Author Archives: Susan Zheng

It’s the end of the program, but only the beginning of my scientific journey. In the past 8 weeks, I have made my first steps into research – and it’s been an amazing experience. During what felt like such a short amount of time, I’ve grown so much as a scientist.

Before the program, I didn’t have an accurate picture of what research was like. Now, I’ve gained a deeper understanding of and appreciation for science. From learning how to clone DNA to understanding the mechanisms of heart regeneration, from reading scientific papers to experiencing the lab environment, from working on an independent project to hearing Duke faculty share about their research, I have a much better understanding of what a scientific career is like. It is something I definitely want to continue to explore.

I’ve learned that science is a lot about asking questions. Whether it’s asking why is this important, what does this do, or how does this work, the root of science is asking questions and striving to find answers. Science is intricate and tricky in this sense. Sometimes, there’s no clear-cut answer. And when there is an answer, it doesn’t always come right away. It’s the scientist’s job to try to crack open this mysterious puzzle, a difficult but highly rewarding task. I think this is what makes science all worth it. You are able to discover things that no one knows, test your curiosities, and contribute to society in meaningful ways.

Walking in to lab on the first day, I’ll admit I was nervous. Here I was, in this room full of expensive, fancy machines I didn’t know how to work and intelligent scientists performing complicated procedures I didn’t understand. Now, however, I’ve gained a sense of confidence and comfort. Don’t get me wrong, there’s still a ton of things I don’t know how to do. I’m still learning. But, every day, I came into lab, excited to work on my project. And every day, I walked away learning something new. Whether it was the new skills I’ve learned, knowledge I’ve gained, or relationships I’ve developed, this experience has been truly valuable. It’s the last day now, and I’m no longer nervous. Instead, I’m more curious, eager, and excited to continue to discover.

I am so grateful to Dr. Grunwald and Jason for all their hard work to make this experience possible for us. I also want to thank the entire Poss lab, especially my PI and my mentor, for giving me the opportunity to work with them and for all their patience, support, and guidance. This experience has truly been a great gateway into research and I can’t wait to see what the future holds for me.

Every week this summer, we had the opportunity to listen to esteemed Duke scientists share about their current research as well as their career paths. Not only was it fascinating to learn about the diverse projects they’ve dedicated their careers to, but it was very intimate to learn about their personal journeys that have made them the successful scientists they are today. It was comforting to hear their stories and to learn that a lot of them did not follow a linear path to become a scientist. Instead, many of them took non-traditional paths that allowed them to explore many different avenues and discover many valuable experiences.

Though I enjoyed listening to all the faculty seminars, Dr. Raphael Valdivia’s talk caught my attention the most. Dr. Valdivia’s lab studies the pathogen chlamydia, a bacteria that is responsible for infecting thousands of men and women with sexually transmitted diseases as well as causing infectious blindness in humans. His work mainly involves identifying the mechanisms of how chlamydia mediates reprogramming of host cells and investigating how they occur. One of the mechanisms he observed is how chlamydia infections prevent cells from undergoing apoptosis, or cell death. I thought it was interesting how chlamydia uses this mechanism to proliferate in cells.

However, what really drew my attention was how personal he was with sharing his story. Dr. Valdivia grew up in Lima, Peru. He obtained his undergraduate education at Cornell University, attended Stanford for his Ph.D. and Berkeley for his post-doc. It wasn’t an easy road for him, however. After not being able to get into grad school right after college, it was his amount of determination to get in after his gap year that really inspired me. He was also faced with many tough decisions, such as having to decide to work in a lab where he values intellectual stimulation and being outdoors where he loves the adrenaline rush of climbing mountains. His gap year helped him decide that his true calling was with science and discovery. He really emphasized how important hard work is. If you’re willing to put in the work that it takes, you can go far. Ultimately, it was this amount of determination and authentic passion he has for his work that I enjoyed hearing the most.

Over the past 6 weeks, I’ve learned a lot. I’ve learned how to pipette the optimal mix of reagents to amplify DNA for PCR. I’ve learned how to clone DNA with a plasmid vector. I’ve learned how to perform ventricle resection on zebrafish. And most importantly, I’ve gained a better idea of what research really is.

Research definitely takes time. Whether it was waiting a day for my bacteria inoculation or 6 hours for my RNA transcription, research actually involves lots of just waiting time. Thankfully, I was able to turn the waiting time into productive work by performing other steps or reading papers. Research also involves a lot of repetition. I can’t even count how many times I ran a PCR and gel this summer. It involves lots of repetition in the sense that repeating procedures makes you better at it. But also, troubleshooting. Sometimes, a step may not work and you may be stuck on one part for a long time, trying to figure out what’s wrong. This involves repeating the step many times and changing one thing at a time, trying all possibilities to get it perfect. I actually enjoyed this troubleshooting process because it was like solving a puzzle to me.

The main part of my project was to create 4 RNA probes for my genes of interest to perform in situ hybridization. This may sound simple to do, just create four strands of complementary RNA. Easy, right? The reality was far from this expected simplicity. In fact, it took over 6 weeks to create three probes (one gene refuses to be amplified and after tons of troubleshooting will still not work) that I just finished this Tuesday. This is really exciting for me because I can finally run all my in situs with my probes. This week will be the week of results where I can see where in whole 3 days post fertilization embryos, 6 week zebrafish hearts, uninjured zebrafish adult hearts, and injured zebrafish adult hearts the genes are being expressed. I cant wait to complete these final stages for my in situs.

In the journey to create RNA probes, I got to learn and experience a multitude of diverse procedures and techniques. Now, I feel much more comfortable performing these protocols and feel that I have a comprehensive overview of the common protocols related to zebrafish. Just the journey and learning everything both conceptually and mechanically have been so rewarding. At this point, results don’t even matter. This experience has been much more valuable (of course, it wouldn’t hurt to get some results).

Slowly by surely, I’ve been putting all the little puzzle pieces together. The past 6 weeks have gone by so quickly, I can hardly believe that the program is drawing near its end. It’s been such an enriching and thrilling experience working in the Poss Lab and I can’t wait to see the final results of my project!

I really enjoyed hearing everyone give their chalk talks this week and learning just how diverse all of our projects are. From plant germination to genetic mutations, gene expression to viruses, each one of us is taking part in really interesting science.

One of the chalk talks that especially caught my attention was Ricardo’s talk about brain-machine interfaces (BMI). A brain-machine interface is a communication pathway between the brain and a system of devices composed of a decoder that interprets electrical signaling in the brain, a machine that translates signals into movement, and sensory feedback that relays signals back to the brain. This network of brain and machine communication allows for the development of brain controlled prosthetic limbs to be used by patients who suffer from paralysis such as quadriplegia. His project focuses on studying the relationship between lag times (the delay between neural firing and actual movement) and unimanual vs. bimanual actions in monkey models. This is done by comparing velocity models and neural firing models for each type of action. Studying lag times can help improve the efficiency of brain-machine interfaces by making movement feel more natural for humans.

What amazes me the most about his project are the possible applications brain-machine interfaces have for human health. The use of BMI in patients who suffer from limb paralysis would allow them to move again, essentially changing their lives. I really found learning about the engineering side of research to be interesting because of this direct application for humans.

I look forward to hearing about his findings as well as all my fellow BSURF researchers’ findings!

No day is the same working in the Poss Lab. Every day consists of new experiments to carry out, new things to learn, and new questions to ask.

The first two weeks of lab largely consisted of shadowing my secondary mentor and learning basic protocols. After gaining experience and comfort in conducting PCR reactions, gel electrophoresis, heart extractions, embryo injections, cloning, and cryosectioning (just to name a few), I have really enjoyed gaining independence in my work.

My project looks at 4 different genes and they’re currently all at different stages in my experiments. I have already ran in situ hybridization for one gene while I’m still at step 1 in trying to isolate the segment of DNA I want for another gene. Thus, every day I continue working on my project, whether it’s the final step for transcribing my RNA probe or trying to troubleshoot a PCR for the tenth time. My days will usually involve running multiple PCR reactions and gels. If my gel runs properly, I can extract the DNA band and purify it. Then, I clone the DNA into a plasmid and transform it in bacteria. After the bacteria grows, I set up a colony PCR to verify the DNA segment and send the plasmid for DNA sequencing. If the DNA sequence looks good, I inoculate more bacteria, extract the DNA with a midi-prep, linearize the plasmid, purify, and transcribe (if all goes smoothly) with many PCR’s and gels in between in order to double check each step. Usually, a step won’t work correctly and I have to try to figure out what the problem is. Troubleshooting a step may take days, so I repeat a step many times, changing one thing at a time in order to determine what is wrong.

Depending on the day, I may also practice embryo injections which involve setting up zebrafish matings the day before. I collect the embryos, prepare the injection mixture, and inject hundreds of zebrafish embryos. I may also need to make cDNA for my PCR which involves dissecting zebrafish hearts, extracting the RNA, and reverse transcribing it to make cDNA. I am usually conducting many experiments at once. While I’m waiting for my PCR, I may be embedding hearts in tissue freezing medium or screening zebrafish for mutants. Some days I am busy going back and forth from the lab to the fish room. While other days I have more waiting time when I can read some papers.

My routine largely consists of the same protocols, but working every day in lab is still exciting. Although creating an RNA probe for each gene involves the same steps, each gene behaves differently. Thus, applying each step to each gene creates different results, so I never know what I’m going to get. Sometimes, things don’t work out so it can be challenging but I enjoy trying to solve the puzzle. I have definitely learned that science takes time but I am excited to discover what it will reveal.

The Poss lab focuses on the concepts and mechanisms of regeneration in zebrafish. Zebrafish are a known animal model system for studying regeneration because of their remarkable ability to regenerate lost tissue after injury. Adult zebrafish are capable of regenerating tissue in the heart, as well as fin, spinal cord, and retina.

Poss, Kenneth D. “Getting to the Heart of Regeneration in Zebrafish.” Seminars in Cell & Developmental Biology 18.1 (2007): 36-45.

In fact, it has been shown that zebrafish are able to regenerate their hearts, not due to stem cells, but the proliferation of spared cardiomyocytes (Poss, Wilson, & Keating 2002).

Poss, Kenneth D., Lindsay G. Wilson, and Mark T. Keating. “Heart Regeneration in Zebrafish.” Science 298.5601 (2002): 2188-190. 1 July 2016.

This picture shows the regeneration of ventricular myocardium in the resected zebrafish heart. After 20% of the ventricle was amputated off, by day 60, no sign of injury remained and the heart is fully repaired.

In contrast, mammals do not have this capacity to regenerate and repair its tissue efficiently.

Poss, Kenneth D. “Getting to the Heart of Regeneration in Zebrafish.” Seminars in Cell & Developmental Biology 18.1 (2007): 36-45.

Thus, injury in the heart often leads to scarring and fibrosis. This makes diseases such as heart disease a significant threat to human health. Studying the mechanisms of regeneration in zebrafish can illuminate factors that may be applicable to the stimulation of human heart regeneration.

My research project focuses on heart development. Specifically, I am looking at 4 different genes and the roles they play in cardiac development and regeneration. The zebrafish heart is divided into two main parts – the atrium and the ventricle. The overall concept of this project is to examine what factors in heart development are responsible in pushing some cells into differentiating into the atrium while pushing other cells into becoming the ventricle. In order to examine these genes’ influence in heart development, I look at whether these 4 genes are atrial specific, meaning they are uniquely expressed in the atrium, or whether there are ventricle specific, meaning they are only present in the ventricle. Two of the genes I am examining were hypothesized to be atrial specific while the other two genes were hypothesized to be ventricle specific.

In order to examine where in the heart these genes are being expressed, I am performing in situ hybridization with adult zebrafish hearts. In situ hybridization is a method that uses a labeled complementary piece of DNA or RNA to locate a segment of DNA or RNA of the gene of interest in tissue (Wikipedia). I will first make a RNA probe that is a segment of RNA complementary to one of the genes of interest. This RNA probe will contain digoxygenin tags that will then be used to immunohistochemically label cells expressing the complementary mRNA. The areas of the heart where the gene is being actively expressed will turn blue. With this method, I will be able to see exactly where in the heart the genes of interest are being expressed. I will also perform in situ hybridization on 6 week old zebrafish to see where the genes are active during the earlier stages of zebrafish life. Furthermore, I will perform in situ hybridization on injured adult zebrafish hearts in order to see where in the heart these genes are being expressed during regeneration and if there are any changes in levels of expression compared to uninjured adult zebrafish hearts. The next step in this project would be to identify possible atrial or ventricle specific enhancers of these genes, clone them in front of a GFP gene, inject into zebrafish embryos, and observe where in the heart these enhancers are active (turns green). Then, CRISPR/Cas9 gene editing would be used to delete the enhancers of these genes and to examine the effects of the deletion on the cardiac development of zebrafish. Overall, with this project I am hoping to find out what roles these four specific genes play in heart development and regeneration.

Unlike the majority of the Poss Lab that focuses on regeneration, my project looks more at heart development. However, development and regeneration are closely linked, so I hope I will be able to contribute information on the roles of these genes in the heart in terms of both cardiac development and regeneration.

Ever since he was a kid, Principle Investigator, Dr. Ken Poss, has always had a love for biology and animals. Dr. Poss began his scientific career at Carleton College, a small school in Minnesota, where he studied biology. The first time he experienced research was his junior year, when he worked in a biochemistry lab. His school fostered a highly interactive atmosphere, such as extremely small classes. In fact, he was the only person in his lab besides his mentor! In 1992, he furthered his studies and attended MIT to pursue his Ph.D. in biology. At the time, he was very interested in new technology in mutant mice. There, he worked in Rudolf Jaenisch’s lab where he experimented with mouse technology and cloning. He then joined Nobel Prize winner Susumu Tonegawa’s lab where he studied the effects of a particular enzyme on learning and memory in mice. He thoroughly enjoyed his time at this lab because he was really able to gain a sense of independence in research. After his Ph.D., Dr. Poss switched fields when he started on his postdoc in Mark Keating’s lab at the Children’s Hospital in Boston. He wanted to be able to apply genetics in a field where he could do independently. At the time, regeneration was a highly unstudied field of work. Thus, he started working with zebrafish and regeneration and became one of the first people to apply molecular biology to regeneration. In 2003, Dr. Poss came to Duke where he became a member of the Department of Cell Biology and was named a James B. Duke professor. He continues to study the mechanisms of heart and tissue regeneration in zebrafish.

Dr. Poss’s favorite part of what he does is being able to be a part of the larger scientific community. With so many fields that he is a part of – zebrafish, heart development, regeneration, embryonic development- he is able to connect with all kinds of people. He enjoys being a part of this wide spread international community of fellow talented scientists.

As the P.I. of his large lab, Dr. Poss no longer conducts experiments but instead manages his lab. However, he loves seeing people in his lab get results. To him, it is just as exciting as getting results himself. His current goal, besides learning more about the mechanisms of regeneration, is to see people from his lab succeed and make discoveries. He enjoys being a part of trainees’ development and to see them grow as scientists.

Key advice Dr. Poss would give to people thinking of going down the path of scientific research is to make smart, key decisions. Research isn’t always about being the smartest or knowing a field inside and out. It is more about being able to embody discovery, exploration, and fearlessness. It is important to view the “unexpected” in a positive way. He thinks that unexpected results are often the most fun, the most important, and the most rewarding. Through these unexpected results, one can contribute to the field and make a big impact.

Thank you Dr. Poss for taking the time to talk to me. Listening to your scientific journey has widened my perspectives on research and has allowed me to reflect on my own path in terms of discovery, exploration, and fearlessness.

A lot of words characterized my first week here:

• I was excited to begin my first real research experience.
• I was nervous that I would make tons of mistakes.
• I was appreciative for everything everyone has done so far – Dr. Grunwald for making this program possible, Jason for supporting us and giving advice, Duke professors for sharing their research experiences, my secondary mentor Matt for guiding and teaching me, and the Poss Lab for letting me work with them this summer!

Conducting real research is a lot different from learning science in a classroom. When I work in the Poss Lab, I’m not conducting experiments everyone has done before in their organic chemistry classes. Real research is open-ended. There are no clear, numbered steps and I never know what I’m going to get. Thus, over the summer, I hope to be able to work, think, and act like a scientist. What does this mean?

I hope to work like a scientist. I hope to be able to understand what real research is like and to gain a deeper understanding of the scientific process at play. I already feel like I have learned a great deal this week. Whether it was learning new lab techniques (I did my first PCR this week…and my second…third…I lost count) as well as understanding the fundamental concepts behind regeneration (what the Poss Lab focuses on), I hope to not just follow protocols and to transfer colorless liquids with a pipette, but to truly understand what is going on. I also expect to make mistakes, in fact I already have. I don’t expect all my experiments to be successful- whether it was my DNA not running properly on gel or my bacterial transformation failing. What’s important, however, are the valuable takeaways in learning from my mistakes.

I also hope to think like a scientist. I hope to always be constantly asking questions (thank you to Matt for patiently answering the endless amount of questions I had) and to be learning something new every day.

Lastly, I hope to act like a scientist. I am excited to continue to build upon my genuine interest for biology. Not only will I be doing what I enjoy every day, I will also be delving deeper into regeneration research as I hope to contribute as a member of a team of researchers at the Poss Lab as well as build long lasting connections with these talented scientists.

This first week has already been everything and more and I look forward to explore what’s to come in the next 7 weeks.