Wednesday, August 26, 2015

Work hard, play hard

I think it was the wise Wiz Khalifa who said "work hard, play hard," a phrase that comes to mind when I think about my summer in Leuven so far. My weekdays are filled with many hours at imec, constantly going back and forth between my cozy office desk and the convergence lab where I conduct my experiments. On the weekends I find myself traveling all over - from little towns in Belgium to bigger, more touristy cities like Rome (where I went this weekend with Gwen and Victoria). Between these two, I haven't been able to sleep in past 9AM. Yet, I find this summer to be really interesting, rewarding, and fun.

I've been able to finish the first part of my project!! It dealt with optimizing PCR efficiency by testing different hydrophobic coatings and seeing which gave high fidelity while still producing the similar results to what we had originally. So while I'm processing data for that part, I'm starting a new, but similar project: a digital droplet PCR that takes approximately 10 minutes rather than 1 hour.

 Rodrigo said that I'll be using the best coating (chosen by the data I got from the first part of my project) and testing different assay and surfactant combinations to find the best one for this process. While I will still be using the same equipment and devices for running the experiment and analyzing the data, I think this will definitely show me other aspects of on-chip PCR that I didn't have time to look at previously. And honestly, the best part is that it only takes a fraction of the time from the regular ddPCR so I'll be able to do more experiments within a day.

Let's talk about my travels: I went to Rome this weekend! I've never been to Italy before and let me just say, every part of it was amazing. The food, the sights, the people - all perfect. I think the weather was a little too hot for me (I got my first sunburn ever) but I just ignored that and cooled down by eating a lot of gelato.

What I liked most about Rome was all the fountains spread across the town. This seems like such an insignificant thing when you compare it to Palatine Hill or the Coliseum. But after spending hours in 34C degree heat, these little spouts seemed like gold to me. I'm being dramatic, yet I do think having these potable drinking fountains were nice especially since it let me avoid spending mucho dinero on the water bottles from tourist traps.

Overall, the past weeks have been wonderful, both work and play wise. I'll definitely keep updating as my new project goes along and as I continue my adventures to Germany this weekend.

---Rachel Bang




Tuesday, August 25, 2015

PCR, programming and Dublin

Since my last blog post, my research project has moved from doing some preliminary testing using a commercially available PCR cycler to a droplet-in-oil PCR setup. The setup is challenging because it involves lots of tiny microfluidic elements, but the process has started to become easier as I gain experience with it.

St Michan's Church
We are using ImageJ and Matlab to analyze our data, so I’ve had to familiarize myself with ImageJ and refresh my memory slightly on Matlab programming. As a computer science minor, I have been enjoying putting some of those skills to practical use! At Imec I think we have settled into our work and have a better understanding of what to expect.

This past weekend, I returned to the English-speaking world by making a trip to Dublin, Ireland. It was my first time traveling alone, but it went smoothly and I’m glad I made the trip! My favorite part of the trip was visiting Bray, a seaside town not far from Dublin. There I was able to hike up a large hill called Bray’s Head to some incredible views of the surrounding sea, town, and mountains. 

Another highlight was a tour of the crypts at St. Michan’s church. There, the constant temperature, the release of methane gas from the ground, and moisture absorbing limestone walls caused the bodies in the crypts to become mummified. The tour was extremely interesting and engaging in large part because the excellent tour guide. Overall I found Dublin to be friendly and enjoyable!

---Gwen Hoffmann

After climbing Bray's Head

Monday, August 24, 2015

The Comfort Zone


While planning this blog, I had a really great idea to do a “Top Five Things I Learned From Leuven” post, with cute little anecdotes illustrating how I’ve changed and what challenges I’ve faced working in this environment. But as I started brainstorming ideas, I realised that everything I was thinking of all fell under the same umbrella, and could be summed up nicely in one sentence:

It’s okay to feel like you have no idea what you’re doing.
From the moment I stepped off the plane and had to search for my luggage, find which train headed to Leuven from signs in a new language, and make my way to our dorm, I was bewildered, confused, and unsure every step of the way - all before even getting to work! Perhaps where I felt it most poignantly was in my second week of work, when I analysed waveguides on my own for the first time. Though I’d used the system several times before, I was still second-guessing myself the entire time getting the laser aligned and the microscope ready. The whole time I wondered to myself, why are they letting me be in charge of this (very expensive) equipment all by myself, when I haven’t even been working for a full week?

Moments like this were a common occurrence: finding the right train to get to Brussels, buying food without understanding what was in it, trying to navigate a completely new city, working on projects at IMEC that were completely new from what I’ve done at Hopkins. I was completely, totally out of my comfort zone.

But from this, I learned. I learned that you have to trust yourself, and trust the skills you didn’t know you had. Though I had never worked with waveguides or optical fibres, within a couple weeks I could analyse entire sets in an hour or two, more efficiently than anyone expected. Though I’d never worked with cardiac cells or micropatterned chips, I worked entirely independently for two weeks while my supervisor was at a conference in the States, and was able to get a lot of good data and refine our protocol along the way. In high school and at Hopkins I’d learned the basics - how to use a microscope, how to culture cells, how the cells actually work, how to analyse and present data. And for the first time, it was up to me to use these skills without anyone looking over my shoulder, and make something meaningful using them. “What am I doing?” turned into “Yeah, I got this,” and I’ve come out of it much more confident in my skills, both in what I’ve been used to doing, and my ability to adapt to new situations and use what I know to solve the problems I’m given.

I’ve also learned how important a supportive team can be. My first time using the fancy confocal microscope, I wasn’t very confident that I would do it right. But two of my team members were there, who offered to answer every question I had and help if I didn’t know how to use the system or something wasn’t working. My supervisor himself, if we were struggling getting something to work, would suggest that we take a water break and just have a few minutes to chat before returning to our work with clearer heads. Even though they’d only known me for a day or two, my team welcomed me with the proverbial open arms, and I never felt like I wasn’t part of the team for a single second. Something as simple as having lunch together every day made the experience much more meaningful than just getting the work done and collecting data - I made new friendships, heard the suggestions of others, and gained practical knowledge pertaining to both the lab and life in Leuven.

So, I learned it was okay to feel like I didn’t know what I was doing. Because I could trust myself and what I know to solve the problems in front of me. Where I stumbled, I could trust my supervisor and my team to be there to help and guide me, or even just make me laugh in a day full of hour upon hour of imaging cells.

Being out of your comfort zone isn’t a bad thing in the least - it’s when you find out how much you can really do and how much you can really grow. Because of that, I’ve learned to trust my own abilities, and how important having a diverse group of people to work with can be. More than anything I’ve learned about heart cells or lens-free imaging, these are the lessons that will stick with me.

--- Rebecca Black

Wednesday, July 1, 2015

This is Not a Microscope

This is not a microscope. This is only an image of a microscope, an image of a lens-free microscope to be exact. This is the first you’ve heard of a lens-free microscope? Well, the technology has been around since the 1950s, although they used mercury lamps instead of lasers, which were invented in 1960. It was developed around the same time as electron holography, which is used in transmission electron microscopes, that we are now familiar with and by the same scientist Dennis Gabor.

This microscope utilizes the principle of digital in-line holography. Very simply the main components are a small laser and a complementary metal oxide semiconductor imaging chip that is used as a platform. It uses a laser which when in contact with an object on a platform creates interference waves which are picked up by the chip, converted via several complex algorithms and displayed on a computer.

Figure 1: Schematic of in-line digital holography. The laser (L) illuminates a pinhole (P) which acts a point light source. Spherical waves are produced from the pinhole. First the waves illuminate the object (O) and produce reference waves ( ¾ )and interference waves (−−−) that constitute the hologram at the screen (C). (http://www.pnas.org/content/98/20/11301.full)

What are the advantages to this microscope? It has a larger field of view than traditional microscopes, which means the data it collects is more likely to be statistically significant. It’s also much smaller and portable, and it’s lack of significant hardware makes it easier to conduct experiments, especially when you want to keep your cells alive in an incubated environment.

At imec we’re using the lens-free imaging to track cancer cell migration. On paper it doesn’t sound that exciting, but in practice it means that the possibility of understanding how cancer cells work in 3-D environments within humans. This is exciting for a lot of reasons including the fact that we can change a variety of variables that will impact these cells. For example, we can treat cells with a chemotactic drug, image them and see how that impacts motility with the general hope that it will halt metastatic process. Of course there are lots of steps in between for these conclusions to be upheld, but in the meantime, I get to run experiments on breast and prostate cancer cells using a lens-free microscope.

Figure 2: Lens-free imaging prototype

A side note: the popular phrase “this is not a pipe” or “ceci n’est pas une pipe,” which was adapted for my title, is from René Magritte’s The Treachery of Images. Magritte is a Belgian surrealist artist who is featured in a four-story exhibition in the Royal Museum of Fine Arts in Brussels. The idea is that the pipe is only a representation since you can’t physically hold the pipe or fill it with tobacco. At the Royal Museum you can see an extensive collection of Magritte’s art as well as works from the Renaissance to the Contemporary periods.

Figure 3: “This Continues Not to be a Pipe” (a successor to “This is Not a Pipe”) featured at the Royal Museum of Fine Arts, Brussels. The original Treachery of Images is currently housed in the Los Angeles County Museum of Arts.

---Victoria Laney

Tuesday, June 30, 2015

"I can turn a three into a heart!"


It’s difficult to believe that we’ve been here for almost a month already! Now that we’ve really settled into a routine at work, the days simply fly by - suddenly it’s almost 5:30 and you wonder where the day went, lost in culture rooms and in front of microscopes.

This week I started work on a new project, one that focuses on a more efficient way of testing clinical drugs on cardiomyocytes (heart muscle cells). Traditional culture of cardiomyocytes uses big disorganised clusters, which don’t resemble the linear arrangement of cells in an actual heart. Because of this, a significant number of drugs are pulled from the market due to heart issues that weren’t seen in clinical trials. Using a chip designed with alternating lines of hydrophobic (water-resistant) and hydrophilic (‘water-loving’, where cells attach) areas, we’re trying to get the heart cells to grow in single-cell lines to mimic their real-life organisation. There’s plenty of work to be done - because these procedures are still fairly early on, we’re testing all different cell densities, materials to seed the cells on, sterilisation methods, and line designs to see which one gives us the best results!

One of the most comedic moments for me was when I was first introduced to the designs we used that had cells attached. Above each pattern of lines is a number to distinguish which pattern it is, which also becomes hydrophilic during the preparation of the chips. As we prepared the samples for the microscope, my supervisor grinned and said, “Want to see something cool? I can turn a 3 into a heart!” And as I looked into the microscope, there it was indeed - heart cells arranged in a perfect number 3, happily beating away!

When we go to actually test the cells, we make use of a lens-free imaging setup. The advantage of this over a traditional microscope is that we get a much wider range of view, and it’s much simpler - instead of needing a big nosepiece and all the different lenses, all we need to do is put a laser source above our sample and a camera below, and hook it up to a laptop. (See the image for a bit more description of what goes on!) Once we collect a few seconds of images of the cells beating, we can adjust the images to yield a time-lapse that shows the propagation of the contraction of the cells as they beat, which looks like a wave rolling across the screen. After studying extensively the mechanics of how the signals are conveyed between cells to cause them to contract this year, seeing it in real life with data we’d collected was incredible!

Outside of work, I’ve made it my mission to try every chocolatier and café in Leuven during my time here, and I have to say that I haven’t been disappointed! I’ve taken trips up to London to visit my boyfriend for a weekend and to Bruges, which is an absolutely gorgeous (if very touristy) town. In Bruges, we visited St. John’s Hospital, which has a big museum with the tools of doctors from its time - all I can say is thank goodness medicine has advanced since the 11th century!

Each week here just gets better and better as I get more into my work, and I’m loving the project that I’m working on!

---Becca Black

Time flies when you are having lab fun


It's crazy how fast time flies. Three weeks have passed and whenever I look at my calender, I’m shocked to see that I’m almost halfway done with my stay here in Europe!

On a work-related note, I've now officially trained for all the biolabs and equipment I have to use and - after several days of not getting the experiment to run - I've gotten pretty good results and data! Right now, I'm focusing on increasing the efficiency of the surface coatings of the micro-channels so I've been in the lab, constantly coating new devices and running experiments. But, working in the lab is fun - more so than sitting in an office cubicle all day.

This past weekend, I went to Antwerp with Gwen, and it was beautiful! I loved being able to relax and walk along the river, then go straight into the shopping district. One thing that was awesome to see was MOMU, a fashion museum for Belgian designers, which isn't something I get to see often.

I lost my all my keys on the train, leaving me temporarily homeless (well, actually I was just staying in the room across from mine. I just didn't have any of my things), but fortunately someone turned them into Leuven Station so I was able to pick them up on Monday. Lesson learned: always check if I have my keys, wallet, and phone before leaving the train.

I'm planning a lot more trips the following weekends until I get back home so I'll definitely be updating as I go along.

---Rachel Bang

Thursday, June 25, 2015

Suit Up


You know that moment in the movies where the protagonist sees something really amazing? The shot gets really wide and you just see the main character standing there with their silhouette and everything they see in front of them? It’s a surprise, a pleasant one that kind of takes their breath away at least for a moment. Well, that’s how I felt as Evelien Mathieu, my supervisor, lead me through the labs in imec.

It sounds corny, I know, but after two days of delays in Newark Liberty Airport I started to get nervous about the prospect of spending 10 weeks in Leuven. I felt like maybe these thunderstorms and flight cancellations were foreshadowing. So when I actually arrived, about 48 hours late, everything seemed to look better.

Initially my time at imec started off slow; adapting to the work environment, learning which floors led to the neuroelectronics lab and which ones led to the warehouse, taking safety training. Then the real work began. We started working on a project that combines lens free imaging and cell migration in microfluidic devices. It consists of three big steps: 1. fabrication of PDMS microfluidic devices in the cleanroom, 2. preparation and seeding of cells in the neuroelectronics lab and 3. imaging of cells using a lens free microscope.

Let’s start with step 1. imec has two state of the art clean rooms, one is class 1 area and the other class 1000 area. The main cleanroom I work in to fabricate devices is class 1 area, which amazingly has one 0.5μm particle per m3. In order to maintain this ultra clean environment everyone has to “suit up” before entering. This entails steel capped shoes, hairnets and a bunny suit in addition to your standard personal protective equipment. Once you’ve got all the gear on you can now proceed to the fabrication area.

Some very trendy steel capped shoes
When you first walk in you can be a little taken aback, the combination of extra suit and the positive pressure makes moving at first a little slow. But you get used to it by the time you arrive in the fabrication area. Both of imec’s cleanrooms are amazing. Tech companies like Dutch ASML, German Aixtron and American Applied Materials use the class 1000 cleanroom to develop semiconductor technologies, while the class 1 is used for lower volume fabrication and production.

To conduct our experiments we need to create PDMS devices with various microchannel designs using a master silicon wafer. From there we cut the devices and adhere them to glass in preparation for imaging. The whole procedure takes more than 24 hours and requires we to suit up about three to four separate times.

While it seems like a hassle, it is really incredible to be able to use new tools that leaders in the bio and nano-tech industries use, and in small way contribute to R&D at imec. Plus it’s pretty cool to get up in the morning, go to work and rock a different kind of suit.

FAB 1-Cleanroom Entry Way
---Victoria Laney