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Plasmids 101: Methylation and Restriction Enzymes

Posted by Marcy Patrick on Jun 30, 2016 10:30:00 AM

Have you ever tried digesting with XbaI or ClaI restriction enzymes and gotten unusual or unexpected results? Or considered why DpnI will degrade your template DNA from a PCR reaction but not the newly synthesized product from a site-directed mutagenesis experiment? The answer to both questions is the same--methylation! Read on to learn about how DNA methylation may affect your restriction digests.

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Topics: Lab Tips, Plasmids 101, Plasmid Cloning

Tips for CRISPR Gene Editing in Mice

Posted by Guest Blogger on Jun 28, 2016 6:59:27 AM

This post was contributed by guest blogger Samantha Young.

The use of CRISPR/Cas9 for gene editing has expanded since its adaptation for use in mammalian cells in 2012-2013. Researchers are now using this system in ever more creative ways, (Wang et al., 2013, Cho et al., 2014). There are several variants of the CRISPR/Cas9 system floating around, and many pre-designed plasmids containing these variants ready for purchase. But what is the easiest and fastest way to use the system in mice? We'll have a post that goes into the mouse genome editing process in a bit more detail in the coming weeks, but, in this post, we will outline a simple method for selecting the guide RNA, validating its efficacy in vitro, and using it in mouse embryos to generate gene modified mouse lines. Hopefully this post will help get your in vivo research up and running as soon as possible!

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Topics: Plasmid Technology, Genome Engineering, Lab Tips, CRISPR

Using Phosphoserine to Study Protein Phosphorylation

Posted by Guest Blogger on Jun 23, 2016 10:30:00 AM

This post was contributed by guest blogger Natalie Niemi, a postdoctoral fellow at the Morgridge Institute for Research in Madison, Wisconsin.

It is commonly cited that approximately one-third of cellular proteins are modified through phosphorylation (1). However, the expansion of studies on protein phosphorylation in an array of model systems coupled with advances in mass spectrometry suggest that phosphorylation is far more prevalent than previously appreciated. PhosphoSitePlus, one of the most inclusive databases of post-translational modifications, identifies a staggering ~250,000 phosphorylation events in the proteomes of higher mammals (2). How can we begin to understand the importance of any of these phosphorylation events on the activity of a given protein?

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Topics: Plasmid How To, Synthetic Biology, Lab Tips, Techniques

Evolution of Lab Techniques

Posted by Guest Blogger on Jun 21, 2016 10:30:00 AM

This post was contributed by guest blogger, Krissy Lyon, a PhD candidate in Neuroscience at Harvard University.

Just as computers, cell phones, and cars become more technologically advanced leaving earlier versions obsolete, the techniques we use in lab are replaced by improved versions that save both time and money. Yet, knowledge of historical techniques comes in handy whether you are perusing classic papers or are brainstorming new technological innovations. Let’s take a look at three historical techniques: southern blotting, restriction mapping, and sequencing gels, as well as their modern equivalents and see what we can learn from their evolution.

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Topics: Fun, Lab Tips, Techniques

How to Keep a Lab Notebook for Bioinformatic Analyses

Posted by Guest Blogger on Jun 2, 2016 10:30:00 AM


This blog post was contributed by guest blogger Kate Palozola

Traditional lab notebooks just won't cut it for bioinformatics. All kinds of biologists are finding themselves using computational approaches to analyze large data sets (myself included) and we are faced with finding the best system to document these types of analyses and their results. We are adept at recording wet-lab experiments using a “traditional” lab notebook; however, keeping track of computation work comes with new sets of challenges. One challenge with computational analyses is to keep track of why you are doing what you are doing. Another common challenge is to keep track of what works, and what does not work. Careful documentation will keep you on task and will prevent you from getting lost in the wide word of informatics.

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Topics: Lab Tips

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