Weekly BioEngineering Talks (Lunch Provided)
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\r\nINVITED SPEAKERS:
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\r\nOrganic electrochemical transistors for enhanced potentiometric sensing of neurochemicals
\r\nDr. Emily Schafer, EPFL Laboratory of Chemical Nanotechnology
\r\nHost: Prof. Nako Nakatsuka
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\r\nData-driven protein engineering for sensing and biosynthesis of new-to-nature thioesters
\r\nDr. Sebastian Barthel, EPFL Laboratory of Synthetic and Applied Microbiology
\r\nHost: Prof. Markus Jeschek
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\r\nBioEngineering Talks mandatory EDBB Seminar Attendance (1st-Year PhD Students)\r\n
In this talk, I'll take a look at three \"microbial vignettes\". In the first, I'll examine how the presence of co-habiting microbes profoundly affects the biology of a human pathogen, Pseudomonas aeruginosa. This is important, because in diseased human airways - where P. aeruginosa is an unwelcome, but common inhabitant - the pathogen invariably shares the infection site with a variety of other microbes. It turns out that these microbial neighbours interact with one another and that these interactions are perturbed by the loss of a quorum sensing \"master regulator\" (LasR) in P. aeruginosa. In the second \"short\", I'll talk about how we are now able to manipulate the rate of evolution of the organism, either by \"stepping on the gas pedal\" or by \"slamming on the brakes\". The ability to do this, in an experimentally-controlled manner, is allowing us to access some novel evolutionary trajectories, and to address some truly fundamental biological questions. Finally, I'll take a fresh look at bacterial biofilms and in particular, examine whether the exopolysaccharide \"bioglue\" that holds these structures together might have additional - possibly more important roles. It turns out that it does, and that the exopolysaccharide matrix acts as a \"net\" to selectively sequester secreted proteins, potentially conferring novel functionalities on the biofilm.
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\r\nBrief Speaker Bio.
\r\nAfter reading for a degree in Biochemistry at the University of Oxford, Martin completed a PhD on bacterial chemotaxis at the Weizmann Institute of Science (Israel), where he was awarded the Wolf Prize for his contributions to the field. Leavuing Israel with a PhD and a [German] wife, he then moved to Toulouse (supported by a long-term EMBO fellowship) where he learned the dark art of x-ray crystallography and solved the structure of a signaling complex involved in bacterial chemotaxis. He then moved back to the UK to take up a post-doctoral position at the University of Cambridge working on quorum sensing in the fascinating plant pathogen, Pectobacterium atrosepticum. There, he developed skills in molecular genetics and demonstrated (for the first time) that quorum sensing molecules bind directly to their cognate LuxR homologs in a range of bacteria. This advance allowed him to secure a Royal Society University Research Fellowship to start his own group - where he learned the hard way that prospective students don't like any project with the word \"plant\" in, and when offered projects on the plant pathogen versus a mammalian pathogen, always went for the latter. Since around 2000, his team's focus has been on understanding better the link between metabolism and virulence in the opportunistic human pathogen, Pseudomonas aeruginosa. He is now Professor of Microbial Physiology and Metabolism at the University of Cambridge.
Photonics Day is a yearly event that aims to promote research discussions and networking among members of the EPFL photonics community, as well as researchers and industry players in the photonics sector. The program includes invited talks from world leaders in the field, a thesis presentation by the winner of the Best EDPO distinction, a scientific picture contest organised by EPC, as well as presentations by students in the Doctoral Program in Photonics, who will compete in the 180-Second Thesis Competition.
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\r\nThis year the Photonics Day will take place on Thursday October 22, 2026 at the EPFL Forum Rolex.
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\r\nParticipation is free and includes lunch. Registration opens in September and is mandatory by October 12, 2026. You’ll find both the registration form and the full program on the same page.
How can we meaningfully interpret neuronal calcium imaging data? Calcium imaging is one of the key methods used to record neuronal activity from the brain of animals. I will outline why the interpretation of calcium signals remains a major bottleneck in understanding neuronal activity and plasticity. I will trace the origins of this problem and how partial solutions have been provided by my own and by others' work, and how these issues are affected by recording conditions and different calcium indicators (e.g., OGB-1, GCaMP6, GCaMP8). I will propose a conceptual path forward that could make calcium imaging a more powerful tool than it currently is.
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Thesis Directors: Dr. S. Joost, Dr A. M. Jaksic
\r\nCivil and Environmental Engineering doctoral program
\r\nThesis Nr. 11653
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\r\nTo take part in the public defense, please contact directly the speaker
Weekly BioEngineering Talks (Lunch Provided)
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\r\nINVITED SPEAKER:
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\r\nAdvancing Multidimensional Single-Molecule localization microscopy: development and applications in nuclear organization
\r\nDr. Bassam Hajj, Institut Curie, Paris
\r\nHost: Prof. Aleksandra Radenovic
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\r\nAbstract:
\r\nSingle-molecule localization microscopy (SMLM) has revolutionized our understanding of biological processes by providing access to spatial scales beyond the diffraction limit of conventional optical microscopy. In the study of the cell nucleus, SMLM has offered unique insights into its organization and function at the nanoscale. Nuclear architecture is structured across multiple spatial scales in three dimensions and is highly dynamic. Understanding the mechanisms that govern nuclear organization therefore requires imaging approaches capable of capturing molecular dynamics across a broad range of spatial and temporal scales and in diverse biological contexts. Although SMLM can routinely achieve spatial resolutions in the tens-of-nanometers range, many biologically relevant structures and processes remain beyond its reach. For example, resolving the precise organization of DNA at the molecular scale remains challenging, as it would require a substantial improvement in spatial resolution over conventional SMLM, while also addressing the high density and degree of molecular compaction within the nucleus.
\r\nOver the years, we have developed complementary strategies to address these challenges by introducing additional dimensions and observables into SMLM measurements. In this presentation, I will first discuss our approaches to three-dimensional single-molecule imaging, including multifocus microscopy and volumetric light-sheet excitation, which enable fast and sensitive imaging over extended volumes and in complex biological samples such as cell colonies. While these approaches provide access to the three-dimensional and temporal dimensions required to investigate nuclear organization, spatial resolution alone is not always sufficient to distinguish molecular arrangements. We have therefore extended SMLM further by implementing polarization-resolved multifocus microscopy (PolMFM), which combines three-dimensional localization with information on molecular orientation.
\r\nI will illustrate how these multidimensional approaches can provide new insights into nuclear organization, with examples spanning different biological systems. In particular, I will present evidence for a long-range, crystal-like organization of DNA within the nuclei of mature sperm cells from crickets, demonstrating how multidimensional imaging can reveal structural features that remain inaccessible to conventional localization microscopy.
\r\nFinally, I will discuss the challenges and opportunities associated with visualizing, analyzing, and interactively exploring the multidimensional datasets generated by these approaches. Together, these developments illustrate how extending SMLM beyond conventional two-dimensional localization can provide new ways to interrogate the organization and dynamics of biological systems at the nanoscale.
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\r\nBio:
\r\nBassam Hajj is a physicist and CNRS researcher at Institut Curie in Paris, where he is a member of the Physics of Cells and Cancer unit and co-leads the “Light-based Observation and Control of Cellular Organization” team. His research focuses on the development of advanced optical microscopy techniques, particularly single-molecule localization microscopy, 3D imaging, and multidimensional approaches for studying cellular organization at the nanoscale.
\r\nAfter completing his PhD at École Normale Supérieure de Cachan on electro-optical microscopy, Bassam joined Janelia Research Campus as a postdoctoral researcher, where he worked on multifocus microscopy for fast and sensitive single-molecule imaging. He subsequently returned to Institut Curie and joined the CNRS as a permanent researcher in 2016.
\r\nHis current research combines innovative microscopy, quantitative image analysis, and data visualization to investigate molecular organization and dynamics, with a particular focus on nuclear organization.
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\r\nSTUDENT SPEAKER:
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\r\nTranscription Factor Dose in Stem Cell Reprogramming: Insights from Single-Cell Multi-Omics
\r\nAngelika Gebhart, Deplancke Lab
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\r\nBioEngineering Talks mandatory EDBB Seminar Attendance (1st-Year PhD Students)\r\n