Riding the roller-coaster that is Graduate School a far ways from home 万里求学路上的浮尘岁月


Fei Sun and Hazel Zhang at conferences in Europe


Fei and Hazel are two graduate students from the Developmental and Stem Cell Biology program. Fei works in the Poss lab and Hazel works in the Alman lab. They have very similar cultural backgrounds and a shared interest in regeneration. Despite such similarities, they have distinct points of views in science and life. Today they share their graduate experiences at Duke:

Fei和Hazel是杜克大学发育与干细胞生物学项目的博士研究生,菲在Dr. Poss的实验室工作,Hazel是Dr. Alman实验室的一员。她们具有相似的文化背景,并且都对组织和器官的修复再生有着浓厚的兴趣;但她们对于科学和生活也都有自己独特的视角和看法。今天让我们来了解一下她们在杜克的求学经历。

Why did you choose your current lab?

你们为什么选择了现在的实验室?

(Fei) I am attracted to the Poss lab because Ken’s science is really conceptual and pioneering. He always focuses on broad questions and has novel ideas. As a graduate student, I am very lucky to be able to initiate a brand-new project based on my own interest. I have the opportunity to build the foundation of my own project from scratch. In addition, the knowledgeable scientific peers in the Poss lab support me grow quickly as a scientist and give me the confidence to face all the challenges in my research.

我(Fei)对Ken的实验室感兴趣最重要的原因是Ken的研究是非常前沿性的和概念性的。 他专注于大的问题并且总会有一些新奇的点子。我觉得最幸运的是在博士期间就可以根据自己的研究兴趣开启一个全新的课题。 与此同时,Ken的实验室里也有一群知识渊博经验丰富的小伙伴支持着我的快速成长,让我更加有信心面对各种挑战。

(Hazel) I joined Ben’s lab because of his scientific ideas, mentoring philosophy, and the lab environment. As a scientist, Ben always has innovative sometimes crazy ideas that would lead the field to a new direction. As a mentor, Ben encourages and supports me to explore different possibilities in my research as well as in life. He provides the training that would be helpful to me regardless of my career choices. In addition, the Alman lab is like a family that everyone supports and cares each other. I am happy in lab every day.

我(Hazel)加入Ben的实验室是因为Ben的科学想法、教育哲学、以及实验室的环境和气氛。作为一个科学家,Ben有很多非常新奇有时候甚至疯狂的点子,这些想法使得他可以把领域的科研带向新的方向。作为导师,无论是在科研还是生活上,Ben都鼓励我去尝试不同的可能性。他所提供的教育会着眼于让我有“成功”的能力,而不局限于成为一个科学家。除此之外,我们的实验室更像是一个大家庭,每一个人都彼此关心、相互支持。因为这些原因,我在实验室的每一天都很快乐。

How are you research experiences in your lab?

你们在实验室的科研经历怎么样?

(Fei) I started with several projects that have open-ended answers. As a new graduate student, such projects were very exciting, but a bit overwhelming. Through those experiences, I learned to ask key questions, manage my time efficiently, and polish my techniques. My current project started at the end of my third year, which left me limited time to accomplish. However, with all previous experiences and Ken’s support, I am able to move quickly and possibly finish it within three years.

(Fei) 我起初尝试过许多开放性和探索性的课题。对于一个新生而言,这样的课题很刺激但是也稍微有点力不从心。但是通过那段时间积累的经验,我学会了如何提出重要的问题,如何管理和安排好自己的时间,同时也磨练了自己的实验技术。我现在的课题是在我博士第三年末开始的。留给我完成课题的时间并不长,但我之前几年接受的训练和Ken的支持让我的课题进展迅速并有望在三年之内完成。

(Hazel) My project focuses on finding therapeutic targets for cartilage tumors. I found that an FDA-approved drug could potentially be redirected to treat these rare diseases. I also found that tumors at different stages could respond to the same treatment distinctively. I also participate in several collaborators’ projects, so that I can work on diverse projects in the field of bone and cancer and build a great publications record.

(Hazel) 我的课题致力于寻找软骨癌的治疗方法。我发现了一个已经被FDA所批准的药物有治疗这些罕见肿瘤的潜力,同时我还发现了不同时期的肿瘤对于同样的治疗有时有着截然不同的作用。在我自己的课题之外,我还参与了许多合作者的科研项目,也因此有机会了解癌症和骨科领域里不同的研究方向并且发表了一些不错的文章。

How do conferences play a part in your graduate school life? 

学术会议对于你们的博士生活有什么样的影响?

(Hazel) Conferences are very important to my Ph.D. training because I could learn about the most cutting-edge research in my field and get helpful advice and feedback from my scientific peers worldwide. In addition, the friends I made at those conferences have helped me a lot both in my research as well as my career development. I have been to Europe and Asia for conferences, but my most memorable experiences are the three conferences in Galveston, Texas. Fortunately, I was elected to be the Chair of the Gordon Research Seminar in Galveston, so I could benefit my coming scientific peers by creating a welcoming supportive environment for them.

(Hazel) 会议在我的博士教育里有着极其重要的作用。每次开会我都可以了解到领域里最新的进展,并且从全世界的同事那里得到很多宝贵的意见和反馈。而且我在各种会议中也交到了非常多的好朋友,他们不仅对我的科研有所助力,在我的职业发展上也有很大的正面影响。我去欧洲和亚洲都开过会,但是我印象最深的还是三次在德州Galveston参加Gordon Research Conference的经历。在2018年的一次会议中,我很幸运地被选为了这一届会议研讨会的主席,这对我以后职业发展非常有帮助,同时我也帮助我的同事们创造一个良好的互相支持的会议环境,让他们在会议里得到最大的收获。

(Fei) I have been to conferences in Europe and several different places in the US. I agree with Hazel that conferences are really beneficial to my research, especially during the project development stage. A lot of the feedback did integrate into my final project. I especially enjoyed smaller conferences with fewer than 100 people because I could have deep conversations with people. I identified many different personalities among the renowned scientists. I find that the scientific community is very diverse and inclusive, and I feel welcome to be part of it.

(Fei) 我参加过一些在美国以及欧洲举行的学术会议。 我很认同Hazel提到的,这些学术会议对我的科研本身帮助很大,特别是在课题的发展阶段。很多会议上得到的建议都最终融入进了我自己的课题中。我特别喜欢一些小而精的会议,因为在这样的会议上很容易有机会和一些著名的科学家进行深度的交流。我看到了这些科学家迥异不同的性格,并感到了这个学术领域的多样性和包容性。

What do you like doing in your spare time?

你在闲暇时间都喜欢做些什么?

(Fei) At Duke, I picked up my music instrument, Gu Qin (an ancient Chinese instrument), after four years of college. I am lucky enough to find a famous musician from China in Cary, NC. I have been polishing my skills and have given many performances in North Carolina with the guidance of her. Music can transcend all boundaries and bridge people with different culture background. I hope I can bring this important part of Chinese culture to more audience in the US and attract more and more people to Chinese history and culture through my music.

(Fei) 来到杜克之后,我捡起了我在大学里丢下了四年的古琴 (一件历史越久的中国乐器)。我很幸运,能够在北卡找到一位来自中国的音乐家。在她的指导下,我开始磨练我的演奏技术并参与了很多当地的音乐演出。音乐可以跨越一切界线,将不同文化背景的人紧紧相连。我希望我能够将中国文化中很重要的这一部分带给更多的美国观众并通过我的音乐吸引更多的人了解中国的历史和文化。

(Hazel) I enjoy doing science education in my spare time. To prepare myself for it, I took the Science Communication course at Duke and served as a teaching assistant for that course afterward. Earlier last year, I gave a small lecture and lab demonstration to a group of underrepresented minority middle school students in collaboration with RNI. This event was to encourage the students to purse research careers in STEM. I also translate scientific articles to Chinese for an online education website Guokr. I think science is more valuable when the public could understand and appreciate it.

(Hazel) 我在空闲时间很喜欢做科普教育。为了更专业更有效地进行科普,我上了一门旨在帮助理工科学生更好的进行科学交流的课程,之后我还担任了那门课的助教。去年早些时候,我和RNI合作给一些少数族裔的中学生们上了一节实验课,希望能激发他们对科学的兴趣,并鼓励他们以后选择理工科相关的职业。平时我还会给一个中文的科普平台果壳网翻译文章。我认为大众对科学的理解和支持会让我们的科研变得更有价值。

How does the Ph.D. training shape you as a person?

PhD 对于你的人生有什么影响?

(Hazel) I learned to be resilient to failure. Doing research is like riding the rollercoaster, full of ups and downs. I believe the ability to identify the root cause for failure and address those problems will help me succeed in my future life and career. Another important thing I learned from my PhD is self-education. There are a lot of novel techniques and knowledge in all disciplines, especially in the field of research. However, we will leave a school in one day. Being able to find the right resources and self-educate is very important.

(Hazel) PhD的经历让我面对失败的时候变得更加坚韧了。科学研究就像是坐过山车,充满了忽上忽下的起伏。我觉得能从失败中发现问题并解决问题的能力,对我未来的人生和事业都会有很大的帮助。通过PhD的训练,我还获得了自我学习的能力。在各行各业,尤其是科研领域,每天都有许多新的技术和知识。我们总有一天要离开学校,因此,能够找到正确的资源并进行自我学习是非常重要的。

(Fei) I learned that process is more valuable than results. Not all the experiments would have expected results. However, I learned to extract useful information from the unexpected ones and solve problems. The skills I gained are more important to the next stage of my life. Furthermore, such experiences give me more courage to face future challenges in my life, because I know that I gain the most from the process.

(Fei) PhD让我明白很多事情过程往往比结果更加重要。不是所有的实验都会获得预期的结果,但是在这些过程中,我学会了积极的面对那些意外的实验结果,并从意外的结果中提取有用的信息,从而帮助我努力寻找解决问题的办法。这些在面对问题和解决问题的过程中收获的能力会让我获益终生。更重要的是,这些经历让我更加勇敢的面对人生道路上的挑战,因为我知道我会在每一次迎接挑战的过程中快速的成长。

 

Durham, Duke, and DSCB: Insights from three DSCB Graduate Students

fruit fly pupa

Fruit Fly pupa. Image by Khanh Vien

Zebrafish scales

Zebrafish scales. Image by Maya Evanitsky.

 

 

 

 

 

 

 

 

The three graduate students (Taylor Hinnant, Khanh Vien, and Maya Evanitsky) running DSCB (Development and Stem Cell Biology) recruitment this year interviewed each other about their research, Duke, Durham, and DSCB:


Could you describe your research in a few sentences?

Taylor – I am a second year in Terry Lechler’s lab where I am currently trying to understand how the microtubule cytoskeleton reorganizes during cellular differentiation using the skin as a model system. I am making tools to figure out how the protein composition of the microtubule organizing center in undifferentiated skin cells changes upon differentiation.

Khanh- I’m a second year in Pelin Volkan’s lab investigating the combinatorial code required to appropriately wire and organize the olfactory system in Drosophila.

Maya – I’m a third year in the Di Talia lab using a systems biology approach to study zebrafish scale development. I’m currently looking into the signaling pathways that control when and where scales first form on the fish.

Why did you choose Duke and the DSCB program in particular?

Taylor- I really liked the flexibility in the courses you can take in your first few years in the DSCB program. Also, the friendly environment created by current students and faculty members during my interview made me feel like I was right at home!

Khanh- I chose Duke because I am particularly interested in the mechanobiology involved in the development of biological shapes and Duke has a very strong network of faculty working on the frontier between biology and physics. And I chose DSCB because I love developmental biology, and knew I wanted to go through graduate school with this emphasis.

Maya – I knew when applying to schools that I wanted to study development and to go to a place where people were friendly and collaborative. Duke and DSCB in particular fit all of this and while I’m not doing the kind of genetics work I first envisioned when applying, I’m really happy with the lab I’m in and the research I’m doing.

What is your favorite/least favorite thing about Durham/North Carolina?

Khanh- Many don’t realize this but Durham has an INCREDIBLE history of activism (that still stands true today). I am from Berkeley/Oakland, CA and Durham’s vibrant and diverse community with a progressive social justice mentality helps me feel safe and at home.

Maya – My favorite thing about Durham is honestly just the general vibe of the city. There’s plenty of things to do without it feeling overwhelming. It’s a very friendly city with an interesting history. My least favorite thing is probably the lack of reliable late night public transit. A lot of buses don’t run very late or very often and the only real alternative is driving or getting a Lyft.

What was the biggest hurdle you faced when starting grad school?

Taylor-When starting grad school, I had difficulty managing my time with so many new styles of courses and rotating through labs doing very different types of science. I definitely had to learn to prioritize my time and focus on big goals.

Khanh- I had a very hard time moving away from the tight knit queer people of color community I had. But I am so glad I am learning how to find and build my own community. I am no longer afraid to move anywhere in the world because I know I can find a home.

What advice would you give a student applying to graduate programs?

Khanh- It’s not a race, no one gets a prize for going to graduate school first. Strive to prioritize what makes you happy and surround yourself with people who want this happiness for you.

Maya – Whatever you do, don’t compare yourself to others. Everyone’s journey in science is unique and hits different roadblocks, so don’t think because other people seem so accomplished that you’re not good enough. Also, ask questions about things that matter to you. Whether it’s science policy, sports, outreach, or just finding friends – make sure the school you choose is holistically a good fit for you. We’re in grad school for science, but you shouldn’t give up your life and interests for it.

The RNI Travel Award and how it enhanced Erez Cohen’s project:

Cell cycle dynamics in the developing Drosophila pylorus. Gray: mitotic cells Green: G1 cells, Magenta: G2/S.I received the Duke Regeneration Next Initiative Graduate Student Travel award to attend the 2019 ASCB|EMBO conference in Washington, D.C. this past December. My research interest is in how developing cells and tissues can adapt to challenges such as acute injury and cell loss within the time frame of development. This question is important given that many tissues, such as our heart and limb digits, show little regenerative capacity as adults yet have a striking capacity for regeneration at a young age. Thus, my project aims to understand how injured organs regenerate under time constraints and in concert with development.

My lab previously identified an organ in the Drosophila hindgut that undergoes regeneration at the developing larval stage following acute injury. During the ASCB|EMBO conference, I presented that this regenerative response is time-limited and occurs in concert with development. To accomplish regeneration within developmental time-constraints, I found that hindgut cells accelerate their cell cycles and undergo additional cell divisions to compensate for severe injury. This work introduces a new genetically tractable model to study regeneration under developmental time constraints.

Receiving the RNI travel award and attending the meeting was instrumental to the advancement of both my research and career goals. The meeting allowed me to interact with peers in my field and receive valuable feedback on my work and project directions. The large scope and the high quality and Photo of Erez Cohenquantity of research of the ASCB|EMBO meeting provided a unique opportunity to expose myself to novel research outside my immediate field – from how tissues and cells interact with each other to the components that makes up the machinery of a single cell. Finally, as a senior graduate student pursuing a career in academia, the RNI travel award provided me with an opportunity to network with potential mentors and peers, as well as to discover new ideas and methods that will be useful for my future career.

Apply for your own travel award by January 31, 2020.  More Details here

 

Regeneration’s Past, Present and Future?

Kenneth PossAn interview with RNI Director – Dr. Kenneth Poss

Tomorrow, countries throughout the world will be ringing in 2020, and over at Duke we can celebrate the four-year anniversary of the official launch of the Regeneration Next Initiative (RNI)! This turn of the decade gives us chance to reflect on and think about the future of the initiative, and the field of regeneration biology. Currently, RNI is led by a committee of co-directors, and works to build a community for and support regeneration and developmental biology researchers at all stages of their careers, in broad areas of expertise. These RNI activities range from student travel grants & post-doctoral fellowships to research conferences, faculty chalk talks, an annual RNI retreat, and to hosting faculty searches. Alongside this work, RNI creates blog posts on the work being done and communicates it to a broader audience through newsletters and social media. An individual that has been with the initiative since its start is Dr. Ken Poss, James B. Duke Professor of Cell Biology and RNI Director. I sat down with Ken and asked him about his past and future perspectives of RNI, the work his lab does, and the impact his experiences have had on him. Check out the interview below.

How did the Regeneration Next Initiative come to be and blossom into what it is today?

It hasn’t changed that much in terms of people since it was launched in the beginning of 2016. We’ve always had the community of faculty studying developmental biology, tissue regeneration, and tissue engineering. And, we’ve always had a focus on the students and post-docs, the various programs, and the labs interested in it. What we didn’t feel we had was a strong sense of community and shared missions, and we didn’t think we were capitalizing on our strengths to build the reputation of the school and have our community flourish as it should be able to.

The School of Medicine ultimately gave us some directive to build a more formalized community interested very broadly in tissue regeneration. It has allowed us to recruit new faculty, gave us funds to invest in people here for post-doctoral fellowships, graduate student travel awards, undergraduate summer fellowships, and various events. . . That’s been the real change: a sense of community, a bit of growth, and a real mechanism of support.

What comes to mind when you talk about regeneration AND developmental biology?

That’s an interesting question because there are many who separate the two, and say that developmental biology might be distinct from regeneration biology. It sounds different, but I equate them. If you think back to studies of regeneration from the mid to late 18th century, these were seminal studies of how hydra regenerate or how salamanders regenerate limbs. It’s fundamental developmental biology for how a tissue forms from the behaviors and division of cells, from a structure that’s ill-defined into a well patterned structure. I see regeneration as a core component of developmental biology.

I also see aging as developmental biology. We’re developing continually, and part of it is through shedding dead tissue or cells and regenerating that. It’s a daily event. As we age we don’t do this as efficiently. This is why the study of embryogenesis, organogenesis, and tissue patterning is an important part of the regeneration community here. I think to understand one, you need to understand the other.

What do you hope to see happen within the initiative in the next five years?

We’ve had great success in stimulating, running, and funding faculty searches. We’ve helped the school invest in six faculty. For four of those faculty, we led and identified the candidate, and successfully recruited them with partnering departments. We’re really happy with the people and ideas that we’ve brought to different parts of Duke! We started off and maybe still believe at its core, that this is a topic where we need to make more discoveries, in most cases, before you can start thinking about therapies.

For many tissues and diseases, more discoveries need to be made on the broad topic of how regeneration happens before you can start thinking about therapies. This is a problem, as some people have jumped onto ideas for therapies that are not based on science. This can be damaging in many ways, mainly to people who think they are being presented with a viable solution.

While there still is a lot to discover, I think we are at a stage now where we’ve engaged multiple aspects and schools here at Duke. Through this, more of the basic scientists and engineers can be thinking about clinical applications and more of the clinical scientists and clinicians can be thinking about how the science is going to inform what they do. I see the next five years as continuing to push the science, but also being more cognizant of the potentials of the field and thinking more about the regenerative medicine space in addition to regenerative biology and discovery science.

Can you give us a snapshot of the range of regeneration research being done in the Poss lab?

My lab is very generally and broadly interested in how and why tissue regeneration occurs. Why it occurs so well in some human tissues (liver, skeletal muscle, blood), why it occurs so poorly in others (the brain, the heart, our limbs), and what explains that. We use the zebrafish, which is particularly good at regenerating some of those structures that we’re bad at. They can regenerate amputated limbs (their fins), severely damaged heart muscle, and a fully severed spinal cord that paralyzes them, which they can regrow and connect from those two severed ends to reverse the paralysis. We study many different tissues in fish. I mentioned the fins, heart, spinal cord, but we also study how they regenerate the bony scales on their surface and their skin that covers those. Recently we’ve been studying their ability to regenerate after a traumatic brain injury.

Studying how regeneration works really well in an animal like the zebrafish, versus a human, gives perspective on what it takes, what the differences might be, and what needs to be tweaked in say a mammal (like a human) to do better at regeneration. Also these other tissues have their own advantages and their own questions. I like to have a wide array of tissues [being researched] so one can see how it seems to be working in one tissue, and can inform the other. Maybe after deep study of these, we can create some kind of common theme or synthesis that explains regeneration better.

 How have you seen the research in your lab change as more work is published in other systems?

Regeneration is a more popular and populated field than it was when I first moved here in 2003. Maybe at the time, there were for instance, only two or three groups studying zebrafish heart regeneration. Now there are several dozen. I think for instance, if you think about heart regeneration as a field, the perspective has changed quite a bit with all the groups entering, both in the fish, and prominently with new angles on how the mouse heart can be provoked to regenerate. Back when I started, the predominant idea was that there were cardiac stem cells that exist in our heart, and can and might be normally replenishing the muscle of our heart. And probably one can take these out, purify, expand them, put them back in, and generate a therapeutic regenerative response for the heart. Now, the field has really changed and that has been largely debunked, and a majority of people in the field have different approaches to regeneration.

One of them aligns with how we think about regeneration, in that in mammals there is likely a way to stimulate the muscle cells to divide and to force them with strong molecular controls to participate in regeneration. That I think is really exciting! What comes with this and this increased number people in the field, is that we naturally, as a lab, have turned our attention to thinking about applications as well. How maybe we can take what we’ve learned in fish to understand how the mouse or mammalian heart can regenerate. I think the biggest change has been the density of groups in the field and that for some tissues, like the heart, we may be ten years or less from a regeneration therapy. It’s always important to try and discover new things and be thinking about knowledge and pure science, but there’s no question everyone is also thinking about how are we able to regenerate human hearts today. I think it’s exciting in that respect!

Your lab recently published a piece on limb regeneration for Development’s advocacy collection- how else do you or members of the lab promote regeneration research advocacy?

I think there is never enough done in this arena, and think we need to continue to increase our efforts. That’s something Amy Dickson, who’s the [RNI] Programs Director, is on. We have opportunities to give lectures, for instance to North Carolina teachers, to bring in middle school kids on tours and into the laboratories here. Our undergraduate program takes a handful of students, but the idea is to give people exposure doing research early on, so they get excited about regeneration research. We try to make appearances where it’s important to advocate science generally, when those are happening locally.

We have an opportunity here because this topic is so clearly relevant to how medicine might happen in this century. I think getting more people excited about it as a possible therapy, getting excited about the science, the idea of a career, and just being knowledgeable, is really important, [especially] on what evidence-based science is versus more hopeful, hype-based ideas. That was one of the goals of putting together the Initiative, to get everyone on the same page about what the science behind some of these ideas really is, and what might not be as rigorous. I think as for advocacy, that starts at Duke, but also it needs to eventually branch out and be transmitted because there are a number of “bad actors” out there pedaling therapies that are not therapeutic at all.

 

How do you balance heading a research lab, being Director of RNI, and having a family?

 

Balance is a word, on a day to day basis, that’s hard to use, but if you average it over many years, I think I’m happy with the balance that I have. It starts with having really great people and working with great people, both in the initiative and the steering committee we have of co-directors. Then of course in the laboratory where I’ve been very lucky to have a stream of really talented graduate students, post-docs, technical staff, and undergraduate students over the last sixteen years. As a lab PI, (unfortunately most PI’s don’t spend a lot of time doing experiments anymore) I’ve always said the experiments are the most difficult part. Writing grants, giving lectures, and reviewing papers, that’s not nearly as difficult as having a whole set of experiments on your shoulders and having to keep those going every day, to interpret, and to pivot.

I think once you get into a position where you’re able to attract great people, then (for me) I found time to be able to try to serve the school in a different way, and I was (and still am) excited to be able to direct this Initiative. The biggest advantage to me is being able to somehow increase or improve the excitement about this topic I’m really excited about. To have more and more people think about it, come to our events, and agree to come here as new faculty. Once the laboratory becomes populated by great people, then you can find time to do that.

Integrating family time is a real challenge, there’s no real equation or answer for that. It’s been challenging especially in the early years as a faculty member here. I find more time now for my kids who are in high school, but they certainly want less of it than they had when they were younger! That’s a battle a lot of people have, and I think unfortunately it keeps some people away from academia. That balance is truly challenging for many people.

How have you handled being a Packers fan transplanted into the middle of Carolina Panther country?

[Mutual chuckles] Yes, I’m from Green Bay, Wisconsin, and I’ve been a Packers fan forever. My most distinguished position was working during their summer training camps serving food or cleaning up during the meals, and I did that for three or four years.

Green Bay is a long way away from here, but it doesn’t change much over the years. I can only visit once a year at most, but I really like following the team and, when I’m able to watch on TV, seeing the scenes of exciting Green Bay. I don’t know if it’s more the football or just the connection to growing up there, but I find that there are a lot of Packers fans around the country. It’s a nice thing to talk about when you can make that connection!

What do you hope to accomplish in this turn of the decade?

This is kind of my mentality to not to make predictions about, or strict goals, like “we are going to discover this,” or “we are going to help contribute to a therapy.” I hope it’s both of those! We definitely want to continue a streak of finding out new things about how regeneration happens, and we want to be more actively involved in trying to tweak the human regeneration machinery. I think what’s exciting about science and how quickly it moves, is how the tools and technologies come unexpectedly, and they get adopted really quick. We can now do things in zebrafish, like insert any DNA sequence we want, wherever we want in the genome. When I started working with zebrafish, it was only very basic stuff we could do.

I hope we will have a comprehensive understanding of the tissues that we study, and how they regenerate, but I also hope in the next ten years to be surprised by some fundamental concept that we find just find one day assessing the data from an experiment. I like accumulating knowledge and knowing a lot about how something happens, but more exciting to me is just the idea that any day you can find something fundamentally unexpected and important. And that’s just as, or more, exciting. So I hope for more of that!


photo of Raymond Allen, DSCB graduate student om tjeInterview by Raymond Allen, DSCB and Biology graduate student – McClay lab – Packer Fan

Catching up with our first RNI Faculty member, Purushothama Rao Tata:

As the year comes to an end, our Programs Director, Amy Dickson, caught up with Regeneration Next’s first faculty hire, Purushothama Rao Tata, to see how his lab is progressing after 3 years at Duke and whats next for them:

ALD: If you had to tell someone abouMEC-1t your research in one or two sentences, what would it be?

PRT: This is what I tell myself and my trainees – We study one of the most important organs that’s highly vulnerable and affects almost everyone on a daily/seasonal basis. We work towards improving repair of damaged lung tissues and cure lung diseases.

ALD: You have been at Duke for 3 years now.  What has been the most surprising aspect of being a PI?

PRT: Yes, it’s been already three years- time flies so fast, particularly when that ticking timer follows you wherever you go. The most surprising thing to me was – how quickly your schedule fills up. My schedule looks almost empty when I look at my calendar a month in advance but surprisingly it fills up in no time. It became more and more obvious when there is a grant deadline. When I was a trainee, all that I had to take care was my experiments and a couple of students who worked with me on the same projects. But now managing the lab members and their projects, managing the budget and other administrative things. Slowly I realized that this is the ‘norm’ and the reality of being a PI. Now, I learn to become more efficient at using my time and doing what I do. Advice from senior faculty and my close interactions with the faculty from RNI affiliated labs helped me accelerate my learning process.

ALD: What is your favorite part of your job? 

PRT: The favorite part of my job is when I see a trainee is genuinely excited about his/her data or the next experiment he/she is going to do. I personally know from my own experiences how gratifying/satisfactory such excitement is. The other part I like is – I get to travel and give talks across the globe. I get to meet new people and hear different perspectives about our work etc.

ALD: Of all time, what is the experiment or project you will never forget?  Positive or negative!

PRT: It’s not a single experiment or project but it’s a collection of observations. But all of them point to one phenomenon – ‘cell plasticity’. During my postdoc time I demonstrated/learned how plastic our cells are. I still continue to explore this property in everything we do.

ALD: What’s coming up for you? Your lab? 

PRT: Many exciting things coming our way in the next one year with some current trainees leaving and some new trainees joining us. Some of our trainees are about to wrap up a couple of manuscripts and they will be ready to move out to explore their own independent research programs. One of the major accomplishments for most PIs is seeing their own trainees move out to build their own nest. I look forward to seeing that in the coming year. Our lab has grown quickly in the last 6 months with the addition of 3 new postdocs. New lab members mean new technical expertise and so new directions. Very exciting times.

How a Torn ACL brought Sofia Hidalgo (c/o 2020) to work in Dr. Amy McNulty’s lab

You recently published an article about culture conditions for in vitro meniscus repair modelling. Briefly describe your breakthrough discovery that led to this publication.Sofia Hidalgo (c/o 2020)

– The McNulty lab works with mesenchymal stem cells and meniscal tissue; however, we had not identified the best media to use when performing experiments involving these two different variables. The media used, specifically the use of serum, has significant impact on the results obtained depending on the substances used per experiment, thus, we decided to investigate this more closely in order to establish a favourable culture medium for both MSCs and tissues.

What excites you about your work?

– There are many aspects about this line of research that excite me. I believe that regenerative medicine is the future and getting the chance to work on stem cell therapies for common orthopaedic injuries will be extremely beneficial for patient outcomes and recovery.

Why did you choose to study in Dr. Amy McNulty’s lab for your undergraduate research project?

– Throughout high school I tore my ACL and injured my meniscus twice. The aftermath of these injuries, and the intricacies of the recovery process made me very interested in meniscus repair strategies, and as I researched potential laboratories for my undergraduate research project, Dr. McNulty’s work caught my attention right away.

What has been your favourite experiment in the lab?

My favourite set of experiments at the lab have been the ones that have used our novel meniscus tissue defect model. Creating this model was tedious, but it allows us to simultaneously investigate many different parameters that promote meniscus repair

Scanning Electron Microscope images of 16% Genipin Meniscus-Derived Matrix Scaffolds. The image is at 1000x (scalebar of 50um).

What’s next for you? Your research? 

– Over the past three years we have worked on optimizing a potential bio scaffold that could be utilized in a clinical setting, but there are many factors that yet have to be studied before that stage can be reached. Currently, I am working on an experiment that combines more clinical parameters, such as dynamic loading. I am planning on working on this project for the remaining part of the year as part of my Senior Thesis project before I graduate in May. After graduation, I am planning on moving to New York and continuing working on this line of research for 2 years before applying to Medical School.

Beyond a Summer in the Lab: Jeffrey Zhong discusses his work in RNI Director, Ken Poss’s lab

Jeffrey Zhong, now as senior at Duke, has worked in Ken Poss’s lab since his freshman year.  Jeffrey work has focused on heart regeneration in both zebrafish and mice.  Jeffrey also had the opportunity to be a part of Regeneration Next’s Summer Undergrad Fellowship:

  1. How was your summer experience in Duke’s RNI/SROP joint summer research program?

It was fantastic and I loved it! The Duke SROP/RNI joint summer research program really was a great opportunity to progress as a student researcher and as an individual. The Duke SROP/RNI joint research program hosted weekly talks by various Duke faculty members in various fields of research and stages of their lives. I found it very helpful when they shared their personal experiences and paths to their current lives, and I gained invaluable insight into research as a career and life in general. The summer research program also helped me to further develop myself professionally by providing opportunities like mock interviews with Duke faculty and giving tips about what makes a good application.

Research always has its ups and downs and having a good community of students and mentors played a major role in how enjoyable the program was. Our cohort had people with various backgrounds in research, with even some having never done it before. Yet, everyone was so excited and curious about engaging in research and you could tell that this enthusiasm was contagious. I loved meeting and bonding with all these students from all different places and backgrounds. In addition, all the directors and supervisors of the program were truly interested in how we were doing and made sure to make us all feel welcome.

We also got to participate in many fun activities around Durham, like visiting the Duke gardens, going to art exhibits, and eating at all the good restaurants around downtown Durham. The most memorable of these was when we went to a Durham Bull’s game on the fourth of July and watched fireworks.

All in all, I believe that spending my summer in Duke’s SROP/RNI joint summer research program was totally worth it and I would definitely recommend taking part in it.

  1. Why did you choose to study regeneration for your undergraduate research project?

I decided to study regeneration for my undergraduate research project because it is a relatively novel and very impactful field of research. The human heart is unable to regenerate well after becoming ischemic, which is why heart attacks are so detrimental to the health of patients. To think how regeneration in zebrafish could be applied and repurposed for humans in the future for biomedical purposes piqued my interest and I’m so glad to have chosen this field of research.

  1. You graduate this year! Where’s next?

I plan on becoming a physician. What specific type of doctor is still up to question, but as of right now I’m thinking of orthopedic surgery. The training that Dr. Poss has provided me in basic science research will surely inspire me to explore the unknowns in whatever field I choose. I can envision becoming a physician scientist to perform disease related research in the future.

 

Undergrad in the Lab: A look into Lily Hiser’s work in the Bursac Lab

Lily Hiser, a junior at Duke, has been working in Dr. Nenad Bursac‘s lab.  Lily is pursuing a degree in Biomedical Engineering

Lily Hiser, undergraduate researcher in the Bursac Lab

What excites you about your work?

To me, tissue engineering is the most exciting area of research in the biomedical field. It is the perfect mixture of biology and engineering, as it takes prowess in both to create a successful tissue. Thinking big picture, I can personally imagine a future where engineering tissues is an everyday part of medical research, whether this is for drug testing, implantable devices, or some other application. Being in such a cutting-edge area of research is such a privilege for me, and I am still amazed every day I go into the lab and see the muscle tissues that we have created working like a muscle should!

  1. Why did you choose to study in Dr. Nenad Bursac’s lab for your undergraduate research project?

Before matriculating into Duke, I had the privilege of doing research in high school at the Wake Forest Institute for Regenerative Medicine. I had never been exposed to that caliber of research before, and I was particularly fascinated by the area of tissue engineering. My experience there propelled me to pursue a degree in biomedical engineering, and I knew that I wanted to do research in tissue engineering while I was at Duke. I had always been impressed with Dr. Bursac’s groundbreaking work, and I knew that doing research in his lab would be an incredible environment for learning and the development of my own research skills. I chose to study in his lab because I knew it was an area of research that I was very passionate about, and I was excited by the opportunity to experience it firsthand.

  1. What has been your favorite project in the lab?

So far, my favorite project in the lab has been my work with the Duchenne muscular dystrophy (DMD) project. DMD is a genetic disorder that causes a mutation in dystrophin, a protein which is important for maintaining muscle structure. Currently, there is no curative treatment for DMD, but there are a variety of drug treatments being developed. However, the animal models which are used for DMD drug testing, particularly the murine models, do not provide realistic modeling of the severity of the disease in humans. DMD can be caused by over 4000 unique genetic mutations, each one causing the disease to present itself in varying severities. The current mouse models only possess two genetic mutations, and it takes over a year for the model to display more advanced disease symptoms. Even then, these models are much milder than what is seen in DMD patients. This project is focused on creating an in vitro, patient-specific human model of DMD, which would more accurately model the various, unique severities of individual patients. My work has been focused on increasing the functionality and accuracy of the model, as well as using the model to test prospective drug treatments.

  1. The Bursac lab has 5 undergraduates working currently in his lab. Is there much overlap in undergrad projects or are you all working on different projects?

For the most part, each of the five undergraduates in Dr. Bursac’s lab is working on his or her own individual projects. Personally, I work very closely with another undergraduate student, Simal Soydan. We were trained together and share a lot of responsibilities on various projects. However, even though all the undergraduates do not work together, we do collaborate as far as communicating about different techniques. If someone has experience with a specific lab technique or expertise in a subject, we are always ready to collaborate and share our knowledge.

  1. What’s next for you? Your research?

As I continue to do research in Dr. Bursac’s lab, I am looking forward to continuing to grow my laboratory technique portfolio, as well as simply learning as much as I can from all of the amazing people I work with. For my research, I am looking forward to continuing to work on the DMD model, particularly with the possibility of testing some prospective gene therapies for DMD patients. Our project is also looking for ways to enhance the ability of the muscle to simulate human biology, specifically by developing methods for incorporating other biological systems, such as immune cells, into the mu

scle model. By doing this, the model will be able to demonstrate how the various DMD treatments affect not only the muscle, but the body as a whole.

Side by side comparison of engineered healthy muscle tissue (left) and DMD model muscle tissue (right)Side by side comparison of engineered healthy muscle tissue (left) and DMD model muscle tissue (right)

5 Questions Challenge with Jieun Esther Park, Ph.D. candidate: Enterocytes in the Vertebrate Gut

LREs in the zebrafish gut shown using fluorescent microscopy and IHC
Jieun Esther Park, Ph.D. candidate in the Bagnat lab took our 5 Question Challenge for her recent publication in Developmental Cell: Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut.  For this publication, Park collaborated with three other Regeneration Next Labs.

What drove you to become an expert on enterocytes?
I don’t know if I can call myself an expert on enterocytes by any means.
But my first project in the lab was characterizing LREs (Lysosome-Rich Enterocytes – specialized enterocytes in zebrafish and pre-weaning mouse) and that’s how I got to start my research on enterocytes. I was fascinated by the distinct characteristics of LREs and I loved studying them in the zebrafish system where I can visually see the cellular processes occurring in these cells. This is how I got to learn a lot about enterocytes over the last few years!

If you could tell the 1st year graduate student version of yourself one thing, what would it be?
Take advantage of lots of opportunities on campus as a student. There are so many certificate programs, classes, outreach programs you can participate in. Take advantage of the resources you have to build the skillsets you want and need!

What experiment or result did you find the most exciting or surprising?
I spent first two years of my graduate school trying to find the direction of my project. I made a lot of CRISPR/Cas9 genetic mutants and zebrafish tools, but I was not sure whether I would see phenotypes with my mutants and whether I will be able to carry out my project to find interesting results. But I took time to develop a very solid assay for quantifying cargo uptake in LREs and then tested one of my mutants (cubn mutant). And when I saw that cubn mutant showed defect in protein uptake, I was so excited!!

Say I’m a high school student, can you briefly describe to me your research and the impact your discovery has on Regenerative Biology?

When you eat food, proteins in your diet are broken down into smaller pieces (called peptides, amino acids) in your stomach & intestine, and then are absorbed by your intestinal cells. However, protein digestion occurs differently in babies during the pre-weaning stage. Babies with immature digestive system cannot digest proteins efficiently in their stomach or intestine. However, they instead have special intestinal cells that gulf up undigested proteins and digest them inside the cells. We named these cells Lysosome Rich Enterocytes (LREs). These cells play a very important function in absorbing and digesting proteins during the pre-weaning stage and they disappear after weaning. Our research looked at how LREs absorb proteins and showed that a defect in LREs leads to slower growth and in serious cases, decreased survival.

Our current research findings do not have direct impact on Regenerative Biology but now we have generated the tools to test how regenerative LREs are. Since LREs are intestinal cells that only exist in neonatal/developing gut in mammals, if they are more regenerative than adult enterocytes, that will lead us to understand and explore the differences in the regenerative capacity of neonate vs adult intestine and the mechanism behind it.photo of Jieun Esther Park, Bagnat Lab graduate student

What prompted you to bridge your work in zebrafish, with a collaboration in the mouse system?

Because we believed LREs are a conserved cell type in zebrafish and pre-weaning stage mammals, we decided to use the mouse system to back up our zebrafish data. We showed that LREs are indeed highly conserved in zebrafish and pre-weaning mouse and that they also share the same molecular machinery for their endocytic function.


Jieune Esther Park is a 6th year graduate student in the Pharmacology program.


Interview by Raymond Allen, DSCB graduate student – McClay Lab.
photo of Raymond Allen, DSCB graduate student om tje

 

 

 

 


If you would like to be a guest writer/social media contributor, please contact Amy Dickson.

5 Question Challenge with Victoria Deneke, Ph.D.: Synchronization in the Cell Cycle

Ahead of her publication in Cell out online today, Victoria Deneke, Ph.D. of the Di Talia lab took our 5 Question Challenge to give us more insight into her time at Duke and her recent work titled: Self-Organized Nuclear Positioning Synchronizes the Cell Cycle in Drosophila Embryos.

What excites you about your work?

One of the most extraordinary moments for me was watching the dynamics and organization that takes place in a developing organism for the first time. I am still in awe of the beauty of development and it is what keeps me motivated to understand more and more how this occurs in living systems.

Briefly describe your breakthrough discovery that led to the publication of this paper?

We have discovered in fly embryos the mechanism by which local biochemical cell cycle signals are integrated with the mechanical properties of the embryo to ensure accurate positioning of the nuclei. We have also shown that this process is necessary to maintain cell cycle synchrony throughout early development. More broadly, our work elucidates how self-organized biochemical and mechanical dynamics can arise in embryos and uncovers an important biological function of cytoplasmic flows.

These findings were made possible by a biosensor, which I was using in my previous studies (Deneke et al., 2016), measuring the activity of Cdk1 and PP1, two important proteins that regulate the cell cycle. One day we were imaging this sensor and we happened to start a movie at a very early time point in development. We immediately noticed that the cell cycle oscillations were distributed in a spatial pattern different from that expected from published studies. Specifically, we saw that oscillations were restricted to a specific location and  gradually expanded during subsequent cell cycles. That observation prompted us to ask whether there could be a functional significance to these local biochemical oscillations and led us to identify the model defined in our new paper (Deneke et al., 2019).

Why is this discovery important to the field of Regenerative Biology?

During regeneration, a damaged organ must heal in order to regain its functional size and shape. At the heart of this process are morphogenetic events that rely on the integration of biochemical and mechanical signals to coordinate growth and proliferation in space and time. Our study provides a novel quantitative model and framework for this integration and will inspire similar studies in more complex multicellular systems.

What was the most memorable experiment in your years in the Di Talia lab (whether it was successful or not)?

Figuring out how to introduce a barrier in the embryo was definitely one of the most memorable experiments in the Di Talia lab. We wanted to know whether the waves of division that we were observing could go through a barrier or not (Deneke et al., 2016). We tried all kinds of things, from using a high-power laser to ‘cauterize’ a part of the egg (think light saber cutting an embryo in half) to using optogenetics to molecularly introduce a barrier. As much as I would have liked for either of these tools to work, they didn’t. The light saber experiment ended up exploding embryos or generating a heat wave that “cooked” the egg, which was cool to watch but not useful for us. We then turned to a paper from the 70s that used what we call in the lab an “embryo guillotine”. This apparatus consists of a dull razor blade that has been mounted on a bar that you can precisely lower with a set of knobs at each end. We contacted the Duke Physics Machine shop to build this for us and we gave it a try. To our surprise, we could introduce a barrier using this method and more importantly, we found that the wave did not go through the barrier, suggesting that diffusion was necessary for the wave to spread.

What comes next for you? Or the research?

I continue to be fascinated by the amazing dynamics and emerging patterns inside living systems, especially during development. I’m intrigued to keep studying dynamical processes, now at the very earliest moments of life, in other words, right after fertilization. I’ll be starting a postdoctoral position in Dr. Andrea Pauli’s lab in September of this year, where I will be studying spatiotemporal coordination following fertilization in zebrafish embryos.

Interested in learning more about the Di Talia lab? Check them out here.  Interested in taking the Regeneration Next 5 Question Challenge about your recently published or upcoming work, email regeneration@duke.edu