STEP reflection

 

  1. Please provide a brief description of your STEP Signature Project.

My STEP project consists of a research initiative that explores the connection between the vitality of retinal ganglion cells and the extent of injury sustained in traumatic brain injuries or TBIs. I was tasked with the immunohistochemistry work on a specific cell type in the retina: Intrinsically Photosensitive Retinal Ganglion Cells or ipRGCs.

  1. What about your understanding of yourself, your assumptions, or your view of the

world changed/transformed while completing your STEP Signature Project?

Before my project truly began in earnest, I had an idealistic point of view in regard to the research process and the world in general. When I previously thought about how research was conducted, I imagined a brand-new high-tech lab equipped with all white, perfectly cleaned receptacles and tools. Inside this lab there would be a scientist who would discover everything they sought to know within one or two experiments. This far from the case. Research is messy, it’s slow and sometimes tedious, but it’s also amazing at the exact same time. Through the process of participating in research, I was reminded of the reason that I fell in love with science in the first place. Everyday working in the lab, I was confronted with the reality of how little we know about the world that we live in and how much we still have to discover. And every day still I got to participate in the chipping away toward a new revelation.

  1. What events, interactions, relationships, or activities during your STEP Signature

Project led to the change/transformation that you discussed in #2, and how did those

affect you?

Overall, one of the biggest catalysts in my transformation of thought was the personal responsibility that I was tasked with throughout this process. Throughout the research process, I had a certain number of tasks that I had to complete. If I were to not complete them, no one else would and the project would suffer as a whole, not just my own personal grade or result as it is with many of my academic classes. It was through this responsibility that I was able to fully curate a level of scientific comfort on my own and truly engage in the scientific process. This enabled me to truly experience what science is at its very roots: a process of trial and error conducted to know just a little bit more about the world.

Additionally, another integral part of my development throughout this process was the scientific freedom that I was allotted by my faculty member. During my time, I was constantly left to my own devices with a task to complete that was vital to the quality, success and overall progression of the project. While initially this was daunting, my faculty member was always available to help me if I needed it and eventually, I gained a fair amount of confidence and comfort working on my own and pondering what it was exactly that I was studying, which cemented the reality and weight of my work.

Overall, I believe that this experience has been an essential part of my development as a student here at Ohio State. Through the responsibility that was bestowed upon me and the scientific freedom that I was granted, I was truly able to gain a deeper understanding of the scientific world. Additionally, I feel as though I was even able to apply many of the concepts that I have learned in the numerous lab classes that I have been enrolled in throughout my 3 years here at Ohio State.

  1. Why is this change/transformation significant or valuable for your life?

This development is very important to me both academically and personally. As of now, I intend on applying to medical school in the near future. This experience is not only very important for admission to medical school, but my success in medical school and even much later on as a medical professional. This is because it has strengthened my understanding of the scientific world and improved my comfort level with the unknown aspect of science, which are both very vital.

Astronomy Research STEP Reflection

My STEP project involved learning about quasars and working to understand a program which analyses quasars. The physical properties of quasars are not well understood, therefore my advisor and his collaborators created a program named SimBAL to estimate the physical properties of quasars. My involvement in the research is mainly in a computer science aspect. I have learned about quasars and studied the program so that we can optimize its use and cut down the time it takes to run it.

Being involved in the research project improved my programming skills greatly. I am relatively fluent in Java but this project involved programming in Python, the language which is becoming the most commonly used programming language in a variety of fields. SimBAL is a data analysis program in that it takes in data, spectra from quasars, and analyses them to produce a result, the physical parameters of the quasar. Thus, I have gained further knowledge about data analysis and how programs work to produce the desired results. Since my involvement in the project focuses on speeding up the program I have gained skills in algorithmic analysis, finding the components of a program which slow it down.

The biggest transformation came in the form of my confidence though. Just being asked to join this project increased my confidence in my astronomy and computer science skills. Then, through working on the project, I have gained confidence in my ability to explain my research, and greater confidence in my understanding of astronomy and computer science.

My advisor was the one who reached out to me about this project. He thought of me because he remembered my interest in computer science and desire to go into data analytics. Simply the fact that I was the person he thought of for this project made me more confident because it showed that I stood out to him and he remembered where my interests were. Our weekly meetings helped me feel more confident in talking about and explaining my research as we spent some time just learning about quasars so I had a strong scientific understanding of the objects we are analyzing.

I also gained confidence in asking questions between our weekly meetings and the information and tasks I was sent. Without asking questions I would have gotten stuck many times, so I had to increase my confidence in asking questions in order to complete the tasks I was given and to better understand both the program and science behind the program. Since most of my tasks involved manipulating the program to produce different plots and diagrams I developed computer science skills. Perhaps one of my proudest moments was when I was able to create a filled contour plot using some of our data, mostly because the result was a pretty graph.

Concurrently with my research this past semester, I was in a CSE class about algorithmic analysis. This class along with my research provided me with a better understanding of what makes a good program and the changes that can be made to optimize a program. In my research we looked at several aspects of SimBAL that can be changed to decrease the running time. These solutions include things from writing it in a different programming language to running it on graphical processing units instead of central processing units. These changes would change nothing about how the program works, they would just speed it up, and we thought of these changes through algorithmic analysis.

Confidence is helpful in every aspect of life. This past semester I found it easier to contact professors when I ran into issues and I have found that I do not have as much anxiety around making phone calls anymore. These skills are both communication based and communication is important in any career, so increased confidence in communication definitely gives me a boost.

My desire is to go into the field of data analytics after graduating so all the programming, data analysis, and algorithmic analysis skills I have built during this project will certainly help in a potential career in data analytics. My project is similar to what I would be doing as a data analyst, just with astronomy data.

This image shows the spectrum of a quasar along with two spectra created by SimBAL which estimate the physical properties of the quasar.

This image shows the spectrum of a quasar along with two spectra created by SimBAL which estimate the physical properties of the quasar.

This image shows a color contour plot describing properties of a quasar.

STEP Project Reflection

For the duration of the semester, I have been collaborating with the Weinberg Computational Lab to learn and conduct experiments in regard to the electrophysiology of the cardiac ventricular cell. Initially this was through studying the effects of ion concentration on the arrhythmogenicity of a guinea pig cell model; however, as the study progressed the course of the long-term project has been refined to study human ventricular cells.

This project has been undeniably insightful in the experience I garnered conducting research as part of an established biomedical engineering laboratory. For the last few months, I have gotten firsthand exposure into how research is conducted as well as a view of what it would look like to hold a position as a research conducting faculty member at a university. The last few months I have worked very diligently on my own research project; however, what I have found are several setbacks on my progress. Initially starting with a project using a guinea pig model, I spent the first couple of months learning how to setup the computational experiments as well as compute different values used to evaluate results. I was able to make some progress that resulted in verifying the model I was using as well as had the opportunity to give a research update to the lab which is typical for researchers to do when coordinating with a group. Unfortunately, shortly after this point I was given an updated objective to begin using a human ventricular model. Having the shift in my research progress was frustrating yet was insightful. Prior to beginning my project, I was familiar with research progress generally being slow. After having my project change scope and in essence having to restart was telling of the different setbacks that can be faced.

Although I faced challenges with the progress, I had some great experiences working on my project. The excitement of problem-solving some of the more complicated issues felt like very rewarding work. Furthermore, being able to connect my results with not only previously established work, but also with clinical manifestations was exhilarating in a way because it validated the time I spent on the project. Having results that connect with real world applications had given me a more concrete understanding of how basic research may be related and applied in an industrial or clinical setting. During the same time that I was working on this project, I was working on a capstone project with a clinical mentor creating an assistive device for patients on dialysis. In a meeting with this mentor, we went over the importance of dialysis as a replacement for kidney function. One example used by the mentor was that if dialysis is missed, the potassium level in the body may get too high and cause an arrhythmia in the patient. During my research, a specific result I had seen is the impact of abnormally low potassium levels on cardiac function. If K+ is too low, then the single cardiomyocyte will enter an arhythmic state; however, if it is too high, I saw no such problem – a result which was unexpected based on what the mentor had spoken to me about what was actually seen clinically. Because of this conversation, I spent time looking into previously published papers that studied both single cardiac cells and cardiac tissue. Looking at both, I was able to distinguish specific issues that arise due to cell-cell communication. If an issue arises in a 2D or 3D model, but not in a single cell model, then the issue is due to the cell communication. As a result, I found a previously published study that showed evidence of increased potassium levels as causing something known as a conduction block, a situation which was indeed due to communication problems between cells. Having made the connection, I was able to verify the results I was able to provide credible reasoning for why I did not see the issue in my single cell model that was seen clinically.

During the course of my project, I was given the opportunity to present my research to the lab group as an update to my progress. This event provided me with practice presenting research which is a typical event for researchers and academic faculty alike. I was given the opportunity to prepare my research in whatever formatting I liked and ended up speaking on the guinea pig model I had initially been working with. Although not an exciting event, the mundane part gave insight into what may be a regular event in a research environment. The ability to communicate with fellow researchers is a must for individuals in that field. Especially when presenting to professional colleagues who have a significant understanding of your research, their feedback can provide significant improvement to the research being conducted. Peers have the ability to see both flaws in current methodology and result interpretation, as well as provide suggestions for improving research and ideas for creative new approaches to solving problems and obstacles in the research process.

A significant portion of my project involved working independently. Because of this the project stressed the ability to be self-sufficient in my work – a concept that goes hand-in-hand with knowing when it is important to reach out to the graduate student I was working with, or even to my PI who is the expect on the field to answer questions. Finding the balance between solving problems on my own in order to have a better understanding and learn more and reaching out to others to answer my questions in order to save time and ensure I am doing things efficiently and correctly is a significant skill I have been able to sharpen throughout the course of this project. The relationship I have built with my project supervisor and the graduate student who I worked closely with on my project has been fundamental to my success. As I mentioned previously, learning to concisely communicate has been a significantly helpful skill that I have developed throughout the course of this project. Through communicating with my graduate mentor, I have been able to learn about forming concise emails, the extent of work I should expect to be motivating myself to complete, as well as the expectations that I would be held to by a more senior member of the research team.

These transformational experiences I have had in the last few months during my STEP project have been greatly insightful into developing my plans for the future. I went into this project hoping to gain experience on what it is like to pursue a career in academia with a heavy dedication on research. My biggest takeaway from this project has been the slow pace that research is carried out at. I saw a number of setbacks in my project specifically, and I see similar pace for my fellow researchers in the lab. This led me to takeaway that I enjoy and want to do research in the future, but I would not want that to be the core of my career. As a result, I look to turn my head toward pursuing a career in medicine – but only after continuing to grow my education as a biomedical engineer by pursuing a master’s degree here at Ohio State (currently with acceptance in the fall). Following my master’s degree, I will be applying for MD/PhD programs. Doing one of these programs will allow me to have a career in medicine, centered around patient care, while opening the door to work on research as a side project throughout my career.

 

Research Reflection

My STEP Signature Project was a research project that I lead in the lab of Dr. Long-Sheng Chang. My research focused on testing the efficacy of a drug on osteosarcoma cells. I performed various experiments, such as western blots, to determine the cells’ protein content after drug treatment.

As a pre-medical student, I had known that I enjoyed interacting with patients; however, I was unsure whether or not I would enjoy the research process as it lacked the patient interaction that I treasured. Yet, during my semester researching, I attended various conferences and heard the stories of how other researchers were making an impact on patients worldwide without actually helping them directly. The initial mindset that I had was that I would not enjoy it as there was no patient interaction. Although I did not have any patient interaction during my time researching, I did learn about the process that it takes for drugs to be approved and how there is a comprehensive approach to ensure the safety of the patients. With this, I had developed a greater appreciation for the works of researchers.

During my time researching, I had the chance to work closely with my Principal investigator, who has been researching for over 30 years. I would come in every weekday at noon and leave around 6 PM or so. On the days that I would arrive early to complete an experiment, I would see my PI already here at the lab. Likewise, on the occasion where I stay late until probably 11 PM or midnight, he is there as well. I realized that he was dedicated to fighting cancer and that he was driven to succeed. This dedication was exceptional and helped me develop a further appreciation for research as it requires a sacrifice to benefit society.

As I spent the semester researching osteosarcoma, I had the unique opportunity to lead my project with the guidance of my PI and the Ph.D. in the lab. I had always known that research was a field that required time and dedication; however, over the course of the semester, I had the chance to experience the required dedication and commitment. As I was performing treating the cells with the drug, somewhere along the way, there was an uneven division of cells that practically threw off the entire experiment. I had no idea until it was near the end of that experiment. Because of something as small as an uneven split of cells, two weeks’ worth of work had gone down the drain. Every step had to be taken with precision and care as even loading a couple of microliters more would result in a result that was not truly reflective of the experiment.

Although there was no patient interaction while researching, I had the opportunity to attend the tumor board meetings where physicians discussed their patients’ treatment courses. During this time, I had the chance to see how the research was directly impacting the patients. The analysis provided the data on what course of treatment should be pursued. Seeing the physicians consider the prior study was an eye-opening experience for me as I was able to see the connection between patient care and research, which I was not actively aware of before this experience.

This experience researching in the lab of Dr. Chang has taught me always to keep an open mind. Although on the surface it may not seem that research would have the same satisfaction of working with patients first hand, this experience has been just as rewarding knowing that I was contributing to the patient care of countless numbers of future patients. I had the chance to learn about how research helps to guide physicians’ choices to achieve the best outcome and care. The mentality will be something that I will take with me as I continue to pursue a medical degree. In the medical field, it is essential always to have an open mind when it comes to listening to the patient and creating a treatment plan. Without an open mind, patient care has been shown to decrease since every person is unique drastically 

Although there was no patient interaction while researching, I had the opportunity to attend the tumor board meetings where physicians discussed the courses of treatment for their patient. It was during this time where I had the chance to see how the research was directly impacting the patients. The research provided the data on what course of treatment should be pursued. Seeing the physicians take into account the prior research was an eye opening experience for me as I was able to see the connection between patient care and research, which was something that I was not actively aware of prior to this experience.

 

User Experience Research for Fluid Earth Viewer

During my STEP project, I was a research assistant in the Virtual Environment, Communication Technology, and Online Research (VECTOR) Lab, within the Ohio State School of Communication. This research assessed the user experience of an interactive website called Fluid Earth Viewer, which displays the planet’s atmosphere and weather patterns in real time. Some of my responsibilities included watching videos of participants interacting with the website, recording my observations, and determine what areas of the site required improvements in usability.

This project was extremely influential in the development of both my career goals as well as my overall global outlook. It exposed me to critical societal problems and forced me to contemplate certain global situations that I had previously been sheltered from. For example, I now hold a greater awareness and understanding of the chilling reality of global climate change; I always believed that climate change is a serious threat to our world, but this experience added urgency to my concerns by showing me all the specific pollutants that plague our air and atmosphere. This project has been part of my inspiration to pursue a career that will hopefully allow me to address climate concerns within my own community—I am certainly not able to immediately institute largescale global climate improvements, but by focusing on bettering my own community, I can promote bottom-up environmental protection and sustainability.

Furthermore, I have gained a greater awareness and appreciation for promoting accessibility in everyday life. I was able to directly observe the frustrations that arise when technology is lacking in usability and accessibility. I now apply the critical thinking I practiced in the VECTOR lab to everyday devices and situations, considering whether something is truly accessible and usable for all people, regardless of ability. Creating a more accessible world leads to a more satisfied and unified community. Lastly, this project was critical in the development of my career goals, by allowing me to witness and participate in an intersection of digital media and the environment. Each week, I was able to study a website that created a truly impressive combination of technology and the environment. Throughout college, I had been torn between my passion for the environment and my passion for English, specifically digital media; my assistantship highlighted the interdisciplinary nature of research and led me to the perfect graduate specialization that will allow me to combine my passions.

The bulk of my time as a research assistant consisted of analyzing videos of participants exploring and completing tasks on the Fluid Earth Viewer website. One of the global projections that concerned me most was the section displaying gases and aerosols in the atmosphere. In participant videos and my own exploration of the website, I was able to see the problematic concentration of gases like Sulfur Dioxide and Carbon Monoxide lurking over our heads. These gases are most prevalent in highly populated, industrious countries, and the Fluid Earth Viewer clearly depicts their overwhelming presence. Being able to fully visualize mankind’s drastic effects on the global climate, instead of merely reading about it online, was quite the wake-up call for myself. I gained an increased urgency for addressing the climate crisis and began to brainstorm how I can cut down on my own contribution to atmospheric pollutants. I have begun to practice more eco-friendly modes transportation, cut down on consumption that creates pollutants, and vote for candidates and legislation that promote renewable energy and environmental conservation.

Arguably more important than the website in the research process were the participants themselves; after all, the website is designed and tailored to their needs and preferences. Some features of the website were quite difficult for participants to locate or use, which is expected in a young, constantly changing web development project. Unfortunately, users often believed that they were the main reason that could not successfully perform a task, and this sense of incompetency is a common side effect of ineffective user centered design. Other times, users were visibly frustrated when the site did not behave the way they expected, and the combination of these problems caused me to start thinking about usability and accessibility outside of the research lab. The overall goal of new technologies, or almost anything made by humans, is to make life easier or more efficient. However, that is not always the case for everyone—objects often neglect certain members of the population, whether intentionally or unintentionally, but user research like that on the Fluid Earth Viewer is an excellent way to combat exclusion or frustration. Listening to community members is essential to enhancing the accessibility of society, and new technologies are not the only things that require considerations as to their accessibility. I hope to contribute to conversations of access in all facets of life—from other newly budding websites to objects as simple as city sidewalks.

My research assistantship opened avenues that allowed me to discover my ultimate passions in life and watch as they all neatly intertwined before me. Throughout the project, I was fascinated by the relationships between the participant, the website, and the environment; each was an equally important component, and constant communication between the parts was required for the whole machine (the research process) to work successfully. For the past year or so I had planned on pursuing a career with technology, but I was unable to let go of my passion for the environment. In fact, I entered college as an Environmental Science major before hesitantly switching to English (which I love). The fusion of the environment and digital media in this research experience showed me the possibility of finding such an interdisciplinary field and led me to search for similar opportunities for my career path, eventually leading me to environmental rhetoric. This subfield of English deals with how people communicate about the environment, and it is part of my intended specialization in graduate school.

Finally understanding that research is not always limited to one particular field, I am now able to combine my passions and confidently pursue a career in academia. This experience cemented my desires to conduct my own research one day as a university professor. I hope to study the relationship between social media and the environment—more specifically, how companies talk about the environment online and what rhetorical strategies prove effective at promoting sustainability, conservation, and environmental policy change. Without this STEP project, I may not have discovered how I could combine my passions for English and the environment nor realize my desire to conduct my own research. I hope to one day design an experiment that will inspire another young research assistant like myself.

-Luke Van Niel

 

This depicts one of the many projections available on the website, in this case Carbon Monoxide buildup in Earth’s atmosphere.

 

This projection displays total precipitable water, or the total amount of water vapor in the air above a unit area of Earth.

STEP Undergraduate Research Reflection

My name is Avidaan Srivastava and I am a third year Physics and Astrophysics double major at The Ohio State University. For my STEP Project, I decided to study and predict a theoretical model of the behavior of Super-Paramagnetic Iron Oxide Nanoparticles (SPIONs) when attached to a DNA Nano-hinge, placed in an external magnetic field. On this Project I worked under Ms. Prerna Kabtiyal, a PhD. student working in Dr. Ezekeil Johnston-Halperin’s Condensed Matter group at the OSU Physics Department.

I have been a part of Dr. Johnston-Halperin’s research group for a year now and the entire experience has been an eye opener for me. As someone who plans on going to graduate school and eventually get a PhD., undergraduate research has been a very important step for me. To say the least, it completely changed my understanding of how reasearch is done.

My idea of research first came from TV shows and movies, like The Big Bang Theory, but it wasn’t until I actually got involved in the process of doing research that I realized how complicated it actually is. The biggest problem I had to face was that we did not know the answer to the question we were asking. My experience is classes and life so far was to ask someone if I wasn’t sure about something. But now, I had to find the answer myself or figure out a way to find it. It was both a challenging and rewarding experience. Challenging because I knew what was to be done and I had to figure out how to do it and for that I had to read and understand quiet a few research papers that contained some complicated physics that I hadn’t learned about at that point. Rewarding because once I did accomplish some task, be it figuring out some part of the computer code I was stuck on, or some physics related topic, it really felt like an achievement.

Another quite important thing I learnt was the ability to work together. Previously when I had worked on group projects, it had mostly been diving the various tasks, individually completing them and finally putting them all together at the end. However, here it did not quite work like that. In my experience working in the Johnston-Halperin research group, the coding aspect of the project was mostly my job and a part of it depended on another member of the group completing their tasks and in turn my worked served as a basis for yet another member’s work, thus it was a system of building on and contributing to the previously done tasks. This always kept me on my toes and gave me the drive to finish my end of the project in a timely manner, which is very important.

Working on this project has been extra challenging this year because of the COVID-19 situation. Thankfully, my side of the project mostly involved computer coding, so it wasn’t affected to an extreme degree, but the overall progress, especially in the experimental side. This reinforced the importance on communication and coordinating with all the members of the research group. Because of that, we were able to make a lot of progress in the theoretical modeling part of the project and once the experimental group has their findings, we can compare it to the our model and finally publish a paper.

Overall, this has been a huge step in my development as a person and for my future career. I have thoroughly enjoyed doing research and this experience has strengthened my passion to pursue a master’s degree and finally a PhD. If there is a thing that living in the pandemic has taught me, it’s that I have to love doing my work, because only then can I actually be productive.

Gadde_STEP_Reflection

Please provide a brief description of your STEP Signature Project. Write two or three sentences describing the main activities your STEP Signature Project entailed.

Collagen type 4 (Col IV) is a tetrameric protein (polymer consisting of 4 monomers) that forms networks within the basement membrane, a thin layer between epithelial cells and underlying tissue. The goal of my STEP project was to identify the binding regions of Discoidin Domain Receptor 1 (DDR1) to Collagen type 4 (col IV) using Atomic Force Microscopy (AFM). The main activities included sample preparation, AFM imaging, and image analysis.

What about your understanding of yourself, your assumptions, or your view of the world changed/transformed while completing your STEP Signature Project? Write one or two paragraphs to describe the change or transformation that took place.

I was able to challenge two assumptions I had about myself. First, I do not have the skills necessary as an undergraduate to be successful with an independent research project. Second, research papers are too complicated for me to be able to dissect and understand. I also realized at least two things about myself during the STEP project. First, that I could critically think through potential solutions. Second, I could get myself out of my comfort zone and collaborate with other principal investigators across the country. Finally, I was able to get an appreciation for how long innovation takes to get from the bench to the bedside for patients.

What events, interactions, relationships, or activities during your STEP Signature Project led to the change/transformation that you discussed in #2, and how did those affect you? Write three or four paragraphs describing the key aspects of your experiences completing your STEP Signature Project that led to this change/transformation.

I started research in Dr. Gunjan Agarwal’s lab in the fall of my sophomore year. Before getting my own independent project, I got published for my work in AFM of collagen in abdominal aortic aneurysms as well as in the intervertebral disk. For both, I relied on the graduate students in the lab for assistance, especially in sample preparation and image analysis. Also, both projects were ongoing, and I felt that I did not understand it at the same depth I could have if I worked on them from the start. These were what led me to wanting an independent research project. However, I doubted that I had the skills to be successful in an independent project. During my time with the STEP project, I have been able to do all the activities on my own. It also is a project I get to see from start to finish for, which gives me the level of detail I would have liked to have from the other projects.

As part of the background work before the project, I was assigned to read a few collagen IV papers. I had to present these in our lab meetings, which added an extra level of stress. At first, looking at papers that were 12-13 pages long was daunting, but I quickly found that the organizations of the papers made them easy to dissect, especially their results. I still struggle with decoding the methods used, but I still think I have a degree of understanding when reading the papers that I did not expect to have.

The first part of the project was finding the right concentration of col IV for AFM imaging. This part went rather smoothly (Figure 1), but I had difficulty when observing the DDR binding to col IV. Initially, I would just let the concentration of col IV and DDR1 sit in a tube for two hours, hoping that the DDR would bind. Then, I would place this solution on a surface that locks the col IV into place (Mica). However, I noticed that the DDR was not binding; Instead, it looks like the col IV was clumping together (Figure 2). This was not ideal, because I needed to see a clean Col IV molecule bind to DDR to map out the binding. We then tried to increase DDR concentration and place the solution in a rocker for the incubation time. Additionally, the PI and I discussed potentially plating the pure Col IV on mica to make it unmovable and then put the DDR on top of that surface for two hrs. I highlight this example to show the immense amount of troubleshooting that research entails.

Another part of the project I will be working on now is looking at a mutated form of Col IV in collaboration with Dr. Douglas Gould. I would laugh if someone told my sophomore self that I would be able to network with researchers across the country. It has definitely been a unique experience in setting up this collaboration.

Finally, through my Pharmaceutical Sciences major, I first was able to see the length of time it takes for an innovative therapy to get from the bench to bedside. The basic science research I am doing is at the start of this long process, and I will not lose sight of the fact that someone 20 years from now could benefit from my work. This also comes with integrity in research because I should not cut corners. Finally, in the era of COVID-19, I think the story of the vaccines are incredible in how they were able to develop, test and distribute a vaccine within a year. However, I think we should realize that this was an exemption, and that innovation takes time to come to fruition.

 

Why is this change/transformation significant or valuable for your life? Write one or two paragraphs discussing why this change or development matters and/or relates to your academic, personal, and/or professional goals and future plans.

As I said above, my STEM project has put research into perspective within the larger drug discovery and development process. I look to continue research in medical school and as a physician, and I will not lose sight of the fact that my work could impact a patient’s care. I also now have the self confidence that I can be successful with an independent research project, which would be an expectation as a medical student.

The networking skills I gained is also important for my career. For starters, a new trend for medical students to boost their residency applications is a research year between M2 and M3. Now, this could be something I go down to California and work more directly with Dr. Gould. Also, I have been told by many career development faculties that who I know is as important as what I know to be successful in my future endeavors.

Finally, critical thinking and troubleshooting comes back as a physician as I know a “one size fits all” approach will not work. So, working alongside my patients like I did with the PI to find the best treatment plan will help me provide the most effective care for my patients.

Figure 1: 1.0ug/ml col IV in PBS

Here, this image of Col IV shows the individual monomers coming together to form some tetramers. The collagen IV strands are well defined and I would expect to see DDR binding to these individual strands.

Figure 2: 1.0 ug/ml col IV in PBS

Here, this image is more representative of the collagen IV I have seen more recently. The strands are not neatly defined and it looks like they are clumped together (example in the blue circle). I would not expect to see any DDR binding to this in the counter samples. We suspect that the effect of letting these samples sit in the fridge (to give time for the counter samples with DDR to bind) is a factor in this clumping with itself.

 

If you have any questions please contact me at my email address (gadde.9@buckeyemail.osu.edu)

Nikhit Gadde

Undergraduate Research STEP Reflection

Hi, my name is Avni Patel, and my STEP project was an Undergraduate Research Project that took place in the Precision Cancer Medicine Lab housed in the Comprehensive Cancer Center at the James Cancer Hospital under the guidance of Dr. Sameek Roychowdhury and Dr. Melanie Krook. My independent project focused on comprehensively characterizing the role of novel FGFR2 gene alterations and how they contribute to the metastatic development of cholangiocarcinoma in patients. 

When I applied to college, I was very adamant about pursuing a pre-medical path, not even having considered all of the other ways in which I could contribute to the field of medicine without being a physician. My first year of my undergraduate career was heavily focused on completing rigorous scientific coursework in biology, chemistry, sociology, etc. As it happens to be, one of the unspoken requirements of being a strong medical school applicant is participating in biomedical research. Thus, at the conclusion of my freshman year of college, I joined the Precision Cancer Medicine lab, and I immediately fell in love with research and everything it had to offer. As I became more proficient in lab techniques and became more comfortable in my lab environment, the idea of pursuing a graduate degree and becoming a cancer biology researcher became an even more promising option.

My STEP project allowed me to fully immerse myself in my own independent research project, truly learning what it means to answer a scientific question from beginning to end. My desire to pursue a career in cancer biology research has become so much more amplified. Importantly, I have realized how important it is to pursue your undergraduate career with an open mind – Ohio State has a multitude of opportunities to offer, and it is so vital to fully explore those options in order to learn what it is that you truly want to do in your professional career. 

One of the most pivotal individuals during my research experience was Dr. Melanie Krook, a research scientist in the Roychowdhury lab. At the start of my research career, Dr. Krook was a postdoctoral fellow who had taken the lead on multiple projects that aim to better understand the FGFR gene and the manner in which the biology of altered FGFR genes plays a role in the development of aggressive cancers. Dr. Krook is easily the best mentor that I have ever had – she is kind, enthusiastic about science, and genuinely values my opinion as a budding scientist. One memorable instance I had was when I was learning how to take care of cells and perfecting my cell culture technique. Cells must be carefully treated and regularly taken care of in order to prevent mycoplasma, or bacterial contamination. Often times, it is difficult to identify the presence of bacterial contamination because cells that require lots of nutrients will turn the solution yellow, just as contamination will. When I initially saw my plates, I saw no reason for concern because I was unable to identify the contamination, but Melanie saw it immediately. However, instead of reprimanding me, she viewed it as a learning experience and explained the science behind the contamination to me. She was aware that as an undergraduate researcher, my experience is limited, and I cannot be expected to be perfect. Thus, she taught me that mistakes are okay and that in science, they are going to occur way more frequently than successes are – and that’s okay. 

Additionally, the development of my own independent project allowed me to develop a vast skill set of lab techniques that will serve me well in my future research endeavors. From basic science techniques such as PCR, gel electrophoresis, bacterial transformation, Western blotting, and RNA extraction to cancer-specific techniques such as drug sensitivity assays, soft agar assays, and colony formation assays, my ability to perform experiments and adjust protocols as needed based on preliminary results has been heavily refined. As I apply to other labs during medical school and graduate school, my breadth of knowledge will make me a much more competitive applicant, and I am appreciative of that. 

Finally, I am very lucky that I joined a lab under Dr. Roychowdhury, who is an MD-PhD. This means that in conjunction with running a research lab, he also sees cancer patients in the clinic one day of the week. Because of this, our research is very multi-faceted: cases from patients in the clinic often inspire new research experiments and the development of new clinical trials. Also, the presence of a multidisciplinary lab containing a bioinformatics team, a clinical laboratory team, and a basic science research team allows for very complex, genomic experiments to take place, and the scope of what we are able to accomplish is much larger than that of simply a bioinformatics lab or simply a basic science lab. Thus, I have gained a much greater appreciation for physician-scientists and am heavily leaning towards applying to those dual-degree programs upon graduating.

As discussed previously, for as long as I have known, I have wanted to be a physician. As a student in the rigorous Biomedical Science major, I knew that undergraduate research was going to be a significant portion of my academic career. However, actually being such a collaborative, supportive lab environment was truly a blessing because many of my peers in my major do not speak as highly of their research experiences as I do. After having experienced the power of a good scientific research community, I am optimistic about immersing myself further in this career field and eventually fostering the same environment for undergraduates in my own cancer research laboratory.

STEP Undergraduate Research Experience

For my STEP Signature Project, I performed research in Kevin Flanigan Research Lab in the Center for Gene Therapy at Nationwide Children’s Hospital in Columbus. Since the beginning of August I have assisted in research projects by learning and performing cell culture, cloning, minipreps, and CsCl preps, as well as assays including PCR, rtPCR, and western blots. I’ve been working in research since my freshman year of college, but this semester was the first time I engaged with the planning process of a project. The original plan for my project changed quite a bit from the beginning of the semester, and is now underway as a time course study of our gene editing therapy in mice. The development of the project and planning took place in August and we have already completed the first two main steps. 

As I’m sure it was for most people, this semester was eventful for me, both in my lab and in my personal life. In the lab, I reaffirmed my understanding that research is not a linear process. Before the pandemic, I planned to research RNA promoters in cells for the duration of the summer. As time progressed however, we developed a new plan for the Autumn semester that fit better with the evolving research of the lab as a whole. The new project was significantly different from anything I had ever worked on before, which was an exciting prospect for me. I helped design a time course study that will investigate the efficacy of our gene editing therapies in a mouse model, which will take place from November to mid-March. I had always thought planning a research project was a somewhat insurmountable task, so getting started was intimidating. With the guidance of my lab mentor, Dr. Anthony Stephenson, however, I was able to brainstorm ideas and develop a working timeline, and we are now well underway with the study. I learned that I am capable of rising to the challenge and adapting my plans to better fit important goals.

My personal life during this time also followed a similar trajectory. Up until this semester, I had always thought I wanted to go to medical school and become a doctor, and I had always overlooked the fact that I didn’t feel quite excited about my future. It seemed like the right career path for me and I didn’t think about it much beyond that. This semester, however, while balancing school work, my research, and studying for the MCAT, I started to realize my lack of excitement for my future might be indicative of a need to reevaluate my plans. Being in my lab significantly helped this realization process. I was surrounded by people in science, and was able to discuss their life paths with them. I learned that almost no one has a linear path from starting college to landing in the right career, and it made me feel much more confident in my decision to assess my options and begin considering a new path. This past semester has transformed my life by making me aware of the need for change in my future, and giving me the confidence to pursue this change.

Deciding to change our research project, and the confidence I developed from successfully doing so, went hand in hand with deciding to change my career plan. This semester was difficult for me because I overloaded my schedule to the point where not even perfect time management could have allowed me to get everything done. I realized I needed to prioritize somehow, and I ultimately decided I would not have time to study for the MCAT that semester. This decision initially came with some fear, as I realized that I might put myself off track for applying for medical school in the spring. As I tried to figure out how to fit everything in, I was struck with the realization that I was putting myself under so much stress to be a competitive medical school applicant, yet the thought of medical school itself and becoming a doctor brought me not much more than a feeling of dread. I realized that I had been working so hard for something that I hadn’t even brought my head above water to ask myself if it was what I actually wanted. Although this realization was a bit scary because I had never thought of myself as doing anything other than medicine, it was also freeing because I realized that I don’t have to continue down this path. Ironically, overworking myself this past semester was perhaps the best thing I could have done, because in evaluating what really mattered to me, I realized what I didn’t want. If I’d had time to study for the MCAT last semester I would probably still be tirelessly working towards a goal that did not bring me joy. 

 

Although deciding that you no longer want to follow your current path while having no working backup plan can be an intimidating thought, I could not have been in a better environment to do so. In my lab I am surrounded by people I look up to, and all of them were willing to discuss my situation with me and offer advice and stories of past experiences. By talking to them I gained the necessary confidence in myself and my feelings about my future to take action. I decided that I really did need to consider my situation and figure out how to make a change. The support from my lab helped me to reach out to my academic advisor, attend career fairs, and make contacts in my new fields of interest. 

In looking into new fields of interest, one career that stood out to me was physical therapy. I worked in a physical therapy office one summer I was in high school, and thoroughly enjoyed my time there. I started to think this might be a career in which I could see myself in the future. When I voiced these thoughts to my lab members, I was offered numerous connections to physical therapists that they knew. My P.I., Dr. Kevin Flanigan, also invited me to shadow him in the clinic, where he introduced me to physical therapists that worked in our building. These connections will help me develop a better understanding of physical therapy as a career, and if I choose to pursue this path they could be valuable career connections in the future.

Overall, this experience was transformational in my life. Not only did I gain valuable academic experience in research, but I began to form a better idea of what I want in my future. My time in the lab helped me to build confidence in myself and my ability to take initiative, and this confidence has spilled over into my personal life as well. I have developed a better idea of what I do and don’t want in my future, and even begun to think about a specific career path. My time in the lab has provided me with valuable advice and connections I would not have otherwise found to further help me in the future. I am very grateful for the time I have spent working in my research lab this past semester and look forward to my continued research in the spring.

STEP Reflection – Undergraduate Research

For my Fellowship, I was the Team Leader for the OhioState team at the 2020 iGEM competition, an international event in which teams create novel projects in the field of synthetic biology. Our project centered around streamlining and promoting genetic biocontainment within our field. Genetic biocontainment is a genetic construct or modification that allows external control of cellular life, and this is generally done as a binary switch between life and death. Biocontainment is a key issue in the implementation of synthetic biology products into the real world, products that have the potential to save countless lives and improve countless more.

I previously had no idea that this kind of tool existed, and now I know that it’s going to be one of the most indispensable tools for the advancement of the synthetic biology field. It had always seemed to me that science had lost a lot of the ingenuity and innovation we see throughout history with, for example, the discovery of DNA and new chemical analysis tools, but this shows me that we still have a long way to go before we’re out of ways to further our fields.

A major part of the iGEM competition is contacting and working with experts in your project’s area of interest. During this project, I met with doctorate students, post-docs, and even a Nobel Laureate! I had always thought that a field as advanced and new as synthetic biology would be difficult to get into and make contacts in, but I’ve already done so. I can use any of these contacts to further myself in this field, and one of my cohorts already secured an internship at MIT in this way!

Furthermore, simply working this closely and for this long with a team required me to develop my interpersonal skills, namely clear communication and getting people to stay productive. As Team Leader, I was charged with organizing the team to optimize our productivity and hold everyone to their commitments and deadlines. With the entire project taking place during the pandemic, I had to accommodate for reduced time and energy for everyone, and we had to narrow our scope to create a high-quality project. Working remotely is always a struggle, and building energy and momentum in a project is nigh impossible. However, we persevered (see photo below for our happy faces!) and secured a Gold Medal, a Special Award nomination, and even a Best in Track award! I’ve never taken lead on anything this large, and certainly not in this circumstance, but it was fun, challenging, and very educational for me to do so!

Genetic biocontainment is a very narrow and under-developed field of study, with very few people devoting much time to it. Much of the work done has been small projects that graduate students have used as a steppingstone to other work. I find this to be a good niche for me to try and fill in my career, as I already have a background in it, and I know exactly who to contact if need be.

The process of researching the initial ideas we had for this project was long and thorough, and I quickly developed a knack for finding the right sources and seeing gaps in knowledge. I’ve also learned how to see the assumptions and real data in papers, and this has made it much easier to boil down papers to the necessary information. I also learned the reverse process, because we had to turn our information into easily understandable graphics and text for a wiki site, poster, and presentation video. Being able to tailor data to a target audience and craft words in a good light for the project is something I’ll be using for my whole life, as every project will have cracks that need to be painted over.

Easily the hardest part of a scientific career is simply getting started. After all, what lab manager wants to hire someone with no experience? And, of course, who you know can be infinitely more important than what you know. This project has given me an excellent start into science in general, and I now have extensive knowledge in a specific field that I may continue to pursue in my career! The STEP fellowship has given me a fantastic opportunity that will make my journey infinitely easier and more enjoyable.