When Do We Get to Zap the Bacteria? - Denis Routkevitch

Hello! This past week and a half has gone by in a whir, and there’s a lot to write about. Hopefully the things I chose are somewhat interesting and representative of my time here.

So far, I really like working at IMEC. Everyone in my group is really nice and always eager to introduce themselves. We all sit together at lunch and I think the camaraderie is really nice. We’re all going bowling on Thursday (a rival group challenged us). My actual work is investigating the electrical properties of bacterial biofilms (a particularly nasty kind of infection that occurs on surfaces from sewers to medical devices) in order to detect and characterize as well as treat them. So far, it’s mainly just been growing and counting bacteria, but we should be getting into the real fun, i.e. zapping bacteria, soon.

Besides work, it’s been really fun starting to explore Belgium. Last weekend, we (the IRES interns) all went to Brussels for the day. There we saw some cool sites, like the Mannekin-Pis (peeing boy), Jeanneke Pis (no-longer-peeing girl), and Grand Place (pictured below). Unfortunately, we missed the peeing dog statue. I also had my first Belgian waffle there, which was unlike anything I was expecting. It tasted like a croissant in waffle form. Belgians say that you’re supposed to eat the waffle plain, but its strawberry season, I’m foreign, and strawberries are delicious.

Leuven itself is a great city. Everyone gets around by bike (there are even special stoplights for bikes). We all rented bikes after the first day of work from a nearby shop. Interns from previous years warned us about these bikes, and it was warranted. Three of us, including me, had problems with our bikes right away. Mine got a flat tire and I had to bike around for about a day on Leuven’s cobble streets before I could get it fixed. Luckily, they fixed it quickly and for free and now we can all ride anywhere we want with light hearts and ever-growing quads.

Well, that’s it for now! There are plenty of other anecdotes, but far too many to write down. Until next time, I’m off to eat some more strawberries.

Never have I seen something so red and delicious in person.

One quarter of Grand Place in Brussels, as depicted my horrendous panorama skills

This leafy wonderland is the view outside my window right now

Meet Our 2017 IRES Student Fellows

Back row (left to right): Kevin Li, Denis Routkevitch, and Diego Alba Burbano
Front row (left to right): Tiffany Hu and Grace Hao

It’s July Already?

Hello again! Us interns are wrapping up our time here at IMEC, which is a crazy thing to think. At the beginning of the summer, late July felt so far away, and yet, it’s arrived. These past few weeks have been busy as we had to give our project presentations. I had a few stressful days before I was able to get nice data to present, but finally giving the presentation and showing the work I’ve done was really fun!

In the lab, I’ve been synchronizing calcium fluorescent imaging and lens-free imaging on cardiac cells to validate lens-free imaging as a method to detect cell contraction. It’s a time-sensitive, complicated procedure, but getting the hang of it and getting good data has been very gratifying. Time passes so quickly in the microscope room--I’ll barely notice that I’ve been tinkering with the system or collecting data for hours.

This past weekend was a four-day weekend thanks to Belgium National Day! To celebrate, Stephanie and I visited Brussels for a day to see all the festivities. We left with more flags and balloons than we came with, and enjoyed the beautiful weather. That evening, I traveled to London to visit my aunt for the weekend, which was incredible. We walked around some of the major historical sights of London, like Big Ben, Parliament, and the River Thames. One of the highlights was visiting St. Paul’s cathedral, where we climbed all 500-odd stairs to the very top for a great view of London, seeing the classic landmarks that we’d just visited from above. We took an hour’s train to Oxford for the weekend, where we did some more sightseeing and learned about the awesome history that envelops the town and university. As my last big trip of the summer abroad, I really enjoyed England and definitely hope to return.

See you next time for my last blog!

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.

Beautiful buildings in Oxford

London view from St. Paul's Cathedral

Murky Thames and Parliament

Radcliffe Camera

Canals and the Clean Room

Canals and the Clean Room

This past weekend, a few of us visited Amsterdam! We were greeted with beautiful weather that framed the famous canals and architecture. One of the highlights was visiting the Anne Frank House, which gave us an amazing and haunting perspective of life in Amsterdam during World War II. I’d read the diary before, but seeing it come to life in the actual warehouse, including the original bookshelf and Anne’s bedroom wall art, made everything feel more real.

After some more sightseeing and enviously watching boaters on the canal, we decided to rent a boat and take it for a (slow!) spin. Lydia’s dream of driving a boat finally came true, even though she didn’t have any sort of boating license. We still made it back in one piece, despite the turns and pass-throughs that often needed all four of us to help steer. Seeing Amsterdam from a canal perspective was definitely worth it!

In the lab, I went on my first clean room visit to cut a large silicon wafer into smaller ones that cells could be grown onto for simulating re-entry mechanisms later on, observed with our lens-free microscope. Preparing to enter the clean room was a twenty-minute process that included putting on steel-toed shoes, a hairnet, a full-body suit, and knee-length boots. Walking around was a bit difficult at first, but eventually I got the hang of it. I’ve never seen clean rooms so enormous and extensive as they are here at IMEC! I also don’t know how people recognize each other in those suits to have conversation--I could barely recognize myself when I peeked in the mirror. Though this was probably my only visit, I’m really excited that I actually saw the clean room and get to say I did some work in it.

Until next time!

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.

Canal's-eye view

Outdoor Market in Amsterdam

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