University of California, Merced View Institution's Website 11 articles published in JoVE Biology Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow Mohammad N. Qasim*1,2, Ashley Valle Arevalo*1,2, Akshay D. Paropkari*1,2, Craig L. Ennis1,2,4, Suzanne S. Sindi3, Clarissa J. Nobile1,4, Aaron D. Hernday1,4 1Department of Molecular and Cell Biology, University of California, Merced, 2Quantitative and Systems Biology Graduate Program, University of California, Merced, 3Department of Applied Mathematics, University of California, Merced, 4Health Sciences Research Institute, University of California, Merced This protocol describes an experimental method and data analysis workflow for cleavage under targets and release using nuclease (CUT&RUN) in the human fungal pathogen Candida albicans. Chemistry Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids Aleksey A. Kocherzhenko1, Sapana V. Shedge2, Pauline F. Germaux1, Mohammad Heidarian1, Christine M. Isborn2 1Department of Chemistry and Biochemistry, California State University, East Bay, 2Department of Chemistry and Chemical Biology, University of California, Merced Here, we present a protocol for parametrizing a tight-binding excitonic Hamiltonian for calculating optical absorption spectra and optoelectronic properties of molecular materials from first-principles quantum chemical calculations. Behavior Continuous Theta Burst Stimulation of the Posterior Medial Frontal Cortex to Experimentally Reduce Ideological Threat Responses Colin Holbrook1, Chelsea L. Gordon1, Marco Iacoboni2 1Department of Cognitive and Information Sciences, University of California, Merced, 2Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles Threats reliably evoke shifts in high-level ideological investment, but little work to date has explored the neural mechanisms underlying these dynamics. This paper describes how continuous theta burst transcranial magnetic stimulation may be employed to test the contribution of the posterior medial frontal cortex (and/or other regions) to threat-related ideological shifts. Immunology and Infection Visualization of Biofilm Formation in Candida albicans Using an Automated Microfluidic Device Megha Gulati1, Craig L. Ennis1, Diana L. Rodriguez1, Clarissa J. Nobile1 1Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced This protocol describes the use of a customizable automated microfluidic device to visualize biofilm formation in Candida albicans under host physiological conditions. Biology Local Field Fluorescence Microscopy: Imaging Cellular Signals in Intact Hearts Yuriana Aguilar-Sanchez*1, Diego Fainstein*2,3, Rafael Mejia-Alvarez4, Ariel L. Escobar5 1School of Natural Sciences, University of California, Merced, 2Centro de Investigaciones Cardiovasculares, Universidad de la Plata and Conicet, 3Facultad de Ingenieria, Universidad Nacional de Entre Rios, 4Department of Physiology, Midwestern University, 5School of Engineering, University of California, Merced In the heart, molecular events coordinate the electrical and contractile function of the organ. A set of local field fluorescence microscopy techniques presented here enables the recording of cellular variables in intact hearts. Identifying mechanisms defining the cardiac function is critical in understanding how the heart works under pathological situations. Engineering High Resolution Phonon-assisted Quasi-resonance Fluorescence Spectroscopy Cyprian Czarnocki1, Mark L. Kerfoot1, Joshua Casara1, Andrew R. Jacobs1, Cameron Jennings1, Michael Scheibner1 1School of Natural Sciences, University of California, Merced The manuscript describes a method of phonon-assisted quasi-resonant fluorescence spectroscopy that incorporates both laser-limited resolution and photoluminescence (PL) spectroscopy. This method utilizes optical phonons to provide linewidth-limited resolution spectra of atom-like semiconductor structures in the energy domain. The method is also easily realized with a single spectrometer optical spectroscopy setup. Engineering Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis Benjamin N. Doblack1, Tim Allis1, Lilian P. Dávila1 1Materials Science and Engineering, School of Engineering, University of California Merced A new computational system featuring GPU-accelerated molecular dynamics simulation and 3D/VR visualization, analysis and manipulation of nanostructures has been implemented, representing a novel approach to advance materials research and promote innovative investigation and alternative methods to learn about material structures with dimensions invisible to the human eye. Engineering Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization Kwyn A. Meagher1, Benjamin N. Doblack1, Mercedes Ramirez2, Lilian P. Davila1 1Materials Science and Engineering, School of Engineering, University of California Merced, 2Computer Science and Engineering, School of Engineering, University of California Merced Accurate modeling of nanohelical structures is important for predictive simulation studies leading to novel nanotechnology applications. Currently, software packages and codes are limited in creating atomistic helical models. We present two procedures designed to create atomistic nanohelical models for simulations, and a graphical interface to enhance research through visualization. Bioengineering Tissue Engineering: Construction of a Multicellular 3D Scaffold for the Delivery of Layered Cell Sheets William S. Turner1, Nabjot Sandhu1, Kara E. McCloskey1 1School of Engineering, University of California, Merced For creation of highly organized structures of complex tissue, one must assemble multiple material and cell types into an integrated composite. This combinatorial design incorporates organ-specific layered cell sheets with two distinct biologically-derived materials containing a strong fibrous matrix base, and endothelial cells for enhancing new vessels formation. Biology Rapid Fibroblast Removal from High Density Human Embryonic Stem Cell Cultures William S. Turner1, Kara E. McCloskey1 1Department of Engineering, University of California, Merced Despite ongoing efforts to transition cultures to feeder-free conditions, the derivation and culture of human embryonic stem cells (hESC) remain largely dependent on co-cultures with mouse embryonic feeders (MEFs). Here, we show a novel methodology for rapidly removing feeders from hESC cultures prior to experimentation. Biology Shrinky-Dink Hanging Drops: A Simple Way to Form and Culture Embryoid Bodies Chi-Shuo Chen1, Jonathan Pegan1, Jesus Luna1, Bing Xia1, Kara McCloskey1, Wei-chun Chin1, Michelle Khine1 1School of Engineering, University of California Merced - UC Merced We show a simple and rapid method to load pre-defined numbers of cells into microfabricated wells and maintain them for embryoid body development.