Author Archives: Ella Gunady

Summer Musings

There’s a beautiful laser-cut wood art piece hanging in the lobby of the Co-Lab entitled “I’m Just Here for the Pizza,” inspired by “the moments in life when we go to an unfamiliar place for a certain reason, and we end up with a completely unexpected and nurturing experience.”

When I first stepped foot in the lab eight weeks ago, I knew I was in for an exciting ride. It has, and continues to be, a “completely unexpected and nurturing experience.” Although I’ve certainly enjoyed learning the basics of working in the lab, be it using a pipette or running a gel, my favorite part of this summer has been learning how to think. I’ve learned that research requires a unique approach to thinking, a different attitude and a certain humility. The ways in which I am challenged to think in the lab are distinct from the ways I am challenged on, say, a math test or a chemistry problem set. While the challenges I encounter on a homework problem or a lab write-up can usually be solved by a quick trip to office hours, I love that challenges in the lab often have no easy answer. Inherent in the nature of research is the idea of not knowing–of standing at the frontiers of what is known and pushing until the boundary moves.

I’ve been pleasantly surprised by the ways in which my lab experience has affected my daily life. As I read more and more about the extent of plastic pollution, I find myself packing wooden utensils and a reusable grocery bag in my backpack as often as I can remember. Instead of dumping dirty plastic containers in the trash, I try to make the effort to rinse and recycle them. While my efforts are just a drop in the ocean, I think that learning about the plastics issue has pushed me to be a better citizen of Planet Earth. In a culture that values efficiency and saving time, I have learned that the “inconvenience” of washing utensils and containers for reuse is, indeed, worth my time. I think this lesson has been as valuable to me as any lesson I’ve learned at the bench.

Of course, I would be remiss not to mention the people who nurtured my experience this summer. I am so thankful to have had wonderful mentors who have guided me as I’ve stumbled along, whether by training me at the bench, teaching me to think critically, or inspiring me with their enthusiasm. I will always be grateful to my lab mentors and the BSURF program for giving me a chance and supporting my summer experience. I’m excited to be continuing in the lab for the rest of the summer and into the school year. Challenges await, but adventure is calling! I couldn’t be more thrilled.

A collection of random thoughts about a film, the microbiome, and the uncertainty of life.

For the past few days I’ve been raving to my friends and family about a documentary I recently watched called Fed Up, which explores the rise of childhood obesity and finds deep roots in the American food industry. The film highlights the ways in which the food industry has sidestepped government efforts to encourage healthy choices–everything from replacing fat with sugars in those appealing “low fat” foods; to aggressively advertising junk food to children and convincing Congress to call pizza a vegetable. 

Since watching this film, I’ve been more conscious about what I consume. It turns out that there are a multitude of reasons to be aware of what you put in your body; Dr. Lawrence David studies one you might not think of–your microbiome.

This Tuesday, Dr. David shared with us his career path and his current research on nutrition and the microbiome, the community of microbes that dwell in your gut. Much of his current research involves feeding people particular foods and studying changes to their microbiomes. How do they study changes to the microbiome? You guessed it–stool samples! While I grimace at the idea of studying other peoples’ stool, Dr. David seemed to think the science is worth it. These are a couple notes I jotted down during his talk:

  1. The microbiome field is the ripe young age of about 15, birthed by the success of the Human Genome Project, which drove down the cost of DNA sequencing. Dr. David pointed out that this new field came about not from a particular hypothesis but from a new technology. Science is full of unexpected surprises!
  2. Dr. David got to go to Thailand for one summer to study his own microbiome during a year-long study. When I got over the initial shock that he took samples of his own stool every day for an entire year, I thought about Dr. David’s actual point when he talked about his experience abroad–his academic path wasn’t confined to a lab or a classroom but took him all the way to Thailand. He got to immerse himself in another culture and indulge in its street food as part of his education and career. Again, science is really full of surprises.
  3. Lady Gaga was at Dr. David’s high school prom! Just thought that was pretty cool.

I’m thankful to have had the opportunity to hear from so many faculty members at Duke–about their successes and setbacks and the windy road that brought them to where they are today. All of their paths are unique, similar only in their promise of unknown adventures and a future that is never certain. And while the idea of uncertainty is daunting, I take comfort knowing that the faculty I heard from embraced uncertainty, took chances and let the currents of life lead them to unexpected places. And despite–or perhaps, because of–all that uncertainty, now they’re all doing what they love, whether that’s studying mantis shrimp, finches–or even stool samples.


Generating a library of mutant enzymes to degrade plastic

As plastic pollution accumulates in the ocean, it becomes a growing threat to marine and human health. Ideonella sakaiensis is a recently discovered bacterium that digests polyethylene terephthalate (PET), the plastic primarily found in single-use water bottles. This bacterium secretes two enzymes, PETase and MHETase, to digest PET and use it as a source of carbon and energy. The process by which PETase and MHETase digest PET is currently too inefficient to be useful for pollution clean-up. The goal of my project was to generate a library of mutant PETase enzymes in order to create a variant of PETase capable of digesting plastic at a rate rapid enough for practical use. To generate this library, we used error-prone PCR, in which Taq and Mutazyme polymerases introduce random mutations while replicating the PETase gene. Individual sequences from the PCR product were obtained through molecular cloning using a 2.1-TOPO vector system and competent DH5alpha E. coli, followed by Sanger sequencing. Sequencing confirmed that error-prone PCR successfully introduced mutations into the PETase gene. Furthermore, successive rounds of error-prone PCR caused an accumulation of mutations within the gene. These mutant PETases will be tested for efficiency in PET digestion in a future study.

New day, fresh page.

My favorite part of life in the lab comes at the start of every day, when I get to flip to a fresh page in my lab notebook. I’ve always loved recording things, so you can imagine my excitement when I got my very own super-official-looking lab notebook, with its pristine black hardcover and exactly 100 pages of green-lined graph paper, each blank page promising a new scientific adventure. 

My lab notebook has become home to protocols, experimental set-ups, data, and observations. More importantly, it has become a way for me to reflect on the successes and failures of my experiments. While each day is inevitably different from the last, my days in the lab–like the pages of my lab notebook–follow a similar pattern.

Objective. Each page of my lab notebook begins with a few notes on my goals for the day, which I discuss with my mentor, Hailey, first thing in the morning. It’s often easy for me to get lost just doing the motions–pipetting and running gels while losing sight of the big picture. Setting clear goals at the beginning of each day has become an important anchor for me this summer, a way to remind myself of how each experiment contributes to the goal of my overall project.

Protocol. In the “Protocol” sections of my lab notebook, I record exactly what I do throughout an experiment, whether that’s setting up a PCR or transforming E. coli. Sometimes, this part of my day consists of pipetting until my hand starts to cramp up. Other times, it consists of setting up a gel and holding my breath as the computer loads the image of my gel to reveal the success or failure of a day’s work.

Results. Here I include observations or pictures describing the results of my experiments. Sometimes with sad face doodles, other times with an excessive number of exclamation points. At the end of each day, Hailey and I discuss our results and what they mean; we troubleshoot and plan for the next day.

Despite the loose structure of every day, I love the dynamic nature of life in the lab. I love that I don’t always know what my week will look like, because each experiment depends on the results of the last. I love the anticipation of walking into each day not knowing whether my experiment will work or not. And from that anticipation, I learn to value my failed experiments as much as my successful ones–each have equally important places in my notebook.

Mouse Makeovers and Helium Voices

The words “Mouse House” kind of freak me out. Every time I hear it mentioned in lab, I can’t help but imagine walking between rows of cages piled ceiling-high, hundreds of beady eyes glowing in the darkness and watching my every move. I’m sure the Mouse House is not the house of horrors that I imagine it to be; nevertheless, I have so much admiration for everyone in BSURF who is working with mice for the first time this summer.

This week, I loved hearing Evelyn give a chalk talk on her experience in the Mooney Lab, researching the ultrasonic vocalizations of mice under the influence of helium. During our first week of BSURF, Evelyn and I sat on the bus together one morning on the way to our labs, and I was so intrigued as she described her project. She mentioned dyeing the backs of some female mice with platinum blonde hair dye to distinguish them from males, and placing mice in chambers with helium to observe changes in their voices during mating. It all sounded worlds away from my own project and was at once fascinating and a little amusing. I mean, can you imagine being a mouse and getting your hair dyed platinum blonde?

I’ve loved reading Evelyn’s blog posts and was excited to hear her give a chalk talk about her project. Two things in particular stood out to me. First, since Evelyn is studying whether or not mice are aware of the change in their voices when exposed to helium, she looks for changes that could indicate this awareness. This includes changes in the pitch, frequency, and amplitude of the mice’s ultrasonic vocalizations, and changes in mating behaviors. I think it’s really cool that Evelyn is studying something as abstract as awareness by observing concrete changes in vocalizations and physical behaviors. I suppose that this is a cornerstone of science as a whole–studying abstract or complicated concepts by observing tangible changes–but this whole science thing is all still new to me, and I’m constantly amazed by the ways in which scientists approach science. 

Second, Evelyn talked about how her lab’s research could have applications to mental disorders like schizophrenia, in which people are unable to distinguish between self-produced and external voices. It’s mind-boggling to me that Evelyn’s project draws a connection between things as seemingly disparate as mice in helium and schizophrenia. I suppose that’s yet another cornerstone of science–drawing connections between vastly different things because those connections help us understand the world a little better. I’m excited to hear about how Evelyn’s project progresses and about her adventures with her new mouse friends!

Spicy Noodles and Words of Wisdom

At my first lab meeting, I was both amused and mildly horrified to watch my PI compete in the Spicy Noodle Challenge. (Think instant noodles whose packaging has pictures of chili peppers with evil eyes. And a chicken breathing fire and holding an about-to-explode bomb.) At my second lab meeting, he walked in with a paper bag, pulling from it an assortment of hot sauces which he carefully laid out in order of spiciness and sampled one by one with wings from Heav Buffs.

When I sat down to chat with Dr. Jason Somarelli for the first time, I knew little about him besides that he had a ridiculously high tolerance for spicy food. I’m thankful to have had the opportunity to hear about his experiences and learn from his wisdom. These were a few of my takeaways:

1. Life is non-linear

Dr. Somarelli received a Bachelor’s degree from Nazareth College, a Master’s degree in biology from the State University of New York at Brockport, and a Ph.D. in Biological and Biomedical Sciences from Florida International University. After completing his post-doctoral training at Duke, he stayed at Duke as a Research Associate and is now a Medical Instructor at the Duke Medical Center and the Director of Research for the Duke Comparative Oncology Group. However, behind this seemingly straightforward, LinkedIn-simple chronology is a story of resilience in the face of disappointment, of a relentless pursuit of education despite a string of rejections from graduate schools, and of a professor at FIU who “believed in [him] when nobody else would.” When life took unexpected turns, Dr. Somarelli turned moments of rejection into opportunities to learn perseverance, a lesson I think must have contributed to Dr. Somarelli’s continued success as a scientist.

2. Science is hard, even for scientists.

“Challenges in science are constant. They’re challenges that you face professionally, but it feels like they’re directed at you, personally.” Dr. Somarelli explained the idea of Imposter’s Syndrome in the scientific community–how incredibly smart scientists feel like they don’t belong and fear being “exposed” as less intelligent than they really are. Tacked above Dr. Somarelli’s desk is an essay published in the Journal of Cell Science titled, “The importance of stupidity in scientific research.” My favorite quote from the article was this: “Science involves confronting our ‘absolute stupidity.’ That kind of stupidity is an existential fact, inherent in our efforts to push our way into the unknown” (Schwartz). After weeks of feeling stupid in the lab, “stupid” has taken on a new, more positive meaning for me, and I take comfort in knowing that embracing stupidity makes great scientists.

3. Science should never be just about you.

One of Dr. Somarelli’s biggest goals is mentoring. “I don’t think I’m going to win a Nobel Prize, but I think my enthusiasm for what I do can bleed through onto people. If I can do that for enough talented people, one of them will be able to revolutionize something. Mentoring has far-reaching consequences,” he told me.

I’ll leave you with something Dr. Somarelli said that I found really beautiful–

“Science is a challenge because you don’t know what you’re doing all the time. It’s equally amazing for that reason.”

I’m so grateful for the opportunity to work with Dr. Somarelli this summer, and excited to witness some more spicy challenges!

Fish tacos with a side of… plastic?

In 2014, Malaysia Airlines Flight 370 disappeared. The world held its breath as week after week, crews in the air and in the water searched for clues. Every once in a while, a glimmer of hope: search teams in the sky spot what they think is debris from the missing plane–only to find out that it’s trash. Carelessly discarded plastic garbage that now wanders on the water like men lost at sea.

Amid the frustrations of the search for Flight 370, a spotlight shone on another tragedy–the fact that we have turned our oceans into massive dumpsters. We dump an estimated 8.8 million tons of plastic into the ocean every single year (National Geographic). The problem is that plastic isn’t biodegradable–with a lifetime of more than 400 years, the plastic garbage in our oceans isn’t going anywhere unless we do something about it.

The fact that our beautiful oceans have become garbage dumps is an outrage in itself, but our negligence has even more far-reaching effects. Every year, marine animals are strangled by plastic debris. Birds starve to death because their guts, so full of plastic, physically can’t hold food. Chemicals from microplastics may even travel up the food chain into the fish tacos on your dinner plate and eventually end up inside you.

This summer, I’m working on a Bass Connections project on the bioremediation of plastic pollution. Our project was inspired by a 2016 paper written by scientists in Japan who isolated a bacterium that secretes enzymes which break down PET, the plastic found in single-use water bottles (See the 2016 paper here). The goal of my project is to create a library of mutant enzymes and select the enzymes which can most effectively break down PET. Hopefully, this project can contribute to future work on a solar-powered bio-reactor that can be used to clean up areas in need of plastic removal.

I’m really excited about my project! And really concerned about the state of Planet Earth…

If you’re interested in learning more about our planet’s plastic problem, I recommend this article and this article, both from National Geographic. And if you’re not into reading, check ’em out anyway! The pictures are pretty darn powerful.

I found the right room!

It’s a hot Monday afternoon. After my first day in the lab, I’m marinating in sweat and being roasted alive in the Durham heat when a girl at the bus stop approaches with a big smile and asks, “Are you a student here? What do you like about Duke?”

She’s a sophomore in high school touring colleges for the week, and I tell her I love basketball, the grass Duke works hard to keep green, and PBJ sandwiches from Div Cafe. And after that, I tell her about what brought me to Duke in the first place — how back in high school I’d always imagined myself doing research in college and how Duke is a Disney World of research opportunities.

I feel so blessed to be here this summer doing exactly what high school me had envisioned — learning really cool science from really smart people and working with a team to solve problems that matter. As part of a Bass Connections team working on the bioremediation of plastic pollution to conserve marine biodiversity, I’m excited to be working with people from all sorts of backgrounds who care about our planet and want to use science to protect it.

Here are a few things I’m anticipating to do this summer:

1. A TON of reading

While articles from PubMed have never been my go-to weekend reads, I’m learning to love dissecting papers related to my Bass Connections project. Reading scientific papers continues to be a challenge for me, and having to Google what seems like every other word can get awfully tedious. But it’s an awesome feeling to finish reading a paper and think, “Hey, I think I sort of get this…”

2. Learning that it’s okay to ask dumb questions!

Multiple times, if necessary. From previous experience, I’ve learned that nodding my head and pretending to understand when someone is explaining Thing A leads to major regret a few conversations down the line, when they start explaining Thing B under the assumption that I understand Thing A. I’m learning to be okay with not understanding things the first (or second or third) time they’re explained to me, and I’m learning to be comfortable with asking, “Can you repeat that?”

I love the quote, “If you’re the smartest person in the room, then you’re in the wrong room.” This past week, it has at times been overwhelming to feel like the opposite of the smartest person in the room. But I am so excited that I’ll be spending my summer lab experience in the right room, surrounded by some incredibly bright minds and hopefully making some progress in our quest to care for Mother Earth.