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Boston University School of Medicine

26 ARTICLES PUBLISHED IN JoVE

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Neuroscience

A Novel Approach for Documenting Phosphenes Induced by Transcranial Magnetic Stimulation
Seth Elkin-Frankston 1, Peter J. Fried 1, Alvaro Pascual-Leone 2, R. J. Rushmore III 1, Antoni Valero-Cabré 1,3
1Department of Anatomy and Neurobiology, Boston University School of Medicine, 2Department of Neurology, Beth Israel Deaconess Med Center, 3Centre de Recherche de l'institut du Cerveau et la Moelle Epinière (CRICM), Centre National de la Recherche Scientifique (CNRS)

Phosphenes are transient percepts of light that can be induced by applying Transcranial Magnetic Stimulation (TMS) to visually sensitive regions of cortex. We demonstrate a standard protocol for determining the phosphene threshold value and introduce a novel method for quantifying and analyzing perceived phosphenes.

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Bioengineering

Biomolecular Detection employing the Interferometric Reflectance Imaging Sensor (IRIS)
Carlos A. Lopez 1, George G. Daaboul 2, Sunmin Ahn 2, Alexander P. Reddington 1, Margo R. Monroe 2, Xirui Zhang 2, Rostem J. Irani 3, Chunxiao Yu 4,5, Caroline A. Genco 4,5, Marina Cretich 6, Marcella Chiari 6, Bennett B. Goldberg 1, John H. Connor 5, M. Selim Ünlü 1,2
1Department of Electrical and Computer Engineering, Boston University , 2Department of Biomedical Engineering, Boston University , 3Center for Advanced Genomics Technology, Boston University , 4Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, 5Department of Microbiology, Boston University School of Medicine, 6CNR (National Research Council), Istituto di Chimica del Riconoscimento Molecolare

Quantitative, high-throughput, real-time, and label-free biomolecular detection (DNA, protein, etc.) on SiO2 surfaces can be achieved using a simple interferometric technique which relies on LED illumination, minimal optical components, and a camera. The Interferometric Reflectance Imaging Sensor (IRIS) is inexpensive, simple to use, and amenable to microarray formats.

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Biology

Generation of Human Induced Pluripotent Stem Cells from Peripheral Blood Using the STEMCCA Lentiviral Vector
Andreia Gianotti Sommer 1, Sarah S. Rozelle 1, Spencer Sullivan 2, Jason A. Mills 3, Seon-Mi Park 1, Brenden W. Smith 1, Amulya M. Iyer 1, Deborah L. French 3, Darrell N. Kotton 1, Paul Gadue 3, George J. Murphy 1, Gustavo Mostoslavsky 1
1Center for Regenerative Medicine (CReM), Boston University School of Medicine, 2Department of Hematology, Children's Hospital of Philadelphia, 3Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia

Here we show a simple and effective protocol for the generation of human iPSCs from 3-4 ml of peripheral blood using a single lentiviral reprogramming vector. Reprogramming of readily available blood cells promises to accelerate the utilization of iPSC technology by making it accessible to a broader research community.

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Advanced Biology

Phage Transduction: A Method to Transfer Ampicillin Resistance from Donor to Recipient E. coli
Alexander Gold 1, Tonya M Colpitts 1
1Department of Microbiology, Boston University School of Medicine & National Emerging Infections Diseases Laboratories

Phage Transduction: A Method to Transfer Ampicillin Resistance from Donor to Recipient E. coli

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Medicine

Utilizing Repetitive Transcranial Magnetic Stimulation to Improve Language Function in Stroke Patients with Chronic Non-fluent Aphasia
Gabriella Garcia 1,2, Catherine Norise 1,2, Olufunsho Faseyitan 1,2, Margaret A. Naeser 3,4,5, Roy H. Hamilton 1,2
1Department of Neurology, Perelman School of Medicine, University of Pennsylvania , 2Center for Cognitive Neuroscience, University of Pennsylvania , 3Veterans Affairs Boston Healthcare System, 4Harold Goodglass Aphasia Research Center, Boston University School of Medicine, 5Department of Neurology, Boston University School of Medicine

We explore the use of repetitive transcranial magnetic stimulation (rTMS) to improve language abilities in patients with chronic stroke and non-fluent aphasia. After identifying a site in the right frontal gyrus for each patient that responds optimally to stimulation, we target this site during ten days of rTMS treatment.

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Neuroscience

In vivo Neuronal Calcium Imaging in C. elegans
Samuel H. Chung *1,2, Lin Sun *1,2, Christopher V. Gabel 1,2
1Department of Physiology and Biophysics, Boston University School of Medicine, 2Boston University Photonics Center

With its small transparent body, well-documented neuroanatomy and a host of amenable genetic techniques and reagents, C. elegans makes an ideal model organism for in vivo neuronal imaging using relatively simple, low-cost techniques. Here we describe single neuron imaging within intact adult animals using genetically encoded fluorescent calcium indicators.

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Immunology and Infection

Vaccinia Reporter Viruses for Quantifying Viral Function at All Stages of Gene Expression
Daniel K. Rozelle 1, Claire Marie Filone 1, Ken Dower 1, John H. Connor 1
1Department of Microbiology, Boston University School of Medicine

We describe the usage of a fluorescent reporter vaccinia virus that enables real-time measurement of viral infectivity and gene expression through the stage-specific expression of spectrally distinct reporter fluorophores. We detail a plate-based method for accurately identifying the stage at which virus replication is affected in response to small molecule inhibition.

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Immunology and Infection

A Mouse Model for Pathogen-induced Chronic Inflammation at Local and Systemic Sites
George Papadopoulos *1, Carolyn D. Kramer *1, Connie S. Slocum 1, Ellen O. Weinberg 1, Ning Hua 2, Cynthia V. Gudino 1, James A. Hamilton 1, Caroline A. Genco 1
1Department of Medicine, Section of Infectious Disease, Boston University School of Medicine, 2Department of Biophysics, Boston University School of Medicine

Animal models have proven to be invaluable tools in defining host and pathogen specific mechanisms that contribute to the development of chronic inflammation. Here we describe a mouse model of oral infection with the human pathogen Porphyromonas gingivalis and detail methodologies to assess the progression of inflammation at local and systemic sites.

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Genetics

Single Molecule Analysis of Laser Localized Psoralen Adducts
Jing Huang 1, Himabindu Gali 1, Julia Gichimu 1, Marina A. Bellani 1, Durga Pokharel 1, Manikandan Paramasivam 1, Michael M. Seidman 1
1Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health

Lasers are frequently used in studies of the cellular response to DNA damage. However, they generate lesions whose spacing, frequency, and collisions with replication forks are rarely characterized. Here, we describe an approach that enables the determination of these parameters with laser localized interstrand crosslinks.

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Medicine

Assessment of Human Adipose Tissue Microvascular Function Using Videomicroscopy
Melissa G. Farb *1, Song-Young Park *1, Shakun Karki 1, Noyan Gokce 1
1Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine

Videomicroscopy systems are used to examine functional properties of isolated adipose tissue arterioles in response to physiological and pharmacological stimuli. This technique can be used to examine microvascular phenotypes in different adipose tissue domains in obese humans.

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Biochemistry

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
Carine Beaupere 1, Rosalyn B. Chen 1, William Pelosi 1, Vyacheslav M. Labunskyy 1
1Department of Dermatology, Boston University School of Medicine

Translational regulation plays an important role in the control of protein abundance. Here, we describe a high-throughput method for quantitative analysis of translation in the budding yeast Saccharomyces cerevisiae.

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Biochemistry

Detection of Detergent-sensitive Interactions Between Membrane Proteins
Nava Zaarur 1, Xiang Pan 1, Konstantin V. Kandror 1
1Department of Biochemistry, Boston University School of Medicine

We describe a protocol for detection of detergent-sensitive interactions between membrane proteins using binding of the sorting receptor, sortilin, to the first luminal loop of the glucose transporter protein, GLUT4, as an example.

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Cancer Research

Long-term Live-cell Imaging to Assess Cell Fate in Response to Paclitaxel
Amanda F. Bolgioni 1, Marc A. Vittoria 1, Neil J. Ganem 1,2
1Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 2Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine

Live-cell imaging provides a wealth of information on single cells or whole populations that is unattainable by fixed cell imaging alone. Here, live-cell imaging protocols to assess cell fate decisions following treatment with the anti-mitotic drug paclitaxel are described.

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Bioengineering

Multimodal Volumetric Retinal Imaging by Oblique Scanning Laser Ophthalmoscopy (oSLO) and Optical Coherence Tomography (OCT)
Weiye Song *1, Libo Zhou *1, Ji Yi 1,2
1Department of Medicine, Boston University School of Medicine, 2Department of Biomedical Engineering, Boston University

Here, we present a protocol to get a large field of view (FOV) three-dimensional (3D) fluorescence and OCT retinal image by using a novel imaging multimodal platform. We will introduce the system setup, the method of alignment, and the operational protocols. In vivo imaging will be demonstrated, and representative results will be provided.

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Genetics

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue
Maria Dafne Cardamone 1, Joseph Orofino 1, Adam Labadorf 2, Valentina Perissi 1
1Biochemistry Department, Boston University School of Medicine, 2Bioinformatic Hub, Boston University

Here we describe a protocol for efficient chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) of brown adipose tissue (BAT) isolated from a mouse. This protocol is suitable for both mapping histone modifications and investigating genome-wide localization of non-histone proteins of interest in vivo.

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Immunology and Infection

Quantification of Antibody-dependent Enhancement of the Zika Virus in Primary Human Cells
Sultan Asad 1,2, Fabiana Feitosa-Suntheimer 1,2, Alexander Gold 1,2, Berlin Londono-Renteria 2, Tonya M. Colpitts 1,2
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.

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Neuroscience

Real-time Video Projection in an MRI for Characterization of Neural Correlates Associated with Mirror Therapy for Phantom Limb Pain
Faddi G. Saleh Velez 1,2, Camila B. Pinto 1,3, Emma S. Bailin 4, Marionna Münger 1, Andrew Ellison 5, Beatriz T. Costa 1, David Crandell 6, Nadia Bolognini 7,8, Lotfi B. Merabet 4, Felipe Fregni 1
1Laboratory of Neuromodulation & Center for Clinical Research Learning, Department of Physical Medicine and Rehabilitation, Harvard Medical School, Spaulding Rehabilitation Hospital, 2University of Chicago Medical Center, Department of Neurology, University of Chicago, 3Department of Neuroscience and Behavior, Psychology Institute, University of Sao Paulo, 4The Laboratory for Visual Neuroplasticity, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, 5Center for Biomedical Imaging, Department of Anatomy and Neurobiology, Boston University School of Medicine, 6Spaulding Rehabilitation Hospital, Harvard Medical School, 7Department of Psychology & Milan Center for Neuroscience, University of Milano-Bicocca, 8Neuropsychological Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Auxologico Italiano

We present a novel combined behavioral and neuroimaging protocol employing real-time video projection for the purpose of characterizing the neural correlates associated with mirror therapy within the magnetic resonance imaging scanner environment in leg amputee subjects with phantom limb pain.

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Immunology and Infection

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
Lin Sun 1, Naoko Kono 2, Hiroyuki Toh 3, Hanbing Xue 1, Kaori Sano 4,5, Tadaki Suzuki 4, Akira Ainai 4, Yasuko Orba 6, Junya Yamagishi 7,8, Hideki Hasegawa 4,5, Yoshimasa Takahashi 9, Shigeyuki Itamura 2, Kazuo Ohnishi 9,10
1Graduate School of Life and Environmental Sciences, University of Tsukuba, 2Center for Influenza Virus Research, National Institute of Infectious Diseases, 3School of Science and Technology, Kwansei Gakuin University, 4Department of Pathology, National Institute of Infectious Diseases, 5Division of Infectious Diseases Pathology, Department of Global Infectious Diseases, Tohoku University Graduate School of Medicine, 6Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, 7Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, 8Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, 9Department of Immunology, National Institute of Infectious Diseases, 10Faculty of Life and Environmental Sciences, University of Tsukuba

Here, we describe protocols for the analysis and visualization of the structure and constitution of whole antibody repertoires. This involves the acquisition of vast sequences of antibody RNA using next-generation sequencing.

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Cancer Research

In Vivo Targeting of Xenografted Human Cancer Cells with Functionalized Fluorescent Silica Nanoparticles in Zebrafish
Xiaodan Qin *1, Fabrice F. J. Laroche *1, Saquib Ahmed M. A. Peerzade 2, Andrew Lam 1, Igor Sokolov 2,3,4, Hui Feng 1
1Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, The Cancer Research Center, Boston University School of Medicine, 2Department of Biomedical Engineering, Tufts University, 3Department of Mechanical Engineering, Tufts University, 4Department of Physics, Tufts University

Described here is a method for utilizing zebrafish embryos to study the ability of functionalized nanoparticles to target human cancer cells in vivo. This method allows for the evaluation and selection of optimal nanoparticles for future testing in large animals and in clinical trials.

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Bioengineering

Fabrication of a Biomimetic Nano-Matrix with Janus Base Nanotubes and Fibronectin for Stem Cell Adhesion
Libo Zhou 1, Anne Yau 1, Wuxia Zhang 1, Yupeng Chen 1
1Department of Biomedical Engineering, University of Connecticut

The goal of this protocol is to show the assembly of a biomimetic nanomatrix (NM) with Janus base nanotubes (JBNTs) and fibronectin (FN). When co-cultured with human mesenchymal stem cells (hMSCs), the NMs exhibit excellent bioactivity in encouraging hMSCs adhesion.

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Biology

Visualization of Replisome Encounters with an Antigen Tagged Blocking Lesion
Jing Zhang *1, Jing Huang *2, Ishani Majumdar 1, Ryan C. James 3, Julia Gichimu 1, Manikandan Paramasivam 4, Durga Pokharel 5, Himabindu Gali 6, Marina A. Bellani 1, Michael M Seidman 1
1Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 2Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, 3Department of Molecular Biology and Genetics, Cornell University, 4Department of Cellular and Molecular Medicine, University of Copenhagen, 5Horizon Discovery, 6Boston University School of Medicine

While replication fork collisions with DNA adducts can induce double strand breaks, less is known about the interaction between replisomes and blocking lesions. We have employed the proximity ligation assay to visualize these encounters and to characterize the consequences for replisome composition.

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Biology

Three-Dimensional Adipocyte Culture as a Model to Study Cachexia-Induced White Adipose Tissue Remodeling
Miguel L Batista Jr. 1,2, Tova Meshulam 2,3, Kathleen Desevin 2, Nabil Rabhi 2, Stephen R. Farmer 2
1Department of Integrated Biotechnology, University of Mogi das Cruzes, 2Department of Biochemistry, Boston University School of Medicine, 3Obesity Research Center, Department of Medicine, Boston University School of Medicine

This protocol describes a three-dimensional (3D) magnetic printing culture system that permits dissection of white adipose tissue (WAT) remodeling induced by a conditioned medium from cancer cells. Using a 3D culture system of UCP1+ adipocytes that express a green fluorescent protein (GFP) allows the study of beige adipocytes contributing to adipose tissue remodeling.

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Medicine

A Retrograde Implantation Approach for Peritoneal Dialysis Catheter Placement in Mice
Saran Lotfollahzadeh 1, Mengwei Zhang 1, Marc Arthur Napoleon 1, Wenqing Yin 1, Josephine Orrick 1, Nagla Elzind 1, Austin Morrissey 1, Isaac E. Sellinger 1, Lauren D. Stern 1, Mostafa Belghasem 2, Jean M. Francis 1, Vipul C. Chitalia 1,3,4
1Renal Section, Department of Medicine, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 2Department of Biomedical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, 3Veterans Affairs Boston Healthcare System, 4Institute of Medical Engineering and Sciences, Massachusetts Institute of Technology

This article describes modifications of a procedure to implant a peritoneal dialysis catheter in a murine model to avoid major technical issues observed with the conventional techniques.

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Medicine

Clinical Application of 24 G Cannula Needle and 3-0 Polypropylene Suture in Vas Deferens Exploration
Jin Wang *1, Wenjia Li *2, Yao He 1, Yuanbin Xia 1, Lin Sun 1, Youpeng Zhang 1, Zhaohui Zhu 1
1Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 2Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

This protocol presents the clinical application of a 24 G cannula and 3-0 polypropylene suture as a simple and effective method for the exploration of the vas deferens.

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Developmental Biology

Generating 3D Spheres and 2D Air-Liquid Interface Cultures of Human Induced Pluripotent Stem Cell-Derived Type 2 Alveolar Epithelial Cells
Rhiannon B. Werder *1,2,3, Jessie Huang *1,2, Kristine M. Abo 1,2, Olivia T. Hix 1,2, Kasey Minakin 1,2, Konstantinos-Dionysios Alysandratos 1,2, Carly Merritt 1,2, Kayleigh Berthiaume 1,2, Andrea B. Alber 1,2, Claire L. Burgess 1,2, Darrell N. Kotton *1,2, Andrew A. Wilson *1,2
1Center for Regenerative Medicine, Boston University and Boston Medical Center, 2The Pulmonary Center and Department of Medicine, Boston University School of Medicine, 3QIMR Berghofer Medical Research Institute

The present protocol describes human induced pluripotent stem cell-derived type 2 alveolar epithelial-like cells (iAT2s). These cells can be cultured as self-renewing spheres in 3D culture or adapted to air-liquid interface (ALI) culture.

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Developmental Biology

Generation of Airway Epithelial Cell Air-Liquid Interface Cultures from Human Pluripotent Stem Cells
Andrew Berical 1,2, Mary Lou Beermann 2, Shingo Suzuki 3, Jake LeSuer 2, Taylor Matte 2, Brian Davis 3, Darrell Kotton 1,2, Finn Hawkins 1,2
1Pulmonary Center, Boston University School of Medicine, 2Center for Regenerative Medicine, Boston University and Boston Medical Center, 3Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center

Recent advances in human induced pluripotent stem cell differentiation protocols allow for the stepwise derivation of organ-specific cell types. Here, we provide detailed steps for the maintenance and expansion of iPSC-derived airway basal cells and their differentiation into a mucociliary epithelium in air-liquid interface cultures.

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