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San Diego State University

20 ARTICLES PUBLISHED IN JoVE

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Biology

Fluorescent Labeling of Drosophila Heart Structures
Nakissa N. Alayari 1,2, Georg Vogler 2, Ouarda Taghli-Lamallem 2, Karen Ocorr 2, Rolf Bodmer 2, Anthony Cammarato 1,2
1Biology Department, San Diego State University, 2Development and Aging Program, NASCR Center, The Sanford Burnham Institute for Medical Research

Here we describe a basic protocol for fluorescent labeling of different elements of heart tubes from larva and adult Drosophila melanogaster. These specimens are well-suited for imaging via fluorescent or confocal microscopy. This technique permits detailed structural analysis of the features of the hearts from a powerful model organism.

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Biology

Semi-automated Optical Heartbeat Analysis of Small Hearts
Karen Ocorr 1, Martin Fink 2, Anthony Cammarato 1,3, Sanford I. Bernstein 3, Rolf Bodmer 1
1Development and Aging Program, The Sanford Burnham Institute for Medical Research, 2Cardiac Electrophysiology Group, Dept. of Physiology, Anatomy and Genetics, The Sanford Burnham Institute for Medical Research, 3Biology Department and Heart Institute, San Diego State University

We have developed a Semi-automated Optical Heartbeat Analysis method (SOHA) for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts. We demonstrate the application of our methodology to the analysis of heart function in fruit fly and embryonic mouse hearts.

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Engineering

Constant Temperature Anemometry: A Tool to Study Turbulent Boundary Layer Flow
Xiaofeng Liu 1, Jose Roberto Moreto 1, Jaime Dorado 1
1Department of Aerospace Engineering, San Diego State University

Constant Temperature Anemometry: A Tool to Study Turbulent Boundary Layer Flow

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Engineering

Aerodynamic Performance of a Model Aircraft: The DC-6B
Jose Roberto Moreto 1, Xiaofeng Liu 1
1Department of Aerospace Engineering, San Diego State University

Aerodynamic Performance of a Model Aircraft: The DC-6B

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Engineering

Turbulence Sphere Method: Evaluating Wind Tunnel Flow Quality
Jose Roberto Moreto 1, Xiaofeng Liu 1
1Department of Aerospace Engineering, San Diego State University

Turbulence Sphere Method: Evaluating Wind Tunnel Flow Quality

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Engineering

Schlieren Imaging: A Technique to Visualize Supersonic Flow Features
Jose Roberto Moreto 1, Xiaofeng Liu 1
1Department of Aerospace Engineering, San Diego State University

Schlieren Imaging: A Technique to Visualize Supersonic Flow Features

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Engineering

Flow Visualization in a Water Tunnel: Observing the Leading-edge Vortex Over a Delta Wing
Jose Roberto Moreto 1, Gustaaf Jacobs 2, Xiaofeng Liu 1
1Department of Aerospace Engineering, San Diego State University

Flow Visualization in a Water Tunnel: Observing the Leading-edge Vortex Over a Delta Wing

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Biology

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Yan Wei Lim 1, Matthew Haynes 2, Mike Furlan 1, Charles E. Robertson 3, J. Kirk Harris 4, Forest Rohwer 1
1Department of Biology, San Diego State University, 2DOE Joint Genome Institute, 3Department of Molecular, Cellular and Developmental Biology, University of Colorado, 4Department of Pediatrics, School of Medicine, University of Colorado

Using the cystic fibrosis airway as an example, the manuscript presents a comprehensive workflow comprising a combination of metagenomic and metatranscriptomic approaches to characterize the microbial and viral communities in animal-associated samples.

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Environment

Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology
Andreas Florian Haas 1, Ben Knowles 1, Yan Wei Lim 1, Tracey McDole Somera 2, Linda Wegley Kelly 1, Mark Hatay 1, Forest Rohwer 1
1Department of Biology, San Diego State University, 2Scripps Institution of Oceanography, University of California San Diego

Here, we present a comprehensive protocol to assess the organic and inorganic nutrient availability and the abundance and structure of microbial and viral communities in remote marine environments.

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Biology

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications
Cameron A. Smurthwaite 1, Wesley Williams 1, Alexandra Fetsko 1, Darin Abbadessa 1, Zachary D. Stolp 1, Connor W. Reed 1, Andre Dharmawan 1, Roland Wolkowicz 1
1Department of Biology, San Diego State University

Since the discovery of the green fluorescent protein gene, fluorescent proteins have impacted molecular cell biology. This protocol describes how expression of distinct fluorescent proteins through genetic engineering is used for barcoding individual cells. The procedure enables tracking distinct populations in a cell mixture, which is ideal for multiplexed applications.

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Immunology and Infection

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Savannah E. Sanchez 1, Daniel A. Cuevas 2, Jason E. Rostron 1, Tiffany Y. Liang 3, Cullen G. Pivaroff 1, Matthew R. Haynes 1, Jim Nulton 4, Ben Felts 4, Barbara A. Bailey 4, Peter Salamon 4, Robert A. Edwards 1,5,6, Alex B. Burgin 7, Anca M. Segall 1, Forest Rohwer 1
1Department of Biology, San Diego State University, 2Computational Science Research Center, San Diego State University, 3Bioinformatics and Medical Informatics Research Center, San Diego State University, 4Department of Mathematics and Statistics, San Diego State University, 5Department of Computer Science, San Diego State University, 6Mathematics and Computer Science Division, Argonne National Laboratory, 7SPARC Committee, Broad Institute

Here, we present phenomic approaches for the functional characterization of putative phage genes. Techniques include a developed assay capable of monitoring host anabolic metabolism, the Multi-phenotype Assay Plates (MAPs), in addition to the established method of metabolomics, capable of measuring effects to catabolic metabolism.

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Immunology and Infection

A Murine Model of Group B Streptococcus Vaginal Colonization
Kathryn A. Patras 1, Kelly S. Doran 1,2
1Department of Pediatrics, Division of Host-Microbe Systems & Therapeutics, University of California San Diego School of Medicine, 2Department of Biology and Center for Microbial Sciences, San Diego State University

The purpose of this protocol is to imitate human group B Streptococcus (GBS) vaginal colonization in a murine model. This method may be used to investigate host immune responses and bacterial factors contributing to GBS vaginal persistence, as well as to test therapeutic strategies.

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Neuroscience

Disruption of Frontal Lobe Neural Synchrony During Cognitive Control by Alcohol Intoxication
Ksenija Marinkovic 1,2, Lauren E. Beaton 1, Burke Q. Rosen 1,3, Joseph P. Happer 4, Laura C. Wagner 1
1Department of Psychology, San Diego State University, 2Department of Radiology, University of California San Diego, 3Department of Neurosciences, University of California San Diego, 4San Diego State University/UC San Diego Joint Doctoral Program in Clinical Psychology

This experiment uses an anatomically-constrained magnetoencephalography (aMEG) method to examine brain oscillatory dynamics and long-range functional synchrony during engagement of cognitive control as a function of acute alcohol intoxication.

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Developmental Biology

A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development
Renat N. Khaliullin 1,2,3, Jeffrey M. Hendel 1,2, Adina Gerson-Gurwitz 1,2, Shaohe Wang 1,4,5, Stacy D. Ochoa 1,6, Zhiling Zhao 1,7, Arshad Desai 1,2, Karen Oegema 1,2, Rebecca A. Green 1,2
1Ludwig Institute for Cancer Research, San Diego, 2Department of Cellular and Molecular Medicine, University of California, San Diego, 3Recursion Pharmaceuticals, 4Biomedical Sciences Graduate Program, University of California, San Diego, 5Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 6Department of Biology, San Diego State University, 7Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco

This work describes a semi-high-throughput protocol that allows simultaneous 3D time-lapse imaging of embryogenesis in 80–100 C. elegans embryos in a single overnight run. Additionally, image processing and visualization tools are included to streamline data analysis. The combination of these methods with custom reporter strains enables detailed monitoring of embryogenesis.

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Biology

Simultaneous Isolation and Culture of Atrial Myocytes, Ventricular Myocytes, and Non-Myocytes from an Adult Mouse Heart
Erik A. Blackwood 1, Alina S. Bilal 1, Khalid Azizi 1, Anup Sarakki 1, Christopher C. Glembotski 1
1San Diego State University Heart Institute and the Department of Biology, San Diego State University

A method is described for the simultaneous isolation of myocytes and non-myocytes from both the atria and ventricles of a single adult mouse heart. This protocol results in consistent yields of highly viable cardiac myocytes and non-myocytes and details optimal cell-specific culture conditions for phenotyping and in vitro analysis.

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Biology

Swabbing the Urban Environment - A Pipeline for Sampling and Detection of SARS-CoV-2 From Environmental Reservoirs
Maria I. Rojas 1,2, Steven S. Giles 3, Mark Little 1,2, Rafael Baron 1,2, Isabella Livingston 1,2, Taylor R. T. Dagenais 3, Jason Baer 1,2, Ana G. Cobián-Güemes 1,2, Brandie White 1,2, Forest Rohwer 1,2
1Department of Biology, San Diego State University, 2Viral Information Institute, San Diego State University, 3Big Rose Web Design, LLC

A citizen science project was designed to recruit San Diego residents to collect environmental samples for SARS-CoV-2. A multilingual web-based platform was created for data submission using a user-friendly mobile device interface. A laboratory information management system facilitated the collection of thousands of geographically diverse samples with real-time outcome tracking.

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Immunology and Infection

Selective Cleaning of Wild Caenorhabditis Nematodes to Enrich for Intestinal Microbiome Bacteria
Emily Morgan 1, Jonah Faye Longares 1, Marie-Anne Félix 2, Robert J. Luallen 1
1Department of Biology, San Diego State University, 2Institut de Biologie de l’École Normale Supérieure

Wild Caenorhabditis nematodes are associated with many microbes, often in the gut lumen or infecting the intestine. This protocol details a method to enrich unculturable microbes colonizing the intestine, taking advantage of the resistance of the dauer cuticle.

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Immunology and Infection

RNA Fluorescence in situ Hybridization (FISH) to Visualize Microbial Colonization and Infection in Caenorhabditis elegans Intestines
Dalaena E. Rivera 1, Vladimir Lažetić 2, Emily R. Troemel 2, Robert J. Luallen 1
1Department of Biology, San Diego State University, 2School of Biological Sciences, University of California, San Diego

Intestinal microbes, including extracellular bacteria and intracellular pathogens like the Orsay virus and microsporidia (fungi), are often associated with wild Caenorhabditis nematodes. This article presents a protocol for detecting and quantifying microbes that colonize and/or infect C. elegans nematodes, and for measuring pathogen load after controlled infections in the lab.

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Environment

Coral Reef Arks: An In Situ Mesocosm and Toolkit for Assembling Reef Communities
Jason L. Baer 1, Jessica Carilli 2, Bart Chadwick 3, Mark Hatay 1, Anneke van der Geer 1, Yun Scholten 4, William Barnes 4, Jenna Aquino 1, Ashton Ballard 1, Mark Little 1, Jared Brzenski 5, Xiaofeng Liu 6, Gunther Rosen 2, Pei-Fang Wang 2, Jose Castillo 5, Andreas F. Haas 4, Aaron C. Hartmann 7, Forest Rohwer 1
1Department of Biology, San Diego State University, 2Energy and Environmental Sciences Branch, Naval Information Warfare Center (NIWC) Pacific, 3Coastal Monitoring Associates, 4Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 5Computational Science Research Center, San Diego State University, 6Department of Aerospace Engineering, San Diego State University, 7Department of Organismic and Evolutionary Biology, Harvard University

Moored midwater geodesic structures called Coral Arks provide a modular, scalable, and vertically adjustable research platform that can be used to build, monitor, and perturb coral reef communities in previously inoperative areas, including offshore.

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Immunology and Infection

T4 Bacteriophage and E. coli Interaction in the Murine Intestine: A Prototypical Model for Studying Host-Bacteriophage Dynamics In Vivo
Nicola Pett 1, Michael Hunter 1, Natalia A. Carranza García 1, Jung Hee Seo 1, Samuel R. Collins 1, Forest Rohwer 2, Lisa C. Osborne 1, Carolina Tropini 1,3,4
1Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2Department of Biology, San Diego State University, 3School of Biomedical Engineering, University of British Columbia, 4Humans and the Microbiome Program, Canadian Institute for Advanced Research

Bacteriophages (phages), viruses that infect bacteria, are an integral component of the gut microbiome. Though these symbiotic inhabitants drive bacterial fitness and population dynamics, little is understood about how they impact gut homeostasis and disease. This protocol studies isolated T4 phages within a mouse model, adaptable to other phage-bacterial pairs.

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