Colorado State University View Institution's Website 35 articles published in JoVE Neuroscience Free-Hand Intracerebroventricular Injections in Mice Richard B. McCosh1, Lauren A. Young1 1Department of Biomedical Sciences, Colorado State University Here, a simple and rapid approach for performing intracerebroventricular injections in mice using a free-hand approach (that is, without a stereotaxic device) is described. Medicine Disposable Dosators Intended for Dry Powder Delivery to Mice Sara E. Maloney1, Ian E. Stewart1, Jeffrey B. Mecham1, Mercedes Gonzalez-Juarrero2, Bernd Meibohm3, Anthony J. Hickey1 1Technology Advancement and Commercialization, RTI International, 2Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 3Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center Pharmaceutical dry powder development necessitates reliable in vivo testing, often using a murine model. Device technology for accurately and reproducibly delivering dry powder aerosols to mice is restricted. This study presents disposable dosators for pulmonary drug delivery at mouse-relevant doses, aiding initial proof-of-concept research. Environment Visualizing Field Data Collection Procedures of Exposure and Biomarker Assessments for the Household Air Pollution Intervention Network Trial in India Karthikeyan D. Rajamani1, Sankar Sambandam1, Krishnendu Mukhopadhyay1, Naveen Puttaswamy1, Gurusamy Thangavel1, Durairaj Natesan1, Rengaraj Ramasamy1, Saritha Sendhil1, Amudha Natarajan1, Vigneswari Aravindalochan1, Ajay Pillarisetti2, Michael Johnson3, Joshua Rosenthal*4, Kyle Steenland5, Ricardo Piedhrahita3, Jennifer Peel6, Maggie L. Clark6, Dana Boyd Barr5, Sarah Rajkumar6, Bonnie Young6, Shirin Jabbarzadeh7, Ghislaine Rosa8, Miles Kirby9, Lindsay J. Underhill10, Anaite Diaz-Artiga11, Amy Lovvorn5, William Checkley12, Thomas Clasen5, Kalpana Balakrishnan1 1Department of Environmental Health Engineering, ICMR Center for Advanced Research on Air Quality, Climate and Health, Faculty of Public Health, Sri Ramachandra Institute of Higher Education and Research (Deemed University), 2Division of Environmental Health Sciences, University of California, Berkeley, 3Berkeley Air Monitoring Group, 4Division of International Epidemiology and Population Studies, National Institutes of Health, 5Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 6Department of Environmental and Radiological Health Sciences, Colorado State University, 7Department of Biostatistics and Informatics, Rollins School of Public Health, Emory University, 8Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, 9Department of Global Health & Population, Harvard, T.H. Chan School of Public Health, 10Cardiovascular Division, Washington University School of Medicine, Washington University, 11Centro de Estudios en Salud, Universidad del Valle de Guatemala, 12Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University We detail the consistent, high-quality procedures used throughout air and biological sampling processes at Indian field sites during a large randomized controlled trial. Insights gathered from the oversight of applications of innovative technologies, adapted for exposure assessment in rural regions, enable better field data collection practices with more reliable outcomes. Biology Hand Dissection of Caenorhabditis elegans Intestines Jessica L. Hill1, Andrew Moore1, Robert T. P. Williams1, Erin Osborne Nishimura1 1Department of Biochemistry & Molecular Biology, Colorado State University The present protocol describes a procedure for isolating intestines from adult Caenorhabditis elegans nematode worms by hand for input in genomics, proteomics, microbiome, or other assays. Immunology and Infection Mycobacterium tuberculosis Extracellular Vesicle Enrichment through Size Exclusion Chromatography Joan M. Ryan1, Karen M. Dobos1, Nicole A. Kruh-Garcia1,2 1Mycobacteria Research Laboratories, Department of Microbiology Immunology & Pathology, Colorado State University, 2BioMARC, Infectious Disease Research Center, Colorado State University This protocol describes size exclusion chromatography, a facile and reproducible technique for enriching Mycobacterium tuberculosis extracellular vesicles from culture supernatants. Biochemistry Identification of RNA Fragments Resulting from Enzymatic Degradation using MALDI-TOF Mass Spectrometry Shawn W. Schowe1, Conner J. Langeberg2, Erich G. Chapman2, Kitty Brown3, Marino J. E. Resendiz1 1Department of Chemistry, University of Colorado, Denver, 2Department of Chemistry & Biochemistry, University of Denver, 3Analytical Resources Core Bioanalysis & Omics, Colorado State University MALDI-TOF was used to characterize fragments obtained from the reactivity between oxidized RNA and the exoribonuclease Xrn-1. The present protocol describes a methodology that can be applied to other processes involving RNA and/or DNA. Biology Bead Loading Proteins and Nucleic Acids into Adherent Human Cells Charlotte Ayn Cialek1, Gabriel Galindo1, Amanda Lynn Koch1, Matthew Neeley Saxton1, Timothy John Stasevich1,2 1Department of Biochemistry and Molecular Biology, Colorado State University, 2World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology Bead loading introduces proteins, plasmids, and particles into adherent mammalian cells. This cell loading technique is inexpensive, rapid, and does not substantially affect cell health. It is best suited for live-cell imaging. Behavior Revised and Neuroimaging-Compatible Versions of the Dual Task Screen Allan M. Aumen*1, Kelly J. Oberg*1, Susan M. Mingils2, Cecelia B. Berkner3, Brian L. Tracy3, Jaclyn A. Stephens1,2 1Molecular Cellular and Integrative Neuroscience Program, Colorado State University, 2Dept. of Occupational Therapy, Colorado State University, 3Dept. of Health and Exercise Science, Colorado State University We developed the original Dual Task Screen (DTS) as a portable, low-cost measure that can evaluate athletes with sports-induced mild traumatic brain injury. We revised the original DTS for future clinical use and developed a neuroimaging-compatible version of the DTS to measure neural underpinnings of single and dual task performance. Behavior The Use of Traditional Fear Tests to Evaluate Different Emotional Circuits in Cattle Courtney Lynd Daigle1, Amanda J. Hubbard1, Temple Grandin2 1Animal Behavior & Welfare Laboratory, Department of Animal Science, Texas A&M University, 2Department of Animal Sciences, Colorado State University Here, we present a protocol to conduct a variety of behavioral tests in cattle that have been designed to evaluate emotions. A battery of behavioral tests (open field test, startle test, bovine zero maze, exit velocity, pen score, and chute score) were conducted to evaluate different components of animal temperament. Chemistry Close-Space Sublimation-Deposited Ultra-Thin CdSeTe/CdTe Solar Cells for Enhanced Short-Circuit Current Density and Photoluminescence Alexandra M. Bothwell1, Jennifer A. Drayton1, Pascal M. Jundt1, James R. Sites1 1Department of Physics, Colorado State University This work describes the complete fabrication process of thin absorber cadmium selenium telluride/cadmium telluride photovoltaic devices for enhanced efficiency. The process utilizes an automated in-line vacuum system for close-space sublimation deposition that is scalable, from fabrication of small area research devices as well as large-scale modules. Environment Detection of Viruses from Bioaerosols Using Anion Exchange Resin Joshua W. Schaeffer1, Jeffrey C. Chandler2, Margaret Davidson1,3, Sheryl L. Magzamen1, Alma Pérez-Méndez4, Stephen J. Reynolds1, Lawrence D. Goodridge5, John Volckens6, Alan B. Franklin2, Susan A. Shriner2, Bledar Bisha7 1High Plains Intermountain Center for Agricultural Health and Safety, Department of Environmental and Radiological Health Sciences, Colorado State University, 2National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 3Western Sydney University, 4Leprino Foods, Inc, 5Department of Food Science and Agricultural Chemistry, McGill University, 6Department of Mechanical Engineering, Colorado State University, 7Department of Animal Science, University of Wyoming An anion exchange resin-based method, adapted to liquid impingement-based bioaerosol sampling of viruses is demonstrated. When coupled with downstream molecular detection, the method allows for facile and sensitive detection of viruses from bioaerosols. Engineering The Diffusion of Passive Tracers in Laminar Shear Flow Manuchehr Aminian1,2, Francesca Bernardi1, Roberto Camassa1, Daniel M. Harris1,3, Richard M. McLaughlin1 1Department of Mathematics, University of North Carolina at Chapel Hill, 2Department of Mathematics, Colorado State University, 3School of Engineering, Brown University A protocol for the study of the diffusion of passive tracers in laminar pressure-driven flow is presented. The procedure is applicable to various capillary pipe geometries. Biochemistry Protein Digestion, Ultrafiltration, and Size Exclusion Chromatography to Optimize the Isolation of Exosomes from Human Blood Plasma and Serum Gustavo Diaz1, Chandler Bridges1, Megan Lucas1, Yong Cheng2, Jeff S. Schorey2, Karen M. Dobos1, Nicole A. Kruh-Garcia1 1Department of Microbiology, Immunology and Pathology, Colorado State University, 2Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame Here, we present a protocol to purify exosomes from both plasma and serum with reduced co-purification of non-exosomal blood proteins. The optimized protocol includes ultrafiltration, protease treatment, and size exclusion chromatography. Enhanced purification of exosomes benefits downstream analyses, including more accurate quantification of vesicles and proteomic characterization. Neuroscience Modified Roller Tube Method for Precisely Localized and Repetitive Intermittent Imaging During Long-term Culture of Brain Slices in an Enclosed System Benjamin B. Fixman*1, Isaac W. Babcock*1, Laurie S. Minamide*1, Alisa E. Shaw1, Marina I. Oliveira da Silva1,2, Avery M. Runyan1, Michael T. Maloney1,3, Jeffrey J. Field1, James R. Bamburg1 1Department of Biochemistry and Molecular Biology and Molecular, Cellular and Integrated Neuroscience Program, Colorado State University, 2IBMC-Instituto de Biologia Molecular e Celular, i3S-Instituto de Investigaçãoe Inovação em Saúde, ICBAS, Universidade do Porto, 3Denali Therapeutics Presented here is a modified roller tube method for culturing and intermittent high-resolution imaging of rodent brain slices over many weeks with precise repositioning on photoetched coverslips. Neuronal viability and slice morphology are well maintained. Applications of this fully enclosed system using viruses for cell-type specific expression are provided. Immunology and Infection Rescue and Characterization of Recombinant Virus from a New World Zika Virus Infectious Clone James Weger-Lucarelli1, Nisha K. Duggal2, Aaron C. Brault2, Brian J. Geiss1, Gregory D. Ebel1 1Department of Microbiology, Immunology, and Pathology, Colorado State University, 2Division of Vector-Borne Diseases, Centers for Disease Control and Prevention This protocol describes the recovery of infectious Zika virus from a two-plasmid infectious cDNA clone. Immunology and Infection Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function Mia J. Smith1,2, Thomas A. Packard1, Shannon K. O'Neill1, Rochelle M. Hinman1, Marynette Rihanek3, Peter A. Gottlieb3, John C. Cambier1,4 1Department of Immunology and Microbiology, University of Colorado School of Medicine, 2Department of Microbiology, Immunology, and Pathology, Colorado State University, 3Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, 4Department of Biomedical Research, National Jewish Health A simple yet effective method that employs magnetic nanoparticles to detect and enrich antigen-reactive B cells for functional and phenotypic analysis is described. Environment Integrating Remote Sensing with Species Distribution Models; Mapping Tamarisk Invasions Using the Software for Assisted Habitat Modeling (SAHM) Amanda M. West1, Paul H. Evangelista1, Catherine S. Jarnevich2, Nicholas E. Young1, Thomas J. Stohlgren1, Colin Talbert2, Marian Talbert3, Jeffrey Morisette3, Ryan Anderson1 1Natural Resource Ecology Laboratory, Colorado State University, 2U.S. Geological Survey, Fort Collins Science Center, 3U.S. Geological Survey - U.S. Department of the Interior, North Central Climate Science Center We demonstrate the utility of remotely sensed data and the newly developed Software for Assisted Habitat Modeling (SAHM) in predicting invasive species occurrence on the landscape. An ensemble of predictive models produced highly accurate maps of tamarisk (Tamarix spp.) invasion in Southeastern Colorado, USA when assessed with subsequent field validations. Bioengineering Delivery of Therapeutic siRNA to the CNS Using Cationic and Anionic Liposomes Heather R. Bender1, Sarah Kane1, Mark D. Zabel1 1Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University The goal of this protocol is to use cationic/anionic liposomes with a neuro-targeting peptide as a CNS delivery system to enable siRNA to cross the BBB. The optimization of a delivery system for treatments, like siRNA, would allow for more treatment options for prion and other neurodegenerative diseases. Environment Removal of Trace Elements by Cupric Oxide Nanoparticles from Uranium In Situ Recovery Bleed Water and Its Effect on Cell Viability Jodi R. Schilz1, K. J. Reddy2, Sreejayan Nair3, Thomas E. Johnson4, Ronald B. Tjalkens5, Kem P. Krueger3, Suzanne Clark6 1Division of Physical Therapy, Department of Orthopedics & Rehabilitation, University of New Mexico, 2Department of Ecosystem Science and Management, University of Wyoming, 3School of Pharmacy, University of Wyoming, 4Department of Environmental and Radiological Health Sciences, Colorado State University, 5Center for Environmental Medicine, Colorado State University, 6College of Pharmacy, California Northstate University Production bleed water (PBW) was treated with cupric oxide nanoparticles (CuO-NPs) and cellular toxicity was assessed in cultured human cells. The goal of this protocol was to integrate the native environmental sample into a cell culture format assessing the changes in toxicity due to CuO-NP treatment. Biology Milk Collection Methods for Mice and Reeves' Muntjac Deer Kassandra Willingham1, Erin McNulty1, Kelly Anderson1, Jeanette Hayes-Klug1, Amy Nalls1, Candace Mathiason1 1Department of Microbiology, Immunology, and Pathology, Prion Research Center, Colorado State University Milk collection from animal models facilitates various research avenues: understanding passive immunity, identifying pathogens responsible for vertical transmission and, through the use of transgenic mice, even commercial production of proteins found in human breast milk. Here we illustrate a simple method for milk collection in mice and Reeves’ muntjac deer. Environment Colorimetric Paper-based Detection of Escherichia coli, Salmonella spp., and Listeria monocytogenes from Large Volumes of Agricultural Water Bledar Bisha1, Jaclyn A. Adkins2, Jana C. Jokerst3, Jeffrey C. Chandler1, Alma Pérez-Méndez4, Shannon M. Coleman4, Adrian O. Sbodio5, Trevor V. Suslow5, Michelle D. Danyluk6, Charles S. Henry2, Lawrence D. Goodridge7 1Department of Animal Science, University of Wyoming, 2Department of Chemistry, Colorado State University, 3Department of Environmental and Radiological Health Sciences, Colorado State University, 4Department of Animal Sciences, Colorado State University, 5Department of Plant Sciences, University of California, Davis, 6Department of Food Science and Human Nutrition, Citrus Research and Education Center, University of Florida, 7Department of Food Science and Agricultural Chemistry, McGill University A protocol involving integrated concentration, enrichment, and end-point colorimetric detection of foodborne pathogens in large volumes of agricultural water is presented here. Water is filtered through Modified Moore Swabs (MMS), enriched with selective or non-selective media, and detection is performed using paper-based analytical devices (µPAD) imbedded with bacterial-indicative colorimetric substrates. Environment Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling Jennifer L Soong1, Dan Reuss1, Colin Pinney1, Ty Boyack1, Michelle L Haddix1, Catherine E Stewart2, M. Francesca Cotrufo1,3 1Natural Resource Ecology Laboratory, Colorado State University, 2Soil Plant Nutrient REsearch, USDA-ARS, 3Department of Soil and Crop Sciences, Colorado State University This method explains how to build and operate a continuous 13C and 15N isotope labeling chamber for uniform or differential plant tissue labeling. Representative results from metabolic and structural labeling of Andropogon gerardii are discussed. Medicine Transabdominal Ultrasound for Pregnancy Diagnosis in Reeves' Muntjac Deer Kelly D. Walton1, Erin McNulty1, Amy V. Nalls1, Candace K. Mathiason1 1Department of Microbiology, Immunology, and Pathology, Colorado State University Transabdominal ultrasound is described as an effective, noninvasive means for assessing reproductive status in Reeves' muntjac deer. These methods can be used to achieve early pregnancy diagnosis and to evaluate fetal viability. Future applications of this technique include estimation of gestational age and effects of maternal disease on fetal development. Behavior P50 Sensory Gating in Infants Anne Spencer Ross1,2, Sharon Kay Hunter1, Mark A Groth1, Randal Glenn Ross1 1Department of Psychiatry, University of Colorado School of Medicine, 2Colorado State University Methods to record auditory P50 sensory gating, a physiological marker of cerebral inhibition which reflects early stages of attention, are described. Environment High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities Colin W. Bell1, Barbara E. Fricks1, Jennifer D. Rocca1, Jessica M. Steinweg2, Shawna K. McMahon3, Matthew D. Wallenstein1 1Natural Resource Ecology Laboratory, Colorado State University, 2Biosciences Division, Oak Ridge National Laboratory, 3Department of Bioengineering, University of Colorado To measure potential rates of soil extracellular enzyme activities, synthetic substrates that are bound to a fluorescent dye are added to soil samples. Enzyme activity is measured as the fluorescent dye is released from the substrate by an enzyme-catalyzed reaction, where higher fluorescence indicates more substrate degradation. Chemistry Rapid High Throughput Amylose Determination in Freeze Dried Potato Tuber Samples Diego Fajardo1, Sastry S. Jayanty2, Shelley H. Jansky1 1USDA-ARS and Department of Horticulture, University of Wisconsin - Madison, 2Department of Horticulture and Landscape Architecture, Colorado State University This protocol describes a high through put colorimetric method that relies on the formation of a complex between iodine and chains of glucose molecules in starch. Iodine forms complexes with both amylose and long chains within amylopectin. After the addition of iodine to a starch sample, the maximum absorption of amylose and amylopectin occurs at 620 and 550 nm, respectively. The amylose/amylopectin ratio can be estimated from the ratio of the 620 and 550 nm absorbance values and comparing them to a standard curve in which specific known concentrations are plotted against absorption values. This high throughput, inexpensive method is reliable and reproducible, allowing the evaluation of large populations of potato clones. Biology Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA Ryan A. Rogge1, Anna A. Kalashnikova1, Uma M. Muthurajan1, Mary E. Porter-Goff1, Karolin Luger1, Jeffrey C. Hansen1 1Biochemistry and Molecular Biology, Colorado State University A method is presented for the reconstitution of model nucleosomal arrays from recombinant core histones and tandemly repeated nucleosome positioning DNA. We also describe how sedimentation velocity experiments in the analytical ultracentrifuge, and atomic force microscopy (AFM) are used to monitor the extent of nucleosomal array saturation after reconstitution. Chemistry Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) Corey D. Broeckling1, Adam L. Heuberger1, Jessica E. Prenni1 1Proteomics and Metabolomics Facility, Colorado State University Non-targeted metabolite profiling by ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS) is a powerful technique to investigate metabolism. This article outlines a typical workflow utilized for non-targeted metabolite profiling of serum including sample organization and preparation, data acquisition, data analysis, quality control, and metabolite identification. Biology In vivo Electroporation of Morpholinos into the Regenerating Adult Zebrafish Tail Fin David R. Hyde1, Alan R. Godwin2, Ryan Thummel3 1Department of Biological Sciences, Center for Zebrafish Research, University of Notre Dame, 2Department of Microbiology, Immunology, and Pathology, Colorado State University, 3Departments of Anatomy and Cell Biology and Ophthalmology, Wayne State University School of Medicine We describe a method to conditionally knockdown the expression of a target protein during adult zebrafish fin regeneration. This technique involves micro-injecting and electroporating antisense oligonucleotide morpholinos into fin tissue, which allows testing the protein’s role in various stages of fin regeneration, including wound healing, blastema formation, and regenerative outgrowth. Immunology and Infection DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat (VNTR) - Fragment Length Analysis (FLA) Ronald W. Jensen1, Jason Rivest1, Wei Li1, Varalakshmi Vissa1 1Department of Microbiology, Immunology and Pathology, Colorado State University Leprosy, caused by Mycobacterium leprae, is still endemic in many places. In order to learn about the spread and mode of transmission of leprosy, it is important to determine which strain of M. leprae has infected a patient. Variable numbers of tandem repeats (VNTR) typing is one such method. Immunology and Infection Non-surgical Intratracheal Instillation of Mice with Analysis of Lungs and Lung Draining Lymph Nodes by Flow Cytometry Manira Rayamajhi1, Elizabeth F. Redente2, Tracy V. Condon1, Mercedes Gonzalez-Juarrero3, David W.H. Riches1,2,4, Laurel L. Lenz1,4 1Department of Immunology, University of Colorado School of Medicine, 2Division of Cell Biology, Department of Pediatrics, National Jewish Health, 3Department of Microbiology, Immunology, and Pathology, Colorado State University, 4Department of Immunology, National Jewish Health We illustrate non-surgical delivery of test materials into the lungs of anesthetized mice via the trachea. This method permits lung exposure to bacterial and viral pathogens, cytokines, antibodies, beads, chemicals, or dyes. We further describe harvesting and processing of lungs and lung draining lymph nodes (LDLNs) for flow cytometry. Biology In vivo and in vitro Studies of Adaptor-clathrin Interaction Daniel Feliciano1, Jarred J. Bultema1, Andrea L. Ambrosio1, Santiago M. Di Pietro1 1Department of Biochemistry and Molecular Biology, Colorado State University Clathrin-mediated endocytosis depends on adaptor proteins that coordinate cargo selection and clathrin coat assembly. Here we describe procedures to study adaptor-clathrin physical interaction and live cell imaging approaches using as a model the yeast endocytic adaptor protein Sla1p. Immunology and Infection Alphavirus Transducing System: Tools for Visualizing Infection in Mosquito Vectors Aaron Phillips1, Eric Mossel1, Irma Sanchez-Vargas1, Brian Foy1, Ken Olson1 1Microbiology, Immunology, and Pathology, Colorado State University Methods for using alphavirus transducing systems to express fluorescent reporters in vitro and in adult mosquitoes are described. This technique may be adapted to express any protein of interest in lieu of or in addition to a reporter. Immunology and Infection Monitoring Immune Cells Trafficking Fluorescent Prion Rods Hours after Intraperitoneal Infection Theodore E. Johnson*1, Brady A. Michel*1, Crystal Meyerett1, Angela Duffy1, Anne Avery1, Steven Dow1, Mark D. Zabel1 1Department of Microbiology, Immunology and Pathology, Colorado State University Here we describe a novel assay for monitoring prion uptake and trafficking by immune cells immediately following intraperitoneal inoculation by purifying and fluorescently labeling aggregated prion rods from infected brain material then monitoring their uptake and movement from the injection site and characterizing the cells mediating these events. Immunology and Infection Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce Bledar Bisha1, Byron F. Brehm-Stecher2 1Center for Meat Safety and Quality, Department of Animal Sciences, Colorado State University, 2Rapid Microbial Detection and Control Laboratory, Department of Food Science and Human Nutrition, Iowa State University This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).