Northwestern University Feinberg School of Medicine 18 articles published in JoVE Neuroscience Biochemical Purification and Proteomic Characterization of Amyloid Fibril Cores from the Brain Arun Upadhyay1, Robert J. Vassar1, Jeffrey N. Savas1 1Department of Neurology, Northwestern University Feinberg School of Medicine This biochemical purification method with mass spectrometry-based proteomic analysis facilitates the robust characterization of amyloid fibril cores, which may accelerate the identification of targets for preventing Alzheimer's disease. Neuroscience Implantation and Control of Wireless, Battery-free Systems for Peripheral Nerve Interfacing Hongkai Wang1,2, Dom D’Andrea1, Yeon Sik Choi3,4, Yasmine Bouricha1, Grace Wickerson3,4, Hak-Young Ahn3, Hexia Guo3,4, Yonggang Huang3,4,5,6, Milap S. Sandhu7, Sumanas W. Jordan8, John A. Rogers3,4,6,9,10,11,12, Colin K. Franz1,3,13 1Laboratory of Regenerative Rehabilitation, Shirley Ryan AbilityLab, Department of Physical Medicine and Rehabilitation, Northwestern University Feinberg School of Medicine, 2Northwestern University Interdepartmental Neuroscience Program, 3Center for Bio-integrated Electronics, Querrey Simpson Institute for Bioelectronics, Northwestern University, 4Department of Materials Science and Engineering, Northwestern University, 5Department of Civil and Environmental Engineering, Northwestern University, 6Department of Mechanical Engineering, Northwestern University, 7Arms and Hands Lab, Shirley Ryan AbilityLab, Department of Physical Medicine and Rehabilitation, Northwestern University Feinberg School of Medicine, 8Division of Plastic and Reconstructive Surgery, Biologics, Shirley Ryan AbilityLab, Northwestern University, 9Department of Biomedical Engineering, Northwestern University, 10Department of Neurological Surgery, Northwestern University, 11Department of Chemistry, Northwestern University, 12Department of Electrical and Computer Engineering, Northwestern University, 13The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine This is a protocol for the surgical implantation and operation of a wirelessly powered interface for peripheral nerves. We demonstrate the utility of this approach with examples from nerve stimulators placed on either the rat sciatic or phrenic nerve. Cancer Research Automated Dissection Protocol for Tumor Enrichment in Low Tumor Content Tissues Charles A. Havnar1, Oliver Zill2, Jeff Eastham1, Jeffrey Hung1, Manana Javey3, Emmanuel Naouri3, Jennifer Giltnane1, Justin M. Balko4, Andrew Wallace2, Nicolas Lounsbury2, Daniel Oreper2, Sarajane Saturnio1, G-Y Yang5, Amy A. Lo1 1Departments of Research Pathology, Genentech, 2Bioinformatics & Computational Biology, Genentech, 3Roche Sequencing Solutions, Hacienda Drive, 4Department of Medicine, Vanderbilt University Medical Center, Medical Center Drive, 5Department of Pathology, Northwestern University, Feinberg School of Medicine Digital annotation with automated tissue dissection provides an innovative approach to enriching tumor in low tumor content cases and is adaptable to both paraffin and frozen tissue types. The described workflow improves accuracy, reproducibility and throughput and could be applied to both research and clinical settings. Medicine Obtaining Quality Extended Field-of-View Ultrasound Images of Skeletal Muscle to Measure Muscle Fascicle Length Amy N. Adkins1,4,5, Wendy M. Murray1,2,3,4,5 1Department of Biomedical Engineering, Northwestern University, 2Department of Physical Medicine & Rehabilitation, Northwestern University Feinberg School of Medicine, 3Department of Physical Therapy and Human Movement Sciences, Northwestern University Feinberg School of Medicine, 4Shirley Ryan AbilityLab, 5Edward Hines, Jr. VA Hospital This study describes how to obtain high quality musculoskeletal images using the extended field-of-view ultrasound (EFOV-US) method for the purpose of making muscle fascicle length measures. We apply this method to muscles with fascicles that extend past the field-of-view of common traditional ultrasound (T-US) probes. Neuroscience Purification of Prominin-1+ Stem Cells from Postnatal Mouse Cerebellum Chandrakanth Reddy Edamakanti1, Puneet Opal1,2 1Davee Department of Neurology, Northwestern University Feinberg School of Medicine Chicago, 2Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine Chicago Demonstrated here is an efficient and cost-effective method to purify, culture, and differentiate white matter stem cells from postnatal mouse cerebellum. Neuroscience Purkinje Cell Survival in Organotypic Cerebellar Slice Cultures Jennifer Rakotomamonjy1, Alicia Guemez-Gamboa1 1Department of Physiology, Northwestern University, Feinberg School of Medicine Organotypic slice cultures are a powerful tool to study neurodevelopmental or degenerative/regenerative processes. Here, we describe a protocol that models the neurodevelopmental death of Purkinje cells in mouse cerebellar slice cultures. This method may benefit research in neuroprotective drug discovery. Behavior Lexical Decision Task for Studying Written Word Recognition in Adults with and without Dementia or Mild Cognitive Impairment Alexandre Nikolaev1, Eve Higby2,3, JungMoon Hyun4, Sameer Ashaie5,6 1Helsinki Collegium for Advanced Studies, University of Helsinki, 2University of California, Riverside, 3California State University, East Bay, 4Hunter College, City University of New York, 5Feinberg School of Medicine, Northwestern University, 6Shirley Ryan AbilityLab This article describes how to implement a simple lexical decision experiment to assess written word recognition in neurologically healthy participants and in individuals with dementia and cognitive decline. We also provide a detailed description of reaction time analysis using principal components analysis (PCA) and mixed-effects modeling. Cancer Research Magnetic Resonance Imaging Assessment of Carcinogen-induced Murine Bladder Tumors Alexander P. Glaser1, Daniele Procissi2, Yanni Yu3, Joshua J. Meeks3 1Department of Surgery, Division of Urology, NorthShore University HealthSystem, 2Department of Radiology, Northwestern University Feinberg School of Medicine, 3Department of Urology, Northwestern University Feinberg School of Medicine Murine bladder tumors are induced with the N-butyl-N-(4-hydroxybutyl) nitrosamine carcinogen (BBN). Bladder tumor generation is heterogeneous; therefore, an accurate assessment of tumor burden is needed before randomization to experimental treatment. Here we present a fast, reliable MRI protocol to assess tumor size and stage. Neuroscience Probing Nicotinic Acetylcholine Receptor Function in Mouse Brain Slices via Laser Flash Photolysis of Photoactivatable Nicotine Matthew C. Arvin1, David L. Wokosin2, Sambashiva Banala3, Luke D. Lavis3, Ryan M. Drenan1 1Department of Pharmacology, Northwestern University Feinberg School of Medicine, 2Department of Physiology, Northwestern University Feinberg School of Medicine, 3Janelia Research Campus, Howard Hughes Medical Institute This article presents a method for studying nicotinic acetylcholine receptors (nAChRs) in mouse brain slices by nicotine uncaging. When coupled with simultaneous patch clamp recording and 2-photon laser scanning microscopy, nicotine uncaging connects nicotinic receptor function with cellular morphology, providing a deeper understanding of cholinergic neurobiology. Cancer Research A Bioluminescent and Fluorescent Orthotopic Syngeneic Murine Model of Androgen-dependent and Castration-resistant Prostate Cancer Jonathan F. Anker1, Hanlin Mok1, Anum F. Naseem1, Praveen Thumbikat*1,3, Sarki A. Abdulkadir*1,2,3 1Department of Urology, Northwestern University Feinberg School of Medicine, 2The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 3Department of Pathology, Northwestern University Feinberg School of Medicine The goal of this protocol is to demonstrate the intra-prostatic injection of prostate cancer cells, with subsequent castration. Orthotopic pre-clinical models of androgen-dependent and castration-resistant prostate cancer are critical to study the disease in the context of a clinically relevant tumor microenvironment and an immunocompetent host. Biochemistry Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation Pan Liu1, Tomokazu Souma1, Andrew Zu-Sern Wei1, Xueying Xie3, Xunrong Luo2, Jing Jin1 1Division of Nephrology and Hypertension, and the Center for Kidney Research and Therapeutics at the Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, 2Surgery-Organ Transplantation, Northwestern University Feinberg School of Medicine, 3School of Biological Sciences and Medical Engineering, Southeast University Mismatches in human leukocyte antigen (HLA) sequences between organ donor and recipient pairs are the major cause of antibody-mediated rejection in organ transplantation. Here we present the use of custom antigen arrays that are based on individual donors' HLA sequences to probe anti-donor HLA alloantibodies in organ recipients. Bioengineering Quantification of Strain in a Porcine Model of Skin Expansion Using Multi-View Stereo and Isogeometric Kinematics Adrian Buganza Tepole1, Elbert E. Vaca2, Chad A. Purnell2, Michael Gart2, Jennifer McGrath2, Ellen Kuhl3, Arun K. Gosain2 1Mechanical Engineering, Purdue University, 2Division of Plastic Surgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, 3Mechanical Engineering, Bioengineering, Cardiothoracic Surgery, Stanford University This protocol uses multi-view stereo to generate three-dimensional (3D) models out of uncalibrated sequences of photographs, making it affordable and adjustable to a surgical setting. Strain maps between the 3D models are quantified with spline-based isogeometric kinematics, which facilitate representation of smooth surfaces over coarse meshes sharing the same parameterization. Biochemistry Method for Identifying Small Molecule Inhibitors of the Protein-protein Interaction Between HCN1 and TRIP8b Ye Han*1, Kyle A. Lyman*1, Matt Clutter2, Gary E. Schiltz3, Quratul-Ain Ismail1, Xiangying Cheng1, Chi-Hao Luan4, Dane M. Chetkovich1,5 1Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University, 2Center for Molecular Innovation and Drug Discovery, Northwestern University, 3Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 4High Throughput Analysis Laboratory, Department of Molecular Biosciences, Northwestern University, 5Department of Physiology, Feinberg School of Medicine, Northwestern University The interaction between HCN channels and their auxiliary subunit has been identified as a therapeutic target in Major Depressive Disorder. Here, a fluorescence polarization-based method for identifying small molecule inhibitors of this protein-protein interaction, is presented. Neuroscience Assessing Primary Neurogenesis in Xenopus Embryos Using Immunostaining Siwei Zhang*1,2, Jingjing Li*1,3, Robert Lea1, Enrique Amaya1 1The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, 2Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 3 This article presents a convenient and rapid method for visualizing different neuronal cell populations in the central nervous system of Xenopus embryos using immunofluorescent staining on sections. Chemistry Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates Ha Yong Song*1, Seong-Hoon Park*2, Hong-Jun Kang1, Athanassios Vassilopoulos1 1Laboratory for Molecular Cancer Biology, Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 2Department of Radiation Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University This protocol describes the required steps to execute in vitro and in vivo deacetylation assays in order to establish the role of proteins as specific deacetylation substrates for sirtuins and further study the role of reversible - lysine acetylation as a post-translational modification. Medicine Bioluminescence Imaging of an Immunocompetent Animal Model for Glioblastoma Aaron J. Clark1, Shayan Fakurnejad2, Quanhong Ma2, Rintaro Hashizume2,3 1Department of Neurological Surgery, University of California San Francisco, 2Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, 3Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine GL261 glioma cells provide a useful immunocompetent animal model of glioblastoma. The goals of this protocol are to demonstrate proper techniques for monitoring intracranial tumor growth using in vivo bioluminescence imaging, and to verify the utility of luciferase-modified GL261 cells for studying tumor immunology and immunotherapeutic approaches for treating glioblastoma. Medicine A Mouse Model for Laser-induced Choroidal Neovascularization Ronil S. Shah1, Brian T. Soetikno1, Michelle Lajko1, Amani A. Fawzi1 1Department of Ophthalmology, Northwestern University Feinberg School of Medicine Here, we present the mouse laser-induced choroidal neovascularization (CNV) protocol, an experimental model that re-creates the vascular hallmarks of neovascular age-related macular degeneration (AMD). Once mastered, it can reliably and effectively induce CNV as a model system to test various experimental measures. Biology Detection of Alternative Splicing During Epithelial-Mesenchymal Transition Huilin Huang*1, Yilin Xu*1, Chonghui Cheng1 1Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine Alternative splicing regulation has been shown to contribute to the epithelial-mesenchymal transition (EMT), an essential cellular program in various physiological and pathological processes. Here we describe a method utilizing an inducible EMT model for the detection of alternative splicing during EMT.