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Immersive 3D Biological Visualization of Proteins and microRNA Using VMD

Olubusayo Oluwagbamila, Rutgers University New Brunswick

Program mentor: Oyewole Oyekoya, Ph.D.     

Project mentor: Olorunseun Ogunwobi, M.D Ph.D.               

Progress Report

Week 1: June 6 – June 10 

This week, I met with Dr. Ogunwobi, studied his work, and drafted my research proposal. I read papers discussing the presence of single-nucleotide polymorphisms (SNPs) on the 8q24 chromosome, the encoding of six miRNAs on the PVT1 loci, as well as the underexpression of miRNA-1205 in prostate cancer. We decided that my role in this project will be  to visualize his research findings, and, along with Dr. Oyekoya, concluded that only certain datasets can be visualized on VMD and Paraview. 

On Friday, I physically attended the CUNYSciCom Symposium at the CUNY Graduate Center. There, I watched CUNY grad students make two presentations on their research: one for scientists and the other for non-scientists. I was especially  intrigued by how most of the presenters were able to simplify their work for audiences from non-scientific backgrounds, without watering it down. They employed analogies to form some connection with their audience, and linked that connection with their research. This method will come in handy for me, so I took some (mental) notes down.  I also watched tutorials on Paraview and VMD, and made attempts at visualizing substances on them.

My goal for next week is to collect data from Dr. Ogunwobi and figure out which datasets can be visualized with my tools. In the meantime, I will continue learning visualization on VMD and Paraview.

 

Week 2: June 13 – June 17

On Monday, I sat in on Dr. Ogunwobi’s weekly lab meeting at the Belfer Research Building. I listened to a few of his undergraduate and graduate students present their progress on the project they were working on. Following that, I was introduced to Fayola, program coordinator at the Hunter College Center for Cancer Health Disparities Research (CCHDR). She was hospitable, giving me a tour of the floor and showing me the different labs and lab equipment used in their research.

The data I needed was under the care of one of Dr. Ogunwobi’s Ph.D. students who had recently graduated, and there had to be some coordination between her and the current lab students. Because of that I was unable to access any data this week. I did however keep working on VMD and learned some cool tricks. Using the lipase 2w22 as a model, I practiced generating a Protein Structure File (PSF) from a Protein Data Bank (PDB) file. I also learnt how to add mutations to a protein, as well as modifying graphical representations of a protein by coloring or drawing method.

During the week, I virtually attended some interesting VR-related presentations. One was a seminar on the Role of Self-Administered VR for On-Demand Chronic Pain Treatment, and the other was a dissertation defense of a Ph.D. nursing candidate. Both presentations contained research on the effects of VR usage on pain, and both research findings demonstrated the positive physical and emotional results VR usage had on patients. This brought to mind the increasing technological advances happening globally, how much the world has changed over the years, and how much the world will change years from now. I find that fascinating, but also ominous. Maybe I watched too many Black Mirror episodes.

My goals for next week are to collect the data from Dr. Ogunwobi’s lab, continue learning VMD, and study other microRNA visualization projects.

 

Week 3: June 20 – June 24

This week, I got access to the data needed for this project. There were a lot of files available (over 6,000!), so I spent a good amount of time sifting through the data and figuring out which ones would be needed for my project. I was able to select files with compatible file types, but I did face some difficulties. I was unable to open these files on either VMD or Paraview, and only got an error message when I tried. My guess is that the problem lies either with the files I have, or with my knowledge of VMD/Paraview. Next week, I will test both hypotheses by going back to the lab to further examine these files, while also watching more tutorials on VMD and PAraview.

I also got to work on myresearch paper this week – I currently have my background/introduction, bibliography and a portion of my methods section complete. I faced some challenges transferring this to the template on Overleaf, and so another goal for next week would be to watch turotials on using Overleaf.

 

Week 4: June 27 – July 1

This week, I spoke to Dr. Wole about the issues I had last week, and he siggested I find similar files from public databases. From the Protein Data Bank, I was able to find four proteins (or their look-alikes) associated with my project: Aurora Kinase A, FRYL, Human Neuron-Specific Enolase-2 and Notch Homolog 2 N-Terminal-Like Protein A & B. I visualized them on VMD, mutated them, and compared the mutated structures with the original. I was hoping to be able to visualize microRNA-1205, or at least the locus PVT1 on chromosome 8p24. Unfortunately, because these molecules are non-protein, and because the Proetin Data Bank only contains information about proteins, I could not visualize them. I searched the web for other open-source databases, or other visualization software. I found a Nucleic Acid Database by Rutgers University (shoutout) and an RNA visualization software called RNA Artist. I could not find any MicroRNA file on the NAD. I tried downloading other files (RNA, DNA) from the NAD and opening them up with RNA Artist, but I kept getting error messages. Next week, I will look more into this.

Since this week marked the end of the first half of this program, I and my peers each made our mid-term presentations on Friday. I had fun putting my PowerPoint slides togather and breaking down the context of my project. Dr. Ogunwobi and I are the only ones in the entire program from Biology/Genetics background, so I enjoyed the challenge of explaining gene expression to Computer Science, Engineering and Art professionals. I also found other projects my peers are working on interesting, and I loved how much progress we all have made on our individual projects. I am looking forward to making more strides in the second half of this program.

 

Week 5: July 4 – July 8

The beginning of this week was a holiday week, so I spent the first couple of days exploring the city. I also spent some time exploring the Nucelic Acid Database and RNA Artist software. Unfortunately, I couldn’t find anything that would be useful for my project, at least not in the next four weeks. They do seem to be interesting visualization tools, however, so I will keep in mind for future projects. This week, I also got a chance to use some VMD extensions. I used the movie maker extension to make both a single-frame movie and a trajectory movie. I did some more digging, and I found a paper that talked about using other VMD extensions for RNA visualization, such as the NetworkVIew extension/plug in. I hope to explore this next week.

 

Week 6: July 11 – July 15

This week, I checked out the NetworkView extension and, unfortunately, it doesn’t have the features I would have liked for my project. Asides from that, I made more VMD videos using different graphic representations. Here’s a close-up video of the Aurora Kinase A protein, and another one of its mutant. I liked this representation because it shows the missing bonds and molecules in the mutant structure.  Also, it’s a visually appealing representation, which would be really interesting to view in VR.

 

 

Week 7: July 18 – Jluy 22

 This week, I worked on visualizing the other proteins associated with my project, similar to the videos I made on Aurora Kinase A. So far, I am done with the visualization aspect of my project, and the next step is to convert these into VR compatible formats.

 

Week 8: July 25 – July 29

This was the final stretch of the program. In this week, I concluded my project my refining the visuals I had created and checking out the VR experience. Due to the techincal obscurity of VMD, I was unable to directly export my visuals  with the VMD VR extension. I was, however, able to work around this and display my visuals through Google Carboard headsets. While this format was less immersive than I had hoped, it did involve virtual reality. I also completed my research paper and submitted it for publication. On the last day of the progrram, I had the opportunity to present my work spanning all eight weeks of the program. Here are some 2D-versions of the 3D visuals I presented:

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My project had its challenges, but it was overall a fulfilling introduction to 3D biological visualization. I am grateful to Dr. Wole for organizaing and enabling this project, and my mentor, Dr. Ogunwobi, for trusting me with his work. VMD appears to be a very useful software with numerous applications. I hope to further explore it independently over the next four weeks.

Final Report

Hunter College
City University of New York
HN-1001T
695 Park Ave
New York, NY 10065

Telephone: +1 (212) 396-6837
Email: oo700 at hunter dot cuny dot edu

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