bunsen

A Lesson Left on the Back Burner

“Don’t get frustrated if you can’t follow my movements,” my mentor says for what seems like the 25th time today, “with practice, you will pick up techniques as well as develop your own.”

I watch him maneuver his hand around a capped test tube, removing the metal lid with his first finger and sterilizing the opening with his second finger curled around the body of the tube before carefully removing however many microliters we need to continue the experiment, then placing the lid back on the test tube. Just a few swift, effective movements.

“Okay,” he says while passing the pipette to me, “your turn.”

I should add that by “sterilizing,” I mean passing the opening of the test tube under the blue flame of a Bunsen burner. All of that without burning himself in less than 30 seconds. How could I possibly follow?

Regardless of the “how,” I know I have to figure it out. I take the pipette with a deep breath. Exhale. He chuckles and says, “take your time, Diego,” inciting a laugh of my own. But I listen to him, and take my time.

With shaky hands, I try to mimic his movements. With shaky hands, I fail to do so. He shows me another way to sterilize the tube and ensure that it doesn’t become contaminated. I keep trying to mimic the movement, and each time I have to use the alternate route, it feels like failure. Day one and the feeling is already there.

For a little while, I forgot about the perfectionist who lives inside of me. I forgot about the person who wrote down every single number after the decimal point that the calculator spit out to make sure my answers were accurate. I forgot about the person who rewrote the same sentence 100 times before deciding it was “okay.” I forgot about the person who never thought anything was good enough if it wasn’t good the first time.

“Very good, Diego!” Carlos says.
“Good?” I say, “I couldn’t do the trick.”
“That’s okay.” He answers, “With practice, you will get it down. I know you can.”

Practice. I remember the perfectionist.

Then I process the last thing he said. Belief. In my abilities.

I’ve known Carlos for about two months now. When I was searching for a lab to work in for the summer, I immediately emailed Professor Diego Acosta-Alvear. The summer before my first year, I spent a lot of my free time sifting through pages of research opportunities and research labs. I found information about the MARC U*STAR program and worked towards it during my first two years. I read about Diego’s lab as a first year and was immediately intrigued by his work. It only made sense that, after receiving a position as a MARC scholar, I went straight to Diego. The first week, I was thrust into the world of RNAs and cell stress responses as he explained his work to me. The second week, I was introduced to the lab.

“Talk to people and figure out what you like best. Remember, this is your summer. Take advantage of your newfound resource,” advised Diego.

As I went around the lab and learned about everybody’s project, one person stood out to me. Carlos. Everybody in the lab had their unique strengths, and Carlos was no exception. He introduced his work to me and I immediately recognized its importance. It was in both the way he delivered his idea, and the way he involved the bigger picture. As I watched him in lab, I realized how much I enjoyed the way he taught others. I witnessed his kindness towards his lab mates and his genuine care about their wellbeing. After a couple of weeks, I asked him if I could join his research team and I started working with him during the last three weeks of spring quarter, mostly shadowing and occasionally doing the work myself.

It has been three weeks of the MARC program, hours of research have given me countless opportunities to practice what I call “THE trick” on the Bunsen burner, as well as many other techniques. I’m no professional, but lately, I’ve been thinking about my growth and feeling proud of my abilities.

Carlos asks me, “how do you feel in the lab?” I confidently respond, “Really good, actually. I love the work, the people, the failure and the success.”

The perfectionist is still there, but it’s a lot quieter now. It’s easy to forget that you are a student and that you are still learning. Don’t let forgetting that become your fallout. It’s an important lesson. Now, when I feel like a failure, I just remember the words of my mentor: “Take your time. Practice. You can do it.”

MARC  Posted by 08 Aug 2019 / 0 comments

The Importance of Research

Our professors make occasional references to the innovative work in the research on campus, but as an undergrad, we barely get a glimpse of what truly goes on in lab. In first-year lab classes, we are introduced to basic laboratory techniques and gain an understanding on lab safety. It is amazing to see how much lab courses mirror experience as an undergraduate researcher.

For example, in my intro bio lab courses, we had multiple lab practicals that tested our pipetting techniques. Getting the technique down seemed simple enough, once you got the hang of it in lab class. It seemed pretty straightforward, and I never gave it much of a second thought. However, in lab, mastering this technique is important to every experiment. Just last week, I was pipetting volumes of 1 microliter, and a quick slip on my finger could have led to us having to redo that part of the experiment. Another example is learning how to use a centrifuge. Without properly balancing the device, the centrifuge could be damaged, or someone could get injured in lab.

For me, there were also aspects of my undergraduate research experience that were somewhat unexpected. Obviously, you can’t learn all the techniques and procedures that you will have to follow in courses, so there is a certain level of on-the-job training, if you will. To me, I felt as if I was playing a game of catch up, working my way up to understand everything my mentor and the other graduate students in our lab was talking about. One big learning gap for me was my lack of prior experience in coding/computer programming. Without any formal experience, my best bet was to take to the internet and start learning MATLAB through online tutorials. In between work on our experiments, I often search up a tutorial or troubleshooting guide, in an ambitious attempt to finish a code that I have been working on for a couple weeks now.

Although you may be the only undergrad in your lab, it helps too keep in mind that you are embarking on a journey that hundreds of students have began before you. As a Gorman scholar, this feeling of self-doubt is further lifted from your shoulders when you talk with undergrads involved in research in other departments, who face similar challenges as you. The CSEP internships are an amazing experience which I’d recommend to any undergraduate. The programs teach you the applications of research, and how you can appreciate the bigger picture of what your project plays a role in accomplishing. An important part of scientific research is that it is incredibly collaborative, as each paper seems to pass the baton onto the next scientist to help solve the larger problem. In the Dey lab, my project involves making improvements to mRNA sequencing technology, and this project can be applied to scientists studying development or localized diseases. Whether or not your undergraduate experience inspires you to pursue a career in research, it is an incredible opportunity that will heighten your appreciation for science as a whole.

Gorman  Posted by 02 Oct 2018 / 0 comments

A Surprising Pollutant Discovery During my Trip to Panamá

For many middle and upper-class Americans, going to another country is a vacation. People traveling out of a comparably wealthy place often expect blue skies, crystal clear waters, and cocktails served to them at a poolside bar. However, for lower class travelers and students trying to explore the world, this picturesque scene is often not in the budget. Luckily, this can very often make for a more realistic and wholesome experience when exploring a new place. I think that this may be because it indirectly helps young travelers avoid taking their “bubble” with them when they get off the plane.

Over summer break, my friends and I found ourselves traveling Central America on a tight budget in an effort to gain new experiences and collect ourselves before our senior years at UCSB. We expected to see the bright blue, lionfish filled waters at every beach once we arrived via speedboat at our popular tourist destination: Bocas Del Toro, Panamá. After the thunderstorms cleared, we were in search for a beach close to the main town, and we stumbled upon Istmito Beach. Istmito was nudged at the crossroads of the local cemetery and a low income neighborhood. At first sight, we saw Panamanian kids playing soccer downstream of a small pier, on which european travelers from the hostel around the corner were sitting and sunbathing. However, when we looked closely at the tides of this beach, strangely enough we saw thousands of tiny balls washing within the black waves. We initially thought that what we were seeing were pebbles.

My research here at UCSB in Michelle O’Malley’s lab has always encouraged me to ask more questions and to be curious about things that seem out of the ordinary. This curiosity seemed to follow me outside of the lab in this case.

After visiting this beach and coming back to UCSB, I took a look at a few of these balls and discovered that what we saw and what the kids swam in appeared to be some synthetic fiber. The resources and encouragement provided by my graduate student mentor allowed me to inspect the sample via microscope. After taking a look, it seemed that the balls were composed of cotton or another type of fiber. This fiber originates from humans, rather than my original hypothesis which was that the balls were composed of algae.

This is a less salient manner of pollution compared to what we see on the news: heaping piles of trash in the middle of the ocean and straws inside of sea turtle’s noses. However, seeing this type of pollution at a local beach raises the point that in less developed parts of the world there are all manner of pollution caused by human presence. In this case and possibly many others, we found this pollution within 2 square miles of crystal clear beaches that are often the foci of Instagram posts about paradise. Unfortunately, this pollution often accumulates and affects the beaches next to the homes of people running stores and hostels, since the town is much less concerned with losing money from tourism in these locations.

At the end of this eye-opening trip to Panamá, I came to understand that being an undergraduate researcher at UCSB has instilled curiosity into my continually developing world view. The fact that the world is saturated with questions is exactly the reason why training to become a scientist is a satisfying and endless endeavor.

Guest Post  Posted by 04 Sep 2018 / 0 comments

The Layers of Medicine: My Summer at Stanford

“Can I get a 5:0 Monocryl and 6:0 Fast Absorbing Gut?” I thought after hearing Dr. Aasi repeat the remark over fifteen times a day through the span of my internship I would get tired of the phrase, but the request was precedent to surgery and watching Dr. Aasi perform surgery was number one on my list of preferred summer pastimes. During the short amount of time I was able to spend at Stanford Medicine shadowing Mohs practitioner and surgical oncologist Dr. Sumaira Aasi, I learned more about the nature of doctors and their teams than I did about the details of medicine. Of course I was intrigued by the effectiveness of Moh’s medicine in removing basal cell carcinomas and the many reasons skin grafts can die after being sutured to an open wound and the exact temperature of liquid nitrogen–all fascinating topics of conversation–but the paramount take away from my summer at Stanford was being able to observe the intricate workings of a hospital clinic.

Dr. Aasi and her team resemble a house of cards. It seems as if they can read each other’s minds, always knowing the whereabouts of every patient’s wandering family members and the next tool Dr. Aasi needs placed in her hand. The team flows, with every factor of the equation solved for. One nurse enters a room as soon as the first exits, the rooms are prepped just in time for the doctor to enter, and the slides are presented at perfect moments between surgeries. There is an unspoken understanding of the way things need to go. My first few days of the observership I was following Dr. Aasi around like a lost puppy, equally befuddled and awed at the clockwork that was their clinic.

The Outside: What Field of Medicine?

Dr. Aasi performs surgeries regarding lesions on the skin that can take the form of basal or superficial squamous cell carcinomas, cysts, lipomas, or keloids. Basal and squamous cell carcinomas are skin cancers that are contained in the outermost layer of the skin, the epidermis. The cells on the topmost layer of skin are called squamous cells, which are constantly shedding and being replaced by basal cells, located in a lower layer of the epidermis. Basal and sqaumous cell cancers are most commonly developed from sun exposure and poor sun protection. They are found in areas such as the face, back of the neck, arms, ears, or hands. The most  common type of skin cancer is a basal cell carcinoma, a slow growing cancer that is minimally invasive and rarely spreads throughout the body. A squamous cell carcinoma is less likely but has a higher likelihood of spreading to other parts of the body because it is found in deeper layers of the skin.

The two main surgical procedures to treat these carcinomas are Mohs surgery and excisions. The Mohs procedure is practiced when there is a skin cancer present on visible areas of the face. Mohs is beneficial because it preserves as much healthy skin as possible and keeps scarring to a minimum. This treatment involves subsequently removing layers of skin that contain malignant cancer cells and immediately sending them to the lab for analysis of leftover tumor. If cancer cells are identified under the microscope, the doctor goes back in to remove another layer of the skin, and the process is repeated until there are no leftover cancer cells. Similar to removing a rotten chunk of an apple, the removed portion is tested for residual impurities. The process is repeated until the patient’s slides are all cleared, Dr. Aasi averaging between one to three stages per patient.

An excision surgery is performed when the skin cancer is located in more conservative areas of the body such as the back, chest, or abdomen. The procedure removes a larger portion of the skin and cuts deeper than Mohs procedure. The doctor incises around a predictable margin for the tumor and immediately sutures the incision without waiting for lab results. Then, the sample is sent to the lab and the team notifies the patient of the results in a few days.

The Middle: What I Learned from Watching Surgery

The first surgery I watched was a Mohs procedure on the outer cartilage of the ear. After the nurses numb the area by administering shots of lidocaine with epinephrine, Dr. Aasi enters and incises around the tumored area. She gently holds and lifts the thin layer of skin using a pair of tweezers. Next she makes systematic cuts under the lifted layer of skin and runs them smoothly up the incised area until the entire sample is cut loose. Dr. Aasi also makes two grid-like cuts along adjacent sides of the incision to orient the sample in relation to the patient’s body. These grid marks help her understand what she is seeing under the microscope. The practice seems routine, almost too easy for Dr. Aasi’s experienced hands. Her steady, composed form makes the evidently complex operation seem simple.

The nurses take care of most residual duties such cautery and pressure dressings between stages, while Dr. Aasi is usually out the door and already halfway to the lab before I can even turn toward the exit. After each stage, the clinic sends the sample of skin to pathology where Dr. Aasi sketches the shape of the sample and applies a different color dye to each edge. These preliminary duties help her visualize a general map of the sample under the microscope. By adding the blue, black, and red dyes, Dr. Aasi distinguishes top from bottom and left from right in relation to the sketch, which is always drawn in regard to the patient’s left shoulder. The pathologists flatten and cut the sample of skin into several slides that are put through an automatic dye machine and then arranged for the doctor to read.

The first time I observed Dr. Aasi viewing specimens under the microscope I was baffled at the speed at which she zipped through the slides and made calls to clear the patient. While all the cells looked like identical blobs to me, she was able to differentiate between  the misshapen island cells of a tumor and the sweat glands, hair follicles, nerves, and normal skin cells the body produces. Over time Dr.Aasi taught me how to distinguish the cluttered, island like appearance of cancer cells from the rest of the body’s creations. Usually colored darker than the surrounding areas, they show up in clusters, resembling nests of irregularly shaped cells. If any tumor is seen under the slide, Dr. Aasi determines which area of the original sample the tumor is in based on the grid marks and dye she placed on the specimen. Characteristic of Mohs, in subsequent stages Dr. Aasi removes skin only from areas where tumor is still present, preserving as much healthy skin as possible.

The Inside: The Lessons That Changed How I View Medicine

While Dr. Aasi operates on patients she often strikes up conversations about random yet intriguing topics. We find ourselves talking about how classy the Obama family is one minute and the next Dr. Aasi will be reminiscing her college days and how she actually had to go to the library and read a book to do research. These spur of the moment exchanges characterize my most valuable glimpses into Dr. Aasi’s life. She discloses stories about her career in medicine, ranging from her experiences as an attending, the hardships of adjusting to new hospitals, and some of the scariest moments she’s had in an operating room. These stories inspire through character, they mean something because they make the hospital come to life, and it’s stories like this I hope I’m able to tell someday.

Through my time at Stanford I learned so much more than I thought I would. Not just about the nature of dermatologic surgery, which proves to be a job for a doctor, artist, and perfectionist all in one, but also about the unforeseeable speed at which life moves and the pure joy that comes from being able to help people. From hearing the stories of hundreds of patients and watching the doctor cure their illnesses, I got a firsthand glance into the miracles of medicine. After witnessing the pain and suffering associated with cancer, I was moved by the resilience of patients faced with circumstances beyond their control. I was stirred by the selflessness of doctors and the amazed by the rhythm of hospital clinics. I learned more from this experience than could ever be written in a textbook, urging me to learn by facing a constant rollercoaster of emotions. But most importantly I learned to never forget sunscreen.

 

Guest Post  Posted by 22 Sep 2016 / 0 comments

A Tale of Two Laboratories

          Perhaps one of the greatest points of contention for a college student is deciding what comes next: academia or industry. Being one of the few fortunate students able to participate in both an internship at an academic neurobiology lab and an internship at a local biotechnology startup company during my spring quarter of sophomore year, I have a few pearls of wisdom for those who do not yet know for certain which type of internship suits them best. And, being a literary art enthusiast who tries her best to entertain herself and her audience when writing blog posts, hereby commences the official entry below:

 

          It was the best of quarters, it was the worst of quarters. All the while completing the last installation of her introductory biology, organic chemistry, and physics courses, a young girl with an ambition larger than her arms could hold endeavored to continue her work in ye old Laboratory of Neurological Sciences while exploring the new realms of agricultural chemistry to help solve her village’s strife with quickly rotting produce.
          Girl, as she preferred to be called, had been enticed by the Industrial Order of Agricultural Science and its proposition to cure local and world hunger with their developing product. She believed her skills would be adequate enough to contribute positively to the order of brilliant, young scientists, and adored the impassioned effort each of the members of the order gave. At the same time, she was just as equally passionate about her work in her village’s Laboratory of Neurological Sciences, and could not bear to part with the project that she and her mentor have worked on for a year together.
          After three months of laborious undertaking with both ye old Laboratory of Neurological Sciences and with the Industrial Order of Agricultural Science, Girl had found herself with much insight to document in her personal journal. The experiences had been fruitful and worth her while, but she had noticed very stark discrepancies between the two research positions that had graced her.
          Her work with the village Laboratory of Neurological Sciences involved much less interaction with her fellow laboratory peers, aside from her own mentor and the principal investigator of the laboratory, although the occasional conversation with an expert in a particular laboratory technique was necessary. She appreciated the independence, however, as having a project tied so closely to her name made her feel as though she were the mother of the project, having to attend and care for the project as it matured into a complete research publication with statistical results that can be shared for the rest of the world. In this realm, she was in charge of herself and her surroundings. There was much flexibility with her project, with many forks in the road as experiments fail and succeed. If one result proved that another path must be taken to discover prospective cures for neurodegenerative disorders, she followed the path, even without entirely knowing what may await her at the end. Ultimately, her research success depended on the amount of effort she was willing to put in; the more seeds one planted, the better the harvest.
          Work with the Industrial Order of Agricultural Science followed a different pace, although the general requirement of her was to perform productive research on a given subject. In this case, the subject had been organic chemistry in the context of preserving agricultural produce. Unlike with the pathway she followed with her work in ye old Laboratory of Neurological Sciences, there was a specific destination to be reached with the Industrial Order of Agricultural Science. She may take a variety of routes to get there, but she had to get there. Deadlines were more strictly enforced; while this aspect may have deterred some from the prospect of an exponential amount of work, she knew she had a team of close colleagues who were almost always available for assistance when needed. The research was a team effort, and each member served as an appendage to the larger body. Projects were often mandated by the head, but without the proper functioning of each body part, the body could not thrive.
          Two laboratories, both with the interest of facilitating research to be of benefit to the populace. And yet, the two laboratories exist as separate worlds with science being the only foundational similarly between the two. As different as the experiences may have been for Girl, she found many benefits in participating in research in both ye old Laboratory of the Neurological Sciences and the Industrial Order of Agricultural Science. And although she had intended for her journal entry to be a determining factor as to what she hoped to pursue in the future, she found herself no further from where she began. Each option was equally as enticing to her. At this point, she knew not which direction to follow, but knew one thing and one thing alone: that as long as she is contributing to the world of scientific research, she is satisfied.

 

          Essentially, having both academic and industrial research experience has not really helped me narrow down my professional pursuits after completing graduate school, but the time will come when the decision will make itself apparent to me. (There’s still some time, thankfully.) As for you, reader, who managed to tolerate my awful attempt at a not-quite-story to explain what I believe to be are the major differences between academia and industry, only you can go forth and experience one or the either (or both) and make a decision for yourself. If possible, explore internships in both fields. If given only one option, even if it is the option that you do not believe is the one you are leaning toward, try it anyway. Personal experience insight is valuable, and research, despite what setting, is research.

EUREKA  Posted by 21 Jun 2016 / 0 comments