Tag Archives: Academic Research

My Research at Tufts: Lipid Nanoparticles

By Jennifer Khirallah, Biomedical Engineering Ph.D. Candidate

Jenn Khirallah holding a gel that analyzed the extracted DNA collected from editing liver cells.

Research at Tufts University spans a wide variety of areas with scientists and engineers that contribute to and advance their fields. I am working in the Xu Lab in the Department of Biomedical Engineering, where we study the use of lipid nanoparticles for small molecule delivery for therapeutic applications.

The Xu lab, located in the Science and Technology Center, is run by Professor Qiaobing Xu. We collaborate with different professors, institutions, and doctors to utilize lipid nanoparticles to deliver a therapeutic cargo for different treatments. These lipid nanoparticles have been designed to target specific organs and cells, such as the liver, lung, spleen, and brain, and therefore acts as a targeted delivery vehicle.

There are many completed and ongoing projects in our lab that have use our lipid nanoparticles in applications such as cancer vaccines, gene editing liver cells, and neurotransmitter-derived lipidoids for brain delivery. I am working on two projects; one project analyzes the use of a liver targeting lipid nanoparticle for treatment of metabolic disorders and the other project aims to analyze and optimize the long-term stability of mRNA-loaded lipid nanoparticles.

I found my passion in this research subject during my various experiences in both research and industry. I worked with different types of nanoparticles for a plethora of applications and eventually found this cutting-edge approach in the Xu lab. The research done in our lab is pushing boundaries and progressing medicine today. Being part of that advancement makes me excited to go to lab every day!

I work extremely independently, and this has pushed me to think more critically and to rely on myself for my needs and goals. I set my own experiments and timelines and am directly responsible for the progress of my projects, which is teaching me about time management, planning, and adaptation. Research has so many bumps that I have learned to adapt in order to save an experiment, which has taught me how to be a quick decision maker under pressure. Overall, the Xu Lab has interesting research and I find the work fascinating. I am grateful to be involved in a laboratory with direct clinical translation and to contribute to the drug delivery field. The technology being developed in this field is revolutionary and can change modern medicine as we know it.

Preparing to Defend

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Preparing to defend my thesis was the most mentally, emotionally, and at times, physically, challenging part of graduate school. After my final field season, I thought it was going to be easy. All I have to do is write. I’ve written a ton. Piece of cake.

I was so wrong.

Yes, as graduate students we write a lot. During my time in graduate school, I wrote scientific papers, grant proposals, popular science articles, blog posts, etc. But I had never written about the same subject so continuously. I started to get sick of my study system (honey bees), which made me sad, because I love honey bees!

When I finally handed my thesis in to my committee, I had to prepare for the actual defense. This was also a challenge. What papers should I read? What is my committee going to ask me? What if they hate my thesis?

In the end, it all worked out. I successfully defended my thesis and the defense was enjoyable! I didn’t need to stress as much as I did.

Preparing to defend your thesis is going to be challenging, but here are some things I realized that may keep you from psyching yourself out too much.

Use a citation manager!

First, a specific piece of advice: start using a citation manager when you get to grad school, keep it updated, and use it consistently! This will make the references section of your thesis much easier to deal with. I didn’t start using a citation manager until year three, and when it came time to write the thesis in year five, I was not happy with past Rachael. I use EndNote but there are many other options and the library hosts workshops on almost all of them.

Keep your committee in the loop.

Throughout your time in graduate school, talk to your committee. Update them on data at committee meetings, discuss methods, ask for suggestions on writing when relevant. If you do this throughout graduate school, your committee won’t be surprised at defense time, and neither will you. If you take the time to get to know your committee members, you may be able to anticipate their questions.

I realize this doesn’t work for that external committee member you may be required to have. When choosing your external committee member, choose someone who knows your field, and read his/her relevant papers. I did this for my external committee member, and I was able to successfully anticipate some of her questions. Also, when it comes to your external member, don’t be afraid to ask around. Ask past graduate students from your lab who they chose and why; ask about their experience in the closed defense.

It doesn’t have to be perfect.

Remember, the written thesis you hand in to your committee is technically a draft. As a perfectionist, this was difficult for me. I was working so hardto make every chapter, every figure, every page, so that it could be publication ready. But with a document that long, it may not be possible in the time you have. And that’s ok. Part of your committee’s job is to suggest edits, which you can then use when/if you publish.

It’s a conversation.

On defense day, I was most worried about the closed defense. What if they hate my research? What if they ask me a question I can’t answer?

Part of these nerves will be alleviated by fostering a relationship with your committee. Also, think of the closed defense as a conversation rather than a “grilling” session. Your committee asks you questions, you answer the questions as best you can. Some questions lead to other questions. It’s just a discussion– a discussion about something you’ve been studying for 4 – 6 years and you know really well.

My closed defense was a fun, productive experience. Sure, I couldn’t answer some of the bigger, theoretical questions, but it was fun to brainstorm and discuss ideas.

Take care of yourself.

Even if you follow all my advice, preparing to defend is going to be difficult. Graduate school is supposed to be hard. Throughout this process (and all of graduate school), remember to take care of yourself.

Countless hours of sitting at a computer takes a toll on your body (this is the physical challenge). Take breaks to stretch or go for a walk. Give your eyes a break from the screen. Drink water. Eat food. (Both sound simple but trust me, you might forget.)

Stay active, whatever that means to you. Do yoga, go for a run, kickbox, get outside, play a board game, grab coffee with friends. And don’t feel guilty about taking time away from school to stay active! Your mental health is important. Your mental health is important. Your mental health is important.

Remember, you are not alone.

Writing a thesis is an inherently isolating process. Don’t let it get to the point where you feel like you’re alone, because you’re not. Talk to past graduate students from your lab (this was my greatest therapy while writing/preparing to defend), attend the graduate writing exchange, visit family, grab coffee with friends (yes, I’m saying it again).

Graduate school takes a village and you have a support system in your mentor, your committee, your friends, your family. Use that support system.

And finally, celebrate!

Following your defense, take time to celebrate your accomplishment! Getting a higher degree takes dedication, ambition, and a lot of hard work. You deserve to be proud of yourself!

Written by Rachael Bonoan, Biology Ph.D. 2018

#GSRS2016

Written by Rachael Bonoan, Biology Ph.D. Candidate

Graduate Student Council (GSC) Academic Chair, Cassandra Donatelli, did a great job soliciting presentations for this year’s Tufts University Graduate Student Research Symposium (GSRS). Throughout the day, there were over 40 different graduate student presentations, representing 20 different departments, from 3 different Tufts schools—Arts, Sciences & Engineering, Sackler, and Fletcher!

Emma Schneider

Of the 15-minute talks I saw (we had so many presenters, there were two sessions going on at once!), one of my favorites was Emma Schneider’s presentation on listening. Emma (pictured right) is a graduate student in the English department who is interested in environmental policy. Emma began her presentation by pointing out that when it comes to environmental policy, there is no lack of people speaking out, there is no lack of data, but there is a lack of listening. Emma then discussed how she analyzes texts about listening to nature, the silence around us, and of course, other people!

Of the shorter, 5-minute talks, the one that stuck out to me most was “MacGyver Robots” given by Vasanth Sarathy (below) of the Computer Science and Cognitive Science Departments. Vasanth is interested in teaching robots how to change how they react to an object based on context. The example Vasanth used was a knife. When picking up the knife to cut something, the robot should pick it up by the handle. When picking up the knife to give it to someone (or something?), the robot should pick it up (carefully!) by the blade. If the robot wants to spin the knife (for what Vasanth called a dangerous game of Truth or Dare), the robot should then grab the knife in the middle. But—asked Dr. Kelly McLaughlin from Biology—why a knife? Why not a pen? Unlike a pen, explained Vasanth, the knife also has a moral context. During the 5-minute presentations, we also learned about the microbes in kimchi, factors affecting conditional probability judgements, facial recognition systems, tail regeneration in tadpoles, and silica nanoparticles (among other things!)

Vasanth Sarathy, a fellow blogger!

Dr. Benjamin Wolfe

Following the 5-minute talks was the keynote by Dr. Benjamin Wolfe from the Biology Department. Ben studies microbes in…cheese (and other fermented foods but cheese is currently his main study system). During his talk, Ben briefly discussed his research (which you should check out!), and then focused on the importance of communication and gave the audience some tips on how to be good communicators.

So—why should we communicate our academic research and how do we do it? In communicating our research, we can understand it better. Ben started with an anecdote—the person who motivates him to communicate his science is his mom. A first generation college student, Ben had to explain his research to his mom in a way that was accessible. Being able to explain his research to his mom—and now cheesemakers—has made Ben understand his research on a deeper level. Also, communicating to the general public can help us to find unexpected things in unlikely places. The picture that Ben is pointing to is a piece of trach (specifically, a cigarette butt) that he picked up off the sidewalk and then put on a nutrient plate to let the microbes grow. This was part of a pop science piece that Ben wrote for a magazine (Lucky Peach).

Which brings me to the “how.” Basically, just do it. Sign up to present at symposia that aren’t specific to your discipline (like the Tufts Graduate Student Research Symposium!), write for magazines that are for the general public, start a blog. Ben also stressed two points that are important for successful communication: visuals and respect. Take pictures of your study system, make infographics, have fun with it! Who doesn’t like a good visual? And importantly, respect your audience and their beliefs. Don’t talk down to them, don’t belittle them; instead, excite them by showing them what they don’t expect (like microbes growing on a cigarette)!

Following the successful keynote was the poster session and reception with wine, cheese, and other refreshments. I presented a poster and found it was a great way to meet other graduate students from other departments and other Tufts schools. (All poster session and reception photos are courtesy of Psychology graduate student Clint Perry.)

If you are interested in checking out some of the other topics covered during the symposium, check out @TuftsGSC on twitter (we live tweeted all day!) and #GSRS2016! Hope to see you there next year!