Author Archives: Kristie Kim

Thank you

As I reflect on the past two months of research, I am filled with an overwhelming feeling: gratitude.

Thank you to the BSURF program for funding my research. Thank you to Dr. Grunwald, Jason Long, and my friends and mentors in the Pendergast lab for dedicating their time and encouragement to create a truly amazing summer research experience.

Research is like baking. I have always enjoyed baking. My favorite baking project to date is making French macarons. These sandwich-like cookies have always intrigued me with the special ruffles on their bottoms called “feet.” With only three ingredients, egg whites, almond flour, and sugar, these cookies are not quite as easy to make as they may seem. After many failed batches of feetless, pancake-like cookies, they no longer emerge from the oven looking like inedible blobs, and that is progress.

The joy. Oh the joy of pulling out delicate little circles of French macaron cookies with their small feet, even if the feet aren’t in perfectly straight lines or the tops of a few cookies have burst open from the baking process. Research is like that. There are joys and there are woes. Each step may seem like another opportunity to make a mistake, but each time one step is complete, it is one step closer to progress. There is joy in knowing that each step counts for something, even if it is only to learn that the batter was overmixed or that a specific antibody does not work.

Admittedly, research is slower than I expected, but somehow I enjoy the whole process, especially the incredible intellectual stimulation as I proceed to answer questions from different angles or analyze the results of each western blot. This summer, I discovered the inner cheerleader inside of me who persistently cheers, “Next time! Next time!” This little pal constantly reinvigorates my optimism towards science.

All of the sudden, I am considering the MD-PhD program as a career path instead of solely pursuing an MD. I know that both pathways can lead to extremely different lifestyles, but I can honestly imagine myself in both. Although newer to me, the research life fascinates me and wakes me up every morning, excited to go to work. I cannot wait to continue conducting research in the Pendergast lab. This summer of research has armed me with the lab techniques and confidence I need to jump back in at full force as I progress my research project, and I am so grateful for that.

So, I leave you with my one final, remaining thought of the summer: thank you.

Me and my poster on the final day of the BSURF program

I wasn’t kidding about the French macarons

The name is Dr. Anne West.

Did you know that three Duke faculty have the name, Anne West? Anne J. West, Anne E. West, and Anne West. The Anne West who directed the faculty seminar this week is Anne West from the Department of Neurobiology.

Dr. West’s convincing argument for the value of basic scientific research captivated my attention. Last week, another Duke faculty member, Kathleen Donahue, began her discussion by asking us about the value of basic scientific research, which, to the average person, does not seem to have practical, real-life applications. This week, Dr. West followed Dr. Donahue’s intriguing introduction to the topic nicely as she also addressed the value of basic scientific research.

On the long whiteboard located at the front of the classroom, Dr. West drew a timeline. As an example, she told the story of CRISPR, the widely popular genome editing technology. When she marked the year 1987 on the timeline and wrote the word, “Archaea” above the year, I must admit I did not see a direct connection to the gene-editing technology. It turns out that in 1987, scientists studying Archaea noticed repeating sequences in Archaea, but did not know what these clustered, interspersed repeats were. When Dr. West mentioned “clustered,” and “interspersed,” I thought, “ah, CRISPR!” (CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats). Later, CRISPRs were found in bacteria, and in 2005, people trying to make better yogurt recognized CRISPR as a defense system for bacteria to protect themselves against phages. In 2012, CRISPR as we know it today was discovered as a method to target and modify genes in living cells.

Although it may be hard to think of the direct, practical applications of “undirected research” to society, this type of research can change lives in the future. Hence, this type of research has considerable value. The sad part is that basic scientific research is being deprived of funding because many fail to perceive the benefits of this type of research to change lives for the better. The discovery of CRISPR as a method to alter the genome is huge, and without the “undirected research” of Archaea, who knows how long it would have taken to reveal this important discovery.

Dr. West mentioned one of her long-term goals to create a book composed of stories about curing diseases, which would challenge people to consider the value of basic scientific research. After listening to Dr. West’s engaging presentation, that is one book I sure would like to read.

Every week I look forward to the faculty seminars more and more. I love to hear about the various life journeys of scientists at Duke. The inspirational faculty talks not only introduce us to the thought-provoking research of highly esteemed faculty at Duke, but also allow us to discuss life goals and the various journeys through life as a scientist with these wonderful people. What an exciting life of exploration it is to be a scientific researcher.

Caution: First Draft

This first draft of my abstract is the result of careful and meticulous revisions to quite a few sentences to reduce the word count to fewer than 200 words. Who knew how tough it would be to fit so many of the ideas swirling around my brain into less than 200 words? Words fly when you’re having fun.

ABSTRACT – Both ABL and DDR kinases appear particularly hyperactive in the context of chemoresistance, in which cancer cells become resistant to chemotherapy. Furthermore, preliminary data suggest that receptor tyrosine kinases, DDR1 and DDR2, are ABL kinase targets. Thus, the hypothesis that DDR and ABL kinases form a feedback loop and that hyperactivation of the ABL-DDR network occurs during therapy resistance was tested. Due to the suggestion that DDR kinases are implicated in subsets of breast and lung cancers, DDR1/2 expression in these cancers was evaluated. It was demonstrated that increased ABL2 activity using the constitutively active form of ABL2 (ABL2-PP) in lung cancer cells induces phosphorylation of DDR1, whereas treatment with the ABL kinase allosteric inhibitor, GNF5, and the ABL and DDR kinase inhibitor, Nilotinib, decreases DDR1 phosphorylation without decreasing total DDR1 amounts. These data suggest that DDR kinases are downstream targets of ABL kinases, which supports the idea that DDR and ABL kinases constitute a novel signaling axis. If hyperactivation of the ABL-DDR network is indeed important during therapy resistance, there is potential that inhibition of the multifunctional ABL kinases through targeted therapy will resensitize cancer cells to the treatment to which they had been resistant before.

To be continued… as I add the results of the experiments I plan to perform next week, fresh from the oven!

Note: “Fresh from the oven” is solely meant to convey the idea that new and not yet acquired data are still to be incorporated into my abstract. I do not actually carry out my experiments in an oven. 😉

Update: For those of you who are interested, here is the final draft of my abstract, in all of its glory:

Novel signaling axis between ABL and DDR kinases in chemoresistance and metastasis: promise for targeted therapy in breast and lung cancers?

In the context of metastasis and chemoresistance in lung and breast cancer cells, the ABL family of tyrosine kinases and the receptor tyrosine kinases, DDR1 and DDR2, have been revealed to be hyperactive. My preliminary data suggest that the DDR kinases are ABL kinase targets. We hypothesize that DDR and ABL kinases form a feedback loop and that hyperactivation of the ABL-DDR network occurs during therapy resistance in subsets of breast and lung cancers. My data demonstrate that increased ABL2 activity using the constitutively active form of ABL2 (ABL2-PP) in lung cancer cells induces phosphorylation of DDR1; however, treatment with the ABL kinase allosteric inhibitor, GNF5, and the ABL and DDR kinase inhibitor, Nilotinib, decreases DDR1 phosphorylation without decreasing total DDR1 expression. These results suggest a novel ABL-DDR signaling axis, and preliminary data suggest that hyperactivation of this pathway may be important during metastasis and therapy resistance. Importantly, we demonstrated that pharmacological inhibition of the ABL kinases resensitizes therapy-refractory tumor cells to standard-of-care chemotherapy.

Choose one, they said. It will be easy, they said.

Last week, all seventeen BSURF fellows presented 8-minute chalk talks to explain their research to the class, and wow, everyone had such interesting research questions. My assignment at the end of all of the presentations: to write about one of my peer’s research.

Every person convinced me of the importance of their research question, which made me really want to know the answers to their questions. Of course, in the research world, answers cannot be obtained within a few seconds from existing data on the Internet. The answers are yet to be discovered. That said, as I listened to the diverse methods that have been formulated in an attempt to answer the overarching research questions, I thought long and hard. How does one devise experimental methods that take into account all possible confounding factors?

One of the many presentations that piqued my curiosity is that of Annika, whose lab focuses on how microbiomes of mice are affected by chronic social defeat. Previous research indicates that gut bacteria are important in brain development and function. What interests me the most is her explanation of the social defeat paradigm, which is used to induce social defeat (as a model for depression) in mice. The method her lab uses involves combining aggressive mice and subject mice in the same cages to encourage the aggressive mice to attack the subject mice. Once the subject mice are, I would assume, terrorized, the subject mice and aggressive mice are divided, but kept in close proximity to each other for 24 hours so that, although the aggressive mice cannot physically abuse the subject mice, the subject mice can still see their attackers. Imagine what it would be like to live in the same room as a bully who had just abused you, with only a glass divider to separate both of you. Now that’s a frightening thought. In the experimental method, the subject mouse must go through the same process ten times, with a different aggressive mouse each time. By the end, the hope is that the subject mice will experience “social defeat” and show symptoms of depression and anxiety. Interesting, right??

Annika’s lab in particular is working on comparing two different methods of extracting DNA from fecal samples and determining the best method. The fecal samples are collected and analyzed from the subject mice before and after they are socially defeated. I wonder how the microbiomes of socially defeated mice compare to the microbiomes of regular, happy mice! I will be excited to have Annika explain her lab’s current data to me at the poster presentation in three weeks. Until then, I must sit here and patiently ponder…

Learning Lab Life Lingo

That’s a lot of L’s.

Not to worry, the L’s are an unfortunate pattern, unrepresentative of this blog post. If you can think of synonyms beginning with, let’s say the letter, W, feel free to comment below.

At this point, I’ve grown much more accustomed to lab life and the basic, daily lingo. Four weeks ago, if someone were to ask me, for example, to split a certain cell line 1:10 onto 3 plates, passage cells once they attain 90%-100% confluency, or, as I perform a western, to dilute a primary antibody 1:5,000 because it produces relatively brighter bands, that person would receive a blank, somewhat bewildered stare. These fundamental concepts of lab life have already become so ingrained into my brain that my lab mentors trust me to do various activities independently such as taking care of my cells and performing western blots. There have even been days where they let me loose the whole day to conduct experiments they had previously taught me. Of course, as the learning process works, I would still ask little, clarifying questions, but I felt like a real scientific researcher confidently walking around with protein samples in hand, instead of following around another lab member.

I’ve never done the same exact activities in lab that I’ve done in a previous day. That is a beauty of research. I don’t go to work expecting to perform the same routine from 9am to 5pm every day. The timing is dependent on the experiments planned for the day. Future experiments are also determined by the results of experiments I do now or have done in the past, and that is exciting. Unpredictable in a sense, which makes lab life exciting. Yes, there are some activities involving taking care of my cell lines that I must attend to every day. However, even the timing for cell passaging and changing media varies day to day, depending on the times that other lab members sign up to occupy the hood.

Something special I’ve noticed about the culture of my lab: we help each other out. I experience this nurturing culture not only in the weekly 2-hour lab meetings, but also in the day-to-day scene. If a lab member working primarily with breast cancer cells needs a lung cancer cell line, another lab member who works primarily with lung cancer cells freely provides a plate of cells from the desired cell line. If a lab member needs to split transduced cells over the weekend, another lab member who has to come in during the weekend anyways graciously offers to split the transduced cells so that the other lab member can take the weekend off. If a lab member needs to leave lab for several days for personal reasons, another lab member is happy to take care of his or her mice in spite of all of the deadlines that need to be met or experiments that need to be run. Cells, reagents, antibodies, and information flow freely throughout the lab. Sometimes while I’m just sitting at my desk, the postdoc in the lab casually says, “Hey Kristie, want a pathology crash course?” or “Hey Kristie, want to watch me harvest mouse lungs?” One minute later, he is showing me on his computer cross sections of the left lung of a mouse that had pneumonia, explaining the versatility of the organ of the lungs, or teaching me the scissors dissection technique of separating tissue by opening the scissors, not cutting down.

The thing about lab life is, I could see myself doing this every day. Working in a lab 10-hours a week during the school year really is not the same as the immersive experience of a summer of research where I can experience every step of the research process. The research I conduct in this lab is still, surprise, fascinating! It is incredibly intellectually stimulating. The excitement from obtaining results and being the first to analyze them is an unparalleled sort of excitement because the reality is, researchers often deal with new information that no one other than themselves has ever produced before. As a researcher, I am not bound by strict time constraints or the same routine every day, but rather I am free to explore the unknown and continually learn and share new, up-to-date knowledge. I could get used to the exciting life and open community of scientific researchers. I really could.

Tyrosine Kinases!

Ever heard of the Philadelphia chromosome? How about imatinib or Gleevec, the highly successful miracle drug most famously used to treat CML (chronic myelogenous leukemia)?

If so, you may have heard of my lab’s focus: the Abl family of protein tyrosine kinases.

When I searched through labs in the Department of Pharmacology and Cancer Biology and came across one with the focus of researching the functions the Abl family of tyrosine kinases, the faintly familiar ideas of the Philadelphia chromosome and Gleevec, which I had associated with the Abl gene, caught my attention. The Philadelphia chromosome represents the abnormal translocation in chromosome 22 found in leukemia cancer cells that results in the Bcr-Abl fusion gene. Imatinib, a chemotherapy medication, hinders the Bcr-Abl tyrosine kinase. Thus, I knew that research in the Pendergast lab, which centers on the exploration of Abl kinases, was sure to be interesting.

Each lab member has an individual project that stems from the Abl kinase focus of the Pendergast lab. Several lab members are utilizing mouse models for their projects. Others, actually all members minus me, continually learn and incorporate creative, new techniques to advance their projects. As for me, I am also learning many new techniques, but ones that have been around for much longer… Nevertheless, I am very grateful to my two lab mentors for taking time off of their own individual research projects to guide me and provide me with the tools I need to conduct research in this lab.

My research project builds on the project of the previous undergrad student in the Pendergast lab, who graduated in May. She focused on triple-negative breast cancer cells, in particular. The goal of my project is to define what role Abl kinases have in the signaling of a specific type of receptor tyrosine kinase (protein) in breast and lung cancer cells. Specifically, I am looking into the role of the interaction between Abl kinases and this particular protein in factors such as cell growth, EMT (epithelial-mesenchymal transition), migration, and invasion.

Now, you may be wondering what exactly is a tyrosine kinase? I will start by explaining one of the roles of phosphate groups. When transferred to a specific protein, a phosphate group can activate that protein. Enzymes (proteins) that add phosphate groups to other molecules, thereby activating the molecules, are called kinases. Tyrosine kinases are a subclass of protein kinases in that they possess the amino acid, tyrosine, to which the phosphate group attaches. Abl genes encode protein tyrosine kinases that activate proteins that are involved in factors such as cell growth and development. A continuous activation of proteins that are involved in important cell processes can lead to cancer, which is caused by an abnormal and uncontrolled division of cells.

Now that you hopefully understand some potentially fatal implications of the interactions of the Abl family of tyrosine kinases with other molecules, you may be wondering, how does one choose which proteins to explore in their interaction with Abl kinases? As my PI, Dr. Pendergast, explained to me, a former postdoc in the lab, along with the previous undergrad, who I mentioned earlier, conducted an unbiased screen for Abl2-induced tyrosine phosphorylated targets, which identified a specific set of kinases to be highly phosphorylated Abl targets. Moreover, it has been shown that these particular kinases are upregulated in breast cancer patients who develop resistance to diverse therapies. Thus, it is worthwhile to investigate and analyze the effects of the signaling axis between Abl kinases and these particular proteins.

Question: how many times can one say, “kinase” in a post? Read the above carefully to find out. 🙂

My research project has involved techniques that include culturing of various breast cancer and lung cancer cell lines, viral transductions, loss- and gain-of-function experiments, immunoprecipitations, and of course, western blots, the bread and butter of our research. I can’t wait to learn even more techniques and practice, practice, practice!

Sherlock Holmes of molecules

“My work is kind of like that of Sherlock Holmes; instead of being a detective of people, I am a detective of molecules.” – Dr. Ann Marie Pendergast

Dr. Ann Marie Pendergast (source:

Dr. Pendergast grew up in just about every other country in Central and South America. In her words, “Guatemala, Mexico, Brazil, Costa Rica, Nicaragua, you name it.” Her dad, who served as a United States diplomat mostly in Latin American countries, met her mom in El Salvador while she was working in the embassy. Hence, Dr. Pendergast’s education up to high school ranged from school to school, mostly Catholic schools, she mentioned, because those were probably the best schools in the various countries. In high school, she learned from teachers who taught at the university and who had very high expectations. Her excellent high school science teachers are the reason for her interest in science and research.

The University of Michigan is where Dr. Pendergast received her bachelor’s degree in Chemistry. However, at the very end of her undergrad years, she took a very interesting class on molecular biology, which influenced her to pursue a minor in molecular biology. For her PhD at the University of California in Riverside, she studied biochemistry, and for her postdoctoral fellowship at UCLA, the molecular biology of cancer. After her postdoctoral fellowship, she arrived here at Duke, where her lab primarily focuses on the role of tyrosine kinases of the Abl family and its effect on pathological conditions such as cancer.

Dr. Pendergast loves everything in cancer biology, especially the history of the field. People such as her mentor’s mentor, David Baltimore, who received the Nobel Prize at the age of 33, started the whole area of oncology by looking at viruses. Studying the way that viruses exploited the genes that eventually became either oncogenes or tumor suppressors excited her.

Concerning the manner in which research is conducted nowadays, Dr. Pendergast noted that the reason that science grew to such high levels in the United States is because there was a big investment in science research. Thus, the premier universities around the world, for research in particular, were in the United States. Over the years, this formula has changed in that the universities are dependent on resources from the government, which does not have a long-term strategy; everything is every 4 years, and budgets are not allocated correctly. There will be damage to the ability of the universities to keep funding research and to keep recruiting new faculty. Dr. Pendergast stressed that this type of uncertainty is unfavorable because if the United States is to remain the leader of the world, there has to be more sustained support rather that this short-term, unstable, and unpredictable support. If this instability continues, other countries, mainly China, will fill the vacuum quickly, which is fine, but the US will lose.

In one of my last questions to Dr. Pendergast, I asked for her advice for aspiring young researchers today. She encourages students to combine the MD and the PhD because the MD-PhD creates more options. She said it is like having two arms instead of just one. For example, the instability in the research part can be balanced with patient care. If, for example, the NIH crumbles or funding disappears, the MD part will still be there. It is an advantage to have both. For some people, it is beneficial even for the questions that people can ask; if you can see what is happening in the real patient world, you can combine it with the molecular world and have a better way to look at potential solutions. You can go from a particular problem and ask the more overarching questions. When Dr. Pendergast was getting her degree, the MD-PhD was not as pervasive as it is now. She sees with her own students that having that option really gives an edge, especially in these uncertain times.

As a student on the pre-med track, I asked Dr. Pendergast if she had ever considered pursuing other careers such as becoming a medical doctor. She was not fond of the idea of doing the same technique over and over again, and therefore, she did not really consider becoming a medical doctor. Rather, she was more interested in the concept of really thinking about the processes and making major breakthroughs.

Some of the most exciting discoveries in her lab have been, for example, the discovery that her lab’s molecules play a role in metastasis. Before that, her lab also identified how chromosomal translocation events induce leukemia and identified the main pathways by which that happens.

I then asked about goals. Her goal is to have fun! She pointed out that the nice thing about science and doing your own research is that you are your own boss. It is not like people who work in companies or under big hospital structures. You do not have to see 100 patients or write reports. You just have to have your own ideas and find out new pathways, new discoveries, and identify new ways of treating diseases. There is a lot more flexibility, and you take your own destiny into your own hands rather than other people telling you what to do. You try to find out how pathways connect to each other and how cancer cells find ways to evade being treated. All of that is really exciting! In science, there is always something new. It is not only doing one thing, it is doing multiple, hundreds of things.

Dr. Pendergast’s enthusiastic personality produced an animated conversation as all of her words and motions were filled with life as always. Boy, am I grateful to have a PI that so easily shares her joy and excitement for research. Both her wisdom and outlook on life are really inspiring for me as I think deeply about my future and how the circumstances we live in will affect me and those around me in the years to come.

No such thing as a dumb question

What a reassuring phrase.

Especially this first week of conducting research in the Pendergast lab, I set out to ask without fear because yes, a minuscule part of me encountered fear: fear that, coming from the only undergrad in the lab, my questions would seem unintelligent, fear that lab members would not have time for me to pester them with my questions, and even fear that in response to my questions, my mentor would discuss complex processes in a way that I did not understand by quickly dropping unfamiliar concepts and large words into every other sentence.

My fears vanished after the first couple of days in lab, not by the assistance of one mentor, but two. My wonderful and enthusiastic PI, Dr. Ann Marie Pendergast, had assigned two mentors to endow me with the knowledge and tools I need to carry out my research project. These two people, along with several other lab members, have not hesitated to assist me in any of my needs or to explain more difficult concepts to me. Sometimes I receive several responses to the same question. Dr. Pendergast has even made herself available to speak with me and guide my project, even in the midst of her very busy schedule full of meetings.

Quick rewind to the beginning of summer break.

It all began with a stack of papers and a textbook titled, “the biology of cancer.” The expectation was that I would have the knowledge level of a graduate student before I began my research in the lab. The fact that I faced this daunting task only invigorated my eagerness to understand the concepts behind my project. Granted, I may have felt utterly lost as I walked into the first lab meeting on Monday as a lab member presented his data, speaking a language filled with various combinations of letters and numbers squished together to represent distinct words. Although my brain swirled with words to look up later, I quickly shook off any feelings of uncertainty as my two mentors introduced me to the wonders of cell culturing and western blotting. I was fascinated.

An accurate word to describe myself this week: fascinated.

Even looking at the product of a western blot I have done fascinates me: straight lines of a variety of sizes indicating the quantity of a specific protein in various cell lines. How will I ever get tired of entering the dark room in anticipation of viewing the Western results of a full day’s work? My lab members could probably answer that question…but that is beside the point.

Of course I had learned general concepts behind basic experiments such as western blotting, but let me tell you. Actually conducting the experiment feels much different than imagining the method as you read through a textbook. I was and still am fascinated using tools and techniques that my fellow lab members probably find monotonous. I remember the first time I observed one of my mentors using the electronic pipette controller. What a cool, sophisticated tool! In addition, the multichannel pipette I observed one of my mentors using for CellTiter-Glo only increased my amazement, along with viewing almost 100% confluent breast cancer cells through a microscope and learning the ways of cell culturing. May I never cease to be enthralled by an electronic pipette controller. What a lovely device.

As I observed my mentors conduct a variety of experiments related to their own projects, I found myself furiously scribbling notes in my handy dandy notebook. With two mentors, I could note the differing techniques each used and the reasons behind each method: the benefit of two mentors instead of just one.

So, based on my first week, what do I expect from my summer research experience?

I expect to ask questions and questions, and more questions. It is truly a great way to learn.

Of course, I also expect to learn new techniques. I hope to apply my current and future knowledge to fully understand and analyze the results of each experiment.

With limited research experience, I expected to be disappointed frequently, whether it was with resulting data or messing up a crucial part of an experiment. On the contrary, fellow lab members have only encouraged me, especially my two very patient mentors, Jake and Courtney. After all, who wouldn’t be encouraged by hearing, “you’re a pro” or even “you ask good questions.” The second compliment is my personal favorite of the week. Maybe my all-time favorite compliment in my academic life.

Furthermore, I expect to grow in confidence as a researcher as I become more familiar with my surroundings over the 8-week period.

I hope to make a contribution to the scientific world this summer from both my expected and unexpected results, no matter how minute or grand the contribution.

And finally, I expect to grow meaningful friendships with the people in my lab and my research fellows this summer. Here’s to a bright and fascinating summer.

My desk ft. my handy dandy notebook

Running and making gels at my lab bench. Can you spot the electronic pipette controller? It’s much cooler in action.