Thursday, July 7, 2016

Optimizing qPCR and optimizing fun

It’s hard to believe that we’re halfway through our stay in Belgium. Work at imec has picked up and all of us are making headway on our projects.

My project is focused on optimizing cycling conditions for ultra-fast qPCR on-chip. Quantitative PCR, or real-time PCR, is similar to traditional PCR, but takes fluorescence measurements during the exponential growth phase of the amplicon. This form of PCR is preferred to qPCR in most applications because it can tell us exactly how much DNA was amplified from the original sample.

Ultra-fast qPCR, as its name would suggest, is an accelerated version of qPCR and can be performed on microfluidic chips. Traditional PCR can take several hours to complete, qPCR around an hour, and ultra-fast qPCR on the order of minutes. However, some complications arise from performing PCR so quickly. One common issue is the formation of primer dimers: primers that have annealed to one another and become amplified. Right now, I’m trying to find what the best cycling conditions and primer concentrations are to avoid the production of PDs. We’re using a new set of tailed and tag primers to circumvent PD amplification, but are running into issues with amplification of the template. I’m running a lot of experiments to see what these optimal conditions are, so hopefully I get some positive results soon!

Aside from work at imec, the other Hopkins students and I have been continuing our weekend travels. Since last time, we’ve been to Brussels and Bruges, which were super fun and beautiful to visit. Brussels is the capital of both Belgium and the EU (well, de facto capital), so it has a great city vibe and lots of buildings, museums, and parks to see. The following weekend we went to Bruges, which has been my favorite Belgian city so far. Cobblestone roads, great church spires, canals, and the famous belfry give Bruges an ancient, yet incredibly charming, feel.

This weekend, my family is here on vacation, so I’ll stay with them in Brussels and take them to some of the cities I’ve visited in Belgium. Next weekend, we’ll meet up again in Paris to spend time with family friends. I’m so glad to have my family here with me, and now that I’ve got the rest of my weekends in Europe planned out, July looks like it’s going to be a fun one!

Stephanie Cai is a rising junior BME with a focus area in Instrumentation. At Hopkins, she is a member of the Wang lab, a leader for Encore Music Group, and on the board for Society of Women Engineers.

Watching the game in Oude Markt, Leuven.

The world-famous Belfry of Bruges.

View of Bruges from the top of the belfry. 
More waffles; this time on a stick.

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