable topic for me personally, is one that is backed by tons of specific literature that I can draw from. But I can’t just have the topic of American history because it is way too broad. At the same time, researching the physics of the bullet that killed Harambe the gorilla is probably too specific. On top of the so-called Goldilocks compromise, there needs to be an academic conversation surrounding the topic so that I can contribute to the field and actually make a contribution. Authors and contributors to the topic must have supporters and dissenters who engage with each other. I also have to feel like my research is significant in someway, again tied to my interest in the topic.

My process of finding a topic is kinda messed up, because I already have my research area and research methods from day 1. Due to aggressive under scheduling in tenth grade, I have an opportunity with an ASU professor to expand on her research. And my opportunity really seems safe, likely, and enjoyable. However, every plan needs a plan B (Harambe wasn’t prepared with a plan B). My secondary plan is to investigate some type of corruption. Previously I really enjoyed exposing the flaws of the pharmaceutical industry, Maryland gambling laws, and North Dakotan fracking laws. 3 days in and I have managed to grasp the academic conversation surrounding my plan A. I still haven’t described my plan A yet for some reason so here it goes: when mutations occur at so called functional sites, the protein folding is significantly altered, but other studies are showing that it doesn’t matter where the mutation occurs because they all result in defects in the protein. My professor, Dr. Ozkan, has already disagreed with them on a special protein. My gig is to see if the LAC1 protein is significantly affected by functional site mutations. The LAC1 protein is linked to lactose intolerance so there is a significant impact to the research at hand for me.

Plan B isn’t really developed, so I better look into that this week (or else RIP Harambe and Ashwath). Thanks for tuning into Episode 1 of Ashwath’s Journey to the center of AP Research. Tune in next week to see if Ashwath changes his meme theme from Harambe to something else.

R.I.P. Harambe