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