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2022 -
Grant Awardees - Early Career

Reconstructing water to land transitions in arthropod evolution combining atoms, genes and fossils

FERNANDEZ Rosa (SPAIN)

CSIC - Institute of Evolutionary Biology - Barcelona - SPAIN

MUÑOZ-GARCIA Ana Belen (SPAIN)

Department of Physics "Ettore Pancini" - University of Naples Federico II - Naples - ITALY

ORTEGA-HERNANDEZ Javier (MEXICO)

Department of Organismic and Evolutionary Biology - Harvard University - Cambridge - USA

Breathing has played a key role in all animal life since its origins more than half a billion years ago. Animals occupy all types of environments, ranging from mountain tops to the bottom of the oceans. Despite this enormous variability of lifestyles, all animals fall within one of three possible categories for breathing: those that breathe air, those that breathe underwater, or those that do a combination of both. The common denominator is that all animals breathe to consume oxygen, a chemical element that can either be a lethal toxin or a vital gas, depending on the circumstances. The transition from breathing underwater to breathing air represents one of the most important steps in animal evolution, as it allowed them to explore dry land for the first time approximately 420 million years ago. However, the precise mechanisms responsible for the water to air transition of breathing and oxygen consumption remain largely unknown due to the complexity of this drastic change in the mode of life of early animals. The objective of this project is to investigate the early evolution of air-breathing among arthropods, animals with jointed legs whose living representatives include arachnids, millipedes, crustaceans and insects. Arthropods represent ideal case studies because they are among the first animals that evolved air-breathing as informed by the fossil record, as well as having well-developed structures for oxygen exchange such as external and internal gills. To better understand how animals acquired the capacity to consume oxygen from breathing air, we will explore this question from three interdisciplinary approaches: 1) We will explore how hemocyanins (the respiratory pigments of arthropods) have evolved through time and will investigate if the oxygen-transporting function in different respiratory structures is due to similar or different genes. 2) We will use the excellent fossil record of arthropods to investigate how respiratory structures have changed over millions of years, from fully marine animals during the Cambrian Explosion, to the first land-dwelling species that show the earliest evidence of adaptations for air-breathing in the Silurian and Devonian. 3) We will use and develop micro- and macroscopic physico-chemical approaches to investigate hemocyanin reactivity and respiratory flux features for different respiratory architectures.
2022 -
Long-Term Fellowships - LTF

Dynamic threat assessment and signal integration by innate immune signaling complexes

FISCH Daniel (.)

. - Boston Children's Hospital - Boston - United States

KAGAN Jonathan (Host supervisor)
Pattern-recognition receptors (PRRs) of the innate immune system sense threats arising from pathogens or tissue injury, respectively known as pathogen or damage-associated molecular patterns (PAMPs/DAMPs). Upon activation, PRRs induce formation of supramolecular organizing centers (SMOCs). SMOCs are the signaling organelles of the innate immune system controlling cytokine production and cell death. SMOC activities were commonly studied in reductionist systems, using pure ligands of individual PRRs. However, during microbial encounters multiple PAMPs are present and likely contribute to SMOC activity, raising the possibility of additive, synergistic or even antagonism responses. To test this, I propose to examine the dynamics of SMOC formation, composition, localization and effector activities using a distinct model system to prior approaches. Specifically, I plan to create CRISPR knock-in macrophages for live cell imaging and spatial proteomics. To offer modularity for PRR stimulation, I plan to use beads as “minimalist microbes”. Their regular, circular shape (and isolation methods for bead-containing phagosomes) allows monitoring protein localization and activities on these minimalist microbes. Combined with the flexibility to attach defined PAMPs, I envision development of a powerful discovery platform. Findings from these synthetic approaches will be scrutinized using primary cells to understand how SMOC assembly with defined ligands in isolation or in combination controls signaling and effector functions. This work will help elucidate how innate immune cells perceive and compute threats in an inflammatory environment and how they decide on an appropriate response.
2022 -
Grant Awardees - Program

Multi-omic reconstruction of flow across the distributed metabolism of early-branching Dracula ants

FISHER Brian Lee (USA)

Entomology - California Academy of Sciences - San Francisco - USA

LEBOEUF Adria (USA)

Department of Biology - University of Fribourg - Fribourg - SWITZERLAND

TEUSINK Bas (NETHERLANDS)

Amsterdam Institute of Molecular and Life Science (AIMMS) - VU University Amsterdam - Amsterdam - NETHERLANDS

Many successes in life are based on collaboration – this extends to the molecular level, where life is fueled by the chemical processes collectively called metabolism. Microorganisms exchange nutrients through cross-feeding, and multicellular organisms are made up of tissues with different metabolic roles and needs. Social insects, where the notion of self is distributed over multiple individuals, take this collaboration still further: Many ant colonies engage in social exchanges of experimentally accessible fluids that contain both exogenously sourced and endogenously produced materials. Larvae of many social insects have been purported to be a ‘digestive caste.’ They are fed exogenously sourced food by adults and return a nutritious fluid whose metabolic functions remain unestablished. The mode of transmission from larvae to adults varies across ant species: In some, larvae voluntarily secrete fluids, while in early-branching ‘Dracula’ ants, adults non-destructively drink larval hemolymph. Such socially exchanged fluids can be analysed to monitor the fluxes of distributed metabolism, making ant colonies apt model systems to study the molecular mechanisms of inter-system communication and division of metabolic labor. We address three key questions (i) what is being exchanged? (ii) what are the functional implications of these exchanges? and (iii) how did these modes of exchange evolve? We combine behavior observations with detailed molecular analyses of four species representing different social feeding modes and evolutionary lineages. We perform proteomics and metabolomics on each colony-tissue and exchanged fluid. Based on genomes and gene expression, we reconstruct metabolic networks for advanced multi-omic data integration to identify active pathways. Novel community-scale metabolic modeling will be used to probe colony-level functionality of social exchange. Critical pathways will be validated with fluorescent metabolite probes in an automated colony- and transmission-tracking system and by genetic or feeding perturbations. This project offers new ways to view social behavior, evolutionary biology, metabolism and the physics of collective behavior. Ultimately, this work will innovate by elucidating the functional role of distributed metabolism, probing its evolution, and providing new tools to study community-level metabolic interactions.
2022 -
Long-Term Fellowships - LTF

Dopaminergic basis of learning temporal regularities in perceptual decisions

FRITSCHE Matthias (.)

. - University of Oxford - Oxford - United Kingdom

LAK Armin (Host supervisor)
Learning from past decisions and their outcomes allows us to make predictions about the future, thereby improving subsequent decisions. Some predictions are formed based on the stability of the world in which past successful decisions tend to remain successful (stable predictions), while others rely on foreseeable dynamic changes in the environment (dynamic predictions). How does the brain learn to make these distinct predictions? I propose to address this question by combining cutting-edge behavioural, neurobiological and computational tools in mice. I will investigate whether the neurotransmitter dopamine, a central component of the brain’s learning circuits, plays a role in this learning process. Specifically, I hypothesize that dopamine regulates distinct prediction strategies through the modulation of neural circuits in two brain areas: the striatum and prefrontal cortex. I will first identify the behavioural signatures of stable and dynamic prediction strategies by training mice to perform visual decisions in environments affording both types of predictions, and will develop computational models of decision-making that capture mouse behaviour. I will then investigate the roles of dopamine in this learning by measuring the release of dopamine in prefrontal cortex and striatum using novel imaging techniques. Finally, I will determine the causal role of dopamine by manipulating dopamine signals in the two brain areas, using optogenetic tools. This research will provide fundamental insights into the neural bases of decision-making, and could shed light on clinical conditions that compromise decision-making and cognition.
2022 -
Grant Awardees - Early Career

Biofilm heterogeneity as an evolutionary mechanism for resilience to complex environments

FUSCO Diana (ITALY)

Physics - University of Cambridge - Cambridge - UK

RUIZ PESTANA Luis (SPAIN)

Civil, Architectural, and Environmental Engineering - University of Miami - Coral Gables - USA

TROPINI Carolina (CANADA)

Dept. of Microbiology and Immunology and School of Biomedical Egineering - University of British Columbia - Vancouver - CANADA

Biofilms are structured communities of bacteria that grow at interfaces and have a remarkable ability to adapt and thrive in a tremendous diversity of hostile environments, including antibiotic-impregnated prosthetic implants. As such, biofilms are the most pervasive life-form on Earth. Our understanding of how biofilms achieve and have evolved this amazing resilience is woefully incomplete, as evidenced by our inability to disrupt detrimental biofilm formation. We hypothesize that phenotypic plasticity and biofilm morphology are coupled and have coevolved to promote optimal adaptation and survival in fluctuating hostile environments. We formulate this hypothesis based on 1) the correlation between biofilm morphology and phenotypic spatial organization 2) the widespread phenotypic heterogeneity among bacterial species, and 3) the multiple mechanisms through which functional and phenotypic diversity may confer advantages to biofilms. While isolated parts of this problem have been investigated, the intrinsic coupling between the mechanics, microbiology and evolution across multiple scales has not yet been explored. Our overall goal is to understand the feedback between cell-to-cell phenotypic heterogeneity, local physico-chemical conditions, and macroscale biofilm morphology, and to elucidate its evolutionary path and role on the amazing resilience of biofilms. Our research plan consists of three aims. First, we will learn the microscopic rules that govern the interplay between mechanical forces and gene expression. Second, we will determine whether and how phenotypic plasticity and associated biofilm morphology in the wildtype confers a fitness advantage to the biofilms. Third and last, we will elucidate how phenotypic heterogeneity could have spontaneously evolved. Our approach consists of a synergistic combination of a bottom-up multiscale modeling framework to map the mechanisms that control the feedback and co-evolution between phenotypic heterogeneity and biofilm morphology, in-vitro microfluidics and top-agar setups to inform and validate the computational models, directed evolution experiments, and in-vivo characterization of gut microbial biofilms to corroborate and revise our in silico understanding of biofilm behavior. The completion of this work will enable an integrated model of the role of heterogeneity in establishing biofilm resilience.
2022 -
Long-Term Fellowships - LTF

Microtechnology-based limbic-cortex axis in 3D: modeling human neurodevelopment and disease

GARONE Maria giovanna (.)

. - Murdoch Childrens Research Institute - Parkville - AUSTRALIA

VELASCO Silvia (Host supervisor)
Stem cell-derived 3D organoid models hold great promise for studying processes of human brain development that would not otherwise be experimentally accessible. The amygdala is the component of the limbic system that regulates emotion and behavior, making extensive connections with the cerebral cortex and hippocampus. Its alterations have recently been highlighted as hallmarks of neurodevelopmental diseases, such as autism spectrum disorder (ASD). Despite recent advances in the generation and characterization of 3D systems replicating brain regions in vitro, models of the amygdala are still missing. Therefore, I propose to develop an innovative method to differentiate human induced pluripotent stem cells (iPSC) into amygdala-like brain organoids (hAmyOs). By using microtechnology-based methods to improve nutrient delivery and exchange, I aim to establish a next-generation 3D system to recapitulate the mutual interactions among the human cortex, amygdala, and hippocampus. By taking advantage of this novel 3D hiPSC-derived cortex-amygdala-hippocampus assembloid system, I will explore aspects of neuronal biology and function involved in human brain development and disease. I will focus on ASD mutant 3D systems to investigate defects of connectivity among defined brain regions with long-term live imaging and functional assays. Moreover, I will leverage single-cell-omics technologies to unbiasedly discover cell-type specific abnormalities and pathogenic mechanisms associated with mutation of ASD genes. Our research will provide a platform to study limbic-cortex connections involved in human development and for modeling circuit organizations and neurodevelopmental diseases.
2022 -
Long-Term Fellowships - LTF

Metabolic and cell–cell interactions of Helicobacter pylori and stem cells of the gastric glands

GEIER Benedikt (.)

. - Stanford University School of Medicine - Stanford - United States

AMIEVA Manuel (Host supervisor)
Virulent strains of the global pathogen Helicobacter pylori (Hp) significantly increase the risk of developing gastric cancer. Recently, Hp has been described to form clonal microcolonies directly on the epithelial surface deep within the gastric glands, where they affect the proliferation and gene expression of epithelial stem cells. My aim is to reveal the molecular details of how these gland-associated Hp strains shape this niche and how virulent strains promote gastric cancer. To study metabolic interactions in situ I have developed an approach combining fluorescence labeling and high-resolution mass spectrometry imaging. I will to translate my approach for analyzing how different Hp strains and epithelial stem cells change their metabolome during colonization of the gastric gland microniche. To reveal the metabolic heterogeneity of Hp microcolonies that grow on the epithelia and to understand the underlying cell-cell interactions, I propose to integrate metabolite imaging with 3D correlative light and electron microscopy. Two experimentally tractable infection models developed by the host lab will serve me as study systems: a chronic Hp infection model of murine stomachs, and a human organoid model that mimics different regions of the gastric gland epithelium. I will infect both systems with genetically modifiable, isogenic Hp strains to show how virulence factors modulate the site-specific metabolism and ultrastructure of epithelial stem cells. Here, I plan to develop a framework to investigate fundamental interactions between microbial strains and human epithelia to shed light on how Hp promotes gastric cancer by colonizing the microniche of the gastric glands.
2022 -
Long-Term Fellowships - LTF

Uncovering the nuclear dynamics of telomeres upon replication stress

GONZALEZ MANJON Anna (.)

. - The University of Sydney - Sydney - AUSTRALIA

CESARE Tony (Host supervisor)
Regulated spatiotemporal nuclear organization is critical for genome function. During my PhD I demonstrated that disrupted chromatin organization at the nuclear lamina can mediate chemotherapy resistance through altered gene expression. As a post-doc, I will explore how dynamic alteration of nuclear spatiotemporal organization promotes genome stability during the replication stress response (RSR). The Cesare lab identified that nuclear actin forces potentiate movement of replication-stressed chromatin, including telomeres, towards the nuclear periphery to facilitate homology directed repair. Telomeres are an exceptional model for this study because straightforward methods exist to induce telomere-specific replication stress and determine telomere interatomic networks. Telomeres are also suitable to live imaging and interact with nuclear domains/condensates during replication stress through unknown mechanisms. Using this telomere model, I will examine the following aims that explore open questions on nuclear dynamics. i) Identify the regulators of RSR-dependent telomere movement using time resolved APEX2 interatomics profiled by mass spectrometry. ii) Characterize how telomere dynamics during replication stress alters both local and global chromatin organization through ChIP, Hi-C/4C, and ATAC-seq methods. iii) Study the consequences of perturbed telomere localization following experimentally directed telomere movement to nuclear domains/condensates. Each aim will include functional interrogation of the revealed pathway/consequences. This study will enhance our understanding of RSR-dependent chromatin dynamics and revel the impact of these processes on genome stability.
2022 -
Grant Awardees - Program

Intracellular voltage control of directional cell migration

GOV Nir (ISRAEL)

Department of Chemical and Biological Physics - Weizmann Institute of Science - Rehovot - ISRAEL

KRISHNAN Yamuna (INDIA)

Department of Chemistry - Gordon Centre for Integrative Science - Chicago - USA

SAEZ Pablo (CHILE)

Department of Biochemistry and Molecular Cell Biology (IBMZ) / Cell Communication and Migration lab - University Medical Center Hamburg- Eppendorf | UKE - Hamburg - GERMANY

Cell migration is pivotal to wound healing, the immune response, and cancer. When a cell moves within a tissue it experiences a complex landscape, facing barriers as well as other cells in set topologies. When cells are moving towards a designated target - referred to as directional migration - they are attracted by specific chemical cues. These cues compel cells to adopt a preferred path along which they often face obstacles that generate bifurcating arms, of which one emerges as the winning direction. One way that cells sense barriers is by activating ion channels on their surface, which changes the membrane potential (MP) across the cell membrane. Due to the lack of tools it was so far impossible to expose the links between MP and directional migration. Ion channels on organelles can also contribute to changes in MP. Migrating cells use polarity as a navigation system, which in turn, is reflected in the organization of organelles - raising exciting questions. How do single cells choose a direction of migration? Do changes in MP at the cell surface and in organelles regulate this decision? Is there a cell-surface-to-organelle axis of communication that drives this decision? We propose to study how cells choose a direction between competing arms formed during movement. We posit that when a moving cell faces a bifurcation, ion channel activity at the plasma membrane changes MP, modifies the local actin flow, thereby contributing to the process of favoring an arm that sets the direction (similar to the front wheel and handle of a bicycle), while organelles at the cell rear respond and contribute to the forward movement (analogous to the back wheel of a bicycle). To test this idea, we will use new technologies that measure MP on the cell surface and in organelles of cells while they are migrating and choosing a direction. The data obtained will be integrated into a theoretical model, which we expect will describe and predict the direction of migration. Indeed, the ability to predict cell migration is an essential precursor to controlling its movement. Controlling cell movement can lead to accelerated wound healing, prevention of metastasis or sculpting of the immune response.
2022 -
Grant Awardees - Program

Trichomes: uncovering principles of forming complex 3-dimensional shapes by cellular morphogenesis

GROSSNIKLAUS Ueli (SWITZERLAND)

Institute of Plant and Microbial Biology - University of Zurich - ZURICH - SWITZERLAND

KONDO Shigeru (JAPAN)

Frontier Bioscience - Osaka University - Suita - JAPAN

While experimental and theoretical studies have provided a deep understanding of the three-dimensional formation of tissues and organs, it largely remains a mystery how a single cell acquires its particular shape. One reason is that the complexity of cellular morphogenesis makes a mathematical description difficult because, in contrast to tissues, cells cannot be used as units in the mathematical model. Furthermore, the many processes that occur simultaneously in a single cell and influence each other, necessitate multi-component, interrelated models. Finally, locally restricted manipulations in specific regions of the cell are required to test certain aspects of the models for cellular morphogenesis. It is thus clear that solving such a complex problem depends on advances in both theory and experiment, requiring a research environment where theoreticians and experimentalists work closely together. We will tackle this problem through cooperation of the Grossniklaus and Kondo groups, specializing in plant developmental biology and mathematical modeling, respectively. The Grossniklaus group will use cell biological, biophysical, and photochemical approaches to investigate the individual processes of trichome morphogenesis. The Kondo group will perform simulations to understand how individual phenomena are integrated to produce the complex morphology of trichomes. Through this interdisciplinary collaboration, we will shed light onto the fundamental principles of cellular morphogenesis.
2022 -
Long-Term Fellowships - LTF

Mapping the neuromodulatory heterogeneity in decision making

HAGIHARA Kenta m. (.)

. - Allen Institute for Brain Science - Seattle - United States

SVOBODA Karel (Host supervisor)
Small groups of neuromodulatory (NM) neurons send brain-wide projections and influence diverse brain functions. Failures of NMs are associated with debilitating neurological and psychiatric disorders. Although NM systems are often thought of as diffuse, there is a complex tapestry of heterogeneity within each system. An outstanding question is how NM systems exert specific effects on circuit subsystems during behavior. Systematic interrogation of this question requires dissecting the diversity of NM cell types and their connectivity to identified target neurons and their NM receptors at multiple spatial scales. In my post-doctoral program, I will take a multi-faceted approach to examine the influence of serotonergic (5HT) neuron types on their postsynaptic targets and on neural ensemble dynamics in frontal cortex. My research will first define sub-types of 5HT neurons in the dorsal raphe projecting to the frontal cortex by combined analysis of transcriptome and whole-brain anatomical reconstruction. I will gain genetic access to these types using enhancer adeno associated viruses. Next, using expansion microscopy and multiplexed immunostaining, I will examine synapse-resolution connectivity of 5HT neuron types by characterizing their post-synaptic receptor subtype distribution in target neurons. Finally, by simultaneously measuring activities of 5HT subtypes and their targets in mice engaged in foraging behavior, I will examine how such heterogeneous 5HT modulation influences population coding underlying economic decision-making. Our approach will provide a blueprint for mapping the NM heterogeneity in general and may reveal new targets for clinical intervention.
2022 -
Cross Disciplinary Fellowships - CDF

Quantum microscopy of neuron electric signals

HANLON Liam (.)

. - École Normale Supérieure Paris-Saclay (ENS Cachan) - Gif-sur-Yvette - FRANCE

TREUSSART Francois (Host supervisor)
MOTHET Jean-Pierre (Host supervisor)
Electrophysiology is the gold standard to study neuron function at sub-µs resolution, but it lacks spatial resolution and is invasive. Various microscopies have been introduced to overcome these limitations and image a number of neuron signals simultaneously at high spatio-temporal resolutions. Voltage-sensitive dyes are one such technology but despite increasing temporal performance, it still lags behind electrophysiology techniques. Hence a sensor of neuronal electrical activity that would combine the high spatial resolution of optical microscopy and the fast time response of electrophysiology is still missing. Recently, quantum properties of atomic size systems have been harnessed in this field such as the Nitrogen-Vacancy (NV) defect in diamond. The NV has rapidly become a table-top equipment used to probe magnetic properties of novel materials at the nanoscale. Its translation to neuron sensing has been demonstrated [Barry2016], but limited to a giant axon with low spatial resolution. To improve such sensor performance I recently proposed a unique theoretical approach in which I harness NV ability to sense an electric field like in electrophysiology in diamond nano-pillars [Hanlon2020]. I now seek to implement neuron NV-electrometry in a laboratory possessing both NV physics and neuro-biology expertise. LuMIn lab at ENS Paris-Saclay will provide such cross-disciplinary expertise. I will conduct my work under the supervision of Prof. Treussart, with key inputs from Prof. Roch (NV magnetometry expert) and Dr Mothet, neurophysiologist. This expertise would allow me to design the NV neuro sensing experiment and test its efficacy against other sensing mechanisms.
2022 -
Long-Term Fellowships - LTF

Understanding the neural mechanism underlying affiliative social behavior

HAYAT Hanna (.)

. - The Regents of the University of California, Los Angeles - Los Angeles - United States

HONG Weizhe (Host supervisor)
Social interactions between individuals are a hallmark of human society and involve two or more individuals engaging with one another. Whereas neural correlates of behaviors such aggression and mating have been studied extensively, little is known about the brain circuits that promote affiliative social interactions, which are crucial to maintain social cohesiveness and to the physical and emotional well-being of social species including humans. One of the most common affiliative behaviors observed across a large range of species is allogrooming, but the neural mechanisms underlying this behavior remain largely unknown. Here I propose to use high-density Neuropixels probe to record simultaneously hundreds of neurons from several brain regions during allogrooming (e.g. one probe can record activity from the medial amygdala, the hippocampus and thalamus simultaneously). Neuropixels enables recordings from local populations of neurons in one region as well as several populations across many regions, an essential step toward better understanding of global activity coordination during behavior. It will give me the opportunity to identify brain regions involved in social grooming, to decipher neuronal activity patterns involved in allogrooming from sensory input to motor output and to understand the inter-play and correlated activity between those regions. Using computational tools, I will build predictive models of behavior based on the brain activity. Investigation of the neural circuitry that controls affiliative social contact may help us understand the deficits of social behavior observed in neuropsychiatric conditions such as autism.
2022 -
Long-Term Fellowships - LTF

Biochemical and structural characterisation of the mycobacterial T4SS-like/T7SS conjugation system

HENNELL JAMES Rory (.)

. - University Medical Center Hamburg-Eppendorf - Hamburg - GERMANY

MARLOVITS Thomas (Host supervisor)
Bacterial conjugation allows the transfer of genetic material between bacterial strains and is associated with the spread of antibiotic resistance and virulence factors. Recent work has discovered a conjugable plasmid (pRAW) in Mycobacterium marinum and related plasmids that are present in up to 50% of natural Mycobacterium isolates, including the Non-Tuberculosis Mycobacteria which often cause infections in immune-compromised patients. Most bacterial conjugation systems use the Type IV Secretion System (T4SS). pRAW encodes a T4SS-like system and a Type VII Secretion System (T7SS) termed ESX-P1. The T4SS-like gene cluster lacks key genes and transposon mutagenesis experiments showed that both the T4SS-like genes and T7SS genes were required for successful conjugation, suggesting that they function together in conjugation. In this project I will structurally and biochemically characterise the components of these T4SS-like and T7SS secretion systems through three main approaches: cryo-electron tomography of secretion systems in native cells, purification of secretion complexes from native cells for biochemical and cryoEM analysis, purification of recombinant secretion complexes from Mycobacterium smegmatis. This work will be carried out in the Marlovits laboratory, where there is expertise in structural biology in collaboration with the Bitter laboratory, where there is expertise in genetics of mycobacteria. Structural and biochemical studies of this complex will enhance our understanding of a fundamental biological process which may contribute to the spread of antibiotic resistance and virulence factors in bacteria that cause a significant disease burden worldwide.
2022 -
Long-Term Fellowships - LTF

Cell-specific functional connectivity of cerebellar outputs for locomotor learning

HERENT Coralie (.)

. - Champalimaud Foundation (Fundação D. Anna de Sommer Champalimaud e Dr. Carlos Montez Champalimaud) - Lisbon - PORTUGAL

CAREY Megan (Host supervisor)
We constantly navigate a complex world filled with uneven terrains that alter our walking pattern. Learning to correct for predictable errors in a changing environment is crucial for smooth and coordinated locomotion. A striking example is the adaptability of locomotor patterns upon exposure to a split-belt treadmill, where opposite limbs move at different speeds. The host laboratory previously showed that mouse, like human, locomotor learning depends critically on the cerebellum and specifically, on neurons projecting to the cerebellar interposed nucleus (IP). Importantly, spatial and temporal components of learning (location and timing of paw placement) proceeded independently, suggesting that they might be dissociable at the circuit level. This proposal aims to identify and characterize the functional connectivity of cerebellar output circuits conveying corrective calibration signals that modify ongoing locomotor movements in space and time. Specifically, we will: 1) Use cutting-edge viral tools to map output circuits downstream of the IP and identify key candidates for spatiotemporal calibration signals; 2) Use high-resolution quantitative behavioral analysis and circuit manipulation to test specific functional roles of projection-defined subsets of IP neurons in locomotor learning; 3) Use optogenetically-guided multi-probe recordings of projection-specific IP neurons during learning to understand how the cerebellum transforms locomotor errors into spatiotemporal calibration of locomotor movements. Overall, this work will reveal unprecedented insights into neural circuits ensuring the adaptability of motor commands, directly relevant for human rehabilitative therapy.
2022 -
Long-Term Fellowships - LTF

Evolutionary, expression, and functional characterization of ancient putative chemosensors

HIMMEL Nathaniel (.)

. - University of Lausanne - Lausanne - SWITZERLAND

BENTON Richard (Host supervisor)
Ligand-gated ion channels (e.g. TRPs, IRs/iGluRs) are critical in animal sensory systems to link recognition of external and internal cues to changes in physiology and behavior. Growing evidence indicates that many of these channel families have origins in the last common eukaryotic ancestor (~2 billion years ago), but their functions outside of Metazoa are poorly understood. Recently, homologs of insect chemosensory receptors (“Gustatory Receptor-like”, GRL) were identified by the host lab in several unicellular species, including chytrid fungi, protists, and alga, many of which are motile and are capable of chemotaxis, leading us to hypothesize that these putative channels function in external stimulus-guided behavioral or physiological responses. I propose to characterize ligand-gated ion channels in these understudied taxa, via three aims: (1) Bioinformatically identify and phylogenetically assess all animal ligand-gated ion channel family homologs across unicellular Eukaryota; (2) Determine channel expression and localization (starting with GRLs) across life stages of select unicellular taxa through RNA-sequencing and immunofluorescence; (3) Determine protein biochemical and functional properties both in vitro (through heterologous cell expression) and in vivo, starting with the chytrid Spizellomyces punctatus GRL1, capitalizing on new genetic tools for this species. My studies will expand our understanding of channel evolution and function across taxa, and potentially reveal molecular mechanisms of sensory-guided behavior and physiology in unicellular eukaryotes, offering insights into the early evolution of chemosensation.
2022 -
Grant Awardees - Program

Molecular determinants of evolutionary conservation in disordered protein regions

HOLEHOUSE Alex (UK)

Dept. of Biochemistry and Molecular Biophysics - Washington University School of Medicine - St. Louis - USA

LEE Hyun (KOREA, REPUBLIC OF (SOUTH KOREA))

Biochemistry - University of Toronto - Toronto - CANADA

WEIJERS Dolf (NETHERLANDS)

Laboratory of Biochemistry - Wageningen University - Wageningen - NETHERLANDS

Intrinsically disordered regions (IDRs) are a ubiquitous class of protein domains found in the majority of eukaryotic proteins. Unlike folded regions, IDRs exist in a conformationally heterogeneous collection of states and lack a single canonical structure. IDRs play essential roles in a wide variety of cellular processes, from the immune response to transcriptional regulation to cell division. Despite their prevalence and crucial cellular roles, our understanding of how IDRs work and what they do in any given context is still in its infancy. Understanding a protein’s function is analogous to understanding that protein’s evolutionary constraints. Evolutionarily significant features are by definition important for protein function, either directly (i.e., catalytic residues in enzymes) or indirectly (i.e., protein stability in folded domains). Given our limited understanding of protein function, it should be of no surprise that our understanding of IDR evolution is also minimal. Rather than a problem, we propose this offers an incredible opportunity to take advantage of evolutionary selection as a design principle that selects for functionally important IDR features. To do this, we require a model system where IDRs are present, essential, and play similar roles across divergent evolutionary organisms. Plant AUXIN RESPONSE transcription FACTORs (ARFs) represent an evolutionarily ancient set of transcription factors that regulate almost every aspect of plant development. ARFs contain folded and well-characterized DNA binding domains, yet most also contain large IDRs that are poorly conserved by any kind of standard alignment-based metric. Importantly, ARF IDRs are critical for normal development. As a result, ARFs offer an unprecedented model to elucidate the determinants of functional selection on IDRs. Our project will integrate molecular biophysics, rational sequence design, and organismal physiology to uncover how changes in ARF IDRs conspire to determine evolutionary fitness.
2022 -
Grant Awardees - Program

Physical regulation of the genome

HOLT Liam (USA)

Dept. of Biochemistry & Molecular Pharmacology, Institute for Systems Genetics - New York University School of Medicine - New York - USA

LEVY Emmanuel (FRANCE)

Dept. of Structural Biology - Weizmann Institute of Science - Rehovot - ISRAEL

TAKINOUE Masahiro (JAPAN)

Department of Computer Science - Tokyo Institute of Technology - Yokohama - JAPAN

Textbook models for biological regulation emphasize active mechanisms of signal transduction and chemical signaling, such as protein phosphorylation. However, cells could also achieve control at a more fundamental level by directly sensing changes to the intracellular physical environment. The cell is highly crowded and far from thermodynamic equilibrium. Molecular crowding decreases molecular motion, and also drives interactions through depletion-attraction. We found that crowding is actively regulated in the cell and can tune phase separation. Active processes increase the effective temperature in the cell, helping to fluidize this extreme environment, and depletion of ATP can lead to glass transitions. Therefore, we hypothesize that the interplay between molecular crowding and active processes plays a global role in determining the rates of biochemical reactions. These effects strongly depend on length-scale, such that each biochemical process can potentially respond differently to physical perturbations depending on the size of molecules involved. Thus, the cell can evolve to increase the rates of some reactions and decrease the rates of others in response to changes in crowding or effective temperature. While appealing, the degree to which changes in the physical environment directly regulate biology has been challenging to test in vivo. Indeed mutation of endogenous molecules that impact the material properties or effective temperature of the nucleus necessarily interfere with host biology, leading to pleiotropic effects and making interpretation impossible. To solve this problem, we will: (i) reconstitute transcription within synthetic DNA nanostructure condensates in vitro (Takinoue lead); (ii) develop analogous protein condensates that anchor to specific DNA loci in vivo (Levy lead); and (iii) leverage large-scale genome engineering (Holt lead) to directly address the hypothesis that transcription can dynamically respond to changes in the physical properties of the environment. More generally, responsiveness of biochemistry to physical regulation could represent a primordial and universal level of regulation. Understanding the principles of physical regulation could help elucidate many unresolved conundrums in biology from cell-size control to mechanobiology and this knowledge would significantly improve our ability to engineer cellular systems.
2022 -
Long-Term Fellowships - LTF

Characterizing how pioneer transcription factors and chromatin structure regulate genome activation

HOPPE Caroline (.)

. - Yale University - New Haven - United States

GIRALDEZ Antonio (Host supervisor)
Zygotic genome activation (ZGA) is a universal step in animal development that involves massive chromatin remodeling and results in priming of cis-regulatory regions and transcriptional activation. In a function conserved across species, pioneer transcription factors (TFs) bind nucleosomal DNA to facilitate opening of regulatory regions to other TFs. In zebrafish, it relies on Nanog, Pou5f3 and SoxB1, yet the specific roles of pioneer TFs and the causal relationship between chromatin architecture and genome activation remain unknown. Further, we lack a holistic understanding of how global chromatin structure is spatially organized and remodeled during genome activation. We will integrate cutting-edge imaging and genomic approaches, including super-resolution, and expansion microscopy to study global chromatin architecture at unprecedented resolution and address these questions at single-cell resolution in zebrafish embryos. We will investigate spatiotemporal behavior of pioneer TF hubs during ZGA, determine interactions of pioneer factors at single molecule resolution and elucidate how promoter-enhancer interactions are modulated in response to pioneer activity. This is a significant shift in both discipline and methodology from my previous research; I will use a new model organism and develop genomic and chromatin probing techniques while leveraging my microscopy expertise, which is a new dimension for the lab. We expect to elucidate the structure/function relationship of chromatin and pioneer factor dynamics, uncover fundamental mechanisms and provide a framework for dynamic chromatin interactions that will be relevant in other contexts.
2022 -
Grant Awardees - Program

Bridging robotics and pollination: Reconstructing a bee’s buzz through micro-robots

JAFFERIS Noah (USA)

Electrical and Computer Engineering - University of Massachusetts Lowell - Lowell - USA

VALLEJO-MARIN Mario (MEXICO)

Dept. of Ecology and Genetics - University of Uppsala - Uppsala - SWEDEN

Bees provide essential services for pollination of both wild and agricultural systems, yet many wild bee populations are currently under threat. There are more than 20,000 species of bees worldwide and understanding how their morphological and ecological diversity translates to variation in function is of timely and urgent importance. Our project leverages a novel implementation of micro-robotics across a multispecies comparison of bees in two continents to disentangle the mechanistic function of buzz pollination, a type of pollination in which bees use powerful vibrations to shake pollen out of flowers. Approximately half of the 20,000 species of bees are thought to be able to buzz pollinate flowers of both wild and agricultural plants (e.g., tomato). These bees encompass an impressive range of morphological diversity, from sweat bees with body sizes of a few tens of milligrams in weight to large bumblebees and massive carpenter bees an order of magnitude heavier. Progress in the study of buzz pollination has been limited by the technical capacity to apply vibrations to flowers in a bee-like manner due to the reliance on large, cumbersome table shakers to mimic bee vibrations. Our project is set apart from previous work by using micro-robotic buzzers designed to capture the main properties of bee pollination buzzes using bee-scale vibrating and grasping mechanisms developed as part of the proposed work. This new approach will allow us to synthesise and apply vibrations capturing the diversity of buzzes produced by evolutionarily diverse types of bees sampled in the UK and North America. We will also investigate how these variations in the vibrations produced by the micro-robotic buzzers determine pollen release from buzz pollinated flowers, allowing us to link bee diversity, mechanical and vibrational properties, and pollen release function. Our project is built upon an international collaboration that brings together expertise in robotics and bee pollination to pursue a multidisciplinary use of micro-robotics for studying the functional diversity in a type of pollination involving thousands of bee and plant species around the world.