In this episode of the Epigenetics Podcast, we caught up with Karol Bomsztyk M.D. and Tom Matula, Ph.D. from the University of Washington and Matchstick Technologies, to talk about their work on DNA and chromatin sonication.
During his career, Karol's research has focused on improving ChIP protocols to make them faster, easier and higher throughput. First, to make ChIP assays faster, Karol and his lab developed "Fast-ChIP". More recently, he adjusted this protocol to improve throughput and "Matrix-ChIP" was born. Tom is an expert in the field of ultrasound and cavitation and the Director of the Center for Industrial and Medical Ultrasound at the University of Washington.
To further improve and speed up the 96-well "Matrix-ChIP" protocol, Karol and Tom teamed up to found Matchstick Technologies and develop a sonication device that would be able to processes each and every well of a 96-well microplate consistently and quickly. The result of this cooperation is the PIXUL Multi-Sample Sonicator that is now available for order from Active Motif.
PIXUL is an ultrasound-based sample preparation platform that was designed completely from the ground up to provide researchers with an easy-to-use tool that is simple to set up, simple to use, and generates consistent results day in and day out. No other sample preparation platform out there can match the power and convenience of PIXUL.
PIXUL was conceived by an epigenetics researcher, and designed and built by ultrasound engineers to take the guesswork out of sample preparation. With PIXUL, sample preparation is no longer an art form, but instead a simple and predictable part of experiments that work every single time.
This interview goes into the mechanism behind sonication-based shearing of DNA and chromatin and highlights how PIXUL is different from existing sonication instruments.
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Effects of DNA Methylation on Diabetes (Charlotte Ling)
Nutriepigenetics: The Effects of Diet on Behavior (Monica Dus)
Investigating the Dynamics of Epigenetic Plasticity in Cancer with Single Cell Technologies (Céline Vallot)
Epigenetic Regulation of Stem Cell Self-Renewal and Differentiation (Margaret “Peggy” Goodell)
Genome-Wide Investigation of Epigenetic Marks and Nucleosome Positioning (Keji Zhao)
The Role of lncRNAs in Tumor Growth and Treatment (Sarah Diermeier)
Unraveling Mechanisms of Chromosome Formation (Job Dekker)
Transcription and Polycomb in Inheritance and Disease (Danny Reinberg)
The Epigenetics of COVID-19
Epigenetic Reprogramming During Mammalian Development (Wolf Reik)
In vivo Nucleosome Structure and Dynamics (Srinivas Ramachandran)
Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret)
The Role of Small RNAs in Transgenerational Inheritance in C. elegans (Oded Rechavi)
Development of Site-Specific ChIP Technologies (Hodaka Fujii)
Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni)
How the "Fragile Nucleosome" Science Community Came to Life (Christine Cucinotta, Melvin Noe Gonzalez)
Epigenetic Influence on Memory Formation and Inheritance (Isabelle Mansuy)
Influence of Dynamic RNA Methylation on Gene Expression (Chuan He)
How to Publish in Nature: Lessons from the ENCODE Consortium (Michelle Trenkmann, Senior Editor at Nature)
The Role of Non-Histone Proteins in Chromosome Structure and Function During Mitosis (Bill Earnshaw)
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