Welcome to the Auditory Development and Connectomics Laboratory at the University of South Florida
Studying the development of neural circuits and the construction of connectomes, or neural wiring diagrams, at nanoscale resolution.
Neural circuit formation is an under-appreciated complete transformation of tissue structure, involving axon extension, the formation of exuberant neural connections, pruning of supernumerary inputs, glial cell proliferation and maturation, and vascular remodeling. These events are coordinated by a multitude of intrinsic and extrinsic factors, which are not well-understood as an integrated process with cellular physiology and anatomy. The ADCL approaches this topic in a unified manner and utilizes innervation of the medial nucleus of the trapezoid body (MNTB) by the calyx of Held (CH) nerve terminal as a model. The CH is the largest mammalian nerve terminal and represents a powerful developmental model for studying synaptic formation and strengthening.
A few (of many) open questions addressed by the ADCL:
- Factors that initiate rapid calyx growth and synapse formation early in development
- Coordination of neural circuit formation by extrinsic factors, such as vascular expansion and myelination
- The role of pre and post synaptic communication during nerve terminal growth and competition
Multi-color confocal microscopy • Lattice light sheet microscopy • Multiphoton microscopy • Volume electron microscopy • Electrophysiology • Ca2+ imaging • Viral vector injections • 3D virtual reality tools
The cochlear nucleus (CN) of mammals and birds (and several other Classes) is the front-end processor for acoustic information in the CNS. Despite considerable study, a systematic census of CN cell types, as well as their peripheral innervation and local connectivity, has not been provided for any species, thereby preventing wholistic understanding of CN function. The ADLC is working to deliver the connectome of the normal, adult mouse CN at ultrastructural resolution, and implement pipelines for large-scale models of neural activity across the CN.
A few (of many) open questions addressed by the ADCL:
- Auditory nerve fiber convergence onto each CN cell type
- Intrinsic neural circuit structure by cell type and compartment
- Defining the synaptic organization of granule cell domains
Light microscopy • Volume electron microscopy • Semi-automated image segmentation and neuron classification • Graph theoretical analysis of connectomes • 3D virtual reality tools
Lab Members and Collaborators
George Spirou – Principal Investigator
Professor / Department of Medical Engineering
Education: M.S., Indiana University, Physiology
Ph.D., University of Florida, Neuroscience
Postdoctoral Fellowship, Johns Hopkins University, Biomedical Engineering
From the time of his graduate training, George has maintained an interest in structure-function relationships in the developing and mature nervous system. His interests wandered into neuroscience from an undergraduate study of physics and philosophy and post-graduate work in physiology. After completing his doctoral degree in neuroscience, and fellowship in biomedical engineering, he led the formation of the Center for Neuroscience at West Virginia University (John W. and Jeannette S Straton Research Chair). The Spirou lab recently moved to join the new Department of Medical Engineering at the University of South Florida (USF). The newly built lab is designed to store and process big imaging data sets, develop tools (3D virtual reality) for their analysis, and conduct functional studies of the developing brain. In his free time, George enjoys history and historical fiction in any medium and running or biking in the beautiful Tampa Bay weather.
Bob Nichol – Laboratory Manager
Education: Ph.D., University of Wisconsin, Neuroscience
Postdoctoral Fellowship, University of Wisconsin, Neuroscience
Bob first developed a strong interest in neuroscience during his undergraduate studies, when he first learned about the brain’s amazing ability to wire, and rewire, itself with unfathomable precision. During his undergraduate classes in developmental neuroscience, Bob realized this was his life’s passion; driven by the singular question, “how can billions of neurons form trillions of synapses with minimal errors?” In graduate school, Bob wanted to contribute to our understanding of brain development and ended up studying the regulation of adhesion signaling proteins during axonal extension and guidance. For this work, he developed techniques to derive human neurons from induced pluripotent stem cells in the laboratory of Dr. Timothy Gomez. His interest in stem cell biology carried over into a Postdoctoral Fellowship position at Wisconsin, where his work focused on examining the effects of dysregulated tau hyperphosphorylation in axonal extension and synaptic function. In addition to his time in academic research, Bob has worked for years as a freelance biomedical writer and editor. Away from the lab, he enjoys music, beach time, hiking, and any outdoor activities with his partner and dog.
Dakota Jackson – Postdoctoral Fellow
Education: Ph.D., West Virginia University, Neuroscience
During his time as a Ph.D. student in the ADCL, Dakota’s research focused on the structural transformation of pre and postsynaptic elements that regulate the growth of the largest nerve terminal in the mammalian brain, the calyx of Held. His interests in the structural plasticity of developing neural circuits led him to his current position as a postdoctoral researcher at USF. In his free time, Dakota can usually be found out with his dog, often with leash and fishing tackle in hand.
Raakhee Shankar – Postdoctoral Fellow
Education: Ph.D., University of Wisconsin, Cellular and Molecular Biology
As a child, I was fascinated by genetics and aspired to be a scientist. To achieve this goal, I joined a neurogenetics lab studying the molecular mechanisms responsible for synaptic recognition in the nematode C. elegans. I continued working with C. elegans for my PhD studies, studying the mechanism of nuclear envelope reformation after mitosis. During this time, I was first introduced to the world of microscopy, electron microscopy being one of them. I was amazed by the ultrastructure of the cell. To expand and hone my skills, I decided to join Dr. George Spirou’s laboratory at USF. In my free time I like to cook, bike, watch movies, and explore the city.
Dan Heller – Graduate Student
Biomedical Engineering Ph.D. Program
Education: B.S., University of Nevada-Reno, Mechanical Engineering
Dan’s initial interests were in the field of mechanical engineering. However, after graduating with his B.S., he began a transitional phase, where he immersed himself in areas related to biomedical sciences, conducted research testing a portable heating/cooling unit for trauma patients who have become hypo-hyperthermic, and taught undergraduate microbiology labs. He initially joined Dr. Spirou’s lab as a Neuroscience Ph.D. student at West Virginia University, investigating the role of astrocytes in developmental myelination processes. In 2019, Dan joined Dr. Spirou at the University of South Florida, where he transitioned into the Biomedical Engineering doctoral program. Dan’s dissertation work is focused on the role of spontaneous activity in the growth and maturation of the calyx of Held during neural circuit formation. When not in the lab, he enjoys music and painting.
Morgan Amick – Graduate Student
Biomedical Engineering Ph.D. Program
Education: B.S., West Virginia University, Biomedical Engineering
Morgan was a part of the third graduating class from the biomedical engineering program at WVU, which lead to a variety of unique experiences. She was able to work on several engineering projects during her undergraduate career, including designing and implementing a prototype for a dual-modality micro-CT/PET scanner used to determine surgical margins during breast tumor excision. She joined Dr. Spirou’s lab in the spring semester of her sophomore year as an undergraduate tracer and quickly developed a passion for neuroscience. She cultivated this passion by continuing her work in the lab for the next 2.5 years and worked her way up to an undergraduate group leader position. After graduation, she decided to continue her education and joined Dr. Spirou after his move to USF. Her interest focuses on glial cell biology, morphology, and development, with an emphasis on astrocytes. In her free time, Morgan loves to travel, read, and volunteer at Clearwater Marine Aquarium on weekends.
Scott Payne – Research Associate
Education: B.S., West Virginia University, Mathematics
M.S., West Virginia University, Mathematics
Scott has conducted academic research in the emerging field of network science for nearly ten years. He began his interest in networks as an undergraduate in mathematics at West Virginia University and eventually earned a master’s degree. Currently, Scott leads a research group that focuses on the development of new mathematical algorithms for the purpose of understanding the relationship between network architecture and biological function in neurons and their representations in connectomic data.
Undergraduate Research Team
Team Brain Development
Anapaula Barrios Gonzalez, Health Sciences, Class of 2021
Kristof Cseh, Biomedical Engineering, Class of 2022
Lara de Vries, Biomedical Engineering, Class of 2022
Ellen Frahm, Biomedical Engineering, Class of 2022
Marla Attalla, Biomedical Engineering, Class of 2023
Alexis Flores, Biomedical Sciences, Class of 2023
Audrey Gabbard, Biomedical Engineering, Class of 2023
Aleah Lynn, Biomedical Engineering, Class of 2023
Sarah Schellhase, Biomedical Engineering, Class of 2023
Andrew Kaiser, Biomedical Engineering, Class of 2024
Sean Carr, Biomedical Engineering, Class of 2022
Zachary Trautz, Biomedical Engineering, Class of 2022
Riya Patel, Biomedical Engineering, Class of 2023
Mirna Beshai, Biomedical Engineering, Class of 2023
Want to join our Undergraduate Research Team?
We are excited to hear from proactive, hard-working young scientists who want the opportunity to work in a laboratory environment. Any interested undergraduates can send their resume/CV and unofficial transcripts to Dr. Bob Nichol, the Spirou lab manager, at firstname.lastname@example.org.
Mark Ellisman, Ph.D.
Department of Neuroscience
University of California, San Diego
Director, National Center for Microscopy and Imaging Research
Paul Manis, Ph.D.
Department of Cell Biology and Physiology
University of North Carolina, Chapel Hill
Henrique von Gersdorff, Ph.D.
Oregon Health and Sciences University
Samuel M. Young, Ph.D.
Department of Anatomy and Cell Biology, Otolaryngology
University of Iowa
Director, Molecular Auditory Research
Mark Culp, Ph.D.
Department of Statistics
West Virginia University
Gianfranco Doretto, Ph.D.
Lane Department of Computer Science and Electrical Engineering
West Virginia University
Edgar Fuller, Ph.D.
Department of Mathematics and Statistics
Associate Director of the STEM Transformation Institute
Florida International University
Peter Mathers, Ph.D.
Departments of Biochemistry, Neuroscience
West Virginia University
CQ Zhang, Ph.D.
Department of Mathematics
West Virginia University
Recent Graduate Students and Postdoctoral Fellows
Ashley Brandebura, Ph.D. • Postdoctoral Fellow, Salk Institute for Biological Studies
Florin Chirila, Ph.D., Postdoctoral Fellow • President and CSO, Spot DX LLC
Paul Holcomb, Ph.D. • Research Engineer, Battelle Memorial Institute, NETL Morgantown
Brian Hoffpauir, Ph.D., Postdoctoral Fellow • Director of Operations, Smithers Avanza, Inc.
Dakota Jackson, Ph.D. • Postdoctoral Fellow, University of South Florida
Garrett Jones, M.D., Resident Fellow • Resident, Otolaryngology, West Virginia University
Brian Kellermeyer, M.D., Resident Fellow • Assistant Professor, Otolaryngology, West Virginia University
Matthew Kersting, M.S. • AI / Machine Learning Scientist, Noblis
Douglas Kolson, Ph.D. • Postdoctoral Fellow, West Virginia University
Glen Marrs, Ph.D., Postdoctoral Fellow • Microscopy Core Facility Director, Wake Forest University
Michael Morehead, M.S. • CEO, IstoVisio, Inc.
Kevin Rowland, Ph.D. • Clinical Professor, University of Houston
Scott Shapiro, M.D., Resident Fellow • Fellow, Otolaryngology, University of Cincinnati
Jesse Thompson, Ph.D. • Research Assistant Professor, Medicine, West Virginia University
Jonathan Wu, M.D., Resident Fellow • Private Practice
Payne S, Fuller E, Spirou GA, Zhang CQ. Automatic Quasi-Clique Merger Algorithm — A hierarchical clustering based on subgraph-density. Physica A: Statistical Mechanics and its Applications. In Press 2022.
Payne S, Fuller E, Spirou GA, Zhang CQ. Diffusion profile embedding as a basis for graph vertex similarity. Network Science. 2021.
Kolson DR#, Heller D#, Brandebura A, Wan J, Ramadan J, Holcomb P, Amick EM, Liu S, Deerinck T, Ellisman M, Qian J, Spirou GA*, Mathers PM*. Astrocyte Ensheathment of Axons Precedes Myelination on Calyx-Forming Axons of the Auditory Brainstem and Coincides with Activation of Myelin Genes. #Co-first authors; *Co-corresponding authors. Under revision.
Jackson D, Holcomb PH, Ellisman M, Spirou GA. Two Types of Somatic Spines Provide Sites for Intercellular Signaling During Nerve Terminal Growth and Maturation. Synapse. 2021. Cover Art.
Srinivasan G, Dagostin A, Leão RN, Balakrishnan V, Holcomb P, Jackson D, Spirou GA, von Gersdorff H. Dendritic speeding of synaptic potentials in an auditory brainstem principal neuron. bioRxiv. 2019. doi: http://dx.doi.org/10.1101/688309.
Sivaramakrishnan S, Brandebura AN, Holcomb P, Heller D, Kolson D, Jackson D, Mathers PH, Spirou GA. Perinatal maturation of the medial nucleus of the trapezoid body. Oxford Handbook of the Auditory System. 2018.
Brandebura AN, Morehead M, Holcomb PS, Heller DT, Kolson D, Jones G, Deerinck TJ, Ellisman MH, Mathers PH, Spirou GA. Glial expansion during neural circuit formation in the auditory brainstem. Dev Neurobiol. 2018. doi: 10.1002/dneu.22633
Pidhorskyi S, Morehead M, Jones Q, Spirou G, Doretto G. syGlass: Interactive exploration of multidimensional images using virtual reality head-mounted displays. arXiv 1804.08197. 2018.
Ryugo, DR and Spirou GA. Giant Synaptic Terminals: Endbulbs and Calyces of the Auditory System. In New Encyclopedia of Neuroscience, edited by LR Squire, TD Albright, FE Bloom, FH Gage and NC Spitzer, Elsevier, Oxford, Great Britain, 2016.
Holcomb PS, Morehead M, Doretto G, Chen P, Berg S, Plaza S, Spirou GA. Rapid and semi-automated extraction of neuronal cell bodies and nuclei from electron microscopy image stacks. Methods Mol Biol. 1427:277-290. 2016. doi: 10.1007/978-1-4939-3615-1_16.
Kolson DR, Wan J, Wu J, Dehoff M, Brandebura A, Qian J, Mathers PH, Spirou GA. Temporal patterns of gene expression during calyx of Held development. Dev Neurobiol. 76:166-189. 2016.
Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. – Sydney Brenner
As part of the ADCL, lab members are encouraged to consider innovative improvements to their methods and their potential commercialization. An example is syGlass 3D VR software (www.syglass.io), which grew out of the need to visualize and work with complex 3D images. An R21 grant led to an initial software product that was later deemed commercializable, and is now supported by NIH Brain Initiative SBIR funding. The lab uses syGlass for file management, collaboration, and analysis, as a daily example of how good ideas can change the way we work. Our next lab discussion of ideas could take your concept into the workflow and then to the marketplace!
A screenshot of the syGlass interface, which is easy to use and enables users to easily choose between multiple 3D images.
The multiplayer function in syGlass allows lab members to meet in VR to discuss data. Using this unique function, ADLC holds lab meetings in VR, resulting in an extremely inventive way to visualize and work with 3D image volumes.
In the news…
Raakhee Shankar joins the ADCL
Raakhee joins the ADCL as an incoming postdoctoral researcher to spearhead all EM-related studies. Raakhee comes in with an extensive background in tissue processing and microscopy, including EM and confocal. Raakhee’s scientific journey began with a strong interest in neurogenetics. As a master’s and Ph.D. student, Raakhee utilized C. elegans as a model system to study the molecular mechanisms of synaptic recognition and nuclear envelope reformation after mitosis, respectively. Raakhee is excited to expand her knowledge and skill base to include studies of the connectome of the mammalian auditory brainstem.
Dan Heller returns from a stint in the von Gersdorff lab at OHSU
Dan has returned to the lab after spending 7 months working at Oregon Health and Sciences University in Portland, OR. Dan worked in the lab of Dr. Henrique von Gersdorff, a frequent collaborator and co-sponsor with the ADCL, and has returned as an expert in multiple challenging electrophysiological techniques (dual patch pre and postsynaptic patch clamp). Dan will use these new skills and expertise to collect preliminary data that will be used in the submission of an NRSA F31 application.
The ADCL bids farewell to two star undergraduates
The ADCL is losing two talented and committed undergraduates this spring. Victoria Moses and Carolyna Yamamoto Alves Pinto are graduating with a Bachelors of Science, as part of the first graduating class in the undergraduate Biomedical Engineering program. They have been integral parts of the ADCL’s success over the last couple of years. Carolyna has largely worked with the Connectomics team and has excelled in learning and implementing computational methods for studying neurobiology. Victoria worked with Morgan (PhD student) on the developmental side of the lab and provided critical work for reconstructing astrocytes in the developing mouse MNTB.
My favorite thing about the lab was the people, Dan (PhD student) was the first person to welcome me into the lab and I remember he was super nice and patient explaining things to me. At the time, I did not know anything about neuroscience, so it was very important to me that he did that, and one of the main reasons I decided to stay. After 7 months in the lab, I decided I wanted to write a thesis and I received great support from Dr. Spirou and Matt Kersting, who helped me throughout the entire year while I worked on my project.
My favorite thing about the lab is how helpful and nice everyone was. I am really going to miss everyone. I also enjoyed learning so much about astrocytes.
What’s next for our star students?
Carolyna will be starting her PhD in Biomedical Engineering at Johns Hopkins University in July. She is a direct-admission to the lab of Dr. Natalia Trayanova, which focuses on computational cardiology. She is very excited to move to Baltimore and looking forward to learning more about human health. Victoria will be starting a masters degree program in prosthetics and orthotics on May 17th at University of Texas Southwestern Medical Center.
Matt Kersting headed off to Noblis
Matt completed his Masters of Science in Biomedical Engineering in December 2020. Next in his journey, he will be heading off to Noblis, where he will work as a Machine Learning Scientist. Noblis is an independent, nonprofit organization that provides federal clients with scientific and technological expertise. In his role, Matt will work as part of a team that researches, develops, and deploys solutions to various national security missions, such as identity management, multimedia, and cyber end-to-end systems. Good luck, Matt!
Dan Heller heads west to strengthen his skills as an electrophysiologist
Dan will spend two months learning multiple challenging electrophysiological techniques (dual patch pre and postsynaptic patch clamp) in the lab of the lab of Dr. Henrique von Gersdorff. Dr. von Gersdorff is a frequent collaborator and co-sponsor with the ADCL, as well as an expert in electrophysiological techniques. Dan will bring his own expertise in transcardial perfusions and brain slicing techniques to the von Gersdorff lab to collect data for his thesis project.
Dakota Jackson completes his Ph.D.
Dakota completed his Doctorate at West Virginia University in Neuroscience. Dakota was a valuable member of the ADCL at WVU and will join the ADCL at USF in January 2021 to work as a Postdoctoral Fellow. Dakota was an author on multiple publications during his graduate years, including a first-author paper recently published in Synapse, titled “Two types of somatic spines provide sites for intercellular signaling during calyx of Held growth and maturation.” He mastered a number of techniques during his time at WVU, and the ADCL is excited to utilize his expertise. Congrats to Dakota!
ADCL opens at USF
The ADCL officially opens at the University of South Florida! The lab is a state-of-the-art facility that includes multiple distinct areas for all steps of the scientific process. The wet lab contains up-to-date equipment for tissue processing, immunohistochemical staining, genetic and molecular manipulations, organotypic cultures, and optogenetic stimulations. The lab contains multiple microscopes for imaging live and fixed tissue, including a multiphoton Hyperscope from Scientifica, as well as an electrophysiology station. Once data is collected, state-of-the-art virtual reality stations allow for data analysis in 3D, using syGlass software, thereby revolutionizing the way data is processed. The data analytics section of the lab contains a BIOS IT 256 TB 4 Dual Socket storage system for tackling large imaging data sets. Greater than 12 work stations are set up for teams of undergrads to aid in the processing of large 3D image volumes. Graduate student and Postdoctoral Fellow work stations are equipped with new, powerful workstations for running 3D data analysis software. Finally, the possesses an amazing view of the USF campus.
Bob Nichol joins the ADCL
Bob joins the ADCL as a laboratory manager. Bob was a graduate student and Postdoctoral Fellow at the University of Wisconsin, where he worked to develop induced pluripotent stem cells as a valuable, high-throughput model for studying human axon guidance. Bob has a variety of research, writing, and editing expertise that will aid the ADCL in accomplishing their goals.
Matthew Melton joins the ADCL
Matthew joins the ADCL as an incoming graduate student. Matthew comes in with a strong background in Physics and Mathematics and a great desire to learn more about neurobiology. He graduated from the University of Florida with an M.S. in Medical Physics and subsequently worked for three years at the McKnight Brain Institute (Burke lab) researching cognitive augmentation through neuroplasticity. Matthew brings a unique skill set to the ADCL, with a strong desire to improve and expand his skills as a scientist.
ADCL awarded NIH RO1 grant, co-sponsored with Dr. Henrique von Gersdorff at OHSU
Dr. Spirou is Co-Investigator on an RO1 grant from the NIH/ National Institute on Deafness and Other Communication Disorders (NIDCD), in collaboration with principal investigator Dr. Henrique von Gersdorff of the Oregon Health and Science University. This project is focused on the biophysical and structural properties of synaptic transmission in the superior olivary complex, a critical region for localizing environmental auditory stimuli. The project will utilize a mixture of high-resolution imaging and electrophysiological techniques to reveal the synaptic mechanisms that regulate action potential timing in the ascending pathways of the auditory brainstem.
We strive to promote a supportive, creative environment that fosters learning and innovation. We are excited to provide opportunities to students who possess a strong work ethic and an inquisitive spirit. We welcome individuals from all backgrounds and work to promote an environment of equality. For any employment-related questions, please contact the ADCL manager, Dr, Bob Nichol, at email@example.com.
Open positions at the ADCL
The ADCL is recruiting graduate students for the incoming class of 2021. We are seeking motivated, hard-working students willing to think broadly and deeply about fundamental topics in brain research. Our lab offers the opportunity to learn a variety of techniques that span a multitude of disciplines. We bring together expertise in biomedical research, engineering, mathematics, and computer science, providing students having different backgrounds and expertise a great environment to thrive and learn from each other. Students will be exposed to a plethora of hands-on, wet lab techniques, as well as microscopy, data analytics, machine learning, coding, and science communication.
Biomedical Engineering Ph.D. program
Postdoctoral Fellow – Brain Development
Applications open February 2021
The ADCL is recruiting a Postdoctoral Fellow to pursue studies in developmental neuroscience. Our approach is wholistic, treating neural circuit formation as a transformation of whole-tissue structure that includes neurons, glia, and vascular cells. This person will utilize optical (2P Ca imaging, optogenetics) and electrophysiological methods to manipulate and monitor multiple cells and cell types simultaneously at perinatal ages to study the formation of the calyx of Held, the largest nerve terminal in the mammalian brain. Candidates with an entrepreneurial spirit can benefit from interaction with our startup company, syGlass (www.syglass.io), and implement new lab methods based in 3D VR/AR for data analytics and science communication. Please contact the ADCL manager, Dr, Bob Nichol, at firstname.lastname@example.org, for more information.
Postdoctoral Fellow – Connectomics
Applications open February 2021
The ADCL is recruiting a Postdoctoral Fellow to pursue their own project in nanoscale connectomics. The overall project goal is to specify the structural and computational basis for parallel processing in a sensory system, which is a fundamental question in neuroscience. We are studying the first CNS station of the auditory pathway, called the cochlear nucleus (CN), using volume electron microscopy. Projects are defined to segment neurons from these very large image volumes, specify neural circuit motifs, establish and discover new cell types, and understand cell function in a computational framework. Candidates with an entrepreneurial spirit can benefit from interaction with our startup company, syGlass (www.syglass.io), and implement new lab methods based in 3D VR/AR for data analytics and science communication. Please contact the ADCL manager, Dr, Bob Nichol, at email@example.com, for more information.
University of South Florida
4202 E. Fowler Ave.
Tampa, FL 33620
Auditory Development and Connectomics Laboratory
12030 USF Cherry Dr.
Interdisciplinary Sciences Building, Room 7037
Tampa, FL 33620
Dr. Bob Nichol
ADCL at the University of South Florida