university of california irvine

10 ARTICLES PUBLISHED IN JoVE

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.

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 Liang¹, Joshua H. Siegle², Jakob Voigts², Matthew Wilson², Michael M. Halassa¹

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.

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.

Biochemistry

Fractionation for Resolution of Soluble and Insoluble Huntingtin Species

Joseph Ochaba^1,2, Eva L. Morozko^2,3, Jacqueline G. O’Rourke⁴, 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

Immunology and Infection

Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes

Saahir Khan¹, Aarti Jain², Omid Taghavian², Rie Nakajima², Algis Jasinskas², Medalyn Supnet², Jiin Felgner², Jenny Davies², Rafael Ramiro de Assis², Sharon Jan², Joshua Obiero², Erwin Strahsburger², Egest J. Pone², Li Liang², D. Huw Davies², Philip L. Felgner²

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.

Biochemistry

Capturing Actively Produced Microbial Volatile Organic Compounds from Human-Associated Samples with Vacuum-Assisted Sorbent Extraction

Joann Phan¹, Joseph Kapcia III¹, Cynthia I. Rodriguez², Victoria L. Vogel³, Daniel B Cardin³, Sage J. B. Dunham³, Katrine Whiteson¹

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.

Medicine

Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome

Jacob Vieira¹, Tara Gallagher², Hui-Yu Sui¹, Sirus Jesudasen³, Katrine Whiteson², George A. O'Toole⁴, Kurt Hanselmann⁵, Peggy S. Lai¹

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.

Biology

Label-Retention Expansion Microscopy (LR-ExM) Enables Super-Resolution Imaging and High-Efficiency Labeling

Sohyeon Park¹, Yinyin Zhuang², 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.

Neuroscience

Head Implants for the Neuroimaging of Awake, Head-Fixed Rats

Mehwish Bhatti¹, Hayden Malone¹, Gabriel Hui¹, 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.

Genetics

Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli

Luis Mota-Bravo¹, Manel Camps², Iván Muñoz-Gutiérrez¹, Andrey Tatarenkov¹, Caison Warner², Isabel Suarez¹, Gerardo Cortés-Cortés²

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.