The Other 99% of Our DNA…Is That Where Cancer Is Hiding?

Cancer, at its core, is caused by genetic changes to cells. Whether by environmental, biological, or lifestyle factors, the regions that regulate the growth and development of cells are disrupted such that the cell begins to multiply uncontrollably. With time, the group of cells grow into a tumor, which can then spread throughout the body, stealing resources and causing physical harm to healthy tissue.

A simple schematic of how cancer develops.

Taking it a step further, it stands to reason that some mutations confer a selective advantage to cancer cells, allowing them to out-compete normal cells and outlast our immune system. Otherwise, it would be difficult to explain how cancers spread so aggressively. These mutations are what we call “cancer drivers”, or in other words, mutations that drive cancer.

Already, there has been extensive literature in this field. Scientists have identified numerous genes linked to cancer. However, the vast majority of these discoveries are made in the protein-coding regions of our DNA. There’s likely a lot more to the picture—after all, the coding region only comprises 1% of the entire human genome.

Along with Dr. Allen, I will be trying to identify cancer drivers in the non-coding regions of the human genome. The plan is to intersect two existing datasets: one from the international Pan-Cancer Analysis of Whole Genomes (PCAWG) study, and one from Dr. Charlie Gersbach, who is a Duke faculty in the Department of Biomedical Engineering. 

The PCAWG study provides a dataset of possible cancer drivers in cancer cell genomes. From over 2,600 whole genome sequences, they were able to identify thousands of SNPs in non-coding sequences by using various computational pipelines and statistical models. However, the study warns that the SNPs they discovered may not all be cancer drivers, since it’s highly unlikely that every identified mutation confers a selective advantage to cancer cells.

This is where Dr. Gersbach’s dataset comes into play. His lab was able to alter specific regions in the non-coding genome to observe the effect it had on the cell. From this, they compiled a list of “essential regulatory elements” in cells, which are regions in the non-coding genome that are critical for cell growth and development. 

The hope from intersecting these two datasets will be to find regions of high density overlap, where the SNPs from the PCAWG study coincide with Dr. Gersbach’s “essential regulatory elements”. If these regions exist, it could provide compelling evidence to confirm that the mutations in that region are indeed cancer drivers.

Although my project is only the first step in a long road, the hope is that, by discovering more cancer drivers, we can improve our capabilities to assess an individual’s risk for cancer based on their DNA, which could prove vital for saving lives. 

Let’s Science From Home!

If things were normal, this would be Week 5 of BSURF. But, a pandemic and a summer class later, here I am, sitting at home, typing up my first blog post. Crazy, isn’t it?

This year’s BSURF program will be drastically different from previous years. Instead of being on campus with the other BSURF fellows, I’ll be working remotely for the next two months, going to Zoom meetings instead of going into the lab. Not all of it is bad news though. There are certain luxuries that come with working from home, such as setting your own schedule, spending time with family, and being able to eat (!) while working. 

Before I get further, a little about my project: under the guidance of Dr. Allen, my PI and mentor,  I’ll be deep-diving into the datasets of two separate studies. The first is the Pan-Cancer Analysis of Whole Genomes (PCAWG) study, which is an international collaboration that yielded groundbreaking research on cancer drivers in non-coding regions of the human genome. In essence, they took over 2,600 whole genome sequences of various cancer types and located potential cancer drivers (read: mutations that cause cancer) in non-coding regions. The second study is by Dr. Gersbach, who is a professor at Duke. His lab recently produced a dataset of “essential elements” in the human genome that regulate normal cell growth. My goal is to intersect these two datasets to see if there are any common hits between them. To put it simply, we’re looking for cause and effect. If, for example, there is a certain essential element that contains many cancer drivers, it would be the first step to confirming the validity of that cancer driver.  Eventually, the hope is to map non-coding cancer drivers to a phenotypic impact.

For the rest of this summer, I have two goals in mind. First, I want to become comfortable with research and the adventure it represents. In more objective terms, I hope to become familiar with the computational knowledge and techniques required to do research in the field of genetics. More importantly, I want to be able to embrace the daunting challenges and uncertainties that come with doing research. Second, I hope to build meaningful and long-lasting relationships with mentors and peers alike. I’m excited to be open-minded and have conversations, whether that’s about research projects, or about anything, really.

Already, research has proven to be an eye-opening experience. Whether it’s deep-diving into literature or emailing for help, I’ve quickly learned research is by no means a linear process. In reading my first paper, I had to read up on three other ones just to understand what was going on. And that’s what I’m coming to really enjoy. There are endless paths to choose from and avenues to explore, and while there will certainly be challenges to embrace, I’ll be ready to adapt, readjust, and push ahead as readily as ever.

Stay tuned, and welcome to the blog!

My workspace from home!

Only the beginning

Eight weeks is almost nothing in the world of science, where experiments are marked in months and results in years. At most, I can say I caught a fleeting glimpse, a snapshot of a singular moment in the scientific process. But even this ephemeral glimpse was saturated with incredibly valuable lessons that do a little more in clearing the uncertainty shrouding my future. In just these short eight weeks, I was able to experience both the highs and lows of scientific research. I got a taste of the beauty and freedom in asking your own questions and creatively crafting your own solutions, while encountering many unforeseen obstacles along the way. Through this process, I am grateful to my mentors Dr. Ru-Rong Ji and Dr. Chris Donnelly for their close mentorship. I am also immensely grateful for Dr. Grunwald and Anna for their support in this journey of discovering what science means to me.  

This summer was truly an immersive experience I had initially hoped for. In the beginning, I could barely differentiate a microglia from and an astrocyte, but now I can explain the distinct roles they play in the pain system as a whole. I got the opportunity to learn many new techniques, such as behavioral tests and immunohistochemistry, and strategies in general that scientists use to elaborately and seemingly effortlessly answer some of the most mind-boggling questions. Through trials and failures, I was also able to experience the struggles of research: time-consuming results and elusive perfection. However, what I enjoyed the most this summer more than learning any technique is thinking like a scientist, from asking questions, to communicating science to diverse audiences, to assessing the validity of scientific methods. Events such as the chalk talks and poster session have shown me that science is always an ongoing conversation that I’d be excited to be a part of. 

What gave me an even greater sense of what science could mean to me were the faculty talks. It was really helpful to hear the distinct perspectives of different faculty and how many different paths can all lead to the same desired result. From their experiences, I have learned to see scientific research as a humbling relationship, where no one can really outlearn science. These scientists are some of the most knowledgeable people in their fields, yet they have the humility to admit they know nothing when in search of new knowledge gaps to investigate. And so, I feel like I am definitely farther along the “chase” of science I had mentioned the first week but I am nowhere near the end. 

You’ll Never Know if You Don’t Go, You’ll Never Shine if You Don’t Glow

What a summer it’s been! I honestly feel like I’ve aged 5 years this summer, but in a good way. No more am I the freshman with no lab skills who can’t cook for herself to save her life.

From my humble beginnings of accidentally dropping a mouse on the floor and getting bitten by BM046 (alias El Diablo), I’ve grown so much as a scientist and a person during my time with the Mooney lab. Growth isn’t really something you realize until you’re looking retrospectively, so I didn’t notice how far I’d come until about week 7. Creating the poster and presenting it in lab meeting and at the poster session really helped me realize how much I learned about vocal communication, mouse courtship behavior, and how helium turns it all upside down. Though I definitely wouldn’t call myself an expert, I gained so much knowledge in a very niche topic of science and gradually got better at communicating it to others. As Dr. G says, science means nothing if you don’t communicate it, and presentation has never been one of my strong suits. But it’s been so gratifying to watch myself grow from giving a half-informed, nervous chalk talk in week 4 to holding my ground during a 45-minute lab meeting presentation in week 8. If you ever need to know ANYTHING about helium affecting mouse ultrasonic vocalizations, I’m your girl.

But besides my new arsenal of intellectual knowledge and laboratory skills, being in a lab surrounded by cool people has just been so much fun. We aren’t workers in cubicles, competing for promotions and passive aggressively shading each other. We’re friends, and I’m thankful the Mooney lab welcomed my shy self into the silliness that punctuates the work day and makes that 9-5 (or sometimes 8-8) just a little more fun. Katie and Valerie had to make a video abstract explaining innate vocalizations, and filmed us all laughing exaggeratedly and crying loudly in the conference room. Marios had a particularly feisty bird that wrestled its way out of his hand and zoomed around the lab for a few minutes, which is apparently pretty common but freaked me out at first. On Jordan’s last day, we got arepas from Guasaca and took a long lunch filled with jokes and fond memories to send him off.

I said it in my very first blog post, but this summer truly cemented what I know about my career, so I’ll say it in all caps: I WANT TO BE A SCIENTIST! Thank you BSURF for being the experience that confirmed my career goals, the springboard for my future, and the best way I could’ve spent my summer. Thank you Dr. Mooney and my mentor Tom for taking on a shy freshman and helping her grow into a confident, inquisitive scientist. Thank you Dr. G for the pep talks and advice along the way and Anna for tirelessly working to feed us breakfast and keep us entertained. Finally, thank you to my fellow bsurfers for making the hours outside of the 9-5 unforgettable. From the food truck rodeo to donut floaties in the Eno Quarry, it was so fun to explore Durham and get to know you all. I can’t wait to see your careers evolve, have an amazing rest of your summers!

If You Don’t Know, Now You Know

This summer has been an amazing experience. I had no idea that I would learn as much as I did when I first started, and I am so glad to have developed a better understanding for the world of science and found my place within it. And I am so thankful to have done it alongside such wonderful people in my lab and in BSURF, thank you all so much!

One of the biggest things I learned or came to realize is how big the world of science is. From the faculty talks, chalk talks, and the poster session I got to hear about the incredibly diverse and important research brilliant people are doing just here at Duke. Previously I had this notion that once you really get fundamental understanding of a topic, you just move on. But this summer I learned there are always more questions to ask and always new perspectives to take. I learned this while working on my own research project, as I needed to approach my problem differently and ask new questions as I learned more. I also learned that science is an incredibly slow process. Everyone says it, but you don’t fully understand it until you’re waiting for the results you really really want to see and they don’t come. But luckily, research doesn’t stop just because BSURF is over. These eight weeks have been a great introduction, but there’s so much more to discover!

The biggest take away for me this summer was that the research you are doing is useless unless you communicate it. Before this summer, I often overlooked this portion of research and thought hands on work in the lab was most important. But I soon realized that posters, papers, and presentations give your work meaning and direction and make it impactful. I am so grateful for the opportunity to both observe and practice this communication of science, and I hope to only get better from here. Again, I am so glad I was apart of this program this summer. I will surely never look at science or fruit flies the same again.

All good things must come to an end

This summer was fulfilling in all the ways I had hoped. I got the chance to meet great people in both BSURF and my lab. I am so glad I was a part of this amazing opportunity and I am saddened that it is over. My career choice was influenced in a positive direction toward research. I realize the potential for knowledge that a career in research can provide. The intrinsic value of discovering something new is something I never realized until I myself was published in a research paper on amitifadine. To keep it simple, research is a lot more interesting than I had realized. While I am not quite certain on my career path right now, I can say without a doubt that a career in research isn’t off the table.

My ideas of science have changed in a positive way as well. I now can see what properly using the scientific method can discover. In high school all the labs I did had a right and a wrong conclusion. This is the first time in my life where there is no right answer as my lab is the first in the world to discover what it did. The experience of working with live rats is one that I thought I would only have the chance to do years after graduation. The fact that I am able to put this on my resume is one that I do not take for granted.

I would like to thank my P.I Dr. Edward Levin for giving me the opportunity to work in his lab. It was a great experience and I definitely plan on coming back sometime in the future. I would also like to thank Dr. Grunwald for allowing me to be a part of this program (especially since he still let me, I passed the deadline).

Unfortunately, all good things must come to an end and I look toward my future at Duke in a brighter light than before BSURF.

See you in a month everyone!

99%Q & 1%A – Part Two

This was the title of my first blog, foreshadowing the ratio of the questions and answers I would gain over the summer. These questions were made apparent within my curiosity-memory project, but more importantly, in the methods and mindsets to which I approach the unknown. 

In my project, my mentor Abby and I had three primary hypotheses—one would be supported, two would be refuted. My mentor and I were mildly stunned by the latter outcomes; the results didn’t corroborate past literature, stumping us during data analysis. Yet after closer examination and a discussion with my PI, Dr. Adcock, I now realize how much continues to remain hidden in the field of research. As research is fundamentally centered around discovery, it is inevitable that we will experience uncertainty in different ways. We can search for an answer, but sometimes the unknown finds you first. As such, we’ve switched just a few gears, and we now hope to examine self-certainty and confidence within our paradigm.

Even with the data disproving our hypotheses, there was truly nothing comparable to the feeling of seeing your results for the first time. For me, the first look was messy, a massive spreadsheet of data that loomed over me; a final boss before obtaining the treasure. Parsing through the data was gratifying, every line of code ultimately leading to a clean graph and a sense of coherence. Only once I’d obtained a graph did I realize the extent of my work this summer, and it was when my laptop spit out that first p-value that I realized that I had stumbled upon discovery. During my interview with Dr. Adcock, she mentioned that there really is nothing like discovery, but only now do I truly understand the extent of her words.

Even so, science isn’t only success. There were days when work was slow, days where I needed help. Collaboration and communication were repeatedly emphasized by Dr. Grunwald, and these qualities were apparent in every faculty talk, every time I asked my mentor to debug my code, and whenever my newfound friends and I would forget a crucial ingredient while making dinner. Through the BSURF programming, I’ve focused my sights. I have a few new goals, such as how I’d like to work in a wet lab setting sometime in the future so that I can experience all that exists in the research field. I have a few new questions, such as do I want to go into academia, or do I want to practice medicine? Do I want to do neurobiology or neurobiology? Do I love working with humans or cells or mice or computers? Yet even with these questions pressing up on me, I’ve become more comfortable with experiencing the unknown. For now, my primary goal is to follow my project through till the end, and I can’t wait to begin the secondary phase once I return for the school year.

I’d like to thank my mentor Abby for her help since the first day I stepped into the lab. She was truly the guiding force behind this project, and I couldn’t have done it without her. I’d like to thank all the members in the lab for their support and encouragement; seeing you all at the poster session truly made my day. Thank you, Dr. Adcock, for taking me in and making my summer research experience possible. Thank you to Anna for the amazing guidance and help over the course of eight weeks, and thank you to Dr. Grunwald for letting us play with/handle your snakes (and of course, being an incredible leader and program director). As I continue to explore new challenges and discoveries, successes and failures, I’ll remember the mentors and the experiences that first propelled me into the unknown.

   

The End But Not Really The End

This summer I was fortunate enough to spend eight weeks conducting research in the Bejsovec Lab. In addition to this research, I had opportunities both explore Durham and learn from faculty as they shared their research journeys with us. Beyond learning about these journeys, BSURF allowed me to think deeply and critically about how I want to spend my remaining years at Duke and the type of person who I wish to become by the end of my undergraduate career.

I believe my summer experience influenced my perceptions about research in a positive way. Before this summer experience, I never had a clear idea of what the life of a researcher looks like, how slow science could be, but at the same time how rewarding failures and successes can be. I believe among the many experiences I’ve had these past eight weeks, the people that I’ve met and the memories created are the best parts of this summer in addition to learning how to conduct research and how to communicate science.

This summer has allowed me to become more certain of the career I would like to pursue in addition to showing me the multitude of routes that I can take to achieve my ultimate end goal. Furthermore, the advice given to us throughout the past eight weeks has not only made me wiser, but certain that the end of BSURF isn’t truly an end.

I would like to thank BSURF and the Bejsovec Lab for providing me an amazing opportunity to learn and observe science, as well as my fellow BSURF-ers for an amazing summer experience.

BSURF may have come to a close, but its impact is timeless

As May turned to June and I found myself on a flight back to Durham, I was nervous, apprehensive, excited, curious. I wasn’t sure what to expect–how I’d get along with the other students in the program, if I would fit in well with the lab, if I would be happy with what I was doing over the summer.

I remember coming into this program with the hopes that it would help me narrow down my list of possible career choices for the future. It did, in the sense that I got to experience a few weeks of being a researcher and had invaluable conversations with people hoping to become a Ph.D., people well on their way to earning one, and people who are already established figures in their field. There was a lot about a career in research that I wasn’t really aware of, and thus a lot that I got to learn about in these past eight weeks. I can’t say for sure that I now know exactly what I want, but I’m really thankful for having had this opportunity.

This summer came with its obstacles–there were nerves in the beginning, mistakes made, failed experiments. Though many had warned me going into this, including Dr. Grunwald, I was still caught off guard by these setbacks. Research is all about discovery, of course, but being so used to academics, where everything already has its own right or wrong answer, tackling the unknown had felt almost like blind grasps at nothing. Not being able to determine exactly what went wrong in our experiments, what to improve for the future, whether it was me making mistakes or possibly faulty materials or reagents–I was overwhelmed by the uncertainty of research. 

But the beauty of research, and what I got to experience a little by the end of my eight weeks, comes with perseverance, embodied in the moment that ignorance turns to enlightenment. After your efforts pay off and you get results, seeing data that confirm your hypothesis or show you something novel or unexpected, these moments–of the euphoria of discovery, and the words of congratulations from your mentor or the surprise on your PI’s face when you inform him of your possible findings–dull every negative thought you might have once had. I’m relieved to have found myself really enjoying my first research experience, through all of its ups and downs, in a way I always hoped I would.

Looking back on my first blog post, I had a lot of other expectations, many of which might have been a little ambitious for just eight weeks. But I’m looking forward to checking off those boxes one by one as I continue my research in the McClay Lab into the upcoming year. 

A big thanks to Dr. McClay, my mentor Esther, and Michael, as well as the rest of the lab, for being so helpful, patient, and welcoming this summer. Thank you, Dr. G and Anna, for the wonderful eight weeks of learning, working, and evolving. On Saturday, I’ll be heading home with a new mindset and greater clarity, coming away from Durham a little wiser and looking forward to the new semester and journeys ahead.

The End of a New Beginning

This summer has been a great learning experience, both in terms of making me more aware of the science community here at Duke as well as helping me develop skills to become a better scientist. I got the opportunity to meet so many amazing people and hear about the exciting research projects they started this summer. The faculty talks exposed me to a wide variety of research topics and made me realize how so much is still unknown about the world. Beyond just learning about science and research, I also developed skills that will be useful during my remaining 3 years at Duke, as well as further into my educational career. I learned how to effectively read and understand the main points of scientific journal articles, and perhaps more importantly, I learned how to communicate my own science, whether it be by presenting a chalk talk, creating a concise abstract, or making a poster to present my findings.

These past 8 weeks in lab has definitely taught me a lot about science in general and how the whole process of research involves a multitude of steps beyond just running an experimental trial. I realized that steps such as doing preliminary testing, planning an experiment, training animals, conducting control trials, collecting data, processing data, and analyzing that data are just as important as the experimental trial in exploring a research question.

Although this summer’s research experience has not greatly influenced my future career choice, it has showed me what one can do with a background in biomedical engineering and how the science we read about can be applied in a laboratory environment. Attending lab meetings and reading journal club articles gave me a better understanding of what biomedical engineering in a neurobiology context means and how we can use various optogenetic methods to explore novel ideas about the brain.

Reflecting on everything that I was lucky enough to experience and accomplish this summer has made me beyond grateful for the BSURF program. Although BSURF has come to an end, I look forward to continuing my journey in the science world!

It’s Over

 

After a grueling, yet rewarding 8 weeks of lab work, BSURF 2019 has concluded.

My summer experience culminated Friday evening with the Duke Summer Undergraduate Research Showcase (pictured above), during which I presented my poster.

This summer has been a whirlwind, to say the least. Feeding mice, analyzing data, and learning about neuroscience all day, every day for 8 weeks was taxing, but extremely influential in my life and my career. Over the past few months, I feel that I accomplished a lot with my project in the Yin Lab, but more importantly, I feel that I’ve solidified a career interest in academic science— I’ve always seen it as a possibility, but thanks to my research, the faculty talks, and other BSURF programming, I know that this career path and this lifestyle are ones that I would enjoy.

I’d like to thank the Yin Lab and Francesco for hosting/mentoring me this summer, as well as the BSURF program for their support and funding this summer. This formative experience wouldn’t have been possible without the support of these people, and I’m grateful for them.

For the future, I remain hopeful. I plan to return to the Yin Lab and continue my work during the semester. I’ll be taking a full slate of courses and I’ll have to reduce my hours, but I’m looking forward to the next steps of my project and undergraduate experience.

Thank You BSURF!

First and foremost the opportunities to glimpse what research is like in BSURF were plentiful. We heard talks from revolutionary scientists and trailblazers, read countless papers, and presented our work in a variety of methods. These activities revealed examples of the larger picture of life as a scientist: asking questions and discovering answers. This picture of science has only made research more compelling and exciting. 

I cannot begin to express my gratitude for Bel, my mentor for the summer. Her exuberance and brilliance will forever baffle me, and I was fortunate enough to observe both her techniques and thought processes in working to answer her hypothesis. With immense help from Bel, I have acquired some technical lab skills as well as some insight into how to communicate science. BSURF has afforded us with invaluable practice in communicating our work, from talking with fellow BSURFers, giving a brief pitch which one might do in an interview, to creating and presenting a scientific poster. Apart from revealing the shortcomings of Powerpoint, creating and then presenting a poster was a very real yet very minuscule experience of moving science forward, that ended up looking like a few members of the Eroglu lab congregating around my poster to exchange ideas.  

In these eight weeks I have found research to involve slow unsuccessful projects. Since I don’t know enough to formulate questions or work on finding answers, I only experienced a microcosm of scientific research. The big picture of what it means to do research is what is the most meaningful and what I want to do. BSURF has cemented this goal in my mind and I am excited to keep working towards it.  

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.

The Start of Something New

I was interested in BSURF because I had never worked in a research lab before, and I was curious about what it was like. I learned some new benchwork techniques and I learned how to use several different machines. Although some parts were tedious, I was never completely bored. A lot of lab work requires vigilance, whether it’s making sure you pipette a certain amount of buffer into each well or making sure the printer does what you want it to do after you run the print program. And when things went wrong, it felt like a puzzle. A frustrating puzzle, yes, but an interesting one as you mentally replay what you did and try to pinpoint what could have gone wrong.

I learned that 90% of the time, experiments don’t run the way you wanted them to, the reagents you need won’t be delivered when you want them to be, and the lab will run out of dichloromethane just when you need it for your experiment. It is easy to get discouraged, and I think in those moments it’s important to remember why you do research. The breast cancer and MRSA D4 assay projects I’m working on can help to democratize access to healthcare in low-resource settings. These projects have the potential to impact many lives, and I’m excited to be a part of that. I can see why people choose a lifelong career in research.

I appreciated my experiences outside of the lab, too. Despite having been in Durham for all of freshman year, I rarely went beyond 9th Street. This summer, I got to simultaneously explore the Durham area and try not to melt in the heat. I tried new restaurants that I can’t wait to return to this fall, I went to the local farmers’ market, and I finally saw a game at the Durham Bulls baseball stadium. I made some new friends in the BSURF program that I don’t think I would’ve met outside this program, and I pretended to be an adult by making dinner for myself and going to bed before midnight.

I want to thank those who made this summer as fun as it was – particularly Dr. Grunwald, Anna, the faculty members and graduate students who spoke to us, and last but certainly not least, Dan and Jake, my mentors. I also want to thank everyone at the Chilkoti Lab who supported and helped me this summer. This post shares the same title as my first blog post because I truly do see the end of the program as a beginning of my adventures in research. I really liked being in a lab this summer, and while my ultimate career goal of increasing worldwide healthcare access hasn’t changed, how I get there might. There are career options that I haven’t considered before, like pursuing a Ph.D. or working in a lab in industry. I look forward to continuing on my adventures in research this fall and beyond.

Navigating Science and Amazing Opportunities!

I started this summer diving in at the deep end with my first lab meeting, where I was taken aback by how much I didn’t know, but excited to begin. Fast forward to my last lab meeting of this summer, and I can’t believe how much I have learned in 8 weeks. At this meeting, I was presenting my work from this summer and I finally began to keep up with (some) of the conversation.

My summer research experience has definitely surpassed my expectations as I have learned more than I could have ever imagined. I have finally got a sense of the literature in my field and worked with my lab mates to learn more about the focus of the lab. I have also learned many new technical skills including western blot analysis and genotyping.

I realized that I want to continue scientific research and thrilled that I will be continuing this project with this lab in the fall. I am very grateful for my lab mates and mentors who helped me develop a passion for what I am studying. Their support and encouragement really pushed me to to be more dedicated to this experience.

In addition, I am so thankful for the bonds and connections I formed with the BSURF community. We had a lot of fun times exploring Durham or even just hanging out at Swift. As a whole, I feel that this summer has been one of immense growth and I am excited to continue navigating this exciting world of science.

So long, farewell!

You really can’t imagine what research is like until you actually do it.  Coming into this summer, I had absolutely no idea what working in a lab would entail.  When my friends and family asked me how I would be spending the summer, I answered that I knew I was working in a biochemistry lab, which was about the extent of my knowledge about what I would be doing.  I obviously didn’t know what I was getting myself into!

That being said, I am so grateful to have had this opportunity this summer!  Transitioning to lab work can be pretty difficult, overwhelming, and scary, but BSURF provided great advising and mentoring and most importantly, a community of other students who were going through the same transition.  I have really loved getting to know everyone, and I hope I have formed connections that will last throughout my time at Duke and beyond.

I have learned a lot about the nature of research and lab work this summer.  First of all, eight weeks is not a lot of time.  By the time I really got a grasp on what I was doing, it was almost time to leave.  I need to devote a lot more time to a project to get rewarding results.  Second, stuff goes wrong.  In fact, sometimes I think it goes wrong more often than it goes right.  There is always some setback or unexpected problem.  Data doesn’t look nice.  I forgot to add ATP to a sample, or I don’t have enough protein to do an important assay.  A machine gives me a crazy error message the one time I’m completely alone in lab with no one to ask for help.  In the words of my mentor, “that’s science.”  Research is not like the lab component of my chemistry class.  It is messy and confusing, and sometimes you have no idea what’s going wrong or right.  However, my final discovery was that research can be incredibly rewarding.  The first time I quantified a protein gel, put the data in Excel, and created a graph that strongly indicated the expected result, I was amazed.  Hours of work had gone into the creation of that data set, and it was an actual result that I could potentially use.  There is really nothing like the feeling of accomplishment that I felt generating that graph or the feeling of seeing my name and results on a 42 x 36 poster.

I am beyond grateful for this experience: this summer was really the perfect time for me to test out the world of research without having to balance the demands of the academic year.  I can’t wait to see where the future takes me, but I am even more excited to keep up with the scientific accomplishments of the friends I have made this summer.  As Dr. G says, science is communication, and I know that the truly amazing people I have met here will have some awesome research to communicate soon!

So goodbye BSURF and thank you!

Opportunity and Community…Thanks BSURF!

This has been a truly amazing summer and an experience I will never forget. I was not expecting to love my lab and the research as much as I do. I was also not expecting to meet so many amazing young scientists and have one of the best summers of my life. It was truly a privilege to be a part of such an amazing program, to be trained by some of the best and brightest, and to be a part of such a tightknit (and better than Huang) community.

When I joined the Sanders lab I knew very little about Parkinson’s Disease and how the mitochondria could possibly play a role in the most common neurodegenerative movement disorder. Now, I know so much about LRRK2 and how the mitochondria can effect the cell in so many different ways. Even though I feel like I know so much, I am excited to keep learning and understanding the science behind the disease in the upcoming fall semester and hopefully for many to come.

I really emjoyed being in lab this semester. I was scared that research would make science feel like a job and would take away my passion for it. In reality, I loved going to lab everyday and I was sad to leave. I was lucky enough to be in a very supportive environment where everyone would help me not only with the physical parts of doing science but also with the deeper understanding. I am very thankful to everyone in the Sanders lab for teaching me so much about the world of science. They taught me to always ask questions, to question my work just as much as the literature, and that communication with other scientists was essential.

At first, I didn’t know why it was important to understand exactly what every reagant or technique we used did. Now, I am so thankful for the small quizzes on what PIC does or where the DNA went in my protein samples. Teaching me about every small step helped me understand the process at large so much better. I believe in the future this knowledge will help me figure out where I made a mistake or maybe even guide my project in new directions.

I am also so thankful for BSURF for providing me this amazing opportunity. I have learned so much in such a short amount of time about research, communicating science, and what the future might hold. The poster session and the lunch was so generous and it was so amazing to see everybody succeed in their labs. If it wasn’t for BSURF I would not have met my amazing peers who I hope to have by my side for the next three years at Duke. We had some amazing times, whether it was at the food truck festival, in the eno, eating in downtown, or simply hanging out at Swift. I’ll miss BSURF, my lab, and my new friends but I’m glad to say I’ll see them all in the fall.

Final Poster Session!

A Reflection Most Cathartic

Hey readers! Well, after 8 short weeks of gratifying summer research, the time has come for me to graduate from the BSURF program. Yesterday I presented the poster I created detailing the research I performed this summer. It felt satisfying to show so many people the work I am so proud of completing. A lot of the people I talked to had little to no experience in cancer research, so it was good practice explaining my project from the most basic level. I also got into some really good conversations with other cancer researchers, and there was one particular PI that I talked to for a while who focused his research on one of the genes I identified as being upregulated in metastasis. It was a lot of fun walking around the poster session and seeing what other students had spent their time researching.

The poster session marked my last day of BSURF, so I think it’s fitting that for my last blog post I will reflect on the summer as a whole. First of all, I am so grateful to Jake (my primary mentor), Ben (another hugely helpful graduate student in the lab), Dr. Pendergast (my PI), Dr. Grunwald (program leader of BSURF), Anna (another program leader of BSURF), and everyone else who helped support my research this summer. That includes the funding provided by the Biological Summer Undergraduate Research Fellowship program as well as the NIH. So much planning went into creating this opportunity to grow as a researcher this summer, and I am extremely appreciative of it all.

As far as my research in the lab, I think I identified both a lot of answers and a lot of questions. My screen of potentially upregulated genes in metastasis revealed 8 ABL kinase-linked genes that are significantly upregulated in the brain metastatic line. I also determined that 5 of these genes were driven by the transcription factor TAZ, a known downstream target of ABL. Many of these genes were kinases or receptors whose upregulation I believe fit the phenotype of a brain metastasis. However, there are still questions to be answered, such as what is/are the transcription factors responsible for the upregulation of the other 3 genes, and what about these genes promoted metastasis? For my assessment of ABL in the EML4-ALK fusion cell line, I showed that although ABL is a functional part of the signal transduction pathway, knocking out ABL has no impact on cell viability. Although this means EML4-ALK isn’t a great model in which to study ABL, this was really useful information for the lab who had not explored this cancer type previously.

It’s also amazing to see how much I grew as a researcher this summer. I began this research experience with the main goal of becoming more independent in the lab. Through a fairly independent research project, a mentor that trusted me to work on my own, and personal perseverance, I was able to improve in my independence. I also learned multiple new techniques, most notably RT-qPCR which was a large part of my project. I also honed my Western Blot skills to the point where Ben trusted me to perform some of his blots for him (they came out very well). Furthermore, since I had never given a poster presentation before, I learned a lot about scientific communication, a skill repeatedly emphasized by Dr. Grunwald. Synthesizing my research into a single poster, and then a single abstract was difficult at first, but after practice much easier. I grew a lot as a scientist this summer, and although there is a long way to go before I’m ready for my future career as a cancer researcher, I am extremely proud of what I accomplished and what I learned this summer.

This is the end of my summer blog series! I hope you enjoyed following along as much as I enjoyed writing. Although it won’t beunder the BSURF title any more, I’m sure I’ll be writing things in the future, hopefully with the journal title “Nature” or “Cell” in there somewhere. See ya then!

-Brennan