Four Research Infrastructure Fellow grants to SciLifeLab
On June 27 the Swedish Foundation for Strategic Research announced the successful recipients of the Research Infrastructure Fellows grants. This year, seven projects were funded. Of those, four were led by researchers affiliated with SciLifeLab.
The aim of the Swedish Foundation for Strategic Research program for Research Infrastructure Fellows is to contribute to career paths for key people who work with the development and operation of research infrastructure at Swedish universities in science, medicine, and technology. Under the Research Infrastructure Fellows program, seven projects will receive SEK 15 million each over a five-year period.
“It is very encouraging to see that SSF clearly acknowledges the importance of imaging techniques from the organism to the molecular level by supporting three projects conceived by members of our platform Cell and Molecular Imaging”, says Marta Carroni, Department of Biochemistry and Biophysics at Stockholm University and Head of Unit of the Cryo-EM Infrastructure Unit at SciLifeLab.
The Centre for Cellular Imaging (CCI) of Gothenburg University, part of the National Microscopy Infrastructure since 2016, offers access, service, and expertise to innovative imaging technologies since 2003.
“With our experience in advanced microscopy imaging, specimen preparation, data processing, and analysis we support the broad needs of our users both in academia and industry. To tackle the challenges of quantitative microscopy at the Centre for Cellular Imaging we will develop “smart microscopy” workflows that use on-the-fly image analysis to continuously monitor the sample, give real-time feedback to the imaging software, and program the microscope to change its parameters during the experiment without human intervention”, says Rafael Camacho, SciLifeLab Integrated Microscopy Technologies, Gothenburg University
In 2021, the CCI was assigned as a SciLifeLab Unit on Correlative Array Tomography (CAT) within Integrated Microscopy Technologies Unit of the Platform of Cellular and Molecular Imaging (CMI). Array Tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore 3D cellular architectures of large samples in extremely fine structural and molecular detail. Performing CAT has many challenges, and results in imaging workflows that are notoriously time-consuming and require high levels of expertise.
“In the framework of this Research Infrastructure Grant, we will focus on increasing the image acquisition speed of CAT in both light and electron microscopy by implementing denoising methods, managing big image data, and automating some of the target identification steps that currently need human intervention”, says Rafael Camacho,
Automation and artificial intelligence are revolutionizing many sectors, from public transport to medicine. Implementing this vision in microscopy, referred to as “smart microscopy” requires a paradigm shift in current technology development and experimental design. It will no longer be the lone scientist sitting in front of a microscope that takes each image.
“We think smart microscopy will be an important trend in years to come. Deep learning is likely to be pivotal, as well as strategies for handling the data deluge associated with automated imaging. We believe that the research community need is well suited to the expertise of advanced Microscopy Core Facilities, such as the Centre for Cellular Imaging, that can take methods and concepts of smart microscopy and make them available to any researcher thanks to the high technical and scientific skill of its staff and the resources available at the infrastructure level”, says Rafael Camacho.
Cryo-Electron Microscopy (Cryo-EM) is a technique used to visualize molecules and obtain their 3-dimensional macromolecular structures using transmission electron microscopy from samples frozen in their physiological buffer at liquid nitrogen temperatures. From being a niche technique, in the last years, cryo-EM exploded to become one of the major techniques for macromolecular structure determination. Small amount of sample is required, and several conformations can be obtained thus allowing biological mechanisms to be deduced. Marta Carroni (SU), Head of Unit of the Cryo-EM Infrastructure Unit at SciLifeLab and Director of the CMI Platform was granted funding to develop Cryo-EM for biomedical applications and drug development.
“I am extremely happy and grateful to receive this SSF grant. This will give the opportunity to make cryo-EM technologies accessible to a broader community of medical researchers studying human health problems or developing drugs. At the same time, the development of specific methodologies for tuning cryo-EM to biomedical applications, such as cryo-EM longitudinal epitope mapping (cryo-EMPEM) and drug screening with electron diffraction, will in itself further the cryo-EM field, says Marta Carroni.
In addition to the development of the technological base of the research infrastructures, such as better instrumentation and working pipelines, the Research Infrastructure Fellow grants focus on the need for skilled experts to achieve success in research and to communicate the science behind the projects to the general public.
”My projects includes also the creation of entertaining content to engage pupils at primary and secondary school, as well as young scientists, to cryo-EM and structural biology at large – I am looking forward to getting started!”, says Marta Carroni.
Johan Rung (UU), Head of Data Centre at SciLifeLab is granted funding to develop a national e-infrastructure for life science data.
SciLifeLab Data Centre’s focus is to strengthen Swedish data-driven life science, working with SciLifeLab infrastructure platforms and researchers to develop new resources and services.
“The scope of the project supported by the Swedish Foundation for Strategic Research, is to build services and resources for sensitive research data, such as data from clinical research studies and precision medicine, says Johan Rung.
Life science research is increasingly becoming not only technology-driven but also data-driven. SciLifeLab coordinates and supports activities throughout the life cycle of data, from project planning, data production, data analysis, and data sharing, to publishing and reuse of data, where researchers are dependent on advanced data analysis and e-infrastructures.
”The areas of use for the infrastructure cover both research and service activities in broad areas of life science, where we integrate research data management with strong IT and data infrastructure. We have our base in open science and the FAIR principles to maximize the impact of Swedish data-driven research in life science”, says Johan Rung.
Umeå Centre for Electron Microscopy (UCEM) is the Umeå lab of the CMI platform, for both Cryo-EM and IMT, a joint resource for research and higher education in electron microscopy techniques. The facilities offer state-of-the-art instruments to prepare, image, and analyze medical and biological samples in 3D as well as structural and chemical characterization of materials at micro, nanometer and Ångström length scales. Linda Sandblad, Scientific director of CMI and SciLifeLab Site Umeå, received the Research Infrastructure grant to develop Cryo-EM and 3D image visualization of molecules, virus, bacteria, cells, and organisms.
“We will use the grant to improve and streamline the possibilities of visualizing cells and microorganisms in 3D. It facilitates basic research to gain insights into molecular mechanisms in cells and organisms and to localize cellular compartments and proteins within living organisms by correlative light and electron microscopy. The methods using both Cryo-EM and Focused Ion Beam (FIB) scanning EM are important for both ecology and infection medicine, bridging current research project needs to SciLifeLabs capabilities – Planetary biology, Pandemic Laboratory Preparedness, and further potential for clinical research, says Linda Sandblad.
More information is available in a news piece by Umeå University.
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