University of California, Riverside

22 articles published in JoVE

• Bioengineering

  
  Direct and Indirect Culture Methods for Studying Biodegradable Implant Materials In Vitro Changlu Xu*¹, Yiqing Chen*¹, Jiajia Lin¹, Huinan H. Liu^{1,2,3 1}Materials 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. Dunn^{2 1}Department 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-Green^{1 1}Department 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 Higby^2,3, JungMoon Hyun⁴, Sameer Ashaie^{5,6 1}Helsinki 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 Aguilar^1,3,4, Hideaki Tsutsui^1,4, Marko Princevac¹, Monica M. Wilhelmus¹, Masaru P. Rao^{1,3,4 1}Department 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 Yu^{1 1}Department 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. Carver^{2 1}Graduate 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 Princevac^{1 1}Department 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. Karginov^{1 1}Cell 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. Shih^{1 1}Department 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 Tsutsui^{1,2,3 1}Department 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 Keogh^{1 1}Department 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. Fiacco^{2,3 1}Graduate 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 Liu^{1 1}Lane 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 Liao^{1 1}Department 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. Binder^{1 1}Division 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. Zhang^{1,3,4 1}Department 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 Kaloshian^{1 1}Department 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. Rao^{1 1}Department 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. Traugh^{2 1}Department 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 Liew^{1 1}UCR 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 Sauer^{1 1}Department 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.