City University of New York

8 ARTICLES PUBLISHED IN JoVE

Immunology and Infection

Derivation of T Cells In Vitro from Mouse Embryonic Stem Cells

Martina Kučerová-Levisohn¹, Jordana Lovett¹, Armin Lahiji¹, Roxanne Holmes², Juan Carlos Zúñiga-Pflücker², Benjamin D. Ortiz¹

¹Department of Biological Sciences, Hunter College and Graduate Center, City University of New York, ²Sunnybrook Research Institute, Department of Immunology, University of Toronto

Mouse embryonic stem cells can be differentiated to T cells in vitro using the OP9-DL1 co-culture system. Success in this procedure requires careful attention to reagent/cell maintenance, and key technique sensitive steps. Here we discuss these critical parameters and provide a detailed protocol to encourage adoption of this technology.

Genetics

Manipulation of Ploidy in Caenorhabditis elegans

Erlyana K. Clarke¹, Katherine A. Rivera Gomez^1,2, Zaki Mustachi¹, Mikaela C. Murph^1,3, Mara Schvarzstein^1,2,3

¹Brooklyn College, Biology Department, City University of New York, ²The Graduate Center, Biology Department, City University of New York, ³Advanced Science Research Center, City University of New York

This method allows for the generation of tetraploid and triploid Caenorhabditis nematodes from any diploid strain. Polyploid strains generated by this method have been used to study chromosome interactions in meiotic prophase, and this method is useful for examining important basic questions in cell, developmental, evolutionary, and cancer biology.

Biology

Visualizing and Tracking Endogenous mRNAs in Live Drosophila melanogaster Egg Chambers

Irina E. Catrina¹, Livia V. Bayer^1,2, Omar S. Omar^1,2, Diana P. Bratu^1,2

¹Biological Sciences Department Hunter College, City University of New York, ²Program in Molecular, Cellular, and Developmental Biology, Graduate Center, City University of New York

Here, we present a protocol for the visualization, detection, analysis and tracking of endogenous mRNA trafficking in live Drosophila melanogaster egg chamber using molecular beacons, spinning disc confocal microscopy, and open-source analysis software.

Behavior

Lexical Decision Task for Studying Written Word Recognition in Adults with and without Dementia or Mild Cognitive Impairment

Alexandre Nikolaev¹, Eve Higby^2,3, JungMoon Hyun⁴, Sameer Ashaie^5,6

¹Helsinki Collegium for Advanced Studies, University of Helsinki, ²University of California, Riverside, ³California State University, East Bay, ⁴Hunter College, City University of New York, ⁵Feinberg School of Medicine, Northwestern University, ⁶Shirley Ryan AbilityLab

This article describes how to implement a simple lexical decision experiment to assess written word recognition in neurologically healthy participants and in individuals with dementia and cognitive decline. We also provide a detailed description of reaction time analysis using principal components analysis (PCA) and mixed-effects modeling.

Genetics

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Ning Zhang^1,2, Shundi Shi², Barney Yoo³, Xiaohong Yuan¹, Wenjia Li⁴, Shenglong Zhang¹

¹Department of Biological and Chemical Sciences, New York Institute of Technology, ²Department of Chemical Engineering, Columbia University, ³Department of Chemistry, Hunter College, City University of New York, ⁴Department of Computer Science, New York Institute of Technology

Here, we describe a detailed protocol for an LC-MS-based sequencing method that can be used as a direct method to sequence short RNA (<35 nt per run) without a cDNA intermediate, and as a general method to sequence different nucleotide modifications in a single study at single-base precision.

Environment

Simulating Impacts of Ice Storms on Forest Ecosystems

John L. Campbell¹, Lindsey E. Rustad¹, Charles T. Driscoll², Ian Halm³, Timothy J. Fahey⁴, Habibollah Fakhraei⁵, Peter M. Groffman^6,7, Gary J. Hawley⁸, Wendy Leuenberger⁹, Paul G. Schaberg¹⁰

¹Northern Research Station, U.S. Forest Service, Durham, NH, ²Department of Civil and Environmental Engineering, Syracuse University, ³Northern Research Station, U.S. Forest Service, North Woodstock, NH, ⁴Department of Natural Resources, Cornell University, ⁵Department of Civil and Environmental Engineering, Southern Illinois University, ⁶Advanced Science Research Center at the Graduate Center, City University of New York, ⁷Cary Institute of Ecosystem Studies, ⁸Rubenstein School of Environment and Natural Resources, University of Vermont, ⁹Department of Forestry and Natural Resources, University of Kentucky, ¹⁰Northern Research Station, U.S. Forest Service, Burlington, VT

Ice storms are important weather events that are challenging to study because of difficulties in predicting their occurrence. Here, we describe a novel method for simulating ice storms that involves spraying water over a forest canopy during sub-freezing conditions.

Experimental Entomology in the Age of Video

Daniel A. Friedman¹, Judith R. Wexler², Sebastian Alvarado³

¹Department of Entomology & Nematology, University of California, ²Department of Ecology, Evolution, and Behavior, The Hebrew University in Jerusalem, ³Department of Biology, Queens College, City University of New York

Experimental Entomology in the Age of Video

Medicine

Mouse Model of Metabolic Dysfunction-Associated Steatotic Liver Disease with Fibrosis

Daniah Khoj^*1, Ryan Huang^*1, Eliza Altvater^*1, Zanib N. Ishfaq¹, Xinyin Jiang¹, Kathleen V. Axen¹, Jorge Matias Caviglia¹

¹Brooklyn College, City University of New York

Mouse model of metabolic dysfunction-associated steatotic liver disease (MASLD) with metabolic dysfunction, hepatic gene expression changes, and liver histopathological alterations that resemble human MASLD, including fibrosis that progresses to advanced fibrosis stage 3. This model can be used in studies of MASLD pathophysiology and in pre-clinical studies of new therapies.