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Beth Kenkel

Beth Kenkel is currently a research scientist at a cell therapy company. She is particularly interested in science communication and viral vectors. Follow Beth on twitter @ElizabethKenkel.

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Four Ways to Package Transgenes That Exceed the Size Limit of Adeno-associated Virus

Posted by Beth Kenkel on Sep 1, 2020 9:15:00 AM

Adeno-associated virus (AAV) has many features which make it a great viral vector, but its packaging capacity is limited to ~4.7kb, or roughly half the packaging limits of lentiviral and adenoviral vectors. While many transgene will fit within this limit, some like prime editing's PE2 enzyme do not. So how do you fit a big gene into a tiny vector like AAV? By breaking the transgene into smaller pieces.

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Topics: Viral Vectors, AAV

Viral Vectors 101: Parts of the AAV Transfer Plasmid

Posted by Beth Kenkel on Aug 11, 2020 9:15:00 AM

So you have this awesome experiment you want to do, but it requires some AAV. You’ve never worked with AAV before, but you aren’t going to let that stop you. Where do you start? Turns out like all good experiments, making AAV starts with some plasmids. You just need three plasmids to start making AAV

  1. the packaging plasmid which contains the structural and packaging genes,
  2. the helper plasmid which contains the proteins needed for the virus to replicate, 
  3. and the transfer plasmid which contains the viral genome.

In today’s blog post, we’ll focus on the AAV transfer plasmid and take a look at each of its parts.

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Topics: Viral Vectors, Viral Vectors 101, AAV

CRISPR 101: Anti-CRISPR Proteins Switch Off CRISPR-Cas Systems

Posted by Beth Kenkel on Jul 23, 2020 9:20:27 AM

Originally published May 23, 2017 and last updated Jul 23, 2020 by Jennifer Tsang.

CRISPR-Cas technology is constantly evolving. Variants of Cas proteins can be used for genome editing, activating gene expression, repressing gene expression, and much more. But there’s one thing that was missing: a way to shut off Cas’s activity. The concern is that the longer Cas remains active in a cell, the greater chances there are for off-target edits to occur. Although methods to switch on Cas activity using light or drugs have been developed, the field lacked an “off-switch” for Cas proteins.

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Topics: CRISPR, CRISPR 101

How to Prepare for an Industry Interview

Posted by Beth Kenkel on Jul 9, 2020 9:15:00 AM

Congratulations, you’ve just landed an interview for an industry job! You’ve worked hard to earn this opportunity and are excited for this next step. But wait, now you feel a little panicked. You’ve never had an industry interview before. What should you do to get ready for this interview?

Maybe the above scenario sounds familiar to you. It was my experience not long ago. I just recently started working in the pharmaceuticals industry after earning my Master’s in 2016 and then working four more years in academia. During my job hunt, I quickly noticed one of the biggest differences between applying for an academic position versus an industry position is the on-site interviewing process.

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Topics: Science Careers, Applying for Jobs, Early Career Researcher

Multiplexed Capture of Promoter-enhancer 3D Chromatin Structures Using CRISPR

Posted by Beth Kenkel on Jul 2, 2020 8:40:00 AM

Originally published Dec 7, 2017 and updated Jul 2, 2020.

Promoters may be the star of gene regulation, but enhancers and chromatin looping play important supporting roles. Enhancers are cis regulatory DNA sequences that, when bound by transcription factors, can increase a gene’s transcription. Sometimes enhancers are located thousands of base pairs away from the gene they regulate, but are brought in proximity by the looping of chromatin, the complex of DNA and proteins that forms chromosomes.

These long range DNA interactions are often detected with chromosome conformation capture (3C) based methods, such as 5C or Hi-C (Han et al., 2018). Think of 3C methods as taking a snapshot of chromatin looping with the photo “developed” by analyzing DNA sequencing data. While “pictures” generated with current 3C methods provide useful information about chromatin interactions, they are grainy so it’s hard to make out the details. To increase the resolution, the Xu lab created a dCas9-based CAPTURE (CRISPR Affinity Purification in situ of Regulatory Elements) method. The original CAPTURE method was published in 2017 and addressed many of the drawbacks of 3C methods, but could only detect chromatin interactions at one location in the genome at a time (Liu et al., 2017). Recently the Xu lab developed CAPTURE 2.0, an updated version of CAPTURE that detects chromatin interactions at hundreds of loci at once (Liu et al., 2020).

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Topics: CRISPR, Other CRISPR Tools

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