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University of Texas at Dallas

19 ARTICLES PUBLISHED IN JoVE

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Biology

Detection of Protein Interactions in Plant using a Gateway Compatible Bimolecular Fluorescence Complementation (BiFC) System
Gang Tian 1, Qing Lu 2, Li Zhang 2, Susanne E. Kohalmi 1, Yuhai Cui 2
1Department of Biology, University of Western Ontario, 2Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada

We have developed a technique to test protein-protein interactions in plant. A yellow fluorescent protein (YFP) is split into two non-overlapping fragments. Each fragment is cloned in-frame to a gene of interest via Gateway system, enabling expression of fusion proteins. Reconstitution of YFP signal only occurs when the inquest proteins interact.

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Medicine

Eye Tracking Young Children with Autism
Noah J. Sasson 1, Jed T. Elison 2
1School of Behavioral and Brain Sciences, University of Texas at Dallas, 2Carolina Institute for Developmental Disabilities, School of Medicine, University of North Carolina at Chapel Hill

Eye tracking has long been used to study gaze patterns in typically-developing individuals, but recent technological advancements have made its use with clinical populations, including autism, more feasible. While eye-tracking young children with autism can offer insight into early symptom manifestations, it involves methodological challenges. Suggestions for best practices are provided.

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Medicine

Staining Protocols for Human Pancreatic Islets
Martha L. Campbell-Thompson 1, Tiffany Heiple 1, Emily Montgomery 1, Li Zhang 1, Lynda Schneider 1
1Department of Pathology, Immunology, and Laboratory Medicine, University of Florida

This video demonstrates procedures for characterization of human pancreatic islets using hematoxylin and eosin (H&E) and immunohistochemistry (IHC). Pancreatic sections from head, body, and tail regions are stained by both H&E and IHC to determine islet endocrine composition (insulin, glucagon, and pancreatic polypeptide), cell replication (Ki67), and inflammatory infiltrates (H&E, CD3). The uncinate region is localized using IHC for pancreatic polypeptide.

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Biology

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
Haipeng Xing 1, Willey Liao 1,2, Yifan Mo 1,2, Michael Q. Zhang 2,3
1Department of Applied Mathematics & Statistics, Stony Brook University, 2Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory, 3Department of Molecular and Cell Biology, University of Texas at Dallas

Our Bayesian Change Point (BCP) algorithm builds on state-of-the-art advances in modeling change-points via Hidden Markov Models and applies them to chromatin immunoprecipitation sequencing (ChIPseq) data analysis. BCP performs well in both broad and punctate data types, but excels in accurately identifying robust, reproducible islands of diffuse histone enrichment.

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Biology

Measurement of Heme Synthesis Levels in Mammalian Cells
Jagmohan Hooda 1, Maksudul Alam 1, Li Zhang 1
1Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas

Altered intracellular heme levels are associated with common diseases such as cancer. Thus, there is a need to measure heme biosynthesis levels in diverse cells. The goal of this protocol is to provide a fast and sensitive method to measure and compare the levels of heme synthesis in different cells.

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Engineering

Atomically Traceable Nanostructure Fabrication
Josh B. Ballard 1, Don D. Dick 2, Stephen J. McDonnell 3, Maia Bischof 4, Joseph Fu 5, James H. G. Owen 1, William R. Owen 1, Justin D. Alexander 1, David L. Jaeger 4, Pradeep Namboodiri 5, Ehud Fuchs 1, Yves J. Chabal 3, Robert M. Wallace 3, Richard Reidy 4, Richard M. Silver 5, John N. Randall 1, James Von Ehr 1
1Zyvex Labs, 2Department of Physics, University of Texas at Dallas, 3Department of Materials Science and Engineering, University of Texas at Dallas, 4Materials Science and Engineering, University of North Texas, 5National Institute of Standards and Technology

We report a protocol for combining the atomic metrology of the Scanning Tunneling Microscope for surface patterning with selective Atomic Layer Deposition and Reactive Ion Etching. Using a robust process involving numerous atmospheric exposures and transport, 3D nanostructures with atomic metrology are fabricated.

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Chemistry

Self-assembling Morphologies Obtained from Helical Polycarbodiimide Copolymers and Their Triazole Derivatives
Oleg V. Kulikov 1, Dumindika A. Siriwardane 1, Gregory T. McCandless 1, Samsuddin F. Mahmood 1, Bruce M. Novak 1
1Department of Chemistry and Biochemistry, University of Texas at Dallas

Here, we present a protocol to prepare and visualize secondary structures (e.g., fibers, toroidal architectures, and nano-spheres) derived from helical polycarbodiimides. The morphology characterized by both atomic force microscopy (AFM) and scanning electron microscopy (SEM) was shown to depend on molecular structure, concentration, and the solvent of choice.

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Bioengineering

Making Conjugation-induced Fluorescent PEGylated Virus-like Particles by Dibromomaleimide-disulfide Chemistry
Zhuo Chen 1, Stacey T. Detvo 2, Elizabeth Pham 3, Jeremiah J. Gassensmith 4
1Department of Chemistry & Biochemistry, University of Texas at Dallas, 2Undergraduate Biology, University of Texas at Dallas, 3Undergraduate Healthcare Studies, University of Texas at Dallas, 4Departments of Chemistry & Biochemistry and Biomedical Engineering, University of Texas at Dallas

Here, we present a procedure to fluorescently functionalize the disulfides on Qβ VLP with dibromomaleimide. We describe Qβ expression and purification, the synthesis of dibromomaleimide-functionalized molecules, and the conjugation reaction between dibromomaleimide and Qβ. The resulting yellow fluorescent conjugated particle can be used as a fluorescence probe inside cells.

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Bioengineering

Environmental Dynamic Mechanical Analysis to Predict the Softening Behavior of Neural Implants
Seyed Mahmoud Hosseini 1, Walter E. Voit 1,2,3, Melanie Ecker 2,3,4
1Department of Chemistry and Biochemistry, University of Texas at Dallas, 2Department of Materials Science and Engineering, University of Texas at Dallas, 3Center for Engineering Innovation, University of Texas at Dallas, 4Department of Bioengineering, University of Texas at Dallas

To allow reliable predictions of the softening of polymeric substrates for neural implants in an in vivo environment, it is important to have a reliable in vitro method. Here, the use of dynamic mechanical analysis in phosphate buffered saline at body temperature is presented.

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Bioengineering

In Vivo Two-Color 2-Photon Imaging of Genetically-Tagged Reporter Cells in the Skin
Thomas A. Szabo-Pardi 1, Nilesh M. Agalave 1, Ashley T. Andrew 1, Michael D. Burton 1
1School of Brain and Behavioral Science, Center for Advanced Pain Studies, University of Texas at Dallas

Morphological changes occur in immune responsive fibroblast cells following activation and promote alterations in cellular recruitment. Utilizing 2-photon imaging in conjunction with a genetically engineered Fibroblast-specific protein 1 (FSP1)-cre; tdTomato floxed-stop-floxed (TB/TB) mouse line and green fluorescently tagged lipopolysaccharide-FITC, we can illustrate highly specific uptake of lipopolysaccharide in dermal fibroblasts and morphological changes in vivo.

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Immunology and Infection

High-Efficiency Generation of Antigen-Specific Primary Mouse Cytotoxic T Cells for Functional Testing in an Autoimmune Diabetes Model
Howard W. Davidson 1, Joseph Ray Cepeda 2, Nitin S. Sekhar 2, Junying Han 2, Ling Gao 3, Tomasz Sosinowski 1, Li Zhang 2
1Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, 2Department of Medicine, Endocrinology, Diabetes & Metabolism, Baylor College of Medicine, 3Scientific Center, Shandong Provincial Hospital affiliated to Shandong University

This article describes a protocol for the generation of antigen-specific CD8 T cells, and their expansion in vitro, with the aim of yielding high numbers of functional T cells for use in vitro and in vivo.

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Biology

Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization
Michael L. Neugent *1, Jashkaran Gadhvi *1, Kelli L. Palmer 1, Philippe E. Zimmern 2, Nicole J. De Nisco 1
1Department of Biological Sciences, University of Texas at Dallas, 2Department of Urology, University of Texas Southwestern Medical Center

This protocol is for the unbiased detection of tissue-associated bacteria in patient biopsies by 16S rRNA in situ hybridization and confocal microscopy.

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JoVE Core

International Expert Consensus and Recommendations for Neonatal Pneumothorax Ultrasound Diagnosis and Ultrasound-guided Thoracentesis Procedure
Jing Liu 1,2, Dalibor Kurepa 3, Francesco Feletti 4,5, Almudena Alonso-Ojembarrena 6, Jovan Lovrenski 7, Roberto Copetti 8, Erich Sorantin 9, Javier Rodriguez-Fanjul 10, Karishma Katti 3, Andrea Aliverti 4, Huayan Zhang 11,12, Misun Hwang 13, Tsu F. Yeh 14, Cai-Bao Hu 15, Xing Feng 16, Ru-Xin Qiu 1,2, Jing-Han Chi 17, Li-Li Shang 18, Guo-Rong Lyu 19, Shao-Zheng He 20, Yan-Fen Chai 21, Zhan-Jun Qiu 22, Hai-Ying Cao 2,23, Yue-Qiao Gao 1,2, Xiao-Ling Ren 1,2, Guo Guo 1,24, Li Zhang 1,2, Ying Liu 1,2, Wei Fu 1,2, Zu-Lin Lu 1,2, Hong-Lei Li 1,2
1Department of Neonatology and NICU, Beijing Chaoyang District Maternal and Child Healthcare Hospital, 2The National Neonatal Lung Ultrasound Training Base, 3Division of Neonatal-Perinatal Medicine, Cohen Children's Medical Center, 4Department of Electronics, Information and Bioengineering, Politecnico di Milano, 5Dipartimento di Diagnostica per Immagini, Ausl della Romagna, S. Maria delle Croci Hospital, 6Neonatal Intensive Care Unit, Puerta del Mar University Hospital, 7Faculty of Medicine, University of Novi Sad, Serbia, Institute for Children and Adolescents Health Care of Vojvodina, 8Emergency Department, University Hospital of Cattinara, 9Division of Pediatric Radiology, Department of Radiology, Medical University Graz, 10Pediatric Intensive Care Unit, Pediatric Service Hospital Joan XXIII Tarragona, University Rovira i Virgil, 11Center for Newborn Care, Guangzhou Women and Children's Medical Center, 12Division of Neonatology, Children's Hospital of Philadelphia, 13Section of Neonatal Imaging, Department of Radiology, Children's Hospital of Philadelphia, 14Maternal Child Health Research institute, Taipei Medical University and China Medical University, 15Intensive Care Unit, Zhejiang Hospital, 16Department of Neonatology, Children's Hospital of Soochow University, 17Department of Neonatology and NICU, Bayi Children's Hospital Affiliated to the Seventh Medical Center of Chinese PLA General Hospital, 18Intensive Care Unit, Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, 19Collaborative Innovation Center for Maternal and Infant Health Service Application Technology, Quanzhou Medical College, 20Department of Ultrasound, Second Affiliated Hospital of Fujian Medical University, 21Department of Emergency Medicine, Tianjin Medical University General Hospital, 22Department of Emergency and Critical Care Medicine, Affiliated Hospital of Traditional Chinese Medicine, 23Department of Ultrasound, GE Healthcare, 24The Neonatal Intensive Care Unit, Fifth Medical Center of Chinese PLA General Hospital

Pneumothorax is a common emergency and critical disease in newborn infants that needs rapid, clear diagnosis and timely treatment. Diagnosis and treatment based on chest X-rays are associated with delayed management and radiation damage. Lung ultrasound (US) provides useful guidance for rapid, accurate diagnosis and the precise thoracentesis of pneumothorax.

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Neuroscience

Preparation of Peripheral Nerve Stimulation Electrodes for Chronic Implantation in Rats
Camilo A. Sanchez 1, Jackson Brougher 2, Kim C. Rahebi 3, Catherine A. Thorn 2
1Department of Bioengineering, University of Texas at Dallas, 2School of Behavioral and Brain Sciences, University of Texas at Dallas, 3Texas Biomedical Device Center, University of Texas at Dallas

Existing approaches for constructing chronically implantable peripheral nerve cuff electrodes for use in small rodents often require specialized equipment and/or highly trained personnel. In this protocol we demonstrate a simple, low-cost approach for fabricating chronically implantable cuff electrodes, and demonstrate their effectiveness for vagus nerve stimulation (VNS) in rats.

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Biology

Isolation of Primary Rat Hepatocytes with Multiparameter Perfusion Control
Inn Chuan Ng *1, Li Zhang *2, Narelle Nichola Yi Ying Shen 3, Yun Ting Soong 4, Chan Way Ng 5, Phoebe Kang Sheing Koh 1, Yan Zhou 3, Hanry Yu 1,3,4,5,6
1Department of Physiology & The Institute for Digital Medicine (WisDM), National University of Singapore, 2College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, 3Mechanobiology Institute, National University of Singapore, 4Institute of Bioengineering and Nanotechnology, A*STAR, 5NUS Graduate School for Integrative Sciences and Engineering, 6CAMP, Singapore-MIT Alliance for Research and Technology

This protocol details the use of a special intravenous catheter, standardized sterile disposable tubing, temperature control complemented by real-time monitoring, and an alarm system for two-step collagenase perfusion procedure to improve the consistency in the viability, yield, and functionality of isolated primary rat hepatocytes.

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JoVE Journal

Genome-wide Analysis of Histone Modifications Distribution using the Chromatin Immunoprecipitation Sequencing Method in Magnaporthe oryzae
Zechi Wu *1, Wanyu Sun *1, Sida Zhou 1, Li Zhang 1, Xinyu Zhao 1, Yang Xu 1, Weixiang Wang 1
1Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Department of Agronomy, Beijing University of Agriculture

Here, we present a protocol to analyze the genome-wide distribution of histone modifications, which can identify new target genes in the pathogenesis of M. oryzae and other filamentous fungi.

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Behavior

Investigating Migraine-Like Behavior Using Light Aversion in Mice
Mengya Wang 1, Bianca N. Mason 2, Levi P. Sowers 3,4, Adisa Kuburas 4, Brandon J. Rea 3,4, Andrew F. Russo 3,4,5
1Department of Neuroscience and Pharmacology, University of Iowa, 2School of Behavioral and Brain Sciences, University of Texas at Dallas, 3Center for the Prevention and Treatment of Visual Loss, Veterans Administration Health Center, Iowa City, IA, 4Department of Molecular Physiology and Biophysics, University of Iowa, 5Department of Neurology, University of Iowa

Rodents are not able to report migraine symptoms. Here, we describe a manageable test paradigm (light/dark and open field assays) to measure light aversion, one of the most common and bothersome symptoms in patients with migraines.

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Neuroscience

Dural Stimulation and Periorbital von Frey Testing in Mice As a Preclinical Model of Headache
Bianca N. Mason 1, Amanda Avona 1, Jacob Lackovic 1, Gregory Dussor 1
1School of Brain and Behavioral Sciences and Center for Advanced Pain Studies, University of Texas at Dallas

The most notable symptom of migraine is severe head pain, and it is hypothesized that this is mediated by sensory neurons innervating the meninges. Here, we present a method to locally apply substances to the dura in a minimally invasive manner while using facial hypersensitivity as an output.

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Genetics

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Belle M. Sharon 1, Neha V. Hulyalkar 1, Vivian H. Nguyen 1, Philippe E. Zimmern 2, Kelli L. Palmer 1, Nicole J. De Nisco 1
1Department of Biological Sciences, University of Texas at Dallas, 2Department of Urology, University of Texas Southwestern Medical Center

This protocol details a comprehensive approach for the culturing, sequencing, and de novo hybrid genome assembly of urinary bacteria. It provides a reproducible procedure for the generation of complete, circular genome sequences useful in studying both chromosomal and extrachromosomal genetic elements contributing to urinary colonization, pathogenesis, and antimicrobial resistance dissemination.

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