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2019 -
Long-Term Fellowships - LTF

Regulating mammalian mitochondrial homeostasis

GUNA Alina-Ioana (CANADA)

Department of Cellular and Molecular Pharmacology - UC San Francisco - San Francisco - USA

WEISSMAN Jonathan (Host supervisor)

Mitochondria are dynamic, multifunctional organelles that are a defining feature of eukaryotic cells. Maintaining mitochondrial homeostasis is essential for normal cellular and organismal physiology. Mammalian cells have roughly ~1,500 mitochondrial proteins, however the vast majority are encoded in the nuclear genome. Therefore, in response to stress, mitochondria must signal their internal states to the nucleus, which can mount a compensatory transcriptional response. Despite the fundamental importance of mitochondrial regulation, the full range of perturbations that disrupt homeostasis, the subsequent signalling cascades and the resultant nuclear responses remain poorly defined in higher eukaryotes. One consequence of mitochondrial stress is the activation of the integrated stress response (ISR), though the mechanism of this remains obscure. I propose to address these aspects of mitochondrial homeostasis in human cells using complementary genetic and biochemical strategies. i) First, I will use a CRISPRi screen to identify factors involved in activation of the ISR. ii) I will use Perturb-seq technology to objectively and systematically establish the full spectrum of stress induced transcriptional responses needed to maintain mitochondrial homeostasis. I will then use the approaches in (i) to explore the exact mechanism for key responses. iii) Finally, I will dissect the role of a new factor TMA7, identified through a previous genetic screen aimed at uncovering genes that sensitize mitochondria to proteotoxic stress. In all cases, the ultimate goal is to delve into the biochemical mechanism of how promising hits are involved in maintaining mitochondrial homeostasis.

2019 -
Long-Term Fellowships - LTF

A forward systems biology approach to investigate the origins and fitness effects of de novo proteins


Département de Biologie - Institut de Biologie Intégrative et des Systèmes - Québec - CANADA

LANDRY Christian (Host supervisor)

Proteins emerging from previously non-coding DNA regions are becoming increasingly appreciated as an important path to creating completely novel functions. However, their path of emergence is very poorly characterized. Comparative genomics studies are finding numerous genes that have emerged from non-coding sequences, providing deep insight into gene evolution. However, these studies provide no insight into the transition from non-coding to coding because these genes have already been shaped by selection. For instance, de novo gene emergence could be frequent but mostly deleterious, or rare but mostly advantageous. In our project, we propose to go beyond classical comparative genomics and force novel proteins to emerge to measure their fitness effects and biochemical properties, and establish the relationship between the two. We will measure the fitness effect of these proteins, confirm their existence and localization, as well as their propensity to interact with other proteins. We will identify protein properties such as length and intrinsic disorder that define the fitness effects and thus the likelihood for a novel protein to emerge. Because many of these biochemical properties are largely defined by nucleotide sequences, our findings will lead to models that directly link de novo gene sequences to fitness effects, allowing us to model gene emergence from sequence composition alone. This will be the first project that is poised to answer the major question of how novel proteins can emerge from previously non-coding sequences.

2019 -
Grant Awardees - Program Grants

In vitro reconstitution of synaptic plasticity: a minimalist approach


Dept. of Pharmacology - Graduate School of Medicine - Kyoto - JAPAN


Division of Life Science - Hong Kong University of Science and Technology - Kowloon - HONG KONG, CHINA


Dept. of Molecular Structural Biology - Max Planck Institute of Biochemistry - Martinsried - GERMANY

Neuronal circuits store information through the mechanism of synaptic plasticity, a process where synaptic transmission is strengthened or weakened. Long-term potentiation (LTP) is a major form of synaptic plasticity. It requires both activation of CaMKII and subsequent trafficking of receptors and other proteins to the postsynaptic site. Despite extensive research, the causative relationship linking these two processes is still unknown. Here, Hayashi (live imaging and electrophysiology), Zhang (structure biology), and Lucic (cryoelectron tomography) will team up and take a unique minimalist approach to reconstitute synaptic plasticity from purified proteins. We will reconstitute postsynaptic density (reconstituted PSD or rPSD) on a glass substrate using a group of key scaffold proteins (PSD-95, SynGAP, SAPAP, Shank, and Homer) and receptor such as NR2B. Once a key process is found in minimal system, we will test if the same mechanisms work in intact neurons. Finally, we will investigate the persistent modification of the rPSD induced by the activation of CaMKII, which is expected to act as a hub for trafficking of various proteins. The network organization of the resulting complexes in vitro and in situ will be determined by cryo-electron tomography. The final goal of this proposal is to understand the minimum essential machinery for activity dependent delivery of postsynaptic proteins.

2019 -
Grant Awardees - Young Investigator Grants

Exploration of the structure/function space of prebiotic to biological proteins


Dept. of Biochemistry - Faculty of Science - Prague - CZECH REPUBLIC


Earth-Life Science Institute - Tokyo Institute of Technology - Tokyo - JAPAN

FRIED Stephen (USA)

Dept. of Chemistry - John Hopkins University - Baltimore - USA

Proteins have evolved to adopt many structures and perform diverse functions by exploring a sequence space spanned by twenty canonical amino acids (AAs). Whilst ten of the AAs were ‘obvious’ choices, as they abounded in the prebiotic world, the other ten were far less accessible prebiotically, thus provoking the question: Why (and how) were these AAs included in the genetic code, and was their inclusion prerequisite for protein evolution to be as successful as it has been? These seeming Gedankenexperiments are directly testable using an interdisciplinary approach we have devised.
Specifically, we propose to synthesize random protein libraries built from reduced (evolutionarily early) and alternative AA alphabets to compare the structure/function-forming potential of the proteinogenic and non-canonical yet prebiotically abundant AAs. The team of Stephen Fried will customize both commercial and home-made cell-free protein translation systems to express protein libraries composed of alternative AA alphabets. The team of Klara Hlouchova will use biophysical approaches to explore the structure-forming potential of the purified libraries. The capacity of the libraries to evince prebiotically-relevant functions will be assessed by the group of Kosuke Fujishima through selections that can relate genotype to phenotype (e.g., mRNA-display). Large sequence space (>10^12) will be analyzed in each experiment and because the same template libraries will be used, the outcomes of both the structural and functional studies will be directly comparable. This would not be possible without coordinated collaboration among the three teams.
Each team member enters the project with a key set of skills and scientific expertise. Klara and her team have a strong background in protein biochemistry, bioinformatics and experience with expression of protein libraries. Kosuke is an astrobiologist with strong experience in RNA molecular biology and his team takes a synthetic biology approach to studying peptide-RNA interactions. Stephen has experience in biophysics and synthetic biology and his newly started lab performs research in protein folding and engineering. This project relies on synergy of the above mentioned disciplines connected by our mutual interest in the origins of life, making it possible to address a broad fundamental biological question in a systematic way.

2019 -
Cross Disciplinary Fellowships - CDF

Deep-tissue voltage imaging in the intact mouse brain


Applied and Engineering Physics - Cornell University - Ithaca - USA

XU Chris (Host supervisor)

Understanding the cellular and molecular mechanisms on memory formation is one of the most important topics in life science and will be highly effective for development of remedies of memory disorders such as Alzheimer’s diseases and dementia. The modification mechanism of the neural network in the brain is a key factor for memory formation, but its understanding is not sufficient yet. The main reason is that direct observation of the neural network modification during memory formation in intact animal brains is still very difficult today. Voltage imaging, which enables direct observation of membrane potential, is a powerful technique for visualization of neural activities ex vivo. In contrast, in vivo voltage imaging in intact mouse brain is highly challenging despite the importance. The difficulty is derived mainly from the following requirements; (i) high signal-to-background ratio in the deep brain of the intact mouse, and (ii) high temporal resolution (<5 ms) for the voltage imaging. In the proposed study, three-photon excitation with near-infrared femtosecond laser will be applied to achieve the condition (i). Three-photon excitation is highly effective because NIR (1300-1700 nm) shows very low scattering from tissues, thus high signal-to-background ratio will be attained. To achieve (ii), an adaptive femtosecond laser source will be applied, making the laser light irradiated only to the regions of interest. The proposed in vivo voltage imaging will be applied to monitor neural network modification in the intact mouse brain during memory formation.

2019 -
Long-Term Fellowships - LTF

Mechanisms underlying distortions in the neural code induced by sensorineural hearing loss


Ear Institute - University College London - London - UK

LESICA Nicholas (Host supervisor)

Hearing loss, ranging from mild to severe, is a detrimental condition linked to decreases in quality of life for those affected. The causes of hearing loss have been extensively studied previously, and few options are available in rescuing hearing loss. Hearing aids have become the standard for treating hearing loss; however, they have only been partially successful due to their limitations when processing sounds in noisy environments. This is due to the fact that hearing loss causes complex distortions in neural activity patterns of the auditory system, which are not fully understood to date. The aim of this project is to identify key features of the neural code for speech that are distorted by hearing loss, and as a result, be able to assess the ability of current hearing aids to correct these distortions. Using recent developments in technology, we will use custom designed multi-channel electrodes to perform large-scale recordings in the inferior colliculus (IC) of the Mongolian gerbil. We will perform these recordings in both anaesthetized as well as awake-behaving gerbils under control and induced hearing loss conditions. We will then assess the neural activity patterns of IC neurons and determine the key distortions caused by hearing loss under differential stimulus conditions mimicking noisy situations. Standard analysis of coherence of speech information will be assessed to understand to what extent certain sounds become distorted under hearing loss. The results of this study will reveal novel insights into how hearing loss creates distortions in the neural code along the auditory pathway, and provide ideas for the efficacy of current and future hearing aids.

2019 -
Grant Awardees - Young Investigator Grants

Evolutionary changes in human hosts and their pathogens during first contact in the New World


Dept. of of Ecology and Evolutionary Biology - Brown University - Providence - USA


Laboratoire de Recherche en Informatique (LRI) - CNRS UMR8623 - Orsay - FRANCE


International Laboratory for Human Genome Research - National Autonomous University of Mexico - Querétaro - MEXICO

In this project we will uncover the evolutionary dynamics in both humans and pathogens in response to epidemics. Recent technology advances enable detection of infectious agents in ancient DNA (aDNA) samples that tie to major historical epidemics. However, we know practically nothing about the dynamic process by which genetic adaptation occurs simultaneously in both the host and pathogen as a consequence of epidemic outbreaks.
We propose to integrate aDNA and sophisticated computational approaches to investigate the selective pressures imposed by the introduction of new pathogens during European colonization of the Americas. Our goals are to characterize the changes in both pathogen and human genetic diversity before and after European colonization to describe: 1) the genetic signatures that were putatively responsible for decimating the Native population, and 2) the selective and demographic processes that conferred adaptation to the colonization environment, especially with respect to pathogen exposure. To this end we will sequence the genomes of at least 30 individuals from before and immediately after colonization, and for the Colonial period we have access to archaeological remains of individuals who were likely victims of epidemics. We will also leverage the metagenomic data produced when sequencing aDNA and quantify the pathogen genetic diversity present in these samples before and after colonization. Lastly, we will use novel statistical methods to identify loci in post-colonization samples that depart from expected proportions of Native American, European or African ancestry to test whether admixture facilitated adaptation.
Our study will leverage temporal genomic data to address a long-standing question of how pathogens have influenced human evolution. As we lack studies quantifying jointly the changes in both pathogen and human diversity across time, this project offers a unique opportunity to directly assess, for the first time, how much evolutionary pressure is experienced within a human population when encountering new pathogens. Our design integrates novel paleogenomics approaches and cutting-edge methods development to leverage longitudinal sequence data of both ancient host and ancient pathogen sequence data to address coevolution with a temporal resolution that has not previously been reached.

2019 -
Grant Awardees - Program Grants

Phase separation of glycolytic machinery as a fundamental mechanism in energy metabolism

HYMAN Anthony (UK)

Dept. of Cell division - Max Planck Institute of Molecular Cell Biology and Genetics - Dresden - GERMANY


Dept. of Cell Biology; Program in Cellular Neuroscience, Neurodegeneration and Repair - Yale School of Medicine - New Haven - USA

Glycolysis is a fundamental energy metabolic pathway which consists of ten enzymatic steps. Unlike the mitochondrion, which is a membrane-bound organelle, glycolytic enzymes are soluble proteins in the cytosol. Based on biochemical evidence, glycolytic enzymes have long been hypothesized to form functional complexes to sustain the rates of glycolysis. This purported complex, called the glycolytic metabolon, was a subject of intense study and debate thirty years ago. Still today we do not yet understand how these purported complexes are organized in cells to sustain local energy metabolism, or their physiological importance. This gap in knowledge results from the fact that when glycolysis was being rigorously examined forty years ago, the techniques did not exist to conclusively answer these questions. The main challenge in addressing these questions lay then, as now, in the ability to both examine the localization of the glycolytic enzymes in living cells, while understanding the biophysical and biochemical mechanisms of their association, and its implications in cellular physiology. We have established a collaboration to address these fundamental questions by making use of our joint expertise in vitro reconstitution and C.elegans physiology, using the energy demands of the C.elegans synapse as a model system.

2019 -
Grant Awardees - Program Grants

Synthetic biocompounds to direct neuronal circuit assembly


Dept. of Basic Neuroscience - University of Geneva - Geneva - SWITZERLAND

LIM Wendell (USA)

Dept. of Cellular and Molecular Pharmacology - University of California, San Francisco - San Francisco - USA

The cerebral cortex is composed of distinct subtypes of neurons organized in circuits allowing high-order functions such as integration of sensory stimuli and sensorimotor transformations. These different neuronal subtypes are connected with neurons located both within and outside of the cortex. Intracortical connectivity is mostly mediated by layer (L) 2/3 neurons, which form synapses with other cortical neurons within and across areas; instead neurons located in L5B project to sub-cerebral targets and are responsible for cortical output.
While the molecular diversity of cortical neurons and their circuit organization is increasingly understood, it is still difficult to genetically manipulate cortical neurons based on which circuits they belong to; the ability to do so would, however, be a critical skill to repair circuits when they are affected by injuries or neurodegenerative diseases. To address this challenge, here we combine our expertise in developmental neurobiology (DJ) and in bioengineering (WL) to develop a strategy to manipulate gene expression in cortical neurons in a circuit-dependent manner. We do so by engineering artificial synaptic contact-dependent signaling cascades to drive new cellular features.
Specifically, we will:
1. Assess the in vitro molecular identity and connectivity of pure populations of L2/3 and L5B cortical neuronal types and manipulate these cellular features by direct reprogramming of L2/3 neurons into L5B neurons (Aim 1).
2. Manipulate gene expression and cellular features of L2/3 neurons in vitro in a synaptic-contact dependent manner by developing a synaptic version of the synthetic notch (synNotch) receptor system (synsynNotch) (Aim 2).
3. Manipulate axonal projections of specific populations of intracortically-projecting neurons in vivo using the synsynNotch system (Aim 3).
Together, these experiments will increase our understanding of the mechanisms controlling cell-type specific circuit assembly and allow us to functionally interrogate this process through circuit-specific manipulation of gene expression.

2019 -
Long-Term Fellowships - LTF

Investigating the role of transposable elements in 3D genome organisation in vivo


Institute of Epigenetics and Stem Cells - Helmholtz Zentrum München - München - GERMANY

TORRES-PADILLA Maria Elena (Host supervisor)

After fertilisation in the early embryo, the epigenetic reprogramming of heterochromatin is thought to be necessary for development. Notwithstanding, the mechanisms driving the de novo formation of heterochromatin are unclear. In somatic cells, transposable elements (TE) are largely heterochromatic and transcriptionally inert. However in the pre-implantation embryo many TE families are highly expressed. Recently, the expression of several TE families has been shown to be necessary for development. However, how TEs drive the developmental program mechanistically is unknown. I propose that their expression is essential for the establishment of heterochromatin, through the formation of long-range chromatin interactions during development. To address this hypothesis, I will establish a targeted DAM-ID protocol to map the genome-wide long-range DNA interactions formed by TE families in vivo, dynamically throughout development. I will develop novel technologies to analyse their chromatin composition and nuclear organisation to uncover the relationship between TE organisation and the establishment of heterochromatin and higher order chromatin structures. To determine the function of TE expression in development, I will perturb their expression and chromatin composition and investigate the ensuing effect on their higher-order organisation, nuclear localisation, and more broadly on heterochromatin formation and development. Finally, I will use the datasets generated in this study to generate a comprehensive model on the mechanisms driving higher order chromatin formation at TEs, and how they influence the local and higher order chromatin architecture in development.

2019 -
Long-Term Fellowships - LTF

Dissecting functional long non-coding RNAs and their working mechanisms


Department of Pathology - Stanford University - Stanford - USA

FIRE Andrew z. (Host supervisor)

It has been well established that eukaryotic genomes produce thousands of short and long non-coding RNAs. Many studies have uncovered the biosynthesis, processing, and functions of small non-coding RNAs. However, whether long non-coding RNAs (lncRNAs) are functional molecules or not has not been clear. Although supporting evidence of functional lncRNAs have been accumulated for the last decade, the working mechanisms of functional lncRNAs are still largely unknown. In this proposal, I aim to 1) identify functional lncRNAs in C. elegans by performing in-depth phenotyping with a large collection of lncRNA knockout mutants, and 2) characterize working mechanisms of the functional lncRNAs by using unbiased genetic and biochemical screen approaches. This study will help unveil mechanisms by which lncRNAs exert functions, and provide insights into how and why eukaryotic genomes contain a large number of the non-coding genetic elements that produce lncRNAs.

2019 -
Grant Awardees - Program Grants

Single-molecule protein sequencing


Dept. of BioNanoScience - Kavli Institute of NanoScience - Delft University of Technology - Delft - NETHERLANDS


Dept. of Physics - Ewha Womans University - Seoul - KOREA, REPUBLIC OF (SOUTH KOREA)

Protein sequencing remains a challenge for small samples. A sensitive sequencing technology will create the opportunity for single-cell proteomics and real-time screening for on-site medical diagnostics. We will use our expertise of single-molecule protein detection and material sciences to develop novel sequencing tools. In particular, we will use graphene mass sensors to measure the mass of proteins with sub-Dalton sensitivity. Utilizing this high sensitivity, we will measure the mass of protein fragments and identify the sequence of the fragments. We will also apply this method for detecting post-translational modifications of single proteins. Ultimately we aim to achieve sequencing of full-length proteins. This proof of concept will open the door to single-molecule protein sequencing and pave the road toward the development of a new, fast, and reliable diagnostic tool.

2019 -
Long-Term Fellowships - LTF

Mechanistic investigation into the driving forces of sensorimotor learning in the visual cortex

JORDAN Rebecca (UK)

Department of Neurobiology - FMI Basel - Basel - SWITZERLAND

KELLER Georg (Host supervisor)

How our brain learns the relationships between movements and the associated sensory feedback is an important question facing neuroscience. Since such sensorimotor relationships are subject to change, sensorimotor learning is crucial for the development of flexible sensory-guided behaviours. One elegant potential solution to this problem would be that the brain generates an internal model of the world that is used to make predictions about the sensory feedback given a certain motor output. Discrepancies between predicted and actual feedback could then be represented as prediction errors, which in turn could be used to update the internal model used to make the predictions. Recent experiments in which sensory feedback was manipulated during movement have revealed neural responses consistent with prediction errors in primary sensory areas of cortex. In primary visual cortex, these responses have been shown to depend on the precise tuning between visual and motor input that is learned with experience. However, both the mechanisms underlying this learning, and the effect of the error-like responses are unknown. In this project, I propose experiments employing a range of techniques, including calcium imaging, in vivo whole cell patching, and optogenetics in order to investigate the driving forces of sensorimotor learning. I will manipulate the activity of single cells in the visual cortex and probe neuromodulatory plasticity signals during visuomotor learning. This will provide a fundamental mechanistic insight into how sensorimotor learning takes place.

2019 -
Long-Term Fellowships - LTF

Explaining evolutionary divergences in epithelial morphogenesis through cell biological innovations


Centre for Organismal Studies - University of Heidelberg - Heidelberg - GERMANY

LEMKE Steffen (Host supervisor)

During early embryonic morphogenesis, naïve epithelia undergo structural changes like bending, folding, stretching, convergent-extension, growth, or even epithelial-to-mesenchymal transitions. Various species show evolutionary divergences in these morphogenetic processes. I propose that such differences in epithelial morphogenesis depend, in part, on physical parameters like tissue area, cell packing, cell aspect ratio, and the pliability of mechanical connectivity between cells. In fly embryos, the blastoderm epithelium undergoes morphogenesis after being defined from a zygote syncytium, in a process called cellularization. The process of cellularization is well described, very stereotypical, and the genetic and molecular players establishing basic cellular properties are known in Drosophila.

I will take advantage of natural diversity that accumulated over 250 million years of fly evolution and resulted in highly different blastoderm epithelia that vary substantially in tissue area, cell packing and cell aspect ratio. The host lab maintains lab cultures for 10+ fly species, including mosquito-related midges and moth flies, scuttle and hover flies, and various drosophilid species, which collectively sample a broad range of natural diversity in the insect order. I propose to compare cell properties and tissue morphogenetic behavior of the embryonic blastoderm in these species, with the aim to identify key genetic innovations underlying the origin of novel tissue properties and divergence in morphogenesis. I will further test how the introduction of these novel genetic elements into more rudimentary systems consequently changes cell properties and epithelial morphogenesis.

2019 -
Long-Term Fellowships - LTF

Mechanistic and structural studies of the RNA m6A writer machinery


Department of Biochemistry - University of Zurich - Zurich - SWITZERLAND

JINEK Martin (Host supervisor)

Post-transcriptional mRNA modifications have emerged as important mechanisms in eukaryotic gene expression control. The most abundant epitranscriptomic mark, N6-adenosine methylation (m6A), affects the processing, translation, and degradation of mRNAs and thus is involved in diverse biological processes including stem cell self-renewal, sex determination, and immunity. Uncovering the m6A molecular mechanisms is crucial to understand its function in gene regulation and shed light on its implicated roles in cancers and psychiatric disorders. Numerous studies have revealed the cellular m6A landscape, defined by writer and eraser enzymes and interpreted by reader proteins. Nevertheless, specific aspects of the m6A pathway, including how mRNAs are chosen for methylation, are not fully understood. Although the m6A mark occurs within a consensus sequence, not all such sites are modified in the transcriptome. It is unclear how the core METTL3/METTL14 methyltransferase complex recognizes its RNA substrates and how additional factors, such as the recently identified MACOM complex, contribute to this mechanism. To address these questions, the proposed research will aim to: (i) characterise the substrate RNA recognition mechanism of the METTL3/METTL14 complex, (ii) define the molecular architecture of the MACOM complex, and (iii) determine the structural and functional links between METTL3/METTL14 and additional m6A writer factors. To achieve these goals, I will combine structural biology with biochemical, biophysical, and functional cell-based assays. Together, these studies will provide fundamental insights into the molecular mechanisms of m6A in epitranscriptomic gene regulation.

2019 -
Grant Awardees - Program Grants

Tracking trade across symbiotic networks


Institute of Ecological Science - Faculty of Earth and Life Sciences - Amsterdam - NETHERLANDS

STONE Howard A. (USA)

Dept. of Mechanical and Aerospace Engineering - Complex Fluids Group - Princeton - USA


Dept. of Living Matter - AMOLF Institute - Amsterdam - NETHERLANDS

TOJU Hirokazu (JAPAN)

Center for Ecological Research - Kyoto University - Shiga - JAPAN

The world is characterized by an unequal distribution of resources. To cope, many organisms evolve symbiotic trade partnerships to exchange commodities they can provide at low cost, for resources more difficult to access. Such trade partnerships allow species to colonize extreme environments and survive resource fluctuations. While the ubiquity and importance of trade partnerships has been established, we do not understand the chemical, physical, and environmental stimuli mediating trade strategies, nor how organisms integrate this information to execute trade ‘decisions’. This is largely because of the lack of tools to quantify symbiotic trade across space and time.
Combining biophysics, fluid mechanics, network theory and evolution, we will develop techniques to track, quantify and predict trade strategies in symbiotic networks formed between plants and their arbuscular mycorrhizal fungal partners – a globally ubiquitous trade partnership fundamental to all terrestrial ecosystems. By visually monitoring the trade of nutrients tagged with fluorescent quantum-dot nanoparticles across scales - from within individual fungal hyphae up to complex plant-fungal networks - we will ask: (1) how do oscillatory flow patterns within fungal networks act to regulate fungal trade decisions; (2) can the fungus manipulate its chemistry and physical architecture to maximize nutrient transport and trade benefits; (3) can trade strategies be predicted by environmental stimuli; (4) what is the influence of the external microbiome on trade behaviors.
Using high-resolution video to track fluorescently tagged nutrients within hyphae, we will be the first to test how the fungal symbiont regulates internal flows to mediate trade. We will develop 2D and 3D time-lapse imaging of network topologies to test the factors driving the optimization of fungal transport routes. We will use transformed in-vitro root systems with precisely controlled nutrient landscapes to correlate specific trade strategies with environmental conditions. We will push the frontiers of tracking trade in whole plant mesocosms by growing plant-fungal networks on transparent farming film, characterizing how synthetic microbiomes affect trade strategies. By integrating the state of the art in imaging, fluid mechanics, and ecological manipulations, we will achieve a quantitative and predictive understanding of organismal trade.

2019 -
Long-Term Fellowships - LTF

Unraveling an interdependency between metabolic cluster for the homeostasis of cellular ATP and Pi


Department of Biochemistry - University of Lausanne - Epalinges - SWITZERLAND

MAYER Andreas (Host supervisor)

Cells face a phosphate challenge. Growth requires a minimal concentration of this limiting resource because intracellular phosphate (Pi) is a compound of nucleic acids modifies most cellular proteins, and is crucial to maintain the cellular ATP/ADP balance. At the same time, cytosolic Pi may not rise much, because elevated cytosolic Pi can stall metabolism. It reduces the free energy that nucleotide triphosphate hydrolysis can provide to drive energetically unfavorable reactions. Cells should hence coordinate their systems for uptake, export and storage of Pi in order to strike the delicate balance between the biosynthetic requirements for Pi and the risks of elevated cytoplasmic Pi. Exploring the signaling mechanisms that guarantee Pi homeostasis is challenging, because intracellular Pi is tightly linked to other metabolites: ATP/ADP, inositol pyrophosphates, and inorganic polyphosphate. These four metabolite classes influence each other's concentrations. I want to dissect this apparently conserved "metabolic cluster" and render the signaling pathways that regulate it accessible. To this end, I will create tools and methods to uncouple these parameters and fix one or several of them to an invariant value. This will allow me to "isolate" the signaling pathways responsible for the homeostasis of these essential parameters and possibly elucidate novel regulatory loops of Pi and energy metabolism.

2019 -
Long-Term Fellowships - LTF

Dissecting the role of intestinal lymphatics in bacteria-derived metabolite transport and signaling


Department of Fundamental Oncology - University of Lausanne - Lausanne - SWITZERLAND

PETROVA Tatiana (Host supervisor)

The gut is a dynamic and complex organ characterized by constant epithelium turnover and crosstalk among various cell types and the microbiota, the ecological community of commensal and, sometimes, pathogenic microorganisms. Changes in the composition of the gut microbiota have been connected to multiple aspects of host physiology and human disease, however relatively few microbe-host interactions have been defined at the level of molecular mechanisms. Here I propose to investigate the role of intestinal lymphatic vasculature in bacteria-derived metabolite transport and signaling. Intestine is richly supplied by lymphatic vessels. Known functions of lymphatic vessels of the gut include dietary fat absorption and transport of immune cells and dietary antigens to regulate tolerance or immune responses. To date, nothing is known about the microbiota-derived metabolites transported by intestinal lymph flow through lymphatic vessels and the role of those metabolites in body homeostasis. My main goal will be to use unbiased metabolomics and other systems biology approaches in combination with genetic animal models to characterize lymph bacteria-derived and host metabolomes and to establish an impact of extrinsic or intrinsic factors such as diet and lymphatic function on production and distribution of such metabolites in the body. I anticipate that the project will uncover previously unknown roles of intestinal lymphatic vasculature and bacterial metabolite signaling in specific target cell populations.

2019 -
Long-Term Fellowships - LTF

Spatio-molecular dissection of the tumor microenvironment


Department of Biology - Broad Institute of MIT and Harvard - Cambridge - USA

REGEV Aviv (Host supervisor)

During the past decade, the tumor microenvironment and in particular its immune cell compartment have moved into the focus of cancer research, offering promising therapeutic opportunities. However, therapeutic approaches targeting the tumor microenvironment, including the highly promising field of immunotherapy, struggle with widespread tumor heterogeneity. To further our understanding of tumor biology and ultimately improve treatment, we need to assess the tumor microenvironment in its complexity and recognize all the different cellular and extra-cellular components as well as their interactions and spatial relations. To this end, I will connect two powerful single-cell technologies, DroNc-seq (providing genomic scale cellular resolution) and MERFISH (providing spatial tissue organization), to create high resolution, spatio-molecular maps of the tumor microenvironment in two tumor types with different etiologies (colon cancer & melanoma). These maps will allow the study of cellular, and by inference, extra-cellular components as well as their physical and effectual interactions, creating an integrated, quantitative image of the tumor microenvironment. Finally, I will apply machine-learning techniques to extract features predictive for different states of the immune cell compartment and establish their relevance through integration with clinical data.

2019 -
Career Development Awards

Exploiting exosome biology to design polyvalent targeting strategies for in situ cell programming


Department of Biomedical Engineering - The University of Tokyo - Tokyo - JAPAN

Engineered mammalian cells have huge potential for next-generation medicine, but their use requires isolation and ex-vivo engineering of patients’ cells with sophisticated biotech instruments, as well as laborious quality checks. One possible approach to address this issue would be selective in situ cellular programming in vivo, but current modalities for gene delivery (e.g. viruses) involve risks due to insufficiently tight specificity and potential safety issues. The aim of my proposal is to apply a “focused discovery” approach to the basic biology of exosomes, which are highly biocompatible, cell-derived nanovesicles, using a range of synthetic/chemical biology tools to identify key control functions in exosomes and receiver cells. Then I will utilize this information to extract design principles for engineering polyvalent targeting layers to deliver exosome cargo to a cell type of interest with extremely high specificity without toxicities, thus enabling in situ cell programming. Specifically, I propose the following three sub-projects. 1. High-throughput exploration of effector proteins that efficiently direct exosomes to target cells in vivo. 2. Discovery of factors in exosome receiver cells that promote exosome uptake. 3. Creation of engineering/loading principles for cell-classifying exosome cargos. The combination of these different targeting layers (polyvalent targeting) should ultimately make it possible to use exosomes to program any desired type of target cells in vivo. This work should contribute to a better understanding of exosome biology, and provide a basis for developing new therapeutic strategies, e.g., for cancer and genetic/metabolic disorders.