The Personalized, Regenerative Medicine of the future will rely on being able to make replacement cells and tissues of choice at will and in a robust, predictive manner. However, key challenges have to be overcome before the promise of personalized stem cell therapeutics becomes a reality. This is because stem cell renewal/differentiation are stochastic processes, precluding the differentiation of a stem cell population into a homogeneously differentiated desired cell type, but also leading to spurious differentiation during renewal. This is thought to partly arise from heterogeneous single-cell signaling states among different cells of a population, which are not measurable using classical ‘population-average’ biochemical methods. A mechanistic understanding of how dynamic signaling processes control differentiation/renewal fates at the single-cell level might therefore significantly improve our capacity to robustly and precisely manipulate cell fates for tissue engineering purposes. We propose to use an integrated interdisciplinary strategy to map the dynamic, single-cell signaling programs that control differentiation/renewal using human Pluripotent Stem Cell (hPSC) differentiation into neural stem cells as a differentiation paradigm. Using multiplexed, genetically-encoded biosensors, we will quantitate hPSC single-cell dynamic signaling states by large-scale, multi-color, multi-day timelapse microscopy across millions of cells, to reveal with unparalleled precision how heterogeneous signaling states correlate with renewal/differentiation fates. Using computer vision approaches, we will automatically segment, track and lineage at scale each of the cells that were induced to self-renew or differentiate, and we will extract a panel of signaling, cell-cycle, pluripotency state, and cell morphodynamics features that quantify these dynamic processes. We will then mine these high-dimensional feature sets to build computational models that identify dynamic single-cell signaling patterns associated with robust fate transitions and predict actionable interventions that might cause those transitions. Lastly, using drug perturbations, and/or microfluidic/optogenetic actuators, we will quantitatively test those predictions by evoking synthetic dynamic signaling states that induce robust fate transitions. Our approach will help to significantly clarify the mechanistic basis of signaling-mediated human stem cell fate decisions, providing new avenues to robustly control stem cell fate. This might help establish a larger framework, broadly applicable to other hPSC lines and differentiation routes.

Embryos develop precisely at the multicellular level. Yet, stochasticity at the single cell level generates local variability in behaviors (e.g. in cell division, cell positioning, and gene expression). How is this apparent contradiction resolved? Do embryos compensate or possibly exploit local variability to adjust or correct patterns?
In mammalian embryos, the first developmental axis forms in the blastocyst when the outer trophoblasts (the future placenta) form a globe with an axis of proliferation/differentiation originating from the cluster of inner embryonic cells (the future embryo).
Here, we will investigate the principles underlying axis formation through a unique combination of stem cell-based embryology, quantitative imaging of the phenome of trophoblasts, and computational and statistical modeling. Using a novel blastocyst model formed solely with stem cells (Nicolas Rivron, The Netherlands), we will tune the embryonic signals and richly quantify the impact on trophoblast phenotypes, and their variability and precision in space (Shantanu Singh, USA), to model cells’ coordination during axis formation (Kyogo Kawaguchi, Japan).
This unique synergy will reveal how individual stem cells resolve the contrasting forces of single cell variability and multicellular guidance (e.g. embryonic inductions, neighbor coupling), to adjust and achieve a level of precision during the generation of an axis.

Osteoderms are hard calcified tissues that form within the skin of some animals. They resemble bone, hence the name, but are fundamentally different in several respects. Crocodile and armadillo skin plates, and turtle shells are among the most familiar examples, reportedly forming a protective armour against external predators and aiding locomotion. However, although less visible, osteoderms are also present in many lizards.
In terms of their shape, spatial distribution, and interaction, lizard osteoderms show the highest diversity in the animal kingdom, yet we know little about what drives this extraordinary diversity, how it is controlled, or how it originated. It could be a biproduct of other genetic differences or, more likely, a natural optimization to enhance osteoderm function, protective or otherwise, under conditions specific to each lizard type.
This project brings together a multidisciplinary team of expert engineers, developmental and evolutionary biologists from the UK, Canada and France to investigate the mechanisms underlying the development, patterning, and evolution of osteoderms in lizards. The team will use a range of advanced techniques (e.g. genetic analysis, material testing, imaging, and computer simulations) to investigate lizard osteoderms from the first molecular signalling events and cellular interactions, through to organismal level. Osteoderm mechanical properties will be characterised both as single units and as sheets so as to understand their function during feeding and locomotion.
This is a basic science project focused on a novel biological tissue and its evolutionary implications, but with a systems approach that may shed light on pathological calcifications, as well as aiding the development of biomimetic materials and structures. Most importantly it will train the next generation of scientists, in a multidisciplinary and international setting, providing them with a fundamental knowledge of biological tissues and a diverse skillset with which to address the global challenges of 21st century.

The gastrointestinal (GI) tract is efficiently organized to protect the host from potential dangerous stimuli and to tolerate commensal microbiota and food antigens. It hosts as many neurons as the spinal cord and more immune cells than all other compartments together. The innervation of the digestive tract is involved in determining the patterns of its movements, control of gastric acid secretion, release of gut hormones, modifying nutrient handling and interacting with the gut immune system. Infections of the GI tract can result in neuronal damage and dysregulation of these functions. The host laboratory has recently demonstrated that upon infection, in response to specific neurotransmitters, macrophages – a subset of innate immune cells – can acquire tissue-protective phenotype and minimize neuronal loss. Both immune and nervous systems are equipped with mechanisms allowing to store and recall information on previously encountered events. On this basis, I aim to examine whether GI infections trigger a neuro-immunological memory supporting tissue repair or response to subsequent infections. This is of fundamental and clinical interest, as interactions between immune and neuronal cells are proposed to be part of several disease processes, ranging from multiple sclerosis to irritable bowel syndrome (IBS).

The cell membrane is a double layer of lipid molecules. It plays a critical role in protecting the cell from its environment and in separating the different processes that take place within its interior. Membranes must change their shape in order for the cell to function, especially during cell division, and this depends on membrane curvature. At present, cells are only known to induce curvature by accumulating lipids in one of the layers or using specialised proteins. Our goal is to investigate a new mechanism of inducing membrane curvature by accumulation of hydrocarbons in the middle of the lipid layers that has not been observed before in nature.
These hydrocarbons are like the components of diesel fuel, and are found in photosynthetic cyanobacteria and algae – some of the most abundant and widespread organisms on Earth. Production of hydrocarbons in cyanobacteria or other microbes could substitute for liquid fuels derived from petroleum. As well, cyanobacteria and algae release hydrocarbons into the environment, where they are degraded by other bacteria that clean up oil spills. However despite their environmental and biotechnological importance, the exact cellular role of hydrocarbons has not been determined.
We recently discovered that hydrocarbons are essential for maintaining optimal cell size, growth and division, processes that require cell membranes to curve and bend, and found that cells lacking hydrocarbons have lipid membranes that are less curved or flexible. We showed that hydrocarbons integrate into the cell membranes, and used computer simulations to predict that this induces membrane curvature. To investigate this further, we have assembled a team of scientists from the UK, Sweden and New Zealand. By combining our different skills, we will analyse how hydrocarbons affect the physical properties of algal and cyanobacterial membranes by 1) running computer simulations; 2) studying membranes purified from algae and cyanobacteria; and 3) carrying out experiments on live cells. Together, these simulations and experiments will allow us to explore and quantify how hydrocarbons affect curvature and other membrane properties, and so conclusively establish the role of hydrocarbons in cells. As well as improving our understanding of biology, this information will assist the use of microbes for biofuel production and oil spill cleanup.

Hypothalamic tanycytes are sensory glia-like cells lining the walls of the 3rd ventricle (3V) that were proposed to respond to a variety of metabolic and environmental stimuli. The preoptic area (POA) is a hypothalamic region involved in thermoregulation whose nuclei are distributed around the 3V. The POA receives input from peripheral temperature receptors but also contains neurons that respond to deep-brain thermal changes, although the exact mechanism of this phenomenon is not clear. Due to the privileged position of tanycytes, with their somata directly contacting the cerebrospinal fluid and processes reaching portal blood vessels, we propose that tanycytes are part of the central temperature-sensing circuitry. This hypothesis is supported by the fact that they express two receptors, TRPM5 and TRPM3, which are known to be temperature-sensitive. In this project I will use transgenic mouse lines and employ a combination of electrophysiological, chemogenetic, optogenetic and imaging techniques to explore the sensory roles of tanycytes, mostly focusing on thermodetection. I will start with characterising sensory capabilities of tanycytes including their responsiveness to temperature changes and analysing their functional diversity. Then I will test whether tanycytes communicate with neurons in the POA and if so, I will attempt to identify the phenotype of these neurons. Lastly, I will perform in vivo experiments to test the effect of chemogenetic activation and inhibition of temperature-sensitive tanycytes on thermal effector responses as well as eating behaviour. Overall, I expect my study to shed light on the role tanycytes play in temperature detection and homeostasis.

Morphological plasticity is a key adaptive process allowing organisms to cope with changes in their environment. In animals, this process has been described in ephemeral organisms (e.g. flies, worms and mice) that typically experience a specific period in which development will respond to environmental signals producing long-lasting changes in animal body. In contrast, animals with extreme longevity are constantly patterning such that they must continuously adjust their developmental and physiological behaviours with the unpredictable fluctuations of food supply. To decipher the logic of such enhanced morphological plasticity, I am using the sea anemone Nematostella vectensis, a cnidarian laboratory model that exhibits a striking ability to adjust developmental patterns to the nutritional status of the environment while having a long lifespan. Based on preliminary data from the host lab, muscle is emerging as a central tissue that mediates the nutrient-dependent development of Nematostella tentacles. I will define this novel property of muscle cells in response to feeding using transgenic reporter lines. In parallel, I will also establish novel genetic tools to manipulate different muscle types and determine their specific contribution to post-embryonic development. I will also perform single-cell sequencing experiments to characterize the potential metabolic and developmental properties of muscles. Altogether, this proposed work will provide new insight into how morphological plasticity is encoded at the cellular and molecular levels in a long-lived animal.

A shared feature of many anxiety disorders is the overgeneralization of fear, the tendency to falsely link together events that have differing emotional significance. In the case of abnormal fear learning this can produce heightened levels of arousal and fear in situations that should be perceived as safe.
Previous studies indicate several distributed brain areas interacting with neuronal networks in the amygdala to modulate the fearful perception of diverse stimuli. It therefore remains largely unknown how changes in synaptic and cellular function (synaptic scale) can influence encoding of fearful stimuli in large cell networks (network scale) and how interaction between brain areas (global scale) finally leads to overgeneralized behavioral responses. Although a few studies have begun to examine neural substrates of fear generalization at the synaptic and network level, to date, no structured and integrated picture has been generated. This major gap exists because no study so far has been able to integrate experimental results across the different scales to generate a complete model of interactions that regulate fear generalization. As a consequence, new therapies and drugs to treat anxiety disorders emerge only slowly with no major discoveries in sight.
In this proposal, we aim to utilize a unique combination of expertise in neurophysiology, optogenetics and advanced brain imaging to study the mechanisms of fear generalization across spatial scales, ranging from synapses to individual neurons, to large-scale, distributed networks across the whole brain. For the first time we will investigate how local amygdalar networks regulate fear generalization within the context of their afferent signals emerging from global brain activity. To connect synaptic, network and global scales, we will develop new innovative technologies such as an fMRI compatible version of a miniaturized microscope for functional Ca2+ imaging to simultaneously monitor whole brain function and local network activity during fear generalization tests in mice. We will complement these studies with in vivo Ca2+ imaging, optogenetics, and ex vivo electrophysiology to identify the distributed inputs and local circuits in the amygdala that generate overgeneralized fear responses.
The goal of our interdisciplinary systems neuroscience/engineering approach is to provide a comprehensive understanding of the neural substrates that trigger overgeneralized fear, thereby generating a novel framework for how anxiety-related behaviors emerge across different brain scales.

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.

Despite effort, it remains incredibly difficult to identify the cellular basis, and/or the causative genetic variants, underlying complex behavior. Understanding how behavior is encoded requires solving a dual problem involving both neurodevelopment and circuit function. Genes build nervous systems; nervous systems are activated to produce behavior. Streelman and Baier will collaborate to develop a unique model system to chart the complex path from genome to brain to behavior, in vertebrates from natural populations. In Lake Malawi, male cichlid fishes construct sand ‘bowers’ to attract females for mating. Bower building is an innate, repeatable natural behavior that we quantify in the lab. Males build two bower types: 1) pits, which are depressions in the sand, and 2) castles, which resemble miniature volcanoes. Species that build these two bower types can interbreed in the lab. Remarkably, first-generation hybrids of pit- and castle- species perform both behaviors in sequence, constructing first a pit and then a castle bower, indicating that a single brain containing two genomes can produce each behavior in succession. Moreover, brain gene expression in these hybrids is biased towards pit- alleles during pit digging, and castle- alleles during castle building. This phenomenon of allele-specific expression matched to behavior is compelling and offers the chance to identify the genome regulatory logic and neural circuitry underlying complex behavior. Streelman’s group will use single-cell RNA-sequencing to pinpoint specific cell populations that mediate context-dependent allele-specific expression in male bower builders. Baier’s team will use genome editing and optogenetic tools to manipulate the neurons that matter in the brains of behaving Malawi bower builders. Our collaborative work will thus identify the neurons responsible for biased allelic gene expression matched to behavior, and then manipulate those neurons to modify behavioral output. Achieving our goals will demonstrate how the genome is activated in particular cell types to produce context-dependent natural social behaviors.

Capturing the dynamic 3D atomic-scale structure of a macromolecular machine while it performs its biological function remains an outstanding goal of biology. Conventional structural tools (e.g. X-ray crystallography, NMR & cryoEM) only provide ‘snapshots’ of stable states along a reaction pathway. Reaction intermediates, and in particular short-lived intermediates, are hard to capture and characterize with such conventional techniques. Here we propose to combine (prior) information from multiple existing static structures of stable states with dynamic datasets of inter-atomic distances obtained by high-throughput non-equilibrium single-molecule FRET (smFRET) measurements in a microfluidic mixer using novel time-resolved multi-pixel single-photon avalanche diode detector. These measurements will be performed on libraries of molecular constructs, sampling multiple inter-atomic distances as function of reaction time. These measured distance distributions will then serve as multiple intra- and inter-domain distance constraints which, together with prior information (available structures), will enable the Rosetta software to achieve large-scale energy optimization-based refinement of time-resolved ‘snap shots’ of complex structures with improved accuracy. These time-resolved Rosetta structures together with intermediary molecular dynamics simulations will allow solving the 3D atomic-level structure of the macromolecule for each sampled reaction time point, eventually producing a 3D structural dynamic movie of the macromolecule in action. To demonstrate the utility of the proposed method, we will solve the dynamic structure of RNA polymerase during transcription initiation (promoter binding, bubble opening, abortive initiation, promoter clearance) and a pair of intrinsically disordered proteins (IDPs) involved in transcription regulation (ACTR and NCBD) that adopt a fully folded structure during a coupled folding and binding reaction. In addition to elucidating outstanding questions in transcription by combining detector developments, high-throughput and time-resolved out-of-equilibrium single-molecule FRET measurements with new experimentally-constrained molecular structure computational approaches, this multidisciplinary project will result in a new generic toolkit applicable to a large array of enzymes, proteins and molecular machines.

To understand how the brain represents the world is a central theme in neuroscience. Neural circuits encode information in terms of rate, timing and synchrony of action potentials arising from the activity of a complex spatial organization of excitatory/inhibitory neurons. The identity of the active neurons at any given time has a profound effect onto the final outcome and regulates fundamental human psychophysical behavior. Attempts to decode the complex behaviors in neurons has led to development of several neuromodulation and sensing tools, by which neural activity can be controlled by microelectrodes or through genetically altering specific neural circuits, ultimately to deliver electrical impulses. Unfortunately, these techniques introduce strong perturbations to the observed system, without reaching the desired spatio-temporal resolution. Experimental approaches that allow non-invasive activation of specific phenotypic groups of neurons could introduce systematic variation of the timing of signals revealing how neural ensembles encode information. Here we propose a novel (nano)tool to alter membrane potential in specific neuronal phenotypes in a spatiotemporally controlled manner.
The nFlare project will develop a novel research paradigm in neuroscience based on a new class of injectable nanodevices delivered to neurons and anchored to their membranes. These nanotools have the ability to depolarize cell membranes or to deliver active biomolecules. Electric or chemical stimulation of single cells will be achieved using deep-penetration near infrared excitation light, to reduce invasiveness.
nFlare core aims are: i) the development of nanodevice components able to generate photoelectrochemical current upon illumination with light; ii) state-of-the-art biochemical functionalization of the nanodevice to target specific neurons and to reduce inflammatory response; iii) applicability of such nanoscale devices as high spatio-temporal neuronal activity modulators in 2D and 3D in vitro neuronal networks followed by in vivo validation.
Selective modulation of neural circuits by artificial stimulation of neuronal membrane or controlled delivery of environmental factors could help answering fundamental neurobiological questions.

How cell differentiation and morphogenesis are coordinated during embryonic development is an open question in developmental biology. The accepted theory sees morphogenesis as a consequence of the cell differentiation events initiated by biochemical signals. However, recent evidence shows that embryonic cells can adjust their differentiation program according to the size and duration of their cell-cell contacts, suggesting that the interplay between biochemical signals and mechanical stimuli determines cell fate. Yet, how these stimuli are integrated in the gene regulatory networks of cell differentiation is largely unknown. Here I will pioneer an evolutionary approach to find conserved mechanisms by which cell-cell contacts regulate gene expression, by comparing two echinoderm species, sea urchin and sea star. In both species, mesendoderm differentiation depends on Wnt/ß-catenin signalling. However, they present different patterns of Wnt/ß-catenin activity and different cell-cell adhesion properties, with sea star cells being far less adhesive than sea urchin cells. Using a combination of live imaging, scRNAseq and theoretical modelling, I will determine how cell-cell contacts regulate mesendoderm cell differentiation in the two species and if variation in cell-cell contact formation underlies the divergence of tissue patterns between sea urchin and star embryos. This study will uncover basic principles of cell differentiation and tissue patterning, broadening our understanding of embryonic development and evolution.

Brain metastasis (BrM) represents the most common brain malignancy, predominantly arising from non-small cell lung cancer, breast cancer and melanoma. We hypothesize that the tumor microenvironment (TME) plays an essential role in the establishment and progression of BrM. The brain is constituted by a unique TME, which includes tissue-resident cell types such as astrocytes and microglia, and critically, the blood-brain barrier (BBB). Cancer cells are able to exploit the brain vasculature for their own benefit, by forming the blood-tumor barrier. This specialized vasculature is an essential TME compartment, as it may suppress anti-tumor responses by blocking immune cell infiltration, specifically of cytotoxic T cells. Indeed, a new perspective to target the tumor vasculature in combination with immunotherapy has recently emerged from studying other cancers; however, this concept has not been explored in BrM to date. Therefore, in the proposed project, I will investigate the biology of two major cellular components of the BBB: endothelial cells (ECs) and pericytes in BrM arising from distinct primary tumors. For this purpose, I will perform transcriptomic analysis of these cell types in patient BrM samples originating from lung, breast or melanoma primary tumors. I will combine this analysis with different experimental approaches available in the host lab, including immunocompetent mouse BrM models and in vitro and ex vivo cell cultures that have been optimized to model the brain TME. This integrated and complementary experimental strategy will facilitate the identification of innovative therapies for BrM to be used alone or in combination with immunotherapies.

Pain sensation, though unpleasant, is considered protective as it provokes aversive behavior from noxious stimuli. Studies show that sensory neurons, which generate the perception of pain and touch, interact with another important protection mechanism, the immune system. Ablation of sensory neurons can alter the skin-resident immune cell response. However, many aspects of this interaction remain uncharacterized.
Cells and antigens from barrier sites, like the skin, are drained and sampled by the lymph nodes (LN). Interestingly, LN are innervated by fibers expressing the sensory neuron derived-peptides Substance P and Calcitonin gene-related peptide. Some of these fibers are found in close proximity to leukocytes. However, their direct impact on immune cell activity is unknown.
This project aims to characterize the effects of sensory neurons in the skin and LN on immune cell behavior. To this aim, we propose to combine chemogenetics to locally activate sensory neurons, with a broad analysis of immune cell responses. Mice expressing Cre under the control of sensory neuronal markers, including the broadly expressed gene Advillin and genes selective for subsets of sensory neurons, will be injected intradermally or in the LN with a viral vector encoding the Cre-dependent expression of the hM3D(Gq) activating receptor. Once validated, this technique will be used to locally activate sensory neurons and characterize subsequent immunological changes using flow cytometry, histological and live imaging techniques. This project can provide new insights into how sensory innervations, which regulate behavior by creating the sensation of touch and pain, shape local immune responses.

A key brain region involved in accurate temporal refinement of motor and also cognitive behaviours is the cerebellum. Cerebellar granule cells (GCs) receive multisensory information from outside the cerebellum via mossy fibres (MF). The prevailing hypothesis is that, in order to learn temporal sequences, the cerebellum requires a rich diversity of GC activity patterns that as a population represent a distributed temporal representation of sensory inputs. But this has never been directly demonstrated. Unpublished network models from the hosting laboratory strongly suggest that their previous findings (input specific diversity of MF-GC synaptic dynamics) are sufficient to generate a diverse GC firing patterns that act as a temporal basis for cerebellar learning. We will use novel high speed two-photon in vivo imaging of GC firing patterns in behaving animals, and examine whether the diversity of GC firing patterns requires functional diversity of MF-GC synapses, and whether this mechanism is specific for different sensory modalities, using optogenetic activation of specific input types. Finally, we will optogenetically inhibit specific MF types to show their influence over specific timescales of eyeblink conditioning, then image the temporal representation in the GC layer before, during and after a temporal learning task. Expected results will included identification of the underlying cellular and circuit mechanism of temporal learning required for fine tuning motor and cognitive processes.

Pancreatic ductal adenocarcinoma (PDAC) remains an incurable disease with a high death rate. PDACs are exceptionally difficult to treat because of high genetic plasticity and encapsulation by cancer-associated fibroblasts (CAFs). Either are due to an altered epigenetic landscape where PDACs and CAFs show a switch towards global chromatin hypo-methylation, and concomitant hyper-methylation of tumor-suppressor genes. As CAFs do not show any mutagenesis, the molecular cause must be found in the tumor microenvironment.

The nutrient microenvironment represents a novel but important aspects of tumor biology. Nutrients are converted into the basic building blocks that fuel cellular proliferation, but also regulate epigenetic modifications. S-Adenosyl-Methionine (SAM) represents a nodal point in one carbon metabolism and is required for methylation of histones and DNA. We therefore propose that metabolism cannot sustain the high SAM requirement of both PDAC and CAF, thus shunting away carbons from epigenetic maintenance. This project therefore aims to map the link between nutrient availability, one carbon metabolism, availability of SAM, and the methylation profile of chromatin. Furthermore, we will establish a genetic sensor and CRISPR-based screening system to visualize the regulation of SAM compartmentalization, and attempt to normalize the epigenome of PDACs and CAFs through engineering of SAM metabolism (EpiSAMe). These studies will shed new insight into the crosstalk between metabolism and epigenetics in PDAC and provide novel molecular for the treatment of this devastating disease.

Genomic instability is a common feature of cancers and can have an important impact on cancer progression and response to treatment. However, the mechanisms underlying cancer genomic instability are not completely understood. While DNA repair defects are thought to be a major cause of this trait, other factors seem to be involved. In the last decade, metabolism has received a lot of attention within the cancer research community. Most of the work has focused on understanding the metabolic requirements of cancer cells for survival and proliferation. However, metabolism does not only provide building blocks for biosynthesis, but it also generates reactive by-products that can damage cellular components such as DNA. Thus, the metabolic alterations characteristic of cancer cells might not only support cancer development by supporting biosynthesis but also by promoting genomic instability.

The aim of this research proposal is to identify changes in the metabolism of endogenous genotoxins in cancer and to elucidate the role of these alterations, particularly in the context of genomic instability. In addition, the potential exploitation of this aspect of metabolism for cancer therapy will be explored. To achieve these goals a diverse range of techniques and study systems will be used, including transcriptomics, metabolomics, CRISPR-based genetic screens, cancer cell lines and mouse models.

In 2014, the Nobel Prize in Physiology was awarded for the discovery of place and grid cells that process spatial cues in the mammalian hippocampal formation;, the key structure for both navigation and episodic memory1. Place and grid cells, and additional cell types form the central building blocks in the current circuit models of navigation in mammals. However, a cohesive picture of how these circuits compute space and enable navigation has not been achieved. In fact, emerging evidence suggest that these navigation circuits are highly diverse in cellular phenotypes and functionality; they do not only map aspects of space but also elements like sound, time, and reward. How neural systems of spatial cognition have evolved outside of the mammalian clade is not clear, and comparative studies are critically needed to gain insights to basic functional constraints and structural requirements underlying these neural circuits.
The international research team of four PIs proposes a broad comparative systems neurobiological approach using teleost fish for integrative studies on higher navigation circuits. These fish are ideal models because they have conquered diverse spatial ecologies and show highly specialized sensory adaptions. Also, their brains exhibit an overall lower complexity to mammals, and are highly accessible to experimental manipulation. To establish systematic research on teleostean spatial cognition, the project combines neuroethological, electrophysiological, neuroimaging, and computational methodologies. Introducing a powerful electrophysiological recording technology in freely-moving fish and generating long-needed anatomical atlas resources, the project analyzes four teleost species with differing spatial ecologies. The team will uncover how different sensory modalities like vision, perception of depth, and active electrolocation are integrated during spatial navigation tasks, thereby investigating how top-down mechanisms modulate sensory integration of spatial learning.
Finally, the team will test specific hypotheses developed in small-scaled laboratory setups in an unconstrained natural environment. Here, the group will measure the activity of neurons in freely moving fish that explore a coral reef habitat. This will be the first ever attempt to analyze brain activity underlying navigation in the wild. Altogether, the project will provide new perspectives on the evolution, function, and mechanism of memory systems in animal navigation.

Prochlorococcus, the smallest photosynthetic organism, has diversified into many ‘ecotypes’ with finely tuned distinct ecological niches. The small and variable genomes of these cyanobacteria encode genes unique to particular habitats. A driving force for gene transfer and evolution in cyanobacteria is phage-mediated. While numerous reports describe lytic cyanophages that infect Prochlorococcus, surprisingly there is only indirect evidence that lysogenic phages – those that spend a portion of their life cycle incorporated into the host genome – exist. The central goals of this proposal are i) to analyze the occurrence of lysogens in wild populations of Prochlorococcus, and ii) to establish a robust protocol for gene editing allowing precise manipulation of the Prochlorococcus genome. The second goal will exploit, but is not dependent upon, advances from the first.
This will be the first study to assess lysogeny across natural Prochlorococcus populations and to develop phage-mediated genetic systems for engineering cyanobacteria. The development of efficient tools for genome editing would be extremely beneficial for understanding Prochlorococcus metabolism. It would allow functional studies for thousands of unannotated genes that influence the relative fitness of different ecotypes in different environments. A unique aspect of my proposal is the employment of a novel synthetic biology strategy to build engineered phages with broad host specificity, and to use them as vehicles for genome editing systems such as CRISPR/Cas9. This technique will be useful for several applications and will further establish Prochlorococcus as a model organism in environmental microbiology.