New faculty Yarui Diao sheds light on DNA non-coding “Dark Matter”

From Regeneration Next Director, Ken Poss, Ph.D.:
On behalf of the Regeneration Next Initiative, I’m excited to welcome Yarui Diao, Ph.D., to Duke University. This month, Yarui joins us as a new Assistant Professor in the Department of Cell Biology. Yarui will also be an affiliate of Regeneration Next and hold an appointment in Orthopaedic Surgery. Regeneration Next partnered with Dean Klotman to recruit Yarui to Duke as part of an open search this past year conducted with the departments of Cell Biology and Biomedical Engineering.

Yarui followed a highly productive training in skeletal muscle regenerative biology with postdoctoral work in Bing Ren’s lab at UCSD, where he applied cutting edge gene-editing techniques to dissect genome regulatory elements at high throughput in stem cells. Here, he intends to explore the gene regulatory mechanisms that control skeletal muscle stem cell activity and is excited to form new collaborations – indeed, his work in both biology and technology spaces should be of interest to many faculty at Duke.

Regeneration Next Executive Director Sharlini Sankaran, Ph.D. spoke with Diao about his research and future plans.

Yarui Diao, Ph.D.

SS: Your research focuses on gene regulatory elements. What are they and why are they important?
YD: As the name suggests, “gene regulatory elements” refer to the non-coding DNA regions which control gene expression. When the human genome was first sequenced in 2003, scientists were surprised to find that only 2% of the human genome was made up of so-called “coding” genes. More than 98% of the sequence was non-coding. In fact, about 15 years ago these non-coding gene sequences used to be called “Junk DNA” or “Dark Matter”, and many people used to think they were non-functional.

But then came the rapid development of the field of epigenetics and next-generation sequencing technologies. These tools allowed us to learn that these non-coding regions of the genome contain extremely critical information to help the cells in our body learn when, where, and how much to turn on or off the gene expression program. These “non-coding” regulatory regions of the genome show highly cell type-specific activity. This activity is what directs cell differentiation – it is what makes our brain cells become brain cells, a muscle cell become a muscle cell, and so on. Each cell type has different morphology, different function, and different gene expression program.  You can think of gene regulatory elements as the “Menu” and “instructions” that tell the cell how develop and how to function.

SS: These elements are very important in cell development and differentiation, but they also play an important role in tissue regeneration. Can you tell us how gene regulatory elements are important in regenerative medicine?
YD: Gene regulatory elements play an important role in almost all biological processes, including tissue regeneration. Let’s take stem cells as an example. In different tissues, there are tissue-specific stem cells, and there are lineage-specific transcription factors that are tightly controlled by gene regulatory elements. These transcription factors need to recognize specific regulatory elements to “turn on” their activity. If we can get a better understand of how gene regulatory elements work, we can get a better understanding of stem cell fate, or how stem cells differentiate into different cell types.

If you get a better understanding of gene regulatory elements, it can help you understand the disease mechanisms that are involved in many degenerative disorders and also in the aging process.  We know that in aging, a lot of tissue types fail to regenerate at the same rate as in younger people, and these have to do with changes in gene regulation.

SS: How did you become interested in this area of research? Tell me a little bit more about your research.
YD: I spent my entire postdoctoral career studying gene regulation, but my interest in tissue regeneration dates back to my PhD studies. I wanted to understand how transcription factors can control stem cell fate (what types of cells the stem cells mature into). I found that the transcription factors need to bind to specific gene regulatory elements to do the job.  At that time, just 5 – 6 years ago, despite the crucial function of these regulatory elements, it was difficult to precisely identify them in the genome because there were no good tools to characterize the 98% of the DNA that consist of these non-regulatory elements.

So for my postdoctoral training, I took a departure from my PhD research of studying muscle stem cells to join Dr. Bing Ren’s lab to study gene regulation. Dr. Ren is well known for using cutting edge technology and tools for studying functions of the non-coding genome. Luckily, at that time, in 2013, there was a new technology called CRISPR-Cas9 that was being developed. This new technology gave me the ability to develop a new method and lead a project to study the functionality of these non-coding gene regulatory elements in a high throughput manner.

In my Ph.D. research I, used muscle stem cells as a model system for studying the gene regulation mechanism centered on a master transcription factor called Pax7. We know that Pax7 regulates muscle development and regeneration. Mice lacking Pax7 show severe defects in muscle stem cell activity and muscle regeneration and growth. Very interestingly, I found that loss of Pax7 causes cells to transition into adipocytes (Fat cells) instead of muscle cells.

Muscle stem cells are isolated (top) and undergo proliferation, differentiation, and fusion to form muscle fibers (bottom row, left to right). The entire process is tightly controlled by gene regulatory elements, whose dysregulation leads to muscular disorders in disease and aging. Image courtesy Yarui Diao.

SS: To clarify – muscle stem cells turned into fat cells? There may be a whole weight-loss industry that would be very interested in this!
YD: Yes. We showed that Pax7 binds to a few non-coding regulatory elements to suppress the fat cells’ fate. Without the Pax7, muscle stem cells that would have become muscle cells, matured into fat cells instead.

SS: What are the future implications of your research for human health and regenerative medicine?
YD: I plan to use muscle stem cells as a model system to understand how gene regulatory networks control muscle stem cell activity. Muscle stem cells are not as “exciting” or popular to study compared to, for example, brain or heart stem cells. The significance of muscle stem cells and their remarkable regenerative potency is often overlooked. We know it’s very hard for the brain to regenerate. It’s very hard for the heart to regenerate. But tissues like muscle and skin have remarkable regenerative ability and we should study them more.

If we look at diseases related to muscular degenerative disorders, I would say there is a very urgent need to understand the mechanisms that control muscle regeneration. For example, there are a lot of patients suffering from disorders like muscular dystrophy and muscular atrophy. Remember, muscles are not just there to support our limb movements. Muscles also control essential functions like moving the ribcage when we breathe – so if you have a defect in your muscle function, it can cause huge life-threatening problems.

There’s another type of condition called cachexia which occurs in patients with some chronic diseases like cancer. Cachexia is a muscle-wasting condition that causes a rapid loss of muscle function. The genetic and epigenetic basis of cachexia was overlooked by both scientists and physicians for many years, because it is not a direct cause of many diseases. But loss of muscle mass and function causes big trouble for patients. Cachexia is one of the provocative questions we need to address in cancer treatment. If we could find a way to manipulate muscle stem cell function, that would be very helpful to restore mobility and strength to these patients.

Also, aging is a condition that affects everyone eventually. Scientists know that in aged mice and aging people, muscle stem cells cannot be properly activated to generate new muscle cells. When injury occurs in older people, these muscle stem cells are less likely to be activated to heal the injury by new tissue formation. So, all these clinical needs are currently unmet mainly due to our limited understanding of the gene regulation mechanisms that control muscle stem cell activity.

SS: What are you looking forward to as you move to Duke?
YD: I’m very excited to establish my own research lab, as anyone would be after years of PhD and postdoctoral training! As I mentioned, I studied muscle stem cells in my PhD, and I studied gene regulatory elements in my postdoc, and I’ve had a long-standing interest in regenerative capacity and disease conditions. When I published my Cell Stem Cell paper during my PhD, I got a lot of phone calls from patients. Even though my research was very far removed from clinical treatments, there was still a lot of interest from patients. This encourages me as a scientist to do a better job of learning how translate this knowledge into future therapies to help people.

At Duke, and in North Carolina in general, there’s a very good environment to collaborate and push forward my research. There are a lot of people working to understand the role of gene regulatory elements in general, and also specifically in muscle stem cell function. For example Charlie Gersbach is a genome engineering expert who is also very interested in muscular disorders, and Ken Poss is a pioneer in heart regeneration who has uncovered tissue regeneration enhancer elements that help zebrafish hearts regenerate. I really look forward to working with these great people, trying to generate new knowledge and make an impact in science.

I’m also very excited to become a teacher. My parents are teachers in China, and my parents-in-law, my grandmother and grandfather, were all teachers. When I was a kid, I thought being a teacher is the best job in the world. I’m so happy to come to Duke to be a researcher in a great environment, but also to become a teacher to help train a new generation of future scientists.

“Fizzy-related” gene regulates organ repair after injury

Most of us take for granted that our bodies and organs have the ability to heal after an injury, but rarely stop to ponder how. We know that the healing process occurs by filling the space created by the injury. This can happen in one of two ways: by making cells bigger (a process called hypertrophy) or by dividing cells to make new ones.  For over a hundred years, scientists have sought to understand why some organs undergo hypertrophy, and if that process has any advantages over cell division.

In a new study published in the journal eLife, Duke researcher Donald Fox, Ph.D., and his team identified a gene, known as “Fizzy related,” that regulates hypertrophy in fruitfly cells after organ injury. They found that in injuries requiring many cell divisions or many rounds of hypertrophy to heal, cell divisions led to organ distortion and loss of permeability, whereas hypertrophy had no substantial effect on the repaired organ.

Intestinal cells in fruitfly larva showing repair after injury. Magenta = intestinal cells, green – cell nuclei. Image courtesy Erez Cohen, Duke graduate student and the paper’s primary author.

These findings may benefit researchers interested in therapeutic organ regeneration, because the results identify a molecular target that could potentially be used to alter an organ’s repair capacity. They also highlight a potential protective effect of hypertrophy in injured tissues. Hypertrophy has been observed in humans, following injury to the liver, heart, or kidney. While often viewed as mal-adaptive and non-regenerative, this study’s results suggest that there may be a protective effect to hypertrophic tissue repair.

Read more about this paper and its implications in the Duke Medical School Blog.

Paper Citation: Cohen E, Allen SR, Sawyer JK, and Fox DT. Fizzy-related dictates a cell cycle switch during organ repair and tissue growth responses in the Drosophila hindgut, eLife 2018;7:e38327 doi: 10.7554/eLife.38327

Cell survival pathway linked to regeneration in aged skeletal muscle

Skeletal muscle stem cells (MuSCs) play a vital role in the repair and regenerative functions of our muscles after injury. As those of us over forty may know firsthand, this function declines with age and contributes to impaired muscle regeneration in older individuals. Despite what you may see in internet ads, there are currently no stem cell injection treatments that can reverse this decline in muscle regeneration function. However, thanks to a new report from Duke University’s Department of Medicine (Hematology), scientists are a step closer to identifying treatments that target molecular pathways related to cell survival. They hope that age- or disease-related muscular degeneration can be slowed or even reversed by identifying and restoring function of these molecular pathways.

Top to bottom muscle stem cells in young, middle-aged, old and geriatric mice. Blue is nuclei, red is cytoplasm and green shows autophagy.

Top to bottom: muscle stem cells in young, middle-aged, old and geriatric mice. Blue is cell nucleus, red is cytoplasm and green shows autophagy. Image courtesy James White

In this recently published report, Duke researcher James White and colleagues identified a molecular pathway that regulates several natural phases of the MuSC cell cycle. This pathway, the AMPK/p27Kip1 pathway, regulates key processes including autophagy (cellular recycling to turn old proteins and other substances into energy and materials for new structures) and apoptosis (cell death). Aging cells tend to exhibit less autophagy and more apoptosis, which ultimately leads to reduced regenerative and repair capacity in older adults.

In the paper, published in the journal Stem Cell Reports, White and colleagues found that the balance between the processes of autophagy and apoptosis is crucial in determining whether an MuSC survives and can assist with muscle repair. They found that MuSCs in aging mice exhibit less autophagy and more apoptosis, and are more susceptible to cell death than the MuSCs of younger mice.

White and colleagues determined that aging MuSCs have dysfunctional signaling of the AMPK/p27Kip1 molecular pathway. When they activated the AMPK/p27Kip1 molecular pathway in old MuSC, they found increased cell proliferation. In addition, restoring AMPK/p27Kip1 signaling increased the survival rate of transplanted aging MuSCs. White and colleagues conclude that this pathway could be an important potential therapeutic target for improving muscle regeneration in older individuals.

Citation: James P. White, Andrew N. Billin, et al, The AMPK/p27Kip1 Axis Regulates Autophagy/Apoptosis Decisions in Aged Skeletal Muscle Stem Cells, Stem Cell Reports, 2018,

Astrocyte-to-neuron signaling is key to building brain connectivity

Duke researcher Cagla Eroglu, PhD and her colleagues have identified a key protein receptor in the brain which regulates development of important connections in the brain. A new research paper published in the Journal of Cell Biology explains how this molecule plays a pivotal part in brain development. Chris Risher, faculty member at Marshall University and a former Postdoctoral Fellow in the Eroglu lab, was the paper’s primary author. Risher says, “this work provides new insight into the development of aberrant synaptic circuitry in conditions like autism, epilepsy, and other neurological conditions.”

An epifluorescence microscopy image of a rat neuron. Bright spots reveal synapses (connection sites). Image courtesy Chris Risher.

The brain is a highly complex organ that enables us to think, remember, move, and perform simple to complicated tasks. These tasks use brain circuits that are made up of connections between cells called neurons. Neurons contact each other at sites known as synapses, and the human brain is estimated to contain trillions of these connections. The way that synapses form in the brain, and how faulty connectivity may lead to brain dysfunction, are still largely unanswered questions in neurobiology.

In the last decade and a half, research has pointed to a non-neuronal basis for regulating synaptic connectivity. Star-shaped “connector” cells known as astrocytes, which far outnumber neurons in the brain, secrete factors that modulate the timing and extent of synapse formation. One of these factors, an extracellular protein called thrombospondin (TSP), was previously shown to promote synapse formation via a receptor, α2δ-1. But the mechanism of synapse formation was not yet known.

Risher used a technique called three-dimensional electron microscopy to study synapse formation in mice brains. In this paper, they show that that α2δ-1 is required for the structural maturation of synapses. They determined that a molecule produced by α2δ-1 stimulates structural maturation of neurons. Mice neurons that lacked α2δ-1 or the molecule it produces remained in an immature state. When they restored the receptor and its functions, the synaptic deficiencies were reversed.

This paper lays the groundwork for future therapies and treatments targeting conditions that are caused by deficient astrocyte-to-neuron signaling. One such drug, the FDA-approved drug gabapentin (Neurontin) is used to treat a variety of neurological conditions and works by targeting TSP and α2δ-1. In humans, defects in TSP, α2δ-1 and their signaling partners have been implicated in autism, epilepsy, and other neurological conditions.

Citation: Thrombospondin receptor α2δ-1 promotes synaptogenesis and spinogenesis via postsynaptic Rac1. Risher, Kim,, Journal of Cell Biology DOI: 10.1083/jcb.201802057 | Published July 27, 2018

Summer Fellow Jack Chang: Thank somebody today

A guest blog by Jack Chang
Mr. Chang is a Regeneration Next Summer Research Fellow in the Karra lab at Duke’s Division of Cardiology. In this blog post, he shares his research experience and reflects on how success depends on more than just individual effort.

My name is Jack Chang and I’m one of the RNI Summer Fellows this year. I’m a rising senior studying biochemistry at the University of Texas at Austin and plan on attending medical school to become a physician. This summer, I’m working in the Karra Lab studying mechanisms of cardiac tissue regeneration in zebrafish larvae, and it’s been an incredible experience. My project involves analyzing the interaction between TGF-b and vegfaa signaling on cardiomyocyte proliferation. To accomplish this, I’m using a confocal microscope to examine the hearts and the software Fiji to quantify cardiomyocytes. By the end, I expect to improve my understanding of the mechanisms of cardiac tissue regeneration in zebrafish and how this can be applied to human hearts.

In lab, I’ve grown tremendously as a scientist. I’ve been able to refine my laboratory research skills, increase my knowledge of the cardiovascular system, and learn how to better assess research. Every day, I learn something new, which is exciting. Being at Duke has been amazing as well. I love interacting with all the bright people I meet and hearing about the amazing accomplishments that have happened and are happening here in Durham.

Chang (Left,white shirt) with Ravi Karra (left, blue shirt), mentor Diana Chong (right, blue shirt) lab members at a celebratory lunch. Photo courtesy Paige DeBenedittis, lab manager (front, purple shirt).

With these highs, however, also come lows. Research can be frustrating and draining. When experiments don’t work, it’s discouraging. Before this program, I had an idealized perspective of research. I expected experiments to run accordingly and for data to be conclusive. But I’ve learned the grinding nature of science and how often finishing an experiment leaves one with more questions than answers. Adjusting to working full-time took time as well. Coming from undergrad’s easy pace, I often came home both physically and mentally exhausted. Being away from friends and family back home is hard as well. I write this to show that there are two sides to every coin and acknowledge that we all go through trials, even when it appears we’re having the time of our lives. So, if you’re feeling down, you’re not alone. Talk to someone about it. Odds are they’re able to empathize with you.

This past week, I got this fortune from a Chinese restaurant. It read:
“People make plans; fate makes the plan successful.”
Agree or disagree?

Initially, I couldn’t disagree more. In fact, when I first read it, I was appalled by this proverb. I posted on social media asking my friends their thoughts and the majority dissented as well. But one friend, whom I respect tremendously, agreed with it. I was confused as to how someone so wise would concur with such a statement. But that got me rethinking if there actually was any truth to it.

If not fate, what makes plans successful? Hard work? Talent? Fortunate circumstances? I think most people would agree that hard work brings success. But I don’t think anyone could argue all of their success in life has come from their own merit. To be fair, hard work does favor success. But how about the times when we got lucky? Or things just seemed to fall into place? For example, me being accepted into this program and coming here wasn’t all because of my own doing. Sure, I earned good grades and sought out research opportunities back home. But I’m fortunate to have friends who encourage me and great role models from my family and professors. Success isn’t dependent on just oneself. It involves factors like privilege, the actions or non-actions of other people, and even some luck.

This summer, I learned how research wasn’t an exception to this idea. To get research done, there was collaboration within a lab, as the PI, lab manager, postdocs, and even undergrads discussed ideas. Information was also shared between labs. Whether it was a joint lab meeting between two groups at Duke or reading a paper written by a lab in China, every day I saw how interwoven science is. PI’s are even dependent on grants to fund their research. With many publications and awards, it’s easy to become arrogant. But research is a team sport, with one piece of evidence being the many authors on a paper. It certainly takes more than an individual effort to account for success.

Being at Duke has been formative not just for my research skills, but also my appreciation for the people around me. Some of the skills I’ve learned include using a confocal microscope and sectioning with a cryostat. But without the guidance of the people in my lab, I would not be as fluent in these techniques, and I’m grateful for the mentors who’ve dedicated their time to training me. Above all, this experience has helped me appreciate how special every day is. I’m lucky to be at a great institution doing research and to work with people who help me be the best I can. Life isn’t just about me, but rather the people who have shaped me to the person I’ve become.

So, thank someone today. It can be your boss, co-workers, or even the cashier at the cafeteria. Show your appreciation for them and acknowledge the role they’ve played in your success. Reflect on the good has happened to you that has helped you reach the success you have today and strive to be that good to someone else. And while there is an “i” in science, you can’t spell it without the other letters.

Stay humble, be grateful, and appreciate the awesome life we all live.

Jack is always down to hear what other people are doing with their time:

Society for Developmental Biology Meeting: Recap Days 3 & 4

Ben Cox, graduate student in the Ken Poss lab, is sharing his experience at the Society for Developmental Biology’s 77th annual meeting in Portland, OR. Here’s his recap of the third and fourth day. Read his recaps of Day 1 and Day 2 .

Day 3:

Boundary between large and small intestine in the fruitfly. Image credit: Jessica Sawyer, Duke University

Day 3 of SDB featured the session that was likely of greatest interest to scientists in Regeneration Next labs. Lucy O’Brien of Stanford chaired the session titled Development Redux: Stem Cells in Regeneration and Homeostasis, and talked about her lab’s work on Drosophila (fruitfly) intestinal stem cells.

Additional highlights included Karen Liu of King’s College London, who studies bone healing in mammals. The work she presented focused primarily on neural crest-derived frontal bone, which is more osteogenic than parietal or mesodermal osteoblasts and heals faster after postnatal wounding. Her lab is working to identify the basis for this differential healing ability, including the role of Sostdc1 as a dual Wnt/Bmp signaling inhibitor.

Kacy Gordon of Dave Sherwood’s lab at Duke presented work on the C. elegans gonad distal tip cell, which the Sherwood lab uses as a stem cell niche model. She studied the interaction of the distal tip cell  and sheath cell Sh1 and found that the interface between the two cells defined a region of germ cell proliferation dependent on actin.

She was followed by Rohan Khadilkar of the University of British Columbia, who studies cell junctions in the lymph gland, a hematopoetic organ, in Drosophila. Through live imaging and RNAi of the extracellular matrix component integrin, his lab showed that the ECM is essential for maintenance of prohemocytes, which will eventually form the hemocytes necessary for immune response to pathogens.

Finally, Regeneration Next director Ken Poss presented work on Vitamin D signaling in cardiomyocyte development, homeostasis, and regeneration. After testing many molecules in a screen using the FUCCI protein system, which consists of fluorescent reporters of cell cycle activation, the Poss lab identified the Vitamin D analog alfacalcidol as a regulator of cardiomyocyte proliferation. Creation of multiple transgenic reporters and signaling mutants confirmed the role of Vitamin D signaling in cardiomyocyte proliferation in all stages of growth and that this effect is dependent on Erbb2 signaling. Further, they showed Vitamin D has broad effects on proliferation and tissue and animal size, not just in cardiomyocytes.

Day 4: The final day was most noteworthy for the award lectures but featured many other talks of interest early in the day. In the Cellular Patterns and Polarity session, Sally Horne-Badovinac from UChicago presented work from her lab, which studies the collective migration of epithelial cells using the Drosophila egg chamber as a model. The egg chamber rotates as it develops as a result of collective migration of follicle cells across the basement membrane. Work from her lab showed that the genes Fat2 and Lar are necessary to specify the leading and trailing edges of these migrating cells. She also showed work on the gene semaphorin-5c, part of a family of genes best known for its role in axon guidance during development. Horne-Badovinac showed that flies with mutations in this gene have a round egg phenotype, and that the gene normally colocalizes with Lar. Her lab has hypothesized that Semaphorin-5c signaling blocks protrusions at the backs of cells, allowing for normal collective migration to occur.

Later, in the Development and the Nucleus session, Rebecca Resnick of Stephen Tapscott’s lab at Fred Hutchison Cancer Research Center investigated the idea of epigenetic memory in development and disease. She showed that the histone variants H3.X and H3.Y, which promote relaxed chromatin and accumulate at the transcription start site of highly expressed genes, are targets of the gene DUX4, a homeobox gene linked to facioscapulohumeral muscular dystrophy. She showed that a burst of this gene during development creates epigenetic memory of the gene expression program through the H3.X and H3.Y histone variants.


The planarian schmidtea mediterranea, which can regenerate its entire body plan after injury. Wikimedia Commons Image by A. Alvarado Sanchez

The final full session of the conference featured awards lectures. Christian Petersen of Northwestern received the Elizabeth D. Hay New Investigator Award and focused more of his talk on recent and ongoing research compared to the researchers who spoke later, perhaps a result of his relative newness to being an investigator. Petersen works in the planarian Schmidtea mediterranea studying regeneration, and trained under Peter Reddien. This planarian can regenerate its entire body plan after severe injury, and it had previously been shown that inhibition of Wnt signaling was necessary to specify regeneration of the head. Thus, when Wnt signaling is inhibited, regeneration results in the formation of two heads. Several years ago, Petersen showed that the gene Zic-1 is required for anterior pole formation and that its inhibition leads to the formation of two tails. Another gene expressed in the anterior during regeneration, Notum, is downstream of Zic-1 but upstream of Wnt signaling. When Notum is knocked down by RNAi, an uninjured planarian will grow a new pair of eyes while keeping the old. However, only the new pair of eyes can regenerate after acute injury. Studies such as these highlight the role of S. mediterranea in understanding basic tenets of positional control genes and how regeneration can make use of information available via pre-existing tissue.

The other award winners were Robb Krumlauf of Stowers, winner of the Edwin G. Conklin Medal, Eric Wieschaus of Princeton, winner of the Society for Developmental Biology Lifetime Achievement Award, and Drew Noden of Cornell College of Veterinary Medicine, winner of the Viktor Hamburger Outstanding Educator Award. These highly accomplished scientists spoke both on their own work and the history of the field, placing the advances they and their immediate colleagues made into the context of multiple centuries of the study of development. It was a fitting end to a conference that featured a spectrum of research ranging from current undergraduates to a Nobel Prize winner in Dr. Wieschaus.

Society for Developmental Biology Meeting: Day 1 recap

Ben Cox, Duke graduate student

Ben Cox, graduate student in the Ken Poss lab, is sharing his experience at the Society for Developmental Biology’s 77th annual meeting in Portland, OR. Here’s his recap of the first day’s activities.

The Society for Developmental Biology (SDB) convened its 77th annual meeting in Portland, OR on Friday evening with a Presidential Symposium. SDB President John Wallingford explained the rationale behind the Symposium’s theme, Developmental Biology from Physicists to Physicians, by highlighting the increasingly common advancements in development pioneered by scientists outside of or adjacent to developmental biology. The session featured speakers with medical, physics, and engineering backgrounds.

Joseph Gleeson of the University of California, San Diego spoke first and presented work from his lab on the mechanisms of Zika virus’s effects on the developing brain. Zika, the first new virus to cause congenital malformation to be discovered since Rubella, causes cell death in the developing brain. Gleeson and his group hypothesized that Zika could impair the cell’s mitotic machinery via the protease it encodes for cleaving proteins required for neurogenesis. They were able to show that not only did the protease cause cell death in human neural precursor cell cultures, but that the flavonoid myricetin rescued some of the negative effects of Zika infection. Next, his group was able to identify binding partners for the Zika protease which are active at the cleavage furrow prior to cytokinesis. Through mass spectrometry, they were able to identify the amino acid residue2 necessary for cleavage by Zika protease. When they mutated this residue, they partially rescued the delay in cytokinesis caused by Zika infection. Gleeson and his group have shone new light on the mechanism of this recently discovered virus and the possibility of treatment with protease inhibitors. Notably, myricetin does not cross the blood-brain barrier, but the potential for other proteases in treatment remains intriguing.

Celeste Nelson from Princeton presented compelling work on the development of lungs in birds and mice. Bird lungs are actually more efficient than their mammalian counterparts because their unidirectional flow prevents mixing of fresh and stale, or partially deoxygenated, air. This feature allows birds to thrive at high elevation, whereas humans and other mammals often struggle in these environments. In comparing lung development in the two species, Nelson and her lab demonstrated that the two species begin with a similar wishbone-shaped structure, but mouse lungs undergo bifurcating branching caused by smooth muscle wrapping around the branches, while bird lungs undergo lateral branching off the side of the main lung structure caused by apical constriction. Her work also included in silico modeling of forces in lung development and light sheet microscopy to address questions about epithelial fusion in avian lungs.

The “Flamingo” portable light sheet microscope, developed by Huisken and colleagues. Photo courtesy Ben Cox

Jan Huisken’s presentation emphasized the physics and engineering themes of the session. Huisken, one of the early innovators in light sheet microscopy, detailed his goal of creating a customizable, affordable light sheet microscopy platform. Light sheet microscopy has diverse applications, including in toto imaging of developing organisms, high speed imaging to capture difficult to image tissues such as the heart, and imaging of fixed and cleared samples. However, Huisken argued that commercial versions of the technology can be prohibitively expensive and quick to become obsolete. Huisken and others had previously developed the openSPIM platform, but he felt it was still too complicated and difficult to upkeep. His group therefore developed the Flamingo, a portable microscope that can be converted into multiple different light sheet setups. He brought the scope to the meeting (sans electronics and software), and it is indeed compact compared to the scopes that can occupy nearly a full room when lasers, lamps, and computers are included.

Renee Reijo Pera of Montana State University shared her group’s work on early human embryo development. Beginning in 2008, they used embryos that had been frozen at the early pronuclear stage, thawed them, and live imaged until the blastocyst stage of development. Because they imaged many embryos, they were able to identify common characteristics of embryos that did or did not survive to the blastocyst stage. One of their findings was that the duration of the first cytokinesis was the primary indicator of success to the blastocyst stage. Thus, they hope to use non-invasive imaging to identify molecularly healthy embryos as early as possible after fertilization to improve the success of IVF. She also shared perspectives and experiences that informed her recent decision to move from Stanford to Montana State University, particularly the desire to broaden the accessibility of scientific education and encourage scientists to move beyond thinking of academic selectivity as inherently good.

Society for Developmental Biology – Day 2 recap

Ben Cox, graduate student in the Ken Poss lab, is sharing his experience at the Society for Developmental Biology’s 77th annual meeting in Portland, OR. Here’s his Day Two recap. You can read his Day One recap here.

A cephalopod specimen. By SEFSC Pascagoula Laboratory; Collection of Brandi Noble, NOAA/NMFS/SEFSC – NOAA photo librairie, Public Domain,

The Evolution and Development session featured broad perspectives on animal variation and methods of studying how such diversity arose. Kristen Koenig of Harvard presented her lab’s work on eye development in the cephalopod. Using the cephalopod Doryteuthis pealeii as a model, she and her group established a description of the stages of eye development, including the formation of the eye placode, optic vesicle fusion, cell differentiation and lens formation. They also assembled an embryonic transcriptome over many stages of eye development and showed that important genes for eye development across the animal kingdom, such as pax6, are active in the cephalopod as well. The most exciting finding she presented was the redeployment for eye development of a suite of genes previously shown to be involved in limb outgrowth in other species. Dlx (distalless) and sp6-9 are deployed in the cephalopod eye during development, and Dr. Koenig showed that like in species who use the Dlx/sp6-9 cassette for limb outgrowth, gene expression is controlled by Wnt signaling. This conservation of genetic signaling across species and organs is a demonstration of the productive union of evolutionary biology and sequencing.

Aniket Gore of the NIH presented work on blind cavefish, who undergo eye degeneration early in development. Gore showed that DNA methylation is highly active during cavefish eye development, and specifically that many genes necessary for eye development are hypermethylated during embryonic stages. Further, chemical inhibition of DNA methylation was able to partially rescue eye development in the cavefish. These findings demonstrate that development can be inactivated epigenetically, in addition to genetically, such as in blind rodents who undergo genetic inactivation of eye development.

Also on the fish evolution front, Dave Parichy presented work on the zebrafish scales, bony tissues whose developmental program shares similarities with other vertebrate skin appendages. Dr. Parichy showed data that implicated FGF and Wnt signaling are both required for scale development in the juvenile zebrafish, and that Wnt regulates ectodysplasin signaling, which was previously shown to be a key player in scale development by Matthew Harris. One of the most interesting findings of Parichy’s group’s work was how another canonical developmental pathway, Hedgehog signaling, affects scale growth. As scales grow out from the trunk of the fish, part of the epidermis actually invaginates under the developing scale. However, when Hh signaling was repressed, the scale plate still formed, but epidermis was unable to invaginate. Parichy concluded his talk by noting the Tulerpeton, a genus of one of the earliest tetrapods, had dermal scales resembling those of teleost fish like the zebrafish, but tetrapods later lost these calcified structures and gained epidermal keratin deposition, e.g. hair and nails. Fish scales thereby represent a fascinating window into the gain and loss of appendages over evolutionary time.

File:Zebrafish (26436913602).jpg

Zebrafish. By Oregon State University (Zebrafish) [CC BY-SA 2.0 (], via Wikimedia Commons

Later in the day, Jeff Rasmussen also gave a talk on fish scales for the Hilde Mangold Postdoctoral Symposium. Dr. Rasmussen is currently a member of Alvaro Sagasti’s lab at UCLA, but will start his own research group at the University of Washington this year. Dr. Rasmussen found his way to scales through his interest in growth of axons in the zebrafish skin. Using several mutants that lack scales, he noticed that axons fail to reorient their polarity when scales are missing or develop improperly. Further, mutants that had patchy scale patterns had denser innervation on areas of the trunk that did have scales than those that did not. In searching for a mechanism by which scales might influence axon growth, Rasmussen noticed that osteoblasts form long lines of cells during scale development prior to innervation and vascularization of the scale. He then prevented scale regeneration by continuous osteoblast ablation and showed that these lines of osteoblasts on the scale, called radii, are necessary to pioneer a pathway that neurons can follow. Rasmussen’s scale work demonstrates a basic developmental principle that diverse cell and tissue types must work in concert to form the complex organ systems of a mature organism.

Hogan reflects on science, history of embryology at Woods Hole

The Woods Hole Embryology course is the longest-running laboratory course in the United States and has trained generations of influential developmental biologists. This year, students were in for a treat as Brigid Hogan, Chair of Duke’s Cell Biology Department, gave the final lecture reflecting on how the field of embryology has evolved and expanded during her career. Hogan is a celebrated embryologist, having pioneered work on transgenic mouse models of development and regeneration. She was the first woman to chair a basic science department at Duke University. She expects to step down as Department Chair in the coming year, but will remain an active Full Professor in the Department.

Hogan (front row center, with white lanyard) with participants and faculty including Sherwood (front low, left) of the 126th Woods Hole Embryology course. Photo courtesy Dave Sherwood.

Hogan said that she was very impressed to learn how the students are using cutting edge techniques in live cell imaging, single cell transcriptomics, and in situ hybridization to tackle big questions in comparative embryology that are still really incompletely understood – like branching morphogenesis and skeletal patterning.

David Sherwood, co-Director of the Embryology course and co-Director of  Duke’s Regeneration Next, shared this photo and note about Hogan’s lecture: “It was a summary of her wonderful, exciting, and challenging scientific path to success. (I had) many favorite parts, but one of the highlights for me was Brigid’s leadership in in situ work in mouse embryos, which has helped to open up the field of mouse embryology.”

Opening my eyes to research

 A guest blog by Dorothea McGowan
Ms. McGowan is a Regeneration Next Summer Research Fellow in the MacLeod lab at Duke’s Department of Dermatology. In this guest post, she shares her experiences and insights from her first research experience.

Dorothea McGowan

On the morning of March 27th, I received an email from Duke University stating I had been accepted to Regeneration Next Summer Fellows program. I immediately felt an onset of emotions. I was beyond ecstatic to be accepted, but was terrified of what would await me. I was a third-year Public Health student graduating a year early and had no previous lab experience. Despite my fears, I decided to accept the fellowship and see how I could grow academically and mentally.

I had many preconceived notions about Duke being an exceedingly competitive field with a cut-throat environment. But I have found out in my time here, that this is simply not true. What I have experienced, is that the research labs are full of some of the world’s most brilliant researchers, but they are also full of the most gracious and accommodating researchers.

Research is an essential aspect of Duke’s fundamental principles; in fact, medical students at Duke participate in a whole year of research as third-year students. Incorporating research into the medical school program allows students to grasp the foundations of research and genuinely understand the work behind the science that they will practice on a daily basis as physicians.

Dorothea (2nd from right) with Dr. Amanda MacLeod (back row, right) and members of the lab. Photo courtesy MacLeod lab

My summer research experience is in the MacLeod lab, which focuses on the mechanisms of Skin Immunity. As a Public Health major my curriculum only briefly focused on the hard sciences, so this was a very new and intimidating experience. Despite my own preconceived notions of feeling intimidated and doltish, I was welcomed into a lab with an extremely conducive learning environment. I felt that I could always ask questions when I needed help and that I always received sincere explanations to the questions I asked. Every lab member has treated me with the utmost respect and patience which has stimulated my own drive to gain as much knowledge as possible. I never once have felt like I wasn’t welcomed in the lab, and that is an essential aspect of creating an encouraging learning environment.

Dr. Amanda MacLeod is not only a brilliant researcher, she is also a compassionate and generous leader of her research laboratory. Dr. MacLeod’s adaptable nature allows her to connect with everyone that sets foot in her lab as well as mentor each person in a way that best fits their own particular way of learning. Dr. Macleod is not just an example of what it means to be a great leader, but sets the standard of what all leaders should want to exemplify. Creating an environment that not only produces top of the line research but also demonstrates an exceptional learning environment is something most people aspire to do, and the MacLeod lab does that with ease.

Before coming to Duke I was sure that Dermatology was the specialty I would pursue in residency, but now I am interested in a variety of specialties. The MacLeod lab has allowed me to see  how different fields of medicine work together to uncover solutions to disease. That has really opened my eyes to other specialties like infectious disease and emergency medicine. It is nice to see that no matter what specialty you chose you can still do research as a PI or a collaborator. Over the past few weeks my own determination to pursue an MD has not wavered but I am now more open to the vast number of specialties and research topics that there are to pursue.

This experience will help me get into medical school. My eyes are opened to a different type of research compared to the research I did as a Public Health professional because of this program. This program has shown me the fundamentals of medical research and allowed me to understand a more quantitative side of research. This will not only be helpful for getting into medical school but will also be helpful when doing research within medical school.

Although my time at the MacLeod lab has been brief, I am able to understand why the researchers produce such quality work as the environment in the lab is a superb teaching and learning environment for all. As my summer progresses, I hope to learn more about how the research done here applies to a whole world perspective. During the end-of-summer presentation on August 3rd, I hope to be able to clearly explain my project to my peers with confidence that I was able to comprehend the process and results well enough to convey them to an audience.