Harvesting Alveolar Macrophages from the Mouse

Harvesting Alveolar Macrophages from the Mouse Using Lung Lavage

Chavez-Santoscoy AV, Huntimer LM, Ramer-Tait AE, Wannemuehler M, Narasimhan B: Harvesting murine alveolar macrophages and evaluating cellular activation induced by polyanhydride nanoparticles. Journal of visualized experiments : JoVE 2012(64):e3883.

Biodegradable nanoparticles have emerged as a versatile platform for the design and implementation of new intranasal vaccines against […]

By |March 15th, 2017|Categories: Protocols, Publications, Respiratory System||0 Comments

Murine Model of DSS-induced Acute Colitis

Murine Model of DSS-induced Acute Colitis

J Vis Exp. 2012 Feb 1;(60). pii: 3678. doi: 10.3791/3678. Investigating intestinal inflammation in DSS-induced model of IBD. Kim JJ1, Shajib MS, Manocha MM, Khan WI. 

Inflammatory bowel disease (IBD) encompasses a range of intestinal pathologies, the most common of which are ulcerative colitis (UC) and Crohn’s Disease (CD). Both UC […]

By |February 27th, 2017|Categories: Gastrointestinal System, Protocols, Publications||0 Comments

Airway Hyperresponsiveness in Murine Tracheal Rings

Assessment of Airway Hyperresponsiveness in Murine Tracheal Rings. Methods Mol Biol. 2013;1032:257-69. doi: 10.1007/978-1-62703-496-8_20.

Isolated tracheal rings have often been used to directly measure the contractile output of airway smooth muscle (ASM). Here, we describe the method for excising murine tracheas, mounting tracheal rings in organ baths, and measuring the isometric forces generated by the ASM when […]

By |February 12th, 2017|Categories: Protocols, Respiratory System||0 Comments

Differential gene and transcript expression analysis of RNA-seq

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn and Lior Pachter: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 2012,  7, 562-578.

Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and […]

Comparison of cell counting methods

Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and considerations for experimental design

Patti C. Zeidler-Erdely, James M. Antonini, Terence G. Meighan, Shih-Houng Young, Tracy J. Eye, Mary Ann Hammer & Aaron Erdely (2016) Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and […]

In vivo Imaging and Tracking of Host-Microbiota Interactions via Metabolic

In vivo Imaging and Tracking of Host-Microbiota Interactions via Metabolic Labeling of Gut Anaerobic Bacteria
Naama Geva-Zatorsky, David Alvarez, Jason E. Hudak, Nicola C. Reading, Deniz Erturk-Hasdemir, Suryasarathi Dasgupta, Ulrich H. von Andrian, and Dennis L. Kasper: Nat Med. 2015 Sep; 21(9): 1091–1100. Published online 2015 Aug 17. doi:  10.1038/nm.3929

“The intestine is densely populated by anaerobic […]

T Lymphocyte Density and Distribution in Human Colorectal Mucosa, and Inefficiency of Current Cell Isolation Protocols

T Lymphocyte Density and Distribution in Human Colorectal Mucosa, and Inefficiency of Current Cell Isolation Protocols
Preza GC, Yang OO, Elliott J, Anton PA, Ochoa MT: T Lymphocyte Density and Distribution in Human Colorectal Mucosa, and Inefficiency of Current Cell Isolation Protocols. PLoS One 2015 Apr 9;10(4):e0122723.

“Mucosal tissues are critical immune effector sites containing complex populations of […]

Isolation and Cytokine Analysis of Lamina Propria Lymphocytes

Isolation and Cytokine Analysis of Lamina Propria Lymphocytes from Mucosal Biopsies of the Human Colon
Bowcutt R, Malter LB, Chen LA, Wolff MJ, Robertson I, Rifkin DB, Poles M, Cho I, Loke P: Isolation and Cytokine Analysis of Lamina Propria Lymphocytes from Mucosal Biopsies of the Human Colon. J Immunol Methods 2015 Jun;421:27-35. 

“Much of our understanding of […]

Defining Human Dendritic Cell Progenitors by Multiparametric Flow Cytometry

Defining Human Dendritic Cell Progenitors by Multiparametric Flow Cytometry

G. Breton, J. Lee, K. Liu, M.C. Nussenzweig: Defining human dendritic cell progenitors by multiparametric flow cytometry. Nat Protoc. 2015 Sep;10(9):1407-22. PMC4607256.

Dendritic cells (DCs) play an important role in the maintenance of mucosal homeostasis and the induction of antigen-specific mucosal immune responses.  DCs develop from bone marrow from increasingly restricted but phenotypically well-defined progenitor […]

By |November 30th, 2015|Categories: 2015, News, Protocols, Publications, SMI Archives||0 Comments

Generating Human Intestinal Tissue from Pluripotent Stem Cells

Generating Human Intestinal Tissue from Pluripotent Stem Cells In Vitro

K.W. McCracken, J.C. Howell, J.M. Wells, J.R. Spence:  Generating human intestinal tissue from pluripotent stem cells in vitro.  Nat Protoc. 2011 Nov 10;6(12):1920-8. PMC3896236

Three-dimensional cultures of mucosal epithelial cells termed organoids are considered the most physiological models of primary epithelial cells in vitro and have […]

By |November 30th, 2015|Categories: 2015, News, Protocols, Publications, SMI Archives||0 Comments