University of California, Riverside View Institution's Website 24 articles published in JoVE Bioengineering Evaluation of Antimicrobial Activities of Nanoparticles and Nanostructured Surfaces In Vitro Patricia S. Holt-Torres1, Yiqing Chen3, Huinan Hannah Liu1,2,3 1Microbiology Graduate Program, University of California, Riverside, 2Department of Bioengineering, University of California, Riverside, 3Materials Science & Engineering Program, University of California, Riverside We introduce four methods to evaluate the antimicrobial activities of nanoparticles and nanostructured surfaces using in vitro techniques. These methods can be adapted to study the interactions of different nanoparticles and nanostructured surfaces with a broad range of microbial species. Bioengineering Automating Citrus Budwood Processing for Downstream Pathogen Detection Through Instrument Engineering Deborah Pagliaccia*1,6, Douglas Hill*2, Emily Dang1, Gerardo Uribe1, Agustina De Francesco1, Ryan Milton2, Anthony De La Torre2, Axel Mounkam2, Tyler Dang1, Sohrab Bodaghi1, Irene Lavagi-Craddock1, Alexandra Syed1, William Grover3, Adriann Okamba4,5, Georgios Vidalakis*1 1Department of Microbiology and Plant Pathology, University of California Riverside, 2Technology Evolving Solutions (TES), 3Department of Bioengineering, University of California Riverside, 4 We engineered, fabricated, and validated an instrument that rapidly processes phloem-rich bark citrus budwood tissues. Compared to current methods, the budwood tissue extractor (BTE) has increased sample throughput and decreased the required labor and equipment costs. Bioengineering Direct and Indirect Culture Methods for Studying Biodegradable Implant Materials In Vitro Changlu Xu*1, Yiqing Chen*1, Jiajia Lin1, Huinan H. Liu1,2,3 1Materials Science and Engineering Program, University of California, Riverside, 2Department of Bioengineering, University of California, Riverside, 3Stem Cell Center, University of California, Riverside We introduce three methods of direct culture, direct exposure culture, and exposure culture for evaluating the in vitro cytocompatibility of biodegradable implant materials. These in vitro methods mimic different in vivo cell-implant interactions and can be applied to study various biodegradable materials. Biochemistry PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase Eduardo Hilario1, Li Fan2, Leonard J. Mueller1, Michael F. Dunn2 1Department of Chemistry, University of California-Riverside, 2Department of Biochemistry, University of California-Riverside This article presents a series of consecutive methods for the expression and purification of Salmonella typhimurium tryptophan synthase comp this protocol a rapid system to purify the protein complex in a day. Covered methods are site-directed mutagenesis, protein expression in Escherichia coli, affinity chromatography, gel filtration chromatography, and crystallization. Medicine Protocol to Create Chronic Wounds in Diabetic Mice Jane Hannah Kim1, Manuela Martins-Green1 1Department of Molecular, Cell and Systems Biology, University of California, Riverside Chronic wounds are developed from acute wounds on a diabetic mouse model by inducing high levels of oxidative stress after a full-thickness cutaneous wound. The wound is treated with inhibitors for catalase and glutathione peroxidase, resulting in impaired healing and biofilm development by bacteria present in the skin microbiome. Behavior Lexical Decision Task for Studying Written Word Recognition in Adults with and without Dementia or Mild Cognitive Impairment Alexandre Nikolaev1, Eve Higby2,3, JungMoon Hyun4, Sameer Ashaie5,6 1Helsinki Collegium for Advanced Studies, University of Helsinki, 2University of California, Riverside, 3California State University, East Bay, 4Hunter College, City University of New York, 5Feinberg School of Medicine, Northwestern University, 6Shirley Ryan AbilityLab This article describes how to implement a simple lexical decision experiment to assess written word recognition in neurologically healthy participants and in individuals with dementia and cognitive decline. We also provide a detailed description of reaction time analysis using principal components analysis (PCA) and mixed-effects modeling. Bioengineering Meso-Scale Particle Image Velocimetry Studies of Neurovascular Flows In Vitro Ryan A. Peck*1, Edver Bahena*1, Reza Jahan2, Guillermo Aguilar1,3,4, Hideaki Tsutsui1,4, Marko Princevac1, Monica M. Wilhelmus1, Masaru P. Rao1,3,4 1Department of Mechanical Engineering, University of California, Riverside, 2Division of Interventional Neuroradiology, University of California, Los Angeles, 3Materials Science and Engineering Program, University of California, Riverside, 4Department of Bioengineering, University of California, Riverside Here we present simplified methods for fabricating transparent neurovascular phantoms and characterizing the flow therein. We highlight several important parameters and demonstrate their relationship to field accuracy. Behavior Gaze in Action: Head-mounted Eye Tracking of Children's Dynamic Visual Attention During Naturalistic Behavior Lauren K. Slone1, Drew H. Abney1, Jeremy I. Borjon1, Chi-hsin Chen2, John M. Franchak3, Daniel Pearcy1, Catalina Suarez-Rivera1, Tian Linger Xu1, Yayun Zhang1, Linda B. Smith1, Chen Yu1 1Department of Psychological and Brain Sciences, Indiana University, 2Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, 3Department of Psychology, University of California, Riverside Young children do not passively observe the world, but rather actively explore and engage with their environment. This protocol provides guiding principles and practical recommendations for using head-mounted eye trackers to record infants' and toddlers' dynamic visual environments and visual attention in the context of natural behavior. Behavior An Electrophysiology Protocol to Measure Reward Anticipation and Processing in Children Katherine K.M. Stavropoulos1, Leslie J. Carver2 1Graduate School of Education, University of California, Riverside, 2Psychology Department, University of California, San Diego This protocol is designed to measure reward anticipation and processing in young children with and without autism. Specifically, the protocol is designed to study the neural correlates of reward during social and nonsocial conditions while controlling for reward between conditions. Engineering Wind Tunnel Experiments to Study Chaparral Crown Fires Jeanette Cobian-Iñiguez1, AmirHessam Aminfar1, Joey Chong2, Gloria Burke2, Albertina Zuniga1, David R. Weise2, Marko Princevac1 1Department of Mechanical Engineering, University of California, Riverside, 2Pacific Southwest Research Station, USDA Forest Service This protocol describes wind tunnel experiments designed to study the transition of a fire from the ground to the canopy of chaparral shrubs. Genetics Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells Erin L. Sternburg1, Kristen C. Dias1, Fedor V. Karginov1 1Cell Biology and Neuroscience, University of California, Riverside Recent advances in the ability to genetically manipulate somatic cell lines hold great potential for basic and applied research. Here, we present two approaches for CRISPR/Cas9 generated knockout production and screening in mammalian cell lines, with and without the use of selectable markers. Behavior Psychophysiological Assessment of the Effectiveness of Emotion Regulation Strategies in Childhood Elizabeth L. Davis1, Parisa Parsafar1, Laura E. Quiñones-Camacho1, Emily W. Shih1 1Department of Psychology, University of California, Riverside (UCR) A detailed protocol for an experimental paradigm to assess the effectiveness with which children regulate emotion is described. Children are randomly assigned to use specific emotion regulation strategies, negative emotions are elicited with film clips, and changes in subsequent psychophysiology index the extent to which emotion regulation is effective. Bioengineering Using Adhesive Patterning to Construct 3D Paper Microfluidic Devices Brent Kalish1, Hideaki Tsutsui1,2,3 1Department of Mechanical Engineering, University of California, Riverside, 2Department of Bioengineering, University of California, Riverside, 3Stem Cell Center, University of California, Riverside We demonstrate the use of patterned aerosol adhesives to construct 3D paper microfluidic devices. This method of adhesive application forms semi-permanent bonds between layers, enabling single-use devices to be non-destructively disassembled after use and to ease folding complex nonplanar structures. Bioengineering Flying Insect Detection and Classification with Inexpensive Sensors Yanping Chen1, Adena Why2, Gustavo Batista3, Agenor Mafra-Neto4, Eamonn Keogh1 1Department of Computer Science and Engineering, University of California, Riverside, 2Department of Entomology, University of California, Riverside, 3Institute of Mathematics and Computer Sciences, University of São Paulo - USP, 4ISCA Technologies We proposed a system that uses inexpensive, noninvasive pseudo-acoustic optical sensors to automatically and accurately detect, count, and classify flying insects based on their flying sound. Neuroscience Inducing Plasticity of Astrocytic Receptors by Manipulation of Neuronal Firing Rates Alison X. Xie1, Kelli Lauderdale1, Thomas Murphy1, Timothy L. Myers1, Todd A. Fiacco2,3 1Graduate Program in Neuroscience, University of California Riverside, 2Department of Cell Biology and Neuroscience, University of California Riverside, 3Center for Glial-Neuronal Interactions, University of California Riverside Here we describe an adaptation of protocols used to induce homeostatic plasticity in neurons for the study of plasticity of astrocytic G protein-coupled receptors. Recently used to examine changes in astrocytic group I mGluRs in juvenile mice, the method can be applied to measure scaling of various astrocytic GPCRs, in tissue from adult mice in situ and in vivo, and to gain a better appreciation of the sensitivity of astrocytic receptors to changes in neuronal activity. Bioengineering Procedure for the Development of Multi-depth Circular Cross-sectional Endothelialized Microchannels-on-a-chip Xiang Li1, Samantha Marie Mearns1, Manuela Martins-Green2, Yuxin Liu1 1Lane Department of Computer Science and Electrical Engineering, West Virginia University, 2Department of Cell Biology and Neuroscience, University of California at Riverside A microchannels-on-a-chip platform was developed by the combination of photolithographic reflowable photoresist technique, soft lithography, and microfluidics. The endothelialized microchannels platform mimics the three-dimensional (3D) geometry of in vivo microvessels, runs under controlled continuous perfusion flow, allows for high-quality and real-time imaging and can be applied for microvascular research. Bioengineering Quantitative FRET (Förster Resonance Energy Transfer) Analysis for SENP1 Protease Kinetics Determination Yan Liu1, Jiayu Liao1 1Department of Bioengineering, Bourns College of Engineering, University of California, Riverside A novel method involving quantitative analysis of FRET (Förster Resonance Energy Transfer) signals is described for studying enzyme kinetics. KM and kcat were obtained for the hydrolysis of the catalytic domain of SENP1 (SUMO/Sentrin specific protease 1) to pre-SUMO1 (Small Ubiquitin-like MOdifier). The general principles of this quantitative-FRET-based protease kinetic study can be applied to other proteases. Neuroscience Thinned-skull Cortical Window Technique for In Vivo Optical Coherence Tomography Imaging Jenny I. Szu1, Melissa M. Eberle2, Carissa L. Reynolds2, Mike S. Hsu1, Yan Wang2, Christian M. Oh2, M. Shahidul Islam2, B. Hyle Park2, Devin K. Binder1 1Division of Biomedical Sciences, University of California, Riverside, 2Department of Bioengineering, University of California, Riverside We present a method of creating a thinned-skull cortical window (TSCW) in a mouse model for in vivo OCT imaging of the cerebral cortex. Medicine Modeling Intracerebral Hemorrhage in Mice: Injection of Autologous Blood or Bacterial Collagenase Paul R. Krafft1, William B. Rolland1, Kamil Duris1, Tim Lekic1, Aaron Campbell2, Jiping Tang1, John H. Zhang1,3,4 1Department of Physiology and Pharmacology, Loma Linda University School of Medicine, 2College of Natural and Agricultural Sciences, University of California, Riverside, 3Department of Anesthesiology, Loma Linda University School of Medicine, 4Department of Neurosurgery, Loma Linda University School of Medicine Clinically relevant animal models of intracerebral hemorrhage (ICH) are needed to extend our knowledge of hemorrhagic stroke and to examine novel therapeutic strategies. In this study, we describe and evaluate two ICH models that implement unilateral injections of either autologous whole blood or bacterial collagenase into the basal ganglia (corpus striatum) of mice. Immunology and Infection High and Low Throughput Screens with Root-knot Nematodes Meloidogyne spp. Hagop S. Atamian1, Philip A. Roberts1, Isgouhi Kaloshian1 1Department of Nematology, University of California, Riverside Two distinct methods to screen plants with root-knot nematodes are described. The described approaches include high-throughput screens with nematodes in a nondestructive manner facilitating the use of these plants in breeding programs. Immunology and Infection Simple and Robust in vivo and in vitro Approach for Studying Virus Assembly Sonali Chaturvedi1, Bongsu Jung2, Sharad Gupta2, Bahman Anvari2, A.L.N. Rao1 1Department of Plant Pathology and Microbiology, University of California, Riverside, 2Department of Bioengineering, University of California, Riverside A simple, efficient and robust way to synchronize the delivery of multiple viral components to plant cells via Agrobacterium-mediated transient expression is described. This approach is amenable for studying replication, encapsidation followed by in vitro reassembly of non-viral components into genome depleted optical viral ghosts suitable for biomedical applications. Biology Amide Hydrogen/Deuterium Exchange & MALDI-TOF Mass Spectrometry Analysis of Pak2 Activation Yuan-Hao Hsu1, Jolinda A. Traugh2 1Department of Chemistry, Tunghai University, 2Department of Biochemistry, University of California, Riverside MALDI-TOF mass spectrometry was successfully utilized to monitor the amide hydrogen/deuterium exchange in protein kinase Pak2 activation. Biology Transfecting and Nucleofecting Human Induced Pluripotent Stem Cells Papri Chatterjee1, Yuri Cheung1, Chee Liew1 1UCR Stem Cell Center, Department of Cell Biology and Neuroscience, University of California Riverside Despite recent advancements in genetic modification, transfection of human embryonic stem cells (HESCs) remains a capricious process. To our knowledge, systematic and efficient methods to transfect human induced pluripotent stem cells (iPSCs) have not been reported. Here, we describe robust protocols to efficiently transfect and nucleofect human iPSCs. Biology Chromatin Immunoprecipitation from Human Embryonic Stem Cells Stephane Bertani1, Alice Kan1, Frank Sauer1 1Department of Biochemistry, University of California - Riverside The differentiation of ESC coincides with cell-type specific changes in the structure and composition of chromatin. The detection of those changes provides valuable insights into the mechanisms that define stemcellness and cell differentiation. Chromatin immunoprecipitation (ChIP) represents a valuable method to dissect the molecular mechanisms underlying stem cell differentiation.