Department of Cell Biology Alumni Newsle er, Fall 2017
Congratulations to Our Recent Graduates
A message from the Chair
Welcome to the first issue of our new, bi‐annual Duke Cell Biology newsletter. Our goal is to highlight some of the activities and successes of the faculty, postdocs, Thomas Pack (Caron Lab) students, and staff, and to keep you up to date on plans Jason Garness (Capel Lab) for the future. We sincerely hope that this resource will help you feel more connected with the department that Matt Foglia (Poss Lab) you helped to build into one of the best. Andrew Muroyama (Lechler Lab) Benjamin Stormo (Fox Lab) Over the past few years there have been some relocations of Cell Biology laboratories. Blanche Capel‘s Jialu Wang (Rockman Lab) team is now on the 4th floor of Nanaline Duke, together with Ken Poss, Chris Nicchitta, and Harold Erickson. Nico Katsanis and the Duke Center for Human Disease Model‐ Dr. Brigid Hogan, George Barth Cell Biology Welcomes ing (CHDM) (chdm.duke.edu) have moved into the Carmi‐ Geller Professor & Chair chael Building. This is a former tobacco warehouse on From CMB Duke Street, a short bus trip downtown from the Medical Center campus. Scott Allen (Fox Lab) Maggie Bara (Tata Lab) The imaging facility on the 3rd floor of Eda Erata (Soderling Lab) Nanaline Duke has expanded in capacity con‐ From DSCB siderably, and now houses a Zeiss 710 inverted Delisa Clay (Fox Lab) confocal, as well as a Leica SP8 upright micro‐ Abigail Leinroth (Hilton Lab) scope with Hybrid (HyD) detectors. Brand new Abdull “AJ” Massri (Tata Lab) to the facility is a Zeiss Lightsheet Z.1 micro‐ Brianna Peskin (Bagnat Lab) scope that allows rapid acquisition of both Leyao Shen (Karner Lab) aqueous and CLARITY cleared sample volumes. Adam Shoffner (Poss Lab) The Light Microscopy Core has also recently acquired a Leica TCS SP8 STED super resolution system capable of resolutions below 30 na‐ From MSTP nometers. We hope that this, too, will be located within the Department. All of this new ca‐ Arvind Konkimalla (Tata Lab) pability involves the generation of large amounts of data, and two high‐end computer work‐ stations with over 40 Tb of storage and various image analysis software packages are availa‐ ble in the imaging suite. In addition, to meet their own research needs and new rules about data storage from the School of Medicine, both the Department and individual labs have Department of Cell Biology been purchasing and setting up large storage and bioinformatics servers. Mark Langan, our Nanaline Duke Building Network Systems Analyst, continues to provide invaluable help in meeting our insatiable IT Room 388 needs. (continued on next page) 307 Research Dr. Duke Box 3709 Durham, NC 27710 Valerie Tornini (Poss Lab)
A message from the Chair (cont.) Other technological advances are also making quite a big impact on the department. Scott Soderling, who is also the director of Graduate Studies, is now director of the Mouse Gene Targeting Core. In this capacity he has spearheaded the utilization of CRISPR/Cas9 methods for genome editing in both mouse embryos and ES cells. With the help of Cheryl Bock, Gary Kucera, and their teams, it is now possible to make knockout mice in two months! They have also developed a new CRISPR‐mediated approach to rapidly generate conditional knockout alleles and GFP fusions. This nov‐ el technique will be described in a publication soon.
In 2016, Ken Poss (left) was made the direc‐ tor of Regeneration Next. This campus‐wide initiative brings faculty, trainees, and staff together to advance research and education in the field of regenerative medicine. You can learn more about this exciting new venture at sites.duke.edu/regenerationnext/ or by contacting the Exectuive Director Sharlini Sankaran, Ph.D., at firstname.lastname@example.org.
In the academic year 2016‐2017, there have been some notable successes in our academic and research enterprises. The primary faculty now number eighteen, with Purushothama Tata, Ph.D., as the newest assistant professor recruit. Cagla Eroglu and Michel Bagnat were both promoted to associate professor with tenure and Michel Bagnat was suc‐ cessful in obtaining an HHMI Faculty Scholar Award. Both Tata and Michel are highlighted in this newsletter. With so much going on, our administra‐ tive staff, led by the indomitable Mollie Sykes, are stretched very thin but continue to do a mag‐ nificent job. Gina Briscoe has transferred to a grants and contracts administrator position in Biomedical Engineering, and they are very lucky to have her. Her job has been taken by Jacquelyn Soderling, who has moved desks but still resides in NanDuke388. Newcomer Kelly Long is now the chair’s assistant as well as assistant to the direc‐ tor of Graduate Studies. She is responsible for editing this newsletter, so if you have any feed‐ back please contact her at email@example.com.
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Graduate Student News For the academic year of 2017‐2018, we have a total of 36 graduate students en‐ rolled. Ten are new affiliates entering their sec‐ ond year, and eleven are third year students who all passed their preliminary exams in the spring. The remainder are in their fourth, fifth, and sixth years preparing for their dissertation defenses, graduation, and life after Duke.
Since the spring semester, the Graduate Student Social Committee has been hosting bi‐ weekly breakfast meetings for the cohort to come together and discuss their projects and lives outside the labs. The organizing committee, spearheaded by Patrick Ferree (Di Talia Lab), con‐ sists of members Sara Payne (Sherwood Lab), Jessie Child (Nicchitta Lab), Kwabena Badu‐ Nkansah (Lechler Lab), and Ceri Weber (Capel Lab). Beginning this year, the students will elect three representatives to serve on the Graduate Student Steering Committee. These individuals will give voice to the student perspective of the department as we continue to grow.
Grad Students Pat Ferree, Woonyung Hur (Di Talia Lab), Eda Erata (Soderling Lab), & Jessie Child. Another opportunity for the students to engage in discussion about science and re‐ search ethics is an interdepartmental group called INSPIRE. This organiza on meets bi‐ weekly, a rac ng twenty to forty a endees. INSPIRE fosters collabora on and community across labs, cohorts, and programs. Current oﬃcers are Gizem Gupur (Lechler Lab), Nora Peterson (Fox Lab), Erez Cohen (Fox Lab) and Patrick Ferree. We are impressed by the level of enthusiasm and engagement that our students have demonstrated, both in their research and community‐building eﬀorts.
Cell Biology—Fall 2017 Newsle er
Faculty Feature: Dr. Michel Bagnat Michel Bagnat, Ph.D., associate professor, was born in Rio Negro, Northern Patagonia, Argentina. He graduated from the Universidad Autónoma de Madrid in Spain. For graduate studies, he went to Germany, to the EMBL in Heidelberg and the Max Planck Institute in Dresden, to study protein and lipid sorting in budding yeast. As a postdoc at UCSF he studied zebrafish genetics and organ development, uncovering novel mechanisms controlling lumen formation and fluid homeostasis in the zebrafish gut. He joined the Department of Cell Biology in 2008 and was promoted to associate professor with tenure in 2016. In the same year, he received an HHMI Faculty Scholar award, a wonderful recognition of the research of his team. The Bagnat lab is exploring the reciprocal relationship between the development of organs and their physiological func‐ tion. Specifically, the lab focuses on how physiological processes such as fluid secretion and nutrition control how organs acquire their shape and size. These questions can only be addressed in vivo and they use the zebrafish gut, notochord, and spine as mod‐ el systems. Their approach combines forward/reverse genetics and genomics, with state‐of‐the‐art imaging and physiological manipulations. Key questions the lab is trying to answer include: (1) What mechanisms control the role of the notochord as a hydrostatic skeleton during embryonic axis elongation and spine formation? (2) What is the role of the notochord in vertebral patterning? (3) How does protein uptake and utilization regulate intestinal differentiation and nutrient sensing? and (4) What are the molecular mechanisms controlling fluid accumulation within intracellular compartments or extracellular lumens? The under‐ lying principle behind these diverse themes is that the morphological and func onal organiza on of ssues generate emerging proper es and epigene c phenomena. These factors, in turn, interact with the endogenous gene c programs to produce the complex pa erns and physiological ac vi es of each organ.
Notochord from a 3‐day old zebrafish embryo: Green shows outer sheath cells, red shows inner vacuolated cells. The notochord acts as a scaﬀold for spine forma on. Scale bar = 100 µm. (Photo: Jennifer Bagwell, Ph.D.).
Recent Faculty Honors, Grants, & Awards Ken Poss—2016 American Heart Associa on Merit Award Sco Soderling (right)—2017 Kahn Neuro‐Technology Development Award Brigid Hogan—2017 Research Mentor Award for Basic Science Blanche Capel (middle)—Elected 2017 President of the Society of Developmental Biology Nico Katsanis (right)—2017 Curt Stern Award from the American Society of Human Gene cs
Graduate student Sara Payne (Sherwood Lab) explains her research to Dr. Bagnat during a Cell Biology retreat poster session.
www.cellbio.duke.edu Phone: 919‐684‐8085
Cell Biology Departmental Retreat 2017 In early May we hosted a retreat for our students, post docs, and faculty at a hotel in New Bern, NC. This provided an opportuni‐ ty for everyone to come together, both intellectually and socially. Under the guidance of CHDM’s Erica Davis, Ph.D., the students organized short talks, poster sessions, and a keynote speaker, Dr. David Parichy from the University of Virginia. They also ar‐ ranged a series of fun ac vi es that helped to bring people together and build morale.
Dept. of Cell Biology Fall 2017 Newsle er
Welcoming New Faculty Member: Purushothama Rao Tata
Tata Lab (from le to right): Pia Weidinger, Hiroaki Katsura (Hogan lab), Yoshihiko Kobayashi, Dr. Tata, A.J. (Abdull) Massri, Arvind Konimalla, Maggie Bara, & Reubin Scheruig
Our newest associate professor, Purushothama Rao Tata, received his Ph.D. from the University of Ulm, Germany, and then moved to Massachusetts General Hospital and Harvard Medical School in Boston for his postdoctoral training. During this time, Tata stud‐ ied some of the cellular mechanisms involved in tissue regeneration and tumorigenesis and uncovered novel cellular plasticity mechanisms through which cells acquire alternate fates. The Tata Lab focuses on understanding cellular ensembles in the context of tissue development, homeostasis, regeneration, and tumorigenesis in diverse epithelial tissues including the lung. Tissues are made of heterogeneous cell types that act in concert to spec‐ ify and confer form and function to a given tissue. Alterations of form and physiologic func‐ tion of tissues are a common hallmark of human diseases, including cancers. Some of the primary interests in the lab are: (1) to define cell‐autonomous signaling and intercellular communications that specify and maintain cellular identities and heterogeneity in normal and disease tissues, (2) to define the cellular and molecular mechanisms that sense and re‐ spond to different forms of injuries, and (3) to better understand the mechanisms through which stem/progenitor cells, or in some cases facultative progenitors, respond to and repair damaged tissues to restore physiological func‐ tions. The Tata Lab uses mouse models of diseases that recapitu‐ late the human disease pathology. In addition, they are also develop‐ ing novel tools to model human diseases ex vivo to better understand the underlying pathological mechanisms. We utilize genetic, live im‐ aging, cell biological, and next generation sequencing technologies, including single‐cell RNA sequencing, to study the behavior of tissues at single cell resolution.