University of California, Riverside

Department of Bioengineering

2016 - 2017 Colloquium




September 28, 2016 Rommie Amaro Shuler Scholar, Director of the National Biomedical Computation Resource
October 12, 2016 Angela Brooks Assistant Professor of Biomolecular Engineering
October 19, 2016 Harvey Borovetz Distinguished Professor of Engineering
November 2, 2016 Hugh Rosen Professor of Chemical Physiology
November 9, 2016 Orestis Kalogirou Fulbright Visiting Scholar
November 16, 2016 Jason Langley MRI Physicist in the Neuroimaging Center
November 30, 2016 Bernard Choi Surgery at the University of California, Irvine
January 4, 2017 Timothy Martens Assistant Professor in the School of Medicine
January 11, 2017 Xiaoping Hu Provost Fellow, Chair of the Department of Bioenineering
January 18, 2017 Song Li Chancellor Professor and Dept. Chair the of Dept. of Bioengineering and of Medicine
January 25, 2017 Arjun Yodh Director of The Laboratory for Research on the Structure of Matter (LRSM)
February 1, 2017 Mark Alber Distinguished Professor of the Department of Mathematics
February 15, 2016 Yuki Oki Assistant Professor of Biology and Division of Biology and Biological Engineering
February 22, 2017 Valentine Vullev Associate Professor of the Department of Bioengineering
March 1, 2017 Raviraj Vankayala Doctoral Scholar of the Department of Bioengineering
March 8, 2017 Taner Akin Director of Undergraduate Studies of the Department of Biomedical Engineering
April 5, 2017 Aleksander Popel Professor of the Department of Biomedical Engineering

All colloquium presentations are held in WCH 205-206 at 11:10am unless otherwise noted.

**click on each image to find out more about each speaker.

September 28, 2016

Rommie Amaro

Rommie AmaroProfessor and Shuler Scholar, Department of Chemistry and Biochemistry; Director, National Biomedical Computation Resource; Co-Director, Drug Design Data Resource, University of California, San Diego

Title: Multi-Scale Dynamics: Molecules to Cells

Abstract: Advances in structural, chemical, and biophysical data acquisition (e.g., protein structures via X-ray crystallography and near atomic cryo-EM, isothermal calorimetry, etc.), coupled with the continued exponential growth in computing power and advances in the underlying algorithms now make the application of computational methods to challenges in biological discovery increasingly possible and, though many challenges remain, increasingly successful. I will discuss how we are developing new capabilities for multi-scale dynamic simulations that cross spatial scales from the molecular (angstrom) to cellular ultrastructure (near micron), and temporal scales from the picoseconds of macromolecular dynamics to the physiologically important time scales of organelles and cells (milliseconds to seconds). Our efforts are driven by the outstanding and persistent advances in peta- and exa-scale computing and availability of multi-modal biological datasets, as well as by gaps in current abilities to connect across scales where it is already clear that new approaches will result in novel fundamental understanding of biological phenomena or new therapeutic avenues.

Biography: Rommie E. Amaro is a Professor and Shuler Scholar in the Department of Chemistry and Biochemistry at the University of California, San Diego. She received her B.S. (Chemical Enginee ring, 1999) and Ph.D. (Chemistry, 2005) from the University of Illinois at Urbana-Champaign. She was a NIH postdoctoral fellow with Andy McCammon (UCSD). Rommie is the recipient of an NIH New Innovator Award, the Presidential Early Career Award for Scientists and Engineers, the ACS COMP OpenEye Outstanding Junior Faculty Award, the 2016 ACS Kavli Foundation Emerging Leader in Chemistry award, and the 2016 Corwin Hansch Award. She is the Director of the NIH P41 National Biomedical Computation Resource and a co-Director of the NIH U01 Drug Design Data Resource. Her research is broadly concerned with the development and application of state-of-the-art computational methods to address outstanding questions in drug discovery and molecular biophysics.

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October 12, 2016

Angela Brooks

Angela BrooksAssistant Professor of Biomolecular Engineering, University of California, Santa Cruz

Title: High-throughput RNA sequencing analysis to examine splicing alterations in cancer

Abstract: Recent whole-exome sequencing studies have identified recurrent somatic mutations in splicing factor genes, including U2AF1/U2AF35 and SF3B1, in multiple cancer types; however, the effects of these mutations on the cancer transcriptome and on cancer biology have yet to be fully elucidated. Using RNA-Seq data from 230 lung adenocarcinomas and 172 acute myeloid leukemias in which U2AF1 is somatically mutated in ~3% of samples, we identified altered splicing events significantly associated with U2AF1 mutations, including altered splicing in known cancer genes. Consistent with the function of U2AF1, we found that the mutation causes altered recognition of 3’ splice site sequences. Continuing our investigation into the effects of splicing factor mutations, we performed a comprehensive transcriptome analysis of SF3B1 mutations in chronic lymphocytic leukemias. SF3B1 mutation was found to dysregulate multiple cellular functions including the DNA damage response, telomere maintenance, and Notch-signaling through altered splicing or altered gene expression. Although we have gained tremendous insight into altered splicing caused by mutations in these genes, short-read RNA-Seq approaches are limited in their ability to accurately quantify full-length transcripts. To gain a complete view of splicing alterations in cancer, we are developing methods for full-length cDNA sequencing with MinION nanopore sequencing with the aim of differential transcript isoform analysis

Biography: Angela Brooks is an Assistant Professor of Biomolecular Engineering at UC Santa Cruz. She was a postdoctoral fellow at the Dana-Farber Cancer Institute and the Broad Institute in the laboratory of Dr. Matthew Meyerson. She was a Merck Fellow of the Damon Runyon Cancer Research Foundation and also received the Dale F. Frey Award for Breakthrough Scientists. She received her Ph.D. in molecular and cell biology with a designated emphasis in computational and genomic biology at UC Berkeley with Dr. Steven Brenner. Dr. Brooks’ research group focuses on identifying cancer genome alterations that disrupt gene regulation, particularly through the regulation of RNA splicing. They are developing computational approaches to analyze genome and transcriptome sequencing data and developing high-throughput experimental approaches to characterize the functional impact of cancer variants.

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October 19, 2016

Harvey Borovetz (Distinguished)

Harvey BorovetzProfessor Department of Bioengineering, University of Pittsburgh

Title: Long-Term Mechanical Circulatory Support in Children

Abstract: Heart failure remains the number one “killer” of Americans in spite of remarkable advances in pharmacologic and medical therapies over the years. For patients who fail to respond, the therapeutic options are few, with cardiac transplantation being the gold standard of care for ~2,000 – 2,500 patients/year in the United States. It is within this setting that mechanical circulatory support devices can fill and have filled an enormous void for many thousands of adult patients who are in refractory heart failure and who have no realistic therapeutic options. Industry continues to develop innovative adult mechanical circulatory support devices which are expected to be introduced in the United States over the course of the current decade. The situation is far different for pediatric patients who do not have the treatment options of Food and Drug Administration (FDA) approved mechanical circulatory support technology that adult patients have. According to statistics from the American Heart Association, approximately one percent of all newborns will present with a structural heart defect. The very limited options available to treat ventricular failure in pediatric patients with congenital and/or acquired heart diseases, especially for infants and children 3 years of age or younger, will be discussed along with NIH/NHLBI funding initiatives to address this unmet clinical need. Also to be discussed is the University of Pittsburgh consortium ongoing development program towards an implantable, miniaturized ventricular assist device for this unique and very special patient population.

Biography: Dr. Harvey Borovetz is distinguished professor and former chair (2002-2013) in the Department of Bioengineering, Swanson School of Engineering at the University of Pittsburgh, a professor of Chemical and Petroleum Engineering, a professor in the Clinical and Translational Science Institute, University of Pittsburgh School of Medicine, a University Honors College Faculty Fellow and, the Robert L. Hardesty Professor in the Department of Surgery, University of Pittsburgh School of Medicine. Within the McGowan Institute for Regenerative Medicine, Dr. Borovetz holds the position of Deputy Director of Artificial Organs and Medical Devices. After receiving his BA in Physics from Brandeis University in 1969, Dr. Borovetz went on to earn an MS and a PhD degree, both in bioengineering, from Carnegie Mellon University in 1973 and 1976, respectively. Dr. Borovetz's current research interests are focused on the design and clinical utilization of cardiovascular organ replacements for both adult and pediatric patients. Since 1986, Borovetz has served as the academic liaison for the University's Clinical Bioengineering Program in Mechanical Circulatory Support. This program supports patients who are implanted with a left ventricular assist device, or bi-ventricular assist devices, as a bridge to cardiac transplantation or bridge to recovery. This work in mechanical circulatory support follows Dr. Borovetz's early efforts in which he helped cardiac surgeons apply extracorporeal membrane oxygenation (ECMO) to treat successfully a large series of neonates in respiratory distress.

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November 2, 2016

Hugh Rosen (Distinguished)

Hugh RosenProfessor of the Department of Chemical Physiology, The Scripps Research Institute

Title: Of Mechanisms And Molecules: From R01 To Intelligent Intervention In MS

Abstract: The lysophospholipid GPCR S1PR1 is a critical regulator of disease processes. Effective multi-point interdiction of difficult to treat autoimmune diseases Multiple Sclerosis and Ulcerative Colitis, with compelling clinical efficacy and safety, have been achieved using a novel therapeutic ozanimod, first discovered and synthesized at TSRI. This is the first New Chemical Entity to emerge from NIH Common Fund discovery efforts and reflects integrating chemistry, biology, structure and discovery to define and modulate control points in pathophysiology for the benefit of patients.

Biography: Dr. Hugh Rosen, MD, PhD has been Professor of The Scripps Research Institute since 2002. He received his MB.ChB (M.D.) from University of Cape Town and his D.Phil. (PhD) in Physiological Sciences at the Sir William Dunn School of Pathology at the University of Oxford as a Royal Commission for the Exhibition of 1851 Scholar. He was elected a Fellow of the Infectious Diseases Society of America, to the Association of American Physicians, a Fellow of the American Academy of Microbiology and to the Henry Kunkel Society. He was Associate Editor of Molecular Pharmacology (2006-14) and on the Editorial board of Journal of Biological Chemistry. He chaired the Molecular Libraries Screening Network Steering Group, a part of the NIH Roadmap, and was PI of the Scripps Research Institute Molecular Screening Center. He was Scientific Founder of Receptos, Inc., now acquired by Celgene, and a co-inventor of ozanimod, a treatment for multiple sclerosis and ulcerative colitis. He recently co-founded BlackThorn Therapeutics , an ARCH Ventures portfolio company. He is an independent director of Regulus Therapeutics since June, 2016. Prior to joining TSRI, Rosen served as Executive Director in Immunology, Rheumatology and Infectious Diseases at Merck Research Laboratories. He serves as Member of Scientific Advisory Board at ActivX Biosciences, Inc. His laboratory discovered a novel mechanism of Immuno-modulation through small molecule alteration of lymphocyte trafficking.

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November 9, 2016

Orestis Kalogirou

Orestis KalogirouProfessor of Physics Aristotle University of Thessaloniki, Greece
Fulbright Visiting Scholar, Center of Systems and Biology – Harvard Medical School

Title: Biomedical Applications of Magnetic Nanoparticles

Abstract: The Kalogirou laboratory is dedicated to studying different aspects of the biomedical applications of Magnetic NanoParticles (MNPs), especially magnetic particle hyperthermia which is among the promising approaches for fighting cancer. MNPs are the subject of basic and applied research due to their unusual and potentially exploitable properties that lead to a wide variety of applications in biomedical fields, such as genetic/tissue engineering, binding of biomolecules, cell separation, cell signaling, gene delivery and gene therapy, contrast enhancement in MRI, site-specific drug delivery, magnetic particle hyperthermia, magnetic diagnostic systems, and magneto-mechanical manipulation on living cells’ growth. In general, hyperthermia therapy is a type of cancer treatment in which the body tissue is exposed to temperature of 41 oC or higher, which is found to be more harmful to cancer cells than to normal healthy cells. Mild hyperthermia is performed at 41-46 oC to stimulate the immune response for non-specific immunotherapy of cancers, while thermoablation is performed at 46-56 oC to kill cancer cells by direct cell necrosis, coagulation or carbonization. Specifically, magnetic particle hyperthermia has emerged as one of the most promising approaches for heat localization. In an alternating magnetic field MNPs generate heat as a result of hysteresis and relaxation losses, which results in heating of the tissue in which MNPs accumulate. Our recent experimental results on magnetic particle hyperthermia, contrast enhancement in MRI and magneto-mechanical effect will be presented.

Biography: Orestis Kalogirou was born in Thessaloniki in 1960. He obtained his BSc in Physics from the Aristotle University of Thessaloniki in 1983 and his PhD in 1988 from the same University. In 1991 he worked as a post-doc in the University of Hamburg and in 1993-1996 as a research fellow in the Institute of Materials Science, NCSR “Demokritos”, Athens. In 1996 he was elected Assistant Professor in the Physics Department of the Aristotle University of Thessaloniki, and in 2010 he became Professor. In 2008-2009 he worked as a Visiting Researcher in the Magnetic Materials Laboratory, Dept. of Electrical and Computer Engineering, Northeastern University. Currently, he is Fulbright Visiting Scholar at Center for Systems Biology, Harvard Medical School. Among his scientific interests are synthesis and study of the structural, electrical and magnetic properties of materials for permanent magnets and lithium battery applications, and biomedical applications of magnetic nanoparticles, in particular magnetic particle hyperthermia.

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November 16, 2016

Jason Langley

Jason LangleyMRI Physicist in the Neuroimaging Center of the University of California, Riverside

Title: MRI biomarkers for detection of Parkinson’s disease

Abstract: Parkinson’s disease is a progressive neurodegenerative movement disorder affecting 1% of the population over the age of 60. Substantia nigra is one of the primary structures affected by Parkinson’s disease and at the time of Parkinsonian symptom onset, up to 50% of melanized neurons have been lost and the opportunity for effective neuroprotection has largely been missed. Despite dozens of attempts, no effective disease-modifying therapy for Parkinson’s disease has been identified. This failure is driven by the lack of well validated neuroimaging biomarkers capable of enhancing the efficiency and success of phase II clinical trials of neuroprotective therapeutics. In this talk, I will give a brief review of MRI principles and discuss how we are developing new imaging markers that can assist in the diagnosis of Parkinson’s disease as well as serve as an outcome measure in clinical trials.

Biography: Jason Langley is the MRI physicist for the Center for Advance Neuroimaging at University of California Riverside. He received his PhD in physics from the University of Georgia and was a postdoctoral fellow at Emory University prior to joining University of California Riverside. Jason’s current research interests are focused on imaging brain changes due to Parkinson’s disease and developing standardized imaging biomarkers for diagnosis of Parkinson’s disease

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November 30, 2016

Bernard Choi

Bernard ChoiAssociate Professor of Department of Biomedical Engineering, Beckman Laser Institute, and Surgery at the University of California, Irvine

Title: Combined Molecular Imaging and Optical Clearing of Thick Ex-Vivo Biological Tissues

Abstract: Recent developments in photonic technologies, optical molecular probes, and transgenic animal models, have led to remarkable advances in visualization of biological structures and processes. Despite these advances, optical imaging in turbid biological tissues remains a challenge due to scattering. In this lecture, I will discuss our research involving the use of chemical agents to reduce scattering in tissues and increase the effective imaging depth of optical imaging techniques. I first will describe the use of simple hyperosmotic chemical agents, such as glycerol and dimethyl sulfoxide, to induce optical clearing of skin. I then will describe recent optical clearing approaches used to perform microscopic molecular imaging of structures in the brain, with a focus on our protocol used to image the cerebral microvasculature and other structures in thick-tissue sections of brain and other organs. Finally, I will present preliminary results from a study in which we applied optical clearing to examine the relationship between intravascular amyloid deposition and formation of cerebral microhemorrhages.

Biography: Bernard Choi, PhD, is an Associate Professor of Biomedical Engineering and Surgery at University of California, Irvine. He is a core faculty member of the Beckman Laser Institute and Medical Clinic, affiliated faculty member of the Edwards Lifesciences Center for Advanced Cardiovascular Technology, and visiting scientist at CHOC Children’s Hospital. He received his BS in Biomedical Engineering from Northwestern University and his MSE and PhD in Biomedical Engineering from The University of Texas at Austin. After completing an Arnold and Mabel Beckman Fellowship at University of California, Irvine, he joined the faculty there as an Assistant Professor. He currently serves as the Associate Chair of Academic Affairs in the Department of Biomedical Engineering, and he has won several teaching awards at University of California, Irvine. He has held several leadership roles in international optics societies, including the American Society for Laser Medicine and Surgery (ASLMS), Optical Society of America (OSA), and SPIE, and he is a Fellow of SPIE. He has published more than 110 peer-reviewed papers and two book chapters. He currently is Principal Investigator of the Microvascular Therapeutics and Imaging (MTI) laboratory in Beckman Laser Institute, and is funded by research awards from the Air Force Office of Scientific Research and National Institutes of Health.

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January 4, 2017

Tim Martens

Tim MartensAssistant Professor in the School of Medicine, Loma Linda University

Title: From Simple Cells to Custom Constructs: A Program in Congenital Cardiovascular Tissue Engineering

Abstract: Congenital heart disease is the most common form of birth defect affecting approximately 1:100 live births or 40,000 babies per year in the United States. Significant advances in operative technique and perioperative management have improved survival for even the most complex lesion sets and allowed for complete repairs in the neonatal period. Often however, these repairs require the use of synthetic materials whose lifespan is limited by their ability to keep pace with somatic growth. A wide range of right-sided lesions present early in life with inadequate or excessive pulmonary blood flow. Common examples include Tetralogy of Fallot with pulmonary stenosis, pulmonary atresia with intact ventricular septum, and truncus arteriosus. Repair of these lesions in infants can be challenging and often employs the use of cadaveric pulmonary arteries and valves also known as homografts. As the child grows, these homografts are prone to calcification and stenosis and commonly require multiple surgeries to replace and “upsize” the conduit during infancy and childhood. Furthermore, as the number of children surviving congenital cardiac operations increases, the need for homograft replacement in adults has also increased leading to a growing population of children and adults with an unmet clinical need. It is not uncommon for a homograft placed in infancy to require three or more operations to allow a child to reach adult age. The end result is certain reoperation with significant risk that increases with each subsequent replacement procedure. Tissue engineering is a rapidly progressing field that combines the use of biologic and synthetic scaffolds with a plethora of cell types and culture conditions in an effort to create suitable constructs for ex vivo modeling and in vivo replacement. The holy grail of pediatric cardiovascular tissue engineering is a construct that (1) is fully functional upon implantation, (2) has the capacity and durability to keep pace with somatic growth, and (3) is composed of non-immunogenic cells and materials. Through the use of extra-cellular matrix-based scaffolds seeded with resident cardiovascular progenitor cells and cultured under physiologic pulsatile perfusion, we can produce a biologic construct that fulfills all of these goals and may greatly reduce the number of operations needed to repair a number of congenital heart defects.

Biography: Tim Martens was born in Flushing, NY and studied Neuroscience at Brown University before returning to New York for medical School. After completing two years of general surgery residency at Thomas Jefferson University in Philadelphia, he entered the laboratory at Columbia University and focused his research efforts on molecular and cellular therapies for myocardial regeneration. This ultimately led to a PhD in tissue engineering under the mentorship of Gordana Vunjak-Novakovic. While in the lab he also completed clinical fellowships in thoracic organ procurement, cellular therapy, and pacemaker and defibrillator surgery. Dr. Martens then resumed his general and adult cardiothoracic surgery training at NYU and developed a keen interest in congenital cardiac surgery. He completed an additional two years of congenital cardiac training with Vaughn Starnes at Children's Hospital Los Angeles before joining the team at Loma Linda University Health Care. His clinical interests include all aspects of congenital cardiac surgery from neonates to adults including mechanical circulatory support and transplantation. He founded the Translational Tissue Engineering Working Group at Loma Linda and is currently investigating the use of bioreactors, scaffolds, and patient-derived stem cells to produce next generation conduits and therapies for congenital cardiac surgery.

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January 11, 2017

Xiaoping Hu

Tim MartensProvost Fellow, Professor, and Chair of the Department of Bioenineering, University of California, Riverside

Title: Alternative Approaches for MR Molecular Imaging with Magnetic Nanoparticles

Abstract: Although iron oxide magnetic nanoparticles are widely used for molecular imaging, particularly cell tracking, there are a number of limitations. First, magnetic nanoparticles usually lead to a signal reduction (i.e. negative contrast) in MRI images, make its effect less prominent and hard to quantify. Second, coating of the particles is required for biomedical applications, modifying the nanoparticle contrasts in MRI images. Third, and more importantly, the use of externally loaded particles is a passive approach, and the resultant contrast diminishes quickly over time and with cell division. In the past decade, my laboratory has worked on remedying these limitations from a number angles. In this talk, I will describe bioengineering efforts in developing more robust, alternative contrast mechanisms, understanding the effects of coating, and using transgenic approaches for generating magnetic nanoparticles or for enhancing the elongating the effect magnetic particle labeling.

Biography: Dr. Hu obtained his Ph.D. in medical physics from the University of Chicago in 1988 and his post-doctoral training there from 1988-1990. From 1990-2002, he was on the faculty of the University of Minnesota, where he became a full professor in 1998. From 2002-2016, he was Professor and Georgia Research Alliance Eminent Scholar in Imaging in the Wallace H. Coulter joint department of biomedical engineering at Georgia Tech and Emory University and the director of Biomedical Imaging Technology Center in the Emory University School of Medicine. Dr. Hu has worked on the development and biomedical application of magnetic resonance imaging for 3 decades. Dr. Hu has authored or co-authored 265 peer-reviewed journal articles. His papers have been cited 18000+ times (h-index: 71). As one of the early players, Dr. Hu has conducted extensive and pioneering work in functional MRI (fMRI), including methods for removing physiological noise, development of ultrahigh field fMRI, systematic investigation of the initial dip in the fMRI signal, Granger causality analysis of fMRI data, and, more recently, characterization of the dynamic nature of resting state fMRI data. In addition to neuroimaging, his group has also made notable contributions to MR molecular imaging. Dr. Hu was a deputy editor of Magnetic Resonance in Medicine from 2005 to 2013 and an Associate Editor of IEEE Transactions on Medical Imaging from 1994 to 2004. He is currently an editor of Brain Connectivity since its inception, an associate editor of Magnetic Resonance in Medicine, and an editorial board member of IEEE Transactions on Biomedical Engineering. He was a member of board of trustees of the international society for magnetic resonance in medicine (2011-2013). He was named a fellow of the International Society for Magnetic Resonance in Medicine in 2004 and a fellow of IEEE and a fellow of American Institute of Medical and Biological Engineering in 2009.

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January 18, 2017

Song Li (Distinguished)

Song LiChancellor Professor and Department Chair the of Department of Bioengineering and of Medicine, University of California, Los Angeles

Title: Mechanobiology of Cell Reprogramming

Abstract: It has largely been accepted that biophysical cues can regulate a variety of cell functions, including signal transduction from the cell membrane through the cytoplasm to the nucleus. The regulation of signaling molecules by biophysical factors represents the early responses of cells, which can lead to the activation of transcriptional factors resulting in differential gene expression and cell functions. On the other hand, recent studies have also demonstrated that biophysical factors have a long-term effect on phenotypic changes, modulating stem cell differentiation and cell reprogramming. The change of cell phenotype stems from the modulation of its epigenetic state, the “memory” of a cell. By using cell reprogramming into induced pluripotent stem cells and neurons as models, I will discuss how biophysical cues such as microtopography, substrate stiffness and fluid shear stress can modulate the cell reprogramming process, through either epigenetic modifications or transcriptional regulation. These findings will lead to new cell engineering approaches for the applications in regenerative medicine, disease modeling and drug screening.

Biography: Dr. Song Li got B.S. and M.S. from Beijing University, and had his Ph.D. and postdoctoral training at UC San Diego. He was a Professor of Bioengineering at UC Berkeley between 2001-2015, and he recently moved to UC Los Angeles in 2016. He is a Chancellor Professor and serves as the Chair of bioengineering department. His research is focused on stem cell engineering, mechanobiology and tissue engineering. His recent work help elucidate the mechanisms of cell reprogramming regulated by biophysical factors and the roles of stem cells in tissue regeneration. Dr. Li has published > 150 papers in various journals including Nature Materials, Nature communications, PNAS, etc. He is also actively involved in the translation of research findings to bioengineering applications. Dr. Li has been elected as a Fellow of American Institute of Medical and Biological Engineering, a Fellow of Biomedical Engineering Society, and a Fellow of the International Academy of Medical and Biological Engineering.

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January 25, 2017

Arjun Yodh (Distinguished)

Arjun YodhJames M. Skinner Professor of Science Director of The Laboratory for Research on the Structure of Matter (LRSM), University of Pennsylvania

Title: Biophotonics with Diffusing Light

Abstract: Functional diffuse optical monitoring of tissue is gaining momentum as a diagnostic in a variety of medical scenarios including functional activation and clinical studies of brain, cancer imaging and cancer therapy monitoring, and investigation of muscle disease. I will review the general problem of spectroscopy and imaging with diffuse light. Then I will describe some recent biophotonics research from my lab that is oriented towards non-invasive monitoring of cerebral hemodynamics in adult/pediatric populations through intact skull and towards imaging cancer.

Biography: Arjun G. Yodh is the James M. Skinner Professor of Science at the University of Pennsylvania (Penn) and Director of Penn’s Laboratory for Research on the Structure of Matter (LRSM) and its Materials Science Research & Engineering Center (NSF-MRSEC). His home department is Physics & Astronomy; he also holds an appointment in the Department of Radiation Oncology in the Medical School and is a member of the graduate group of the Department of Bioengineering. Yodh obtained his BSc from Cornell University in 1981 and his PhD from Harvard University in 1986. He then worked at AT&T Bell Laboratories as a post-doctoral associate. He joined the Faculty at Penn in 1988. Professor Yodh is an experimenter in the areas of soft condensed matter physics and biomedical optics. Yodh’s biomedical research is oriented towards diffuse optical imaging and monitoring of deep tissue physiology, i.e., millimeters to centimeters below the tissue surface. His laboratory carries out fundamental studies of light transport, image reconstruction and optical technology development; in parallel, the lab identifies relevant clinical problems and applies these methodologies therein. Current research explores the potential of these tools for functional imaging/monitoring in brain and breast, for monitoring tumor hemodynamics during cancer therapy, and for investigation of patients with critical limb ischemia. In soft matter science he is known for experiments manipulating, measuring and using entropic forces to control assembly in colloidal suspensions, for use of temperature-sensitive polymers and microgel spheres in studies of crystal phase transitions and glass micromechanics, for observations of ellipsoidal particles ranging from their Brownian motion to their affect on coffee-rings, and finally for research with lyotropic liquid crystals including carbon nanotube solubilization in water.

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February 1, 2017

Mark Alber

Mark AlberDistinguished Professor of the Department of Mathematics, University of California, Riverside

Title: Combined multi-scale computational and experimental study of the impacts of cell properties on mitotic cell rounding in developing epithelia

Abstract: How individual epithelial cells coordinate multicellular processes is still poorly understood due to the inherent complexity of emergent systems-level behavior. Generating and testing hypothetical novel biological mechanisms combining multiple spatial and time scales requires creation of multiscale computational models that can span subcellular to tissue levels. Mitotic rounding (MR) during cell division is critical for the robust segregation of chromosomes into daughter cells and is frequently perturbed in cancerous cells. MR has been studied extensively in individual cultured cells, but the physical mechanisms regulating MR in intact tissues are still poorly understood. A cell undergoes mitotic rounding by simultaneously reducing adhesion with its neighbors, increasing actomyosin contraction in the cortex, and increasing the osmotic pressure of the cytoplasm. Whether these changes are purely additive, synergistic or impact separate aspects of MR is not clear. Specific modulation of these processes in dividing cells within a tissue is experimentally challenging, because of off-target effects and the difficulty of targeting only dividing cells. General computational models for investigating in detail epithelial mechanotransduction, especially MR, require biologically calibrated submodels capable of representing non polygonal cell shapes, and simulating the membranes as well as cytoplasm of individual cells as separate entities. To accomplish this, a novel multi-scale sub-cellular model, called Epi-scale, was developed for simulating mechanical properties of cells in the developing columnar epithelium of the wing disc which consists of a single layer of cells. First, the model was calibrated using experimental observations of a biological model system of epithelial tissue growth, the Drosophila wing imaginal disc. The calibrated model simulations predict that increase in cross-sectional area of mitotic cells is solely driven by increasing cytoplasmic pressure. MR however is not achieved within biological constraints unless all three properties (cell-cell adhesion, cortical stiffness and pressure) are simultaneously regulated by the cell. A particular advantage for the Epi-Scale modeling environment is its extensibility toward investigating complex biological processes involving multiple cell types and interactions between cells and extracellular matrix, including morphogenesis, wound healing and metastasis. Identifying the control systems for tissue homeostasis is important for understanding the underlying causes of birth defects, chronic wounds and cancer.

Biography: Mark Alber earned his M.S. (with honors) in applied mathematics at the Moscow Institute of Technology and his Ph.D. in mathematics at the University of Pennsylvania under the direction of J. E. Marsden (UC Berkeley and Caltech). He held several positions at the University of Notre Dame including most recently Vincent J. Duncan Family Chair in Applied Mathematics. He is currently Distinguished Professor in the Department of Mathematics and Director of the Center for Mathematical and Computational Modeling in Biology and Medicine, University of California, Riverside. Dr. Alber was elected a Fellow of the American Association for the Advancement of Science (AAAS) in 2011. He is currently a Deputy Editor of the PLoS Computational Biology, Associate Editor of the Bulletin of Mathematical Biology and Member of the Editorial Board of the Biophysical Journal. His research interests include computational biology and multi-scale modeling of blood clot formation, epithelial tissue growth, cancer invasion, bacterial swarming and microtubule dynamics.

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February 15, 2017

Yuki Oka

Yuki OkaAssistant Professor of Biology and Division of Biology and Biological Engineering, California Institute of Technology

Title: Central and Peripheral Control of Thirst

Abstract: Appetite represents an important basis of body homeostasis. There are two key elements for this innate drive; central motivation and peripheral sensation. How the brain integrates internal motivation and external sensations to drive appropriate behavior (i.e., eating, drinking) is an unsolved problem in neuroscience, resolution of which could have significant implications for treatment of appetite-related disorders. In this talk, I will describe the neural mechanisms how the central and peripheral sensory signals regulate thirst and water drinking behavior using physiology, genetics and optogenetics manipulation.

Biography: Yuki Oka is an Assistant Professor of Biology at the California Institute of Technology. After receiving his B.S. in biochemistry (2002) and his Ph.D. (2007) at the University of Tokyo, Oka went on to his receive his postdoctoral in neuroscience at the University of California, San Diego (2009) and Columbia University (2014). The goal of Oka’s research is to understand how the brain process external and internal body information to control behaviors. Throughout my research training, he has focused on the processing of sensory stimuli, specifically in mammalian chemosensory systems. In graduate work at The University of Tokyo, he explored odorant coding mechanisms in the mammalian olfactory system. His postdoctoral studies at Columbia University applied genetics, physiology and behavioral approaches to elucidate molecular and cellular mechanisms of mammalian salt taste detection. This study revealed that the taste system plays an important role in salt homeostasis by regulating salt intake. As an investigator at California Institute of Technology, Oka focus is on understanding of neural basis controlling homeostatic regulation. Specifically, he uses body fluid homeostasis as a model system to investigate the mechanisms for (1) detection of internal fluid balance, (2) processing of depletion signals in the brain, and (3) translation of such brain signals into specific motivated behaviors. They aim to dissect and control neural circuits underlying each of these steps by combining multidisciplinary approaches including genetics, pharmacology, optogenetics and optical/electrophysiological recording techniques.

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February 22, 2017

Valentine Vullev

portrait of Valentine VullevAssociate Professor of the Department of Bioengineering, University of California, Riverside

Title: Bioinspired Molecular Electrets: Synthetic “Proteome” for Engineering Charge-Transfer Systems

Abstract: The ability to control charge transfer at molecular and nanometer scales represents the ultimate level of electronic mastery, and its impacts on electronic, energy and other applications cannot be overstated. As electrostatic analogues of magnets, electrets possess ordered electric dipoles that present key paradigms for directing transduction of electrons and holes. We undertake a bioinspired approach in the design of molecular electrets based on anthranilamides.[J. Phys. Chem. Lett. 2011, 2, 503–508] Similar to protein helices, the anthranilamides possess intrinsic dipoles originating from ordered amide and hydrogen bonds, i.e., they are composed of non-native anthranilamide (Aa) derivatives.[J. Org. Chem. 2013, 78, 1994-2004] Unlike proteins, however, the bioinspired molecular electrets have extended pi-conjugation along their backbones providing a means for efficient charge transfer. The anthranilic molecular electrets are polypeptides of non-native amino acids. This feature offers unexplored routes for bringing principles of proteomics into the de novo designs of electronic molecular systems and materials. In analogy, 22 proteogenic native alpha-amino acids, each with a different single side chain, are the building blocks of proteins with countless structural and functional characteristics yielding the amazing diversity of life on our planet. Therefore, a similar set of Aa residues with different electronic properties should prove most essential for the design of molecular electrets with a wide range of charge-transfer properties. Unlike the native amino acids, each of the Aa residues has two side chains that we selectively alter. Electrochemical and spectroelectrochemical studies revealed that the electronic properties of an anthranilic residue depend not only on the type of a substituent, but also on its exact position [J. Phys. Chem. Lett. 2016, 7, 758-764]. This regio-dependence of properties offers a larger diversity in anthranilamide residues than what native-type amino acids can offer, demonstrating once again the clear advantage of bioinspired over biomimetic or biomediated approaches. The bioinspired molecular electrets, indeed, rectify the kinetics of charge separation, i.e., they act as molecular diodes [J. Am. Chem. Soc. 2014, 136, 12966-12973]. The rates of electron transfer along the electret dipoles are faster than the rates against the dipoles. For processes with small driving forces, the modulation of the energies of the charge-transfer states accounts for the observed rectification trends. This Franck-Condon effect on the observed kinetics is in excellent agreement with the accepted notion for charge-transfer in dipolar systems. For processes with a large graving force such as charge-recombination, however, the observed rectification is a corollary of the asymmetry in the electronic coupling. This unprecedented demonstration of the synergy between the electronic-coupling and the Franck-Condon effects on charge-transfer kinetics led us to exploration and discovery of new mechanism for gating and suppressing undesired charge recombination [J. Am. Chem. Soc. 2016, 138, 12826-12832]. Our synthetic “proteome” along with the mechanistic discoveries provide a wealth of knowledge and unprecedented paradigms for molecular engineering focusing on energy science and organic electronics.

Biography: Prof. Val Vullev was born in Bulgaria. He attended the National Gimnazia (High School) for Science and Math “Dr. Acd. Ljubomir Chakaloff,” Chemistry Major, where he was involved in research on nitrogen fixation and transition-metal electrochemistry. Val Vullev started his higher education at Sofia University “St. Kliment Ohridski” where in addition to majoring in Chemical Physics and Physical Chemistry, he completed a degree in Theory and History of Diplomacy. After moving to U.S., he received academic scholarships to complete his undergraduate studies in chemistry and physics at Keene State College. V. Vullev obtained his Ph.D. in chemistry from Boston University under the supervision of Prof. Guilford Jones. His research was in the areas of photochemistry and biophysics, encompassing polypeptide biomimetics of solar-energy-conversion systems and macromolecular self-assembly. To expand his expertise in surface science, Val Vullev joined the group of Prof. George Whitesides at Harvard University, as a postdoctoral fellow. His postdoctoral research was in the areas of optofluidics, molecular electronics and single-molecule biophysics. In 2006, Val Vullev moved from the Northeast to Southern California. Presently, he is an Associate Professor of Bioengineering at UCR. He is also a member of the Department of Chemistry, the Department of Biochemistry and the Materials Science and Engineering Program. His current areas of research encompass photoinduced charge transfer in de novo designed bioinspired electrets, optomicrofluidics, photoactive and bioactive interfaces, and photophysics of organic agents for imaging and other biomedical applications.

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March 1, 2017

Raviraj Vankayala

portrait of Raviraj VankayalaPost-Doctoral Scholar of the Department of Bioengineering University of California, Riverside

Title: Engineering Multi-functional Nanostructures Derived from Inorganic, Organic and Biological Materials for Light-Based Theranostics

Abstract: Development of theranostic nanostructures may offer both diagnosis and treatment functions in tackling various diseases at high spatial resolution. In the first segment of the talk, I will describe the efforts in developing various nanostructures derived from inorganic materials for simultaneous multi-modal imaging and photodynamic therapy (PDT) of cancers. Although these nanostructures show excellent imaging and phototherapeutic capabilities, their toxicity, immunogenicity, and biodegradability are the most critical concerns for clinical translation. To circumvent these limitations, the second segment of the talk will be focused on the engineering of hybrid nanostructures derived from organic and biological materials, specifically comprised of genome-depleted plant-infecting brome mosaic virus and erythrocytes doped with FDA-approved NIR chromophore, indocyanine green (ICG). We refer to these materials as Optical Viral Ghosts (OVGs) and NIR erythrocyte-mimicking transducers (NETs). The optical properties, enhanced fluorescence imaging capabilities, effects of size on the in vivo biodistribution and abilities to image and treat blood clots using these nanoconstructs will be discussed.

Biography: Raviraj Vankayala earned his M.S in Applied Environmental Chemistry from Andhra University, India and his Ph.D. in Chemistry from National Tsing Hua University (2012), Taiwan under the supervision of Prof. Kuo Chu Hwang. Later on, he had his postdoctoral training in the same lab until 2015. During his Ph.D. and postdoctoral training at National Tsing Hua University, he was actively involved in exploring novel functional nanomaterials as gene carriers and photodynamic therapeutic reagents for destruction of tumors. Some of his recent works were published in various reputed journals, including, Advanced Materials, Advanced Functional Materials, Angewandte Chemie, Biomaterials and Small. Raviraj Vankayala joined Professor Anvari’s lab at University of California Riverside in September 2015 as a postdoctoral research fellow. His current focus was on the fabrication of optical nanoconstructs derived from plant viruses and red blood cells for imaging and phototherapy applications.

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March 8, 2017

Taner Akkin

portrait of Taner AkkinDirector of Undergraduate Studies of the Department of Biomedical Engineering, University of Minnesota

Title: Visualizing and mapping the brain at microscopic resolution with serial optical coherence scanner

Abstract: Large-scale brain imaging and mapping at microscopic resolution is feasible with intrinsic optical contrasts. Serial optical coherence scanner, which combines a multi-contrast optical coherence tomography and a tissue slicer, distinguishes white matter and gray matter and visualizes nerve fiber tracts that are as small as a few tens of micrometers. Axonal birefringence highlights the location and myelination of nerve fibers, while the axis orientation contrast indicates the fiber alignment in the plane. A method to extract the inclination angle that completes the 3D orientation will be presented as well. The scanner could reveal biomarkers for disease onset and progression and support development of therapeutics. If time permits, I will present a summary of another study that is on optical imaging of neural action potentials.

Biography: Taner Akkin received his BSc (1995) and MSc (1997) degrees in electrical and electronics engineering from Çukurova University, Turkey, and his PhD degree (2003) from the University of Texas at Austin. After postdoctoral studies at Harvard Medical School/Wellman Center for Photomedicine, Massachusetts General Hospital, he joined the Department of Biomedical Engineering at the University of Minnesota (2005), where he is an associate professor. He develops optical imaging systems to study neural structure and function.

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April 5, 2017

Aleksander S. Popel

portrait of Taner AkkinProfessor of Department of Biomedical Engineering, Johns Hopkins University

Title: Systems Biology of Cancer – a Bioengineering Insight

Abstract: Cancer is a devastating disease that affects millions of people worldwide. In the US, 1,700,000 new cancer cases will be diagnosed in 2017 with 600,000 deaths. It is a complex disease that involves processes at the molecular, cellular, tissue and organism level. Thus, a combination of multiscale computational systems biology and modern experimental high-throughput approaches is necessary to understand and eventually find cures for the disease. The complex interactions between cancer and stromal cells is a hallmark of cancer. I will discuss our experimental studies in which we investigate cell interactions via secreted factors (secretomes) and how these factors facilitate tumor progression and metastasis. We use this knowledge to build multiscale computational models that describe signaling pathways and ligand-receptor interactions, 3D spatial distribution of ligands and drugs, and cellular and tissue processes using a combination of differential equations and agent-based modeling. Stromal cells include blood and lymphatic endothelial cells, and immune cells such as macrophages and T cells. I will discuss emergent studies in systems biology and systems pharmacology applied to immunotherapy, including targeting immune checkpoints that shows promise in several type of cancer. In summary, cancer systems biology is emerging as a powerful methodology that will play an important role in defeating cancer; bioengineering is uniquely equipped to be a major player in this fight.

Biography: Aleksander S. Popel, Ph.D., is a Professor of Biomedical Engineering at the Johns Hopkins University School of Medicine. He also holds appointments as a Professor of Oncology and a member of the Sidney Kimmel Cancer Center. His areas of expertise are systems biology and computational biology & medicine. He published over 300 scientific papers in these areas. He served as a Visiting Professor at MIT and Harvard University. He received the Eugene M. Landis Award from the Microcirculatory Society. He delivered keynote addresses for The Virtual Physiological Human (VPH) European Union Physiome Project, and Next-Generation Integrated Simulation of Living Matter Project in Japan; he was C. Forbes Dewey Distinguished Lecturer in Biological Engineering at the Massachusetts Institute of Technology, delivered A.C. Suhren Lecture at Tulane University, Robert M. and Mary Haythornthwaite Distinguished Lecturer at Temple University, and Kawasaki Medical Society Lecturer in Japan. He is an elected Fellow of the American Institute of Medical and Biological Engineering, American Heart Association, American Physiological Society, and American Society of Mechanical Engineers, and an Inaugural Fellow of the Biomedical Engineering Society. He has been a member of editorial boards of biological and biomedical engineering journals. He served in an advisory role to biotech and pharmaceutical companies. He regularly serves on grant review boards and advisory panels at the National Institutes of Health, and other US and international funding agencies.

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More Information 

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Department Information

Department of Bioengineering
205 Materials Science & Engineering

Hours: 8:00 AM - 5:00 PM
Tel: (951) 827-4303
Fax: (951) 827-6416

Potential Undergraduate Students:
Undergraduate Admissions

Potential Graduate Students:
Professor Jiayu Liao

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