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University Of Massachusetts Amherst

6 ARTICLES PUBLISHED IN JoVE

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.

Engineering

Patterning via Optical Saturable Transitions - Fabrication and Characterization

Precious Cantu¹, Trisha L. Andrew², Rajesh Menon¹

¹Department of Electrical and Computer Engineering, The University of Utah, ²Department of Chemistry, The University of Wisconsin-Madison

We report that the diffraction limit of conventional optical lithography can be overcome by exploiting the transitions of organic photochromic derivatives induced by their photoisomerization at low light intensities.^1-3 This paper outlines our fabrication technique and two locking mechanisms, namely: dissolution of one photoisomer and electrochemical oxidation.

Chemistry

A Filter-based Surface Enhanced Raman Spectroscopic Assay for Rapid Detection of Chemical Contaminants

Siyue Gao¹, Jessica Glasser¹, Lili He¹

¹Department of Food Science, University of Massachusetts Amherst

A procedure for fabrication and performing the filter-based surface enhanced Raman spectroscopic (SERS) assay for the detection of chemical contaminants (i.e., pesticide ferbam and antibiotic ampicillin) is presented.

Genetics

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Blake L. Joyce^1,2, Asher K. Haug-Baltzell³, Jonathan P. Hulvey⁴, Fiona McCarthy⁵, Upendra Kumar Devisetty^1,6, Eric Lyons^1,2,3

¹BIO5 Institute, University of Arizona, ²The School of Plant Sciences, University of Arizona, ³Genetics GIDP, University of Arizona, ⁴Biology Department, University of Massachusetts Amherst, ⁵School of Animal and Comparative Biomedical Sciences, University of Arizona, ⁶CyVerse, University of Arizona

This protocol outlines a comparative de novo transcriptome assembly and annotation workflow for novice bioinformaticians. The workflow is available for free entirely through CyVerse and connected by the Data Store. Command line and graphical user interfaces are used, but all code needed is available to copy and paste.

Chemistry

Reactive Vapor Deposition of Conjugated Polymer Films on Arbitrary Substrates

Nongyi Cheng^1,2, Trisha L. Andrew^2,3

¹Department of Chemistry, University of Wisconsin-Madison, ²Department of Chemistry, University of Massachusetts Amherst, ³Department of Polymer Science and Engineering, University of Massachusetts Amherst

This paper presents a protocol for reactive vapor deposition of poly(3,4-ethylenedioxythiophene), poly(3,4-propylenedioxythiophene), and poly(thieno[3,2-b]thiophene) films on glass slides and rough substrates, such as textiles and paper.

Chemistry

Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry

Zachary J. Kirsch¹, Blaise G. Arden¹, Richard W. Vachet^*1,2, Patanachai Limpikirati^*3

¹Department of Chemistry, University of Massachusetts Amherst, ²Molecular and Cellular Biology Program, University of Massachusetts Amherst, ³Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University

The experimental procedures for performing diethylpyrocarbonate-based covalent labeling with mass spectrometric detection are described. Diethylpyrocarbonate is simply mixed with the protein or protein complex of interest, leading to the modification of solvent accessible amino acid residues. The modified residues can be identified after proteolytic digestion and liquid chromatography/mass spectrometry analysis.