FMI Young Investigator Seminar Series

Advances in AI now make it possible to mine unprecedentedly large and multimodal biomedical datasets for mechanisms that could transform scientific discovery, diagnostics and therapy. Yet, without formal guarantees of identifiability, these models risk producing representations and predictions that are scientifically ungrounded and clinically unreliable. Identifiability refers to the statistical property of being able to infer structure from data relating to the actual causal or generative processes rather than arbitrary representations.
In this talk, I first present recent advances in representation learning for uncovering mechanisms directly from neural time-series data. I then turn to foundation models, presenting new methods for interpretability that map their learned representations to semantic concepts understandable to human experts. Such a tight integration of theoretically grounded AI for mechanism discovery paired with semantic interpretability offers a path toward AI systems that are both scientifically valid and clinically reliable.

Gustatory systems drive critical survival behaviors such as feeding, foraging, and social interactions. However, gustation remains one of the least mapped sensory modalities at the connectome level. In the first part of my talk, I will present our efforts to map the first complete wiring diagram of Drosophila adult gustatory system using comparative connectomics on existing datasets. We mapped all feeding motor neurons and traced complete sensory-to-motor pathways to feeding, foraging, endocrine, and social behavior circuits. The emerging circuit architectures reveal distinct circuits for nutrient assessment, motor control, neuroendocrine regulation, and courtship. In the second part of my talk, I will talk about how we dissect neural-circuit mechanisms underlying physiological state-specific regulation of food intake by dissecting sensorimotor pathways controlling the feeding microstructure. First, we show that different sensory neuron populations control frequency and duration of feeding bursts suggesting that distinct sensorimotor pathways regulate these feeding motor programs. We combined connectomics, high-resolution behavioral analysis and neurogenetic manipulations to map neurons downstream of a set of gustatory receptor neurons that are important for sustaining feeding on proteinaceous food. Our approach revealed the identity of a group of interneurons (Sustain neurons) that specifically regulate the duration of feeding bursts in a protein feeding-specific way. We further showed that Sustain neurons control the feeding motor neurons that are involved in ingestion, but not in proboscis extension. Our study demonstrates how low-level motor actions are controlled by distinct sensorimotor pathways to orchestrate the higher order feeding microstructure based on the physiological needs of the animal.

DNA viruses are lifelong companions of humankind. Often clinically silent, they persist within us for decades. While many infections appear benign, mounting evidence links persistent DNA viruses to chronic inflammatory conditions and complex diseases, including cancer, neurodegeneration, and autoimmune disorders. These associations expand our understanding of viral infection beyond acute disease and position DNA viruses as long-term modulators of human health. A central theme emerging across diverse DNA viruses is their intimate relationship with the mitochondrion. By reshaping mitochondrial metabolism, rewiring energy production, and tuning innate immune signaling, viruses create a cellular environment that supports persistence and enables periodic reactivation. Yet the molecular principles governing these processes remain poorly understood. Our work seeks to illuminate how latent and persistent DNA viruses exploit mitochondrial function to control the switch between dormancy and replication. To meet this challenge, we combine cutting-edge structural biology—including X-ray crystallography, single-particle cryo-electron microscopy, and in situ cryo-electron tomography—with integrative approaches spanning biochemistry, biophysics, cell biology, and virology. By resolving viral and host machineries at near-atomic resolution and integrating structural insight with cellular function, we aim to define the fundamental principles that govern viral persistence—and to translate this knowledge into a new generation of antiviral strategies: therapeutics that not only block replication, but disrupt the long-term viral–host equilibrium underlying chronic disease.

Ribosomes have recently emerged to directly function in gene regulation. Our lab focuses on how regulation of gene expression is directly executed by the ribosome, particularly in the innate immune response. Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. We study a fundamentally new mode of gene regulation I discovered as a postdoc, by which rRNA regions exposed on the outer shell of the ribosome called rRNA expansion segments (ESs) bind to selective transcripts to control mRNA- and species-specific translation (1, 2). Ribosomes have thereby evolved the ability to discriminate which proteins are made for selective translation via rRNA. rRNA ESs consist of a multitude of highly variable, tentacle-like rRNA structures that extend from the conserved rRNA core in eukaryotes with largely unknown roles in translation. This work unravels species-specific, selective mRNA-rRNA interactions on the ribosome for translation. We combine innovative RNA biochemistry and RNA-based technology development with model systems ranging from yeast to macrophages. Further, we designed a platform to screen for favourable mRNA features for optimized RNA therapeutics (3) and have recently employed a toolbox for IRES-characterization including circular RNAs (4). My lab aims to decipher how rRNA-directed specialized translation is employed by the ribosome in the innate immune response.

Pathogens deploy effector proteins to manipulate host processes, yet the functions of most pathogen open-reading frames (ORFs) remain unknown. To address this, we developed a scalable functional genomics platform to systematically profile thousands of diverse effectors. Our "eORFeome" collection contains 3,843 effector ORFs from a broad range of viruses and bacteria. Using a barcoded lentiviral library, we conducted high-throughput functional screens to identify effectors modulating key host pathways, including NFκB, p53, interferon signaling, MHC-I display, cGAS-STING, inflammasome activation and apoptosis. These screens not only recovered established effectors, but also assigned functions to hundreds of previously uncharacterized proteins and revealed unexpected, novel activities for known effectors. Among our key discoveries, we found that human adenoviral i-leader proteins (13.6K) suppress surface MHC-I by targeting the TAP transporter. We identified HHV6A U14 as a potent p53 antagonist that sequesters and stabilizes p53. Furthermore, we discovered that herpesvirus U21 and US30 proteins are potent inhibitors of STING signaling, with U21 promoting STING’s lysosome-dependent degradation. This work introduces a powerful framework for large-scale functional annotation of pathogen effectors, uncovering novel mechanisms of host-pathogen interaction and providing a rich resource for future investigations into protein function and therapeutic target discovery.

Heat shock provokes a dramatic reorganization of the eukaryotic nucleus. Transcription is broadly reprogrammed, and membraneless nuclear bodies form, dissolve, or change in composition within minutes. Despite decades of study, we still lack a clear understanding of how these structures assemble and what they actually do. Using C. elegans embryos, we are dissecting the nuclear response to heat shock and finding that repetitive elements play a central and recurring role. We have identified the scaffolds for three distinct nuclear bodies that are remodeled by heat shock. Each is nucleated by a different class of repetitive sequence, spanning DNA transposons, tandemly repeated genes, and a non-coding RNA. These bodies concentrate key regulators of transcription and RNA processing, and their perturbation alters gene expression under stress. Functional homologues of these structures exist in other animals, yet their physiological significance has remained elusive. The genetic tractability of C. elegans now allows us to delete or modify the underlying scaffolds and study the consequences in a living animal. Our work suggests that repetitive elements are not passive passengers in the genome but active organizers of nuclear space, particularly when cells are challenged by stress.

Learning from social feedback is fundamental for flexible behavior across species, and deficits in such flexibility can impair social well-being. To investigate the neural basis of social flexibility, we studied male Drosophila melanogaster, a genetically accessible model of social behavior. Building on work showing that past social experience influences male courtship behavior (Roemschied et al., Curr Biol 2026), we developed a novel framework to test how distinct forms of social feedback from female flies shape the function of courtship-related neurons in males. We created ‘alternate social realities’ by pairing males with females that either displayed atypical backward-walking responses to an approaching male (using closed-loop optogenetic activation of neurons driving female backward walking, Bidaye et al., Science 2014), or behaved normally. Following these experiences, we characterized the function of distinct sets of male neurons, spanning visual sensory, brain, and premotor levels, using a novel approach that has not yet been used in adult flies (but nematodes and fly larvae, Hernandez-Nunez et al., eLife 2015; Gepner et al. eLife 2015): optogenetic neural stimulation with stochastic light patterns (covering a broad range of neural dynamics) paired with automated behavioral identification to uncover the neurons’ roles across the full behavioral repertoire. Males exposed to backward-walking females showed altered neural-behavior mappings in key neurons involved in courtship, requiring different stimulation patterns to elicit comparable behaviors relative to controls – indicating social modulation of neural function. The level of modulation depended both on neuron type and target behavior. Preliminary analysis suggests that dopamine synthesis is required for social modulation of visual neurons. This integrative approach—combining real‑time behavioral tracking, closed‑loop neural manipulation, stochastic optogenetic profiling, and behavioral classification—demonstrates how past social experience modulates a behavioral readout of neural dynamics to guide future interactions. By modeling how individuals update internal representations in response to social feedback, this work introduces a novel system for studying the neural basis of adaptive social behavior.

Collective behaviours—such as animals moving or foraging together—allow animals to pool effort, reduce risk, and increase fitness. These behaviours are traditionally explained by simple rules that each individual follows. Yet animals are far from identical; their experiences uniquely shape their brains and behaviour. How do collectives stay coordinated when members are not interchangeable? To address this question, my group investigates the neural circuits underlying collective behaviour and how they are modified by an animal’s past experience. We use collective digging in fruit fly larvae as a model, in which animals align and synchronise their movements to dig more effectively for food. We have shown that early-life social experience shapes individual foraging strategies and is required for the formation of coordinated digging groups. By combining large-scale neuronal inactivation with whole-brain connectomics, we have identified pathways linking sensory inputs to the descending circuits controlling collective digging. These include candidate circuits for the bilateral integration of mechanosensory signals from neighbouring larvae, an essential computation for group coordination. We are now generating new synapse-resolution connectomes to investigate how social experience reshapes these circuits. Together, our work aims to determine how neural circuits support collective behaviour, and how individuals with different experiences and brain wiring can strengthen group coordination or cause it to collapse.

TBA

TBA

Acute malnutrition remains a leading cause of childhood morbidity and mortality worldwide. Ready-to-Use Therapeutic Food (RUTF) has proven highly effective in treating severe acute malnutrition; however, its high production costs and reliance on imported ingredients limit large-scale accessibility. Currently, RUTFs reach only about 30% of children in need—an alarming gap exacerbated by recent cuts in food aid budgets.
alarming gap exacerbated by recent cuts in food aid budgets. To address this challenge, novel, plant-based RUTF formulations were developed using regionally available ingredients optimized for protein quality and micronutrient content. Beyond traditional assessments focused solely on weight gain, a preclinical study in rats evaluates broader indicators of recovery, including micronutrient status, linear growth, bone quality, and gut health—factors critical for long-term metabolic resilience.
Preliminary findings demonstrate that the new RUTF formulations enhanced recovery from malnutrition, producing superior gains in weight, length, and bone quality compared to a commercial RUTF. Moreover, significant shifts in caecal and stool microbiome composition, as assessed by bacterial 16S rRNA gene sequencing, and metabolomic profiles following RUTF intervention highlight complex gut-mediated responses to nutritional therapy.
These results underscore the potential of locally derived, nutritionally optimized RUTF formulations as cost-effective, sustainable, and holistic interventions to combat childhood malnutrition and inform future clinical translation.

Cell extrusion is essential for homeostatic self-renewal of the intestinal epithelium. Extrusion is thought to be triggered by crowding-induced compression of cells at the intestinal villus tip. In this study, we found instead that a local “tug-of-war” competition between contractile cells regulated extrusion in the intestinal epithelium.
We combined quantitative live microscopy, optogenetic induction of tissue tension, genetic perturbation of myosin II activity, and local disruption of the basal cortex in mouse intestines and intestinal organoids.
These approaches revealed that a dynamic actomyosin network generates tension throughout the intestinal villi, including the villus tip region. Mechanically weak cells unable to maintain this tension underwent extrusion. Thus, epithelial barrier integrity depends on intercellular mechanics.

Sporadic reports have highlighted that chemical matter initially designed to inhibit a protein can sometimes also enable its degradation. Crucially, the degradation often governs superior drug action. Among others, this has been observed for kinase inhibitors. However, we lack an understanding of frequency, generalizability, and mechanistic underpinnings of such phenomena. To close this gap, we established dynamic abundance profiles of 98 kinases after cellular perturbations with 1570 kinase inhibitors, revealing 160 selective instances of inhibitor-induced kinase destabilisation.
Kinases prone to degradation are frequently annotated as HSP90 clients, affirming previously reporter chaperone deprivation as one important route of destabilisation. Detailed investigation of inhibitor-induced degradation of the three kinases LYN, BLK and RIPK2, however, revealed differentiated, yet common mechanistic logic. The inhibitors elicit degradation by inducing a kinase state that is efficiently cleared by the native degradation routes. Mechanistically, these effects manifest by changes in activity, localisation, or multimerisation, and can be prompted by direct target engagement or network effects. We further extended our observations to the non-kinase IDO1. We similarly uncovered that a suite of inhibitors and degraders enables supercharging native turnover, in this scenario, however, by inducing a structural state that is more permissive to endogenous E3 engagement.
In sum, our data indicates that inhibitor-induced degradation is a frequent event and positions supercharging of endogenous degradation circuits as an alternative to classical proximity-inducing degraders.

Recent advances in CRISPR/Cas9 genome engineering have enabled efficient base editing (C>T and A>G transitions) without introducing double-stranded breaks. Combined with adult stem cell (ASC)-derived organoid technology, this offers powerful opportunities for disease modeling and gene repair.
We established streamlined pipelines to rapidly generate isogenic ASC-derived organoid models using phenotype- or transfection-based selection strategies. Within six weeks, these systems yield sufficient material for functional assays. We demonstrate the versatility of this platform across hepatocyte and intestinal organoids. Using cytosine and adenine base editors, we model CTNNB1 hotspot mutations in hepatocyte organoids and observe mutation-dependent beta-catenin localization. We further multiplex base editing to activate oncogenes (e.g., PIK3CA) and inactivate tumor suppressors (e.g., APC, TP53) using dual SpCas9 and SaCas9 systems.
Finally, we model colorectal cancer in a single step by introducing five key mutations simultaneously. These results highlight the broad potential of base editing for generating precise and complex human disease models. To further enhance the applicability of our system, we developed an RNP-based delivery platform optimized for organoids and primary human cells. This approach significantly increases editing efficiency compared to plasmid-based methods and enables rapid, transient delivery of CRISPR tools without genomic integration. The high efficiency and flexibility of this system make it ideally suited for both functional studies and therapeutic genome engineering in clinically relevant settings.

Cortical functions such as learning and memory are commonly attributed to the fast communication within synaptic circuits. However, several major cell types in the cortex are classified by their strong expression of neuropeptides and all major cortical cell types express neuropeptide receptors. How cortical neuropeptides modify signaling intracellularly and how they affect synaptic transmission in cortical circuits remain largely unknown.
We use electrophysiological recordings and various optical sensors to identify the mechanisms through which neuropeptides modulate cortical functions. The development of new CRISPR-based strategies to selectively manipulate neuropeptidergic pathways in specific neuronal circuits allows us to investigate their functions in learning and memory. In my talk, I will provide insights into the functions and effects of several cortical neuropeptides and outline future directions.

Facial appearance is one of the most variable morphological traits in humans, influenced by both rare and common genetic variants that can impact facial form between individuals and in disease. Large deletions and chromosomal translocations far upstream of the SOX9 gene are associated with Pierre Robin sequence (PRS), a human craniofacial disorder characterised by underdevelopment of the lower jaw and frequently associated with cleft palate. We previously identified extreme long-range enhancer clusters at the PRS disease locus (including EC1.45, 1.45Mb upstream of SOX9) that regulate SOX9 expression during development, and whose ablation impacts jaw morphology and fitness in mouse models.
In this talk, I will leverage the distinct morphology of the Neanderthal lower jaw, to explore how DNA sequence changes within EC1.45 may have contributed to altered facial morphology across recent hominin evolution. Using zebrafish as a model, we explore impacts to enhancer regulatory activity and jaw morphology driven by single nucleotide changes during craniofacial skeletal development. I will further discuss how 3D genome topology impacts the action of long-range enhancers of SOX9, implicating a role for CTCF-anchored stripe-associated structural elements that help to facilitate enhancer-promoter interactions. Ultimately, through an improved understanding of gene regulatory mechanisms at a human disease locus, we hope to better predict and interpret how DNA sequence alterations contribute to facial shape variation within the population, and drive dysmorphology in disease.

Access to genetic information within the cell nucleus is regulated by the distribution of nucleosomes, which are the basic unit of chromatin. Local access to specific genomic regions is facilitated by repositioning nucleosomes to enable transcription and other nuclear processes.
Nucleosome positioning is primarily regulated by ATP-dependent chromatin remodeling enzymes (CRs) that belong to the Snf2-type helicase family. These enzymes disrupt histone-DNA contacts by consuming ATP. The functions of CRs can be redundant or essential, complicating their study in vivo. To address this, we employ a unique bottom-up approach, in which we reconstitute chromatin in vitro using purified proteins and a yeast genomic plasmid library.
To elucidate the diverse remodeling functions of CRs, we add purified CRs in combination with various transcription factors to the in vitro reconstituted chromatin. The resulting changes in nucleosome positioning are monitored using MNase-seq. Depending on the type of CR used, we observe distinct nucleosome positioning patterns. Furthermore, we have expanded our in vitro reconstitution approach to explore the 3D genome organization of reconstituted chromatin, discovering a role for CRs in the 3D genome organization of S. cerevisiae.

Proteins organise the genome across multiple length and time scales. How proteins collectively bridge these scales to generate structure remains an open question. In this talk, I will discuss our work on dissecting physical mechanisms of genome self-organization, and how these principles can be linked to transcription and DNA damage repair. To tackle these questions, we use interdisciplinary approaches that combine single molecule biophysics, reconstitution biology, and theory. I will describe how protein condensation acts as an organizing principle of genome organization, generating forces on DNA that then act as active enzymatic scaffolds.

In the one-cell C. elegans embryo, asymmetric protein distribution is driven by complex feedback loops. Concentration gradients of the RNA-binding proteins MEX-5 and MEX-6 in the anterior cytoplasm were shown to regulate the patterning of other factors, including the mitotic kinase PLK-1. The gradient of MEX-5 forms through differential diffusion, but the mechanisms behind MEX-6 and PLK-1 gradients, as well as their reciprocal regulation, are still not fully described.
Using an integrated approach at the interface between physics and biology, we explore how these proteins establish concentration gradients and how they are interconnected. We reveal that PLK-1 promotes the enrichment of MEX-5 and MEX-6 at the anterior through different feedback loops, suggesting a model where intricate polarity circuitries are essential for faithful polarity establishment and maintenance.

Regulatory T (Treg) cells are a dedicated immunosuppressive T cell subset defined by expression of the lineage-specific transcription factor Foxp3.
Treg cells continuously suppress the onset of lethal multi-organ autoimmune inflammation and act as critical modulators of immune responses to pathogens and tumors.
How Foxp3 controls Treg cell differentiation and function is still poorly understood. The seminar will discuss the development of new genetically-modified mouse models that reveal unique requirements for Foxp3 within two distinct Treg cell subpopulations responsible for inducing tolerance to food and commensal microbes or the suppression of anti-tumor immunity.

Explaining the activity of a recorded neuronal population from its known properties still poses a great challenge, not just because of the many local agents that shape the output of a circuit, but due to the impact of long range connections from other brain regions. To explore this problem, I use conductance based computational models to unravel how local and global components of a network shape their Slow Wave Activity (SWA). This allowed us to study the interaction of local properties and long range connections shapes the SWA of a population and its neighbors, as well as how the sequential propagation of active “Up” states lead to the emergence of axis of propagation.
I will talk about relevant features of cortical Up states that are modulated by stiff properties of the local circuit as opposed to others that are sensitive to the level of excitability of the whole network and the input coming from neighbor populations. Additionally, I will show how our simulations guided in vivo experiments that explored the substrate of the directionality of travelling waves during SWA.
We expect these results to motivate future research exploring and comparing cortical circuits through the analysis of their Up states.

Hippocampal mechanisms of spatial cognition give rise to a number of interlinked phenomena: spatial coding by neuronal population, phase precession, and theta-oscillation-bound sequences.

In the first half of the talk I will present a series of results that link these phenomena to the spontaneous natural behavior of the rat.

Using high resolution 3D tracking we detect, classify and discover exploratory behavioral states. We demonstrate that hippocampal pyramidal and inhibitory populations conjunctively code for both space and behavioral state.

In the second half I will introduce a newly developed virtual reality system for freely-moving rodents and their application for dissection of rodent behavior and hippocampal function.

Using this system we demonstrate that under conflict between idothetic and allothetic inputs hippocampal spatial representation is consistent with the weighted multisensory integration of these two inputs.

Cellular movement plays a pivotal role in organismal development, immune responses, tissue maintenance, and cancer dissemination. Leveraging immune cells as a highly motile model, this talk will discuss fundamental principles of cellular movement through complex tissue microenvironments and the role of cytoskeletal organisation, cell polarity, and membrane dynamics.

Additionally, I will present some of our latest discoveries, wherein we unveil an unforeseen breakage of an intracellular organelle during cellular pathfinding.

Most animals have a bilaterally symmetric body plan, which emerges during embryonic development. While how symmetries are broken along the left-right axis is well studied, how tissues emerge with the same shape, size and at the same position on the two sides remains much less explored. In this talk, I will discuss the major discoveries from my postdoc, where using zebrafish embryos as a model system and light-sheet microscopy, we established that somites often develop with subtle left-right asymmetries, which gets corrected.

We further used a tissue mechanics approach to describe the underlying mechanism of error correction and show that symmetry evolves over time.

In the end, I will broadly link this to what our newly-established lab is planning to do to take forward this idea of symmetry as an emergent property in developing embryos.

Tumor tissues are mechanically altered across multiple spatial scales, from the subcellular to the tissue level, and these changes contribute to cancer progression.

Effects of mechanically altered microenvironments on tumor cells are well studied in a systematic manner using bioengineered 3D in vitro models.

Previous studies indicate that tumor spheroids adapt their growth and mechanical properties when grown in confining 3D microenvironments. Still, the temporal dynamics and molecular basis of this mechanical adaption remain poorly understood.

Here we cultured tumor spheroids grown from single cancer cells in mechanically well-defined biohybrid ECM mimicking hydrogels.

Growth in stiffened hydrogels was associated with changes in cell morphology, gene expression, and spheroid growth. Brillouin microscopy in-situ mapping revealed that cells tumor spheroids altered their mechanical properties under confinement and when starting to invade the surrounding matrix.

Within few days, transitions from single cells to multicellular structures were associated with drastic cell volume decreases and higher Brillouin frequency shifts.

Drugs interfering with cell-cell junctions and intermediate filaments but not F-actin filaments nor microtubules affected the mechanical phenotype of cells measured by Brillouin microscopy.

Taken together, our study provides insights into how tumor cells adapt their volumes and mechanical properties to microenvironment stiffness and confinement and when forming multicellular and invasive structures, which are relevant aspects in tumorigenesis and tumor progression.

The actin cytoskeleton is involved in cell shape and organization of the intracellular space.

To do so, actin is organized in a variety of dedicated architectures, in a spatiotemporally regulated manner using hundreds of different building blocks.

Changing their availability or their localization allows the cell to tune its properties, thus affecting cell morphology, mechanics and gene expression profiles which feedbacks into the process of determination of cell identity.

The Reymann team is studying how actin architectures are spatiotemporally controlled in the different cell types found in the early C. elegans embryo and how some actin specificities are linked with the differentiation process.

By the use of in vivo endogenous fluorescent labeling of actin binding proteins using CRISPR/Cas9 techniques as well as state of the art live imaging techniques and quantitative image analysis, we are studying in the early embryonic cells, the dynamics of individual actin binding proteins and how differences of content or dynamics arise along the lineage.

Genetic engineering is also allowing us to reproduce human actin mutations linked to rare diseases (Non-Muscle Actinopathies) in the model organism C. elegans.

We aim at a better characterization of the molecular, cellular and developmental consequences induced by these mutations, thus providing clues regarding the human genotype to phenotype correlation.

In the last decade, adult stem cell-derived organoids have become versatile tools in disease modelling and bioengineering.

The possibilities to expand healthy human tissue of almost every organ and control its differentiation states makes these 3D tissue models a suitable platform for studies in diverse research areas. Among these are host-microbiome interactions, where numerous clinical associations await functional validation.

Here, I highlight our recent advances in modelling cancer-microbiome interactions using organoids and organs-on-chips. I discuss approaches to expose human intestinal organoids to cancer-associated bacteria and the various read-outs which can provide mechanistic insights into their crosstalk.

A particular focus is laid on genotoxic bacteria that can induce mutations in cancer genomes and on intracellular bacteria and their roles in colorectal cancer disease progression and metastasis.

The hippocampal formation is a complex system of neurons and circuits that plays a crucial role in learning and memory. In particular, the CA1-DG axis of the hippocampus is a region that consists of multiple layers with distinct neuron types and inputs from different circuits which are essential for memory formation and retrieval.

When these networks are simultaneously activated, they generate complex signals composed of a wide variety of electrophysiological patterns. By identifying and denoising these patterns, we can gain insights into the mechanisms underlying neuronal operations and their contributions to learning and memory.

In this talk, I will provide an overview of the electrophysiological profile of the CA1-DG axis, including both well-known patterns and novel ones that have not been previously reported. Furthermore, I will showcase how electrophysiological patterns can be used as a powerful tool for studying the function and cellular basis of specific neural circuits.

Pregnancy is associated with striking physiological adaptations that prepare the female body for the challenges of motherhood.

Becoming a mother also requires behavioral adaptations such as robust parental behavior.

Classical studies in rats suggest that such adaptations can already occur during pregnancy, but how pregnancy hormones remodel parenting circuits to instruct preparatory behavioral changes remains unknown.

We find that action of estradiol (E2) and progesterone (P4) on galanin (Gal)-expressing neurons in the medial preoptic area (MPOA) is critical for pregnancy-induced parental behavior.

E2 silences MPOAGal neurons but increases their excitability, whereas P4 permanently remodels this circuit by recruiting excitatory synaptic inputs.

This remodeling results in more efficient encoding of parental behavior and stronger and more selective responses to pup stimuli.

Our work thus demonstrates that pregnancy hormones remodel parenting circuits in anticipation of a future behavioral need.

The resilience of the intestine makes it an attractive system to address questions, such as how organs use diverse strategies for regeneration.

My laboratory focuses on (1) niche signals that regulate intestinal stem cell (ISC) function and (2) the mechanical niche-ISC interactions that modulate regeneration.

1. Throughout life, the activity of niche signals changes in response to injury, and ISCs need to respond accordingly to fulfill tissue function. Thus, how do stem cells interpret fluctuating niche signals?

We found that during high Wnt activity observed in regeneration, canonical WNT ligands activate non-canonical Wnt signaling via a DLG1-ARHGAP31-CDC42 axis required for renewal.

2. After damage, crypts undergo morphological changes to restore their pre-injury shapes, and a major open question is how such repair occurs.

We found that telocytes envelop crypts in a contractile mesh and mechanically direct crypt morphology during development and regeneration. Further, in response to stretch, telocytes upregulate Slit3, which promotes epithelial regeneration.

Thus, telocytes provide mechanical cues that establish crypt morphology during development and restore it after injury.

Previous work by the Siegelbaum lab and others has shown that the hippocampal dorsal cornu ammonis 2 (dCA2) region is necessary for social memory, i.e., for the ability to recognize a familiar conspecific. Social memory is in turn necessary for avoidance or approach based on past negative or positive experiences.

Here, we show within a social fear conditioning paradigm that the dCA2 region is required for the dissociation of a safe from a threatening conspecific independent of the degree of familiarity.

Opto- or chemogenetic silencing of dCA2 dampens this dissociation and dCA2-silenced mice display a behavioral phenotype of social fear generalization. This behavioral discrimination is associated with a change of a memory for safe and threatening conspecifics, and the accuracy of this encoding is strongly related to behavioral discrimination performance.

Importantly, we find that dCA2 is not required for a dissociation of safe vs. threatening objects, underlining the specialization of dCA2 to the social domain. This thus demonstrates the relevance of the CA2 region for the regulation of social behavior beyond the processing of social novelty.

The mammalian small intestine is a tube-like structure with an inner epithelial lining facing the lumen. This layer is organized into absorptive villi protruding into the lumen and proliferative crypt compartments invaginating into the underlying mesenchyme. The structural and functional maturation of the intestine is only achieved following fetal development.

It remains unclear how the immature fetal intestine transitions into the mature structure enabling tissue function and how this is orchestrated at the cellular and molecular level. Furthermore, our knowledge on the extent of microenvironmental influence on these processes remains limited. Here we investigate how morphogen signalling and tissue mechanics emerging from intestinal niches influence cell fate during tissue maturation.

Firstly, our work focuses on intestinal regionalisation – the process that enables the emergence of anatomically distinct compartments allowing differential processing of food and nutrient absorption. Secondly, we investigate how tissue geometry affects the genesis of differentiated cells during tissue maturation.

These studies enable the refinement of regional identity and maturation-associated functionality of intestinal cells derived from pluripotent sources via manipulation of specific environmental signals such as morphogens or tissue geometry. Moreover, our platforms will allow unprecedented investigation of intestinal development as well as disease and will facilitate the generation of intestinal tissue for transplantation-based therapies.

The recent advancement of MRI-based tools for mapping brain function in rodents provides a great platform for discovering the determinants of functional (dys)connectivity, whether genetic mutations, environmental risk factors, or specific cellular and circuit dysfunctions. 

In my talk, I will describe our most recent contributions to the field, underlining the drawbacks of utilizing such a technique while also emphasizing the novel opportunities that this technology can provide.

I will also discuss how perturbational techniques can be used to dissect the fundamental aspects of fMRI coupling and reveal the causal contribution of neuromodulatory systems to brain network activity, with a particular emphasis on the locus coeruleus / noradrenergic system.

These examples highlight how rodent functional imaging has the potential to increase our understanding of the origins and drivers of human functional connectivity.

Relevant papers:
[1] Zerbi et al., Neuron, 2019
[2] Grimm et al., bioRxiv, 2022

Fast synaptic inhibition shapes neuronal responses and network activity in the mammalian brain. This inhibitory process is principally mediated by the activation of ionotropic GABA-A receptors (GABA_ARs). Despite their fundamental role, the manner by which GABA_ARs shape activity in the awake cortex is unknown. In this talk, I will present novel in vivo gramicidin perforated patch-clamp recordings that show GABA_AR-mediated synaptic signalling is predominantly shunting in pyramidal neurons of the awake mouse cortex. I will then demonstrate that this results from relatively depolarised GABA_AR equilibrium potentials (E_GABAAR), which arise due to the high levels of synaptic activity that characterise the awake state. To investigate the functional implications, I will present how we constructed a neural network model to show that the awake E_GABAAR and associated shunting inhibition allow for decoupled cortical networks that can better discriminate incoming stimuli. These findings support the idea that GABA_AR-mediated synaptic signalling adapts to the activity state of the cortex to optimise network function.

High-fidelity dynamical measurements of animal body kinematics and neural activity are becoming increasingly prevalent in neuroscience enabling the study of network-wide information processing in the brain.

However, given the high degree of freedom of neural systems and experimental limitations, any practically conceivable measurement is fundamentally incomplete, which can introduce biases in their interpretation.

My talk will focus on two methods that achieve measurement-independent representations of dynamical systems in neuroscience and beyond. First, I will discuss an efficient 3D animal pose estimation method that overcomes challenging experimental situations where animal poses are occluded from a given camera or where only a single camera is available.

I will illustrate the versatility of this method through examples of different animal systems. Second, I will ask how to combine and compare measurements whose identity is uncertain due to anatomical variations or changes in experimental setups. I will describe an unsupervised method involving geometric deep learning and statistical topology to jointly embed a priori incompatible measurements in a shared space, where they can be compared.

Through this shared representation, our method can detect changes in the latent system parameters and can serve as an unbiased means to understand the dynamic effect of experimental interventions.

Papers

Gosztolai, A.*, Günel, S.*, Rios, V.L., Abrate, M.P., Morales, D., Rhodin, H., Fua, P. and Ramdya, P. LiftPose3D, a deep learning-based approach for transforming 2D to 3D poses in laboratory animals. Nature Methods, 18, 975–981 (2021)

Gosztolai, A., Peach, L.R, Arnaudon, A., Barahona, M., Vandergheynst, P., Geometric deep learning detects transitions in dynamical systems based on topological features, in preparation

Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood.

Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition.

In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders.

The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning.

Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.

Oncoproteins of the MYC family are major drivers of human tumorigenesis with MYCN amplification underlying the genesis of high-risk neuroblastoma. Current models propose that the oncogenic potential of MYC proteins stems from their universal binding to active promoters in a heterodimer with MAX, where they induce tumor- specific gene expression patterns. Interestingly, we have previously shown that MYCN recruits the nuclear exosome, a 3’-5’ ribonucleolytic complex, to expressed genes, where it limits the accumulation of stalled RNA Polymerase II (RNAPII), and thus prevents conflicts with ongoing replication[1].

Based on these observations and the known role of the exosome in RNA processing, we investigated the involvement of RNAs in MYCN interactions. Gradient fractionation provides direct evidence that MYCN exists in two distinct separable complexes: one is the well-known heterodimer with MAX, and the second is a stable high molecular weight protein complex containing the exosome and RNAPII but not MAX. Notably, RNA is required for the stability of the latter complex. Utilizing enhanced crosslinking and immunoprecipitation (eCLIP), we found that MYCN associates with a large number of intronic RNAs independently of DNA binding. Importantly, further eCLIP and nascent transcriptomics show that the same sites are also bound by the RNA exosome. Mass spectrometry analysis of the high molecular weight MYCN complex reveals a striking prevalence of RNA binding proteins, including the RNA exosome and its targeting complexes. Finally, proximity ligation assays show that MYCN stabilizes the interaction of the nuclear exosome with RNAPII.

Our results demonstrate the existence of a stable MAX-independent MYCN protein complex arising from MYCN’s association with nascent mRNAs. We propose that the balance between the DNA- and RNA-bound MYCN complexes is controlled by accumulation of intronic RNA at promoters and postulate that MAX-free MYCN complexes remove RNAPII from chromatin following failed splicing or R-loop formation. We hypothesize that clearing stalled RNAPII is critical for the rapid growth of tumour cells and underpins the ability of MYC oncoproteins to enhance transcription rates on large groups of genes.

[1]Papadopoulos, D. et al. MYCN recruits the nuclear exosome complex to RNA polymerase II to prevent transcription-replication conflicts. Mol Cell, doi:10.1016/j.molcel.2021.11.002 (2022)

Acute myeloid leukemia (AML) patients have a 5-year overall survival of only 30%. Furthermore, most AML therapies, such as Anthracyclines in combination with Cytarabine (AraC), do not permanently eradicate the disease and most of patients will experience a relapse or have a refractory AML. Therefore understanding the biology of AML cells and resistant cells is an upmost priority to improve current chemotherapy and second line therapy possibilities.

While autophagy was described to be important in healthy hematopoiesis, reports demonstrated that deregulated autophagy can favor AML development. Autophagy mediates degradation of cytosolic components, such as protein aggregates and organelles, via transporting targeted component to lysosomes for degradation.

We are therefore aiming at understand the impact of autophagy and lysosomes on AML cells in therapy response using cell lines and primary samples in close collaboration with pathologists. We believe that our projects will open new avenue on autophagy-based therapy in AML.

In the last part of my talk, I will briefly introduce you to our exciting Innosuisse project on ex-vivo blood platelet generation as an alternative to blood donation.

Mechanical signals have emerged as an important determinant of tissue homeostasis, development and disease.

Through mechanotransduction, forces can induce changes in gene expression, cytoskeleton organization, and intercellular adhesion, so as to affect cell size, shape, number, motility and fate.

In turn, the alteration of cell properties will generate forces to its the environment and shape the tissue. However, how would mechanical and biochemical signals coordinate to control cell specification and tissue pattern formation is still elusive.

This talk will present a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity, and also our recent findings on mechano-chemical coupled collective cell migration.

We have assembled the first single-cell transcriptomic/organoid atlas of epithelial cell evolution during metastasis in patients. In a cohort of 90 matched synchronously resected normal/primary/metastatic samples from 31 colorectal cancer (CRC) patients, including six longitudinally collected secondary metastasis, we find that while the transition from normal to primary tumor involves dedifferentiation to an LGR5+ cancer cell (CSC) state, metastasis involves progressive plasticity (not seen before in metastatic mouse CRC models), with developmental expansion to noncanonical gene expression programs, including squamous and neuroendocrine programs, exacerbated by neoadjuvant therapy.

Diffusion component analysis is indicative of a two steps transition from primary to metastatic states, involving first a reprogramming to a fetal-like progenitor state conserved across multiple patients, followed by divergent transdifferentiation into diverse lineages, which we validated using multiplex immunofluorescence. In a biobank of 29 organoid lines generated from the same patient cohort, including matched normal/primary/metastatic organoids from 6 individuals, we find that intestinal stem cell media selects for LGR5+ CSC cell expansion, leading to loss of cellular heterogeneity over time.

By replacing intestinal growth factors with metastasis-specific factors, we find that metastatic organoids can readily adapt and grow in non-intestinal conditions and express diverse gene programs, unlike matched primary tumor organoids from the same patients.

Chemotherapy-mediated epithelial disruption is a potent inducer of fetal reprogramming and transdifferentiation. Accordingly, metastasis but not primary tumor organoids from the same patients display efficient metastatic outgrowth when xenografted into the liver.

Our results suggest that epithelial disruption during metastasis and therapy induces conserved cancer cell autonomous multipotential progenitor states, with local microenvironmental cues determining the selection of discrete lineage programs during metastatic outgrowth. In turn, our identification of a conserved progenitor state across multiple metastatic cancers suggests opportunities for therapeutic targeting.

We are currently screening transcription factors for their capacity to promote entry into the progenitor state and pharmacological compounds with the potential to interfere with metastatic plasticity.

Cell size impacts cellular biosynthesis and stem cell fitness. How cell size is controlled, especially in a crowded multicellular context, is poorly understood.

We analyzed the growth of single epidermal stem cells during in vivo homeostatic turnover.

We find the G1/S transition is cell size-dependent, where smaller-born stem cells spend longer and grow more during their G1 phase. We find that in agreement with previous quantitative models, the dilution of RB1 (retinoblastoma protein) by cell growth may couple G1/S transition rate to stem cell size.

We further find that in intestinal organoids, as intestinal stem cells commit to differentiation, the size-dependence of G1/S transition remains invariant despite faster cell growth rates.

Our results of cell size control in 3D contexts contrasts with how cell size is controlled in the majority of 2D cell cultures, where cell size variation remains correlated across many cell cycles.

In the cortex the interplay between excitation and inhibition determines the resolution of neuronal representations. However, while the receptive fields of excitatory neurons are often fine-tuned to the encoded feature, the principles governing the tuning of inhibitory neurons are still poorly characterized.

To characterise the relationship between excitatory and inhibitory tuning, we focused on the head-direction cortex (the postsubiculum), a circuit characterised by a relatively simple feature space. Excitatory head-direction neurons are fine-tuned to a specific direction of the head in the horizontal plane, which allowed us to fully map the receptive fields of individual neurons at high resolution during natural behaviours. In contrast to excitatory cells, the tuning of fast-spiking inhibitory interneurons was broad and heterogeneous.

In order to compare the tuning resolution of the two populations independently of tuning curve shape, we transformed their head-direction tuning curves from the spatial domain to the spatial frequency domain. We found that inhibitory tuning curves were broadly tuned in the spatial domain but fine-tuned in the spatial frequency domain, resulting in various radial symmetries in their head-direction tuning. In addition, the average spatial frequency spectrum of fast-spiking interneuron populations was virtually indistinguishable from that of local excitatory cells but differed from that of the upstream thalamic inputs, suggesting that the tuning resolution of inhibitory interneurons precisely matches that of local excitatory cells.

Together, these findings provide evidence that the resolution of neuronal tuning is an intrinsic property of local cortical networks, shared by both excitatory and inhibitory cell populations.

A long-standing question in developmental biology is how a simple embryonic epithelium builds complex 3D organs during embryogenesis. A critical step during vertebrate heart development is trabeculation, during which the myocardial epithelium transforms from a monolayer to a topological 3D meshwork.

Trabeculae are multicellular ridges critical for heart function and anomalous trabecular morphology leads to cardiac defects and embryonic lethality.

We have recently shown that local differences in the mechanical properties of CMs trigger this morphological symmetry breaking. CMs with higher mechanical tension delaminate stochastically to seed the trabecular layer, and this mechanical segregation is also sufficient to induce their differential fate. Eventually, these single trabecular cells grow into multicellular ridges, which remodel to form macroscopic topological trabecular meshwork thereby thickening the myocardial wall.

How a developing heart acquires these crucial anatomical structures remains unknown. By exploiting excellent tractability of zebrafish heart with cross-disciplinary tools, my lab aims to decode the design rules underlying this morphogenetic transition.

In this seminar, I will be discussing some of our previous and current findings explaining how morphological complexity is built up during cardiac trabeculation.

Multicellular systems exploit physical principles to self-organize in space and time.

Using theoretical approaches from soft matter physics, we investigate the role of interfaces and boundaries in directing the spatial organization of multicellular systems across diverse contexts.

I will present recent work on follicle patterning in the avian skin, the role of tissue interfaces in facilitating luminogenesis, and the mechanics of embryo-uterus interactions during implantation.

Using these examples, I will discuss how biologically tuned mechanical processes drive pattern formation and morphogenesis.

While the role of the nuclear lamina in the organization of heterochromatin is well studied, much less is known about the involvement of the second compartment from the nuclear periphery, the nuclear pores.

Using oncogene-induced senescence as a model, I have previously demonstrated that nuclear pores can impact the organization of chromatin, not only at the nuclear periphery but also in the entire nucleus with consequences on the expression of the genes involved in a senescence-specific secretory pathway.

In particular, the nuclear pore protein TPR is necessary for the exclusion of heterochromatin from the nuclear pores by a completely unknown mechanism.

Our current work aims at uncovering the mechanisms by which TPR can affect chromatin organization.

No-reflow following ischemic stroke, a brain attack that affects millions each year, challenges the current therapeutic strategies. Contractile vascular smooth muscle cells (vSMCs) play a pivotal role in cerebral blood perfusion, yet, their role in recovery from cerebral ischemia is unknown.

Here, by using a new animal model compatible with live imaging and functional Ca2+ in vivo imaging, we found ischemic attack can permanently dampen the spontaneous arteriolar vasomotion as well as vSMC's Ca2+ oscillation despite the successful reperfusion.

Notably, cell-specific enhancing Ca2+ fluctuation via enhancing mito-ER contact in vSMCs, blood reperfusion efficiency in the ischemia area, neurodegeneration, and behavior recovery all were significantly ameliorated.

Our findings demonstrated the importance of reserve arteriolar spontaneous vasomotion in preventing the peri-infarcted region from transitioning to the core region, which usually is caused by secondary no-reflow.

This study suggests a potential avenue of manipulating the basal vasomotion to treat ischemic stroke via decreasing no-reflow.

Bioelectric signals include membrane potentials, physiological ion currents, and long-range electric fields. These signals are not confined to action potential propagation, but also govern wound healing, regeneration, and development.

To study the role of bioelectric signals in tissue homeostasis which are poorly understood, epithelial cell lines with defined transepithelial electric potential difference were used as model systems. Using a novel microfluidic platform, we biophysically perturbed or reinforced the transepithelial potential using an external E-field of similar strength as the endogenous one.

On the one hand, perturbing the transepithelial potential led to disruption of normal cell shape, tissue architecture, cell-cell adhesion, and cell division/extrusion rates. On the other hand, reinforcing this potential even rescued non-confluent tissue organization of E-cadherin knock-out cells.

These observations were accompanied by an out-of-plane mechanical force that was measured, and we propose an electroosmosis framework to explain them. Future work will investigate molecular mechanisms and their physiological relevance.

An outstanding question in embryo development is how spatial patterns are formed robustly, despite large scale cellular re-arrangement required during tissue morphogenesis.

In the zebrafish spinal cord, thirteen distinct cell types are specified along the ventral-to-dorsal axis to form stripe-like patterns, under the instruction of opposing gradients of Shh and BMP/Wnt. The Shh signal is noisy, resulting in cells specified in a mixed pattern initially. In addition, concurrent morphogenetic movement could further disrupt patterns. Nevertheless, the stereotypic stripe-like patterns still form reproducibly.

To understand how adhesion-based mechanism may assist in patterning robustness, we developed two cell-based mechanical assays based on micropipette aspiration to measure adhesion forces and preferences among three types of spinal cord neural progenitors (p3, pMN, and p0 cells).

Interestingly, each cell type exhibited preference to stabilize homotypic contact and adhered more strongly to cells of the same type. Subsequent genetic analyses revealed three adhesion molecules (N-cadherin, Cadherin 11, and Protocadherin 19) that are differentially expressed among the three cell types, forming a three-molecule adhesion code. When the adhesion code is perturbed, the adhesion preference to cells of the same type is lost, and the neural progenitor pattern in the spinal cord is disrupted in vivo. Both the cell fate and adhesion code are co-regulated by the common upstream morphogen signal Shh.

We propose that robust patterning in tissues undergoing morphogenesis results from a previously unappreciated interplay between morphogen gradient-based patterning and adhesion-based self-organization.

Mitochondria are dynamic, double-membrane organelles involved in many essential eukaryotic functions such as energy production and cellular stress pathway integration.

Their ability to perform these functions fundamentally depends on their dynamic remodeling both within the entire cellular mitochondrial network population and within their distinct outer and inner mitochondrial membranes.

Combining cryo-electron tomography (cryo-ET) with cryo-fluorescence microscopy provides an opportunity to correlate bulk mitochondrial network morphologies with membrane ultrastructures to gain mechanistic insight into factors regulating cellular stress signaling.

However, quantifying ultrastructural features of pleomorphic organelles in three dimensions is challenging, as is defining the significance of observed changes induced by specific cellular perturbations.

To address this challenge, we established a semi-automated workflow to segment organellar membranes and reconstruct their underlying surface geometry in cryo-ET.

To complement this workflow, we developed an open source suite of ultrastructural quantifications, integrated into a single pipeline called the surface morphometrics toolkit.

We applied this workflow with cryo-fluorescence microscopy to correlate bulk mitochondrial network morphology with membrane ultrastructure of individual mitochondria in the presence and absence of endoplasmic reticulum (ER) stress.

Using our toolkit, we demonstrate ER stress promotes adaptive remodeling of ultrastructural features of mitochondria including spacing between the inner and outer membranes, local curvature of the inner membrane, and spacing between mitochondrial cristae.

Our toolkit offers an opportunity for quantifying changes in organellar architecture on a single-cell level using cryo-ET, and future potential for extending this approach towards guided subtomogram averaging of membrane-embedded proteins.

Proper tissue function is imparted by both the structure and the cellular composition of the tissue. The mammalian intestine is an exquisite example of this: the continuous ribbons of crypts and villi serve to maximize the absorptive surface area.

Meanwhile, there are several specialized secretory cell types required for fluid and pH balance, hormone sensing and secreting, and mucus secretion. Aberrations in tissue architecture or cell fate specification can result in loss of homeostasis and can contribute to disease pathogenesis.

I will present how alterations in epithelial-fibroblasts interactions alter intestinal architecture to drive intestinal hyperproliferation and the initiation of polyposis.

Moreover, I will describe a novel cell type in the intestinal epithelium of humans and rats that is specialized for fluid secretion. We are defining its cell fate specification program and the contributions it makes to cystic fibrosis pathophysiology using a novel rat organoid system.

Animal and human social networks are shaped by multiple selection pressures, including the need to ensure efficient group functioning and communication while simultaneously limiting the spread of infectious diseases.

It has been hypothesised that social animals could further reduce epidemic risk in the presence of pathogens by altering the transmission properties of their social networks, yet there is little evidence for such pathogen-triggered network changes.

We tested this hypothesis experimentally in colonies of the ant Lasius niger using a combination of automated behavioural tracking, controlled exposure to an infectious pathogen, precise quantification of individual pathogen load, and temporally-explicit transmission simulations.

We first describe important constitutive properties of the ant social network that simultaneously inhibit overall transmission and isolate valuable individuals (queen, brood and young workers) from disease sources.

We then show that the ants adaptively respond to the presence of an infectious pathogen by reinforcing key disease-inhibitory properties of their social network, conferring additional disease defence to the colony.

Finally, we show that these network changes result from early behavioural changes in both pathogen-exposed workers and their untreated nestmates, increasing the spatial and social segregation between individuals.

Our results indicate that the alteration of social organisation in response to pathogen entry is an effective strategy to mitigate the effects of disease in social groups.

The foundation of the mammalian body plan is established in early embryogenesis. Yet, our knowledge of early mammalian development remains limited by current technical boundaries, such as the inability to visualize in vivo development and the paucity of embryonic material for high-throughput screens.

To overcome these barriers, much work over the recent years has been dedicated to developing sophisticated in vitro engineering approaches, exploiting the self-organizing properties of embryo-derived stem cells.

We previously developed strategies to model mouse gastrulation dynamics in 3D, allowing us to investigate how single cells interact and organise to build embryos.

Using these tools, together with ex vivo embryo culture systems, we study principles of lineage patterning; specifically, the intercellular metabolism-signalling axis that controls dynamic cell decisions in the developing embryo.

Understanding these interconnected cellular events will be vital for advancing developmental and reproductive health, offering a unique opportunity to understand the cellular and molecular mechanisms behind early miscarriage and congenital pathologies.

Many models of motor control emphasize the role of sensorimotor cortex in movement, principally through the direct axonal projections corticospinal neurons (CSNs) make to the spinal cord. In addition to their intimate access to motor output, CSNs also possess strikingly expansive supraspinal axon collaterals. The functional organization of these supraspinal projections, and what information is encoded in their activity, was largely unknown.

I used a suite of intersectional anatomical methods to map the input and output organization of CSNs, revealing dorsolateral striatum as the preeminent target of collateral innervation.

The striatum is composed of two distinct populations of spiny projection neurons (SPNs) defined in part by the expression of dopamine receptor type 1 (D1) or type 2 (D2).

Using optogenetics-assisted electrophysiological circuit mapping, I found CSNs innervate both principle striatal cell types, but on average formed more synapses on D1 SPNs compared to D2 SPNs.

This connectivity bias was reflected in the spinal cord: CSNs that target D1 or D2 SPNs synapsed in different regions of the spinal cord, and asymmetrically targeted two types of spinal interneurons.

I combined multiphoton imaging of CSNs, transsynaptic rabies tracing from D1 or D2 SPNs, and a sequential lever press task to characterize the information encoded in the activity of CSNs and their collaterals in DLS.

Contrary to more conventional perspectives, CSN populations encode not only individual movements and muscle output, but also higher-order information related to the onset and offset of motor sequences. Furthermore, similar patterns of complex activity are broadcast by CSN populations targeting different downstream striatal circuits.

These results reveal a logic of coordinated connectivity between forebrain and spinal circuits, where separate CSN modules broadcast similarly complex information to downstream circuits, suggesting that differences in postsynaptic connectivity dictate motor specificity.

Our rhythmic world has been a driving force for organisms to evolve a clock to anticipate such daily rhythms. Similarly, our own circadian biology leads to body rhythms that parasites experience.

Malaria is a parasitic disease whose major symptom is fever. Malarial rhythmic fevers are a consequence of the synchronous bursting of host’s red blood cells (RBCs) on completion of the malaria parasite asexual cell cycle.

How is this bursting synchronous across the parasite population?
Are parasites following host cues or do they also have a clock to anticipate host daily rhythms?

Through a combination of infection challenges where we manipulate the environment or rhythms of the host by infections of circadian mutant hosts, we probed the rhythms of the parasites. We found that without any external cue to the parasites, their transcriptome remains rhythmic with ~60% of parasite transcripts being expressed once a day.

Thus, we propose malaria parasites to have intrinsic clocks. Parasite rhythms are aligned to the host daily rhythms but are generated by the parasite, possibly to anticipate its circadian environment.

The Allen Institute has been collecting and sharing large-scale, standardized datasets since the original Allen Brain Atlas was launched in 2006.

More recently, the Institute has brought this approach to the domain of in vivo physiology, by building platforms for surveying visual responses in the brains of awake, head-fixed mice. Using Neuropixels probes, we measured the spiking activity of nearly 100,000 neurons across 58 recording sessions.

Each experiment included simultaneous recordings from up to 8 cortical and thalamic visual areas, as well as adjacent regions in the hippocampus and midbrain. All of the data has been made publicly available via the AllenSDK Python package and NWB files hosted on the DANDI Archive.

In this talk, I will present some of the findings from of our own analysis of this dataset, including evidence for hierarchical processing in mouse visual system.

I will also highlight results from the more than 30 publications and preprints that have used this dataset so far.

Finally, I will discuss our plans for the recently launched Allen Institute for Neural Dynamics, where we will scale up our Neuropixels recordings to measure cell-type–specific interactions across the entire mouse brain.

While mechanisms of embryonic development are well conserved among mammals, the progression speed tends to be slower in larger species.

To study differences in time between species, my group uses in vitro systems. We have recently recapitulated the segmentation clock, oscillatory gene expression during early development, from human and mouse pluripotent stem cells. The oscillation period of the human segmentation clock is 5-6 hours, while the mouse period is 2-3 hours.

We found that this period difference between species stems from slower biochemical reactions in human cells, including slower protein degradation and longer delays in gene expression processes.

Now we are extending this approach of cross-species comparison to other mammalian species, including cows and rhinos, and other developmental processes. In parallel, we develop genetic tools to manipulate developmental processes and organoids.

Embryo development entails the generation of diverse cellular identities and tissues morphologies. Cells need to take the right decision, at the right location, at the right time, and this decision needs to be coordinated with concurrent changes in tissue organisation.

The mechanisms that ensure the tight coordination between cell fate decisions and tissue shape changes remain poorly explored. To address this question, my group focuses on the development of the mammalian embryo at the time of implantation into the uterus, a developmental stage that involves a global transcriptional and morphological transformation. We have recently developed a new 3D culture platform that maintains mouse pluripotent cells as self-renewing organised epithelial structures.

Under these conditions, cells closely recapitulate the organization and transcriptional profile of the embryonic epiblast tissue of early post-implantation mouse embryos. Moreover, we have uncovered a functional relation between epithelial architecture and pluripotency maintenance.

Our work establishes these 3D epiblast stem cells as a tractable model of the post-implantation embryo. We are currently applying this system to deconstruct the complexity of mammalian development.

A major challenge in the field of tissue engineering is the generation of new materials that can support angiogenesis, wherein endothelial cells from existing vasculature invade the surrounding matrix to form new blood vessels. To proceed, material design criteria based on natural tissue characteristics are needed, but currently lacking because we do not know how extracellular matrix (ECM) properties affect angiogenic sprouting and ultimately, blood vessel formation. Due to the complex nature of native ECMs, it is difficult to identify the role of individual matrix properties.

Here, we have developed synthetic hydrogels with independently tunable properties, which are integrated into a microfluidic platform that mimics the process of angiogenesis in vitro.

In this talk, I will present our efforts to understand how matrix stiffness, adhesiveness and degradative properties jointly regulate angiogenic sprouting, and importantly, vascular lumen formation.

How information is transmitted between cells to govern development and tissue homeostasis in time and space remains a central question in biology. In particular, the role of signaling dynamics in this control is still largely unknown.

While dynamic signalling has been found in various multicellular model systems, its function and mechanism has mainly been studied in cultures of single cells.

We employ a combination of ex vivo and in vitro culture systems with high-resolution imaging of dynamic signalling reporters and microfluidics-based perturbation of signalling dynamics to dissect the function of such dynamics both during embryonic development and adult tissue homeostasis.

Here, I will discuss our latest findings on the role of signalling dynamics in the segmenting mouse embryo and homeostasis of the adult small intestine.

Turing gene regulatory networks are prominent models to study multi-cellular self-organization but it is still unclear how they can drive different self-organizing behaviors.

Here we use an automated algebraic method to derive a topological atlas of self-organizing Turing networks that can generate periodic patterns, traveling waves or noisy amplifying patterns.

The atlas reveals that different self-organizing behaviors are grouped into distinct topological clusters that are characterized by specific network feedbacks.

These clusters are connected together by multi-functional networks that can transition between self-organizing behaviors upon feedback modulations.

These transitions can explain changes in patterning dynamics such as the progression from axis formation into somitogenesis that is observed during early embryonic development.

Our analysis also reveals that feedbacks on cell-autonomous nodes play a central role in canalizing the noise of the system by controlling the speed and precision of pattern formation.

Taken together, our results show that changes in network topology and feedback modulations can drive continuous transitions between Turing behaviors, providing a novel framework to study the evolution and development of multi-cellular self-organization.

Dr. Rajan and her lab design neural network models based on experimental data, and reverse-engineer them to figure out how brain circuits function in health and disease.

They recently developed a powerful framework for tracing neural paths across multiple brain regions— called Current-Based Decomposition (CURBD). This new approach enables the computation of excitatory and inhibitory input currents that drive a given neuron, aiding in the discovery of how entire populations of neurons behave across multiple interacting brain regions.

Dr. Rajan’s team has applied this method to studying the neural underpinnings of behavior. As an example, when CURBD was applied to data gathered from an animal model often used to study depression- and anxiety-like behaviors (i.e., learned helplessness) the underlying biology driving adaptive and maladaptive behaviors in the face of stress was revealed.

With this framework Dr. Rajan's team probes for mechanisms at work across brain regions that support both healthy and disease states - as well as identify key divergences from multiple different nervous systems, including zebrafish, mice, non-human primates, and humans.

Revealing the developmental functional engagement of inhibitory cells is key to understanding the emergence of higher-order cortical processing in mammals. There is a plethora of GABAergic inhibitory neurons present in the cortex, the maturation and impact of which is not well understood.

The upper layers (layers 1-3) are considered an evolutionary newer addition to the cortex and are thought of as a hub that integrates bottom-up and top-down information. We postulate that inhibitory cell development and participation in cortical processing of upper cortical layer activity is key in regulating information flow across cortical areas and hence organizing higher order sensory processing.

We work under the hypothesis that more complex cortical processing begins at the end of the second week after birth (postnatal day 14 - P14), since it is at this time point that a large increase in locomotor and exploratory behavior of mice is observed, which is accompanied by the beginning of whisking.

In this talk I will present some of our work that has focused on unraveling how upper cortical layer GABAergic cells of the whisker somatosensory cortex of mice are developmentally embedding and functionally impacting brain circuits and sensory processing before versus after P14.

In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex. Chromosome separation in anaphase is triggered by separase that cleaves the cohesin subunit Scc1 (also known as Rad21). Separase is activated by degradation of its inhibitors securin or cyclin B, but the molecular mechanisms of separase regulation are not clear.

We used cryogenic electron microscopy (cryoEM) to determine the structures of human separase in complex with either securin or Cdk1-cyclin B1-Cks1. In both complexes, separase is inhibited by pseudosubstrate motifs that block substrate binding at the active site and at nearby docking sites. As in Caenorhabditis elegans and yeast, human securin harbors its own pseudosubstrate motifs. In contrast, Cdk1-cyclin B1 inhibits separase by deploying pseudosubstrate motifs from intrinsically disordered loops in separase itself.

One autoinhibitory loop is oriented by Cdk1-cyclin B1 to block the active sites of both separase and Cdk1. Another autoinhibitory loop blocks substrate docking in a cleft adjacent to the separase catalytic site. A third separase loop contains a phosphoserine that initiates complex assembly by binding to a conserved phosphate-binding pocket in cyclin B1.

Our study reveals the diverse array of mechanisms by which securin and Cdk1-cyclin B1 bind and inhibit separase, providing the molecular basis for the robust control of chromosome segregation.

To understand how an organized multi-cellular embryo forms from a single fertilized egg, we need to examine all the intermediate steps between the one-cell stage and the adult stage which involve individual cell spatial positioning, cell proliferation dynamics and morphogenesis together with cell differentiation.

To study these different aspects, developmental biology has grown into a data intensive science with the development of high-throughput imaging and multi-omics technologies leading to very large datasets that cannot be explored by hand. Machine learning is a versatile set of techniques that can help make sense of these large datasets with minimal human intervention.

We will present here, on one hand, new mathematical and computational approaches to explore very large datasets of individual cell morphological features. And on the other hand, to understand individual cell relationships to patterns of gene expression, we will present our recent progress in data integration between microscopy techniques and transcriptomics data based on machine learning.

Circadian rhythms orchestrate many physiological functions and behavioral aspects around a day in almost all living forms.

The circadian clock is an endogenous time tracking system that which anticipates and coordinates adaptation to daily environmental fluctuations. The circadian system is hierarchically organized, and a master pacemaker located in the brain synchronizes subsidiary clocks in the rest of the organism.

Adequate synchrony between central and peripheral clocks ensures fitness and potentiates a healthy state. Conversely, circadian misalignment leads to several pathological conditions, such as obesity and metabolic syndrome.

At the molecular level, the clock machinery is expressed in almost every cell in the organism and consists of an intricate network of feedback loops in transcription and translation which imposes 24-h cycles in gene expression across all tissues.

In our laboratory, we have been exploring how certain metabolites can reset the phase of the molecular clock and uncouple transcriptional oscillations. We hypothesize that these findings can set the basis for novel chrono-therapeutical approaches to treat metabolic dysfunction.

RNA polymerase (Pol) II is regulated during all stages of transcription to ensure appropriate gene expression. In metazoans, Pol II frequently pauses in the region proximal to the promoter through its association with two protein complexes, DRB-sensitivity inducing factor (DSIF) and negative elongation factor (NELF). Release from pausing into active elongation is mediated by the kinase, P-TEFb.

To understand how pausing and pause release are regulated, we reconstituted mammalian paused and activated Pol II complexes and resolved their structures by cryo-EM. The structures along with biochemical assays show how NELF enhances Pol II pausing and how elongation factors compete with NELF to promote active elongation. Finally, we have recently determined how Pol II is stimulated to transcribe rapidly using an allosteric interaction with the elongation factor RTF1.

Together, our results provide the foundation for understanding the molecular basis of promoter proximal gene regulation and transcription through chromatin.

Why tissue regeneration occurs in some animals but not in others remains enigmatic, and it is not clear why even some closely related species have different responses to the same type of injury.

Using naturally regenerating African spiny mice in comparative RNA-seq based approaches with poorly regenerating mammals, we investigate the molecular mechanisms that promote regeneration in different spiny mouse organs.

Fluorescence lifetime imaging (FLIm) is an optical spectroscopic imaging technique capable of real-time assessments of tissue properties in clinical settings. Label-free FLIm is sensitive to changes in tissue structure and biochemistry resulting from pathological conditions, thus providing optical contrast to identify and monitor the progression of disease. We are translating this imaging technology to the operating room. In this talk I will describe two projects that are at different stages of clinical translation.

The first project focuses on detecting brain tumors with an intraoperative FLIm device integrated into the surgical workflow. There is an unmet need to identify the tumor infiltrative edge of glioblastoma multiforme, the most devastating form of brain cancer, because accurate resections lead to longer survival rates. The infiltrative edge is however difficult to assess grossly during surgery and current tools (including pre-operative MRI and 5-ALA fluorescence-guided surgery) provide limited accuracy. We are exploring the use of FLIm to provide distinctive autofluorescence information from areas with different degrees of tumor cellularity that allow to better identify positive resection margins intraoperatively.

The goal of the second project is to identify and monitor gastrointestinal inflammation with a FLIm prototype device for intraluminal imaging on animal models. Gastrointestinal (GI) diseases such as colorectal cancer or inflammatory bowel diseases are difficult to diagnose in the early stages due to the lack of clear symptoms and techniques with enough sensitivity to detect early inflammatory changes. Gut dysbiosis, an altered balance of the gut microbiota, is central to early manifestations of GI disorders, causing metabolic changes on the gut epithelial cells that are susceptible to elicit tissue autofluorescence contrast. We propose an intraluminal FLIm approach that is compatible with in vivo imaging, for detecting signs of dysbiosis with the goal to develop a clinical tool for early screening of GI diseases.

Both projects will provide an overview of the wide range of processes, skills, and multidisciplinary integration required to translate optical imaging tools from the laboratory work bench to the bed side in the operating room.

One of the biggest challenges in neuroscience is to understand how neural circuits in the brain process, encode, store, and retrieve information. Meeting this challenge requires tools capable of recording and manipulating the activity of intact neural networks in freely behaving animals. Head-mounted miniature fluorescence microscopes are among the most promising of these tools. Taking advantage of the past decade of advancements in fluorescent neural activity reports, these microscopes use wide-field single photon excitation to image activity across large populations of neurons in freely behaving animals. They are capable of imaging the same neural population across months and in a wide range of different brain regions.

Initiated six years ago, the Miniscope Project -- an open-source collaborative effort-- aims at accelerating innovation of miniature microscope technology while also extending access to this technology to the entire neuroscience community. Currently, we are working on advancements ranging from optogenetic stimulation and wire-free operation to simultaneous optical and electrophysiology recording. Through continued optimization and innovation, miniature microscopes will likely play a critical role in extending the reach of neuroscience research and creating new avenues of scientific inquiry.

Episodic memory is a unique type of memory that enables us to mentally re-experience specific episodes in the past.

During memory encoding, a continuous stream of experience is segmented into episodes each of which encodes a temporally organized sequence of events.

Memory-related sequential neuronal activity patterns have been identified in the hippocampus, a brain region essential for episodic memory formation.

However, it is unclear how the hippocampus can parse behavior-level boundaries and encode individual segments of experience.

Here, we investigate the circuit-level mechanism that slices experience into units such as behavioral trials and in turn triggers the expression of the memory-related hippocampal neuronal sequence.

Projects like ENCODE, HCA or the 1+MG project have been generating and will generate PetaBytes of data that are freely accessible to all researchers. This is posing completely new challenges to our community but also a lot of opportunities.

In this talk we will cover the bioinformatic advantages over the last years, with a specific focus on Conda, Containers and the Galaxy framework. We will explain how those projects and freely available global compute infrastructures enables scalable and reproducible science to cope with the mentioned challenges.

Understanding the neuronal basis of need-based motivational drives, such as thirst and hunger, has been a major goal in neuroscience and psychology for over a century. These drives, which maintain homeostasis by directing an animal’s behavior to satisfy specific physiological needs important for survival, are fundamental regulators of behavior. However, it has remained unclear how the activity of neurons sensing physiological state cause an animal to engage in specific motivated behaviors (e.g., eating or drinking) to maintain homeostasis.

I studied the motivational mechanisms underlying thirst, a drive vital for survival that is easily and rapidly induced in mice. Using a new transgenic mouse line that enabled Cre recombination in activity-defined populations of neurons, I was able to obtain highly specific and efficient genetic access to hypothalamic neurons that are activated upon water deprivation, and which integrate signals from cells that directly sense the animal’s physiological need for water. Through a series of molecular profiling, optogenetic, and activity recording experiments, I found that these thirst neurons form a specific cell type and encode a neural regulator of thirst that acts through aversive reinforcement.

It remained unclear how this small population of genetically-defined thirst neurons could shape the animal’s overall behavior. To answer this question, I developed a new approach using large-scale extracellular electrophysiology to map the flow of activity through an unprecedented ~24,000 single neurons in 34 regions of the mouse brain during thirst-motivated behavior. These experiments revealed both widespread neural correlates of sensory input and behavioral output and, surprisingly, a brain-wide neural activity state encoding thirst that could be causally induced through optogenetic stimulation of hypothalamic thirst neurons. These results are significant both in revealing the basic mechanisms of thirst, and in suggesting a new way to study the neural basis of behavior at the level of brain-wide activity patterns.

Transcriptional regulatory regions in the genome including promoters and distal acting enhancers play fundamental roles for development and disease.

Genetic variants associated with human phenotypic traits and disease risk are enriched within cis-regulatory elements (CREs).

However, heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types.

Therefore, we optimized single cell ATAC-seq protocols using droplet based and combinatorial barcoding based strategies for use on more than 25 flash frozen primary human and mouse tissue types including brain and heart.

Misregulation of gene expression in human hearts can result in cardiovascular diseases that are leading causes of morbidity and mortality worldwide. The limited information on the genomic location of candidate cis-regulatory elements (cCREs) in distinct cardiac cell types has restricted our molecular understanding of these diseases.

Using single nucleus ATAC-seq, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure.

We further discovered cardiovascular disease-associated genetic variants enriched within these cCREs including candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs.

Two such risk variants residing within a cardiomyocyte-specific cCRE at the KCNH2/HERG locus resulted in reduced enhancer activity compared to the non-risk allele.

Finally, we found that deletion of the cCRE containing these variants decreased KCNH2 expression and prolonged action potential repolarization in an enhancer dosage-dependent manner.

Overall, this comprehensive atlas of human cardiac cCREs provides the foundation for illuminating cell type specific gene regulation in human hearts during health and disease.

Animals encounter different types of sensory signals depending on their natural habitats and lifestyles.

This can serve as an evolutionary driving force for each species to optimize its sensory systems for processing those signals that appear more frequently and are relevant for survival.

The optimality of the sensory processing has been broadly supported from a viewpoint of coding efficiency; however, here I would like to present and discuss two pieces of evidence that are inconsistent with what the efficient coding hypothesis implies on the mouse retina.

First, extracellular recordings from the optic tract of awake mice show that the retinal physiology in vivo violates the energy minimization principle.

Second, the analysis of the natural image statistics indicates that the functional dorsoventral division of the mouse retina is not optimal for efficiently encoding natural scenes in the UV-green spectra.

These data thus suggest that the mouse retina should have evolved under selective pressures beyond the coding efficiency, such as visual ethological demands.

Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs).

Here, I will present how rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity.

By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm at the onset of gastrulation undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value.

We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables.

We further explore the cellular mechanisms controlling the precision of this PT showing that it depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity.

Finally, our more recent results suggest that the early germ layers in zebrafish occupy different rigidity regimes of the rigidity percolation phase space which may be important in their early segregation at the onset of gastrulation.

Every day we make decisions critical for adaptation and survival.

We repeat actions with known consequences. But we also draw on loosely related events, to infer and imagine the outcome of entirely novel choices.

These inferential decisions are thought to engage a number of brain regions, however the underlying neuronal computation remains unknown.

In this talk I will show how a cross-species approach in humans and mice can be used to reveal the functional anatomy and neuronal computation underlying inferential decisions. I will show that during successful inference, the mammalian brain uses a hippocampal prospective code to forecast temporally-structured learned associations.

Moreover, during resting behaviour, short-timescale coactivation of hippocampal cells represent inferred relationships in sharp-wave/ripples, thereby “joining-the-dots” between events that have not been observed together but lead to profitable outcomes.

Computing mnemonic links in this manner may provide a general mechanism to build a cognitive map that stretches beyond direct experience, thus supporting flexible behavior.

ATP-dependent chromatin remodelers are macromolecular machines that govern the arrangement and composition of nucleosomes across eukaryotic genomes.

Understanding the mechanisms of these enigmatic enzymes promises to reveal core principles of genome regulation and maintenance.

However, the complexity of remodelers and their chromosomal substrates poses a major challenge for modern structural biology.

In my talk, I will discuss the recent breakthroughs which provided high-resolution cryoEM insights into all four families of remodelers.

I will highlight the emerging structural and mechanistic principles with a particular focus on multi-subunit SWI/SNF and INO80/SWR1 complexes.

A conserved architecture comprising a motor, rotor, stator and grip suggests a unifying mechanism how stepwise DNA translocation enables large scale reconfigurations of nucleosomes.

A molecular circuitry involving the nuclear actin containing module establishes a framework for understanding allosteric regulation.

By using whole genome chromatin reconstitutions, we probed these insights in a biochemically defined yet genome wide manner.

We identified DNA shape/mechanics motifs, distinct from known DNA sequence preference of histones, as sufficient information for nucleosome positioning.

Our findings establish a molecular mechanism for robust and yet adjustable +1 nucleosome positioning adjacent to gene promoter regions and, more generally, remodelers as information processing hubs that enable active organization and allosteric regulation of the first level of chromatin.

Emergence of multicellular forms (tissues, organs and organisms) from cells through changes in their shape, size, number and organization is central to understanding the process of morphogenesis.

While molecular players are known, we do not know how the activity of genes and proteins is translated into 3D structures in space and time.

Preexisting spatial cues, species-specific geometry and extraembryonic signaling centers, confound studying these processes in vivo.

We have recently shown that 3D cell aggregates from different species (mouse embryonic stem cells and zebrafish blastula cells, which we term gastruloids and pescoids respectively) generate spatial asymmetries in gene expression and cell behavior within otherwise equivalent groups of cells, to develop a global coordinate system (body axes) de novo.

Combining light-sheet imaging with genetic labelling of cells we are now gaining some insights into the spatio-temporal precision and species-independent manner, with which such 3D embryonic cell aggregates generate the major body axes even in the absence of any embryonic information.

Using these embryonic organoids, as a minimal alternate system, sufficient to generate embryonic axes, we aim to understand early development in embryos as an emergent phenomenon of the self-organization of pluripotent cells.

Probing the molecular and functional properties of neural ensembles is essential for understanding how these networks give rise to circuit function and animal behavior.

I specialize in using molecular and optical approaches to study different types of neuronal signaling in the brains of awake behaving mice.

During my Ph.D. with Professor Karl Deisseroth, I studied the diverse firing properties of projection-defined prefrontal cortex neurons using real-time, cellular-resolution imaging techniques for recording activity from sparse projection pathways.

To allow investigations into the molecular cell-types of these activity- and projection-defined neurons, during my postdoctoral work with Professor Alice Ting I further developed and applied technologies inspired by synthetic biology to gain genetic access to activated cell ensembles.

I coupled single-cell RNA sequencing with a light- and calcium-dependent transcription reporter, FLiCRE, to map out a specific functional and molecular pathway in the brain.

This circuit could be genetically accessed and stimulated using FLiCRE to demonstrate that these neurons drive aversive behaviors in mice.

Together, these emerging technologies have revealed highly-resolved cortical cell-types defined by their transcriptome, projection targets, and activity patterns during behavior.

Future application of FLiCRE along with further development of new technologies will pinpoint the molecular mechanisms by which diverse neural pathways regulate downstream circuits and behavior.

Human pluripotent stem cells can reproducibly organize into embryo-like and organ-like structures.

Efforts to produce pure cell populations for applications such as regenerative medicine are hampered by variability and heterogeneous cell fate outcomes.

In both cases the same biology is at play: developmental gene circuits give rise to endogenous signaling patterns in space and time that in turn give rise to cell fate patterns.

How cells establish these endogenous signaling patterns, and how those signals are then interpreted to give rise to different cell fates is poorly understood.

Recent work has shown that signaling patterns are not static and that cells may respond to different features of the dynamic signaling history such as the rate of signal change, raising the question of how the high dimensional space of possible signaling histories maps to the space of cell fates.

I will report on our ongoing work to answer these questions, which focuses on the cell fate decisions associated with gastrulation and early post-gastrulation development.

Perceptual decision-making is characterized by widespread patterns of activity in the brain. Yet our understanding of the neuronal pathways that support these processes remains very limited.

We studied thalamocortical and cortico-cortical circuits involved in goal-directed sensorimotor transformations in mice performing a whisker-based discrimination task to understand how tactile sensations can be used to drive decisions. As mice learn to perform this task, on one end of the nervous system, tactile stimuli are encoded in the somatosensory pathways while on the other end, motor commands are issued reflecting decisions made.

Subdivisions of the whisker somatosensory thalamus project to cortex in a region-specific and layer-specific manner. A clear anatomical dissection of these pathways and their functional properties during whisker sensation is lacking. Here, we revealed parallel non-overlapping thalamic pathways with distinct representations of tactile and decision-related information during goal-directed sensorimotor task.

At the cortical level, wide field calcium imaging helped identified the secondary somatosensory cortex (wS2) and premotor cortex (M2) as part of the cortical network involved in sensorimotor transformation. Two-photon calcium imaging of large populations of neurons across layers of wS1, wS2 and M2 showed increase functional specialization along this pathway.

In particular, we found that projecting neurons in wS2 displayed decision-related responses suggesting that these neurons are important for the initiation of the upcoming movement generated in M2 cortical network. This was further corroborated with optogenetics manipulations of cortical activity during task execution.

Together these results highlight a shift in sensorimotor representations in the cortex underlying whisker-based goal-directed behavior.

Embryonic Stem cells (ESCs) show a robust yet plastic identity as they are capable of maintaining an efficient self-renewing state with a fast cell cycle while being responsive to external clues that lead to cell differentiation.

A core regulatory network formed by pluripotency transcription factors is responsible to maintain ESCs in this plastic pluripotent state. During mitosis chromatin is compacted, most transcription factors (TFs) are evicted from chromatin and transcription is globally downregulated.

To maintain PS cell identity, it is therefore required that transcription re-initiates at the appropriate set of genes after mitosis completion. Recently, it has been shown that some pluripotency TFs are able to bind to a subset of their target sites during mitosis.

This phenomenon, known as mitotic bookmarking, may represent a mechanism to maintain the memory of active transcription and therefore cell identity. Moreover, waves of intense transcription have recently been observed during mitotic exit and early interphase by using metabolic labeling of RNA in synchronized populations of HUH7 human hepatoma cells.

However, these studies did not consider that mitotic-arrested cell populations progressively de-synchronize and therefore the reported measurements are performed on mixture of cells at different internal cell-cycle times. Moreover, the treatment used for synchronization represents a considerable perturbation and therefore the gene expression dynamics in free cycling cells may differ substantially. Furthermore, it is still not fully understood the precise regulatory mechanism that drive gene expression dynamics during the cell cycle.

In my team, in particular, we try to address the following questions:

1) What is the precise gene expression dynamics during the cell cycle in ESCs?
2) How gene-specific mRNA synthesis and degradation rates change during the cell cycle?
3) What are the key transcriptional regulators that drive transcription dynamics during the cell cycle?

To address these questions, we have performed single-cell RNA sequencing of mouse ESCs and human fibroblast and infer the cell-cycle state progression of each cell applying advance machine learning methods; estimate transcription and degradation rates during the cell cycle using a biophysical model of gene regulation; and, identify key TFs underlying the transcriptional dynamics using linear regression models that relates gene expression with TF activity dynamics.

Overall, we believe that our results open the possibility to shed new light on the interplay between pluripotency maintenance, cell differentiation and the cell cycle.

Cognitive function requires holding multiple hypotheses in mind and interpreting sensory information differently depending on prior experience.

Here, we examined the cortical substrates of this process in a novel spatial inference task through modeling and electrophysiology in mouse Retrosplenial cortex (RSC).

We find evidence that spatial coding in RSC changes depending on previous landmarks the mouse has seen, which correlates with how much information the mouse has about its position.

We then examine whether this encoding of spatial information gained from previous sensory input could form the basis by which new sensory input is interpreted.

To build an interpretable model of this process, we trained a recurrent neural network on a simplified version of our task, and found that this network can correctly interpret otherwise ambiguous sensory information by exploiting local recurrent dynamics.

We then find that the activity dynamics in RSC fulfill the requirements for performing a similar computation.

In sum, we find that the population activity in RSC is capable of assigning different interpretations to otherwise ambiguous sensory inputs by encoding previous experience in a way where its attractor dynamics lead to different interpretations of identical subsequent sensory inputs.

Many developmental processes involve the emergence of intercellular fluid and luminogenesis. This often results in a build up of hydrostatic pressure and signalling molecules in the lumen. However, the potential roles of lumina in cellular functions and tissue morphogenesis have yet to be fully explored.

Using mouse blastocyst as a model, we show that hydraulic force during lumen expansion leads to robust control of blastocyst size and cell fate specification1. We further showed that lineage segregation of the inner cell mass (ICM) can be guided by biochemical signalling cues from within the lumen2.

Notably, spatial segregation of the epiblast and primitive endoderm in the ICM is characterized by differential cellular dynamics and a fluid-solid transition in the overall ICM material property.

The interplay between hydraulics, signalling and tissue mechanics provides a unified framework in understanding tissue morphogenesis3, which we argue have important implications in understanding mammalian follicle development.

References

1. Chan CJ, Costanzo M, Ruiz-Herrero T, Mönke G, Petrie R, Bergert M, Diz-Munoz A, Mahadevan L, Hiiragi T. Hydraulic control of mammalian embryo size and cell fate. Nature (2019) 571:112-116.

2. Ryan AQ, Chan CJ, Graner F, Hiiragi T. Lumen expansion facilitates epiblast-primitive endoderm fate specification during mouse blastocyst formation. Developmental Cell (2019) 51, 1-14.

3. Chan CJ, Hiiragi T. Integration of luminal pressure and signalling in tissue self-organisation. Development (2020) 147:dev181297

Accurate chromosome segregation in eukaryotes requires the coordinated action of hundreds of proteins. Subsets of these, named kinetochores, attach centromeric chromatin to the microtubules of the mitotic or meiotic spindle.

Kinetochores are crucial for accurate cell division: they couple the force of depolymerising microtubules to chromosome movement and delay the onset of anaphase until all chromosome-spindle attachments are correct.

The main microtubule binder in the kinetochore is Ndc80, a 65 nm long tether-like complex. In a human kinetochore, ~200 Ndc80 complexes connect a centromere to ~15 microtubules.

How does this lawn of Ndc80 bind dynamic microtubules and how is microtubule-attachment regulated during mitosis?

To address those questions, I reconstituted the kinetochore-microtubule attachment site from purified components and, together with colleagues, compared how the kinetochore-microtubule interface is regulated in a minimal in vitro system and in dividing cells.

Our work provides a quantitative description of microtubule binding under force and a molecular explanation for causes and consequences of Ndc80 multivalency.

Post-implantation embryogenesis is a highly dynamic process comprising multiple lineage decisions and morphogenetic changes that are inaccessible to deep analysis in vivo.

The developmental engineering of embryo-like structures from stem cells in vitro can overcome this impediment.

Gastruloids are aggregates of mouse embryonic stem cells that resemble the organized gene expression space of the post-occipital embryo (i.e. an "embryo without a head"), but lack proper morphogenesis, e.g. presomitic mesoderm does not condense into somites and neural cells do not form a neural tube.

We recently discovered that the addition of the extracellular matrix surrogate Matrigel could transform the organized gene expression space of gastruloids into highly organized “trunk-like structures” (TLSs) with embryo-like architecture, comprising the neural tube and bilateral somites.

Comparative single-cell RNA sequencing analysis confirmed that this process is highly analogous to mouse development and follows the same stepwise gene-regulatory program.

Tbx6 knockout TLSs developed additional neural tubes mirroring the embryonic mutant phenotype, and chemical modulation could induce excess somite formation. TLSs thus reveal an advanced level of self-organization and provide a powerful platform for investigating post-implantation embryogenesis in a dish.

In my talk, I will give an overview of the development and benchmarking of the TLS system and discuss how it can be utilized to achieve quantitative biological insights.

Regulation of information flow in the brain is critical for many forms of behavior.

In the first part of my talk, I will focus on mechanisms that regulate interactions between brain regions and describe how information flow from the sensory cortex can be gated by state-dependent frontal cortex dynamics during decision-making in mice.

In the second part, I will focus on information flow within the frontal cortex microcircuitry and present a new optical method that I developed for rapid mapping of local connectivity in vivo.

Combining connectivity mapping with a novel paradigm of mouse innate behavior revealed a columnar structure in the frontal cortex and the existence of neurons that function as network hubs, which had an unexpectedly high number of connections and strong influence on neighboring neurons.

Finally, I will show that analyses of interactions between >20,000 neurons, recorded simultaneously across multiple cortical areasand different brain states, revealed a hitherto unknown parcellation of the mouse cortex into functional modules, calling for revision of existing definitions of cortical regions.

Taken together, these results pave a road to study how neuronal interactions on different spatial scales give rise to behavior.

Establishment of correct gene expression patterns is crucial for organism development and their perturbation is a key event in the manifestation of many diseases including cancer.

Binding of transcription factors (TFs) to cis-regulatory elements (CREs) opens chromatin and leads to the recruitment of multiple co-factors that activate or repress transcription.

CRE activation typically requires the binding of multiple TFs, however the precise mechanisms underlying their coordinated action are largely unknown. Current bulk assays used to map TF occupancy average binding events arising from millions of individual cells, not informing on the dependencies that organize their binding at CRE.

To move beyond this boundary, we have adapted Single Molecule Footprinting (SMF) to quantify the binding of TFs at mouse regulatory regions.

Detecting multiple TF binding events on single DNA molecules has enabled us to determine TF co-binding frequencies in vivo. Systematic analysis of the co-occupancy patterns of thousands of TF pairs reveals widespread evidence of cooperative binding independently of the identity of the factors involved.

We find that genomic distance between motifs, but not their strict spatial arrangement within CREs determines their degree of co-occupancy. Moreover, TF co-binding is prevalent at CREs with high nucleosome occupancy, suggesting that cooperative binding is required for maintaining chromatin open at regulatory regions.

These findings elucidate the binding cooperativity mechanism used by transcription factors in absence of strict organisation of their binding motifs, a characteristic feature of most of enhancers.

Natural environments are dynamic, necessitating rapid learning and flexible behavior to maximize reward. In the framework of reinforcement learning, memories of previous interactions with the environment form value representations - the basis for reward predictions.

We have explored the neural basis of these reward memories, how they are maintained, how they are updated, and how they drive behavior.

In one study, we trained mice on a dynamic foraging task in which they chose between alternatives that delivered reward with changing probabilities. Mice were sensitive to changes in reward contingencies and shifted behavior rapidly to maximize reward. We found that neurons in the medial prefrontal cortex, including projections to the dorsomedial striatum, persistently maintained memories of previous choices/outcomes and causally drove future decisions and the vigor of those actions.

In another study, we trained rats to associate cues with probabilistic delivery of rewards. We made the unexpected discovery that the ventral pallidum, a basal ganglia structure, encoded reward prediction errors, a necessary teaching signal to update reward memories. This activity bidirectionally modulated the vigor of reward-seeking behavior.

In contrast to a long-held view that ventral pallidum serves as a relay, these representations were much weaker in its primary input structure, the nucleus accumbens. Taken together, this work better defines the neural architecture of reinforcement learning.

Animals use memories of previous experiences to guide behavior in a flexible manner. The hippocampus and associated cortical structures play a key role in learning and memory processes. The synchronous spiking of cell ensembles in these circuits supports the encoding and recall of behaviorally relevant information, while neural oscillations coordinate inter-areal communication. In the first part of the talk, I will present novel evidence on the existence of dedicated entorhinal-hippocampal circuits and physiological mechanisms for different types of learning in rodents. The lateral (LEC) and medial (MEC) entorhinal cortex receive inputs from two distinct streams of cortical hierarchy (the ‘what’ and ‘where’ paths) and convey these neuronal messages to the hippocampus. I will show how this two inputs engage different hippocampal cellular populations in a task-dependent manner and how optogenetic manipulations that impair the precision timing of spikes affect learning performance and interareal communication. Hippocampal cells that have been active during a recent experience are reactivated during highly synchronous network events known as sharp-wave ripples (SWRs). This “replay” of behaviorally relevant sequences during SWRs after a new experience is believed to mediate memory maintenance and behavioral planning. In the second part of the talk, I will provide causal evidence on how the sequential activation of place cell ensembles during ‘offline’ periods contribute to memory.

Transcription of eukaryotic protein-coding genes requires RNA polymerase II (Pol II).

During transcription, RNA polymerase II transcribes a chromatinized DNA template.

Pol II passage, however, is impaired by nucleosomes and requires elongation factors including chromatin remodellers and histone chaperones that facilitate chromatin transcription.

To understand the mechanistic basis of nucleosome passage, we have obtained multiple cryo-electron microscopy (cryo-EM) structures of transcribing RNA polymerase II from the yeast Saccharomyces cerevisiae engaged with a downstream nucleosome core particle and additional factors.

The structures and biochemical data provide a structural basis to investigate the interplay of Pol II, transcription factors, chromatin remodellers, histone chaperones, and nucleosomes.

Contractile cell types are universally present in animals and fundamental to animal morphogenesis and behavior.

Contractions of individual, scattered cells underlies amoeboid cell migration, which is prevalent in both adult organisms and embryos, while tissue-scale collective cell contractility underlies both embryonic morphogenesis and adult motricity.

However, the origin of animal contractile cell types remains obscure. As the sister-group of animals, choanoflagellates hold the promise of illuminating the evolutionary origins of animal cell biology.

Intriguingly, choanoflagellate genomes encode an extensive complement of homologs to animal contractility genes, suggesting the involvement of (yet unidentified) contractile processes in their life history.

Here, I report on the recent discovery of both individual and collective cell contractility in choanoflagellates.

Under confinement, the model choanoflagellate Salpingoeca rosetta rapidly undergoes a phenotypic switch from a flagellate to an amoeboid cell phenotype that resemble animal migratory cells in both structure and function.

This represents an unexpected expansion of the known phenotypic repertoire of choanoflagellates and suggests an ancient origin for animal crawling cells, in line with the temporal-to-spatial transition hypothesis for the origin of animal cell types.

Finally, collective cell contractility has also been recently discovered in a newly discovered colonial choanoflagellate isolated from a Carribean island, that undergoes rapid and reversible whole-colony inversion in response to external photic and mechanical stimuli.

Homologous recombination(HR) is a ubiquitous DNA double-strand break (DSB) repair mechanism that promotes cell survival and genomic stability.

HR entails a potentially genome-wide homology search step, carried out along a conserved RecA/Rad51-ssDNA nucleoprotein filament (NPF) assembledon each DSB ends 1–3.

This search is subdued to the NPF-dsDNA collision probability with any given loci. However, whether chromatin spatially reorganizes following a DSB, and how it in turn influences the homology search process, remains undefined.

Here we characterize the local and genome-wide spatial reorganization of chromatin following DSB formation, and show that they influence homology search in multiple ways.

Cohesin folds chromosomes into cohesive arrays of ~20 kb long chromatin loops as cells arrest in G2/M.

Locally, the DSB-flanking regions interact in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin and HR proteins.

This local structure blocks cohesin progression, constraining the extending NPF at loop base and promoting side-specific NPF-dsDNA interactions.

Functionally, cohesin-mediated loop folding (but not sister chromatid cohesion) restrains homology search intra-chromosomally, which provides a kinetic advantage for identification of intra- over inter-chromosomal homology.

Together with pastin vitrodata, our results suggest that cohesins act as general facilitators of homology search, by promoting both 1D scanning upon loop expansion and localized 3D inter-segmental contact sampling upon global reorganization of chromatin conformation.

In order to survive and reproduce, animals must produce a diverse range of innate and learned behaviors in a flexible and context-dependent manner.

The computational task of forming an internal representation of an animal’s environment and translating that to the selection of goal-directed actions is dependent on the coordinated activity of multiple brain areas.

Working with experimentalists to dissect the neural correlates of behavior in multiple interconnected hypothalamic nuclei of freely behaving mice, we uncover striking differences in how animals’ motivational states and behaviors are represented across neural populations.

Combined with neuronal cell type data, these observations inform a new model of the joint control of behavioral decision-making by multiple interacting neuronal populations.

SARS-CoV-2 is the coronavirus responsible for the current COVID-19 pandemic.

Normal human coronaviruses cause the common seasonal cold that cause mild respiratory symptoms.

Why SARS-CoV-2 is capable of spreading so effectively among humans, why it infects organs other than the lung, why it causes neurological symptoms such as loss of taste and smell, is not clear.

The SARS-CoV-2 Spike (S) is a viral surface protein that binds the receptor ACE2 and is essential for host cell attachment and entry.

We noticed that furin protease cleavage of S at the S1/S2 boundary liberates a sequence that conforms to the C-end Rule [R/K]-X-X-[R/K] at the S1 C-terminus.

We found that this C-end Rule binds directly to the cell surface receptor neuropilin-1 (NRP1) - in non-infected cells, NRP1 has roles in ligand internalisation, angiogenesis and regulation of vascular leakage. We further showed that depletion of NRP1 by CRISPR/Cas9, blockade of the S1-NRP1 interaction with NRP1 antagonist or anti-NRP1 mAbs significantly reduced SARS-CoV-2 infectivity in human tissue culture cells.

Thus, NRP1 is a second receptor for SARS-CoV-2 that promotes viral infectivity, and is a target for therapeutic intervention of COVID-19.