The Center for Microbial Dynamics and Infection will host a special recording of the podcast "This Week in Microbiology" (TWiM) on October 16, 2019. Sponsored by the American Society for Microbiology, TWiM is one of the most popular science podcasts in the country.  The podcast will focus on one or two recent papers from CMDI members, who will join the hosts in discussing the work in front of an audience.  

The podcast will focus on two recent papers by CMDI labs.

The first (Lewin et al. 2019, PNAS) presents the intriguing finding that an oral pathogen does better (higher fitness) in the wound environment when it infects alongside microbes from different (non-oral) environments, compared to microbes native to the oral environment.  This effect appears to be related to an expanded metabolic repertoire provided by the non-natives, and is also tied to a core set of genes essential for success during co-infection. 

The second (Beatty et al. 2019, Science Advances) focuses on a different system: the complex microbial community on corals. The study shows that the ability of coral water (sterilized washes of coral fragments) to suppress a known pathogen declines in corals on reefs subjected to overfishing compared to reefs in marine protected areas. This effect coincides with subtle differences in the coral microbiome. 

Both studies highlight the importance of microbial interactions, a core theme of CMDI. Both are lead-authored by two young scientists: recently graduated CMDI graduate student Deanna Beatty and postdoctoral researcher Gina Lewin.   

"Implanted Neurotechnology to Understand and Restore Arm and Hand Function"

Jennifer Collinger, Ph.D.
Assistant Professor
Department of Physical Medicine & Rehabilitation
University of Pittsburgh

Watch via Livestream

ABSTRACT
After a cervical spinal cord injury, restoration of arm and hand function is a top rehabilitation priority.  A brain-computer interface (BCI) can tap into sensorimotor information that remains intact in the brain and bypass the injured spinal cord to control an assistive device that may help the user regain function. Intracortical BCIs have allowed people to control reaching and grasping movements using their neural activity. However, BCIs users have primarily relied on visual feedback which may be insufficient for tasks involving object manipulation.  Recently, we showed that intracortical microsimulation of somatosensory cortex can generate focal sensations that feel like they originate on the BCI users hand and that can be graded in intensity. Our current BCI study participant was able to use restored tactile sensations to improve performance on object transfer tasks. The time required to grasp the objects was reduced when ICMS feedback was provided as compared to visual feedback alone, likely due to increased certainty about the timing of object contact. Sensory feedback is particularly critical for dexterous and complex movements that are essential for many activities of daily living. We have also begun to investigate the role of motor cortex in modulating grasp force across a variety of task conditions.  Across all experiments, we identified a large transient neural response during periods of active force application, as well as a tonic neural response during periods of constant force application.  Interestingly, the relative strength of the transient and tonic neural components changes with task complexity suggesting a reallocation of cortical resources to accommodate the task requirements.  This has implications for BCIs, which must account for contextual changes in order to maintain consistent performance.   

BIO
Jennifer Collinger, PhD, is an Assistant Professor in the Department of Physical Medicine and Rehabilitation at the University of Pittsburgh and a Research Biomedical Engineer at the Pittsburgh VA R&D Center of Excellence.  Dr. Collinger’s research interests are related to the use of neuroprosthetics to restore function for individuals with upper limb paralysis or loss. Specifically, she is developing intracortical brain-computer interface technology for individuals with tetraplegia. She also uses non-invasive imaging tools to study sensorimotor control and neuroplasticity after spinal cord injury or amputation.
 

The Bioengineering Seminar Series is co-hosted by the Parker H. Petit Institute for Bioengineering and Bioscience, and the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

Michael Borich, D.P.T., Ph.D.
Assistant Professor
Division of Rehabilitation Medicine
Emory University School of Medicine

“Perturbation-imaging Approaches to Study Functional Contributions of Cortical Activity to Human Movement”

The ability to learn and produce skilled movements is required for humans to successfully engage with each other and their environment. A principal role of the brain is to guide current, and plan future, movements based on past actions and potential rewards. In this talk, I will describe ongoing work in our lab employing multiple approaches to investigate the functional contributions of brain activity to normal and abnormal human movement. I will discuss how transcranial magnetic stimulation (TMS), a form of non-invasive brain stimulation, can be used both characterize and modulate cortical activity and connectivity during movement. I will also describe our recent findings showing abnormal TMS-evoked cortical reactivity post-stroke that is related to persistent paretic arm impairment. Lastly, I will discuss preliminary work applying alternative perturbation paradigms to study brain-behavior relationships in health and disease.

NEW TWO-SPEAKER FORMAT for 2019-2020!

@ 8:30  A.M.

F. Levent Degertekin, Ph.D.
George W. Woodruff Chair in Mechanical Systems and Professor of Mechanical Engineering
Georgia Tech

"Microscale Systems and Sensors for Ultrasound and Magnetic Resonance Imaging"

ABSTRACT
Levent Degertekin's group performs modeling, design and implementation of microscale ultrasound devices and integrated systems for a broad range of medical applications spanning from catheter based intravascular and intracardiac ultrasound imaging systems, ultrasound imaging of the brain and skull, to acousto-optical sensors for safer magnetic resonance imaging (MRI).

RESEARCH
F. Levent Degertekin's research focuses on understanding of physical phenomena in acoustics and optics, and utilizing this knowledge creatively in the form of microfabricated devices. The research interests span several fields including atomic force microscopy (AFM), micromachined opto-acoustic devices, ultrasound imaging, bioanalytical instrumentation, and optical metrology. Degertekin's research group, in collaboration with an array of collaborators, has developed innovative devices for applications such as nanoscale material characterization and fast imaging, hearing aid microphones, intravascular imaging arrays for cardiology, bioanalytical mass spectrometry, and microscale parallel interferometers for metrology.

@ 9:00 A.M.

John Oshinski Ph.D.
Associate Professor
Wallace H. Coulter Department of Biomedical Engineering
Emory University and Georgia Tech
Associate Professor
Department of Radiology
Emory University School of Medicine

"Measuring Brain Tissue Motion and Cerebrovascular Blood Flow with MRI"

RESEARCH
John Oshinski's research is focused on developing cardiovascular imaging applications that directly impact patient care.  His work includes development of cardiovascular imaging for understanding physiology,  elucidating disease mechanisms, and evaluating treatment efficacy.  Specific applications include development of cardiovascular magnetic resonance imaging (MRI) for assessing myocardial function and vascular hemodynamics.

"Learning to Program Cellular Machines: Harnessing Cells to Treat Disease, Build Tissues, and Elucidate Design Principles"

Wendell Lim, Ph.D.
Professor of Cellular and Molecular Pharmacology
Biochemistry and Biophysics and Pharmaceutical Chemistry
Investigator, Howard Hughes Medical Institute    
Byers Distinguished Professorship
University of California San Francisco

Abstract
The eras of molecular biology and genomics have given us an unprecedented picture of the molecular components underlying living systems. Nonetheless, our understanding of how these components are assembled to generate precision physiological systems remains far less developed.  To approach this problem, we and others have been using synthetic biology methods to empirically explore how molecular components can be used to construct novel cellular functions. Using these approaches, we have shown that we can reprogram living cellular machines that carryout new novel precision functions, including therapeutic immune cells that precisely recognize and eliminate cancer cells, or cells that self-organize into tissues.  By merging our understanding of cellular machines with our knowledge of our bodies and its diseases, we envision the development of a mature field of cell engineering with a toolbox of optimized molecular parts and circuit architectures, as well as disease and  "GPS" sensors that allow the cell to target specific sites in the body or brain.  Such a platform will allow us to rapidly and flexibly prototype and design cells that can identify sites of disease or degeneration and execute precisely targeted and controlled therapeutic actions. 

Biography
Wendell Lim is the Byers Distinguished Professor and Chair of the Department of Cellular and Molecular Pharmacology at the University of California San Francisco, and an Investigator of the Howard Hughes Medical Institute. He received his A.B. in Chemistry, summa cum laude, from Harvard College, his Ph.D. in Biochemistry and Biophysics at the Massachusetts Institute of Technology and completed his postdoctoral training at Yale University. His research focuses on the design principles of molecular circuits that govern cell decision-making and responses. His lab has made contributions in understanding the molecular machinery of cell signaling and how molecular modules have been used in evolution to build novel new behaviors. Most recently he has been a pioneer in the emerging field of synthetic biology, exploring how these design principles can be harnessed to engineer cells with customized therapeutic response programs.  He is an author of the textbook, Cell Signaling (Garland Science 2014) and was the founder of the cell therapy biotech startup, Cell Design Labs, which was acquired by Gilead Biosciences in 2017.

A community lunch will be served immediately following the presentation.

“Specialized Properties of Adult Muscle Stem Cells”

Foteini Mourkioti, Ph.D.
Assistant Professor
Department of Orthopaedic Surgery
Perelman School of Medicine
University of Pennsylvania

Muscle stem cells play a major role in muscle regeneration. Following muscle injury, muscle stem cells become active, proliferate, and fuse with the surrounding tissue, allowing for the full regeneration within a few days. Pax7 is a marker of muscle stem cells that is conserved across many species, including humans. To look at muscle stem cells in vivo in a live animal, a Pax7EGFP mouse model was generated by inserting an enhanced green fluorescent protein (EGFP) cassette in the Pax7 gene (Tichy et. al., Skeletal Muscle, 2018). This allowed for the expression of EGFP driven by endogenous promoter and regulatory elements. Using 2-photon microscopy, we were able to visualize for the first time muscle stem cells in vivo and have identified unique and novel properties of these cells that have never been reported previously. Moreover, the study of muscle regeneration has primarily relied on retrospective analysis of static images from tissue section histology. Our system allows for longitudinal studies of muscle regeneration in a substantial reduced number of experimental animals and gives us the opportunity to test therapeutic interventions to reveal how early pathological symptoms correlate with later disease outcomes. 

The Mourkioti lab has a long-term interest in understanding the fundamental aspects of skeletal muscle and cardiac function in normal or diseased conditions and in the practical aspects of manipulating these functions by using animal models and tissue engineering approaches for treatment intervention.

The Bioengineering Seminar Series is co-hosted by the Parker H. Petit Institute for Bioengineering and Bioscience, and the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

Maryam Shanechi, Ph.D.
Assistant Professor
Viterbi Early Career Chair in Electrical and Computer Engineering
Viterbi School of Engineering
University of Southern California

“Neural Decoding and Control of Multiscale Brain Networks: From Motor to Mood”

In this talk, I first discuss our recent work on modeling, decoding, and controlling multisite human brain activity underlying mood states. I present a multiscale dynamical modeling framework that allows us, for the first time, to decode mood variations and identify brain sites that are most predictive of mood. I then develop a system identification approach that can predict large-scale brain network dynamics (output) in response to electrical stimulation (input) to enable closed-loop control of brain activity. Finally, I demonstrate that our modeling framework can uncover multiscale neural dynamics from hybrid spike-field activity in monkeys performing unconstrained movements and can further combine information from multiple scales of activity and model their different time-scales and statistical profiles. These models, decoders, and controllers could facilitate future closed-loop therapies for neurological and neuropsychiatric disorders and help probe neural circuits.

NEW TWO-SPEAKER FORMAT for 2019-2020!

@ 8:30 A.M.

Sam Brown, Ph.D.
Associate Professor
School of Biological Sciences
Georgia Tech

"Conditional Strategies for Effective and Evolutionarily Robust Infection Control"

ABSTRACT
I will discuss recent theory and experimental work to address the antibiotic resistance crisis via treatment strategies that are conditioned on diagnostics. I will show that reversing the rise in AMR is possible, but requires diagnostic information during both point-of-care and periodic microbiome surveillance (e.g. as part of an annual health check). 

RESEARCH
Microbial model systems offer unparalleled access to the molecular mechanisms and ecological forces that together shape evolution, making them powerful systems for addressing fundamental behavioural, ecological and evolutionary questions. In our work, these questions include – why cooperate? Why communicate? Why kill your host? At the same time, a continual lab challenge is to consider – what are the practical implications of our discoveries? Can they drive novel therapeutics or diagnostics? Do they point to unappreciated epidemiological or evolutionary risks? Can we develop sustainable, evolution-proof therapeutics?


@ 9:00 A.M.

Cassie Mitchell, Ph.D. @ 9:00 a.m.
Assistant Professor
Wallace H. Coulter Department of Biomedical Engineering
Georgia Tech and Emory University

"Literature Mining Strategies for Predictive Medicine"

ABSTRACT
This talk will focus on newer approaches and tools for text mining of biomedical relationships and concepts from the 28+ million PubMed publications.  A real case study will illustrate how literature mining using biomedical concept graphs can be used to derive new actionable insights for disease etiology, treatment discovery, clinical care support, and research prioritization.

RESEARCH
Cassie Mitchell’s research goal centers around expediting clinical translation from bench to bedside using data-enabled prediction. Akin to data-based models used to forecast weather, Cassie’s research integrates disparate, multi-scalar experimental and clinical data sets to dynamically forecast disease.  Cassie is the principal investigator of the Laboratory for Pathology Dynamics, which uses a combination of big data, machine learning, biostatistics, and informatics-based techniques to identify complex disease etiology, predict new therapeutics, and optimize current interventions.  Cassie’s research has predominantly targeted neuropathology, but her research applications in predictive medicine expand across all clinical specialties, including cancer, pediatrics, and cardiovascular medicine.

"Smart Photonic Biomaterials for Diagnostic and Therapeutic Applications"

Sei Kwang Hahn, Ph.D.
Professor
Biomedical Nanomaterials Lab
Department of Materials Science and Engineering
POSTECH, Korea
Department of Chemical Engineering
Stanford University

ABSTRACT
Advances in photonics have stimulated significant progress in medicine with many techniques now in routine clinical use. However, the finite depth of light penetration in tissue is a serious constraint to clinical applications. Here, we developed implantable light-delivery devices using biodegradable polymers. With this light delivery system, we demonstrated photochemical tissue bonding (PTB) for wound healing with a Rose Bengal (RB) dye, achieving a full thickness (410 mm) wound closure of porcine skin. In addition, we successfully demonstrated the facilitated PTB using hyaluronic acid (HA) – RB conjugate and upconversion nanoparticle (UCNP). The UCNP emitting red and green light in the skin tissue by skin-penetrating near infrared (NIR) laser illumination could activate the RB dye and crosslink the collagen, inducing skin repair and deep tissue wound healing. Furthermore, we developed cell-integrated poly(ethylene glycol) hydrogels for in vivo optogenetic sensing and therapy. Real-time optical readout of encapsulated heat-shock-protein-coupled fluorescent reporter cells made it possible to measure the nanotoxicity of cadmium-based quantum dots in vivo. Using optogenetic cells producing glucagon-like peptide-1, we performed light-controlled therapy and obtained improved glucose homeostasis in diabetic model mice. Finally, we developed a smart contact lens composed of biosensors, drug delivery systems, and power sources for the treatment of diabetic retinopathy as a model disease. This presentation will provide the current state-of-the-art smart photomedicines for further clinical applications.

BIO
Sei Kwang Hahn obtained his B.S., M.S., and Ph.D. in the Department of Chemical and Biomolecular Engineering at Korea Advanced Institute of Science and Technology (KAIST). As the youngest Ph.D. at LG Chemical Group in 1996, he started his research on biodegradable polymer and then sustained release formulation of hGH, which was successfully commercialized in Korea under the trade name of Declage® in 2007. From 2001, he did his post-doctoral research with Prof. Allan Hoffman in the Department of Bioengineering at the University of Washington. After that, he worked for long acting formulation of various biopharmaceuticals at the Roche Group, Chugai Pharmaceutical Co. in Japan for more than three years. Since 2005, he has worked as a professor in the Department of Materials Science and Engineering at POSTECH, and an adjunct professor in the School of Interdisciplinary Bioscience and Bioengineering and in the Department of Creative IT Engineering at POSTECH. He was a consultant for Johnson & Johnson in New Jersey in 2008 and made a collaboration project contract with Hoffman-La Roche. In 2012, he joined in the Wellman Center for Photomedicine, Harvard Medical School and Massachusetts General Hospital for his sabbatical research supported by LG Yeonam Fellowship. Currently, he is a visiting professor at Stanford University starting from Feb 1, 2019. He was the Samsung Future Technology Committee Member for 2016-2018 and the Presidential Advisory Council on Science and Technology for 2017-2019. He is the founder and CEO of PHI BIOMED Co. He received the Controlled Release Society Award in 2018, the Minister of Health and Welfare Award in 2017, the Korean President Award in 2015 and Korean Minister of Education Award in 2013. He published more than 120 SCI journal papers including Nature Photonics, Nature Communications, Progress in Polymer Science, Advanced Materials, and ACS Nano, and filed more than 130 Korean and international patents. He is one of the editorial board members of ACS Biomaterials Science and Engineering, ACS Applied Bio Materials, Biomacromolecules, and an Associate Editor of Biomaterials Research.

The Bioengineering Seminar Series is co-hosted by the Parker H. Petit Institute for Bioengineering and Bioscience, and the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University.

A Petit Institute Seminar, jointly hosted by GT Neuro

Vince Calhoun, Ph.D.
Professor
Distinguished University Professor
Department of Psychology
Georgia State University

Vince Calhoun, Ph.D., has secondary appointments in Computer Science, Math, Neuroscience and Physics at Georgia State University, with additional appointments at Georgia Institute of Technology (Electrical and Computer Engineering, Biomedical Engineering) and Emory University (Neurology, Radiology, Psychiatry, Biomedical Engineering)

Calhoun is the founding director of the tri-institutional Center for Translational Research in Neuroimaging and Data Science, which is focused on improving our understanding of the human brain using advanced analytic approaches with an emphasis on translational research such as the development of predictive biomarkers for mental and neurological disorders. The use of big data approaches and neuroinformatics tools to capture, manage, analyze, and share data is also a major emphasis.

Calhoun develops techniques for making sense of brain imaging data. The use of flexible/data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However, such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. Because each imaging modality has limitations, the integration of these data is needed to understand the healthy and especially the disordered human brain. He has created algorithms which map dynamic networks of brain function, structure, and genomics and how these are impacted while being stimulated by various tasks or in individuals with mental illness such as schizophrenia. He has released multiple software tools as well as advanced neuroinformatics tools for data management and sharing.

Calhoun is the author of more than 650 peer-reviewed journal articles and over 750 technical reports, abstracts and conference proceedings. Much of his career has been spent on the development of data driven approaches for the analysis of brain imaging data. He has won over $100 million in NSF and NIH grants on various topics including the incorporation of prior information into independent component analysis (ICA) for functional magnetic resonance imaging, data fusion of multimodal imaging and genetics data, and the identification of biomarkers for disease.

Calhoun is a fellow of the Institute of Electrical and Electronic Engineers, The Association for the Advancement of Science, The American Institute of Biomedical and Medical Engineers, the International Society of Magnetic Resonance in Medicine, and the American College of Neuropsychopharmacology (ACNP). He is also a member and regularly attends the Organization for Human Brain Mapping, the International Society for Magnetic Resonance in Medicine, the International Congress on Schizophrenia Research, and the ACNP. He is also a regular grant reviewer for NIH and NSF. He has organized workshops and special sessions at multiple conferences. He is currently chair of the IEEE Machine Learning for Signal Processing (MLSP) technical committee. He is a reviewer for many journals and is on the editorial board of the Brain Connectivity and Neuroimage journals and serves as Associate Editor for Journal of Neuroscience Methods and several other journals.