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18 ARTICLES PUBLISHED IN JoVE

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Biology

Fluorescence Activated Cell Sorting of Plant Protoplasts
Bastiaan O. R. Bargmann 1, Kenneth D. Birnbaum 1
1Center for Genomics and Systems Biology, Department of Biology, New York University

A method for isolating specific cell types from plant material is demonstrated. This technique employs transgenic marker lines expressing fluorescent proteins in particular cell types, cellular dissociation and Fluorescence Activated Cell Sorting. Additionally, a growth setup is established here that facilitates treatment of Arabidopsis thaliana seedlings prior to cell sorting.

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Neuroscience

How to Create and Use Binocular Rivalry
David Carmel 1,2, Michael Arcaro 3,4, Sabine Kastner 3,4, Uri Hasson 3,4
1Department of Psychology, New York University, 2Centre for Neural Science, New York University, 3Department of Psychology, Princeton University, 4Neuroscience Institute, Princeton University

Binocular rivalry occurs when the eyes are presented with different images at the same location: one image dominates while the other is suppressed, and dominance alternates periodically. Rivalry is useful for investigating perceptual selection and visual awareness. Here we describe several easy methods for creating and using binocular rivalry stimuli.

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Neuroscience

Large-scale Recording of Neurons by Movable Silicon Probes in Behaving Rodents
Marie Vandecasteele 1,2, S. M. 1, Sébastien Royer 1,3, Mariano Belluscio 1, Antal Berényi 1, Kamran Diba 1,4, Shigeyoshi Fujisawa 1, Andres Grosmark 1, Dun Mao 1, Kenji Mizuseki 1, Jagdish Patel 1, Eran Stark 1, David Sullivan 1, Brendon Watson 1, György Buzsáki 1
1Center for Molecular and Behavioral Neuroscience, University of New Jersey, 2Center for Interdisciplinary Research in Biology, Collège de France, 3Janelia Farm Research Campus, Howards Hughes Medical Institute, 4Deptartment of Psychology, University of Wisconsin at Milwaukee

We describe methods for large-scale recording of multiple single units and local field potential in behaving rodents with silicon probes. Drive fabrication, probe attachment to the drive and probe implantation processes are illustrated in sufficient details for easy replication.

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Behavior

Automated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction
C. R. Gallistel 1, Fuat Balci 1,2, David Freestone 1,3, Aaron Kheifets 1, Adam King 4
1Department of Psychology, Rutgers University, 2Department of Psychology, Koç University, 3Center for Neural Science, New York University, 4Department of Mathematics & Computer Science, Fairfield University

Fully automated system for measuring physiologically meaningful properties of the mechanisms mediating spatial localization, temporal localization, duration, rate and probability estimation, risk assessment, impulsivity, and the accuracy and precision of memory, in order to assess the effects of genetic and pharmacological manipulations on foundational mechanisms of cognition in mice.

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Medicine

Coordinate Mapping of Hyolaryngeal Mechanics in Swallowing
Thomas Z. Thompson 1, Farres Obeidin 1, Alisa A. Davidoff 2, Cody L. Hightower 1, Christohper Z. Johnson 1, Sonya L. Rice 1, Rebecca-Lyn Sokolove 1, Brandon K. Taylor 1, John M. Tuck 1, William G. Pearson, Jr. 3,4
1Medical College of Georgia, Georgia Regents University, 2Department of Communicative Sciences and Disorders, New York University, 3Department of Cellular Biology & Anatomy, Georgia Regents University, 4Department of Otolaryngology, Georgia Regents University

Coordinate mapping is a method of documenting salient features of hyolaryngeal biomechanics in the pharyngeal phase of swallowing. This methodology uses image analysis software to record coordinates of anatomical landmarks. These coordinates are imported into an excel macro and translated into kinematic variables of interest useful in dysphagia research.

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Behavior

Using the Activity-based Anorexia Rodent Model to Study the Neurobiological Basis of Anorexia Nervosa
Tara Gunkali Chowdhury 1, Yi-Wen Chen 1, Chiye Aoki 1
1Center for Neural Science, New York University

Here we present a protocol to induce activity-based anorexia (ABA) in female adolescent mice. ABA is a condition of hyperactivity evoked by imposing food restriction on rodents with access to a running wheel. This phenomenon is being used as a model to study the underlying neurobiology of anorexia nervosa.

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JoVE Core

Ultrasound Images of the Tongue: A Tutorial for Assessment and Remediation of Speech Sound Errors
Jonathan L. Preston 1,2, Tara McAllister Byun 3, Suzanne E. Boyce 2,4, Sarah Hamilton 4, Mark Tiede 2, Emily Phillips 2, Ahmed Rivera-Campos 4, Douglas H. Whalen 2,5,6
1Department of Communication Sciences and Disorders, Syracuse University, 2Haskins Laboratories, 3Department of Communicative Sciences and Disorders, New York University, 4Department of Communication Sciences and Disorders, University of Cincinnati, 5Program in Speech-Language-Hearing Sciences, City University of New York Graduate Center, 6Department of Linguistics, Yale University

Ultrasound imaging can be used to display the shape and movements of the tongue in real time during speech. The images can be used to determine the nature of speech sound errors. Visual feedback of the tongue can be used to facilitate improvements in speech sound production in clinical populations.

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Medicine

Minimally Invasive Transverse Aortic Constriction in Mice
Aung Moe Zaw 1, Connor M. Williams 2, Helen K. W. Law 3, Billy Kwok Chong Chow 1
1School of Biological Sciences, The University of Hong Kong, 2College of Arts and Science, New York University, 3Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University

Minimally invasive transverse aortic constriction (MTAC) conserves the essentials of regular transverse aortic constriction (TAC) while eliminating the use of a ventilator with tracheal intubation. It proves to be a highly desirable method for high-throughput studies on left ventricular overload, particularly in translational studies.

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Biochemistry

Nitrogen Cavitation and Differential Centrifugation Allows for Monitoring the Distribution of Peripheral Membrane Proteins in Cultured Cells
Mo Zhou 1, Mark R. Philips 1
1Langone Medical Center, New York University

Here we present protocols for detergent-free homogenization of cultured mammalian cells based on nitrogen cavitation and subsequent separation of cytosolic and membrane-bound proteins by ultracentrifugation. This method is ideal for monitoring the partitioning of peripheral membrane proteins between soluble and membrane fractions.

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Neuroscience

Chronic Transcranial Electrical Stimulation and Intracortical Recording in Rats
Gábor Kozák 1, Tamás Földi 1, Antal Berényi 1,2
1MTA-SZTE "Momentum" Oscillatory Neuronal Networks Research Group, Department of Physiology, University of Szeged, 2New York University Neuroscience Institute, New York University

This detailed protocol describes transcranial stimulation electrode placement on the temporal bone in order to investigate the short- and long-term effects of transcranial electrical stimulation in freely moving rats.

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Neuroscience

Preparation of the Rat Vocal Fold for Neuromuscular Analyses
Charles Lenell 1,2, Adrianna C. Shembel 1, Aaron M. Johnson 1
1NYU Voice Center, Department of Otolaryngology-Head & Neck Surgery, New York University School of Medicine, 2Communicative Sciences and Disorders, New York University

This protocol describes methods used to prepare rat vocal folds for histochemical neuromuscular study.

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Biology

High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression
Federica M. O. Sartori 1, Cassandra Buzby 1, Yevgeniy Plavskin 1, Mark L. Siegal 1
1Center for Genomics and Systems Biology, Department of Biology, New York University

Yeast growth phenotypes are precisely measured through highly parallel time-lapse imaging of immobilized cells growing into microcolonies. Simultaneously, stress tolerance, protein expression, and protein localization can be monitored, generating integrated datasets to study how environmental and genetic differences, as well as gene-expression heterogeneity among isogenic cells, modulate growth.

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Biology

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Gunjan Dixit 1, Ying Zheng 1, Brian Parker 2, Jiayu Wen 1
1Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, 2Department of Biology, New York University

Alternative splicing (AS) and alternative polyadenylation (APA) expand the diversity of transcript isoforms and their products. Here, we describe bioinformatic protocols to analyze bulk RNA-seq and 3' end sequencing assays to detect and visualize AS and APA varying across experimental conditions.

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Genetics

Rapid Isolation of Wild Nematodes by Baermann Funnel
Sophia C. Tintori *1, Solomon A. Sloat *1, Matthew V. Rockman 1
1Department of Biology and Center for Genomics & Systems Biology, New York University

This protocol outlines a method for efficiently extracting live nematodes from natural substrates in the field.

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Biology

Laser Microdissection for Species-Agnostic Single-Tissue Applications
Alyssa Woronik 1,2, Karin Kiontke 1, Raya S. Jallad 1, R. Antonio Herrera 3, David H. A. Fitch 1
1Center for Developmental Genetics, New York University, 2Sacred Heart University, 3Baylor School

A protocol is described that uses laser microdissection to isolate individual nematode tissues for RNA-sequencing. The protocol does not require species-specific genetic toolkits, allowing gene expression profiles to be compared between different species at the level of single-tissue samples.

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Biology

Sample Preparation for Rapid Lipid Analysis in Drosophila Brain Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging
Yuki X. Chen *1,5,6, Kelly Veerasammy *1,2, Jun Yin *3, Tenzin Choetso 1,4, Tiffany Zhong 7, Muniyat A. Choudhury 1,4,5, Cory Weng 1,4,5, Ethan Xu 8, Mayan A. Hein 9,10, Rinat Abzalimov 2, Ye He 1
1Advanced Science Research Center, Neuroscience Initiative, the City University of New York, Graduate Center New York, 2Advanced Science Research Center, Structural Biology Initiative, the City University of New York, Graduate Center, 3National Institute of Neurological Disorders and Stroke, National Institutes of Health, 4The City College of New York, CUNY, 5Macaulay Honors College, CUNY, 6Graduate School of Public Health and Health Policy, The City University of New York, 7Princeton University, 8Ardrey Kell High School, 9The Borough of Manhattan Community College, CUNY, 10Gallatin School of Individualized Study, New York University

The aim of this protocol is to provide detailed guidance on the proper sample preparation for lipid and metabolite analysis in small tissues, such as the Drosophila brain, using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging.

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Cancer Research

Phospholipid Mediator Induced Transformation in Three-Dimensional Cultures
Abhijith Kuttanamkuzhi 1, Libi Anandi 1,2, Vaishali Chakravarty 1,3, Mayurika Lahiri 1
1Biology Department, Indian Institute of Science Education and Research, 2Department of Biology, Center for Genomics and Systems Biology, New York University, 3Enveda Therapeutics India Pvt Ltd.

The present protocol describes the setting up of 3D 'on top' cultures of a non-transformed breast epithelial cell line, MCF10A, that has been modified to study Platelet Activating Factor (PAF) induced transformation. Immuno-fluorescence has been used to assess the transformation and is discussed in detail.

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Behavior

Assessing Human Spatial Navigation in a Virtual Space and its Sensitivity to Exercise
Alana J. Smith 1, Noor Tasnim 2, Zach Psaras 3, Daphne Gyamfi 4, Krishna Makani 4, Wendy A. Suzuki 3, Julia C. Basso 1,4,5
1School of Neuroscience, Virginia Tech, 2Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, 3Center for Neural Science, New York University, 4Department of Human Nutrition, Foods, and Exercise, Virginia Tech, 5Center for Health Behaviors Research, Fralin Biomedical Research Institute at VTC

Here, we present a novel, brief, and active spatial navigation task that assesses both spatial navigation and episodic memory ability. Importantly, spatial navigation and episodic memory were associated with one another, and this task demonstrated sensitivity to exercise.

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