Author Archives: Caroline Gamard

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!

I was struck by Dr. Sheila Patek’s talk about her scientific journey, particularly because she faced a completely unexpected challenge that wasn’t something I previously would have considered a roadblock for scientists: politics.  Dr. Patek’s research almost lost funding when it was identified by a senator as something that was an unnecessary use of taxpayer dollars.  Dr. Patek researches extreme movement in animals such as mantis shrimp and trap-jaw ants, which admittedly does sound like something that is not immediately necessary to move the field of science forward.  However, plenty of scientific research seems to be based on learning more about the world for the sake of learning more about the world, not learning for the sake of advancing technology or saving humanity.  Isn’t learning for the sake of learning what science is all about?  That’s what I thought before Dr. Patek told us about how her research was challenged for being unnecessary and how she was told that it was not worth the time or money that she poured into it.  I never considered that this would be a challenge for a researcher, someone who spends his/her life learning about the world.

Dr. Patek’s talk taught me three important lessons that I will remember as I grow as a scientist:

1. Learning more about the world for the sake of learning more about the world is of the utmost importance. We should study everything, however seemingly insignificant and try to gain as great an understanding of our world as we can.  That’s our job as scientists.  If something gives me a greater understanding of some aspect of the world, it’s worth doing, even if I can’t immediately see the applications or the way that it advances society.  It doesn’t have to solve a human problem to be important.  The study of how mantis shrimp resolve conflict is just as important as the study of neuroscience, cancer biology, or evolution.  Just because one has more obvious implications for humans does not make it more important.
2. That being said, all research has implications for humans. Although Dr. Patek’s research was challenged for its lack of relevance, she proved that it does have really important applications in engineering and technology and our understandings of evolution and physics.  Although these applications are not immediately obvious, they still exist and are of great importance.
3. It’s important to stand up for ourselves and what we love and believe. When Dr. Patek was challenged, she did not sit idly by and lose funding.  She met with the senator on Capitol Hill to convince him that her research deserved funding, and she also spoke about the importance of research on PBS.  Dr. Patek’s bravery and perseverance in the face of adversity are truly inspiring to me, and the lesson I learned from her actions about standing up for knowledge and standing your ground is extremely relevant inside and outside of lab.

I highly recommend everyone watch Dr. Patek’s PBS Newshour segment.  She speaks so eloquently about why research is important for its own sake, and it’s a very inspiring message, especially for us as the next generation of researchers: https://www.youtube.com/watch?v=hb0hxuM-TeM

Inhibition of HipA to Reduce Multidrug Tolerance in E. coli

The HipBA operon is a bacterial toxin-antitoxin module that plays a crucial role in multidrug tolerance in E. coli.  HipA, the toxin, is a kinase that functions by phosphorylating translation factors, inhibiting translation in the cell and inducing a state of dormancy in which cellular processes that are targeted by antibiotics are shut down, allowing the cell to evade antibiotic poisoning.  The goal of my research is to identify molecules that bind to HipA and inhibit its kinase activity.  HipA autophosphorylates, so its activity can be measured by its phosphorylation.  To measure phosphorylation, wild-type HipA is completely dephosphorylated using a phosphatase enzyme, and its phosphorylation after the addition of ATP can be visualized through a ProQ Diamond Phosphoprotein Gel Stain.  This assay can be repeated with wild-type HipA in the presence of target molecules that are believed to inhibit its kinase activity.  A lack of autophosphorylation in the presence of a molecule indicates that this molecule inhibits HipA and could be a potential molecule of study for the development of an antibiotic.

I really enjoyed Evelyn’s chalk talk on the ultrasonic vocalizations of mice because it presented a fascinating solution to a question I never would have thought to ask.  Her overarching question is whether or not mice are aware of their own vocalizations.  Before hearing her talk, I never would have considered the fact that mice might not be aware of their own vocalizations or that this ability that humans have to distinguish between self-generated and foreign sounds is actually pretty special.  Furthermore, once this interesting question was posed, a very creative way to test it was generated.  I admire the way her lab came up with a unique solution to a unique question.

In a nut shell, the lab tests whether mice can distinguish between self-generated and other noises by giving them helium and seeing how/if they react to the raised pitch of their voices.  If they adjust their vocalizations to a lower pitch or lower the volume of their vocalizations, it could indicate that they can distinguish which sounds they are producing and that they can discern that they sound different than usual and adjust accordingly.

However, even more interesting than the idea of giving mice helium to see if they notice when their voice changes is the important implications that it has for humans.  I was also impressed by this aspect of the presentation because while this research seems interesting and relevant to the study of neuroscience in mice, it is not immediately clear how it applies to humans.  Evelyn explained that this research can be applied to the study of schizophrenia, as people with schizophrenia often have difficulty distinguishing between self-generated and other sounds.  Thus, research on the ultrasonic vocalizations of mice can be used to better understand a disorder that affects hundreds of thousands of people and is not currently well understood.  That’s one of the most amazing things about science and research that I’ve discovered this summer: it always has broader implications that can make our world a better place.

So thanks Evelyn for the fascinating talk!  I can’t wait to learn what you discover!

Dr. Richard Brennan began his research journey at Boston University.  He started as a chemistry major but switched to biology, although he maintained his interest in chemistry, which ultimately led him to the field of biochemistry.  He was also interested in history and English, and he emphasized to me the importance of the humanities in science.  Without the ability to communicate, science is meaningless, and scientists need to be good writers in order to effectively write informative and intelligible papers.  Thus, Dr. Brennan’s interest in language and English proved especially beneficial for his life of publishing papers and writing reviews.  This advice from Dr. Brennan made me appreciate the interdisciplinary curriculum I enjoy at Duke: my humanities classes are just as crucial in preparing me for a career in research as my science classes.

The summer after his sophomore year of undergrad, Dr. Brennan participated in a summer research fellowship much like BSURF during which he decided that he might like to pursue research as a career.  After graduating from Boston University, Dr. Brennan went to Cornell University for graduate school, but he quickly realized that he needed to take a break before continuing his education.  He left and took a position as a technician at a hospital in Boston.  This taught me that there isn’t a set career path to research: it’s okay and even important to take breaks and explore other options and fields.  Later, Dr. Brennan returned to school and earned his PhD at the University of Wisconsin and then went to the University of Oregon for his postdoctoral fellowship.  Dr. Brennan emphasized to me the importance of good mentorship: he took his first job at a medical school in Portland because it was geographically close to his mentor at the University of Oregon, allowing them to continue to work together.  He became a full professor at the medical school in Portland.

After seventeen years, Dr. Brennan moved to MD Anderson Cancer Center in Houston to establish a structural biology center there.  However, after six years, he was offered a job as the Chair of the Department of Biochemistry at Duke University.  Dr. Brennan emphasized how much he enjoys working with students and how he thinks graduate students are essential to laboratory research.  Accepting the position at Duke would allow him to work with highly motivated graduate students, and Duke had an excellent grad student to faculty member ratio in its biochemistry labs which would allow the Brennan lab to bring in many graduate students.  Furthermore, a position as chair of the department would allow Dr. Brennan to build a strong department at an already great school.  Needless to say, Dr. Brennan accepted the position at Duke, and the rest is history.

One takeaway from Dr. Brennan’s journey is that amazing opportunities are often unexpected: he was not looking to leave MD Anderson, but he received an amazing offer to do what he loves most at Duke.

Dr. Brennan truly loves students and teaching.  He believes graduate students are what make research labs great, and he also believes that all faculty members should teach.  Dr. Brennan teaches everything from courses on grant writing to x-rays to his specialty, structural biochemistry, and he usually has at least two undergraduate students in his lab each year.

While Dr. Brennan loves research because of the unique opportunity it gives him to observe something that has never before been observed and to understand something that has never before been understood, he offered me some warnings about the nature of the field.  He encouraged me to study topics that interest me, rather than those considered “hot” in science right now.  Brilliant research is being done everywhere, but not all of it is recognized because not all of it focuses on what is considered new and important in the field at the time.  Focus on what you love, not on what will win you awards and national recognition.

Dr. Brennan’s final advice to me was to seize all the opportunities available to me and try as many different research settings as possible until I find one in which I feel truly comfortable and happy.  There are many different research experiences, and I cannot know how I really feel about conducting research after this one experience, however great it may be.  I should never close myself to other opportunities just because I am comfortable where I am: Dr. Brennan loved his job at MD Anderson, but he was open to a change and got to create an amazing department at Duke, where he is very happy.

TL;DR: Always be on the lookout for new opportunities and never stop pursuing what interests you!

While many people (not Dr. G) fear snakes or spiders, I have been afraid of antibiotic resistant bacteria since I read a book about it in middle school.  But unlike my other fears, I don’t want to avoid antibiotic resistant bacteria.  I want to do something about it.  That’s one of the reasons why the Brennan lab stood out as a good match for me this summer.

My project in the Brennan lab is primarily focused on a bacterial toxin called HipA (high persistence A), a protein that mediates multidrug tolerance through a mechanism known as persistence.  Essentially, during times of stress, such as the presence of antibiotics in an environment, HipA causes bacterial cells to enter a dormant state in which all cellular activity stops.  During this time, antibiotics are not effective against them because the functions targeted by antibiotics are shut down.  After a period of time, the levels of HipA in the cell decrease, and the cell returns to normal functioning.  These cells are known as persisters because they survive antibiotic treatment.  You can learn more about bacterial persistence here.  The Brennan lab is collaborating with a drug discovery company to find molecules that bind with HipA, potentially reducing its ability to induce dormancy.  In the future, these findings could lead to improvement of antibiotics.

My project involves isolating HipA from E. coli that are engineered to overexpress it, or make much more of it than they usually would.  HipA is a kinase, which means that it transfers phosphate from ATP to other molecules, and its activity can be measured by its ability to autophosphorylate, in which it uses its kinase abilities to phosphorylate itself.  I can treat HipA with the drug precursors to determine if any of them can inhibit HipA’s autophosphorylation, since if HipA cannot phosphorylate itself, this is an indication that it has lost its function as a kinase.  My longterm goal is to determine which, if any, of the drug precursors inhibit HipA’s function.  You can read more about HipA and phosphorylation here.

Field trip to the lemur center!