Kansas State University 14 articles published in JoVE Neuroscience P300-Based Brain-Computer Interface Speller Performance Estimation with Classifier-Based Latency Estimation Nazmun N. Khan1, Taylor Sweet1, Chase A. Harvey1, Seth Warschausky2, Jane E. Huggins3,4, David E. Thompson1 1Brain and Body Sensing Lab, Mike Wiegers Department of Electrical & Computer Engineering, Kansas State University, 2Adaptive Cognitive Assessment Laboratory, Department of Physical Medicine and Rehabilitation, University of Michigan, Ann Arbor, 3Direct Brain Interface Laboratory, Department of Physical Medicine and Rehabilitation, University of Michigan, Ann Arbor, 4Direct Brain Interface Laboratory, Department of Biomedical Engineering, University of Michigan, Ann Arbor This article presents a method for estimating same-day P300 speller Brain-Computer Interface (BCI) accuracy using a small testing dataset. Genetics Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter Changkun Hu*1, Tyler Doerksen*2, Taylor Bugbee1, Nicholas A. Wallace1, Rachel Palinski2,3 1Division of Biology, Kansas State University, 2Kansas State Veterinary Diagnostic Laboratory, Kansas State University, 3Department of Diagnostic Medicine/Pathobiology, Kansas State University Presented here is sgRNA/CAS9 endonuclease and next-generation sequencing protocol that can be used to identify the mutations associated with double strand break repair near the CD4 promoter. Bioengineering Photodegradable Hydrogel Interfaces for Bacteria Screening, Selection, and Isolation Niloufar Fattahi1, Niloy Barua1, André J. van der Vlies2, Ryan R. Hansen1 1Tim Taylor Department of Chemical Engineering, Kansas State University, 2Department of Materials Science and Engineering, The Pennsylvania State University The use of photodegradable hydrogels to isolate bacterial cells by utilizing a high-resolution light pattering tool is reported. Essential experimental procedures, results, and advantages of the process are reviewed. The method enables rapid and inexpensive isolation of targeted bacteria showing rare or unique functions from heterogeneous communities or populations. Immunology and Infection Separation of Bioactive Small Molecules, Peptides from Natural Sources and Proteins from Microbes by Preparative Isoelectric Focusing (IEF) Method Raja Veerapandian1, Anuja Paudyal1, Adeline Chang1, Govindsamy Vediyappan1 1Division of Biology, Kansas State University The objective is to fractionate and isolate bioactive small molecules, peptides from a complex plant extract, and proteins from pathogenic microbes by employing liquid-phase isoelectric focusing (IEF) method. Further, the separated molecules were identified and their bioactivity confirmed. Developmental Biology Protein Extract Preparation and Co-immunoprecipitation from Caenorhabditis elegans Li Li1, Anna Y. Zinovyeva1 1Division of Biology, Kansas State University This method describes a protocol for high-throughput protein extract preparation from Caenorhabditis elegans samples and subsequent co-immunoprecipitation. Behavior Noninvasive, In-pen Approach Test for Laboratory-housed Pigs Lindsey E. Hulbert1, Eduarda M. Bortoluzzi1, Yunzhi Luo1, Jared M. Mumm1, Morgan J. Coffin1, Gina Y. Becker2, Pamela J. Vandevord3, Elizabeth M. McNeil3, Tim Walilko4, Zin Z. Khaing5,6, Laila Zai4,5 1Animal Sciences and Industry, Kansas State University, 2DynaSim Technical Services, INC, 3Center for Injury Biomechanics, Virginia Polytechnic Institute and State University, 4Applied Research Associates, Inc., 5Lucent Research, LLC, 6Department of Neurological Surgery, University of Washington This protocol describes a new behavioral test—the human approach test in the pigs' home pen—to detect functional deficits in laboratory pigs after subconcussive traumatic brain injury. Immunology and Infection In Vitro Transcribed RNA-based Luciferase Reporter Assay to Study Translation Regulation in Poxvirus-infected Cells Pragyesh Dhungel1, Fernando Cantu1, Candy Hernandez1, Zhilong Yang1 1Division of Biology, Kansas State University We present a protocol to study mRNA translation regulation in poxvirus-infected cells using in vitro Transcribed RNA-based luciferase reporter assay. The assay can be used for studying translation regulation by cis-elements of an mRNA, including 5’-untranslated region (UTR) and 3’-UTR. Different translation initiation modes can also be examined using this method. Immunology and Infection Quantification of Antibody-dependent Enhancement of the Zika Virus in Primary Human Cells Sultan Asad1,2, Fabiana Feitosa-Suntheimer1,2, Alexander Gold1,2, Berlin Londono-Renteria2, Tonya M. Colpitts1,2 1Department of Microbiology, Boston University School of Medicine, 2National Emerging Infectious Diseases Laborator, Boston University School of Medicine, 3Department of Entomology, Kansas State University We describe a method to evaluate the effect of pre-existing immunity against dengue virus on the Zika virus infection by using human serum, primary human cells, and infection quantification by quantitative real-time polymerase chain reaction. Chemistry An Experimental Protocol for Femtosecond NIR/UV - XUV Pump-Probe Experiments with Free-Electron Lasers Daniel Rolles1, Rebecca Boll2,3, Benjamin Erk2, Dimitrios Rompotis2, Bastian Manschwetus2 1J.R. Macdonald Laboratory, Department of Physics, Kansas State University, 2Deutsches Elektronen-Synchrotron DESY, 3European XFEL GmbH This protocol describes the key steps for performing and analyzing pump-probe experiments combining a femtosecond optical laser with a free-electron laser in order to study ultrafast photochemical reactions in gas-phase molecules. Biology A Versatile Model of Hard Tick Infestation on Laboratory Rabbits Consuelo Almazán1, Sarah Bonnet1, Martine Cote1, Mirko Slovák2, Yoonseong Park3, Ladislav Šimo1 1Unité Mixte de Recherche (UMR) Biologie moléculaire et immunologie parasitaires (BIPAR), Institut national de la recherche agronomique (INRA), Ecole Nationale Vétérinaire d'Alfort, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris-Est, 2Institute of Zoology, Slovak Academy of Sciences, 3Department of Entomology, Kansas State University We have developed a simple and versatile system to feed hard ticks on laboratory rabbits. Our non-laborious protocol uses easily accessible materials and can be adjusted depending on the requirements of the various experimental settings. The method allows comfortable monitoring and/or sampling of ticks during the entire feeding period. Engineering Fabricating Reactive Surfaces with Brush-like and Crosslinked Films of Azlactone-Functionalized Block Co-Polymers Mohammadali Masigol1, Niloy Barua1, Bradley S. Lokitz2, Ryan R. Hansen1 1Chemical Engineering Department, Kansas State University, 2Center for Nanophase Materials Sciences, Oak Ridge National Laboratory Surface fabrication methods for patterned deposition of nanometer thick brushes or micron thick, crosslinked films of an azlactone block co-polymer are reported. Critical experimental steps, representative results, and limitations of each method are discussed. These methods are useful for creating functional interfaces with tailored physical features and tunable surface reactivity. Cancer Research Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy Vaibhav Murthy*1, Dalton Dacus*1, Monica Gamez2, Changkun Hu1, Sebastian O. Wendel1, Jazmine Snow1, Andrew Kahn1, Stephen H. Walterhouse1, Nicholas A. Wallace1 1Division of Biology, Kansas State University, 2Bristol Medical School, Translational Health Sciences, University of Bristol Repair of double-strand DNA breaks is a dynamic process, requiring not only formation of repair complexes at the breaks, but also their resolution after the lesion is addressed. Here, we use immunofluorescence microscopy for transient and long-lasting double-stranded breaks as a tool to dissect this genome maintenance mechanism. Biology RNAi Trigger Delivery into Anopheles gambiae Pupae Kimberly Regna1, Rachel M. Harrison1, Shannon A. Heyse1, Thomas C. Chiles1, Kristin Michel2, Marc A. T. Muskavitch1,3 1Biology Department, Boston College, 2Division of Biology, Kansas State University, 3Discovery Research, Biogen RNA interference (RNAi) is an extremely valuable tool for uncovering gene function. However, the ability to target genes using RNAi during pre-adult stages is limited in the major human malaria vector Anopheles gambiae. We describe an RNAi protocol to reduce gene function via direct injection during pupal development. Biology Chitosan/Interfering RNA Nanoparticle Mediated Gene Silencing in Disease Vector Mosquito Larvae Xin Zhang*1, Keshava Mysore*2,3, Ellen Flannery3,4, Kristin Michel1, David W. Severson3,4, Kun Yan Zhu5, Molly Duman-Scheel2,3,4 1Division of Biology, Kansas State University, 2Department of Medical and Molecular Genetics, Indiana University School of Medicine, 3Eck Institute for Global Health, University of Notre Dame, 4Department of Biological Sciences, University of Notre Dame, 5Department of Entomology, Kansas State University Here we describe a procedure for inhibiting gene function in disease vector mosquitoes through the use of chitosan/interfering RNA nanoparticles that are ingested by larvae.
