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Yale School of Medicine

48 ARTICLES PUBLISHED IN JoVE

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Biology

Functional Imaging with Reinforcement, Eyetracking, and Physiological Monitoring
Vincent Ferrera 1,2,3, Jack Grinband 1,3, Tobias Teichert 1, Franco Pestilli 1, Stephen Dashnaw 3, Joy Hirsch 1,3
1Department of Neuroscience, Columbia University, 2Department of Psychiatry, Columbia University, 3Department of Radiology, Columbia University

This presentation demonstrates the use of fMRI to study neural circuits that underlie decision-making. Simple perceptual tasks are combined with appetitive and aversive reinforcements to investigate how outcomes affect decision processes.

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Bioengineering

Engineering Biological-Based Vascular Grafts Using a Pulsatile Bioreactor
Angela H. Huang 1, Laura E. Niklason 1,2
1Department of Biomedical Engineering, Yale University, 2Department of Anesthesiology, Yale University School of Medicine

Our group has developed a bioreactor culture system that mimics the physiological pulsatile stresses of the cardiovascular system to regenerate implantable small-diameter vascular grafts.

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Bioengineering

Procedure for Lung Engineering
Elizabeth A. Calle *1, Thomas H. Petersen *2, Laura E. Niklason 1,3
1Department of Biomedical Engineering, Yale University, 2Department of Biomedical Engineering, School of Medicine, Duke University, 3Department of Anesthesia, Yale University

We have developed a decellularized lung extracellular matrix and novel biomimetic bioreactor that can be used to generate functional lung tissue. By seeding cells into the matrix and culturing in the bioreactor, we generate tissue that demonstrates effective gas exchange when transplanted in vivo for short periods of time.

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Behavior

Method for Simultaneous fMRI/EEG Data Collection during a Focused Attention Suggestion for Differential Thermal Sensation
Pamela K. Douglas 1,2, Maureen Pisani 2, Rory Reid 1, Austin Head 2, Edward Lau 2, Ebrahim Mirakhor 3, Jennifer Bramen 2, Billi Gordon 2, Ariana Anderson 2, Wesley T. Kerr 2, Chajoon Cheong 4, Mark S. Cohen 1,2
1Neuropsychiatric Institute, University of California, Los Angeles, 2Laboratory of Neuroimaging Technology, University of California, Los Angeles, 3Yale School of Medicine, 4Korean Basic Science Institute

We present a protocol for concurrent collection of EEG/fMRI data, and synchronized MR clock signal recording. We demonstrate this method using a unique paradigm whereby subjects receive ‘cold glove’ instructions during scanning, and EEG/fMRI data are recorded along with hand temperature measurements both before and after hypnotic induction.

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Neuroscience

Measuring the Subjective Value of Risky and Ambiguous Options using Experimental Economics and Functional MRI Methods
Ifat Levy 1,2, Lior Rosenberg Belmaker 1, Kirk Manson 1, Agnieszka Tymula 3, Paul W. Glimcher 3,4,5
1Section of Comparative Medicine, Yale School of Medicine, 2Department of Neurobiology, Yale School of Medicine, 3Center for Neural Science, New York University , 4Department of Psychology, New York University , 5Department of Economics, New York University

Using functional MRI and behavioral methods to determine the neural representation of the subjective value of risky and ambiguous options in the human brain.

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Biology

Reprogramming Human Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) Using Retroviral Vector with GFP
Kun-Yong Kim 1, Eriona Hysolli 1, In-Hyun Park 1
1Yale Stem Cell Center, Department of Genetics, Yale School of Medicine

A method to generate human induced pluripotent stem cells (iPSCs) via retrovirus-mediated ectopic expression of OCT4, SOX2, KLF4 and MYC is described. A practical way to identify human iPSC colonies based on GFP expression is also discussed.

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Medicine

Immunohistochemical Staining of B7-H1 (PD-L1) on Paraffin-embedded Slides of Pancreatic Adenocarcinoma Tissue
Elaine Bigelow 1,2, Katherine M. Bever 1,2, Haiying Xu 1,2,3, Allison Yager 1, Annie Wu 1,2,4, Janis Taube 3,5, Lieping Chen 6, Elizabeth M. Jaffee 1,2,5,7,8, Robert A. Anders 1,2,5,8, Lei Zheng 1,2,4,5,7
1The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 2Department of Oncology, The Johns Hopkins University School of Medicine, 3Department of Dermatology, The Johns Hopkins University School of Medicine, 4Department of Surgery, Johns Hopkins University School of Medicine, 5The Sol Goldman Pancreatic Cancer Center, The Johns Hopkins University School of Medicine, 6Yale Cancer Center, Yale School of Medicine, 7The Skip Viragh Center for Pancreatic Cancer, The Johns Hopkins University School of Medicine, 8Department of Pathology, The Johns Hopkins University School of Medicine

B7-H1 (PD-L1) and its binding to PD-1 provide a major tumor-induced immunosuppressive signal in the tumor’s microenvironment. An immunohistochemical staining technique to characterize the expression and localization of B7-H1 in pancreatic adenocarcinoma is described here.

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Clinical Skills

General Approach to the Physical Exam
Jaideep Talwalkar 1
1Internal Medicine, Yale School of Medicine

General Approach to the Physical Exam

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Clinical Skills

Comprehensive Breast Exam
Alexandra Duncan 1, Tiffany Cook 1, Jaideep S. Talwalkar 2
1GTA, Praxis Clinical, 2Internal Medicine and Pediatrics, Yale School of Medicine

Comprehensive Breast Exam

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Clinical Skills

Observation and Inspection
Jaideep Talwalkar 1
1Internal Medicine, Yale School of Medicine

Observation and Inspection

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Clinical Skills

Abdominal Exam IV: Acute Abdominal Pain Assessment
Joseph Donroe 1
1Internal Medicine and Pediatrics, Yale School of Medicine

Abdominal Exam IV: Acute Abdominal Pain Assessment

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Clinical Skills

Peripheral Vascular Exam
Joseph Donroe 1
1Internal Medicine and Pediatrics, Yale School of Medicine

Peripheral Vascular Exam

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Clinical Skills

Peripheral Vascular Exam Using a Continuous Wave Doppler
Joseph Donroe 1
1Internal Medicine and Pediatrics, Yale School of Medicine

Peripheral Vascular Exam Using a Continuous Wave Doppler

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Clinical Skills

Percussion
Jaideep Talwalkar 1
1Internal Medicine, Yale School of Medicine

Percussion

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Clinical Skills

Pelvic Exam II: Speculum Exam
Alexandra Duncan 1, Tiffany Cook 1, Jaideep S. Talwalkar 2
1Praxis Clinical, 2Internal Medicine and Pediatrics, Yale School of Medicine

Pelvic Exam II: Speculum Exam

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Clinical Skills

Palpation
Jaideep Talwalkar 1
1Yale School of Medicine

Palpation

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Clinical Skills

Pelvic Exam I: Assessment of the External Genitalia
Alexandra Duncan 1, Tiffany Cook 1, Jaideep S. Talwalkar 2
1GTA, Praxis Clinical, 2Internal Medicine and Pediatrics, Yale School of Medicine

Pelvic Exam I: Assessment of the External Genitalia

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Clinical Skills

Proper Adjustment of Patient Attire during the Physical Exam
Jaideep Talwalkar 1, Joseph Donroe 1
1Internal Medicine, Yale School of Medicine

Proper Adjustment of Patient Attire during the Physical Exam

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Clinical Skills

Auscultation
Jaideep Talwalkar 1
1Internal Medicine, Yale School of Medicine

Auscultation

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Clinical Skills

Pelvic Exam III: Bimanual and Rectovaginal Exam
Alexandra Duncan 1, Jaideep S. Talwalkar 1
1Internal Medicine and Pediatrics, Yale School of Medicine

Pelvic Exam III: Bimanual and Rectovaginal Exam

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Clinical Skills

The Comprehensive Infant Examination
Heather Collette 1, Jaideep Talwalkar 1
1Yale School of Medicine

The Comprehensive Infant Examination

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Clinical Skills

Toddler and Preschool Child Exam
Heather Collette 1, Jaideep Talwalkar 1
1Yale School of Medicine

Toddler and Preschool Child Exam

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Clinical Skills

Adolescent Exam
Heather Collette 1, Jaideep Talwalkar 1
1Yale School of Medicine

Adolescent Exam

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Clinical Skills

The 4 M’s Framework: Case History and Physical Examination of Older Adults
Jennifer A. Ouellet 1, Jaideep Talwalkar 1
1Yale School of Medicine

The 4 M’s Framework: Case History and Physical Examination of Older Adults

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Clinical Skills

Accessibility to Clinical Care for People who use Wheelchairs
Yetsa Tuakli-Wosornu 1,2, Jaideep Talwalkar 1
1Yale School of Medicine, 2University of Pittsburgh

Accessibility to Clinical Care for People who use Wheelchairs

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Clinical Skills

Using Point of Care Ultrasound to Augment Acquisition of Physical Exam Skills: Organs
Joseph H. Donroe 1, Rachel Liu 1
1Yale School of Medicine

Using Point of Care Ultrasound to Augment Acquisition of Physical Exam Skills: Organs

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Clinical Skills

Using Point of Care Ultrasound to Augment Acquisition of Physical Exam Skills: Knee and Shoulder
Joseph H. Donroe 1, Rachel Liu 1
1Yale School of Medicine

Using Point of Care Ultrasound to Augment Acquisition of Physical Exam Skills: Knee and Shoulder

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Clinical Skills

Mental Status Examination
Carmen Black 1, Matthew Goldenberg 1, Jaideep Talwalkar 1
1Yale School of Medicine

Mental Status Examination

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Clinical Skills

Using Point of Care Ultrasound to Augment Acquisition of Physical Exam Skills: Veins and Arteries
Joseph H. Donroe 1, Rachel Liu 1
1Yale School of Medicine

Using Point of Care Ultrasound to Augment Acquisition of Physical Exam Skills: Veins and Arteries

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Clinical Skills

Physical Exam Considerations for People who use Wheelchairs
Yetsa Tuakli-Wosornu 1,2, Jaideep Talwalkar 1
1Yale School of Medicine, 2University of Pittsburgh

Physical Exam Considerations for People who use Wheelchairs

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Neuroscience

Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection
Urmi Bandyopadhyay 1,2, Wayne A. Fenton 1, Arthur L. Horwich 1,2, Maria Nagy 1,2
1Department of Genetics, Yale School of Medicine, 2Howard Hughes Medical Institute

High-quality total RNA has been prepared from cell bodies of mouse spinal cord motor neurons by laser capture microdissection after staining spinal cord sections with Azure B in 70% ethanol. Sufficient RNA (~40-60 ng) is recovered from 3,000-4,000 motor neurons to allow downstream RNA analysis by RNA-seq and qRT-PCR.

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Bioengineering

Use of Label-free Optical Biosensors to Detect Modulation of Potassium Channels by G-protein Coupled Receptors
Matthew R. Fleming 1, Steven M. Shamah 3, Leonard K. Kaczmarek 1,2
1Department of Pharmacology, Yale School of Medicine, 2Department of Cellular and Molecular Physiology, Yale School of Medicine, 3X-BODY Biosciences

Optical biosensor techniques can detect changes in mass near the plasma membrane in living cells and allow one to follow cellular responses in both individual cells and populations of cells. This protocol will describe detection of the modulation of potassium channels by G-protein coupled receptors in intact cells using this approach.

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Biology

Live Cell Imaging of Primary Rat Neonatal Cardiomyocytes Following Adenoviral and Lentiviral Transduction Using Confocal Spinning Disk Microscopy
Takashi Sakurai 1,2, Anthony Lanahan 2, Melissa J. Woolls 2, Na Li 2, Daniela Tirziu 2, Masahiro Murakami 2
1Max-Planck-Institute for Molecular Biomedicine and Institute of Cell Biology, 2Department of Internal Medicine, Yale Cardiovascular Research Center and Section of Cardiovascular Medicine

This protocol describes a method of live cell imaging using primary rat neonatal cardiomyocytes following lentiviral and adenoviral transduction using confocal spinning disk microscopy. This enables detailed observations of cellular processes in living cardiomyocytes.

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Behavior

fMRI Validation of fNIRS Measurements During a Naturalistic Task
J. Adam Noah 1, Yumie Ono 2, Yasunori Nomoto 2, Sotaro Shimada 2, Atsumichi Tachibana 3, Xian Zhang 1, Shaw Bronner 1, Joy Hirsch 1,5
1Department of Psychiatry, Yale School of Medicine, 2Department of Electronics and Bioinformatics, Meiji University, 3Department of Histology and Neurobiology, Dokkyo Medical University School of Medicine, 4ADAM Center, Department of Physical Therapy, Movement and Rehabilitation Sciences, Northeastern University, 5Department of Neurobiology, Yale School of Medicine

We present a method to compare functional brain activity recorded during a naturalistic task using fNIRS with activity recorded during fMRI.

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Behavior

Examination of Rapid Dopamine Dynamics with Fast Scan Cyclic Voltammetry During Intra-oral Tastant Administration in Awake Rats
Robert J. Wickham 1, Jinwoo Park 2, Eric J. Nunes 3, Nii A. Addy 1,3,4
1Interdepartmental Neuroscience Program, Yale University, 2Department of Biotechnical and Clinical Laboratory Sciences, School of Medicine and Biomedical Sciences, University at Buffalo, 3Department of Psychiatry, Yale School of Medicine, 4Department of Cellular and Molecular Physiology, Yale School of Medicine

Rapid fluctuations in extracellular dopamine (DA) mediate both reward processing and motivated behavior in mammals. This manuscript describes the combined use of fast scan cyclic voltammetry (FSCV) and intra-oral tastant administration to determine how tastants alter rapid dopamine release in awake, freely moving rats.

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Use of Decellularized Mammalian Lung Tissues to Study Cell: Matrix Interactions
Christina N. Blaul 1,2, Jenna Balestrini 3,4, Hongyi Pan 5, Julia Winkler 5, Erica L. Herzog 5, Huanxing Sun 5
1NSF Funded Biomedical MD-PhD REU in affiliation with Yale School of Medicine, Yale Pathology Department, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, 2School of Natural Sciences: Molecular and Cellular Biology, University of California, Merced, 3Department of Anesthesiology, Yale School of Medicine, 4Cell Bioprocessing, Draper, 5Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine

This study presents an ex vivo platform based on decellularized lung tissue to study cell: matrix interactions in the healthy and diseased adult lung.

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Developmental Biology

Culturing of Retinal Pigment Epithelial Cells on an Ex Vivo Model of Aged Human Bruch's Membrane
Hui Cai 1, Jie Gong 1, Lucian V. Del Priore 1, Tongalp H. Tezel 2, Mark A. Fields 1
1Department of Ophthalmology and Visual Science, Yale School of Medicine, 2Edward S. Harkness Eye Institute, Columbia University School of Medicine

The goal of this protocol is to demonstrate the culturing of retinal pigment epithelial (RPE) cells on aged and/or diseased human Bruch's membrane. This method is suitable to study RPE cell behavior on a compromised extracellular matrix.

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Neuroscience

Cannula Implantation into the Cisterna Magna of Rodents
Anna L.R. Xavier 1, Natalie Linea Hauglund 1, Stephanie von Holstein-Rathlou 1, Qianliang Li 1, Simon Sanggaard 1,2, Nanhong Lou 3, Iben Lundgaard 3,4, Maiken Nedergaard 1,3
1Center for Translational Neuromedicine, Division of Glial Therapeutics, University of Copenhagen, 2Department of Anesthesiology, Yale School of Medicine, 3Center for Translational Neuromedicine, Division of Glial Therapeutics, University of Rochester Medical Center, 4Department of Experimental Medical Science, Wallenberg Center for Molecular Medicine, Lund University

Here we describe a protocol to perform cisterna magna cannulation (CMc), a minimally invasive way to deliver tracers, substrates and signaling molecules into the cerebrospinal fluid (CSF). Combined with different imaging modalities, CMc enables glymphatic system and CSF dynamics assessment, as well as brain-wide delivery of various compounds.

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Genetics

Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization
Fani Memi 1, Daniela Tirziu 2, Irinna Papangeli 3
1Department of Cell and Developmental Biology, University College London, 2Yale Cardiovascular Research Group, Section of Cardiovascular Medicine, Yale School of Medicine, 3Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Yale School of Medicine

micro-RNAs (miRNAs) are short and highly homologous RNA sequences, serving as post-transcriptional regulators of messenger RNAs (mRNAs). Current miRNA detection methods vary in sensitivity and specificity. We describe a protocol that combines in situ hybridization and immunostaining for concurrent detection of miRNA and protein molecules on mouse heart tissue sections.

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Medicine

Predicting Treatment Response to Image-Guided Therapies Using Machine Learning: An Example for Trans-Arterial Treatment of Hepatocellular Carcinoma
Aaron Abajian 1, Nikitha Murali 1, Lynn Jeanette Savic 1,2, Fabian Max Laage-Gaupp 1, Nariman Nezami 1, James S. Duncan 3, Todd Schlachter 1, MingDe Lin 4, Jean-François Geschwind 5, Julius Chapiro 1
1Department of Radiology and Biomedical Imaging, Yale School of Medicine, 2Department of Diagnostic and Interventional Radiology, Universitätsmedizin Charité Berlin, 3Department of Biomedical Engineering, Yale School of Engineering and Applied Science, 4Philips Research North America, 5Prescience Labs

Intra-arterial therapies are the standard of care for patients with hepatocellular carcinoma who cannot undergo surgical resection. A method for predicting response to these therapies is proposed. The technique uses pre-procedural clinical, demographic, and imaging information to train machine learning models capable of predicting response prior to treatment.

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Developmental Biology

In Vitro Assays to Evaluate the Migration, Invasion, and Proliferation of Immortalized Human First-trimester Trophoblast Cell Lines
Edwina P. Kisanga 1, Zhonghua Tang 1, Seth Guller 1, Shannon Whirledge 1
1Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine

Here, we present a highly accessible protocol for evaluating the cell movement in human trophoblast cells using three in vitro assays: the scratch assay, the transwell invasion assay, and the cell proliferation assay.

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Immunology and Infection

Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells
Tenaya K. Vallery 1, Joan A. Steitz 2
1Norfolk Academy, 2Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale School of Medicine

We describe a protocol utilizing fluorescence in situ hybridization (FISH) to visualize multiple herpesviral RNAs within lytically infected human cells, either in suspension or adherent. This protocol includes quantification of fluorescence producing a nucleocytoplasmic ratio and can be extended for simultaneous visualization of host and viral proteins with immunofluorescence (IF).

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Genetics

Expression, Purification, and Liposome Binding of Budding Yeast SNX-BAR Heterodimers
Mengxiao Ma 1, Shreya Goyal 2, Christopher G. Burd 1, Richard J. Chi 2
1Department of Cell Biology, Yale School of Medicine, 2Department of Biological Sciences, University of North Carolina at Charlotte

Here, we present a workflow for the expression, purification and liposome binding of SNX-BAR heterodimers in yeast.

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Neuroscience

Combined Infusion and Stimulation with Fast-Scan Cyclic Voltammetry (CIS-FSCV) to Assess Ventral Tegmental Area Receptor Regulation of Phasic Dopamine
Robert J. Wickham 1, Makenzie Lehr *1, Lauryn Mitchell *1, Nii A. Addy 2,3
1Department of Psychology, Elizabethtown College, 2Department of Psychiatry, Yale University, 3Department of Cellular and Molecular Physiology, Yale University

The goal of this protocol is to directly manipulate ventral tegmental area receptors to study their contribution to subsecond dopamine release.

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Bioengineering

Engineered Lung Tissues Prepared from Decellularized Lung Slices
Katherine L. Leiby 1,2, Ronald Ng 1, Stuart G. Campbell 1,3, Laura E. Niklason 1,4
1Department of Biomedical Engineering, Yale University, 2Yale School of Medicine, 3Department of Cellular and Molecular Physiology, Yale School of Medicine, 4Department of Anesthesiology, Yale School of Medicine

This protocol describes a method to generate reproducible, small-scale engineered lung tissues, by repopulating decellularized precision-cut lung slices with alveolar epithelial type 2 cells, fibroblasts, and endothelial cells.

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Biochemistry

Self-Assembly of Microtubule Tactoids
Prashali Chauhan 1, Sumon Sahu 1,2, Niaz Goodbee 1, Sophia Martin 1, Hong Beom Lee 1, Ruell Branch 1, Jennifer M. Schwarz 1, Jennifer L. Ross 1
1Physics Department, Syracuse University, 2Department of Molecular Biophysics and Biochemistry, Yale School of Medicine

This article presents a protocol for the formation of microtubule assemblies in the shape of tactoids using MAP65, a plant-based microtubule crosslinker, and PEG as a crowding agent.

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Biology

Generation and Manipulation of Rat Intestinal Organoids
Eleanor Zagoren *1, Anderson K. Santos *1,2, Nadia A. Ameen 3,4, Kaelyn Sumigray 1,5,6
1Department of Genetics, Yale School of Medicine, 2Department of Pediatrics, Yale School of Medicine, 3Department of Pediatrics/Gastroenterology and Hepatology, Yale School of Medicine, 4Department of Cellular and Molecular Physiology, Yale School of Medicine, 5Yale Stem Cell Center, Yale School of Medicine, 6Yale Cancer Center, Yale School of Medicine

Here, we present a protocol to generate rat intestinal organoids and use them in several downstream applications. Rats are often a preferred preclinical model, and the robust intestinal organoid system fills the need for an in vitro system to accompany in vivo studies.

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Biology

Optimizing Visualization of Axonal Transport of Endogenous Cargo by Fluorescence Microscopy in Living Caenorhabditis elegans
Oliver Glomb 1, Mengya Lyu 1, Shaul Yogev 1
1Department of Neuroscience, Yale School of Medicine

The paper describes the optimization of fluorescence microscopy acquisition parameters to visualize the axonal transport of endogenous labeled cargos at single-neuron resolution in a living nematode.

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