Technique: Probe Phage Genomes for Host Binding Proteins

Posted by Guest Blogger on Sep 29, 2016 10:30:00 AM

This post was contributed by guest blogger, Jessica Sacher, a microbiology PhD student at the University of Alberta studying with the Szymanski lab.

Reasons to Study How a Phage Recognizes Its Host

Bacteriophages (viruses that prey on bacteria) may be the most numerous and most diverse biological entities on our planet, but we still know collectively little about how they infect and influence the evolution of their bacterial prey. Currently, receptor binding proteins (RBPs, the host recognition factors of phages) constitute one of the most popular classes of phage proteins to study. These are highly useful for the biotech industry, which is in the process of capitalizing on phage RBPs as diagnostic tools and therapeutics. In addition, the strategic use of whole phages as therapeutics, which is also gaining a lot of new traction lately (1, 2), depends on knowledge of the structure(s) a given phage will recognize on a host cell.

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Topics: Protocols, Techniques, Microbiology

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

Genome engineering using Cas9/gRNA Ribonucleoproteins (RNPs)

Posted by Joel McDade on Apr 21, 2016 10:30:00 AM

CRISPR has quickly become the preferred system for genome engineering due to its simplicity, as it requires only Cas9 and a guide RNA (gRNA).  Choosing the correct method to deliver both Cas9 and gRNAs to your target cells is absolutely critical as failure to adequately express either component will result in a failed experiment.  In our previous blog post entitled “CRISPR 101 - Mammalian Expression Systems and Delivery Methods” we provided a general overview of the most common ways in which you can deliver Cas9 and gRNAs to your target cells and discussed a few key advantages and disadvantages of each method. In this blog post, we will go into greater detail about why and how Cas9/gRNA Ribonucleoprotein complexes (Cas9 RNPs) are being used for genome engineering experiments and provide a general framework for getting started with Cas9 RNPs in your research.

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Topics: Genome Engineering, CRISPR, Techniques

Tips for Titering Your Lentiviral Preps

Posted by Meghan Rego on Mar 15, 2016 10:30:00 AM


The day has arrived; you’ve painstakingly cared for your packaging cell line, prepped your DNA, transfected and harvested your lentivirus. Now it’s time to move ahead with your infection and make your stable cell line. While we’ve all experienced the pressure to move a project forward, transductions should not be rushed into. Before you start any transduction, you should always titer your virus - that is determine the amount of virus you actually have in your prep. Taking time to properly titer your virus will not only ensure that your infection is designed in the best possible way but it may also save you time in the long run. Read on for an overview of the titering options and the benefits and drawbacks of different methods (for comprehensive protocols for all of the methods discussed here refer to
Kutner et. al.).

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Topics: Techniques, Viral Vectors

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