Author Archives: Casey Kuka

Thoughts on the Summer

Wait, it’s week eight already? NO!! Stop! Wait! I want to keep going. . .

This summer has been such a valuable experience. I’m just going to list some of my favorite takeaways and such, based on my experience in lab and listening to the wise words of the faculty speakers:

1. I’ve been reminded that being obstinately persistent and hard-working will consistently serve you well.

A book I recently read, aptly titled Lab Girl*, sums this up nicely:

“Any sign that the newbie regarded his or her time as of any value whatsoever was a bad omen, and the loss of so many hours’ work was a telling trial of this principle. As a corollary, clear your mind and go home, distract yourself for the evening, and come back fresh the next day to start over. The other is to immediately resubmerge, put your head under and dive to the bottom, work an hour longer than you did last night, and stay in the moment of what went wrong. While the first way is a good path toward adequacy, it is the second way that leads to important discoveries.”

A woodpecker doesn’t drill a hole into a tree by poking at the bark once or twice then taking a two hour break. Hacking and pecking and picking at a problem or question while it’s still fresh in your mind is the best approach to making any progress. This is good news for me because I have used this method in school and extracurriculars for as long as I can remember, having a tendency to obsess over things, losing sleep and pulling my hair out until I figure them out. It’s not always fun, but when you finally, finally solve your problem, the satisfaction can’t be beat. It was encouraging to have this program drive that point home in me again.

*highly recommended book, after just eight weeks in a lab I could relate to it in a way I never could have before and it made me laugh and think and look at plants in a new way. promptly obtain a copy and read it. this has been a PSA

2. I’ve started filling my toolbox of science-related skills!

At the beginning of this summer, I knew vaguely how to operate a centrifuge and had used a micropipette perhaps twice. Now I’ve collected a variety of lab skills and know-how: operating centrifuges of all shapes and sizes for cells and bacteria, using sterile technique and the cell culture fun that comes with it, dexterity in the operation of micropipettes, multi-channel pipettes, and motorized pipettes (henceforth rewarding myself the title of “Pipette Ninja”), PCR and gel electrophoresis, protein production and purification, western blotting. . . and blah, blah, blah. I’m just excited because this learning and acquiring new skills and using them to potentially generate new knowledge has probably been one of my favorite parts of summer. I want to keep going and filling my toolbox! And pipetting things. I love pipetting things. . .

3. The lab is not a glamorous place.

There’s a lot of work that happens that isn’t actually going to produce data. Instead, it just gets you one-sixteenth of a step closer to producing data. Take protein production and purification in E. Coli, for example: it’s a 3-day long process involving two liters of bacteria in LB broth that produces just one milliliter of proteins to use in your experiments (if you’re lucky!). Also, a lot of work isn’t actually going to produce data just because it isn’t going to produce data. Experiments fail often. Repetition is routine. There’s also a lot of waiting for things — waiting for cells to incubate or a gel to run or a film to develop.  Science is slow. Finally and most importantly of all, the lab is, overall, a smelly place. I’ve started a definitive list of Odoriferous Things in the Lab and I’m going to share it with you:

  1. E. Coli: Just disgusting. No words.
  2. Beta-mercaptoethanol: gasoline + hard-boiled eggs with a light touch of farty funk
  3. The mice used in experiments: pet store, ultra-concentrated
  4. The autoclave that day someone decided to throw some used mouse bedding in it: inside-out colon

Generally, one or more of these smells will assault your delicate olfactory neurons each day in the lab.

4. I still have no idea what I’m doing.

And that’s okay! BSURF has exposed me not only to real science in general, but also so many different types of science that are all so interesting. When I entered Duke, I, like 99% of everyone else, was premed. And I still am! Only now I’m also considering the merits of pursuing a PhD. And an MD/PhD. And still just the MD. I plan to just keep working hard and enjoy the ride, doing things I am genuinely interested in, and let things unfold. If the faculty seminars have taught me anything, it’s that no matter how certain you are about your future, it will probably turn out exactly how you didn’t think it would, but you still find yourself exactly where you want to be. So why worry?

((That’s a wrap! Before I close out my final blog post of the summer, I want to express my sincere gratitude to Trinity College for funding BSURF, and Dr. G and Jason for helping make it the experience it was: a rich summer of reflection, frustration, and late night laughter with awesome people. It’s been a blast!))



“There is Always a Path,” Science Outreach, and Chlamydia

This title suggests a blog post that’s all over the place, right? Well, I wanted to talk about all three aspects covered in one faculty seminar this summer so hold on to your hats. Whee!

I’ve truly enjoyed all of the faculty speakers this summer; it was great to hear about their individual paths to Duke, and to learn about their research and how they got interested in their specific fields. I ultimately decided to choose Dr. Raphael Valdivia to talk about, though Dr. Kontos, Dr. Williams, and Dr. Gersbach were all close runners-up (for very different reasons!).

Dr. Valdivia’s talk resonated with me for multiple reasons. Most importantly, Dr. Valdivia was adamant that if you are willing to put in the effort and seize available opportunities, you can achieve anything you are striving for. As he said, “There is always a path.” As someone whose mantra has been “hard work always pays off” ever since I practiced a beam routine for a gymnastics meet 30+ times and placed first for it eight years ago, hearing a researcher at Duke speak similarly about getting where he is today was encouraging. He also offered some unique advice, such as being open to new experiences as a scientist and not becoming comfortable with just working in the lab day in and day out, and reading papers outside your area of expertise for new ideas.

Another topic Dr. Valdivia touched on was scientific outreach efforts, and the importance of educating the public on scientific matters. This is also something I’m very interested in, because there is so much misinformation out in the vast and shifting oceans of the World Wide Web. As an avid reader of food blogs, I’ve seen a lot of blogs promoting various lifestyles for optimal health, which is great. . . until they spread false or poorly researched information, influencing their sometimes huge following of readers into believing things like, oh, cooking honey makes it toxic (

Here’s a paragraph that’s a particular gem in case you were too lazy to click the link:*

“In addition, Ayurvedic dietary principles warn that consuming honey that has been cooked, baked or added to hot liquids contributes to ill health over time. The reason is because honey that is cooked becomes like glue. The molecules then tend to adhere to mucous membranes in the digestive tract producing toxins, called ama. The literal meaning of ama is undigested food or toxins stuck within the digestive tract. It is considered to be the root cause of most ill health in Ayurveda with heated honey one of the most difficult forms to detoxify.”

All right. Okay. Someone has clearly never learned the basics of human digestion, yet is acting like an expert and causing this information to be circulated. And the author’s readers thank her for sharing this IMPORTANT information, never again to expose honey to any form of heat before consuming it for fear of coating their GI tract with honey glue.


Science outreach is incredibly important to preventing misinformation like this being spread, and it’s something I hope to try getting more involved in beyond posting comments attempting to refute information on blogs.

I went off on a tangent there, but I’ll get back to Dr. Valdivia now to wrap up because what he studies is also cool: chlamydia infections. Chlamydia bacteria can infect a cell and prevent it from undergoing apoptosis in response to this rude intruder. Thus, when the cell divides, it splits into two cells with the chlamydia bacteria. Then those divide, and so on, resulting in scores of cells infected with the freeloading bacteria. Dr Valdivia’s lab studies how the bacteria take over and prevent cell death from occurring, and he showed us a few videos of cells dividing and spreading the chlamydia. Microbiology is just the coolest!

Thanks for sharing your science, words of wisdom, and path to success, Dr. Valdivia!

*Just for fun, here is another one of my favorite misinformation/pseudoscience posts by a food blogger who clearly never took a science class:

This is a hilarious post for multiple reasons, not least of which she’s bashing airplanes for not having the air in the cabin be 100% pure oxygen (omg there’s nitrogen being pumped in too! *Gasp,* it’s a conspiracy)

A Wooden Roller Coaster

In my irrational subconscious, I feared the summer might go something like this:

Walk into the lab. Never fully grasp what the heck was going on. Cost the lab thousands of dollars on reagents flushed away in countless botched experiments. Spill something worth the entirety of my fellowship stipend*. Break some extravagantly expensive piece of equipment. Accomplish nothing more than generating a small landfill worth of pipette tips and earning the title of “that mathematically inept undergrad (who also broke that extravagantly expensive piece of equipment).” Definitely never get results, leading to shame and dishonor upon myself.

Instead, it’s gone more like this:

Walked into the lab. Sort of understood what the heck was going on. Repeated one experiment six times without ever improving the results and questioned my skill (or lack thereof) as a scientist, until it was determined that one of the chemicals used in the experiment was faulty (weight lifted, but, SERIOUSLY?!??!?!!). Spilled nothing — yet (knock on wood! KNOCK ON WOOD!!). Aspirated liquid up into a mechanical pipette and had a small panic attack until I learned the issue was easily rectified by replacing the relatively cheap filter (SIGH of RELIEF). Accomplished generating a small landfill worth of pipette tips and earned the self-proclaimed title of “that mathematically inept-when-being-watched undergrad,” along with stumbling upon a paper that helped my mentor and PI greatly with a project and running experiments that actually succeeded (excitement!).

So it’s going better than I expected, is what I’m saying.

I got my first results around week four, which was relieving (“My poster will not be a barren landscape!”), gratifying (I can do science after all omg), and exciting because they look pretty, too — all graphical and columnar and ombre-colored (sorry, but you should know by now: Casey = science nerd). I’m still working on some other experiments but should have results for those soon as well. It’s definitely not been a water slide-smooth ride to the finish — more like a wooden roller coaster, with lots of little bumps and ridges that are irritatingly unpredictable, but keep things from becoming dull. There have been setbacks (dead cells *sad face*), problems (ionomycin that’s a DUD!) and, of course, plenty of user error (let’s leave our cells out of the incubator overnight! yay!**), but I’ve come to just say “Welp, that’s science,” and take it in stride. Every day is different, and that makes it interesting. The summer has slid by so quickly and I can’t believe our poster session is almost upon us; it’s been a rich and fulfilling learning experience in the Abraham lab and I’m not ready for my project to end!


*Not that I would expect anyone would trust me so early on to be unsupervised with a $4,000 bottle of something. Heh.

**Amazingly, this little brain fart did not kill my cells (C166s are tough little suckers), the experiment somehow still worked, and you’ll probably see the results on my poster. HA!

Chalk Talk Reflection: The Gut and the Brain

First off, everyone’s projects sound so interesting! I’m such a nerd but it was so cool to finally get a glimpse of what everyone else is working on this summer. From heart tissue regeneration to brain technology that can help paraplegics  walk, BSURF fellows are working on some really awesome stuff. One of the talks I found especially intriguing was Chad’s project on enteroendocrine cells and neurons. As a huge foodie, the topic of how the gut and brain interact is something I’m really interested in (quick deviation for a cool article about there being taste receptors in the gut:, so it was exciting to learn about some of the research happening in that area. Enteroendocrine cells are cells in the gut that have projections called “neuropods” that are similar to the axon in a neuron, leading to the question of whether the enteroendocrine cells are able to communicate with nerve cells via their unique anatomy. Chad’s project is focusing on proving that a connection between these neuropods and nerves in the gut exist. Hormones are typically responsible for sending messages about whatever is going on in the GI tract to the brain, so it’s fascinating that there is possibly a way for the gut to communicate directly with the brain. It would be interesting to also know why such direct communication is necessary, along with the type of communication being conveyed — is it about pain, fullness, etc.? — and how that might be applied in the future in terms of human health.

Once again, I truly enjoyed listening to everyone’s talks this weeks. Thanks for sharing your research!

A Day in the Life: Cells, Cells, and more Cells

When your research project depends on delicate little organisms known as “cells,” day-to-day life in the lab is always a bit different. Regardless, my days usually begin the same way: I come into lab in the morning, vaguely sticky from my bike ride there in the humid morning sun, and dump my backpack in my mentor’s office. I grab my lab notebook and head into lab, where I pull on my gloves and start removing bottles of media (basically just a solution that provides a nice, utopian environment for cells) and any other solutions I might need for experiments or procedures that day out of the 4° (aka the refrigerator) and place them in a water bath to bring them to room temperature. Then I check on my cell cultures. Cells are basically fragile, very boring pets that cling to the bottom of a culture flask, happily growing into a single layer, and they have to be looked after for optimum health.


a happy home for cells. . . usually

source: Thermo Fisher Scientific

When they’ve almost completely covered the bottom of the flask (that is, reached “confluency”), they are ready for use in experiments. Or, they must be “split” — collected and divided amongst multiple new flasks — so they can continue proliferating. However, sometimes they don’t behave as you want. If it’s a bad day, you walk into the lab, excited to get started on your experiment. You open the incubator, obtain your flask of cells presumably bathing happily in their bright pink media, and check them under the microscope only to see — what! — the cells have detached from the bottom of the flask and are drifting languidly, a guarantee that they are quite dead and possibly contaminated. Sadly casting away any thoughts of advancing science even one timid step forward, you bleach your cells and send them down the drain, along with all of the other fluids you used to prepare them since you’ll never know exactly where the contamination originated. Then you have to make new media and prepare a new flask of cells from your frozen stock, and then there’s nothing to do but wait until the next day when your previously frozen cells have readjusted to their new life in the warm belly of the incubator. If it’s a good day, your cells are alive and ready for whatever experimental abuse you throw their way. If it’s a really good day, you’re able to put in a full day’s worth of work, and the experiment you’ve been working on for the past few days works out and you get beautiful, tangible, blessed results. Most days are usually just good days.

Once my reagents have come to room temperature, I spray down the hood where all work that requires a sterile environment takes place with 70% ethanol and wipe it down. Then I remove all of my stuff from the water bath and attack them with healthy squirts of ethanol. (Once you’ve had your cells get contaminated, you will never take disinfecting your bottles of solutions lightly ever again.) Then I wipe them down with paper towels and place them in the hood. Now I can finally remove my flask or plate of cells from the incubator and get to work. A lot of times, if I’m doing an experiment rather than just cell culture upkeep, this involves pipetting various treatment solutions onto cells on plates, and then putting them back in the incubator to essentially marinate overnight. Other times an experiment may require that cells sit only 10-30 minutes or so as you wait for reactions to occur. Overall, I spend a lot of time waiting for things. This is when I basically just chill in my mentor’s office and read papers or a book. Once my cells have sat for as long as necessary, I can then treat them with a buffer that causes the solution to change color depending on what happened between the cells and treatment. Next I usually run diagnostic tests on them with a plate reader, a cool little machine that hits the wells of cells with a laser and spits out a number for each well that corresponds to the intensity of the color in each well, which can in turn be placed in excel and translated into a nice graph.

If I’m lucky, I go eat lunch with the lab technician, Taylor, at around noon. Sometimes I go earlier, and sometimes much later — it all just depends on what procedures I had to do in the morning. Regardless, it always means a nice 30 minute socialization break at a table outdoors.

After lunch, I sometimes don’t have much else to do. I may have another experiment to run or perhaps one to finish, or I might just have to take care of my cells. If there’s nothing I need to do, I will usually follow Taylor around as she works on various procedures around the lab, and sometimes she will also teach me how to do some of the procedures (Example: I was able to run my first PCR and gel electrophoresis yesterday! Very exciting, I know). If Taylor’s busy, I will hang out in my mentor’s office again until he comes to get me and show me how to do something. Although some days I’ve been able to finish everything before lunch, I am typically able to leave lab at around 4.

And that’s a wrap of a day in the life of this amateur scientist!

If You Give a Mast Cell an Antigen


This is a slightly longer post than usual, but I didn’t want to gloss over anything important and risk comprehension for the sake of brevity. Also, I’m just really excited about my project and its future applications (I even added some quick cell watercolors to augment your learning because 1. art is fun and 2. I really had nothing better to do), so this is also me nerding out. Heh. So with that, let’s forge ahead!

You’re out at a restaurant with your family and decide to splurge on dessert; in particular, a fudge brownie sundae. Upon its arrival, it appears as magnificent as it sounded on the menu: a squat slab of dense cake, oozing gooey bits of chocolate chips, supporting a smooth scoop of vanilla ice cream, all topped with a delicate, twirling ripple of whipped cream. After only a few bites of this indulgence, however, your chest tightens. Your throat feels like it’s trying to suffocate itself which has greatly compromised your ability to breathe. You realize your dessert of choice is a hazard to your health not due to its extravagant calorie count, but rather the fact that it must have been in contact with peanuts some way or another, which, unluckily for you, you are deathly allergic to. At a young age, your immune system took offense to this lowly legume, and now you’re being rushed to the hospital in anaphylactic shock all due to your forgetting to question whether your dessert of choice had been created in a peanut-free environment.

What’s happening here? Clearly your body has rejected something it considers a threat to your health and therefore evil, but what’s behind this dramatic response?

In two words: mast cells!

A type of white blood cell involved in allergies and  fighting off pathogens, mast cells can be found at an array of sites around the body, most predominantly mucosal tissue (tissue that comes into contact with the outer world often, such as your sinuses) and the vasculature. Mast cells are stuffed with granules, which are essentially small sacks containing mainly proteases (enzymes that break down proteins) and some chemical compounds such as histamine. Mast cells also sport antibody receptors on their membrane that will bind with antigens when any are present in the body.

mast cell. . . aka cellular bean bag

When this occurs, a complex reaction pathway is triggered in the cell that ultimately leads to the release of the mast cell’s granules. The mast cell can regenerate new granules later, but what about the ones released? Well, they’re having a grand time causing havoc, either on pathogenic invaders or, in the case of an allergic reaction, on the body itself. 

When mast cells located around blood vessels come in contact with an antigen, degranulation occurs and the granules are released into the interstitial fluid and inevitably the bloodstream. The inner lining of blood vessels is made up of endothelial cells, which are simply a type of epithelial cell, and these cells endocytose (a fancy way to say “eat”) the granules. This choice of snack is just as poor as that of the hypothetical person with a peanut allergy eating something contaminated with peanuts, and the cells die, detaching from the basement membrane of the blood vessel. This leaves holes in the blood vessel, allowing fluid to rush in and the blood vessels to dilate, ultimately leading to a drop in blood pressure corresponding to anaphylaxis. So what exactly is it about the granules that triggers this cell death? That’s where my project for the summer comes in.

here’s the TL;DR version for your viewing pleasure

Mast cell granules contain, among other compounds, three different proteases that are unique to mast cells: tryptase, carboxypeptidase A, and chymase. It’s hypothesized that chymase is responsible for killing the endothelial cells. So, my summer thus far is focused on in vitro (basically, in a plastic plate and not something living — that would be in vivo and, well, super awesome) tests of this hypothesis, involving collecting granules from RBLs (Rat Basophilic Leukemia cells, which behave similarly to mast cells) to place on plates of cultured endothelial cells in varying amounts and seeing if the endothelial cells die. Then, to confirm that it is the chymase that is the main problem and not other compounds, the experiment will be run with a chymase inhibitor, and the amount of cell death will again be determined and compared to that of the experiment run without a chymase inhibitor. From there, the type of cell death must be determined (apoptosis, which is “clean” cell death? Or pyroptosis, which is basically cells exploding?). These are the first steps necessary in the process to eventually considering the use of an antichymase drug to use in tandem with an antihistamine to help completely squelch the symptoms of an allergic reaction. There’s a long way to go before that point, but I’m excited to be working on the very beginnings of such a project!


Always Ask “Why”: The Distinguished Career of Dr. Soman Abraham

It’s 4:00 a.m. The sun is snuggled sleepily behind the horizon, and even the birds are still snoozing. Dr. Soman Abraham, PhD, however, is already awake — and in fact, may have been awake for a full hour already, toiling away on papers and writing grant proposals. At 6:00 a.m., he takes a walk with his wife, and by 8:00, he’s in the lab, ready to spend the next ten and a half hours of his day there.

Such motivation to start his day at what many would consider an ungodly hour of the morning indicates that Dr. Abraham has found his passion in life. Was an academic career involved in researching mast cells something he always aspired to? Well, not exactly. Dr. Abraham began building his path to research at Ahmadu Bello University in Nigeria, where his fascination with microorganisms and how they caused disease through processes invisible to the unaided eye led him to major in microbiology. From there, he went on to Newcastle University in England for his PhD, where he began studying the bacterium E. coli and its methods of attack in urinary tract infections (UTIs). It was at this point that Dr. Abraham, greatly influenced by his mentor at Newcastle, decided he wanted to pursue postdoctoral training, thus cementing his journey to a career in academics. After postdoc training at the University of Tennessee in Memphis, where he worked on developing a vaccine for UTIs, he traveled to Umeå University in northern Sweden for a year for further training with E.coli, this time focusing on their genetics. From there, he returned to the United States, where he went to Washington University in St. Louis to continue working on studying E. coli and vaccines for UTIs. Soon, however, his research would take a twist.

In 1995, while at WashU, Dr. Abraham was examining the tissue of infected mice when he happened to glimpse some mast cells around the area. He became curious about the mast cells, since, at the time, no one really knew much about them, other than the fact that they had been implicated in allergic reactions. After further observation, Dr. Abraham discovered that mast cells would release their granules (essentially small bundles full of enzymes) in response to bacterial invasion. In 1996, he published a paper on this topic that ended up Nature, a prestigious scientific journal, and cracked the field of study on mast cells wide open.

In 1997, Dr. Abraham came to Duke (hooray!), where his lab studies salmonella, yersinia pestis (the bacterium responsible for the bubonic plague, or “Black Death”), and the dengue virus, all in the context of mast cells. What does he enjoy most about research? Not working at the lab bench! His impatience with the tedious work of such things as pipetting and following protocols to the letter leads him to stay, for the most part, away from hoods and centrifuges. What he finds most enjoyable about research is the fact that he gets to consider questions that others have not addressed before, and enjoys coming up with new hypotheses and discussing them with others. It is this teamwork in puzzling out an idea that he finds most pleasurable. Additionally, he loves to mentor trainees, finding satisfaction in watching them develop and grow as scientists. His advice for novices in research? Always ask “why”: why is this being done? Why are we doing it like that? In Dr. Abraham’s opinion, there is no better way of proving your knowledge of a subject than being able to understand it well enough to translate it into layman’s terms. And that, of course, means asking questions.

Everyone has to start somewhere, just as Dr. Abraham did years ago, as an undergraduate who only knew he was interested in bacteria. Today, he teaches PhD students in multiple areas including pathology and immunology, is the director of graduate studies in pathology and the director of the Duke Summer Research Opportunity Program, and runs a lab not only at Duke, but also at Duke-NUS Medical School in Singapore, where he likely continues to ask “why?” every day, continuing to stretch the boundaries of knowledge on mast cells and their potential in preventing disease.

I Messed Up: Week 1 Adventures of an Amateur Scientist

“I think I made a mistake.”

These were not words I wanted to be saying to my secondary mentor, Haewoong, but, alas; I couldn’t hide out at my workspace in the biosafety cabinet forever and hope things would magically resolve themselves. As he quizzed me on the steps I had followed, it quickly became clear that I had made a small but fatal error in the notes I had frenziedly scribbled down while watching Haewoong perform the procedure the previous day. This is not the first time I’ve made a careless mistake, and it definitely won’t be the last. However, it’s these little mistakes that teach me the most; mainly because I will remember the error forever and therefore never repeat it!

It’s the end of my first week in the Abraham lab, and I’ve already made countless little blunders, from setting my micropipette to aspirate the wrong amount of liquid to throwing the coverslip for the hemocytometer* away (whoops) to messing up my experiment of the week on its second to last step. But one of the main reasons I’m here for BSURF is to learn, and learning involves making mistakes. During this program, I hope to learn as much as possible about techniques in a biology lab and gain more skill with the instruments used. I also hope to become more familiar with the theory behind why certain methods are used for certain experiments so that I can one day use that knowledge to formulate my own experiments and contribute to the research on mast cells that’s happening in the Abraham lab. Finally, I hope to gain a better understanding of what exactly the life of a research scientist entails on a daily basis. It’s only been one week, but I feel like I’ve already learned so much and can’t wait for the weeks to come!

Also, before I go, here’s a picture of the cells I’m working with this summer just because science pictures are fun:

Screen Shot 2016-06-18 at 10.14.08 AM


These are Rat Basophilic Leukemia cells. Basophils are a type of white blood cell that behave similarly to mast cells, and this cancerous line of them will divide and prosper almost indefinitely, making them ideal for use in research. I’ll be talking about these a lot more in future posts!

*A hemocytometer is a special microscope slide with a grid on it that makes it easy to count cells. (It also requires a special coverslip that apparently is not disposable. Heh.) It’s not the most exciting piece of equipment, but, to a science nerd like me, I have to admit I find it quite cool. And helpful!