EMBL Seminars

Abstract
The NGS landscape has evolved rapidly in the past decades leading to the need for library preparation and sequencing solutions compatible with challenging and vanishingly low sample inputs that maintain data quality. Watchmaker Genomics utilizes a novel enzyme engineering and multidimensional reaction optimization to develop NGS library prep solutions that enhance data integrity, minimize bias, and improve sequence accuracy.

We highlight the advantages of this development approach with our RNA Sequencing portfolio which achieves a rapid, single day workflow with significantly improved data quality compared to existing commercial products, particularly when dealing with low input or degraded samples. The library prep kits are compatible with both established and emerging short read platforms, creating a versatile solution for highly sensitive applications.

About the speaker 
Ariele has over 15 years experience with Next Generation Sequencing, starting with assay development across a variety of organizations. Her experience includes migrating QC assays from Sanger to NGS based methods, as well as development & launch of NGS based library prep and sequencing services at both clinical and non-clinical service providers. She continued in development of library prep reagents before moving to applications and customer support.

Please Register: https://embl-org.zoom.us/meeting/register/tJwscumgrz0oHdUV-GGdlB4OV0CjETxtX8GD

Abstract
All enveloped viruses enter cells by inducing the fusion of their lipid envelope with the membrane of a target cell to release their genomic cargo into the cytoplasm for infection. Our structural studies over the years have shown that the gene coding for the membrane fusion protein (MFP) of viruses from otherwise unrelated families - flaviviruses, rubiviruses, alphaviruses, bunyaviruses - derive a from a distal common ancestor that underwent divergent evolution. These proteins constitute a separate structural class of MFPs (termed class II) and require an chaperoning accompanying protein (AP) to be functional as an AP/MFP heterodimer.  The trigger of their membrane-fusogenic activity is dissociation of the AP/MFP heterodimer upon binding of protons in the acidic environment of an endosome following receptor-mediated endocytosis. The MFP released from the heterodimer then undergoes a major conformational change that drives the fusion of the viral envelope with the endosomal membrane. Class II MFP homologs are also functional in eukaryotic cells, the most notable example being protein HAP2, present in the male gamete (sperm) and responsible for the fusion with female gametes to form a zygote. The identification of HAP2 in organisms in the most distant branches of the eukaryotic tree suggests that it was present in the last eukaryotic common ancestor (LECA), which already underwent sexual reproduction.  Our studies suggest that this eukaryotic homolog uses the same mechanism as its viral homologs to drive membrane fusion, although no AP has been identified, and the trigger of the membrane fusion reaction is not yet known. Despite its importance in eukaryotic biology, the molecular mechanism of fertilization is therefore still not understood. In my presentation, I will discuss the implications of the homology with the viral proteins for understanding gamete fusion in molecular terms, as well as the prospects to combat eukaryotic pathogens such as Plasmodium, the aetiologic agent of malaria..

About the speaker
Felix Rey graduated in physics at Instituto Balseiro in Bariloche, Argentina. He then did a PhD thesis in structural biology at the Université de Paris-Sud (Orsay, France) and specialized in virus structure at Harvard University, USA. After being junior group leader (CNRS ATIPE program) and then Director of the Structural Molecular Virology laboratory of the CNRS at Gif-sur-Yvette, Felix Rey moved to Institute Pasteur in Paris. His laboratory studies the mechanism of membrane fusion used by enveloped viruses to enter cells. His work has led first to the identification of a separate structural class of viral membrane fusion proteins. He then showed that they are related to eukaryotic proteins, in particular one that drive sgamete fusion in numerous eukaryotic organisms during sexual reproduction. Félix Rey also made important contributions to understand the interactions of viral proteins with their cell receptors and the identification of epitopes targeted by neutralizing antibodies against pathogenic viruses, providing important insight for the development of novel immunogens in an epitope-focused reverse vaccinology approach.

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Connection details
Zoom*: https://embl-org.zoom.us/j/96561764037?pwd=0AoNepG1KaaQUeR8JoQlknPE7QDItb.1 (Meeting ID: 965 6176 4037, Password: 666024)

Abstract
The oncofetal RNA binding protein Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) is a key player in a wide array of malignancies. Here we demonstrate that IGF2BP3 is required for MLL-AF4 driven leukemogenesis and define the underlying post-transcriptional regulatory mechanisms through which IGF2BP3 drives this process in vivo. 

Abstract
Bacteria often grow in biofilms, cell clusters held together by a self-produced matrix. This lifestyle promotes physiological differentiation, making it difficult to control bacterial growth. My group studies the multicellular physiology of Pseudomonas aeruginosa, a bacterium that is metabolically versatile, produces a diverse set of virulence factors, and is a major cause of biofilm-based infections. To visualize and investigate the mechanisms underpinning differentiation in biofilms, we use fluorescent reporters and deuterium labeling, paired with various microscopic techniques applied to thin sections and live samples. We have shown that biofilm subpopulations employ distinct strategies, such as the use of oxygen-scavenging complexes and endogenous electron-shuttling compounds called phenazines, to support metabolic activity. We have also observed that such metabolic differentiation correlates with increased drug tolerance. Additionally, our characterization of P. aeruginosa biofilms has uncovered a virulence factor called the “refractile body” (R-body) a nanomachine that extends into a spear, thought to damage to host cells from within. R-body production is stochastic within biofilms, consistent with the idea that R-body-producing bacteria disable phagocytes and thereby protect their kin from engulfment. Broadly, our work provides insights that are specific to the communal lifestyle and that can inform efforts to control the growth of biofilms in diverse contexts that are relevant for human health and society.

About the speaker
I am an associate professor at Columbia University, where I founded my research group 14 years ago. Prior to that, I studied yeast membrane dynamics and obtained my PhD at the BZH Heidelbergin the laboratory of Christian Ungermann, then studied bacterial biofilm physiology at Caltech and MIT as a postdoc in Dianne Newman’s group.

The Dietrich lab conducts curiosity-driven research on cellular communication and metabolism in biofilms. P. aeruginosa, an opportunistic and metabolically versatile pathogen, is the focus of our studies. We seek to understand the mechanisms driving physiological differentiation when cells grow in groups (packed together), the consequences of physiological heterogeneity for intercellular and interspecies interactions, and the impact of such heterogeneity on our ability to treat to disease. We also love to follow up on unexpected findings, such as (i) effects of light on biofilm physiology, and (ii) the formation of proteinaceous nanospears by P. aeruginosa! 

Connection details
Zoom*:Join Zoom Meeting 
https://embl-org.zoom.us/j/96133916944?pwd=qLHtisk0zJA06EvDsXPEopkSk2qHu0.1

Meeting ID: 961 3391 6944 
Passcode: 268344 

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
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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*: Join Zoom Meeting 
https://embl-org.zoom.us/j/93051446608?pwd=BoAPoKk13lgiaMmUarAYaAcajwLmUY.1

Meeting ID: 930 5144 6608 
Passcode: 495498 

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.