Best Poster Awards – In Situ Structural Biology Workshop

The EMBO Workshop: In Situ Structural Biology: From Cryo-EM to Integrative Modelling was our final virtual conference of 2020, but there was no trace of Zoom fatigue amongst the 466 participants who joined us from 6 – 8 December!

80 international researchers presented their posters during the two posters sessions on the following topics:

  • Biophysical analysis in cells
  • COVID-19
  • Imaging across scales
  • Integrative modelling
  • Molecular sociology
  • Structural analysis in situ
  • Structural biology

Each of the participants had the chance to vote for their favourite poster, resulting in two posters winning the Best Poster Award kindly sponsored by EMBO Press.  Here are the winners:

New insights on the catalytic mechanism of arsenite oxidase

PHOTO: Filipa Engrola

Authors: Filipa Engrola, Márcia Correia, Teresa Santos-Silva, Maria Romao, (UCIBIO@FCT-NOVA, Portugal)

Arsenic (As) and antimony (Sb) are two metalloids that, due to anthropogenic and natural causes, pose an environmental  threat, considered as priority pollutants by the World Health Organisation and the United States Environmental Protection Agency. Although the safety guards recommend a maximum of 10 μg/L of As and Sb in drinking water, these values are exceeded in many regions worldwide, with no remediation approach that is simultaneously effective, clean and economically sustainable [1,2]. The ancient bioenergetic enzyme arsenite oxidase (Aio), from microorganisms Rhizobium sp. NT-26 (NT-26 Aio) and Alcaligenes faecalis (A.f. Aio), is currently being studied for its use as a biosensor and in bioremediation processes. Both Aio enzymes contain a large subunit (AioA) that harbours a
molybdenum centre and a [3Fe-4S] cluster, and a small subunit (AioB) that possess a Rieske [2Fe-2S] cluster and have demonstrated to oxidise AsIII, as well as SbIII, into the easier to remove and less toxic forms of AsV and SbV, respectively [3,4]. Aiming to elucidate the catalysis mechanism of the enzymes, a combination of expression and purification of the proteins, crystallisation, structural analysis, enzyme kinetics and affinity tests were
conducted. X-ray structures of the ligand-free form of the enzyme had been previously determined (PDB: 4AAY, 5NQD and 1G8K [3,5,6]). In our work, Aio crystals in complex with two different forms of the substrate analogue – Sb oxyanions, with a reaction kinetic 6500 times slower than AsIII [6] – diffracted up to ca 1.8 Å resolution. The structures show the reaction intermediates bound at the active site, with a μ-oxo bridge binding Sb to the Mo atom. Analysis of bond lengths and geometry of the ligands at the Mo active site allowed us to revisit the catalytic mechanism of As oxidation [7], contributing to the understanding and future biotechnological application of this family of enzymes in water treatment.

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Allosteric hotspot in the main protease of SARS-CoV-2

PHOTO: Léonie Ströhmich

Authors: Léonie Strömich, Sophia N Yaliraki, (Imperial College London, UK)

Since the beginning of 2020 we have seen the coronavirus SARS-CoV-2 causing a global pandemic with almost 34 million cases and over 1 million deaths worldwide [as of 01.10.2020] [1.] As a result, we have seen a surge in research efforts to develop effective treatments for the underlying disease, COVID-19. One approach is to target the main protease (Mpro) of SARS-CoV-2 as it is essential for virus replication in an early step of the viral life cycle [2.] Most efforts are centred on inhibiting the orthosteric binding site of the enzyme. However, considering allosteric sites on the protein allows for more selective drug design and widens the chemical search space. Here, we report an allosteric hotspot in the SARS-CoV-2 Mpro dimer by using novel atomistic graph theoretical methods: Markov transient analyses follow the propagation of a random walker on a graph and have been shown to successfully identify allosteric communication in catalytic proteins [3.] We further score the so identified allosteric hotspots against random sites in similar distances and thus identify a statistically significant putative allosteric site in the SARS-CoV-2 Mpro. We then simulate a binding event at this hotspot region using data from a recent XChem fragment screen by the Diamond Light Source [4.] which provides a starting point for rational drug design. This study uses highly efficient network theoretical models to shed light on allosteric communication and uncovers putative allosteric sites in the SARS-CoV-2 main protease. This provides a valuable contribution to the ongoing efforts to find a cure against COVID-19 by broadening the horizon for drug discovery efforts.

References:
[1.] Official World Health Organization COVID-19
dashboard: https://covid19.who.int (Accessed: 01.10.2020).
[2.] Hilgenfeld, R. (2014). FEBS Journal, 281(18), 4085-4096.
[3.] Amor, B., Yaliraki, S. N., Woscholski, R., & Barahona, M. (2014) Molecular BioSystems, 10(8), 2247-2258.
[4.] Douangamath, A., Fearon, D., Gehrtz, P., Krojer, T., Lukacik, P., Owen, C. D., … Walsh, M. A. (2020) Nature Communications, 11, 5047.

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Best Poster Awards – Cancer Genomics

The 4th EMBL Conference: Cancer Genomics (4 – 6 November 2019) brought together over 240 scientists in the field of cancer research to present the latest findings in cancer functional genomics, systems biology, cancer immunogenomics and epigenomics, as well as their translation and clinical impact.

123 posters were presented at the two poster sessions, out of which two were selected as the winners by popular vote. 

Infinite sites violations during tumour evolution reveal local mutational determinants

Jonas Demeulemeester is a postdoctoral researcher at the Francis Crick Insitute in UK. PHOTO: Jonas Demeulemeester

Authors: Jonas Demeulemeester (1), Stefan C. Dentro (2), Moritz Gerstung (2), Peter Van Loo (1)

The infinite sites model of molecular evolution requires that every base in the genome is mutated at most once. It is a cornerstone of (tumour) phylogenetic analysis, and is often implied when calling, phasing and interpreting variants or studying the mutational landscape as a whole. It is unclear however, whether this assumption holds in practice for bulk tumour samples. Here we provide frameworks to model and detect infinite sites violations, identifying 24,459 in total, including 6 candidate biallelic driver events, in 700 bulk tumour samples (26.3%) from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes project. Violations generally occur at mutational hotspots and their frequency and type can accurately be predicted from the overall mutation spectrum. In melanoma, their local sequence context evidences how not only ETS, but also NFAT-family transcription factor binding creates hotspots for UV-induced cyclobutane pyrimidine dimer formation. In colorectal adenocarcinoma, violations reveal hypermutable special cases of the trinucleotide mutational contexts identified in POLE-mutant tumours. Taken together, we reveal the infinite sites model breaks down at the bulk level for a considerable fraction of tumours. These results warrant a careful evaluation of current pipelines relying on the validity of the infinite sites assumption, especially when scaling up to larger sets of mutations and lineages in the future.

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(1) The Francis Crick Institute, United Kingdom, (2) EMBL-EBI, United Kingdom


The other award-winning poster was:

Understanding the early impact of activating PIK3CA mutation on cellular and genetic heterogeneity presented by Evelyn Lau, UCL Cancer Institute, United Kingdom


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Best Poster Awards – Seeing is Believing

For the 5th time, the EMBL Advanced Training Centre played host to 466 researchers and imaging specialists at the EMBO|EMBL Symposium: Seeing is Believing – Imaging the Molecular Processes of Life (9 – 12 October 2019), where cutting-edge applications illustrated how imaging can answer biological questions and capture the dynamics of life. 

Out of the 248 posters presented, 2 stood out from the rest and were awarded a poster prize based on popular vote. Here we present the abstracts and posters of the winners.

CalQTrace: Simultaneous Calculation and Quantification of 100,000 immune activation Traces at single-cell resolution using CNN

Liliana Barbieri is a doctoral student at the Biomedical Imaging Doctoral Training Centre, University of Oxford, UK. PHOTO: Liliana Barbieri

Authors: Liliana Barbieri (1), Kseniya Korobchevskaya (2), Azeem Ahmad (3), Huw Colin-York (1), Aurelien Barbotin (4), Glykeria Karanika (1), Loic Peters (5), Isabela Pedroza-Pacheco (4), Angela Lee (1), Lena Cords (1), Anish Priyadarshi (3), Dominic Waithe (6), Jana Kohler (6), Christoffer Lagerholm (6), Balpreet Singh Ahluwalia (3), Marco Fritzsche (2)

Quantification of immune cell activation is essential to the understanding of their effector function. Tracing activation signatures like cellular calcium release and the expression of surface markers in response to activation signals allows the classification of the course of immune cell activation from early triggering events to late differentiation. However, robust quantitative platforms for such measurements represent a major challenge, restricting the analysis to small single-cell population or more recently to cell ensembles with high-dimensional parameter analysis tools. Here, we introduce a combination of a convolutional neural network-based CalQTrace (Calculation and Quantification of Trace) software, together with a Graphical User Interface, and an optical high-throughput light-sheet platform, allowing the simultaneous fully automated quantitation of immune cell activation traces of >100,000 live immune cells. CalQTrace enables user-independent statistically robust classification and quantification of multiple fluorescent activation markers including calcium, CD25+/- expression, and cell viability tracking single cells in space and time within a 5 mm x 5 mm large-field-of-view, opening-up unprecedented insights into physiological activation tracing in living immune cells.

(1) MRC Human Immunology Unit, University of Oxford, United Kingdom
(2) Kennedy Institute for Rheumatology, University of Oxford, United Kingdom
(3) The Arctic University of Norway, Norway
(4) University of Oxford, United Kingdom
(5) University College London, United Kingdom
(6) Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom

Poster currently not available


Bleaching-insensitive STED microscopy with exchangeable fluorescent probes

Mike Heilemann is a Principal Investigator at Johann Wolfgang Goethe-University, Frankfurt, Germany. PHOTO: Mike Heilemann

Authors: Christoph Spahn (1), Florian Hurter (1), Mathilda Glaesmann (1), Jonathan Grimm (2), Luke Lavis (2), Hans-Dieter Barth (1), Marko Lampe (3), Mike Heilemann (1)

Photobleaching affects image quality and resolution in fluorescence microscopy, and thus limits the extractable information. This is in particular relevant for super-resolution microscopy where typically high laser intensities are used. In order to minimize photobleaching, we repurposed the use of exchangeable fluorescent probes, as used in single-molecule localisation microscopy methods such as Point Accumulation for Imaging in Nanoscale Tomography (PAINT) [1], for STED microscopy. We demonstrate pseudo-permanent labeling of target structures and constant exchange of photobleached fluorophores. This concept allows for whole-cell, 3D, multi-color and live-cell STED microscopy [2]. Using transiently binding hydrophobic dyes and fluorophore-labeled major minor groove binders [3, 4], we visualised the nanostructure of chromatin, cell membranes and organelles in bacterial and mammalian cells in 3D. To expand the range of targets, we employed oligonucleotide-labeled antibodies that transiently bind fluorophore-labeled oligonucleotides, as used in single-molecule super-resolution imaging with DNA-PAINT [5], and demonstrate multi-color STED imaging.

References:
[1] Sharanov and Hochstrasser, PNAS 103 (50), 18911-18916 (2006)
[2] Spahn et al., Nano Letters 19 (1), 500-505 (2019)
[3] Lukinavičius et al., Nature Communications 6, 8497 (2015)
[4] Spahn et al., Scientific Reports 8, 14768 (2018)
[5] Schnitzbauer et al., Nature Protocols 12(6), 1198-1228 (2017)

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(1) Johann Wolfgang Goethe-University Frankfurt, Germany
(2) HHMI – Janelia Research Campus, United States of America
(3) EMBL Heidelberg, Germany


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