University of Houston View Institution's Website 27 articles published in JoVE Medicine An Epithelial Abrasion Model for Studying Corneal Wound Healing Prince K. Akowuah1, Angie De La Cruz1, C. Wayne Smith2, Rolando E. Rumbaut2,3, Alan R. Burns1,2 1College of Optometry, University of Houston, 2Children’s Nutrition Research Center, Baylor College of Medicine, 3Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center Here, a protocol for creating a central corneal epithelial abrasion wound in the mouse using a trephine and a blunt golf club spud is described. This corneal wound healing model is highly reproducible and is now being used to evaluate compromised corneal wound healing in the context of diseases. Biochemistry Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis Yuhong Wang1 1Department of Biology and Biochemistry, University of Houston Single molecule fluorescence energy transfer is a method that tracks the tRNA dynamics during ribosomal protein synthesis. By tracking individual ribosomes, inhomogeneous populations are identified, which shed light on mechanisms. This method can be used to track biological conformational changes in general to reveal dynamic-function relationships in many other complexed biosystems. Single molecule methods can observe non-rate limiting steps and low-populated key intermediates, which are not accessible by conventional ensemble methods due to the average effect. Biology Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples Justin A. Courson1, Paul T. Landry1, Thao Do1, Eric Spehlmann2, Pascal J. Lafontant2, Nimesh Patel1, Rolando E. Rumbaut3,4, Alan R. Burns1,4 1College of Optometry, University of Houston, 2Department of Biology, DePauw University, 3Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center, 4Children’s Nutrition Center, Baylor College of Medicine This protocol outlines a routine method for using serial block-face scanning electron microscopy (SBF-SEM), a powerful 3D imaging technique. Successful application of SBF-SEM hinges on proper fixation and tissue staining techniques, as well as careful consideration of imaging settings. This protocol contains practical considerations for the entirety of this process. Immunology and Infection High-throughput Screening of Chemical Compounds to Elucidate Their Effects on Bacterial Persistence Prashant Karki1, Mehmet A. Orman1 1Department of Chemical and Biomolecular Engineering, University of Houston In this method paper, we present a high-throughput screening strategy to identify chemical compounds, such as osmolytes, that have a significant impact on bacterial persistence. Environment Ammonia Fiber Expansion (AFEX) Pretreatment of Lignocellulosic Biomass Shishir P. S. Chundawat1, Ramendra K. Pal1, Chao Zhao1, Timothy Campbell2, Farzaneh Teymouri2, Josh Videto2, Chandra Nielson2, Bradley Wieferich3, Leonardo Sousa3, Bruce E. Dale3, Venkatesh Balan4, Sarvada Chipkar5, Jacob Aguado5, Emily Burke5, Rebecca G. Ong5 1Department of Chemical and Biochemical Engineering, Rutgers-State University of New Jersey, 2Michigan Biotechnology Institute (MBI), 3Department of Chemical Engineering and Materials Science, Michigan State University, 4Engineering Technology Department, Biotechnology Program, College of Technology, University of Houston, 5Department of Chemical Engineering, Michigan Technological University Ammonia fiber expansion (AFEX) is a thermochemical pretreatment technology that can convert lignocellulosic biomass (e.g., corn stover, rice straw, and sugarcane bagasse) into a highly digestible feedstock for both biofuels and animal feed applications. Here, we describe a laboratory-scale method for conducting AFEX pretreatment on lignocellulosic biomass. Engineering Evaluation of an Exclusive Spur Dike U-Turn Design with Radar-Collected Data and Simulation Yang Shao1, Hongtao Yu1, Huan Wu2, Xueyan Han1, Xizhen Zhou1, Christian G. Claudel3, Hualing Zhang4, Chen Yang5 1 This protocol describes the process of solving a microscopic traffic problem with simulation. The whole process contains a detailed description of data collection, data analysis, simulation model build, simulation calibration, and sensitive analysis. Modifications and troubleshooting of the method are also discussed. Developmental Biology A Layered Mounting Method for Extended Time-Lapse Confocal Microscopy of Whole Zebrafish Embryos Sanat Upadhyay1, Leoncio Vergara2, Pranjali Shah2, Jan-Åke Gustafsson3,4, Ioannis Kakadiaris1,4, Maria Bondesson5 1Computational Biomedicine Lab, Texas Institute of Measurement Evaluation and Statistics, University of Houston, 2Institute of Biosciences and Technology, Texas A&M Health Science Center, 3Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, 4Department of Biosciences and Nutrition, Novum, Karolinska Institutet, 5Department of Intelligent Systems Engineering, Indiana University This article describes a method to mount fragile zebrafish embryos for extended time-lapse confocal microscopy. This low-cost method is easy to perform using regular glass-bottom microscopy dishes for imaging on any inverted microscope. The mounting is performed in layers of agarose at different concentrations. Biochemistry Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation Emily A. Brown1,2, Steven C. Neier3,4, Claudia Neuhauser5, Adam G. Schrum6,7,8, Stephen E.P. Smith1,2,9 1 Quantitative Multiplex Immunoprecipitation (QMI) uses flow cytometry for sensitive detection of differences in the abundance of targeted protein-protein interactions between two samples. QMI can be performed using a small amount of biomaterial, does not require genetically engineered tags, and can be adapted for any previously defined protein interaction network. Biochemistry Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution Heng Yin1, Shoujun Xu1, Yuhong Wang2 1Department of Chemistry, University of Houston, 2Department of Biology and Biochemistry, University of Houston Dual DNA ruler assay is developed to determine the mRNA position during ribosome translocation, which relies on the dissociation forces of the formed DNA-mRNA duplexes. With single-nucleotide resolution and capability of reaching both ends of mRNA, it can provide mechanistic insights for ribosome translocation and probe other nucleic acid displacements. Biology Concurrent EEG and Functional MRI Recording and Integration Analysis for Dynamic Cortical Activity Imaging Thinh Nguyen*1, Thomas Potter*1, Christof Karmonik2, Robert Grossman2, Yingchun Zhang1,3 1Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, 2Department of Neurosurgery, Houston Methodist Hospital and Research Institute, 3Guangdong Provincial Work Injury Rehabilitation Center An EEG-fMRI multimodal imaging method, known as the spatiotemporal fMRI-constrained EEG source imaging method, is described here. The presented method employs conditionally-active fMRI sub-maps, or priors, to guide EEG source localization in a manner that improves spatial specificity and limits erroneous results. Immunology and Infection A Protocol to Characterize the Morphological Changes of Clostridium difficile in Response to Antibiotic Treatment Bradley Endres1, Eugénie Bassères1, Tasnuva Rashid1, Long Chang2, M. Jahangir Alam1, Kevin W Garey1 1Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, 2Department of Electrical and Computer Engineering, University of Houston Antibiotic efficacy is most commonly determined by conducting killing kinetic studies and measuring colony forming units (CFUs). By integrating scanning electron microscopy (SEM) with these standard methods, we can distinguish the pharmacological effects of treatment between different antibiotics. Bioengineering Image-guided, Laser-based Fabrication of Vascular-derived Microfluidic Networks Keely A. Heintz1, David Mayerich2, John H. Slater1,3 1Department of Biomedical Engineering, University of Delaware, 2Department of Electrical and Computer Engineering, University of Houston, 3Delaware Biotechnology Institute This protocol outlines the implementation of image-guided, laser-based hydrogel degradation to fabricate vascular-derived, biomimetic microfluidic networks embedded in poly(ethylene glycol) diacrylate (PEGDA) hydrogels. These biomimetic microfluidic systems may be useful for tissue engineering applications, generation of in vitro disease models, and fabrication of advanced "on-a-chip" devices. Neuroscience A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains Antonio J. Tito1, Shebna Cheema2, Mian Jiang2, Sheng Zhang1,3 1Center for Metabolic and Degenerative Diseases, The Brown Foundation Institute of Molecular Medicine, Programs in Human and Molecular Genetics and Neuroscience, The Graduate School of Biomedical Sciences at Houston, The University of Texas Health Science Center at Houston, 2Department of Natural Sciences, University of Houston - Downtown, 3Department of Neurobiology and Anatomy, McGovern Medical School, The University of Texas Health Science Center at Houston The adult Drosophila brain is a valuable system for studying neuronal circuitry, higher brain functions, and complex disorders. An efficient method to dissect whole brain tissue from the small fly head will facilitate brain-based studies. Here we describe a simple, one-step dissection protocol of adult brains with well-preserved morphology. Medicine Modeling Myotonic Dystrophy 1 in C2C12 Myoblast Cells Rui Liang*1, Wei Dong*1,3, Xiaopeng Shen1, Xiaoping Peng1,3, Angie G. Aceves1,2, Yu Liu1 1Department of Biology and Biochemistry, University of Houston, 2Department of Economics, University of Houston, 3Department of Cardiology, The First Affiliated Hospital of Nanchang University In this protocol, we present the procedures in establishing myotonic dystrophy 1 myoblast models, including optimized C2C12 cell maintenance, gene transfection/transduction, and myocyte differentiation. Chemistry Facile Preparation of 4-Substituted Quinazoline Derivatives Daniel Z. Wang1, Lesong Yan2, Lingmei Ma1 1School of Science and Computer Engineering, University of Houston-Clear Lake, 2Airgas Specialty Gas, Airgas USA LLC A protocol for facile preparation of 4-substituted quinazoline derivatives from 2-aminobenzophenones, thiourea and dimethyl sulfoxide is presented. Behavior A Novel Experimental and Analytical Approach to the Multimodal Neural Decoding of Intent During Social Interaction in Freely-behaving Human Infants Jesus G. Cruz-Garza1, Zachery R. Hernandez1, Teresa Tse1,2,3, Eunice Caducoy1,3, Berdakh Abibullaev1, Jose L. Contreras-Vidal1,2 1Laboratory for Noninvasive Brain-Machine Interface Systems, Department of Electrical and Computer Engineering, University of Houston, 2Department of Biomedical Engineering, University of Houston, 3Department of Biology and Biochemistry, University of Houston This protocol presents a novel methodology for the neural decoding of intent from freely-behaving infants during unscripted social interaction with an actor. Neural activity is acquired using non-invasive high-density active scalp electroencephalography (EEG). Kinematic data is collected with inertial measurement units and supplemented with synchronized video recording. Chemistry Confocal Imaging of Confined Quiescent and Flowing Colloid-polymer Mixtures Rahul Pandey*1, Melissa Spannuth*1, Jacinta C. Conrad1 1Chemical and Biomolecular Engineering Department, University of Houston Confocal microscopy is used to image quiescent and flowing colloid-polymer mixtures, which are studied as model systems for attractive suspensions. Image analysis algorithms are used to calculate structural and dynamic metrics for the colloidal particles that measure changes due to geometric confinement. Neuroscience The FlyBar: Administering Alcohol to Flies Kim van der Linde1, Emiliano Fumagalli2, Gregg Roman2, Lisa C. Lyons1 1Department of Biological Science, Florida State University, 2Department of Biology and Biochemistry, Biology of Behavior Institute, University of Houston Drosophila has emerged as a significant model system for dissecting the cellular and molecular underpinnings of behavioral responses to alcohol. Here we present a protocol for the collection of alcohol sensitivity data in a circadian context that can be easily applied to other experiments and is well-suited for undergraduate research. Environment Tracking Microbial Contamination in Retail Environments Using Fluorescent Powder - A Retail Delicatessen Environment Example Sujata A. Sirsat1, Kawon Kim1, Kristen E. Gibson2, Phillip G. Crandall2, Steven C. Ricke2, Jack A. Neal1 1Conrad N. Hilton College of Hotel and Restaurant Management, University of Houston, 2Center for Food Safety, Department of Food Science, University of Arkansas The overall goal of this study was to demonstrate the potential cross contamination mechanism of foodborne pathogen Listeria monocytogenes in a retail deli setting. This methodology may be applied to a variety of different environments to track pathogen contamination. Medicine Profiling of Estrogen-regulated MicroRNAs in Breast Cancer Cells Anne Katchy1, Cecilia Williams1 1Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston Molecular signaling through both estrogen and microRNAs are critical in breast cancer development and growth. Estrogen activates the estrogen receptors, which are transcription factors. Many transcription factors can regulate the expression of microRNAs, and estrogen-regulated microRNAs can be profiled using different large-scale techniques. Chemistry Qualitative Identification of Carboxylic Acids, Boronic Acids, and Amines Using Cruciform Fluorophores Thimon Schwaebel1, Rio Carlo Lirag2, Evan A. Davey1, Jaebum Lim2, Uwe H. F. Bunz1, Ognjen Š. Miljanić2 1Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, 2Department of Chemistry, University of Houston Cross-conjugated cruciform fluorophores based on 1,4-distyryl-2,5-bis(arylethynyl)benzene and benzobisoxazole nuclei can be used to qualitatively identify diverse Lewis acidic and Lewis basic analytes. This method relies on the differences in emission colors of the cruciforms that are observed upon analyte addition. Structurally closely related species can be distinguished from each other. Behavior Simultaneous Scalp Electroencephalography (EEG), Electromyography (EMG), and Whole-body Segmental Inertial Recording for Multi-modal Neural Decoding Thomas C. Bulea1,2, Atilla Kilicarslan2, Recep Ozdemir2,3,4, William H. Paloski3,4, Jose L. Contreras-Vidal2,4,5 1Functional and Applied Biomechanics Group, National Institutes of Health, 2Laboratory for Non-invasive Brain-Machine Interface Systems, Department of Electrical and Computer Engineering, University of Houston, 3Department of Health and Human Performance, University of Houston, 4Center for Neuromotor & Biomechanics Research, University of Houston, 5Department of Biomedical Engineering, University of Houston Development of an effective brain-machine-interface (BMI) system for restoration and rehabilitation of bipedal locomotion requires accurate decoding of user's intent. Here we present a novel experimental protocol and data collection technique for simultaneous non-invasive acquisition of neural activity, muscle activity, and whole-body kinematics during various locomotion tasks and conditions. Immunology and Infection Quantitative High-throughput Single-cell Cytotoxicity Assay For T Cells Ivan Liadi1, Jason Roszik2, Gabrielle Romain1, Laurence J.N. Cooper2, Navin Varadarajan1 1Department of Chemical and Biomolecular Engineering, University of Houston, 2Division of Pediatrics, Research Unit 907, University of Texas MD Anderson Cancer Center We describe a single-cell high-throughput assay to measure cytotoxicity of T cells when incubated with tumor target cells. This method employs a dense, elastomeric array of sub-nanoliter wells (~100,000 wells/array) to spatially confine the T cells and target cells at defined ratios and is coupled to fluorescence microscopy to monitor effector-target conjugation and subsequent apoptosis. Neuroscience Local and Global Methods of Assessing Thermal Nociception in Drosophila Larvae Abanti Chattopadhyay*1, A'Tondra V. Gilstrap*1,2, Michael J. Galko1,3,4 1Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, 2Scholars Academy/MARC Scholar, University of Houston-Downtown, 3Genes and Development Graduate Program, University of Texas Graduate School of Biomedical Sciences, 4Neuroscience Graduate Program, University of Texas Graduate School of Biomedical Sciences In this article, we demonstrate assays to study thermal nociception in Drosophila larvae. One assay involves spatially-restricted (local) stimulation of thermal nociceptors1,2 while the second involves a wholesale (global) activation of most or all such neurons3. Together, these techniques allow visualization and quantification of the behavioral functions of Drosophila nociceptive sensory neurons. Biology Experimental Manipulation of Body Size to Estimate Morphological Scaling Relationships in Drosophila R. Craig Stillwell1, Ian Dworkin2, Alexander W. Shingleton2, W. Anthony Frankino1 1Department of Biology & Biochemistry, University of Houston, 2Department of Zoology, Michigan State University Morphological scaling relationships capture and describe organismal shape. We present a method to measure morphological scaling relationships across the natural range of body sizes in fully metamorphic insects. Using a simple diet manipulation we increase the distribution of trait sizes, permitting the accurate description of how shape and size co-vary. Immunology and Infection Finger-stick Blood Sampling Methodology for the Determination of Exercise-induced Lymphocyte Apoptosis James Navalta1, Brian McFarlin*2, Richard Simpson2, Elizabeth Fedor1, Holly Kell1, Scott Lyons1, Scott Arnett1, Mark Schafer1 1Department of Kinesiology, Recreation, and Sport, Western Kentucky University, 2Department of Health and Human Performance, University of Houston Exercise is capable of inducing apoptosis in immune cells. There are various measurement limitations, particularly relating to the amount of time required to isolate and treat a blood sample prior to the assessment. Demonstrated is a rapid and minimally invasive procedure for the analysis of exercise-induced lymphocyte apoptosis. Medicine Acute Myocardial Infarction in Rats Yewen Wu1, Xing Yin2, Cori Wijaya2, Ming-He Huang1, Bradley K. McConnell2 1Department of Internal Medicine, Division of Cardiology, University of Texas Medical Branch, 2Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston (UH), Texas Medical Center The rat model of acute myocardial infarction (AMI) is useful to study the consequence of a MI on cardiac pathophysiological and physiological function.