EMBL Events’ Post

Will 2025 be the year that you increase your bioinformatics, omics and/or data science knowledge and skills? Take a look at our current 2025 course programme as well as other great courses and conferences run by EMBL Events. Find out more about our 2025 courses: https://lnkd.in/dRaihKYC #bioinformatics #datascience #omics #genomics #proteomics #sciencetraining #sciencelearning #EMBL #EMBLEBI

I'm excited to share that I'll be presenting at the 3rd International Spatial Biology Congress: Europe in The Hague, Netherlands on 11-12 July 2024. My talk will focus on the critical role of multimodal spatial data in translational research, particularly within the therapeutic area of oncology. Looking forward to discussing how the integration of pathology data with additional tissue components, like spatial transcriptomics or proteomics, can transform our approach in the translational setting. This fusion of data offers fresh perspectives for research and holds the potential to improve patient outcomes. I hope to see many of you there! #SpatialBiology #TranslationalResearch #Oncology #Histopathology #DigitalPathology

This week, we celebrate the exciting news that David Baker, Demis Hassabis, and John Jumper received the 2024 #NobelPrize in #Chemistry for their revolutionary work on computational protein design and protein structure prediction. Their work has already had immense impact in the field of #biochemistry, as covered in this accessible and informative article by Yasemin Saplakoglu 👉 https://lnkd.in/eFWiM76h This Quanta Magazine piece features interviews with two of the Nobel Prize winners alongside other experts in the field, including Anastassis Perrakis: group leader within Oncode Accelerator’s #ArtificialIntelligence Platform, group leader and head of the division of #Biochemistry at The Netherlands Cancer Institute, professor of Macromolecular Structures at Utrecht University, and Oncode Institute Investigator. 💬 Professor Perrakis says: “The work that received yesterday's Nobel prize has completely transformed the way we approach questions about the mechanism of proteins to understand basic biology and design new drugs and therapeutics. The impact in cancer research is already starting to show, and I am confident that in the next few years we will see applications of protein design in - for example - making therapeutic antibodies for specific (neo)antigens, and applications of protein structure prediction to better understand mutations that lead to cancer or result in drug resistance. And, of course, I anticipate a boost in computer-aided drug development.” 🔎 For a deeper dive into the work of Professor Perrakis and his team, including Ida de Vries, Robbie P. Joosten, Daniel Álvarez Salmoral, Razvan Borza & Maarten Hekkelman, take a look at: ⏺ The tools they have developed for enriching AlphaFold models with ligands and cofactors: https://alphafill.eu/ ⏺ A first public view of their brand-new server for analysing AlphaFold 3 models, a development supported by PhD research on Artificial Intelligence within the Oncode Accelerator program: https://alpha-bridge.eu/ #cancerresearch #structuralbiology #drugdiscovery #AlphaFold #chemnobel #computationalbiology #AI #AIforGood | The Nobel Prize | Google DeepMind

Very powerfull tools!

✨ Lab Showcase Series, Episode 11: Borner Lab ✨ This week in our Lab Showcase Series, we’re diving into the fascinating world of the Borner Lab at the Max Planck Institute of Biochemistry! 🧬🔬 Led by Dr. Georg H H Borner , the lab is pioneering research in Microbial Functional Genomics , focusing on the intricate processes within cells that are essential for life. 🧫🔍 🔍 Key Research Highlights: ✨ Dynamic Organellar Maps: The Borner Lab is at the forefront of developing mass-spectrometry-based approaches to subcellular protein localization, creating detailed and dynamic maps of organelles. 🦠 🔬 Proteomic Microscope: These organellar maps are not just static images; they are used to study protein movements and cellular processes, including membrane trafficking and signaling. This approach is crucial for understanding the inner workings of cells. 📈🔧 🧠 AP-4 Pathway: The team investigates the AP-4 complex, a key player in protein export from the trans-Golgi network (TGN), and its role in intellectual disability and spastic paraplegia. Understanding this pathway could lead to breakthroughs in treating these conditions. 🧠🔍 🧬Autophagy and AP-4: The lab also explores how deficiencies in AP-4 affect autophagy, particularly through the sorting of the ATG9A protein, linking it to AP-4 pathology. This research is vital for unraveling the complexities of cellular maintenance and disease. 🔄🧪 For more insights into their cutting-edge research, visit: 🔗 Lab Website: https://lnkd.in/gDt6_JC6 ✍🏻Credits: Poster: Smrutimayee Prusty Content: Shruti Gajbhiye #LabShowcaseSeries #NGSF #BornerLab #Research #Labs #MaxPlanckInstitute #MicrobialGenomics #Proteomics #CellBiology #AP4Pathway #Autophagy

Researchers from the Bhogaraju Group at EMBL Grenoble have come up with a new method named Ub-POD to study a critical protein modification process called ubiquitination. Ubiquitination plays an integral role in diverse cellular functions, and its dysregulation contributes to many human diseases, including neurodegeneration and cancer. Current methods for mapping ubiquitination interactions are highly resource-intensive, which limits their use and scalability. The simplicity of Ub-POD and the use of common chemicals means that it can be used in any lab that has basic molecular biology facilities. https://lnkd.in/dPtE47P4 Sagar Bhogaraju Urbi Mukhopadhyay

Visualizing cells in the context of their environment can put an ocean of data within your view. With over 600 biomarkers available in our MACS® Antibody portfolio, you can see what no one has before and make new discoveries. #SpatialBiology #MACSima #highplex #proteomics #antibodypanels

Visualizing cells in the context of their environment can put an ocean of data within your view. With over 600 biomarkers available in our MACS® Antibody portfolio, you can see what no one has before and make new discoveries. Our pre-tested antibodies fit seamlessly in any spatial workflow and are suitable for FFPE-, PFA-, or acetone-fixed tissues or cells. If your research is missing depth, take advantage of our limitless proteomics with the MACSima™ Platform. Learn more about antibodies for diving into spatial biology: 👉 https://ow.ly/wZ3B50SCZFa #SpatialBiology #MACSima #highplex #proteomics #antibodypanels

Congratulations to Lucia Bellanova for the Best Poster award at the XXVII Congresso Nazionale 2024 of the Italian Society for Pure and Applied Biophysics (SIBPA)! For more info about the work of Lucia and her team check https://lnkd.in/dtKxqkRS SENSING NITRIC OXIDE WITH A FLUORESCENT PROTEIN Real-time quantitative visualization of nitric oxide (NO) concentration at the single cell level is fundamental to achieve a direct and accurate determination of NO dynamics. To this aim, development of genetically encoded fluorescent sensors (GES) is of fundamental relevance. The field is still poorly explored and only a few GES have been so far developed and proposed for monitoring intracellular NO levels 1. The recent finding that the blue-emitting fluorescent protein mTagBFP2 is sensitive to NO in the micromolar range suggested new development strategies 2. Protein mutants and mass spectrometry demonstrated that S-nitrosylation of Cys residues is at the basis of the observed reduction in emission intensity and lifetime in response to NO exposure. The potential of this GES for monitoring intracellular NO was shown on HeLa cells transiently expressing mTagBFP2. In this work, we present a more accurate study on the dynamics of S-nitrosylation of Cys residues in mTagBFP2. S-nitrosylation of mTagBFP2 was induced by the NO donor MAHMA nonoate and the changes in fluorescence intensity and lifetime were monitored as a function of time. From the overall change, it was possible to obtain a better estimate of the Kd for the reaction. We have also explored the response of mTagBFP2 to the NO donors S-nitrosoglutathione (GSNO) and S-nitroso-N-acetylpenicillamine (SNAP). Experiments on mTagBFP2 mutants containing a single Cys residue show that two of the three Cys residues in mTagBFP2 are responsible for the changes in fluorescence emission. Further experiments on bacterial and mammalian cells expressing mTagBFP2 and its mutants, are underway. Funded by the European Union – Next Generation EU-PRIN 2022PNRR P2022F4WR8_001 “A molecular platform for intracellular nitric oxide sensing”.

I'm thrilled to announce the publication of our paper "Mapping cellular interactions from spatially resolved transcriptomics data" in Nature Methods! As co-first author alongside James Zhu and Dr. Yunguan Wang, I'm incredibly proud of this work and grateful for the opportunity to contribute to advancing our understanding of cell-cell communications. I want to extend my sincere thanks to my PIs, Tao Wang and Yang Xie, for their guidance and support throughout this project. Our new computational tool, Spacia, is specifically designed for single-cell resolution spatial transcriptomics technologies like MERSCOPE, Xenium, and CosMx. Spacia overcomes key limitations of existing methods by: - Achieving single-cell resolution detection of cell-cell communications - Not being limited to prior interaction databases or ligand-receptor relationships - Using a multiple instance learning (MIL) framework to model multiple-sender-to-one-receiver relationships explicitly Some exciting biological findings from our work include: - Revealing how tumor microenvironment cells induce EMT and lineage plasticity in prostate cancer - Identifying differential roles of γδ T cells in healthy livers versus liver cancers You can check out the full paper here: https://lnkd.in/gt2A3qBm GitHub link to Spacia: https://lnkd.in/g2DXPJKx #SpatialTranscriptomics #ComputationalBiology #Bioinformatics #CancerResearch