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The University of Texas MD Anderson Cancer Center

24 ARTICLES PUBLISHED IN JoVE

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Bioengineering

High-resolution Fiber-optic Microendoscopy for in situ Cellular Imaging
Mark Pierce 1, Dihua Yu 2, Rebecca Richards-Kortum 1
1Department of Bioengineering, Rice University, 2Department of Molecular and Cellular Oncology, The Univeristy of Texas M. D. Anderson Cancer Center

In many biological and clinical situations it is advantageous to study cellular processes as they evolve in their native microenvironment. Here we describe the assembly and use of a low-cost fiber-optic microscope which can provide real time imaging in cell culture, animal studies, and clinical patient studies.

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JoVE Journal

Local and Global Methods of Assessing Thermal Nociception in Drosophila Larvae
Abanti Chattopadhyay *1, A'Tondra V. Gilstrap *1,2, Michael J. Galko 1,3,4
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.

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Biology

Rapid Generation of Amyloid from Native Proteins In vitro
Stephanie M Dorta-Estremera 1, Jingjing Li 1, Wei Cao 1
1Department of Immunology, The University of Texas MD Anderson Cancer Center

Proteins can either adopt a native structure or misfold into insoluble amyloid. Conditions that favor the misfolding pathway lead to the formation of different types of amyloid fibrils. The methods described here allow rapid conversion of native proteins into amyloid in vitro.

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Immunology and Infection

Assessing the Development of Murine Plasmacytoid Dendritic Cells in Peyer's Patches Using Adoptive Transfer of Hematopoietic Progenitors
Haiyan S. Li 1, Stephanie S. Watowich 1,2
1Department of Immunology, The University of Texas MD Anderson Cancer Center, 2The University of Texas Graduate School of Biomedical Sciences

This protocol describes experimental procedures to assess the differentiation of plasmacytoid dendritic cells in Peyer’s patch from common dendritic cell progenitors, using techniques involving FACS-mediated cell isolation, hydrodynamic gene transfer, and flow analysis of immune subsets in Peyer’s patch.

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Bioengineering

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Uri Rozovski 1, Inbal Hazan-Halevy 2, George Calin 3, David Harris 4, Ping Li 4, Zhiming Liu 4, Michael J. Keating 4, Zeev Estrov 4
1Division of Hematology, Davidoff Cancer Center, Rabin Medical Center, 2The Center of Nanoscience and Nanotechnology, Tel Aviv University, 3Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 4Department of Leukemia, The University of Texas MD Anderson Cancer Center

Herein we propose a strategy to study the effect of a transcription factor of interest on the microRNA transcriptome using publically available data, computational resources and high throughput data from microRNA arrays after transfecting cells with small hairpin (sh)RNA targeting a transcription factor of interest.

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Neuroscience

Assessing Primary Neurogenesis in Xenopus Embryos Using Immunostaining
Siwei Zhang *1,2, Jingjing Li *1,3, Robert Lea 1, Enrique Amaya 1
1The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, 2Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 3Department of Craniofacial Development and Stem Cell Biology, Dental Institute, King's College London

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.

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Developmental Biology

Imaging Cleared Embryonic and Postnatal Hearts at Single-cell Resolution
Wasay M. Shaikh Qureshi 1, Lianjie Miao 1, David Shieh 1, Jingjing Li 1, Yangyang Lu 1, Saiyang Hu 1, Margarida Barroso 1, Joseph Mazurkiewicz 2, Mingfu Wu 1
1Department of Molecular and Cellular Physiology, Albany Medical College, 2Department of Neuroscience and Experimental Therapeutics, Albany Medical College

We describe a protocol to volumetrically image fluorescent protein labeled cells deep inside intact embryonic and postnatal hearts. Utilizing tissue-clearing methods in combination with whole mount staining, single fluorescent protein-labeled cells inside an embryonic or postnatal heart can be imaged clearly and accurately.

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Biology

Sample Preparation for Mass Cytometry Analysis
Ryan L. McCarthy 1, Aundrietta D. Duncan 1, Michelle C. Barton 1
1Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center

This article describes the collection and processing of samples for mass cytometry analysis.

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Cancer Research

Intracarotid Cancer Cell Injection to Produce Mouse Models of Brain Metastasis
Chenyu Zhang 1, Frank J. Lowery 1, Dihua Yu 1
1Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center

Brain metastasis has become an urgent unmet medical need as its incidence has increased while therapeutic options have remained palliative. Creating experimental animal models of brain metastasis via intracarotid arterial injection of cancer cells facilitates mechanistic studies of the disease biology and evaluation of novel intervention regimens.

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Neuroscience

Novel Assay for Cold Nociception in Drosophila Larvae
Heather N. Turner 1,2,5, Christian Landry 3, Michael J. Galko 1,2,4
1Department of Genetics, UT MD Anderson Cancer Center, 2Neuroscience Program, Graduate School of Biomedical Sciences at Houston, 3ProDev Engineering, 4Genes and Development Program, Graduate School of Biomedical Sciences at Houston, 5Section of Neurobiology, University of Southern California

Here we demonstrate a novel assay to study cold nociception in Drosophila larvae. This assay utilizes a custom-built Peltier probe capable of applying a focal noxious cold stimulus and results in quantifiable cold-specific behaviors. This technique will allow further cellular and molecular dissection of cold nociception.

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Genetics

Analysis of the c-KIT Ligand Promoter Using Chromatin Immunoprecipitation
Pingyu Zhang *1, Andres Rojas *1, Boris Blechacz 1
1Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center

DNA-protein interactions are essential for multiple biological processes. During the evaluation of cellular functions, the analysis of DNA-protein interactions is indispensable for understanding gene regulation. Chromatin immunoprecipitation (ChIP) is a powerful tool to analyze such interactions in vivo.

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Engineering

Guidelines and Experience Using Imaging Biomarker Explorer (IBEX) for Radiomics
Rachel B. Ger 1,2, Carlos E. Cardenas 1,2, Brian M. Anderson 1,2, Jinzhong Yang 1,2, Dennis S. Mackin 1, Lifei Zhang 1, Laurence E. Court 1,2,3
1Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 2UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, 3Department of Imaging Physics, The University of Texas MD Anderson Cancer Center

We describe IBEX, an open-source tool designed for medical imaging radiomics studies, and how to use this tool. In addition, some published works that have used IBEX for uncertainty analysis and model building are showcased.

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Medicine

Radiation Planning Assistant - A Streamlined, Fully Automated Radiotherapy Treatment Planning System
Laurence E. Court 1, Kelly Kisling 1, Rachel McCarroll 1, Lifei Zhang 1, Jinzhong Yang 1, Hannah Simonds 2, Monique du Toit 2, Chris Trauernicht 2, Hester Burger 3, Jeannette Parkes 3, Mike Mejia 4, Maureen Bojador 4, Peter Balter 1, Daniela Branco 1, Angela Steinmann 1, Garrett Baltz 1, Skylar Gay 1, Brian Anderson 1, Carlos Cardenas 1, Anuja Jhingran 5, Simona Shaitelman 5, Oliver Bogler 6, Kathleen Schmeller 7, David Followill 1, Rebecca Howell 1, Christopher Nelson 1, Christine Peterson 8, Beth Beadle 5,9
1Department of Radiation Physics, University of Texas MD Anderson Cancer Center, 2Department of Radiation Oncology, Stellenbosch University and Tygerberg Hospital, 3Departments of Radiation Oncology and Medical Physics, Groote Schuur Hospital and University of Cape Town, 4Department of Radiation Oncology, University of Santo Tomas Hospital, Benavides Cancer Institute, 5Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, 6Academic Affairs, University of Texas MD Anderson Cancer Center, 7Department of Gynecological Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, 8Department of Biostatistics, University of Texas MD Anderson Cancer Center, 9Department of Radiation Oncology, Stanford University

Radiation therapy is a highly complex cancer treatment that requires multiple specialists to create a treatment plan and provide quality assurance (QA) prior to delivery to a patient. This protocol describes the use of a fully automated system, the Radiation Planning Assistant (RPA), to create high-quality radiation treatment plans.

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JoVE Core

Applicability Analysis of Assessment Methods for Morphological Parameters of Corroded Steel Bars
Dawang Li 1,2, Ping Li 1,2, Yingang Du 3, Ren Wei 1,2
1Department of Civil Engineering, Shenzhen University, 2Guangdong Province Key Laboratory of Durability for Marine Civil Engineering, Shenzhen University, 3Department of Engineering and the Built Environment, Anglia Ruskin University

This paper measures the geometry and the amount of corrosion of a steel bar using different methods: mass loss, calipers, drainage measurements, 3D scanning, and X-ray micro-computed tomography (XCT).

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Immunology and Infection

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems
Yunfei Hu 1, Huahai Chen 1, Ping Li 2, Baiyuan Li 1, Linyan Cao 1, Changhui Zhao 1, Qing Gu 2, Yeshi Yin 1
1Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 2College of Food and Biological Engineering, Zhejiang Gongshang University

Described here is a protocol to investigate the interactions between endobiotics and human gut microbiota using in vitro batch fermentation systems.

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Cancer Research

Enhanced Viability for Ex vivo 3D Hydrogel Cultures of Patient-Derived Xenografts in a Perfused Microfluidic Platform
Lindsey K. Sablatura 1, Kristin M. Bircsak 2, Peter Shepherd 3, Karla Queiroz 4, Mary C. Farach-Carson 1,5,6, Pamela E. Constantinou 1,7, Anthony Saleh 2, Nora Navone 3, Daniel A. Harrington 1,5,6
1Department of BioSciences, Rice University, 2Mimetas US Inc, 3Department of Genitourinary Medical Oncology Research, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 4Mimetas B.V., 5Department of Bioengineering, Rice University, 6Department of Diagnostic and Biomedical Sciences, The University of Texas Health Science Center, 7Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center

This protocol demonstrates methods to enable extended in vitro culture of patient-derived xenografts (PDX). One step enhances overall viability of multicellular cluster cultures in 3D hydrogels, through straightforward removal of non-viable single cells. A secondary step demonstrates best practices for PDX culture in a perfused microfluidic platform.

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Immunology and Infection

Cigarette Smoke Exposure in Mice using a Whole-Body Inhalation System
Daniel E. Morales-Mantilla 1,2, Xinyan Huang 3,7, Philip Erice 1,3, Paul Porter 4, Yun Zhang 1,5, Mary Figueroa 6, Joya Chandra 6, Katherine Y. King 2, Farrah Kheradmand 4,8, Antony Rodríguez 3,8
1Program in Immunology, Baylor College of Medicine, 2Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine, 3Department of Medicine - Immunology Allergy and Rheumatology, Baylor College of Medicine, 4Department of Medicine, Pulmonary, Critical Care, Sleep Medicine, Baylor College of Medicine, 5Department of Pathology and Immunology, Baylor College of Medicine, 6Department of Pediatrics, Research and Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 7Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, 8Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center

This protocol demonstrates the study of the pathophysiologic effects of cigarette smoke (CS) with a whole-body inhalation (WBI) exposure system (WBIS) built in-house. This system can expose animals to CS under controlled repeatable conditions for research of CS-mediated effects on lung emphysema and hematopoiesis.

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Behavior

An Improved Assay and Tools for Measuring Mechanical Nociception in Drosophila Larvae
Roger Lopez-Bellido 1, Michael J. Galko 1,2,3
1Department of Genetics, The University of Texas MD Anderson Cancer Center, 2Neuroscience Graduate Program, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, 3Genetics and Epigenetics Graduate Program, Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center

The goal of this protocol is to show how to perform an improved assay for mechanical nociception in Drosophila larvae. We use the assay here to demonstrate that mechanical hypersensitivity (allodynia and hyperalgesia) exists in Drosophila larvae.

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Cancer Research

Modeling Brain Metastasis Via Tail-Vein Injection of Inflammatory Breast Cancer Cells
Xiaoding Hu *1,2, Emilly S. Villodre *1,2, Wendy A. Woodward 2,3, Bisrat G. Debeb 1,2
1Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 2Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, 3Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center

We describe a xenograft mouse model of breast cancer brain metastasis generated via tail-vein injection of an endogenously HER2-amplified inflammatory breast cancer cell line.

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Cancer Research

Expanding the Comprehension of the Tumor Microenvironment using Mass Spectrometry Imaging of Formalin-Fixed and Paraffin-Embedded Tissue Samples
Leticia Campos Clemente 1, Ou Shi 1, Frank Rojas 1, Edwin Roger Parra 1
1Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center

In the era of cancer immunotherapy, interest in elucidating tumor microenvironment dynamics has increased strikingly. This protocol details a mass spectrometry imaging technique with respect to its staining and imaging steps, which allow for highly multiplexed spatial analysis.

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Cancer Research

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
Saxon Rodriguez *1, Baohua Sun *1, Salome McAllen 1, Mei Jiang 1, Edwin Roger Parra 1
1Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center

Multiplexed barcoding image analysis has recently improved the characterization of the tumor microenvironment, permitting comprehensive studies of cell composition, functional state, and cell-cell interactions. Herein, we describe a staining and imaging protocol using the barcoding of oligonucleotide-conjugated antibodies and cycle imaging, which allows for the use of a high-dimensional image analysis technique.

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Medicine

Radiation Planning Assistant - A Web-based Tool to Support High-quality Radiotherapy in Clinics with Limited Resources
Laurence Edward Court 1, Ajay Aggarwal 2, Hester Burger 3, Carlos Cardenas 4, Christine Chung 1, Raphael Douglas 1, Monique du Toit 5, Anuja Jhingran 1, Raymond Mumme 1, Sikudhani Muya 6, Komeela Naidoo 5, Jerry Ndumbalo 6, Tucker Netherton 1, Callistus Nguyen 1, Adenike Olanrewaju 1, Jeannette Parkes 3, Willie Shaw 7, Christoph Trauernicht 5, Melody Xu 8, Jinzhong Yang 1, Lifei Zhang 1, Hannah Simonds 9, Beth M. Beadle 10
1The University of Texas MD Anderson Cancer Center, 2Guy’s and St. Thomas’ Hospital, 3Groote Schuur Hospital and University of Cape Town, 4University of Alabama at Birmingham, 5Tygerberg Hospital and Stellenbosch University, 6Ocean Road Cancer Institute, 7University of the Free State, 8University of California-San Francisco, 9University Hospitals Plymouth NHS Trust, 10Stanford University

This protocol describes a series of automated tools designed for high-quality radiotherapy autocontouring and autoplanning that are being packaged into a web-based service to maximize robustness and scalability while minimizing operational costs.

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Bioengineering

A Computational Modeling Approach to Investigate the Influence of Hyperthermia on the Tumor Microenvironment
Anna Bottiglieri 1, Rahul A. Sheth 2, Punit Prakash 1
1Department of Electrical and Computer Engineering, Kansas State University, 2Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center

The article describes a protocol to simulate the transient temperature profiles and the coupled spatiotemporal variation of the interstitial fluid pressure following the heating delivered by a dipolar radiofrequency hyperthermia system. The protocol can be used to assess the response of biophysical parameters characterizing the tumor microenvironment to interventional hyperthermia techniques.

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Cancer Research

Facilitating Repeat Intracarotid Injections in Mouse Models by a Novel Injection Site Repair Technique
Daniel Ledbetter 1, Joy Gumin 1, Lynette Phillips 1, Chibawanye Ene 1, Yuzaburo Shimizu 1,2, Frederick F. Lang 1
1Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, 2Department of Neurosurgery, Juntendo University

Repair of the intracarotid artery in a mouse model after injection returns blood flow to the artery without negatively impacting the distribution of the injected material. Injection site repair facilitates subsequent injections through the same artery and prevents cerebral ischemia in mouse strains that lack a complete Circle of Willis.

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