Insights from Priyamvada Jayaprakash. Connect at Her LinkedIn Profile. She’d love to discuss her PhD experience with you and get insights on opportunities related to tumor immunotherapy.

Challenges I Faced During my Ph.D

I love Biology

Biology has always fascinated me. Understanding how cells and their environment team up to create a functioning organism mesmerizes me. So, without a second thought, I decided to pursue my Bachelors in Biotechnology when I was a senior in high school. During my coursework, I gained an introduction to diverse areas spanning genetics, biochemistry, cell biology and immunology. I learned to appreciate not only the complexities of organisms at a molecular level but also the fact that some of these molecular underpinnings can be explored and manipulated for the betterment of people. Towards the end of my 4 years, I realized that my passion for science wasn’t quelled by my undergraduate education and I pursued my scientific journey by accepting a PhD position in the University of Southern California (USC), Los Angeles. My thesis was on understanding the importance of secreted heat shock proteins (Hsps), Hsp90α and Hsp90β, in wound healing and breast cancer metastasis.

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Like any other PhD student, I spent the initial few months (and a lot of time in the future) reading and understanding “literature”. This meant a thorough knowledge and understanding of what findings have been accomplished in my research area- what ideas have worked and more importantly, not worked. Fellow researchers would definitely know “Pubmed”, an extremely useful database from NCBI (National Center for Biotechnology Information), that lets you search for papers of a specific area- all in one location. I cannot emphasize enough how much literature is important in the life of a PhD. It is especially important for a a naïve undergraduate like me from a foreign land, with no previous experience in a research lab.

Question. What are the downfalls of “literature search” in general vs. PubMed specifically? Or are they the same?
Priya: Searching in general gives a lot of redundant and irrelevant information such as random articles/blog posts etc, most of which are not helpful. But I feel Pubmed search is more streamlined to identify publications of interest. To the best of my knowledge, finding papers is either through Pubmed or a general Google search.

The Research Process is Inefficient

Hence, it came as a shock to me when I realized Pubmed is probably the only database that lets you search for papers in one go. More appalling was the lack of accessibility to all journals and papers one might need. Most journals charge an “article processing fee” for making research work “open access” and unfortunately, many labs are not financially equipped to pay such fees. As a result, research is not freely available to everyone in a timely manner. This is further exacerbated by the fact that the research environment is for the most part competitive, rather than collaborative. A number of my friends and myself have been instructed to be cautious while sharing interesting findings that were still unpublished. Conferences are a great resource of getting to know what’s out there, but most labs are skeptical about sharing their new findings in the fear of getting “scooped”. However, an ideal research environment is one where everyone focuses on asking the right scientific questions, identifies relevant ways to answer the questions, establishes productive collaborations and works toward the betterment of the society. We should create a forum where researchers are able to share their findings with an open mind and get ideas from fellow colleagues- our scientific progress can only be improved by engaging more scientific minds.

Question. This supports ResearchGate. Do you think it adequately solves your challenges? What’s missing?
Priya: Honestly, I need to use ResearchGate more to comment on it. But from what I know, more scientists need to be part of it and be made aware of it as well.

Funding Issues have changed Science

In the recent past, there has also been a rapid decline in funding. NIH funding is being allocated to projects that have a high probability of being a success. Hence “risky” projects have taken a back seat, which means innovation, the most important quality of a research, is at stake. I did my PhD in a lab that was hit by the funding decline. The lab worked at the junction of basic and translational research. We performed in vitro experiments and identified secreted Hsp90α as an important pro-motility factor. We then performed in vivo experiments in mice and pigs to prove the importance of the protein in wound healing and breast cancer metastasis. Compared to labs that worked on drug screening, my PhD lab, similar to most labs, focused on identifying something that could definitely benefit people, in the long run. Hence, I had to restrict my ideas to experiments that we could afford. The funding decline also meant that scientists were not open to trying out new things. Scientists feared any change and “played safe” with their ideas. The goal has now become “publish or perish”.

Question. What does this physically mean? Is your research stifled?
Priya: The funding decline did not affect access to literature. My experience is mainly from inability to buy the right reagents/chemicals required for research. Recombinant proteins and antibodies are expensive and sometimes, you prefer buying these only from specific companies due to the quality. Thus, in case of a funding decline, you either do not buy the reagents you need or you settle for one of less quality. Thus research does get stifled.

Question. What does it mean to “play safe” and not really expand scientific discovery?
Priya: I can comment on this from the perspective of a researcher working in cancer biology. Cancer is a complex and heterogenous disease and 1) multiple targets are required to treat the disease 2) multiple approaches to identify the targets are required. Thanks to modern technology, there are high throughput screening methods to simultaneously identify multiple targets specifically expressed by cancer cells. However, these methods are expensive to execute and many labs are unable cannot afford them. Thus, many target proteins are understudied, which means the number of “druggable” targets in cancer patients are being understudied.

From the point of view of a lab with low funding, identifying a single protein that is specifically expressed by cancer cells can fetch them a paper and therefore more funding. This highlights the “publish or perish” scenario, but does nothing to advance scientific contributions to cancer research. In other words, “playing safe” affects scientific progress globally.

Research Lacks the Right Tools

As a graduate student, there were a lot of things I learned, apart from the science. I spent a lot of time identifying the right reagents for my experiments. Any student who has done western blotting will know that many times antibodies either a) do not work, b) have a lot of background noise or c) have non-specific binding. Not all antibodies work for all purposes. Hence, antibodies from a specific company may not all be amazing. Even though I use literature as a starting point, it requires a lot of trial and error, which means a lot of time and effort on the my part. But, not many resources have helped with this. I used VWR as an online resource to purchase reagents. However, VWR is merely a database that lists different companies offering a specific product. It provides no information on how good the product is.

Hmm, this gets me thinking…I’m happy spending time on Amazon getting a case for my iPhone. Amazon gives me a table comparing different vendors, with specific features of each vendor, the associated product, the price and reviews of each. Why can’t there be an Amazon for science? It would make a huge difference to my professional life. I would highly appreciate a resource that does this and provide reference papers that have used the product. Similar to the star ratings we find on Amazon or eBay, it would be very helpful and time saving for researchers if there were a good rating system for life science reagents too.

Identifying the right protocol is a challenging task too. We need to conserve time and resources…it would be a great help if some online platform provided references to other researches that have already standardized the protocol, along with information on the reagents used.

Question. How do you currently search for protocols and products?
Priya: Currently, I use a general Google search to look for protocols and VWR for most of my purchases. The problem is mainly that I get a lot of redundant and irrelevant information. In addition, it is difficult to verify if the protocols have been standardized and come from a reputed lab or institution. Also, there’s no proof if the protocol has worked for them or not. Hence, if I have a visual evidence (aka reference papers), it is more convincing.

Conclusions and More Ideas

I consider myself very fortunate to have obtained admission into a prestigious graduate program in the United States. I came to the country with no prior experience. When I look back, I think that certain tools may greatly benefit many young students. One tool I can think of is a visual pathway explorer. Biological processes are dynamic in nature and I have always wanted resources that can teach me a specific biological process more visually. Currently, I use YouTube for this purpose, but it does not have videos for everything. I think it would be amazing to have an interactive tool where a pathway/process is taught illustratively and questions can be posted on the website, which will be addressed by experts. Imagine how many ideas can be sprung out of this simple idea!

Science is fascinating, but with challenges of failure and lack of accessibility to resources, it can get pretty frustrating too. Thus by providing the right accessibility to constructive collaborations, the right protocols, and the right reagents, the life of scientists can be more productive.

Question. If you wanted to make research more efficient. What kind of company would you make? What products would it have? Assuming you have an unlimited budget and/or time.
Priya: I would create a company that acts as a liaison between labs and service/reagent companies. For example, for my research, I would need diverse products ranging from a specific custom-made cell line, lentiviral knockdown systems, CRISPR/Cas9 reagents, specific transgenic mouse models or diverse services ranging from microarray analyses, RNA seq analysis etc. Diverse types of companies provide these reagents and services. For example, IDT is the company I use to generate my oligo constructs for cloning while I use Jackson labs for mouse models and Affymetrix for microarray services.

My company would be like a liaison that obtains the needs of specific lab (s) and get in touch with these diverse companies. Every lab can create a profile on the company website and use it as a single portal to add these diverse orders. My company would communicate with the different companies and provide the reagents & services to the labs. This will be the service wing of the company. In addition, my company will also provide analyses software for the different high throughput techniques at a subsidized rate for customers. If feasible, certain bioinformatic analyses might also be performed by my company for a subsidized rate.

In addition, my company will also have a scientific wing where I would have a board of expert scientists, postdoctoral researchers and other experts in different fields, for eg, neuroscience, immunology, proteomics etc. If a lab is confused about how to address a specific goal, they can post the questions via their profile on my company website and they will be addressed by the respective experts.

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SciPrice and SciGine are Solving Challenges in Research

Many of the challenges that Priya has outlined are now being tackled by SciPrice and Scigine.

SciPrice is a marketplace for antibodies which focuses on providing all the information possible for each product. It’s an Amazon for Science.

Scigine provides protocols for Biology from reputed journals along with the materials that were used. In combination with SciPrice, both services help make research more efficient.

Thank you for reading!

By Karthik Raman, PhD

I am a PhD Bioengineer specialized in utilizing heparan sulfate and heparin for drug delivery to brain tumors. My expertise lies in the interface between polymer chemistry, protein biochemistry, and cellular biology.

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