Indiana University - Purdue University at Indianapolis (IUPUI) View Institution's Website 10 articles published in JoVE Medicine A Reproducible Cartilage Impact Model to Generate Post-Traumatic Osteoarthritis in the Rabbit Julian Dilley*1,2,3, Hessam Noori-Dokht*3,4,6, Abhijit Seetharam1, Margaret Bello1,3, Aaron Nanavaty1,3, Roman M. Natoli2,3, Todd McKinley1,2,3, Zachary Bault5, Diane Wagner2,3,6, Uma Sankar1,3 1Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, 2Department of Orthopaedic Surgery, Indiana University School of Medicine, 3Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, 4School of Mechanical Engineering, Purdue University, 5Large Animal Resource Center, Indiana University School of Medicine, 6Department of Mechanical and Energy Engineering, Indiana University-Purdue University Indianapolis The open medial femoral condyle impact model in rabbits is reliable for studying post-traumatic osteoarthritis (PTOA) and novel therapeutic strategies to mitigate PTOA progression. This protocol generates an isolated cartilage defect of the posterior medial femoral condyle in rabbits using a carriage-based drop tower with an impactor head. Bioengineering Practical Considerations for the Design, Execution, and Interpretation of Studies Involving Whole-Bone Bending Tests of Rodent Bones Olivia N. Reul1, Ashtin M. Anneken1, Rachel K. Kohler1, Dyann M. Segvich1, Joseph M. Wallace1 1Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis Mechanical testing of rodent bones is a valuable method for extracting information regarding a bone's susceptibility to fracture. Lacking proper practical understanding, the results may be overinterpreted or lack validity. This protocol will serve as a guide to ensure mechanical tests are performed accurately to provide valid and functional data. Chemistry Gas Chromatography-Mass Spectrometry Paired with Total Vaporization Solid-Phase Microextraction as a Forensic Tool Kymeri E. Davis*1, John V. Goodpaster*1,2 1Department of Chemistry & Chemical Biology, Indiana University - Purdue University Indianapolis, 2Forensic & Investigative Sciences Program, Indiana University - Purdue University Indianapolis Total Vaporization Solid Phase Microextraction (TV-SPME) completely vaporizes a liquid sample whilst analytes are sorbed onto a SPME fiber. This allows for partitioning of the analyte between only the solvent vapor and the SPME fiber coating. Biology Artificial Intelligence Approaches to Assessing Primary Cilia Ruchi Bansal1, Staci E. Engle1, Tisianna K. Kamba1, Kathryn M. Brewer1, Wesley R. Lewis2, Nicolas F. Berbari1,3,4 1Department of Biology, Indiana University-Purdue University Indianapolis, 2Nikon Instruments Inc., 3Stark Neurosciences Research Institute, Indiana University, 4Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine The use of artificial intelligence (Ai) to analyze images is emerging as a powerful, less biased, and rapid approach compared with commonly used methods. Here we trained Ai to recognize a cellular organelle, primary cilia, and analyze properties such as length and staining intensity in a rigorous and reproducible manner. Behavior The Participant-Reported Implementation Update and Score (PRIUS): A Novel Method for Capturing Implementation-Related Data Over Time Edward J. Miech1,2,3,4,5, Nicholas A. Rattray1,2,3,6, Dawn M. Bravata1,2,3,5, Jennifer Myers1,3, Teresa M. Damush1,2,3,5 1VA Precision Monitoring (PRIS-M) QUERI, Richard L. Roudebush VA Medical Center, 2William M. Tierney Center for Health Services Research, Regenstrief Institute, 3VA Health Services Research & Development Center for Health Information and Communication (CHIC), Richard L. Roudebush VA Medical Center, 4Department of Emergency Medicine, Indiana University School of Medicine, 5Department of Internal Medicine and Geriatrics, Indiana University School of Medicine, 6Department of Anthropology, Indiana University-Purdue University Indianapolis This protocol describes a novel method for collecting and analyzing data related to ongoing implementation called the Participant-Reported Implementation Update and Score (PRIUS). The PRIUS method allows for the efficient and systematic capture of data over time and from multiple viewpoints in healthcare settings. Chemistry Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry Elijah N. McCool*1, Rachele Lubeckyj*1, Xiaojing Shen1, Qiang Kou2, Xiaowen Liu2,3, Liangliang Sun1 1Department of Chemistry, Michigan State University, 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 3Center for Computational Biology and Bioinformatics, Indiana University School of Medicine A detailed protocol is described for the separation, identification, and characterization of proteoforms in protein samples using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS). The protocol can be used for the high-resolution characterization of proteoforms in simple protein samples and the large-scale identification of proteoforms in complex proteome samples. Engineering Cooling an Optically Trapped Ultracold Fermi Gas by Periodical Driving Jiaming Li1, Leonardo F. de Melo1, Le Luo1 1Department of Physics, Indiana University–Purdue University Indianapolis (IUPUI) We present a parametric driving method to cool an ultracold Fermi gas in a crossed-beam optical dipole trap. This method selectively removes high-energy atoms from the trap by periodically modulating the trap depth with frequencies that are resonant with the anharmonic components of the trapping potential. Biochemistry Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach Dilrajkaur Panfair1, Andrew R. Kusmierczyk1 1Department of Biology, Indiana University-Purdue University, Indianapolis (IUPUI) This protocol uses both subunit coexpression and postlysis subunit mixing for a more thorough examination of recombinant proteasome assembly. Medicine Cell Population Analyses During Skin Carcinogenesis Dongsheng Gu1, Qipeng Fan1, Jingwu Xie1 1Department of Pediatrics, Wells Center for Pediatric Research, IU Simon Cancer Center, Indiana University Carcinogenesis is a process involving interactions between cancer cells and the cancer microenvironment. To dissect the molecular events, one needs to isolate different cell populations at different stages during cancer development. Using a mouse model for basal cell carcinoma, we describe a protocol for cell analyses during carcinogenesis. Bioengineering Generation and Recovery of β-cell Spheroids From Step-growth PEG-peptide Hydrogels Asad Raza1, Chien-Chi Lin1 1Department of Biomedical Engineering, Purdue School of Engineering and Technology, Indiana University - Purdue University at Indianapolis The following protocol provides techniques for encapsulating pancreatic β-cells in step-growth PEG-peptide hydrogels formed by thiol-ene photo-click reactions. This material platform not only offers a cytocompatible microenvironment for cell encapsulation, but also permits user-controlled rapid recovery of cell structures formed within the hydrogels.
