A working qPCR chip and a quirky Belgian fest

The last few weeks have been filled with some truly wonderful memories and it’s going to be hard to narrow it down to just a few, but I’ll try my best! Work at imec has been going steady; unfortunately, the testing I was doing with tag primers didn’t end up working, but we have found a working master mix for qPCR on-chip. I’ll be spending the rest of my time at imec testing a variety of conditions to see what enzymes and cycling protocols work best for the on-chip setup.

We also had to give our midterm presentations last week for our project advisors, imec colleagues, and the people back at Hopkins. It was really neat to hear in detail about the work Lakyn, Lydia, Chris, and Michael have been doing with their mentors. Everyone enjoyed the presentations and our hard work was rewarded with a nice reception of Belgian beers and snacks afterwards.

Now, onto the weekend travels. On the second weekend of July, I went to Paris and to spend more time with family and friends. The weather was perfect for wandering the streets. We strolled through the immaculately maintained Jardin des Plantes, where we were surprised to find some very cute kangaroos sunbathing, and by the Seine River. On my second day there, we went to the Louis Vuitton Foundation, which ended up being one of my favorite museums this summer. Enormous curved panels, checkered with vibrant colored glass, cover the exterior of the museum. The main exhibition had a few collections of modern Chinese paintings, sculptures, and films on display, which were equally as wonderful to look at. I returned to Leuven Sunday night completely exhausted, but so happy that I got to fit in so many new experiences in Paris.

The next weekend, Lydia, Chris, Lakyn, a few of our other friends, and I went to Ghent for the annual Gentse Feesten. We had heard through the grapevine that Gentse Feesten was a legendary Belgian festival that we simply could not miss, and I’m so glad that we went! Ghent really lit up (literally!) at night: there were hundreds of food and drink stands, concert stages, and quirky art booths scattered throughout the city. Our adventures lasted well into the night and I can comfortably say that the Belgians know how to have a good time.

And lastly, this past weekend I got to celebrate my birthday with my boyfriend here in Belgium. He came down from Scotland where he’s doing research at the University of Glasgow through the Vredenburg scholarship. We wandered around in Leuven and Bruges, and I couldn’t have imagined a better way to spend the weekend.

We have just one more weekend and nine working days left until it’s time to return to the States. I feel like we’ve just gotten into the swing of things, and now we have to prepare to go back. But if I’ve learned anything in the past two months, it’s that you can pack a lot into a short amount of time and that’s what I fully intend on doing.

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.

The exterior of the Louis Vuitton Foundation

Lydia, me, Lakyn, and Chris on top of Gravensteen Castle in Ghent.

Gentse Feesten at sundown.

Looking up from one of the terraces inside of the Louis Vuitton Foundation.

Strolling through the Jardin des Plantes with my parents.

Summer Reflections

Hello all! After ten weeks in Europe, I am back in the United States!

The end of my internship involved working more with the 3D printer to create the last two prototype lenses. I spent much time working with a lab member, Rachid, to troubleshoot problems with the CAD files and resin that led to frequent failure of the 3D printer. We successfully printed one of the lenses that I was able to test experimentally in the lab and obtain preliminary waveform data. My mentors informed me that they intend to continue with my project after I leave and will keep me updated!

Hopefully I can continue using the engineering techniques I learned like finite element analysis and signal processing in my future research and coursework like Systems and Controls. Experience with CAD and 3D printing will also be helpful for creating prototypes for BME Design Teams, which I will be applying for junior year!

Returning to the US felt strange after spending such a long time in Europe. Leuven was basically my home for ten weeks. I adapted to the language barrier and new lifestyle over several weeks, but it all ended abruptly with returning my imec badge one day and flying out the next. Over the last two weeks, I enjoyed my last Liege waffle covered in dark Belgian chocolate at Gaufry’s in Leuven and traditional Flemish beef stew. Chris, Lakyn, Stephanie, and I spent our last night in Leuven at Oude Markt.

After enduring the 8-hour flight back, I was excited to see the ocean and an abundance of dining options (especially large breakfasts which were only available in London!). At the same time, I miss the architecture, desserts like chocolate and waffles, and spicy meals like the European version of Chicken Tikka Masala and the Samourai sauce in Durum wraps.

All in all, this was by far the most exciting summer of my life! I visited seven countries and did my first paid internship and first experience working in industry. The cultural immersion, professional networking, and engineering experience make this summer exciting, productive, and unforgettable.

  

Michael Signorelli is a second year biomedical engineering student.

Flemish Beef Stew

A sunset from my window at Wisteria in the nights before I left

The 'joys' of human subject testing

Ah, the joys of human subject testing. Let’s begin with the positive aspects: the process of collecting EEG data from volunteers at IMEC has left me with a new appreciated for biologists everywhere. Sure, circuits and code can break in horrifyingly puzzling, strange, and exasperating ways, but if you follow basic rules and techniques and avoid physically crushing anything you can almost always make machines work. Living beings are a whole different can of worms. If you’re not getting good EEG signal, it could be that the subject’s brain just doesn’t work like you think it does. There could be interference from sweat or hair. They might not be focusing on the task at hand, so you could be recording brain waves related to weekend plans rather than motor intention. Of course, you have all the normal equipment problems on top of biological factors, so your troubles could also be related to battery, wireless interference, loose electrodes, or the ever-fickle gods of engineering.

At this point I’m more than halfway through data collection, so if all goes well I’ll finish up next week. That would leave me with the rest of the summer to work on classifying EEG signals into motor intentions and hopefully use my shiny new data to add a no-movement class. This week I realized I need a way to quantify signal strength, so I’ve been working my way through various MATLAB toolboxes comparing function outputs. My goal is to find a way to exclude bad trials so they don't unnecessarily confuse my classifier.

Outside of work, Lakyn and I went to Paris last weekend! We were fortunate to have my friend Tristan as a native guide; with his help we saw tourist attractions like the Eiffel Tower, Notre Dame, the Arc de Triomphe, and the Louvre, then caught the Pride parade marching down the Seine. That evening we ate in the student quarter, watched Italy play Germany in an Irish pub and danced our way through the night. Despite all that, I think my favorite thing about Paris is the bread. Lakyn and I stopped by a bakery on Saturday morning for a baguette and it was so good I nearly cried.

It’s July 8th now and I can’t believe I’m halfway through my internship. Yesterday I got my cast off and tonight Lakyn, Olli, and I are catching a train to Amsterdam, where we’ll meet my friend Ally and spend the weekend exploring. This whole summer feels like something out of a storybook whenever I stop to process it. I’m planning to make the most of the time I have left by finishing the human subject testing, fine-tuning the gesture classification process, and developing exclusion criteria for bad trials. That’s a reasonably optimistic agenda for one month, and it’s likely I’ll only accomplish two of those three goals. But if I can’t be optimistic during a summer abroad in Europe, when can I?

Lydia Carroll is a 21-year-old biomedical engineer on her first excursion to the European mainland. In her free time she enjoys taking things apart, putting them back together, volunteering with the Maryland SPCA, and reading any paperback novel she can get her hands on. 

Me wearing the EEG headset and recording myself.

The Pride parade marching downtown along the Seine.

Notre Dame

Two Belgian Wins and a Belfry

Since my last blog post, us IMEC interns have definitely kept busy: working, exploring Leuven, taking day trips, and the occasional grocery store visit have made us more accustomed to living here. Being in Belgium for the summer has been especially exciting thanks to Eurocup! This past week, we saw Belgium win against Sweden and Hungary, which sent the team to quarterfinals. For the Sweden game, we staked out a spot in Oude Markt two hours early, and barely made it in time to find a place to watch one of the large TVs on display in the street. The square was full of thousands of enthusiastic Belgian fans, each dressed in red with a Stella Artois in hand. When Belgium finally scored in the second half, the crowd went wild! It’s hard to describe what happened, but it was crazy and I’m pretty sure none of us had experienced anything like that goal in Oude Markt.

This past weekend we took a day trip to Bruges, a city I’d been hyping up for a long time because I’ve seen a movie that takes place there. I wasn’t disappointed--Bruges ended up being my favorite city so far, with its canals, cobblestone streets, and quaint red buildings. We climbed a 366-step spiral staircase to get to the top of the famous Belfry, which had an amazing view of the city. The “great Belfry weather” (quote by Chris) was perfect for exploring the many historical landmarks and buildings that call Bruges home.

At IMEC I’ve been getting the hang of the lens-free imaging set-up, which once seemed to have a million pieces that each needed adjusting whenever you needed to move the set-up to another place. Luckily there’s not a million pieces, and it’s been a really useful tool to see and quantify heart cell contractions without the use of cell-toxic dyes. Last week I spent some time simulating re-entry loops in cardiac tissue by making holes in the cell monolayer, which can make the action potential of the contraction move in cool-looking patterns.

Lakyn Mayo is a rising junior in Materials Science and Engineering at Johns Hopkins University and an IMEC intern with the Johns Hopkins INBT IRES program. She likes dogs, mountains, and getting lost running in new places.

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.

Lab Work, Presentations, Paris, and London

My research in the last few weeks have primarily been experimental testing of acoustical systems in the Clinical Lab and 3D printing additional lenses to test. I worked with a function generator to create sinusoidal waveforms in bursts that lead to an ultrasound transducer to create far field plane waves in water. The waves pass through the lens and the amplitude of the resulting waver were measured using a hydrophone. The signal was observed and recorded along with the input signal and the trigger using an oscilloscope. I conducted further processing and analysis of the signal using Python. For the 3D printing, I am learning and working through the entire process of using the high quality ultraviolet printer including designing the CAD files, cleaning the final product, and curing the resin. We are printing two additional lensed to test.

Last week, the other JHU interns and I created presentations for a review meeting so others in the Life Science Technologies department at imec and in the Institute of Nanobiotechnology at JHU could learn about what we are working on. It was an enjoyable way to showcase my project and see what the other JHU interns were working on in the newer labs. At the end of the internship, I will also give a small presentation to my group at imec to show my work through the last two weeks.

On the weekends, I am continuing to travel to nearby areas of Europe. The last two weekends have included trips to France (Paris and Versailles) and England (London). My trip to France was generally short and rushed in order to fit in both Paris, Versailles, and the train rides there and back in only two days. I still did have the opportunity to visit the major tourist attractions like the Eiffel Tower, the Louvre, and the Palace of Versailles. However, two days was not enough to see the less-touristy areas of Paris and gain a true understanding of the culture there.

The past weekend, I traveled to London with Chris Argento. We had a four-day weekend due to holidays in Belgium last week, so we had ample time to visit amazing attractions like the British Museum, Houses of Parliament, and Tower of London along with exploring various neighborhoods, parks, and restaurants. Of all the cities I visited, London had by far the best food and public transportation. The city was very comfortable and exciting at the same time – definitely a place I would go to again.

All that remains are two weeks at work and a trip to Prague. Then, this amazing program is over, and I have to find another reason to go back and live in Europe!

Michael Signorelli is a second-year Biomedical Engineering undergraduate at Johns Hopkins University

A famous Full English Breakfast at Regency Cafe

View from the Eiffel Tower

The London Eye at night

Brussels, Bikes, and Brainwaves

Brussels, it turns out, has a Grand Place. Seriously, that’s the name of its central square, as I found out when I visited with the other interns last weekend. The skeptical side of my mind senses an ages-old translation error here, but for whatever reason it is now ingrained in the local psyche and written on maps. To be fair, the square is impressive: every building touching the Grand Place is liberally coated in gold accents and decorated with carved stone figures that probably predate the Gutenberg printing press. Besides seeing the Grand Place, Lakyn, Stephanie, Michael, Chris and I also visited three local art museums and caught the Belgium—Ireland game at a local pub. The entire country is avidly following the European Cup, so we joined an exuberant crowd in cheering Belgium on to the elimination rounds. It was awesome.

This has been an eventful week for a number of reasons. Academically, I’m gearing up to do some human subject studies with our EEG headset. Until now I’ve been analyzing old data and using it to test my classification algorithms (read: if I multiply this fancy matrix by that fancy matrix, can I tell if the subject is wiggling his right hand?). However, my real goal this summer is to add a no-movement state to the classifier, and none of our past experiments have no-movement data. This means it is my job to abduct – excuse me, recruit – fellow IMEC employees to sit still while wearing the headset so I can record no-movement data. It should make for a nice break from coding.

Unfortunately, not all breaks are the pleasant sort. Thanks to two consecutive bike crashes this week, I now have a fracture in my left wrist and right knee. Fortunately Belgian health care is merciful beyond reason: in addition to getting two days off work to recover, IMEC is covering my medical bills. All I have to do is recover and exchange my rental bike for one with handlebars. Oh yes, the handlebars came off while I was riding it. Twice.

Despite how it sounds, I’m basically fine and ready to get back to work and exploring. I made it to the Belgium vs. Sweden game last week on foot, but it’ll be nice to be able to bike again. This week I’m hoping to get my protocol for human testing approved and maybe even tidy up my algorithms a bit before we start recording. It turns out there’s a second set of old data that I haven’t tried to classify yet, so I’m cautiously optimistic that it might yield some useful information. Outside of work, my primary goal is to catch all the upcoming Belgium soccer games. My secondary goal is to not crash off my bike again. Priorities.

Lydia Carroll is a 21-year-old biomedical engineer on her first excursion to the European mainland. In her free time she enjoys taking things apart, putting them back together, volunteering with the Maryland SPCA, and reading any paperback novel she can get her hands on. 

From left to right: me, Lakyn, and Stephanie in Brussel’s Grand Place.

Oude Maarkt in Leuven before the Belgium vs. Sweden game.

Olli and Chris geared up for the Belgium vs. Sweden game.