Author Archives: Skylar Montague Redecke

During his summer with BSURF, Zach is working with the McClay lab (which actually shares a space with the Wray Lab where I am working this summer). Dr. McClay is known for dedicating his career to mapping the gene regulatory network (GRN) of the model organism sea urchins. GRNs are very complex, specific, and intricate; many genes may be influencing the expression of one gene, and one gene may be influencing the expression of many genes. Zach is taking up a small part of the sea urchin embryo GRN, specifically looking at the gene Astacin-4, expressed in immune cells in the sea urchin. Very little is known about Astacin-4, but Zach is dedicated towards figuring it out – asking questions such as what genes are upstream, what genes are downstream, when it is activated, how long it takes to become activated, and what its primary function is. What is known about Astacin-4 is that it is expressed in cells known as blastocoels, located on the left side of the early developing sea urchin embryo. Establishing a GRN is a long and tedious process that includes continuously conducting a protocol known as in situ hybridizations. In simple terms, in-situs are conducted by throwing a cocktail of antibodies and G markers together with the developing embryo to see where and when Astacin-4 is expressed. By manipulating the system through gene inhibition or upregulation, the GRN of Astacin-4 can slowly be uncovered and mapped. Once the GRN for Astacin-4 has been defined, it may have applications in all types of other organisms, such as humans.

Every day in the lab consists of different experiments to conduct, exciting protocols to learn about, and new lessons take home. In the mornings, I work with my mentor Carl, a PhD student in Dr. Wrays lab, to assist him in the various questions he is asking as he continues to solidify what his PhD research question is. On some days I may be transforming cells, harvesting virus, or just routinely feeding and passaging my HEK 293T cells. One thing that stays constant is the schedule my cells are on to be passaged. On Mondays the cells get passaged 1:15 – meaning that the cells are detached from the plate and 1/15^th of them are transferred to a new plate – and on Thursday the cells get passaged 1:20. Even though the process may seem tedious and repetitive, it has taught me important pipetting skills and how to correctly work under sterile conditions in the hood.

In the afternoons, I work with Micah, a first-year graduate student in Dr. Wray’s lab – as he begins tackling his thesis involving induced pluripotent stem cells (iPSCs). Working with the HEK 293T cells has been a good introduction to cell culturing, but iPSCs seem to be a whole different story. They require routine checking, special environments, and delicate handling. Every day, I look at the iPSCs under the microscope to make sure that they are working towards confluency (proliferating until they cover the entire plate) and look healthy; then, I feed them by changing their media and look at them again to make sure they haven’t been disrupted too much. These cells are also passaged once a week to help discourage differentiation of the cells. Eventually, I will work towards differentiating them into neural progenitor cells that can be used to study various characteristics.

Outside of my work with the iPSCs, Micah teaches me various valuable skills and protocols used in the lab. So far, I have learnt how to cryopreserve cells and virus, prepare lentivirus, make competent cells, digest plasmids using restriction enzymes, conduct gel electrophoresis, make a viral titre, and do a maxi/mini prep. I have greatly enjoyed getting more comfortable with the motor skills and protocols used in a genomics lab.

Outside of my time in the lab, I spend time reading different research papers, learning about protocols online, or attending weekly lab meeting. During my spare time, I spend time with friends, cooking meals, going to the gym, and reading books. So far, this summer has been exactly what I hoped for.

Similar to me, Dr. Wray (my PI) grew up across the pond, a ways away from where he was originally from. After graduating from his high school in India, he already knew that he would follow a career in biology. Dr. Wray obtained his Md/PhD from Duke studying Sea Urchin development and transcriptional regulation. As a visual learner, he loved that you could watch as the transparent sea urchin embryo matures within a few weeks. After doing 2 postdocs on Australian Sea Urchins at various established institutions, Dr. Wray found himself back at Duke to lead his own lab and become a professor. He teamed up with Dr. Mclay, his former Sea Urchin mentor, and they both lead a cutting edge lab side by side, still supporting and  learning from each other.

When asked about the most rewarding parts of his job, Dr. Wray said that the mentoring and teaching parts of his job are just as rewarding as the research he does at the bench. He mentioned that while mentoring others, you constantly have to learn and adapt to each of your mentees, because everyone requires different support – some people need structure, some people need help troubleshooting, and others may just want to bounce ideas back and forth. Even more rewarding to Dr. Wray was seeing his mentees go on to do amazing things, sometimes even surpassing him in his own accomplishments.

Even though Dr. Wray has stepped away from the bench and is doing more administrative responsibilities in his role at the moment, he hopes that in a few years’ time he will transition back to answering complex questions at the bench. When he started his work on sea urchin gene regulation, the basic lab tools and technology were just at their infancy. Genetics research has made leaps and bounds – such as the use of CRISPR and iPSCs – since he first started, and he is excited about the new questions he can ask and systems he can uncover.

When asked about his current job at Duke, Dr. Wray proudly revealed that he feels like he’s in his dream environment. Duke has a really special culture that is highly collaborative, filled with students and other professors who are eager to learn, discover, and make an impact at all levels. And with the medical school nearby, you can easily collaborate with doctors, a perfect match when focusing your research on helping others and saving lives.

I’ve learnt a great deal working in Dr. Wray’s lab these past few weeks. Not only is the research cutting edge, but the lab culture is collaborative, and the PI is involved and supportive; I look forward to everything I have to learn in the coming weeks. A special thanks to Dr. Wray for all the lessons – outside of Bio203L – he has taught me so far.

Chimpanzees share almost 99% of our DNA, yet the way our brain functions, our morphology, our phylogeny, our phenotype, and multiple other factors differ greatly. So how can this be the case? The drivers for these differences lay within the non-coding parts of our DNA – specifically the gene regulatory system. These DNA sequences, instead of coding for a specific protein, tell our genes when to turn on and at what level they should be expressed at what time. Because of these nucleotide differences, genes in the human forebrain have allowed humans to grow smarter, and genes in chimpanzees have allowed them to build a stronger and more resilient immune system.

This summer, I will be working with the Wray lab under Micah, a first-year graduate student at Duke. Even though I will only be working on a small part of the greater project, the end goal of this research project is to investigate evolutionary differences between chimpanzees and humans at the gene regulatory level. More specifically, chimp-human hybrid induced pluripotent tetraploid cells will be cultured to see how DNA from the chimp will interact with DNA from the human, and to see how the gene regulation in the hybrid cells differs from just the human or chimp cells. From this, we can tell what factors affect gene regulation in both species that lead to the different phenotypes observed. This technique can then be further used to look at disease specific differences that could give us insight into how chimpanzees are better adapted for some diseases than humans are, and why.

Even though I hope to see this project to completion eventually, my specific role in the lab this summer will be to work with human induced pluripotent stem cells (hiPSC’s) to differentiate them into neural progenitor cells. To complete this, iPSC’s must first be thawed and cultured in petri dishes. Their stem cell properties must be confirmed using antibody markers that detect specific transcription factors. Next, the stem cells must be differentiated into neural progenitor cells (NPC’s) using a range of different factors such as noggin to direct their gene expression. The identity of these cells must then be confirmed using antibody markers once again for specific transcription factors expressed by human NPC’s. Once these human NPC’s have been produced, multiple tests can be run to gain insight into their cis and trans gene regulatory systems to get a better understanding of how they work in vivo.

I look forward to getting more comfortable with the lab, learning new bench techniques, and making an impact on the greater scope of this project.

The first and only lab project I took up was during my senior year of high school. I engaged in a year-long supplementary research course that pairs students with an advisor as we develop a hypothesis, research proposal, and presentation on a topic of our choice. I focused my research on antibacterial herbs on the African continent that have the capability of inhibiting bacterial growth. The end goal (cut short – somewhat ironically – by COVID-19) was to synthesize these herbs into an all-natural hand sanitizer, allowing communities to sanitize and protect themselves by using the natural compounds found in their backyards. I only had access to a tiny incubator with an ancient dial to regulate the temperature, an autoclave that could fit about 2 conical flasks, and a Soxhlet extraction apparatus. Even though, I felt like a scientist in my beat-up safety goggles as I meticulously poured agar into petri dishes and streaked them with bacteria I had collected from around campus.

As I walked into Dr. Wray’s lab – the lab I am working with while participating in B-SURF – I knew that the learning curve would be steep. The incubators had options to regulate not only temperature, but humidity and CO2 levels; the lab benches were covered with all types of fancy gadgets, glassware, and tools I soon hope to get my hands on; and everyone was deeply engaged in some sort of fancy intricate experiment. My goal for the end of the summer is to make this place my home and hub for creativity.

I hope to develop the seemingly effortless muscle memory required for efficient one-handed opening of tubes, the ability to deep dive into research papers as I apply an analytical lens to decipher the methods and results produced, and to build the confidence to develop my own experiments and execute them in the lab. The goal would be to end the summer a little less clumsy and lost then when I started. And if I find out that the lab just isn’t the place for me (which seems highly unlikely, but I’ll keep the option open), the experience will be just as important – as even in science, every failed experiment is a step closer to the solution.