News: Goodbye Koen and welcome Cleo, Martijn, Niels and Simon

After recently defending his PhD thesis titled “Pinpointing macromolecular motion. Single-particle tracking fluorescence microscopy advances and applications” with distinction (cum laude!), Koen Martens left the group for a postdoc position in the lab of Dr. Ulrike Endesfelder (CMU, Pittsburgh). All the best, Koen, you will be missed!

A big welcome to Martijn Gobes and Cleo Bagchus who both joined the group for their MSc thesis. Martijn will improve our computational workflow for super-resolution microscopy (his first ImageJ plugin for fast temporal median filtering is available here). Cleo will continue our work on single-particle tracking in live cells together with Simon van de Els, who joined the lab as a (semi) post-doctoral research assistant.

Last but not least, we welcome Niels Zijlstra as a guest scientist from the Cordes lab in Munich. Niels will work on combining the miCube platform with spectrally resolved super-resolution imaging.

News: IPM-3 and R2I proposals granted

Good news! Two proposals got granted!

For the first one (IPM-3, Innovation Program Microbiology, an initiative from the Laboratory of Microbiology at Wageningen University and Research), we will use single-particle tracking Photo-Activated Localisation Microscopy (sptPALM) to study CRISPR-Cas in live bacteria. Looking forward collaborating with Raymond Staals from the Laboratory of Microbiology. A one-year post-doc position will be available, please contact me (with CV) for further details.

For the second, the Road-to-Innovation business development grant, we will work on a neat idea for spectrally resolved single-molecule localisation microscopy.

News: Welcome to Mariska Brüls and Dani Kortekaas

With Mariska, the third PhD student in our NWO funded LocalBioFood project on super-resolution based localisation of biomolecules at food-related interfaces has started. Mariska started her PhD thesis in the Voets lab in Eindhoven and will relocate to our lab in early 2022.

Dani started his BSc thesis in the lab during Covid-19 times. He will look into improving our computational workflow for single-particle tracking in live cells.

News: Welcome to Ezra Bekkering

Ezra just started his BSc thesis in a new project together with the Laboratory of Microbiology (Wen Wu & Dr. Raymond Staals). He will work on visualising CRISPR-Cas interactions in live bacteria using sptPALM.

Publication: Direct visualization of native CRISPR target search in live bacteria reveals Cascade DNA surveillance mechanism

J.N.A. Vink, K.J.A. Martens, M. Vlot, R.E. McKenzie, C. Almendros, B. Estrada Bonilla, D.J.W. Brocken, J. Hohlbein, S.J.J. Brouns, Molecular Cell, 77, 39-50.e10, 2020, [link], preprint here [link]

CRISPR-Cas systems encode RNA-guided surveil-lance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism andkinetics of target search and its impact on CRISPRprotection levels have remained unknown. Here, wevisualize individual Cascade complexes in a native type I CRISPR-Cas system. We uncover an exponential relation between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunitCas8e, Cascade spends half its search time rapidly probing DNA (30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and affect CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.

Graphical abstract

News: Welcome to Šarūnė Ivanovaitė and Elmar van der Wijk

Šarūnė recently started her Erasmus+ internship in the group. She will characterise a variety of fluidic devices that we got our hands on including devices for high throughput smFRET screening, trapping of bacteria and establishing DNA curtains. Elmar started his MSc thesis and will utilise new DNA constructs for smFRET based studies of ARF transcription factor binding.

News: Welcome to Abbas Jabermoradi, Ben Tumulero, Vincent Boerkamp, and Sven Koens

Great to see so many people joining the group. Abbas started his PhD thesis on super-resolution based localisation of biomolecules at food-related interfaces. Ben (BSc thesis, BIP) started illuminating bacteria using the PAINT technique. Vincent (MSc thesis, BIP) supports Koen in his quest to monitor particle diffusion in meat replacers. Last but not least, Sven (BSc thesis with BIC & BIP) will study the influence of control elements to the transcription factor binding.

Some PAINT data by Ben

Sample1_celldivision_+BF

News: Welcome to Suyeon Yang and George Vogelaar

Suyeon joined the group in November 2018 for her PhD thesis. She will study lipid oxidation at oil/water interfaces using super-resolution microscopy. George just started his MSc thesis to study diffusion of dCas9 in Lactococcus lactis using single-particle tracking PALM.

News: The miCube moved to Github

Our open (single-molecule) microscopy project, the #miCube, is now on Github [link]!  The page shows a detailed and updated overview of the components, some information on phasor-based SMLM, and many links to similar open hardware projects.