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university of california irvine

10 ARTICLES PUBLISHED IN JoVE

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Medicine

Permanent Cerebral Vessel Occlusion via Double Ligature and Transection
Melissa F. Davis *1,2, Christopher Lay *1,2,3, Ron D. Frostig 1,2,3,4
1Department of Neurobiology & Behavior, University of California, Irvine, 2The Center for the Neurobiology of Learning and Memory, University of California, Irvine, 3The Center for Hearing Research, University of California, Irvine, 4Department of Biomedical Engineering, University of California, Irvine

We describe a highly reproducible method for the permanent occlusion of a rodent major cerebral blood vessel. This technique can be accomplished with very little peripheral damage, minimal blood loss, a high rate of long-term survival, and consistent infarct volume commensurate with the human clinical population.

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Neuroscience

Design and Fabrication of Ultralight Weight, Adjustable Multi-electrode Probes for Electrophysiological Recordings in Mice
Philip M. Brunetti *1, Ralf D. Wimmer *1, Li Liang 1, Joshua H. Siegle 2, Jakob Voigts 2, Matthew Wilson 2, Michael M. Halassa 1
1The Neuroscience Institute, New York University Langone Medical Center, 2Department of Brain and Cognitive Science, Massachusetts Institute of Technology

Understanding the neural substrates of behavior requires brain circuit ensemble recording. Because of its genetic tractability, the mouse offers a model for circuit dissection and disease mimicry. Here, a method of designing and fabricating miniaturized probes is described that is suitable for targeting deep brain structure in the mouse.

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Biology

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis
Edmund Ong 1,2, Catherine Cahill 1,2,3
1Department of Anesthesiology and Perioperative Care, University of California Irvine, 2Department of Biomedical and Molecular Sciences, Queen's University, 3Department of Pharmacology, University of California Irvine

Receptor trafficking modulates signaling and cell responsiveness to ligands and is, itself, responsive to cell conditions, including ligand-induced signaling. Here, we describe a powerful and flexible technique for quantitatively assessing drug-induced receptor trafficking using immunolabeling and colocalizational analysis.

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Biochemistry

Fractionation for Resolution of Soluble and Insoluble Huntingtin Species
Joseph Ochaba 1,2, Eva L. Morozko 2,3, Jacqueline G. O’Rourke 4, Leslie M. Thompson 1,2,3
1Department of Psychiatry and Human Behavior, University of California Irvine, 2UCI MIND, University of California Irvine, 3Department of Neurobiology and Behavior, University of California Irvine, 4Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center

A method is described for fractionation of insoluble and soluble mutant huntingtin species from mouse brain and cell culture. The method described is useful for characterization and quantification of huntingtin protein flux and aids in analyzing protein homeostasis in disease pathogenesis and in the presence of perturbations

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Immunology and Infection

Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes
Saahir Khan 1, Aarti Jain 2, Omid Taghavian 2, Rie Nakajima 2, Algis Jasinskas 2, Medalyn Supnet 2, Jiin Felgner 2, Jenny Davies 2, Rafael Ramiro de Assis 2, Sharon Jan 2, Joshua Obiero 2, Erwin Strahsburger 2, Egest J. Pone 2, Li Liang 2, D. Huw Davies 2, Philip L. Felgner 2
1Division of Infectious Diseases, Department of Medicine, University of California Irvine Health, 2Vaccine Research and Development Center, Department of Physiology, University of California Irvine

We present a protocol for using a protein microarray constructed by printing influenza antigens onto nitrocellulose-coated slides to simultaneously probe serum for multiple antibody isotypes against over 250 antigens from different virus strains, thus allowing measurement of the breadth of serum antibodies across virus subtypes.

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Biochemistry

Capturing Actively Produced Microbial Volatile Organic Compounds from Human-Associated Samples with Vacuum-Assisted Sorbent Extraction
Joann Phan 1, Joseph Kapcia III 1, Cynthia I. Rodriguez 2, Victoria L. Vogel 3, Daniel B Cardin 3, Sage J. B. Dunham 3, Katrine Whiteson 1
1Department of Molecular Biology and Biochemistry, University of California Irvine, 2Department of Ecology and Evolutionary Biology, University of California Irvine, 3Entech Instruments Inc.

This protocol describes the extraction of volatile organic compounds from a biological sample with the vacuum-assisted sorbent extraction method, gas chromatography coupled with mass spectrometry using the Entech Sample Preparation Rail, and data analysis. It also describes culture of biological samples and stable isotope probing.

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Medicine

Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome
Jacob Vieira 1, Tara Gallagher 2, Hui-Yu Sui 1, Sirus Jesudasen 3, Katrine Whiteson 2, George A. O'Toole 4, Kurt Hanselmann 5, Peggy S. Lai 1
1Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, 2Department of Molecular Biology & Biochemistry, University of California, Irvine, 3Department of Medicine, Massachusetts General Hospital, 4Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 5Swiss i-research and teaching institute

The goal of this protocol is to develop a model system for the effect of hyperoxia on cystic fibrosis airway microbial communities. Artificial sputum medium emulates the composition of sputum, and hyperoxic culture conditions model the effects of supplemental oxygen on lung microbial communities.

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Biology

Label-Retention Expansion Microscopy (LR-ExM) Enables Super-Resolution Imaging and High-Efficiency Labeling
Sohyeon Park 1, Yinyin Zhuang 2, Xiaoyu Shi 1,2,3
1Center for Complex Biological Systems, University of California Irvine, 2Department of Developmental and Cell Biology, University of California Irvine, 3Department of Chemistry, University of California Irvine

A protocol of label retention expansion microscopy (LR-ExM) is demonstrated. LR-ExM uses a novel set of trifunctional anchors, which provides better labeling efficiency compared to previously introduced expansion microscopies.

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Neuroscience

Head Implants for the Neuroimaging of Awake, Head-Fixed Rats
Mehwish Bhatti 1, Hayden Malone 1, Gabriel Hui 1, Ron D. Frostig 1,2,3
1Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, 2Department of Biomedical Engineering, School of Engineering, University of California, Irvine, 33Center for Neurobiology of Learning and Memory, University of California, Irvine

A detailed new procedure for functional imaging of awake, head-fixed rats is described.

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Genetics

Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
Luis Mota-Bravo 1, Manel Camps 2, Iván Muñoz-Gutiérrez 1, Andrey Tatarenkov 1, Caison Warner 2, Isabel Suarez 1, Gerardo Cortés-Cortés 2
1School of Biological Sciences, University of California Irvine, 2Department of Microbiology & Environmental Toxicology, University of California Santa Cruz

Conjugation mediates horizontal gene transfer by mobilizing plasmid DNA across two different cells, facilitating the spread of beneficial genes. This work describes a widely-used method for the efficient detection of conjugative plasmid transfer, based on the use of differential markers in the conjugative plasmid, donor, and recipient to detect transconjugation.

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