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Before I started writing for the Addgene blog, sharing Chemistry Cat memes was how I used social media as a scientist. I mean, I had a LinkedIn page and a Twitter handle, but I wasn’t using them to my professional advantage. It wasn’t until I wrote a blog post about a research paper that explored how scientists connect on Twitter that I realized 1) a lot of scientists are using social media professionally, and 2) I needed to start using Twitter.

My lab's vector of choice is AAV, with nearly every experiment requiring AAV. Before joining my lab, I had never worked with AAV, so naturally I had to package some virus for my first experiment. It was a bit intimidating, but I had my lab’s protocols and some great co-workers to help me out. Even with these tools, I found myself writing AAV production tricks into the margins of my protocol. While these tips weren’t critical to the experiment, they definitely made my life easier!  In this post, I’ll share some AAV production, purification, and titration tips, while also summarizing the basic steps and analyses needed for packaging AAV.

Genome-wide CRISPR/Cas9 screens are a high-throughput systematic approach for identifying genes involved in a biological process. These screens provide an alternative to genome-wide RNAi screens, which although highly effective, are affected by low on-target efficacy, non-specific toxicity, and off-target effects. The flaws of RNAi screens are well characterized and strategies exist to control for these faults. However, it’s still unclear if similar pitfalls exist for CRISPR screens and how best to design these screens to controls for flaws. Recently the Bassik Lab at Stanford developed a new genome-wide CRISPR knockout screen to analyze the following unanswered questions about CRISPR screen design.

Sometimes it feels like DNA and protein get all the attention.There are numerous ways to detect DNA-protein interactions or to analyze chromatin states (CHIP-seq, FAIRE-seq, Cut & Run) and to detect protein-protein interactions (yeast-two hybrid, Co-IP, BioID),  and that’s just to name a few. But what if you want to study RNA-protein interactions? The characterization of RNA-protein interactions has lagged behind, likely due to limitations of current means to detect RNA-protein interactions. To address this need, the Khavari lab at Stanford created the RNA-Protein interaction detection (RaPID) method. RaPID borrows the E. coli biotin ligase BirA* from BioID and allows a researcher to identify proteins that bind an RNA motif of interest in living cells.

Kinases: they regulate many proteins, with ~1/3 of human proteins predicted to be phosphorylated on at least one site. Phosphorylation is particularly important for regulating signal transduction and measuring kinase activity at the single-cell level can aid in drawing connections between signaling activity and cell phenotype. One method for monitoring live single-cell kinase activity is FRET, but FRET reporters are challenging to design and difficult to multiplex. The Covert Lab provides an alternative tool with their Kinase Translocation Reporters (KTRs) whose cellular localization serves as a proxy measurement of kinase activity. The key advantage of KTRs is that they are easy to create and simple to multiplex.