University of San Diego

5 ARTICLES PUBLISHED IN JoVE

Bioengineering

Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices

Gordon D. Hoople^*1, Andrew Richards^*2, Yan Wu², Albert P. Pisano³, Kun Zhang²

¹Department of Engineering, University of San Diego, ²Department of Bioengineering, University of California, San Diego, ³Department of Mechanical and Aerospace Engineering, University of California, San Diego

Gel-seq enables researchers to simultaneously prepare libraries for both DNA- and RNA-seq at negligible added cost starting from 100 - 1000 cells using a simple hydrogel device. This paper presents a detailed approach for the fabrication of the device as well as the biological protocol to generate paired libraries.

Engineering

Building Langmuir Probes and Emissive Probes for Plasma Potential Measurements in Low Pressure, Low Temperature Plasmas

Peixuan Li^*1, Noah Hershkowitz^*1, Gregory Severn^*2

¹Department of Engineering Physics, University of Wisconsin, ²Department of Physics & Biophysics, University of San Diego

The main goal of this work is to make it easier for research groups unfamiliar with Langmuir probes and emissive probes to use them as plasma diagnostics, especially near plasma boundaries. We do this by demonstrating how to build the probes from readily available materials and supplies.

Bioengineering

Quantifying Cytoskeleton Dynamics Using Differential Dynamic Microscopy

Hannah N. Verwei¹, Gloria Lee², Gregor Leech², Irene Istúriz Petitjean³, Gijsje H. Koenderink³, Rae M. Robertson-Anderson², Ryan James McGorty²

¹Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, ²Department of Physics and Biophysics, University of San Diego, ³Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology

Differential dynamic microscopy (DDM) combines features of dynamic light scattering and microscopy. Here, the process of using DDM to characterize reconstituted cytoskeleton networks by quantifying the subdiffusive and caged dynamics of particles in vimentin networks and the ballistic motion of active myosin-driven actin-microtubule composites is presented.

Biology

Reconstituting and Characterizing Actin-Microtubule Composites with Tunable Motor-Driven Dynamics and Mechanics

Mehrzad Sasanpour¹, Daisy H. Achiriloaie^1,2, Gloria Lee¹, Gregor Leech¹, Maya Hendija¹, K. Alice Lindsay³, Jennifer L. Ross³, Ryan J. McGorty¹, Rae M. Robertson-Anderson¹

¹Department of Physics and Biophysics, University of San Diego, ²W. M. Keck Science Department, Scripps College, Pitzer College, and Claremont McKenna College, ³Department of Physics, Syracuse University

This paper presents protocols for engineering and characterizing tunable three-dimensional composite networks of co-entangled actin filaments and microtubules. Composites undergo active restructuring and ballistic motion, driven by myosin II and kinesin motors, and are tuned by the relative concentrations of actin, microtubules, motor proteins, and passive crosslinkers.

Design and Building of a Customizable, Single-Objective, Light-Sheet Fluorescence Microscope for the Visualization of Cytoskeleton Networks

Nathan Felcher¹, Daisy Achiriloaie¹, Brian Lee², Ryan McGorty³, Janet Sheung^1,2,4

¹W.M. Keck Science Department, Scripps College, ²W.M. Keck Science Department, Claremont McKenna College, ³Department of Physics and Biophysics, University of San Diego, ⁴W.M. Keck Science Department, Pitzer College

This protocol describes in detail how to build a single-objective, light-sheet fluorescence microscope and its usage for visualizing cytoskeleton networks.