Florida International University 12 articles published in JoVE Chemistry Histone Modification Screening using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Time-Of-Flight Mass Spectrometry Meiby Fernandez-Rojas1, Cassandra N. Fuller1, Lilian Valadares Tose1, Matthew Willetts2, Melvin A. Park2, Natarajan V. Bhanu3, Benjamin A. Garcia3, Francisco Fernandez-Lima1,4 1Department of Chemistry and Biochemistry, Florida International University, 2Bruker Daltonics Inc., 3Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 4Biomolecular Sciences Institute, Florida International University An analytical workflow based on liquid chromatography, trapped ion mobility spectrometry, and time-of-flight mass spectrometry (LC-TIMS-ToF MS/MS) for high confidence and highly reproducible "bottom-up" analysis of histone modifications and identification based on principal parameters (retention time [RT], collision cross section [CCS], and accurate mass-to-charge [m/z] ratio). Biology Analysis of Extracellular Vesicle-Mediated Vascular Calcification Using In Vitro and In Vivo Models Sophie K. Ashbrook1, Ana M. Valentin Cabrera1, Mohammad Shaver1, Joshua D. Hutcheson1 1Department of Biomedical Engineering, Florida International University This paper presents the methodology for obtaining and assessing vascular calcification by isolating murine aortas followed by extracting calcified extracellular vesicles to observe the mineralization potential. Biology A High-Throughput Comet Assay Approach for Assessing Cellular DNA Damage Yunhee Ji*1, Mahsa Karbaschi*2, Abdulhadi Abdulwahed*3, Natalia S. Quinete4, Mark D. Evans5, Marcus S. Cooke1 1Oxidative Stress Group, Dept. Cell Biology, Microbiology and Molecular Biology, College of Arts and Sciences, University of South Florida, 2Cepheid (Danaher Corp.), US Technical Operations, 3Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, 4Department of Chemistry and Biochemistry, Institute of Environment, Florida International University, 5Leicester School of Allied Health Sciences, Faculty of Health and Life Sciences, De Montfort University The comet assay is a popular means of detecting DNA damage. This study describes an approach to running slides in representative variants of the comet assay. This approach significantly increased the number of samples while decreasing assay run-time, the number of slide manipulations, and the risk of damage to gels. Chemistry Controlled Odor Mimic Permeation Systems for Olfactory Training and Field Testing Lauryn E. DeGreeff1,2, Alison G. Simon3,4, Michael S. Macias3, Howard K. Holness2, Kenneth G. Furton2 1Chemistry Division, US Naval Research Laboratory, 2International Forensic Research Institute, Florida International University, 3Formerly of International Forensic Research Institute, Florida International University, 4Formerly of National Research Council Post-Doctoral Fellowship Program, US Naval Research Laboratory The Controlled Odor Mimic Permeation System is a simple, field-portable, low-cost method of odor delivery for olfactory testing and training. It is constructed of an odorant retained on an adsorbent material and contained inside of a permeable polymer bag allowing controlled release of the odorant vapor over time. Immunology and Infection Purification of High Yield Extracellular Vesicle Preparations Away from Virus Catherine DeMarino*1, Robert A. Barclay*1, Michelle L. Pleet1, Daniel O. Pinto1, Heather Branscome1,2, Siddhartha Paul3, Benjamin Lepene4, Nazira El-Hage5, Fatah Kashanchi1 1Laboratory of Molecular Virology, School of Systems Biology, George Mason University, 2American Type Culture Collection (ATCC), 3ATCC Cell Systems, 4Ceres Nanosciences, Inc, 5Department of Immunology and Nano-medicine, Herbert Wertheim College of Medicine, Florida International University This protocol isolates extracellular vesicles (EVs) away from virions with high efficiency and yield by incorporating EV precipitation, density gradient ultracentrifugation, and particle capture to allow for a streamlined workflow and a reduction of starting volume requirements, resulting in reproducible preparations for use in all EV research. Environment Chemical Analysis of Water-accommodated Fractions of Crude Oil Spills Using TIMS-FT-ICR MS Paolo Benigni1, Rebecca Marin1, Kathia Sandoval1, Piero Gardinali1, Francisco Fernandez-Lima1 1Chemistry and Biochemistry, Florida International University The low-energy water-accommodated fraction (LEWAF) of crude oil is a challenging system to analyze, because over time, this complex mixture undergoes chemical transformations. This protocol illustrates methods for the preparation of the LEWAF sample and for performing photo-irradiation and chemical analysis by trapped ion mobility spectrometry–FT-ICR MS. Immunology and Infection Characterization of Human Monocyte-derived Dendritic Cells by Imaging Flow Cytometry: A Comparison between Two Monocyte Isolation Protocols Gloria Figueroa1, Tiyash Parira1, Alejandra Laverde1, Gianna Casteleiro1, Amal El-Mabhouh2, Madhavan Nair1, Marisela Agudelo1 1Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, 2Millipore Sigma This study compares two different methods of human monocyte isolation for obtaining in vitro dendritic cells (DCs). Monocytes are selected by adherence or negatively enriched by magnetic separation. Monocyte yield and viability along with MDDC viability, proliferation and CD11c/CD14 surface marker expression will be compared between both methods. Behavior A Treatment Package without Escape Extinction to Address Food Selectivity Jessica Weber1, Anibal Gutierrez, Jr.1 1Department of Psychology and the Center for Children and Families, Florida International University Feeding difficulties are a common problem for children with developmental disorders, including autism, and behavioral interventions often include escape extinction. Recent research has begun to evaluate treatments that do not include escape extinction. This manuscript describes a multicomponent treatment package that does not use escape extinction to treat feeding difficulties. Medicine Brain Source Imaging in Preclinical Rat Models of Focal Epilepsy using High-Resolution EEG Recordings Jihye Bae1, Abhay Deshmukh1, Yinchen Song1, Jorge Riera1 1Biomedical Engineering, Florida International University This video introduces the preparation, recording, and source analysis procedures of high-resolution EEG on sedated rats with a particular preclinical model of focal epilepsy under noninvasive conditions. Bioengineering Electrospun Fibrous Scaffolds of Poly(glycerol-dodecanedioate) for Engineering Neural Tissues From Mouse Embryonic Stem Cells Xizi Dai1, Yen-Chih Huang1 1Department of Biomedical Engineering, Florida International University Synthesis and fabrication of electrospun long fibers spanning a larger deposit area via a newly designed collector from a novel biodegradable polymer named poly(glycerol-dodecanoate) (PGD) was reported. The fibers were able to support the growth of cells derived from mouse pluripotent stem cells. Chemistry Submillisecond Conformational Changes in Proteins Resolved by Photothermal Beam Deflection Walter G. Gonzalez1, Jaroslava Miksovska1 1Department of Chemistry and Biochemistry, Florida International University Here we report an application of the photothermal beam deflection technique in combination with a caged calcium compound, DM-nitrophen, to monitor microsecond and millisecond dynamics and energetics of structural changes associated with the calcium association to a neuronal calcium sensor, Downstream Regulatory Element Antagonist Modulator. Bioengineering Protocol for Relative Hydrodynamic Assessment of Tri-leaflet Polymer Valves Sharan Ramaswamy1, Manuel Salinas1, Rob Carrol2, Karla Landaburo1, Xavier Ryans1, Cynthia Crespo1, Ailyn Rivero1, Faris Al-Mousily3,4, Curt DeGroff3, Mark Bleiweis3, Hitomi Yamaguchi2 1Tissue Engineered Mechanics, Imaging and Materials Laboratory, Department of Biomedical Engineering, Florida International University, 2Department of Mechanical and Aerospace Engineering, University of Florida, 3College of Medicine, University of Florida, 4King Faisal Specialty Hospital and Research Center, Jeddah, Saudi Arabia There has been renewed interest in developing polymer valves. Here, the objectives are to demonstrate the feasibility of modifying a commercial pulse duplicator to accommodate tri-leaflet geometries and to define a protocol to present polymer valve hydrodynamic data in comparison to native and prosthetic valve data collected under near-identical conditions.
