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The 6th Brazil School for Single-Particle Cryo-EM 2014

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Joined: 5 May 2009

As a graduate student doing an EM project in a non-EM lab I had spent a few months searching for a good course that would focus on what I needed to learn. I already had experience preparing samples and collecting data, but I was a novice when it came to data processing and analysis. The Brazil School’s focus on single particles seemed perfect for what I needed in order to move forward with my project.

After 20 hours of traveling from Seattle, I arrived at the São Paulo airport and found the rest of the group, who were being chaperoned by our designated liaison Roosevelt. Roosevelt immediately made us feel at ease and comfortable, while facilitating introductions and conversations between the students. We all piled into a large passenger van and began the bumpy and curvy two-hour drive to the village of Socorro. I had no idea what to expect, other than that Socorro was small and rural. The drive was scenic, and as we watched out the window, we began to see São Paulo city fade away and we transitioned into farmland and forest. It was winter in Brazil, so temperatures were actually quite cold when we first arrived (~14˚C). The hotel in Socorro had no heating in the rooms, but they did provide extra blankets that were more than enough to keep us warm in the evening.

As someone who is fairly shy around new people, I greatly appreciated the effort that the instructors and organizers made to facilitate interactions. I learned that the other students came from a variety of backgrounds - from new graduate students learning the basics of EM, to faculty with expertise in crystallography who were interested in bringing EM techniques to bear on their research projects. The small course size, together with the concentrated instruction, allowed the participants and organizers to see each other not just as colleagues, but as friends.

Each day consisted of lectures on practical and theoretical aspects of EM data processing in parallel with a hands-on sessions using IMAGIC and/or Frealign to process a sample set of cryo data on worm hemoglobin (picture). Those who brought their own data were able to work through the same steps with that data. We were also given overviews of other software packages such as Relion and Appion. After courses were done for the day, students and instructors gathered informally at the pool, the game room, or a local boteco (hole-in-the-wall Brazilian bar with very cold and cheap drinks!), and continued discussions of EM topics or simply enjoy getting to know one another.

The second week brought warmer temperatures, the blooming of the ipê-amarelo trees (picture), and the chance for students to give short talks on their own research. I took the leap and gave a talk, and after showing my preliminary negative stain data, I received helpful feedback about how to improve the quality of my samples and the processing of my data. Having personalized instruction on how to optimize my EM analysis was one of the most valuable parts of the course. I was also able to pick up pieces of general knowledge from instructors and students who had more experience than me throughout the course. The quality of instruction was so high that concepts in single particle EM and structural biology which had eluded me in my own graduate coursework and independent research were quickly made clear in a matter of days or often through a single lecture or conversation.

The average day was packed full of information and computing work, so we had two free days that we could use to catch up on coursework or to join a group on a leisure activity. These activities included zip-lining, visiting a cachaçaria (cachaça distillery), exploring a farm, or hiking up some of the many viewpoints on the hills around the area. Several participants were able to capture beautiful photographs of birds and scenery (picture), and on a couple evenings, many of us gathered together to observe the clear night sky of the Southern hemisphere for the first time.

The group was quite international, yet due to the structure of the course and the amount of personal interaction built into each day, there were few communication barriers and we quickly formed a very collegial and incredibly fun community. A scheduled churrasco meal (Brazilian barbecue) evolved into an evening filled with delicious food, karaoke, dancing, and live music, thanks to the impromptu efforts of some of the organizers.

At the Brazil School, we learned about Fourier transforms, CTF correction, multivariate statistical analysis, common-lines reconstruction methods and many other important concepts in single-particle EM. Equally important, however, we formed friendships and collaborations with the other participants and organizers that will go beyond our time in Socorro (picture).

       -- Patrick Nygren