EMBL Seminars

Abstract
The essential but enigmatic functions of sleep must be reflected in physical changes sensed by the brain's sleep-control systems. In Drosophila, a handful of sleep-inducing neurons adjust their electrical output to sleep need, via the antagonistic regulation of two potassium conductances: the leak channel Sandman suppresses activity during waking, whereas voltage-gated currents through Shaker support tonic firing during sleep. Insight into the sleep need-dependent regulation of these ion channels is beginning to furnish a molecular interpretation of sleep pressure, uncover the cellular processes responsible for its accumulation and discharge, and hint at some of the physiological roles of sleep.

Abstract
The accelerating rate of data production in biology and the remarkable breakthroughs in AI
seem like a match made in heaven. Yet, physics offers a different perspective for the future of biology:
in Einstein's words, "it is the theory that decides what we can observe". I will discuss some attempts to
follow this road and to thereby clarify the assumptions that underlie how we think about the molecular
complexity the confronts us.

About the speaker
Jeremy Gunawardena is Associate Professor of Systems Biology in the Department of
Systems Biology at Harvard Medical School. He is a pure mathematician by training. He did his PhD
in algebraic topology at Trinity College, Cambridge, where he was elected to a Research Fellowship.
He then spent several years in industry at Hewlett-Packard Research Labs, where he founded HP's
basic research programme in Europe. He returned to academic life at Harvard Medical School, where
his lab studies cellular information processing using a combination of mathematical, computational and experimental methods.

Connection details
Zoom*: https://embl-org.zoom.us/j/93818978353?pwd=UkRHZDBIN1gybGNhRDJQN1VJWExTQT09

ID: 93818978353
Passcode: 781768

Please note that the talk will 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
[In addition to the usual “visible” spectral range, which is commonly used for image detection in scientific and especially in light microscopy applications, there are neighboring spectral ranges like UV and deep UV on one side and “shortwave infrared” (SWIR) on the other side which allow to see and detect features, characteristics and spectral fingerprints, which cannot be seen in the visible part of the spectrum. In this presentation available SWIR image sensor technologies will be discussed and an introduction to a new InGaAs camera system will be given, which allows to access the visible, the NIR and the SWIR range of the spectrum. Camera applications like in-vivo microscopy or digital surgery microscopy will be shown.].

Connection details
Zoom*https://embl-org.zoom.us/j/2431602777 (Meeting ID: 2431602777, Password: 719364) 

Abstract
Both normal human differentiation and development, as well as induced cell reprogramming into a pluripotent state, involves major reconfiguration of the epigenome that is critical for the transformation of cellular identity and function. Highly orchestrated gene regulatory programs govern the emergence and maturation of diverse cell states during the formation of complex organs during development, while resetting of the epigenome is required for reversion to pluripotency. However, failure to correctly reshape epigenome and transcriptional states during these processes can lead to undesired cell identities and dysfunction. In this presentation, I will discuss our research into the natural formation and artificial reprogramming of human cell identities.

Abstract
[An introduction into the theory and technology of modern scientific cameras. Important parameters will be explained and discussed, and some examples will be shown. New directions like sub-electron noise image sensors and SPAD-arrays will be shown.].

Connection details
Zoom*: [https://embl-org.zoom.us/j/3528126808?pwd=WEZuRXlZTG83MzgvV2FId1R3STVBUT09] (Meeting ID: [352 812 6808], Password: [2LCN7s])
*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
Meiosis represents a battleground between chromosomes which vie for transmission and evolutionary success. This competition can profoundly shape chromosomal architectures and the evolution of chromatin proteins that are essential for fertility and viability, leading to an 'arms race' dynamic that drives their rapid evolution relentlessly. I will discuss how arms races during male and female meiosis have driven the evolution of protamines and centromeric proteins respectively.

Abstract
[Understanding gene regulation and single-cell heterogeneity often requires information about both protein expression and RNA including the profiling of full-length (antigen-specific) B cell and T cell receptors. There are few technologies that allow concurrent examination of both types of molecules in a single experiment with a single readout. We kindly invite you to this informative hybrid seminar about microwell based scRNAseq, multiomics and its applications in various scientific fields].

Program:
[10:30 – 11:00   Introducing single-cell multiomics with the BD Rhapsody™ HT analysis system and its innovations

Ray van Haaren, Senior Single-Cell Solution Architect, BD Biosciences 

11:00 – 11:20   Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

Dominik Vonficht, Scientist Stem Cells and Cancer DKFZ Heidelberg

11:20 – 11:40   Probing enhancer function with targeted perturbation sequencing using BD Rhapsody™ HT Xpress

Dewi Moonen, Scientist Genome Biology Unit, EMBL Heidelberg  

11:20 – 11:40   New and exciting single particle applications to study phytoplankton

Dr. Antonella Ruggiero, Scientist Developmental Biology, EMBL Heidelberg].

Connection details
Zoom*: [https://embl-org.zoom.us/j/94316335407?pwd=cGlZZWNOdnhEOERtWjVMeDFYR25IQT09] (Meeting ID: [94316335407], Password: [621356])
*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
 Interactions between biological macromolecules, including proteins and nucleic acids, are at the core of most processes in living organisms, and their deregulation can have pathological consequences. Knowledge of the 3D structure of these assemblies provides invaluable insight into understanding and modulating their function. The difficulties of experimental structure determination have motivated the development of many computational prediction methods over the last fifty years, and the most recent of these methods have achieved amazing success. I will present methodological approaches to protein complex structure prediction, including contributions to the improvement of protein-protein docking and recent developments related to the increasing use of deep learning strategies, such as AlphaFold. I will also present an ongoing research project to predict protein-RNA interaction structures using a combination of evolutionary and omics data, such as RNA binding motifs obtained from high-throughput experiments. In particular, we are using structural data analysis to investigate how selection pressures affect the evolution of protein-RNA interfaces across species, identifying areas of conservation and plasticity. Overall, recent and current computational developments are paving the way for a more integrative view of macromolecular interaction networks.

About the speaker
 Jessica Andreani is a CEA researcher in computational biology and bioinformatics at the Institute for Integrative Biology of the Cell (Paris-Saclay, France). Her research focuses on the structural prediction of macromolecular assemblies, in particular protein-protein and protein-nucleic acid interactions. To this end, her methodological interests include the integration of diverse sources of information, such as evolutionary and omics data, as well as deep learning approaches.

Meet the speaker
To meet with the speaker informally after the talks,sign up here https://docs.google.com/document/d/1ZgVFVkLDPzHDeyZ3VAALYYHOloeGlPCTqDjp22OJeA4/edit We especially encourage predocs and postdocs to take advantage of this opportunity.

Connection details
Zoom*: [link] https://embl-org.zoom.us/j/99727907551?pwd=WjNuZkV0UDdRU1Y0Qlpob3ppS1JJUT09 ID : 997 2790 7551 Code : 024126

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
Cell images contain a vast amount of quantifiable information about the status of the cell: for example, whether it is diseased, whether it is responding to a drug treatment, or whether a pathway has been disrupted by a genetic mutation. We aim to go beyond measuring individual cell phenotypes that biologists already know are relevant to a particular disease. Instead, in a strategy called image-based profiling, often using the Cell Painting assay, we extract hundreds of features of cells (or other biological samples, such as tissues or whole organisms) from images. Just like transcriptional profiling, the similarities and differences in the patterns of extracted features reveal connections among diseases, drugs, and genes.

About the speaker
Dr. Carpenter is an Institute Scientist at the Broad Institute of Harvard and MIT. Her research group develops algorithms and strategies for large-scale experiments involving images. The team’s open-source CellProfiler software is used by thousands of biologists worldwide and their Cell Painting assay has been adopted throughout the pharma industry to accelerate drug discovery. She leads industry-wide consortia such as JUMP-Cell Painting and OASIS. 

Her PhD is in cell biology from the University of Illinois, Urbana-Champaign and her postdoc in high-throughput image analysis was at the Whitehead Institute for Biomedical Research and MIT’s CSAIL (Computer Sciences/Artificial Intelligence Laboratory). Carpenter has been named an NSF CAREER awardee, an NIH MIRA awardee, and is listed in Deep Knowledge Analytics’ top-100 AI Leaders in Drug Discovery and Advanced Healthcare.

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*: [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
How information encoded within our genomes directs our development is fundamental to understanding how genetic alterations drive evolutionary change, normal-range variation, and human developmental disorders. The face is an excellent system for investigating how changes in genotype impact morphology as it is one of the most divergent structures that forms during development and around one-third of human congenital disorders are associated with craniofacial defects. Increasingly, mutations in the non-coding genome are implicated in Mendelian developmental disorders, for example, enhancer clusters (ECs) greater than 1.25 megabases upstream of SOX9 are frequently ablated in Pierre Robin sequence (PRS) patients exhibiting lower jaw hypoplasia. We previously characterised the activity of these ECs in facial progenitor cells (cranial neural crest cells, CNCCs) and quantified the impact of EC ablation on gene expression and craniofacial morphological development. To explore mechanisms facilitating extreme long-range regulation at this locus, we leveraged optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS EC activation. We observed pronounced changes in locus topology during CNCC differentiation from pluripotent stem cells and determined that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies – an observation made possible through analysis of ORCA single chromatin fibre traces. We further identified two CTCF-bound elements, within the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain’s 3D geometric centre, bridge enhancer-promoter contacts and when ablated diminish SOX9 expression. Together, we provide mechanistic insights into gene regulation over ultra-long genomic ranges, involving distal enhancer clusters and structural elements that mediate architectural stripe formation.

Abstract
All cells, eukaryotic and prokaryotic, face the threat of viral infections and develop anti-viral systems to fight them off. The constant arms race between cells and their viruses leads to the diversification of these defense systems. Thus, hallmarks of immunity in diverse domains such as plants, animals or bacteria are completely different. However, the unveiling of novel anti-phage defense systems in prokaryotes lead us to revisit this paradigm. In this seminar, I will discuss the discovery of novel prokaryotic anti-viral systems that show conservation with eukaryotic ones and discuss the implications of these conservation for both prokaryotes and eukaryotes.

About the speaker
Aude Bernheim is a microbiologist interested in how bacteria defend themselves against their viruses. She did her PhD in the Pasteur Institute in Paris studying the evolution of CRISPR-Cas systems and her post-doc in the Weizmann Institute in Israël focusing on the discovery of novel prokaryotic immune systems. She currently leads a lab at the Pasteur Institute exploring the molecular diversity of microbes. She's also an activist for a more inclusive and diverse science (both for people and the science itself).

Zoom Connection details
Zoom*https://embl-org.zoom.us/j/96019475133?pwd=TG03OVpHKzhVRHpjQVpZMW5sM2FiZz09

Meeting ID: 960 1947 5133 
Passcode: 184690 

Please note that the talk will 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.