EMBL Seminars

Abstract
Electron cryotomography (cryo-ET) is a powerful technique for investigating the structure and distribution of biological macromolecules directly inside cells. However, the physiology of a cell is influenced by its environment, and performing cryo-ET experiments within cells grown in isolation does not fully replicate the complexity found in vivo. This limits our understanding of intracellular structure within the broader context of whole tissues and organs. The application of cryo-ET within tissues is hindered by multiple technical bottlenecks, particularly the reproducible vitrification of samples and the fabrication of thin sections from thick (≥100µm) specimens. Here, I will demonstrate the workflow developments that have enabled routine analysis of mouse hippocampus by cryo-ET. The optimisation of high-pressure freezing protocols to ensure complete sample vitrification, and the application of plasma-sourced focused ion beam milling and cryo-lift-out has enabled ≥700 tomograms spanning the mouse hippocampus CA1 to be generated. This has allowed us to visualise the molecular detail of both synaptic transmission and the cytoskeletal organisation of the CA1 neuropil. This approach is generalisable and has been extended to multiple brain regions and other mouse tissues, opening the possibility to study many pressing structural biology questions within the most native context. 

About the speaker
[Biographical information about the speaker].

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Attachments
[Link to a file (for example a pdf of the seminar’s programme) - the file can be uploaded on the intranet]

Connection details
Zoom*: [link] (Meeting ID: [XXXXXXXXX], Password: [XXXXXXX])

Please note that the talk will yes/not be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.

Abstract
Macromolecules dynamically segregate into phase-separated assemblies, establishing a fundamental organizational principle for membraneless compartments within the cell. While the constituents of biomolecular condensates have been extensively characterized, we still lack clarity regarding both the regulatory mechanisms controlling their formation and the biological significance of their stress-induced assembly. Here, we identify the evolutionarily conserved ubiquitin-like modifier Urm1 as a critical driver of stress-induced phase separation. Termed urmylation, this post-translational modification directs the strategic sequestration of stress-vulnerable proteins into protective nuclear and cytoplasmic condensates. Urmylation-deficient cells show impaired condensate formation and accumulate ubiquitinated proteins under stress, suggesting that urmylation shields vulnerable proteins from non-specific ubiquitination and prevents collateral damage to the proteome during stress exposure. We propose that Urm1 acts as a reversible molecular adhesive that drives the protective phase separation of essential proteins during stress, a mechanism critical for safeguarding proteome integrity under adverse conditions.

Abstract
Large Language Models (LLMs) like ChatGPT are transforming the way we do science and very prominently how we analyse scientific data. In this talk, I will introduce the fundamentals of LLMs and their emerging multimodal extensions, such as Vision-Language Models (VLMs). Computer scientists seek to enable analysis of biological images using VLMs, turning images into numbers and insights ideally directly. I will discuss current capabilities and limitations of these models for bio-image analysis and highlight the unique potential of LLMs for automating data analysis workflows through code-generation. Emphasizing practical examples, I will demonstrate how LLM-driven code-generation accelerates data exploration, preprocessing, and quantitative analysis in bio-image data science.

Abstract
[Strain-level variation within the human microbiome is a major determinant of functional capacity, pathogenic potential, and host interaction. However, resolving such variation remains a significant challenge. Sequencing-based methods, while powerful, require deep coverage, elaborate bioinformatics pipelines, and time-consuming workflows to achieve strain-level accuracy—making them costly and impractical for large-scale or time-sensitive applications.

We present DynaMAP, a rapid, sequencing-independent metagenomics platform based on high-density optical DNA mapping. By directly imaging fluorophore-labeled high-molecular-weight DNA extracted from human stool and other complex samples, DynaMAP generates long, single-molecule optical maps that preserve structural features specific to individual strains. These maps are matched against a curated reference database of nearly 20,000 microbial genomes, enabling strain-level identification up to 99.8% average nucleotide identity (ANI) resolution.

We benchmark DynaMAP on mock communities, standardized microbial panels, and real human fecal samples, and show that it achieves taxonomic profiles highly concordant with shotgun metagenomics, but with reduced complexity, same-day turnaround time, and affordable cost. Crucially, DynaMAP avoids the need for genome assembly or computationally intensive strain-calling algorithms, enabling accessible and scalable microbiome analysis.

Our results demonstrate that DynaMAP enables same-day, strain-resolved profiling of gut microbiota, with potential applications in clinical diagnostics, microbial infection monitoring, and routine microbiome monitoring in research and healthcare settings.].

About the speaker
[Arno Bouwens is the R&D Director at Perseus Biomics, a pioneering biotechnology company transforming microbiome analysis through optical mapping of metagenomic DNA. With a strong foundation in engineering, Arno brings deep expertise in the development of complex optical and electronic systems.

He earned his PhD in 2013 from the École Polytechnique Fédérale de Lausanne (EPFL), specializing in advanced biomedical imaging technologies. His postdoctoral research at KU Leuven, Université Libre de Bruxelles (ULB), and EPFL focused on DNA mapping techniques and optical implementations of machine learning.

Before joining Perseus Biomics, Arno worked as a senior systems engineer at a Belgian SME, where he developed optical metrology tools and satellite imaging hardware. Drawing on his multidisciplinary background in research, systems engineering, and data engineering, he now leads the development of high-precision, high-throughput data generation technologies tailored to life sciences applications.].

Connection details
Zoom*: [https://embl-org.zoom.us/j/93113530119?pwd=B5ifSphC0TrPbCO8uWMGmbIbbLVNoX.1] 

Abstract
Memory formation relies on a bidirectional interplay between synaptic plasticity and nucleus-templated transcriptional programs, but how precisely this interplay is orchestrated by epigenetic mechanisms remains to a large extent unknown. In this talk, I will showcase our recent efforts to better understand this aspect from two angles. First, we have found that chromatin plasticity in the mouse brain is a key determinant for memory allocation, the process by which neurons become recruited into the memory trace: When we increased chromatin plasticity by enzymatic overexpression of histone acetyl transferases (HATs), neurons with elevated histone acetylation were preferentially recruited into the encoding ensemble and memory retention was enhanced, while optogenetic silencing of the epigenetically altered neurons prevented memory expression. Second, we have found that after learning, the epigenetic make-up of a single locus in the encoding ensemble is necessary and sufficient to bidirectionally alter memory performance across different phases of memory consolidation. Together, these findings stipulate that before and after memory encoding, epigenetic mechanisms play a pivotal role as molecular memory aids. 

Abstract
[Text for abstract].

About the speaker
[Biographical information about the speaker].

Meet the speaker
To meet with the speaker informally after the talks,sign up here [add link]. We especially encourage predocs and postdocs to take advantage of this opportunity.

Attachments
[Link to a file (for example a pdf of the seminar’s programme) - the file can be uploaded on the intranet]

Connection details
Zoom*: [https://embl-org.zoom.us/j/96374261689?pwd=TnNxRWtQY2lyc2pSa2JpY3NGcDlhZz09] (Meeting ID: [963 7426 1689], Password: [DBU])

Please note that the talk will yes/not be recorded.
*For the FAQ section, as a zoom participant, please use either the chat function (the host will read out your question) or the “raise your hand” function and turn on your microphone.