Here is the link to my presentation.

https://drive.google.com/open?id=0B7vpDX2wvVN_ekVIZm1hOW8zbVk

Week 9

This entire week was spent cataloging the runs on the wes machines. This basically entailed sitting in front of computers all day typing in data into excel sheets. And yes, it was just as boring as it sounds. So instead of boring you all with the details of my wonderful week, I shall share with you pictures of my lab and what I do.

The workspace

This is where my supervisors primarily work at. As you can see, there is a lot of equipment in the picture. However, I do not know what most of it is used for. I only work with the stuff immediately surrounding the blue pad in the front of the picture.

Close up of workspace and equipment

Pretty neat, isn't it. The only thing missing from the picture is a tray full of ice and samples, because my supervisor would yell at me for pulling those out just for a picture.

full lab bench

Here's a picture of the entire lab bench. Despite what it looks like, we do not use the space for hopscotch. At least most of the time.

The Freezer

Open Freezer

Here is the infamous freezer that I always complain about. I'm surprised that I haven't lost my fingers to hypothermia after all of the time that my hands have spent in the freezer. Well, it's not that cold, but my fingers are numb after a full day in there. And that's just about everything in the lab, that I use at least.

Week 8

This week, just like last week, turned out to be quite dull and uneventful due to my project being halted temporarily while the problems with the wes machine are dealt with.

On Tuesday, I helped my supervisors Sarah and Bret run a plate that had various samples from different regions, using various antibodies and biological markers, to try and diagnose what is causing the issue with the wes. After we ran the plate, I helped with some paper organization and lab clean up.

On Wednesday, I came into work and realized that we had used an expired plate for the previous day's run, so we had to rerun the plate. After that, I helped with more paperwork before calling it a day.

On Thursday, we again reviewed an article during the lab meeting, and I watched as all of the others critiqued the paper very thoroughly. After the lab meeting, I shadowed other researchers and generally helped around the lab.

On Friday, I spent the morning talking with two researchers about building 1/6 scale World War II R/C tanks until Sarah came in. I then shadowed other researchers for the remainder of the day, as well as cleaning up the lab and making it tidy.

Week 7

This week, for once, was very uneventful.

The problems with the antibodies still hadn't been resolved, so I didn't have much to do on Monday. In the morning, I worked on sorting out the samples for the hippocampus region so that we would know where they were when we got to that point. After that, I went to lunch and worked on my study design for the rest of  the day.

On Tuesday, I spent the entire day working on my study design because the problems with the wes had still not been fixed, and I could do nothing to help because many of the problems were occurring outside of my control.

On Wednesday, after waking up at 5:30 as usual to get to the Arizona Biomedical Collaborative at 7:30 as usual, my supervisor Sarah told me that there was absolutely nothing to do in the lab that day, so she said that I could go home early. At least I got to take a long nap after I got home.

On Thursday, during our weekly lab meeting, we discussed changes in the NIH's standards on data reporting. The other lab member's gave me valuable tips on how to carefully take notes on everything that I do and on how to properly report my data. The remainder of the day was spent cleaning all of the excess ice that was built up in the freezers. Hopefully the problems with the wes will be sorted out by next week.

Week 6

This week, like most of the previous weeks, started out normally, only to later spiral into chaos.

On Monday, I became the most efficient worker and my supervisor, Caitlin, and I were able to quickly finish four plates, which is the maximum that we can fulfill in one day. We were both really excited because we had just finished half of the work for that entire section of the brain samples that we needed to test. The next day, however, we quickly realized that things were not going as well as we thought.

On Tuesday, my main supervisor, Sarah, came in, saw our results, and very quickly deemed that all of our tests had been messed up, and that we had to redo them. It turned out that one of the antibodies that we were using had expired, but we had no way of knowing that because the antibody was made in the lab, so it doesn't come with an expiration date or anything. I was kind of bummed that we had to redo all of our plates, but what made me feel worse was the thought of all of the money that went down the drain from all of the wasted materials. The rest of the day, I worked on my study design, which is basically an outline for a paper that one wants to publish. I doubt that I will be publishing anything, but my supervisor wants me to practice as this will be a valuable skill in the future when I do other research.

On Wednesday, instead of running all of the plates again, we decided to change some our methods and rerun one plate, just to see if the changes would have much of an effect. The rest of that day was spent working on my study design as well.

On Thursday, we had our normal weekly meetings. This week, Matt, one of the lab researchers, presented his preliminary proposal for a project that he was about to start. The rest of the lab researchers gave him plenty of advice and tips, and that was basically all that happened during the meeting. Afterwards, I had to fish out some old samples in the -80 C freezer before I left  early to go on a hiking trip with my family.

Week 5

After a week off for spring break, I felt ready to get back to work on my project and maybe gather a lot of useful data for my project as well.

But this week was again not only unique but also a very informative experience.

On Monday, I finished the two Wes plates I needed to collect all the data for the S1BF region of the mice brain samples that I am using. For the plates themselves, I ran two plates testing for Glypican 4 in S1BF samples from animals whose brains were removed and frozen one to seven days post injury to complete that region.

During that day as well, I had a meeting with Dr. Theresa Thomas and my senior advisor, Sarah. There, we began with a discussion of the progress that we made so far with the project, but we digressed to the topic of the challenges facing students who pursue the medical profession and the characteristics that are needed to truly elevate yourself from the pack. All in all, the meeting was very informative and a unique learning experience, especially given that Dr. Thomas sits on the board of admissions for the University of Arizona Medical School.

On Tuesday, I started running Wes plates for the MPFC (mid pre frontal cortex) region of the mice brain. Specifically, I ran the preliminary plate that we use to determine which samples will run well with the others. After that, I gathered samples from the MPFC region that need to be used for future plates and put them into one box for safe storage in the freezer for easier access later on. I then called it a day after that.

On Wednesday, my senior advisor, Sarah, advised me to study the Compass software that I use to interpret the Wes results and to become more comfortable with using it. This may seem relaxing, but the 452 page long user’s manual that I had to read made it hard to take it easy. After a few hours tinkering with Compass, I aided our lab manager, Bret, in his study on cage dividers and their effect on mice aggression. I got to go the vivarium, where the living mice are, and though I did not get to touch them, I got to operate the rotarod machine that we were using that day to run tests on the mice.

On Thursday, we had yet another lab meeting. At this week’s lab meeting, we had an extensive discussion about the new batman v superman movie for about half an hour before we got down to business. Bret gave a presentation about his LPA study and asked for suggestions on how to improve it. Though I was of no help, the others gladly gave him advice on how to improve his study. After the meeting, I helped Sarah with some paper filing and general organization and then I helped Bret with his studies using the rotarod once again.

Week 4

This week at the Arizona Biomedical Collaborative was kind of hectic.

On Monday, I ran some more Wes plates with my secondary adviser Caitlin. I ran plates for the second half of the samples from the S1BF region of mice brain samples. My results indicated that the run was completed successfully as compared to the disastrous run of the same plate a few days ago. After I completed the Wes plates, I took a break for lunch and organized my notebook and my materials.

On Tuesday, things went perfectly for the first time since I came to the lab. That day, I had to run another wes plate with Sarah, and within a matter of minutes everything was set up, the rest of the process went as smoothly as it could, and we were done by lunchtime. After that, I worked on organizing the lab and Sarah's lab notebook, which was very messy and all over the place. Overall, it was a pretty relaxed day without much craziness.

Wednesday, on the other hand, was a complete disaster. I got to prepare a wes plate by myself for the first time, and I was really excited. However, I was making mistakes from the get-go till the end. Every step that I could mess up, I did. At the end of it all, the results looked like an ekg  that went wild. I would have looked at it as an opportunity to learn from all the possible mistakes that I could make, but considering how much the plate itself costs, plus the materials that were put into the plate and the time it took to the raise the mice before removing their brains, it was kind of hard to focus on anything but the cost.

On Thursday, at the weekly lab meeting, I learned again what not to do in lab studies along with learning some new facets of the medical industry. Overall, I had a very light work day, and after doing some organizing and setting a wes plate for my senior advisor, Sarah, to run, I called it a day.

Week 3

This past week at the Arizona Biomedical Collaborative started out normally enough.

On Monday, Caitlin, my secondary advisor, and I ran some more Wes plates. Since we had finished running Wes plates testing for Neuroligin-1 and Glypican-4 in the VPM (ventral posteromedial nucleus) region of the mice brain samples, we then proceeded to attempt to run Wes plates for the S1BF region. It started out with a hitch when we couldn’t find all of our samples. In the end, we managed to get what we needed and we ran two plates. I then did some housekeeping and bookkeeping work and proceeded to call it a day.

On Tuesday, Caitlin was not in the lab, so my main supervisor Sarah Ogle decided that I assist the Research Lab manager, Bret, on his study involving cage dividers and the reduction of aggression on mice in their cages. So, for that entire day, I assisted Bret by keeping track of the amount of time a specific rat in the cage spent in a tunnel created by the cage divider.

On Wednesday, Murphy’s Law reared its head.

At 9, Sarah told me to gather the samples that we were supposed to have already prepared for the protein extraction of brain tissue from specific regions. But the whole process soon turned into a fiasco due to both mistakes on my part as well as misplacement of sample tissues in previous studies. The main problem was that the samples that we needed that contained the hippocampus chunks had been extracted by three different teams at three different times and were all labeled three different ways. That made it a huge a pain to find all the samples that we needed to run the tests. Truth be told, it took us nearly two and a half hours to find all of our samples to run a protein extraction and then the protein assay. After a nerve racking rest of the day, I was still able to finish everything in a reasonable amount of time.

On Thursday, in lieu of the recent developments (see Wednesday), Sarah assigned me the task of noting down which samples we could find for the hippocampus region of the brain. The region had been used by many different people and as a result were scattered across the lab for me to find. After a few hours of noting down, I finished and now have a comprehensive list of where all of my samples are, so the next few weeks should run smoothly, hopefuly.

Week 2

My second week at the Arizona Biomedical Collaborative was a unique experience.

It started off normal enough. On Tuesday, I, with the help of my research supervisors Sarah and Caitlin, ran some more tests on the Wes machine.We did the normal procedure of preparing the samples and filling out a plate, and we were able to finish a decent amount of work for the day.

On Wednesday, the craziness began. One of my supervisors, Caitlin, was not able to make it, and my other supervisor, Sarah, is one of the busiest people in the department as she is always running around helping out everybody and she is also involved in a various number of projects, and that day she had planned to spend the entire time that I was there in a section of the lab that I do not have clearance to enter, believing that Caitlin would show up to help me out. Since my supervisors were not there to tell me what to do, I thought that it was going to be an easy, relaxed day. Boy, was I wrong. One of the other lab workers decided to put me to the task of cleaning and organizing the freezers. This doesn't sound that bad, but when you have to remove boxes full of slides from freezers set to -80 C and rearrange them in a room at 4 C for four hours, it gets kinda bad. The worst part about it was that the gloves I wore for the entire process were the same type of latex gloves that are used for class dissections, so I could not feel my fingers for the rest of the day. The second worst part was that I didn't even finish organizing half of a freezer, so I will probably have to do this again in the near future.

The highlight of the week had to be on Thursday, during the weekly lab meetings where everyone discusses the issues in the lab and any new findings that have been made. There is also a presentation by one of the researchers every week, and this week Matt, the one who had to present, had not gathered enough data for a proper presentation, so he shared an article that he thought was relevant to the majority of the researchers in the lab. It turns out that he had only read the abstract before sending it to all of the other researchers, and it also turned out that the article he had selected was utter crap. So the next two hours were spent ripping apart the article in a thorough fashion, and they turned the presentation into a session to teach me and the other interns about how not to write a scientific paper.

Friday went back to normal to some degree, but due to the lack of organization in a freezer that I did not have a chance to organize, we were not able to find the proper samples, and we spent most of the day finishing leftover busy work. And that's how this week went.

Week 1

My first week at the Arizona Biomedical Collaborative at the Translational Neurotrauma Lab can be wholesomely described as an entirely new and alien experience.

Before joining the research efforts at the ABC, I had a very preconceived notion about the nature of the research. I thought that the professor controls everything within the lab and dictates every responsibility to high school interns out of a sense of untrustworthiness. Also, I thought that to pursue research was to throw yourself into the fire immediately with some training and you proceeded under the watchful eye of the professors and lab interns.

All of these notions were proven a mix of truths and untruths.

Anyways, here is a brief overview of what I accomplished this week.

On Monday, I learned all about the materials needed to properly run the Wes machine, a tool that simulates a western blot and cuts the run time down from two days to three hours, and where they were all stored, which is important information to consider for experiments.

Due to my supervisor being extremely busy on Tuesday, I was exempt from going to the lab as she would not be there to guide me.

On Wednesday, I ran a sham plate for the samples from the VPM region of the brain for Sprague Dawley rats to ascertain which samples would be appropriate to run with the injured samples. Sham is the term used to refer to uninjured rats, and the VPM is one of the regions of the brain that we are looking at.

On Thursday, I participated in a lab meeting with all the personnel in the lab. There, we discussed specific projects that other lab personnel were pursuing as well as addressing problems and solutions to many issues in the lab. Afterwards, we watched a presentation on a study on the reduction of aggression in mice after the addition of a corrugated plastic cage divider, where it was ascertained that a cage divider heavily affected aggression levels in mice in a positive manner. Then, lab personnel offered other avenues to pursue as well as improvements to make on the experiment. After the lab meeting, my advisor then again extensively reviewed the steps needed to run the Wes machine again and I wrote the steps in my lab notebook.

On Friday, I began creating WES plates for the actual study that I am helping in. It took me three hours to gather all of the materials and fill the plate due to unforeseen problems, but I was still able to run two plates in the end.

Prologue

Hi everyone.

I am Rohith Malladi and am currently a senior at BASIS Scottsdale. I have been learning at BASIS since I was in fifth grade. I have taken many classes during my education period, such as AP Biology and AP Chemistry, that I have enjoyed very much. Those two classes in particular helped me figure out what I wanted to do with my future, and more specifically, my Research Project.

This blog will document my work during the period of my Senior Research Project. The Senior Research Project is endeavor offered to senior students at BASIS Scottsdale that allows them to conduct research instead of having to come to school for the third trimester. While performing my research, I will regularly update this blog on my research, as well as with pictures, I hope. At the end of the period, I will be giving a presentation on my research and findings. Successful completion of this project results in graduation with high honors.

The research is being done through the University of Arizona Medical School and it relates to brain trauma. Specifically, we will be conducting research on translational brain trauma in mice. Recently, there have been many cases of unexplained symptoms occurring in patients who had recently suffered traumatic brain injuries.The symptoms began showing up several months after the brain injury occurred, so very few have linked the new symptoms with the brain injuries. Through our research, we wish to learn the causes of these symptoms, how to treat these symptoms, and how to prevent these symptoms from occurring during initial treatment for the traumatic brain injury.

We are currently in the animal testing stage of the research. In a separate lab, researchers are inducing brain trauma onto mice and recording their behaviors. After the behavior has been thoroughly documented, the brains of the mice are sent to our lab. We have the duty of creating slides of the brains and then analyzing the chemical and anatomical changes that occurred due to the induced brain trauma. We are hoping to discover the pharmacological causes of the delayed symptoms, and have conducted various trials. As I am only a high school intern, I have not been given access to very much hard data, but I hope that we will be able to reach some results before the end of this project period.