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Mobile-CRISPRi: Bringing CRISPRi to Diverse Bacteria

Posted by Beth Kenkel on Apr 4, 2019 8:53:46 AM

The vast majority of bacteria are undomesticated which limits the tools scientists can use to study them. For example, gene knockdown with CRISPR interference (CRISPRi) has been limited to lab-adapted bacteria because it has been challenging to introduce CRISPRi machinery into diverse bacteria species. Existing protocols can transfer CRISPRi into a single bacterial strain, such as a B. subtilis, or a narrow range of bacterial species, such as the human gut bacteria B. thetaiotaomicron, Mycobacterium, Pseudomonas, and E. coli. However, many non-model bacterial species lack genetic tools.

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Topics: CRISPR, CRISPR Expression Systems and Delivery Methods

What's New in CRISPR - Spring 2019

Posted by Jennifer Tsang on Mar 21, 2019 8:47:48 AM

In this quarterly blog series, we’ll highlight a few of the new CRISPR plasmids available at Addgene. We will still periodically focus on specific CRISPR plasmid tools more in-depth, but we hope that this blog series will help you find new CRISPR tools for your research.

 

 

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Topics: CRISPR

Targeted Mutagenesis with EvolvR

Posted by Beth Kenkel on Feb 21, 2019 8:15:26 AM

Mutagenesis is a tool that both evolution and molecular biologists use to tinker with DNA. Making changes to a DNA sequence can help scientists identify and/or facilitate the evolution of new phenotypes, and forward genetics harnesses this at a large scale by screening diverse libraries of genetic variants. Several methods for generating mutant libraries exist, but none provide a means to continuously diversify all nucleotides within a user-defined genomic region. EvolvR, a CRISPR-Cas9 based targeted mutagenesis method developed by the Dueber Lab at Berkeley, provides a new approach for generating novel genetic variants in bacteria. Read on to learn about the key components of EvolvR and its potential applications.

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Topics: CRISPR, Other CRISPR Tools

CrispyCrunch: High-throughput Design and Analysis of CRISPR+HDR Experiments

Posted by Guest Blogger on Feb 7, 2019 9:16:20 AM

This post was contributed by Greg Dingle, a software engineer with the Chan Zuckerberg Initiative.

We hereby announce the general availability of new a tool for CRISPR scientists––CrispyCrunch! CrispyCrunch is a web app that helps scientists design and analyze batches of CRISPR samples.

We invite you to jump in and try it out, or take a look at our live examples: experiment or analysis. In the rest of this article, we'll explain the thinking behind the tool, its key features, how it works, and how to use it.

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Topics: CRISPR, Other CRISPR Tools

CRISPR 101: CRISPR-mediated Plant Base Editors

Posted by Guest Blogger on Jan 3, 2019 8:35:29 AM

This post was contributed by Kutubuddin Molla, a Fulbright Visiting Scholar at the Pennsylvania State University.

Imagine you are dealing with a defective gene, Xm, the sequence of which is identical to the correct gene, Xw, except for a single base. If you heard about CRISPR, one question probably comes to mind: can CRISPR be applied to fix the defective base precisely?

Until 2016, precise single base changes were only possible through exploiting the homology-directed repair (HDR) pathway which occurs in cells at low frequencies and relies on the efficient delivery of donor DNA to facilitate repair. Since the development of CRISPR-mediated base editing (BE), these types of repairs can now be done more efficiently than before. A base editor precisely changes a single base with an efficiency typically ranging from 25-75%, while the success of precise change via HDR limited to 0-5%. This blog post covers a brief review of different basic BE technologies and their adaptation for plant genome editing.
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Topics: CRISPR, Plant Biology, CRISPR 101, Base Editing

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