University of Massachusetts

6 ARTICLES PUBLISHED IN JoVE

Biology

Computer-assisted Large-scale Visualization and Quantification of Pancreatic Islet Mass, Size Distribution and Architecture

Abraham Kim¹, German Kilimnik¹, Charles Guo¹, Joshua Sung¹, Junghyo Jo², Vipul Periwal², Piotr Witkowski³, Philip Dilorio⁴, Manami Hara¹

¹Department of Medicine, University of Chicago, ²Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, ³Department of Surgery, University of Chicago, ⁴Diabetes Division, University of Massachusetts

Novel computer-assisted methods of large-scale procurement and analysis of immunohistochemically stained pancreatic specimens are described: (1) Virtual Slice capture of the entire section; (2) Mass analysis of large-scale data; (3) Reconstruction of 2D Virtual Slices; (4) 3D islet mapping; and (5) Mathematical analysis.

Biology

A Matrigel-Based Tube Formation Assay to Assess the Vasculogenic Activity of Tumor Cells

Ralph A. Francescone III¹, Michael Faibish¹, Rong Shao^1,2,3

¹Molecular and Cellular Biology Program, Morrill Science Center, University of Massachusetts, ²Pioneer Valley Life Sciences Institute, University of Massachusetts, ³Department of Veterinary and Animal Sciences, University of Massachusetts

A tube formation assay is used to evaluate vascular activity of tumor cells.

Neuroscience

Measuring Neural Mechanisms Underlying Sleep-Dependent Memory Consolidation During Naps in Early Childhood

Tamara Allard^*1, Tracy Riggins^*1, Arcadia Ewell¹, Benjamin Weinberg¹, Sanna Lokhandwala², Rebecca M. C. Spencer^2,3

¹Department of Psychology, University of Maryland, ²Department of Psychological and Brain Sciences, University of Massachusetts, ³Neuroscience and Behavior, University of Massachusetts

This protocol describes methods used to examine neural mechanisms underlying sleep-dependent memory consolidation during naps in early childhood. It includes procedures for examining the effect of sleep on behavioral memory performance, as well as the application and recording of both polysomnography and actigraphy.

Biochemistry

Platform Incubator with Movable XY Stage: A New Platform for Implementing In-Cell Fast Photochemical Oxidation of Proteins

Danté Johnson¹, Benjamin Punshon-Smith², Jessica A. Espino¹, Anne Gershenson³, Lisa M. Jones¹

¹Department of Pharmaceutical Sciences, University of Maryland Baltimore, ²Technology Research Center, University of Maryland Baltimore County, ³Department of Biochemistry and Molecular Biology, University of Massachusetts

A new static platform is used to characterize protein structure and interaction sites in the native cell environment utilizing a protein footprinting technique called in-cell fast photochemical oxidation of proteins (IC-FPOP).

Environment

Rapid Testing of Resistance of Timber to Biodegradation by Marine Wood-Boring Crustaceans

Lucy S. Martin¹, J. Reuben Shipway^1,2, Marc A. Martin¹, Graham P. Malyon¹, Mou Akter¹, Simon M. Cragg¹

¹University of Portsmouth, ²Microbiology Department, University of Massachusetts

This protocol presents a method for assessing the feeding rate of the wood-boring crustacean, Limnoria, by measuring faecal pellet production. This method is designed for use in non-specialist labs and has potential for incorporation into standard testing protocols, to evaluate enhanced wood durability under marine conditions.

Biology

Alignment of Synchronized Time-Series Data Using the Characterizing Loss of Cell Cycle Synchrony Model for Cross-Experiment Comparisons

Sophia A. Campione¹, Christina M. Kelliher², David A. Orlando³, Trung Q. Tran⁴, Steven B. Haase¹

¹Department of Biology, Duke University, ²Department of Biology, University of Massachusetts, ³Orlando Data Science LLC, ⁴Department of Computer Science, Duke University

One challenge of analyzing synchronized time-series experiments is that the experiments often differ in the length of recovery from synchrony and the cell-cycle period. Thus, the measurements from different experiments cannot be analyzed in aggregate or readily compared. Here, we describe a method for aligning experiments to allow for phase-specific comparisons.