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University of California Berkeley

10 ARTICLES PUBLISHED IN JoVE

Neuroscience

Stereotaxic Surgery for Excitotoxic Lesion of Specific Brain Areas in the Adult Rat

Elizabeth D. Kirby¹, Kelly Jensen², Ki A. Goosens³, Daniela Kaufer^1,4

¹Helen Wills Neuroscience Institute, University of California Berkeley, ²Office of Laboratory Animal Care, University of California Berkeley, ³McGovern Institute for Brain Research & The Department of Brain and Cognitive Science, Massachusetts Institute of Technology, ⁴Integrative Biology Department, University of California Berkeley

Targeted ablation of specific brain region(s) by infusion of an excitotoxin using stereotaxic coordinates is described. This technique could also be adapted for infusion of other chemicals into the rat brain.

Engineering

Failure Analysis of Batteries Using Synchrotron-based Hard X-ray Microtomography

Katherine J. Harry^1,2, Dilworth Y. Parkinson³, Nitash P. Balsara^2,4,5

¹Department of Materials Science and Engineering, University of California Berkeley, ²Materials Science Division, Lawrence Berkeley National Laboratory, ³Advanced Light Source Division, Lawrence Berkeley National Laboratory, ⁴Department of Chemical and Biomolecular Engineering, University of California Berkeley, ⁵Environmental Energy Technology Division, Lawrence Berkeley National Laboratory

Synchrotron-based hard X-ray microtomography is used to image the electrochemical growth of dendrites from a lithium metal electrode through a solid polymer electrolyte membrane.

Bioengineering

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Jackson T. Del Bonis-O’Donnell¹, Abraham Beyene¹, Linda Chio¹, Gözde Demirer¹, Darwin Yang¹, Markita P. Landry^1,2

¹Department of Chemical and Biomolecular Engineering, University of California Berkeley, ²California Institute for Quantitative Biosciences (QB3), University of California Berkeley

We present a protocol for engineering the corona phase of near infrared fluorescent single walled carbon nanotubes (SWNTs) using amphiphilic polymers and DNA to develop sensors for molecular targets without known recognition elements.

Genetics

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

Joanna M. Feehan^*1,2, Katherine E. Scheibel^*1, Salim Bourras³, William Underwood⁴, Beat Keller³, Shauna C. Somerville¹

¹Department of Plant and Microbial Biology, University of California Berkeley, ²John Innes Centre, Norwich Research Park, ³Department of Plant and Microbial Biology, University of Zürich, ⁴USDA-ARS Sunflower and Plant Biology Research Unit

Described here is a method for the extraction, purification, and quality control of genomic DNA from the obligate biotrophic fungal pathogen, powdery mildew, for use in long-read genome sequencing.

Behavior

Novel Object Recognition and Object Location Behavioral Testing in Mice on a Budget

Jiyeon K. Denninger¹, Bryon M. Smith¹, Elizabeth D. Kirby^1,2,3

¹Department of Psychology, Ohio State University, ²Department of Neuroscience, Ohio State University, ³Center for Chronic Brain Injury, Ohio State University

Here we provide a protocol which includes comprehensive instructions for the economical establishment of murine object location and novel object recognition behavioral testing, including the design, cost, and construction of required equipment as well as execution of behavioral testing, data collection, and analysis.

Genetics

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Carly V. Weiss^1,2, Julie N. Chuong³, Rachel B. Brem^1,3

¹Department of Plant and Microbial Biology, University of California Berkeley, ²Department of Biology, Stanford University, ³Buck Institute for Research on Aging

Reciprocal hemizygosity via sequencing (RH-seq) is a powerful new method to map the genetic basis of a trait difference between species. Pools of hemizygotes are generated by transposon mutagenesis and their fitness is tracked through competitive growth using high-throughout sequencing. Analysis of the resulting data pinpoints genes underlying the trait.

Bioengineering

Patterning the Geometry of Human Embryonic Stem Cell Colonies on Compliant Substrates to Control Tissue-Level Mechanics

Jonathon M. Muncie^1,2, Roberto Falcón-Banchs¹, Johnathon N. Lakins², Lydia L. Sohn^1,3, Valerie M. Weaver^2,4,5,6

¹Graduate Program in Bioengineering, University of California San Francisco and University of California Berkeley, ²Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, ³Department of Mechanical Engineering, University of California Berkeley, ⁴Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, ⁵UCSF Comprehensive Cancer Center, Helen Diller Family Cancer Research Center, University of California San Francisco, ⁶Department of Anatomy, Department of Bioengineering and Therapeutic Sciences, and Department of Radiation Oncology, University of California San Francisco

Extracellular matrix ligands can be patterned onto polyacrylamide hydrogels to enable the culture of human embryonic stem cells in confined colonies on compliant substrates. This method can be combined with traction force microscopy and biochemical assays to examine the interplay between tissue geometry, cell-generated forces, and fate specification.

Bioengineering

Simple, Affordable, and Modular Patterning of Cells using DNA

Katelyn A. Cabral¹, David M. Patterson², Olivia J. Scheideler¹, Russell Cole³, Adam R. Abate^4,5,6, David V. Schaffer^7,8, Lydia L. Sohn⁹, Zev J. Gartner^2,6,10

Here we present a protocol to micropattern cells at single-cell resolution using DNA-programmed adhesion. This protocol uses a benchtop photolithography platform to create patterns of DNA oligonucleotides on a glass slide and then labels cell membranes with commercially available complementary oligonucleotides. Hybridization of the oligos results in programmed cell adhesion_.

Biology

Methods for Rearing the Parasitoid Ganaspis brasiliensis, a Promising Biological Control Agent for the Invasive Drosophila suzukii

Marco Valerio Rossi-Stacconi¹, Xingeng Wang², Amanda Stout², Lorenzo Fellin^1,3, Kent M. Daane⁴, Antonio Biondi⁵, Judith M. Stahl⁴, Matthew L. Buffington⁶, Gianfranco Anfora^1,3, Kim A. Hoelmer²

¹Research and Innovation Centre, Fondazione Edmund Mach, ²Beneficial Insects Introduction Research Unit, Agricultural Research Service, United States Department of Agriculture, ³Center for Agriculture, Food and Environment, University of Trento, ⁴Department of Environmental Science, Policy and Management, University of California Berkeley, ⁵Department of Agriculture, Food and Environment, University of Catania, ⁶Systematic Entomology Laboratory, Agricultural Research Service, United States Department of Agriculture

Ganaspis brasiliensis-a larval parasitoid of Drosophila suzukii (a global invasive fruit crop pest)-has been approved or is considered for introduction into Europe and the United States for biological control of this pest. This article provides protocols for both small-scale and large-scale rearing of this parasitoid.

Bioengineering

Mechano-Node-Pore Sensing: A Rapid, Label-Free Platform for Multi-Parameter Single-Cell Viscoelastic Measurements

Andre Lai^*1, Rachel Rex^*2, Kristen L. Cotner¹, Alan Dong³, Michael Lustig^1,3, Lydia L. Sohn^1,2

¹Graduate Program in Bioengineering, University of California, Berkeley and University of California, San Francisco, ²Department of Mechanical Engineering, University of California, Berkeley, ³Department of Electrical Engineering and Computer Sciences, University of California, Berkeley

Presented here is a method to mechanically phenotype single cells using an electronics-based microfluidic platform called mechano-node-pore sensing (mechano-NPS). This platform maintains moderate throughput of 1-10 cells/s while measuring both the elastic and viscous biophysical properties of cells.