University of California, Santa Cruz View Institution's Website 12 articles published in JoVE Environment Field Collection and Laboratory Maintenance of Canopy-Forming Giant Kelp to Facilitate Restoration Phoebe D. Dawkins1, Andrea Paz-Lacavex2, Evan A. Fiorenza1, Makena A. Rush1, Rodrigo Beas-Luna3, Julio Lorda4, Luis Malpica-Cruz5, Jose M. Sandoval-Gil5, Tristin A. McHugh6, Min K. Han1, Matthew E. S. Bracken1, Joleah B. Lamb1 1Department of Ecology and Evolutionary Biology, University of California, Irvine, 2Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 3Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 4Facultad de Ciencias, Universidad Autónoma de Baja California, 5Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, 6The Nature Conservancy This protocol describes the field collection and regular laboratory maintenance of substrates seeded with canopy-forming giant kelp for use in restoration trials to address the success and limitations of the 'green gravel' technique in field settings. 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. Developmental Biology Generation of Mosaic Mammary Organoids by Differential Trypsinization Stefany Rubio1, Oscar Cazares1, Hector Macias1, Lindsay Hinck1 1Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz The mammary gland is a bilayered structure, comprising outer myoepithelial and inner luminal epithelial cells. Presented is a protocol to prepare organoids using differential trypsinization. This efficient method allows researchers to separately manipulate these two cell types to explore questions concerning their roles in mammary gland form and function. Bioengineering Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior Francesco Carrara1, Douglas R. Brumley2, Andrew M. Hein3, Yutaka Yawata4,5, M. Mehdi Salek1, Kang Soo Lee1, Elzbieta Sliwerska1, Simon A. Levin6, Roman Stocker1 1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, 2School of Mathematics and Statistics, University of Melbourne, 3Institute of Marine Sciences, University of California, Santa Cruz, 4Faculty of Life and Environmental Sciences, University of Tsukuba, 5Microbiology Research Center for Sustainability, University of Tsukuba, 6Department of Ecology and Evolutionary Biology, Princeton University A protocol for the generation of dynamic chemical landscapes by photolysis within microfluidic and millifluidic setups is presented. This methodology is suitable to study diverse biological processes, including the motile behavior, nutrient uptake, or adaptation to chemicals of microorganisms, both at the single cell and population level. Biology Novel Method of Plasmid DNA Delivery to Mouse Bladder Urothelium by Electroporation Chuan Yu*1, Ofir Stefanson*1, Yueli Liu1, Zhu A. Wang1 1Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz We describe a novel method for the delivery of DNA plasmid into the urothelial cells of mouse bladder in vivo through urethra catheterization and electroporation. It offers a fast and convenient way for generating autochthonous mouse models of bladder diseases. Biochemistry A Tailored HPLC Purification Protocol That Yields High-purity Amyloid Beta 42 and Amyloid Beta 40 Peptides, Capable of Oligomer Formation Christopher J. A. Warner1, Subrata Dutta1, Alejandro R. Foley1, Jevgenij A. Raskatov1 1Department of Chemistry, University of California, Santa Cruz Herein we report a tailored HPLC purification protocol that yields high-purity amyloid beta 42 (Aβ42) and amyloid beta 40 (Aβ40) peptides, capable of oligomer formation. Amyloid beta is a highly aggregation prone, hydrophobic peptide implicated in Alzheimer's disease. The amyloidogenic nature of the peptide makes its purification a challenge. Neuroscience Two-Photon in vivo Imaging of Dendritic Spines in the Mouse Cortex Using a Thinned-skull Preparation Xinzhu Yu1, Yi Zuo1 1Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz Time-lapse imaging in the living animal provides valuable information on structural reorganization in the intact brain. Here, we introduce a thinned-skull preparation that allows transcranial imaging of fluorescently labeled synaptic structures in the living mouse cortex by two-photon microscopy. Behavior Study Motor Skill Learning by Single-pellet Reaching Tasks in Mice Chia-Chien Chen1, Anthony Gilmore1, Yi Zuo1 1Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz Persistent practice improves the precision of coordinated movements. Here we introduce a single-pellet reaching task, which is designed to assess the learning and memory of forelimb skill in mice. Medicine Gene-environment Interaction Models to Unmask Susceptibility Mechanisms in Parkinson's Disease Vivian P. Chou1, Novie Ko1, Theodore R. Holman2, Amy B. Manning-Boğ1 1Center for Health Sciences, SRI International, 2Department of Chemistry and Biochemistry, University of California-Santa Cruz Lipoxygenase (LOX) isozymes can generate products that may increase or decrease neuroinflammation and neurodegeneration. A gene-environment interaction study could identify LOX isozyme-specific effects. Using the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of nigrostriatal damage in two LOX isozyme-deficient transgenic lines allows for comparison of the contribution of LOX isozymes on dopaminergic integrity and inflammation. Biology Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli Chris Troll1, David Alexander1, Jennifer Allen1, Jacob Marquette1, Manel Camps1 1Department of Microbiology & Environmental Toxicology, University of California Santa Cruz - UCSC Here we demonstrate a simple protocol to create a random mutant library for a given target sequence. We show how this method, which is performed in vivo in Escherichia coli, can be coupled with functional selections to evolve new enzymatic activities. Biology Bacterial Gene Expression Analysis Using Microarrays Sinem Beyhan1, Fitnat Yildiz1 1Department of Environmental Toxicology, University of California Santa Cruz - UCSC Biology Vibrio cholerae: Model Organism to Study Bacterial Pathogenesis - Interview Fitnat Yildiz1 1Department of Environmental Toxicology, University of California Santa Cruz - UCSC
