NCMM visit to MIMS, Umeå, to learn the A-Z of cryo-EM

Ahmad Ali Ahmad is a postdoctoral researcher in the Sekulic Group at NCMM. He is currently spending time in the group of Dr. Linda Sandblad, director of the Umeå Core Facility for Electron Microscopy (UCEM), based at Umeå University.

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Ahmad Ali Ahmad with Dr Linda Sandblad at the Umeå Core Facilty for Electron Microscopy (UCEM). Photo: Nora Lehotai, MIMS

Ahmad’s research involves biochemical and structural studies to examine the centromeric chromatin, a specific part of the chromosome which is important for cell division. A functional centromere is vital for accurate cell division. As Ahmad describes, “To have accurate cell division you need a working centromere, and this is what we are trying to understand. We want to know what makes a centromere functional, how it works, how it controls cell division, and also how it ensures that this cell division is accurate.”

“Problems with cell division lead to a different outcome in terms of DNA distribution in the daughter cells, something which is often observed in cancer cells. We therefore want to understand how the centromere is built. To do this, we express centromere-building proteins in bacteria. We then purify them and assemble centromeric protein-DNA complexes to enable us to study them more closely. These complexes are very big and often heterogenous so we cannot use regular common structural techniques like X-ray crystallography, which is why we need to use cryo-EM. 

cryo-EM facilities available in Umeå, as part of the Nordic EMBL Partnership

Norway currently does not have a cryo-EM facility, however, researchers at NCMM and within the Nordic EMBL Partnership can travel to use facilities at the other Partnership nodes. The Umeå Core Facility for Electron Microscopy (UCEM) is supported by MIMS, which is the Swedish node of the Nordic EMBL Partnership. The core facility is therefore open for use by researchers from the other Nordic nodes. The Director of the facility is Dr Linda Sandlblad, who is also a MIMS team leader. 

As Ahmad explains: “As we don’t have cryo-EM in Norway, we then thought about how we could make use of the facilities available at the other Nordic EMBL Partnership nodes. Both, Dr. Nikolina Sekulic, group leader, and myself had already participated in courses organised by SciLifeLab in Sweden where we interacted with Dr. Linda Sandblad and she kindly offered to host me in Umeå. My visit was initially planned for April, but it had to be rescheduled due to the COVID-19 outbreak. However, I am now half-way through a four-month visit to Umeå.” 

Training means all aspects of cryo-EM can be performed by Ahmad

The time in Umeå will ensure that Ahmad is ready to take on projects involving cryo-EM from start to finish. As he describes, “I’m learning the A-Z of cryo-EM! This means learning everything from sample preparation, screening, collecting data, and then also processing this data. I’m learning how to do each of the steps so that I can take this aspect of our research and run it from start to finish. I’m working on different projects which are all at different levels, so I am collecting data at the same time as I’m processing data. It’s busy but I’m learning a lot.”

Ahmad’s acquired knowledge will be a great asset, not only for him and his career but also for the Sekulic lab, NCMM, and wider Norwegian science in general. Steps are currently being taken towards establishing a Norwegian cryo-EM facility, so it will be important that Norway-based researchers are trained in the latest techniques. 

As Ahmad and Nikolina agree, “Science is moving very fast and, if we want to stay competitive with other researchers in our field, we have to make this system work for us while we wait for national cryoEM facility.”

Mobility grant from the Norwegian Research Council made visit possible

“I was able to come thanks to a grant from the Norwegian Research Council. The grant has very specific terms and requires that I go abroad to visit a lab and learn a new technique, so this was perfect for me. The grant has also given me an extension for my postdoc, so I have time to learn these new skills and use them with my project, although unfortunately the delay in my visit due to the COVID-19 outbreak has shortened the implementation phase.” explains Ahmad. 

How important are these kinds of opportunities for young researchers, and how do they benefit your group’s research?

“Since cryo-EM is a fast developing technique that is indispensable for our project, it has been even more important to learn all about it. Also while I’m physically based here, we have wider access to the facilities. It’s therefore easier for me to take advantage of the extra instrument time and local expertise, rather than operating remotely from Oslo.” 

“Aside from the benefits to my project and the group’s research, this time in Umeå has been a fantastic opportunity for me and for my career. It’s also interesting to see how things work at another node of the Nordic EMBL Partnership. It’s different being based with a platform like the cryo-EM facility in Umeå, rather than in a remote user group like we have at NCMM. It’s useful to see how a platform operates and how they receive and approach projects. It’s also good to learn how we can better coordinate with the group in Umeå once I’m back in Oslo; I know more about how to explain the project to them and what information needs to be included to get the best possible job done.” 

Are you being mentored by a specific group leader?

“Dr. Linda Sandblad is my main contact and mentor here and I’m working as a part of her group. We have weekly meetings where we discuss my project and other ongoing projects that the facility is working on. I’m also working closely with Dr. Michael Hall who is helping me to collect data. As a trained crystallographer and cryo-EM facility manager, Michael has extensive experience working with protein structures and always gives me great suggestions and ideas. I’m really benefitting from his and Linda’s support and training.” 

Do you have any advice for other researchers about travelling to learn new techniques and skills?

“I really recommend that people travel and learn from other experts abroad and expand their network. I feel really lucky to have had this opportunity; I’m learning a new technique, I’m visiting a new city and working and learning from a whole new group of researchers. Whilst it was a little difficult to organise due to the COVID-19 restrictions, it has definitely been worth it.” 

The situation posed COVID-19 and the resulting travel restrictions will hopefully be resolved in the near future, and that more of these exchange visits will be possible. As Ahmad concludes, “Nothing quite matches gaining hands-on experience in an established environment.” There is certainly a lot more expertise waiting to be exchanged within the Nordic EMBL Partnership.

 

Published Oct. 23, 2020 12:04 PM - Last modified Oct. 28, 2020 9:35 AM