Category Archives: BSURF 2017

Throughout the program we’ve had the opportunity to hear from a variety of researchers at Duke. They have studied everything from CRISPR to bird song varieties, but have all shared one thing: their passion. Everyone who spoke had a clear passion for their work and a true love of science. It was inspiring to hear how so many people made successful careers for themselves that include their personal interests of discovery and innovation.

One talk that really struck me was from Dr. Anne West. Dr. West’s research was interesting to me from the start because it is in my intended field, but she also delivered such a powerful presentation on the importance of basic science research. Her presentation talked about the serendipity of finding CRISPR in archaea in the 1980s and how that discovery has led to a massive revolution in research today. Those findings will be able to alter medical treatment for a myriad of diseases, including Duchene’s Muscular Dystrophy. Dr. West made a convincing, easy to follow, and powerful case for funding basic science research. She communicated with the audience in a way that many people would relate to, by bringing up how a disease affected a child. She gave her audience hope at the end, a clear understanding of how basic science research that was completely unrelated to a disease could become applicable to its treatment, and she did it all without using scientific jargon. I was impressed with her project idea and her future plans to collect these stories and turn them into a book. Her ability to use research that she was working on, science that she knew, personal experiences that she had, and an opinion that she believed in all at once was impressive. I was already planning on getting a Science and Society certificate from Duke, but now I might have an avenue by which to pursue my interests in conveying the importance of science to the general public. I hope that Dr. West’s project turns into a book that educates the public and our politicians about the importance of basic science and how drastically basic science can impact our society.

Dr. Stephen Nowicki lied to us. While I’m not a fan of lying, this lie was ~for science~, which made it acceptable. This lie, while small in size, made a big difference. The difference was between “pa” and “da” – a miniscule change of breath. This difference, clear to us, shows our categorical thinking: something is “pa” because its not “da”. Birds also, amazingly, display categorical thinking in their song. If it is not the correct song, the song has no meaning, just like how saying “dause” means nothing to humans (while the word “pause” makes sense). Birds from Pennsylvania do not understand the songs of birds from New York because of these slight changes (who knew birds had accents?). Throughout the faculty seminars this summer, I have noticed a trend: discovering connections in the world. I thought Dr. Nowicki’s research was incredibly cool because it uncovered more interconnectedness in the natural world. Additionally, I have been working in an animal behavior lab and Dr. Nowicki’s research sparked my interest into another side of animal behavior research I had never seen before!

Happy accidents are those moments of sheer luck and coincidence in life that we’ve learned to cherish whenever they should pop up. We don’t really think about them though. We never take the time to reflect on them, to think where we might be in life should they have never occurred. Dr.Mohamed Noor made me think critically about happy accidents and for that reason I’d like to talk about what I gathered from his talk.

Dr.Mohamed’s talk woke me up from a deep sleep. Literally. I was face-down on the table when he walked in rambling about evolution and genetics. He went on to give a riveting talk about his path he followed as a scientist, the theory of evolution in the context of today’s society, and his own work. As a group we discussed possible solutions for communicating the theory of evolution to lay audiences in a way that they could be receptive to. He played us some example recordings of fly courtship ‘songs’ that were part of some of the work hs has done in speciation. However, the part about his talk that I really resonated with was the happy accident that occurred during the research project he was undertaking during graduate school.

Dr.Noor told us about amazing data he was able to produce during a graduate project that put him in the spotlight as an evolutionary biologist. He discussed it with humility and humor as he described how the amazing results were almost all sheer luck, a happy accident if you will. I found it interesting that Dr.Noor was so open about this. Where would he be if it hadn’t been for this happy accident. Would I be calling him ‘Dr.’ today? If someone had not sent me a snapchat of the Duke application two days before it was due, would I even be here today? I don’t have the answers to these questions or how my life would be different today but I do know it doesn’t matter. I’m so grateful for having been able to follow the path that I was set on by a trail of happy accidents. However, even if I hadn’t been ended up at Duke and at this program I would still know my future lies in science. I would have come to this realization in some other way in some alternate timeline. The paths we follow and the lives we live can seem so haphazard and random but what we can control is what we feel and know on the inside. No happy accident can change that.

As I mentioned in a previous blog post, my schedule revolves around my meals. To me, seminars primarily mean the time of day where I drag myself up ten million flights of stairs to French Family and finally get to reenergize with some granola bars, fruit, OJ, and yogurt (thanks for the new yogurt, Jason!)

While I love having seminars because it means getting to eat, there’s an added bonus of going: learning about other research that faculty members are doing. The seminar that struck me the most was Dean Steve Nowicki’s. Steve is my academic advisor, and I’ve heard a lot of his stories including his research. I’m not sure if it’s because I wasn’t eating when I first heard it, but I never fully understood the research he was doing until he came and presented to us — and wow am I glad I finally understand it!

Steve’s research investigates how birds communicate using various biological approaches. After taking genetics and evolution in the Spring, I was able to have the capacity to fully understand his presentation. It was amazing how he was able to connect how birds learn to communicate with humans. One anecdote that he brought up was the inability to hear certain phonemes and growing up bilingual, I completely understood. I remember my parents trying to pronounce Walmart and not being able to enunciate the l’s and the r’s.

Another interesting point he brought up was the difference between songs of birds from Pennsylvania and New York. I asked a question about how this affects mating, and Steve said that birds in Pennsylvania won’t even recognize the songs of birds from New York. This led me to think about how the Biological Species Concept is applied. If females won’t pick up the courtship songs of males, when are the regional birds considered different species?

One of the faculty talks that stood out the most to me was Dr. Charles Gerbasch’s talk. After his talk I realized that his name had sounded pretty familiar. It then hit me that back when I was researching universities to attend, Dr. Gerbasch’s lab had struck my interest back then as well. Research like his had been one of the reasons I later decided to attend Duke.

One thing that really stood out to me about Gerbasch is that he places a strong emphasis on the overlap of the various fields of science. Gerbasch emphasized that as science becomes more advanced, the more intermixed the various disciplines of science become with each other. Thus while Gerbasch majored in chemical engineering, he is also well versed in other fields of science such as genetics and molecular biology. Seeing how various fields of science intermingle with each other is something I find very interesting and hope to find in a career.

Cutting-edge research is currently being conducted at the Gerbasch lab. The lab is using various genetic-engineering methods to research ways to improve treatment for patients of an abundance of diseases and disabilities. I really enjoyed hearing how open-minded the Gerbasch lab is to experimenting with various methods.

Overall, I really enjoyed the faculty seminars. Being an undergraduate who has little idea what type of career I want to pursue, it was interesting seeing the journey these various faculty members took to end up in their careers. I also enjoyed hearing all of the life lessons and perspectives on science the various faculty members shared and I learned a lot from the insights they had to share.

I thoroughly enjoyed these seminars. Not only did I learn more about other research that I might not have thought of exposing myself to, but I also got to know how these researchers became…researchers. To be completely honest, it’s nice hearing from the researchers who didn’t see themselves as researchers from their early undergraduate years.

Out of all of the seminars, it was really difficult to choose only one to talk about, so I’ve decided to pick two! I promise to keep it short-ish.

First up, Dr. Anne West, since her seminar is still fresh in this forgetful brain of mine. One question that she brought up was why she wanted to be a basic scientist. There are so many people who really look for research that will show immediate/direct benefits in real world applications. However, like what Dr. West explained through her captivating storytelling, basic science is so essential. Without it, we wouldn’t be able to progress as much as we have thus far. The fact that CRISPR was essentially discovered 30 years before it became popular in the science world is just mind blowing. Research that might seem pointless at first, might have a very important role in the future. On top of that, her research is really interesting. I wasn’t aware that neurons could change so much so quickly.

She really reminded me of why I like science so much; why I want to become a researcher. My love for epigenetics just keeps increasing!

Next up: Dr. Gersbach. His lab really interested me because he said that even though he’s known to be fiddling around in biomedical engineering, his colleagues don’t really consider him and his lab to be “biomedical engineering”. Instead, his lab and interests lie in many different fields, which is completely relatable. Who is only interested in one very specific topic their whole life? (okay, probably quite a few people, but I rest my case) He doesn’t want to limit himself. Out of all of this research this summer, I’ve kind of learned that each lab is a bit isolating. You could become lost within the narrow scope that your lab focuses on and not know what’s going on in the rest of the researching world. The fact that Dr. Gersbach is so willing to explore other fields and defy, I guess, labels is pretty cool. His research itself is very interesting because, even though I have absolutely no knowledge about engineering, I become completely intrigued whenever gene editing or genetic engineering is brought up (I’m a genome/epigenome freak, what can I say). It’s just so interesting to me, that I’d be willing to read articles upon articles on it (maybe).

Can you sense how interested and excited I am with all of this science? Can you? Because I think I can.

I guess all this proves that…science is cool.

Limitations to dopamine D2 ligands for antipsychotic efficacy.

The D2 receptor has often been examined as the target for antipsychotic drugs due to its distribution in critical areas of the brain involved in movement and reward. Beta-arrestin biased drugs such as UNC9994 function as antagonists through G-protein signaling and partial agonists through beta-arrestin signaling, which has been shown to decrease psychotic properties while minimizing unwanted side effects. Of the five dopamine receptors, D2 closely mirrors D3 and D4. Therefore, it has been proposed that these novel therapeutics may be having an effect on the dopamine D3 and D4 receptors. Using BRET assays with HEK293 cell lines, aripiprazole and its congener UNC9994 have been tested on the dopamine D2-D4 receptors, and their effects were recorded as dose-response curves. By comparing the effect of the drugs to the effect of the natural ligand dopamine, it has been discovered that these agents do have an effect at the D3 and D4 receptors. Due to the role of non-D2 dopamine receptors in contributing to many of the symptoms of schizophrenia, novel therapeutic agents remain to be developed that could have the receptor specificity needed to attenuate psychotic phenotypes while minimizing unwanted side effects.

In the Caron lab, my project has largely been testing new schizophrenia drugs on the dopamine receptors. Because my interests in the sciences have largely revolved around pharmacology and cell biology, I have usually approached the concept of neuropsychiatric disorders as a dysregulation of neurotransmitter systems that can be fixed by the administration of a molecular substance (i.e. drug). This would involve knowledge of the receptor and the subsequent effects it has on the cell. This approach to these disorders focuses on abating symptoms once they are present in a patient (or forced in an animal model), and does not truly examine the causes of such disorders (but merely the effects). Thus, I was quite fascinated to hear about some of my colleague’s labs which focus on proposed causes for certain disorders, like the role of gut microbiota in contributing to depression.

One chalk talk that really grabbed my attention was the one given by Annika Sharma. In the talk, she stressed that experiments transferring fecal matter from a depressed mouse (mice eat poop) into a healthy mouse was able to induce depression in the healthy mouse, suggesting a role for the gut microbiota in facilitating connections with the brain (i.e. the gut-brain access). It is also known that Major Depressive Disorder (MDD) patients have altered microbial compositions and many metabolites which play a role in depression are byproducts of gut microbiota. I was also rather shocked by the way in which her lab generates what it calls the social defeat paradigm. Essentially, to create a depressed mouse, it is left in the company of older, more aggressive mice that beat it up. The lab then extracts fecal matter from the depressed mouse and is able to run any series of tests that they want to determine, for instance, the presence or absence of certain metabolites. Overall, I was just interested in learning the many different ways in which researchers have approached certain disorders.

For me, each day of the week in the Caron lab is dedicated to a different procedure with the overall goal of generating data for my project. Thanks to my dedicated mentor who goes to lab on Sunday, I am able to run three rounds of BRET in a week.

On Mondays, I transfect the cells that my mentor split the day before. I also split cells for transfections on Tuesdays. On Tuesdays, I split the transfected cells to a 96 well plate for BRET and transfect the cells split on Monday. On Wednesday, I am able to finally use the BRET machine and see if my transfections and plating reveal any interesting results. Like is expected for good science, I try to achieve many rounds of similar results with BRET assay to assure that the data is not due to error on my part. Thus, I run BRET on Thursdays and Fridays as well.

While the BRET assay is my main objective in lab, it is not the only thing I do. Each time I transfect, I have to use some DNA from the stocks we keep in the fridge. After many rounds of BRET, the DNA starts to run low. Therefore, I occasionally engage in cloning projects in order to make more DNA. Sometimes, I am lucky that other people in the lab have glycerol stocks of the DNA I need. If so, I am able to utilize a Qiagen MidiPrep in order to extract more DNA. However, if no glycerol stocks are available, I have to transform the DNA in bacteria and let the bacteria grow up copies for me.

In addition to all of these small mini cloning projects, I did partake in a fairly lengthy cloning project that lasted an entire week. I attached a fluorescent probe to the D3 receptor.

So, this is how I have been keeping busy in lab. Sometimes, if I finish everything I have to in a day (or if there ends up being too few cells to split), my mentor will keep me busy with random projects that usually involve new techniques. One thing is for sure, there is never a boring day in the Caron lab.

Astrocytes are a non-neuronal cell population in the brain which perform many important functions, including regulating synapse formation and function and helping to form the blood brain barrier. Despite the importance of these cells in vivo, little is known about how they carry out these critical functions. Protein Tyrosine Phosphatase Receptor Z1 (PTPRZ1) is a transmembrane protein which is heavily expressed in astrocytes and oligodendrocytes, another non-neuronal cell in the brain. While some function has been found for PTPRZ1 in controlling oligodendrocyte maturation, little is known about the function of the protein in astrocytes. The present study investigates the role of this protein by determining its location of action, its expression across development, and finally what it is doing in astrocytes. To determine the location in which PTPRZ1 is acting, immunohistochemistry (IHC) was used on mouse brain sections. These tests showed expression of PTPRZ1 along the branches of astrocytes, with a co-localization between the PTPRZ1 and our astrocyte marker GFP. We also found the protein to be present on western blot in the brains of mature animals. We plan to continue this work by investigating PTPRZ1 levels over different developmental time-points using western blot and quantitative PCR analysis.

Identifying the endoreplication pathway in Cryptococcus neoformans

Aaliyah Davy                                                                                                                     Mentors: Ci Fu, PhD., Joseph Heitman, MD., PhD.                                             Department of Molecular Genetics and Microbiology

Cryptococcus neoformans is an opportunistic fungal pathogen that affects the immunocompromised and rarely, the immunocompetent. The fungus has two different sexual cycles- that is, bisexual and unisexual. Central to bisexual reproduction is cell and nuclear fusions that are indicative of ploidy duplication and the yeast-hyphal morphology transition. In this study, we investigated the currently unidentified endoreplication cycles that these cells go through to attain ploidy replication in the unisexual cycle. We hypothesized that one of six cell cycle genes we have chosen, that have differential expression throughout unisexual reproduction, will have some impact on the pathway. To test this, we generated gene deletion constructs with dominant selectable marker neomycin (G418), and conducted biolistic transformation on the unisexual strain XL280α. Transformants were streaked on additional G418 plates and verified by PCR. We tested whether deletion of these genes impact unisexual reproduction. This endoreplication pathway has also been linked to the formation of titan cells (greatly enlarged versions of the pathogen) in host infection, so we tested the significance of these genes in titan cell formation as well.

Exposure to polycyclic aromatic hydrocarbon (PAH) chemicals is widespread due to their presence in emissions from tobacco smoke, wood stoves, and organic fuel burning throughout the world. Many PAHs are classified as carcinogens, and prior studies have shown an increase proliferation in an estrogen-receptor positive human breast adenocarcinoma cell line due to exposure to low doses of a complex PAH mixture. The objective of this study was to observe the effects of the same PAH chemical mixture on an aggressive human inflammatory breast cancer cell line using a 3D tumor emboli assay. We hypothesized that greater concentrations of PAH mixture would lead to greater tumor emboli growth. Cells were seeded in ultra-low attachment well plates and once emboli were formed, they were treated with different concentrations of PAH mixture, called Elizabeth River Sediment Extract (ERSE). Microscopic and statistical analysis revealed that low nanomolar doses of ERSE result in greater tumor emboli size compared to untreated emboli, in a dose-dependent manner. There was a positive correlation between emboli size and increased ERSE concentration, although a high micromolar ERSE dose was cytotoxic to the cells. Collectively, these results suggest that low-dose exposure to this PAH mixture can enhance growth of aggressive breast cancer cells, and may have a wider and more substantial impact on cancer progression and outcome.