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University of California, Riverside

21 ARTICLES PUBLISHED IN JoVE

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Biology

Monitoring Acupuncture Effects on Human Brain by fMRI
Kathleen K. S. Hui 1, Vitaly Napadow 1, Jing Liu 1, Ming Li 1, Ovidiu Marina 1,2, Erika E. Nixon 1, Joshua D. Claunch 1, Lauren LaCount 1, Tara Sporko 1, Kenneth K. Kwong 1
1Department of Radiology, Massachusetts General Hospital and Harvard Medical School, 2William Beaumont Hospital

FMRI and physiological monitoring is used to study the effects of Acupuncture on the central and peripheral nervous systems. Acupuncture mobilizes a limbic-paralimbic-neocortical network, with great overlap with the default mode network, to modulate neurological activity, possibly related to its autonomic effect in the peripheral nervous system.

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Bioengineering

Procedure for the Development of Multi-depth Circular Cross-sectional Endothelialized Microchannels-on-a-chip
Xiang Li 1, Samantha Marie Mearns 1, Manuela Martins-Green 2, Yuxin Liu 1
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.

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Bioengineering

Flying Insect Detection and Classification with Inexpensive Sensors
Yanping Chen 1, Adena Why 2, Gustavo Batista 3, Agenor Mafra-Neto 4, Eamonn Keogh 1
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.

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Bioengineering

Using Adhesive Patterning to Construct 3D Paper Microfluidic Devices
Brent Kalish 1, Hideaki Tsutsui 1,2,3
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.

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Immunology and Infection

SILAC Based Proteomic Characterization of Exosomes from HIV-1 Infected Cells
Collins Cheruiyot 1, Zemplen Pataki 1, Robert Williams 1, Bharat Ramratnam 2,3, Ming Li 3
1Brown University, 2COBRE Center for Cancer Research, Lifespan Laboratories, Rhode Island and Miriam Hospitals, 3Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School, Brown University

Here, we describe a quantitative proteomics method using the technique of stable isotope labeling by amino acids in cell culture (SILAC) to analyze the effects of HIV-1 infection on host exosomal proteomes. This protocol can be easily adapted to cells under different stress or infection conditions.

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Genetics

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells
Erin L. Sternburg 1, Kristen C. Dias 1, Fedor V. Karginov 1
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.

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Engineering

Wind Tunnel Experiments to Study Chaparral Crown Fires
Jeanette Cobian-Iñiguez 1, AmirHessam Aminfar 1, Joey Chong 2, Gloria Burke 2, Albertina Zuniga 1, David R. Weise 2, Marko Princevac 1
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.

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Genetics

Embryo Microinjection and Transplantation Technique for Nasonia vitripennis Genome Manipulation
Ming Li 1,2, Michelle Bui 1,2, Omar S. Akbari 1,2
1Department of Entomology and Riverside Center of Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, 2Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego

Microinjection of Nasonia vitripennis embryos is an essential method for generating heritable genome modifications. Described here is a detailed procedure for microinjection and transplantation of Nasonia vitripennis embryos, which will greatly facilitate future genome manipulation in this organism.

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Medicine

Protocol to Create Chronic Wounds in Diabetic Mice
Jane Hannah Kim 1, Manuela Martins-Green 1
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.

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Behavior

An Electrophysiology Protocol to Measure Reward Anticipation and Processing in Children
Katherine K.M. Stavropoulos 1, Leslie J. Carver 2
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.

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Behavior

Gaze in Action: Head-mounted Eye Tracking of Children's Dynamic Visual Attention During Naturalistic Behavior
Lauren K. Slone 1, Drew H. Abney 1, Jeremy I. Borjon 1, Chi-hsin Chen 2, John M. Franchak 3, Daniel Pearcy 1, Catalina Suarez-Rivera 1, Tian Linger Xu 1, Yayun Zhang 1, Linda B. Smith 1, Chen Yu 1
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.

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Bioengineering

Meso-Scale Particle Image Velocimetry Studies of Neurovascular Flows In Vitro
Ryan A. Peck *1, Edver Bahena *1, Reza Jahan 2, Guillermo Aguilar 1,3,4, Hideaki Tsutsui 1,4, Marko Princevac 1, Monica M. Wilhelmus 1, Masaru P. Rao 1,3,4
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.

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Neuroscience

Evaluation of Hemisphere Lateralization with Bilateral Local Field Potential Recording in Secondary Motor Cortex of Mice
Yunan Chen 1,2, Ming Li 3, Ying Zheng 3, Li Yang 1
1School of Life Sciences, Guangzhou University, 2Institute for Brain Research and Rehabilitation, South China Normal University, 3School of Life Sciences, South China Normal University

We present in vivo electrophysiological recording of the local field potential (LFP) in bilateral secondary motor cortex (M2) of mice, which can be applied to evaluate hemisphere lateralization. The study revealed altered levels of synchronization between the left and right M2 in APP/PS1 mice compared to WT controls.

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Behavior

Lexical Decision Task for Studying Written Word Recognition in Adults with and without Dementia or Mild Cognitive Impairment
Alexandre Nikolaev 1, Eve Higby 2,3, JungMoon Hyun 4, Sameer Ashaie 5,6
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.

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Genetics

Embryo Microinjection Techniques for Efficient Site-Specific Mutagenesis in Culex quinquefasciatus
Michelle Bui 1, Ming Li 1, Robyn R Raban 1, Nannan Liu 2, Omar S Akbari 1,3
1Section of Cell and Developmental Biology, University of California, San Diego, 2Department of Entomology and Plant Patholog, Auburn University, 3Tata Institute for Genetics and Society, University of California, San Diego

This protocol describes microinjection procedures for Culex quinquefasciatus embryos that are optimized to work with CRISPR/Cas9 gene editing tools. This technique can efficiently generate site-specific, heritable, germline mutations that can be used for building genetic technologies in this understudied disease vector.

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Biology

Pupal and Adult Injections for RNAi and CRISPR Gene Editing in Nasonia vitripennis
Elena Dalla Benetta *1, Duverney Chaverra-Rodriguez *1, Jason L. Rasgon 2, Omar S. Akbari 1
1Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 2Department of Entomology, The Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, The Pennsylvania State University

Here, we describe methods for efficient pupal and adult injections in Nasonia vitripennis as accessible alternatives to embryo microinjection, enabling functional analysis of genes of interest using either RNA-silencing via RNA interference (RNAi) or gene knockout via CRISPR/Cas9 genome editing.

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Immunology and Infection

Ubiquitous and Tissue-specific RNA Targeting in Drosophila Melanogaster using CRISPR/CasRx
Ruichen Sun 1, Daniel Brogan 1, Anna Buchman 1, Ting Yang 1, Omar S. Akbari 1
1Division of Biological Sciences, Section of Cell and Developmental Biology, University of California

This article outlines a detailed protocol for using the RNA-targeting Cas13D enzyme (RfxCas13D) in flies.

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Bioengineering

Direct and Indirect Culture Methods for Studying Biodegradable Implant Materials In Vitro
Changlu Xu *1, Yiqing Chen *1, Jiajia Lin 1, Huinan H. Liu 1,2,3
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.

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Developmental Biology

Microdissection and Dissociation of the Murine Oviduct: Individual Segment Identification and Single Cell Isolation
Kelly C. Radecki 1, Mary Y. Lorenson 1, David G. Carter 2, Ameae M. Walker 1
1Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 2Microscopy and Imaging Core Facility, University of California, Riverside

A method for microdissection of the mouse oviduct that allows collection of the individual segments while maintaining RNA integrity is presented. In addition, non-enzymatic oviductal cell dissociation procedure is described. The methods are appropriate for subsequent gene and protein analysis of the functionally different oviductal segments and dissociated oviductal cells.

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Developmental Biology

Rapid and Efficient Spatiotemporal Monitoring of Normal and Aberrant Cytosine Methylation within Intact Zebrafish Embryos
Sarah Avila-Barnard 1, David C. Volz 1
1Department of Environmental Sciences, University of California, Riverside

This paper describes a protocol for the rapid and efficient spatiotemporal monitoring of normal and aberrant cytosine methylation within intact zebrafish embryos.

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Bioengineering

Evaluation of Antimicrobial Activities of Nanoparticles and Nanostructured Surfaces In Vitro
Patricia S. Holt-Torres 1, Yiqing Chen 3, Huinan Hannah Liu 1,2,3
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.

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