Stony Brook University

7 articles published in JoVE

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

JoVE 4273 12/10/2012

Haipeng Xing¹, Willey Liao^1,2, Yifan Mo^1,2, Michael Q. Zhang^2,3

¹Department of Applied Mathematics & Statistics, Stony Brook University, ²Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory, ³Department of Molecular and Cell Biology, University of Texas at Dallas

Our Bayesian Change Point (BCP) algorithm builds on state-of-the-art advances in modeling change-points via Hidden Markov Models and applies them to chromatin immunoprecipitation sequencing (ChIPseq) data analysis. BCP performs well in both broad and punctate data types, but excels in accurately identifying robust, reproducible islands of diffuse histone enrichment.

Chemoselective Modification of Viral Surfaces via Bioorthogonal Click Chemistry

JoVE 4246 8/19/2012

Frederick A. Rubino, Yoon Hyeun Oum, Lakshmi Rajaram, Yanjie Chu, Isaac S. Carrico

Department of Chemistry, Stony Brook University

Adenovirus particles are engineered to contain either the unnatural amino acid analogue azidohomoalanine or the azido sugar O-GlcNAz. The azide group of each is chemoselectively ligated via "click" chemistry reactions as a means of viral surface modification.

Measuring Fast Calcium Fluxes in Cardiomyocytes

JoVE 3505 11/29/2011

Urszula Golebiewska¹, Suzanne Scarlata²

¹Department of Biological Sciences and Geology, Queensborough Community College, ²Department of Physiology & Biophysics, Stony Brook University

We present a method to isolate rapid (microsecond) calcium events from slower fluxes in living cells using laser scanning confocal microscopy. The method measures fluorescence intensity fluctuations of calcium indicators by recording line scans of several hundred pixels in a cell. Histogram analysis allows us to isolate the time scales of different calcium fluxes.

Establishment of Epstein-Barr Virus Growth-transformed Lymphoblastoid Cell Lines

JoVE 3321 11/08/2011

Joyce Hui-Yuen^1,2, Shane McAllister^1,2, Siva Koganti², Erik Hill², Sumita Bhaduri-McIntosh^1,2,3,4

¹Stony Brook Children's Hospital, State University of New York at Stony Brook, ²Department of Pediatrics, State University of New York at Stony Brook, ³Department of Molecular Genetics, State University of New York at Stony Brook, ⁴Department of Microbiology, State University of New York at Stony Brook

We describe a method for generating transformed B cell lines using Epstein-Barr virus. We also illustrate a novel assay that can identify B cells destined to undergo transformation as early as three days after infection.

Derivation of Enriched Oligodendrocyte Cultures and Oligodendrocyte/Neuron Myelinating Co-cultures from Post-natal Murine Tissues

JoVE 3324 8/21/2011

Ryan W. O'Meara^1,2, Scott D. Ryan¹, Holly Colognato³, Rashmi Kothary^1,2,4

¹Regenerative Medicine Program, Ottawa Hospital Research Institute, ²Department of Cellular and Molecular Medicine, University of Ottawa, ³Department of Pharmacological Sciences, Stony Brook University, ⁴Department of Medicine, University of Ottawa

This article describes methods to derive enriched populations of murine oligodendrocyte precursor cells (OPCs) in primary culture, which differentiate to produce mature oligodendrocytes (OLs). In addition, this report describes techniques to produce murine myelinating co-cultures by seeding mouse OPCs onto a neurite bed of mouse dorsal root ganglion neurons (DRGNs).

Studying the Integration of Adult-born Neurons

JoVE 2548 3/25/2011

Yan Gu, Stephen Janoschka, Shaoyu Ge

Department of Neurobiology & Behavior, State University of New York at Stony Brook

A way to study the integration of newborn dentate granule cells in adult animals is described. This technique uses an engineered retrovirus to label newborn neurons, followed by electrophysiological recordings to determine in vivo functional integration.

A Cell-to-cell Macromolecular Transport Assay in Planta Utilizing Biolistic Bombardment

JoVE 2208 8/27/2010

Shoko Ueki¹, Benjamin L. Meyers¹, Farzana Yasmin², Vitaly Citovsky²

¹Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, ²Bio-Medical Engineering Department, NED University of Engineering and Technology

Macromolecular trafficking between plant cells can be assessed by transiently expressing a fluorescently-tagged protein of interest and analyzing its intra- and intercellular distribution by confocal microscopy.