University of Massachusetts View Institution's Website 7 articles published in JoVE 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. Environment Rapid Testing of Resistance of Timber to Biodegradation by Marine Wood-Boring Crustaceans Lucy S. Martin1, J. Reuben Shipway1,2, 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. 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). Bioengineering Microfluidic Device for Recreating a Tumor Microenvironment in Vitro Bhushan J. Toley*1, Dan E. Ganz*1, Colin L. Walsh1, Neil S. Forbes1 1Department of Chemical Engineering, University Of Massachusetts Amherst We present the procedure for fabrication and operation of a microfluidic device that recreates heterogeneous tumor microenvironments in vitro. The variability in apoptosis within tumor tissue was quantified using fluorescent stains and the effective diffusion coefficient of the chemotherapeutic drug doxorubicin into tumor tissue was evaluated. Biology A Matrigel-Based Tube Formation Assay to Assess the Vasculogenic Activity of Tumor Cells Ralph A. Francescone III1, Michael Faibish1, Rong Shao1,2,3 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. 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 Mammary Epithelial Transplant Procedure Karen A. Dunphy1,2, Luwei Tao3, D. Joseph Jerry1,2 1Department of Veterinary and Animal Sciences, University of Massachussetts, 2Pioneer Valley Life Sciences institute, 3Molecular and Cellular Biology, University of Massachussetts This article demonstrates the procedure developed by DeOme KB et al. (1959) and the sparing procedure developed by Brill B et al. (2008) for clearing the 4th inguinal mammary fat pad of a pubescent mouse in preparation for transplantation of mammary fragments, mammary epithelial cells, or mammary tumor cells.