ERC FUNDED PROJECTS

Humans diverged from our closest living relatives, chimpanzees and other great apes, 6-10 million years ago. Since this divergence, our ancestors acquired genetic changes that enhanced cognition, altered metabolism, and endowed our species with an adaptive capacity to colonize the entire planet and reshape the biosphere. Through genome comparisons between modern humans, Neandertals, chimpanzees and other apes we have identified genetic changes that likely contribute to innovations in human metabolic and cognitive physiology. However, it has been difficult to assess the functional effects of these genetic changes due to the lack of cell culture systems that recapitulate great ape organ complexity. Human and chimpanzee pluripotent stem cells (PSCs) can self-organize into three-dimensional (3D) tissues that recapitulate the morphology, function, and genetic programs controlling organ development. Our vision is to use organoids to study the changes that set modern humans apart from our closest evolutionary relatives as well as all other organisms on the planet. In ANTHROPOID we will generate a great ape developmental cell atlas using cortex, liver, and small intestine organoids. We will use single-cell transcriptomics and chromatin accessibility to identify cell type-specific features of transcriptome divergence at cellular resolution. We will dissect enhancer evolution using single-cell genomic screens and ancestralize human cells to resurrect pre-human cellular phenotypes. ANTHROPOID utilizes quantitative and state-of-the-art methods to explore exciting high-risk questions at multiple branches of the modern human lineage. This project is a ground breaking starting point to replay evolution and tackle the ancient question of what makes us uniquely human?

1 500 000 €

Start date: 2019-06-01, End date: 2024-05-31

This interdisciplinary proposal has the objective to greatly enhance our understanding of fundamental biomineralization processes involved in the formation of calcium carbonates by marine organisms, such as corals, foraminifera and bivalves, in order to better understand vital effects. This is essential to the application of these carbonates as proxies for global (paleo-) environmental change. The core of the proposal is an experimental capability that I have pioneered during 2008: Dynamic stable isotopic labeling during formation of carbonate skeletons, tests, and shells, combined with NanoSIMS imaging. The NanoSIMS ion microprobe is a state-of-the-art analytical technology that allows precise elemental and isotopic imaging with a spatial resolution of ~100 nanometers. NanoSIMS imaging of the isotopic label(s) in the resulting biocarbonates and in associated cell-structures will be used to uncover cellular-level transport processes, timescales of formation of different biocarbonate components, as well as trace-elemental and isotopic fractionations. This will uncover the origin of vital effects. With this proposal, I establish a new scientific frontier and guarantee European leadership. The technical and scientific developments resulting from this work are broadly applicable and will radically change scientific ideas about marine carbonate biomineralization and compositional vital effects.

2 182 000 €

Start date: 2010-07-01, End date: 2015-06-30

In mammals, transcriptional control of many genes relies on cis-regulatory elements such as enhancers, which are often located tens to hundreds of kilobases away from their cognate promoters. Functional interactions between distal regulatory elements and target promoters require mutual physical proximity, which is linked to the three-dimensional structure of the chromatin fiber. Chromosome conformation capture studies revealed that chromosomes are partitioned into Topologically Associating Domains (TADs), sub-megabase domains of preferential physical interactions of the chromatin fiber. Genetic evidence showed that TAD boundaries restrict the genomic range of enhancer-promoter communication, and that interactions between regulatory sequences within TADs are further fine-tuned by smaller-scale structures. However, the mechanistic details of how physical interactions translate into transcriptional outputs are totally unknown. Here we propose to explore the biophysical mechanisms that link chromosome conformation and long-range transcriptional regulation using molecular biology, genetic engineering, single-cell experiments and physical modeling. We will measure chromosomal interactions in single cells and in time using a novel method that relies on an enzymatic process in vivo. Genetic engineering will be used to establish a cell system that allows quantitative measurement of how enhancer-promoter interactions relate to transcription at the population and single-cell levels, and to test the effects of perturbations without confounding effects. Finally, we will develop physical models of promoter operation in the presence of distal enhancers, which will be used to interpret the experimental data and formulate new testable predictions. With this integrated approach we aim at providing an entirely new layer of description of the general principles underlying transcriptional control, which could establish new paradigms for research in epigenetics and gene regulation.

1 500 000 €

Start date: 2018-01-01, End date: 2022-12-31

We have developed a new numerical method to consistently compute atmospheric trace gas and aerosol chemistry and cloud processes. The method is computationally efficient so that it can be used in climate models. For the first time cloud droplet formation on multi-component particles can be represented based on first principles rather than parameterisations. This allows for a direct coupling in models between aerosol chemical composition and the continuum between hazes and clouds as a function of ambient relative humidity. We will apply the method in a new nested global-limited area model system to study atmospheric chemistry climate interactions and anthropogenic influences. We will focus on the Mediterranean region because it is a hot spot in climate change exposed to drying and air pollution. The limited area model will also be applied as cloud-resolving model to study aerosol influences on precipitation and storm development. By simulating realistic meteorological conditions at high spatial resolution our method can be straightforwardly tested against observations. Central questions are: - How does the simulated haze-cloud continuum compare with remote sensing measurements and what is the consequence of abandoning the traditional and artificial distinction between aerosols and clouds? - How are cloud and precipitation formation influenced by atmospheric chemical composition changes? - To what extent do haze and cloud formation in polluted air exert forcings of synoptic meteorological conditions and climate? - Can aerosol pollution in the Mediterranean region exacerbate the predicted and observed drying in a changing climate? The model system is user-friendly and will facilitate air quality and climate studies by regional scientists. The project will be part of the Energy, Environment and Water Centre of the newly founded Cyprus Institute, provide input to climate impact assessments and contribute to a regional outreach programme.

2 196 000 €

Start date: 2009-01-01, End date: 2014-12-31

Clouds and precipitation play a crucial role in the Earth's energy balance, global atmospheric circulation and the water cycle. Despite their importance, clouds still pose the largest uncertainty in climate research. I propose a new approach for studying anthropogenic effects on cloud fields and rain, tackling the challenge from both scientific ends: reductionism and systems approach. We will develop a novel research approach using observations and models interactively that will allow us to “peel apart” detailed physical processes. In parallel we will develop a systems view of cloud fields looking for Emergent Behavior rising out of the complexity, as the end result of all of the coupled processes. Better understanding of key processes on a detailed (reductionist) manner will enable us to formulate the important basic rules that control the field and to look for emergence of the overall effects. We will merge ideas and methods from four different disciplines: remote sensing and radiative transfer, cloud physics, pattern recognition and computer vision and ideas developed in systems approach. All of this will be done against the backdrop of natural variability of meteorological systems. The outcomes of this work will include fundamental new understanding of the coupled surface-aerosol-cloud-precipitation system. More importantly this work will emphasize the consequences of human actions on the environment, and how we change our climate and hydrological cycle as we input pollutants and transform the Earth’s surface. This work will open new horizons in cloud research by developing novel methods and employing the bulk knowledge of pattern recognition, complexity, networking and self organization to cloud and climate studies. We are proposing a long-term, open-ended program of study that will have scientific and societal relevance as long as human-caused influences continue, evolve and change.

1 428 169 €

Start date: 2012-09-01, End date: 2017-08-31

Proper and controlled expression of genes is essential for normal cell growth. Chromatin modifying enzymes play a fundamental role in the control of gene expression and their deregulation is often linked to cancer. In recent years chromatin modifiers have been considered key targets for cancer therapy and this demands a full understanding of their biological functions. Previous biochemical and structural studies have focused on the identification of chromatin modifying enzymes and characterization of their substrate specificities and catalytic mechanisms. However, a comprehensive view of the biological processes, signaling pathways and regulatory circuits in which these enzymes participate is missing. Protein arginine methyltransferases (PRMTs), which methylate histones and are evolutionarily conserved from yeast to human, constitute an example of chromatin modifying enzymes whose functional and regulatory networks remain unexplored. I propose to use complementary state-of-the-art genomic and proteomic approaches in order to identify the protein networks and cellular pathways that are linked to PRMTs. In parallel, I will identify novel regulatory circuits and define the molecular mechanisms that control methylation of specific histone arginine residues. I will utilize the yeast S. cerevisiae as a model organism because it allows genetic, biochemical and genomic approaches to be combined. Most importantly, many of the pathways and mechanisms in yeast are highly conserved and therefore, the findings from this study will be pertinent to human and other eukaryotic organisms. Establishing a global cellular wiring diagram of PRMTs will serve as a paradigm for other chromatin modifiers and is imperative for assessing the efficacy of these enzymes as therapeutic targets.

1 498 279 €

Start date: 2011-01-01, End date: 2016-06-30

Over the past decade small RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) have been shown to carry pivotal roles in post-transcriptional regulation and genome protection and to play an important part in various physiological processes in animals. miRNAs can be found in a very wide range of animals yet their functions were studied almost exclusively in members of the Bilateria such as insects, nematodes and vertebrates. Hence studying their function in representatives of non-bilaterian phyla such as Cnidaria (sea anemones, corals, hydras and jellyfish) is crucial for understanding the evolution of miRNAs in animals and can provide important insights into their roles in the ancient ancestor of Cnidaria and Bilateria. The sea anemone Nematostella vectensis is an excellent model for such a study since it can be grown in large numbers throughout its life cycle in the lab and because well-established genetic manipulation techniques are available for this species. Our preliminary results indicate that miRNAs in Nematostella frequently have a nearly perfect match to their messenger RNA (mRNA) targets, resulting in cleavage of the target. This mode of action is common for plant miRNAs, but is very rare in Bilateria. This finding together with my recent discovery of a Nematostella homolog of HYL1, a protein involved in miRNA biogenesis in plants, raises the exciting possibility that the miRNA pathway existed in the common ancestor of plants and animals. Here I suggest to bring together an array of advanced biochemical and genetic methods such as gene knockdown, transgenesis, high throughput sequencing and immunoprecipitation in order to obtain - for the first time - a deep understanding of the biogenesis and mechanism of action of small RNAs in Cnidaria. This will provide a novel way to understand the evolution of this important molecular pathway and to evaluate its age and ancestral form.

1 499 587 €

Start date: 2015-05-01, End date: 2020-04-30

Over 100 types of distinct modifications are catalyzed on RNA molecules post-transcriptionally. In an analogous manner to well-studied chemical modifications on proteins or DNA, modifications on RNA - and particularly on mRNA - harbor the exciting potential of regulating the complex and interlinked life cycle of these molecules. The most abundant modification in mammalian and yeast mRNA is N6-methyladenosine (m6A). We have pioneered approaches for mapping m6A in a transcriptome wide manner, and we and others have identified factors involved in encoding and decoding m6A. While experimental disruption of these factors is associated with severe phenotypes, the role of m6A remains enigmatic. No single methylated site has been shown to causally underlie any physiological or molecular function. This proposal aims to establish a framework for systematically deciphering the molecular function of a modification and its underlying mechanisms and to uncover the physiological role of the modification in regulation of a cellular response. We will apply this framework to m6A in the context of meiosis in budding yeast, as m6A dynamically accumulates on meiotic mRNAs and as the methyltransferase catalyzing m6A is essential for meiosis. We will (1) aim to elucidate the physiological targets of methylation governing entry into meiosis (2) seek to elucidate the function of m6A at the molecular level, and understand its impact on the various steps of the mRNA life cycle, (3) seek to understand the mechanisms underlying its effects. These aims will provide a comprehensive framework for understanding how the epitranscriptome, an emerging post-transcriptional layer of regulation, fine-tunes gene regulation and impacts cellular decision making in a dynamic response, and will set the stage towards dissecting the roles of m6A and of an expanding set of mRNA modifications in more complex and disease related systems.

1 402 666 €

Start date: 2016-11-01, End date: 2021-10-31

Seismic tomography images of the Earth's interior are key to the characterisation of earthquakes, natural resource exploration, seismic risk assessment, tsunami warning, and studies of geodynamic processes. While tomography has drawn a fascinating picture of our planet, today's individual researchers can exploit only a fraction of the rapidly expanding seismic data volume. Applications relying on tomographic images lag behind their potential; fundamental questions remain unanswered: Do mantle plumes exist in the deep Earth? What are the properties of active faults, and how do they affect earthquake ground motion? To address these questions and to ensure continued progress of seismic tomography in the 'Big Data' era, I propose new technological developments that enable a paradigm shift in Earth model construction towards a Collaborative Seismic Earth Model (CSEM). Fully accounting for the physics of wave propagation in the complex 3D Earth, the CSEM is envisioned to evolve successively through a systematic group effort of my team, thus going beyond the tomographic models that individual researchers may construct today. I will develop the technological foundation of the CSEM and integrate these developments in studies of large-earthquake rupture processes and the convective pattern of the Earth's mantle in relation to surface geology. The CSEM project will bridge the gap between regional and global tomography, and deliver the first multiscale model of the Earth where crust and mantle are jointly resolved. The CSEM will lead to a dramatic increase in the exploitable seismic data volume, and set new standards for the construction and reproducibility of tomographic Earth models. Beyond this project, the CSEM will be openly accessible through the European Plate Observing System (EPOS). It will then offer Earth scientists the unique opportunity to join forces in the discovery of multiscale Earth structure by systematically building on each other's results.

1 367 500 €

Start date: 2017-01-01, End date: 2021-12-31

Cells use circuits of interacting proteins to respond to their environment. In the past decades, molecular biology has provided detailed knowledge on the proteins in these circuits and their interactions. To fully understand circuit function requires, in addition to molecular knowledge, new concepts that explain how multiple components work together to perform systems level functions. Our lab has been a leader in defining such concepts, based on combined experimental and theoretical study of well characterized circuits in bacteria and human cells. In this proposal we aim to find novel principles on how circuits resist fluctuations and errors, and how they can be controlled by drugs: (1) Why do key regulatory systems use bifunctional enzymes that catalyze antagonistic reactions (e.g. both kinase and phosphatase)? We will test the role of bifunctional enzymes in making circuits robust to variations in protein levels. (2) Why are some genes regulated by a repressor and others by an activator? We will test this in the context of reduction of errors in transcription control. (3) Are there principles that describe how drugs combine to affect protein dynamics in human cells? We will use a novel dynamic proteomics approach developed in our lab to explore how protein dynamics can be controlled by drug combinations. This research will define principles that unite our understanding of seemingly distinct biological systems, and explain their particular design in terms of systems-level functions. This understanding will help form the basis for a future medicine that rationally controls the state of the cell based on a detailed blueprint of their circuit design, and quantitative principles for the effects of drugs on this circuitry.

2 261 440 €

Start date: 2010-03-01, End date: 2015-02-28

"Land-climate interactions mediated through soil moisture and vegetation play a critical role in the climate system, in particular for the occurrence of extreme events such as droughts and heatwaves. They are, however, poorly constrained in current Earth System Models (ESMs), leading to large uncertainties in climate projections. These uncertainties affect the quality and accuracy of projections of temperature, water availability, and carbon concentrations, as well as that of projected impacts on agriculture, ecosystems, and health. In the past years, in-situ and remote sensing-based datasets of soil moisture, evapotranspiration, and energy and carbon fluxes have become increasingly available, providing untapped potential for reducing associated uncertainties in current climate models. The DROUGHT-HEAT project aims at innovatively exploiting these new information sources in order to 1) derive observations-based diagnostics to quantify and isolate the role of land-climate interactions in past extreme events (""Diagnostic Atlas""), 2) evaluate and improve current ESMs and constrain climate-change projections using the derived diagnostics, and 3) apply the newly gained knowledge to frontier developments in the attribution of climate extremes to land processes and their mitigation through ""land geoengineering"". The DROUGHT-HEAT project integrates the newest land observational datasets with the latest stream of ESMs. Novel methodologies will be applied to extract functional relationships from the data, and identify key gaps in the ESMs' representation of underlying processes. These will build on physically-based relationships, machine learning tools, and model calibration. In addition, they will encompass the mapping and merging of derived diagnostics in space and time to reduce ""blank spaces"" in the datasets. The project is unprecedented in its breadth and scope and will allow a major breakthrough in our understanding of the processes leading to heatwaves and droughts."

1 952 285 €

Start date: 2014-09-01, End date: 2019-08-31

This proposal aims to constrain the late accretion history of the Earth and the differentiation of the earliest silicate reservoirs in planets. Highly siderophile elements (HSE) constrain the late accretion of material onto the Earth; a process that potentially delivered water to Earth. During core formation, HSE strongly partition into metal. Once core formation ceases, newly accreted HSE-rich material will significantly contribute to the HSE budget of the Earth’s mantle. The HSE are more abundant in the Earth’s mantle than predicted from low temperature partitioning experiments and feature nearly chondritic relative abundances. This implies a significant late accretion of chondritic material (“the late veneer”). This idea is challenged by high pressure/temperature experiments indicating that the HSE were left in the behind in the mantle during core formation, thereby calling into question the late veneer. To address this issue, I propose the setup of new isotopic tracers and utilize (i) nucleosynthetic anomalies and (ii) stable isotope systematics of the HSE to determine the origin of HSE in the Earth’s mantle. Unravelling this issue is a major advance in understanding planetary accretion. Formation of the earliest silicate reservoirs probably occurred contemporary to late accretion. Global differentiation in terrestrial silicate reservoirs may have taken place within the first 30 million years of the Earth’s formation based on Sm-Nd isotope data. This timing has been debated on various grounds. The 92Nb-92Zr decay system is a potentially powerful chronometer to further constrain this issue. Its usefulness, however, has been hindered by uncertainties of the initial 92Nb abundance in the solar system. I propose to obtain unequivocal evidence from old differentiated meteorites to settle this debate. The results will have implications for understanding early silicate differentiation on asteroids and - depending on the initial 92Nb abundance - the Earth and Mars.

1 994 545 €

Start date: 2012-04-01, End date: 2017-12-31

Animals constantly face complex environments consisted of multiple fluctuating cues. Accurate detection and efficient integration of such perplexing information are essential as animals’ fitness and consequently survival depend on making the right behavioral decisions. However, little is known about how multifaceted stimuli are integrated by neural systems, and how this information flows in the neural network in a single-neuron resolution. Here we aim to address these fundamental questions using C. elegans worms as a model system. With a compact and fully-mapped neural network, C. elegans offers a unique opportunity of generating novel breakthroughs and significantly advance the field. To study functional dynamics on a network-wide scale with an unprecedented single-neuron resolution, we will construct a comprehensive library of transgenic animals expressing state-of-the-art optogenetic tools and Calcium indicators in individual neurons. Moreover, we will study the entire encoding process, beginning with the sensory layer, through integration in the neural network, to behavioral outputs. At the sensory level, we aim to reveal how small sensory systems efficiently encode the complex external world. Next, we will decipher the design principles by which neural circuits integrate and process information. The optogenetic transgenic animals will allow us interrogating computational roles of various circuits by manipulating individual neurons in the network. At the end, we will integrate the gathered knowledge to study how encoding eventually translates to decision making behavioral outputs. Throughout this project, we will use a combination of cutting-edge experimental techniques coupled with extensive computational analyses, modelling and theory. The aims of this interdisciplinary project together with the system-level approaches put it in the front line of research in the Systems Biology field.

1 498 400 €

Start date: 2014-02-01, End date: 2019-01-31

Differentiation events in mammalian development involve stable resetting of transcriptional programs, which entails changes in the epigenetic state of target sequences defined by modifications of DNA and bound nucleosomes. These recently identified epigenetic layers modulate DNA accessibility in a positive and negative manner and thus could make genetic readouts context-dependent and dynamic. The proposed project aims to quantify the epigenetic contribution to cellular differentiation as a key event in development. By applying parallel genomic approaches we will comprehensively define the epigenome and its plasticity during cellular commitment of pluripotent murine stem cells into defined terminally differentiated cells. We will focus on DNA methylation and its interplay with several histone modifications as a way to achieve stable gene silencing. The resulting global profiles will gain insights into targeting principles and generate statistical, predictive models of regulation. From these mechanistic models will be derived and tested by genetically interfering with genetic and epigenetic regulatory pathways and by dissecting DNA sequence components involved in specifying targets. These experiments aim to unravel the crosstalk between epigenetic regulation and cell plasticity, the underlying molecular circuitry in pluripotent and unipotent cells and ultimately help to incorporate epigenetic regulation into current transcriptional regulatory models.

1 085 000 €

Start date: 2008-10-01, End date: 2013-09-30

"Gene expression in living cells is a most intricate molecular process, occurring in stages, each of which is regulated by a diversity of mechanisms. Among the various stages leading to gene expression, only transcription is relatively well understood, thanks to Genomics and bioinformatics. In contrast to the vast amounts of genome-wide data and a growing understanding of the structure of networks controlling transcription, we still lack quantitative, genome-wide knowledge of the mechanisms underlying regulation of mRNA degradation and translation. Among the unknowns are the identity of the regulators, their kinetic modes of action, and their means of interaction with the sequence features that make-up their targets; how these target combine to produce a higher level ""grammar"" is also unknown. An important part of the project is dedicated to generating genome-wide experimental data that will form the basis for quantitative and more comprehensive analysis of gene expression. Specifically, the primary objectives of our proposed research plan are: 1) to advance our understanding of the transcriptome, by deciphering the code regulating mRNA decay 2) to break the code which controls protein translation efficiency 3) to understand how mRNA degradation and translation efficiency determine noise in protein expression levels. The proposed strategy is based on an innovative combination of computational prediction, synthetic gene design, and genome-wide data acquisition, all culminating in extensive data analysis, mathematical modeling and focused experiments. This highly challenging, multidisciplinary project is likely to greatly enhance our knowledge of the various modes by which organisms regulate expression of their genomes, how these regulatory mechanisms are interrelated, how they generate precise response to environmental challenges and how they have evolved over time."

1 320 000 €

Start date: 2008-09-01, End date: 2013-08-31

Our working hypothesis is that tumorigenesis is an evolutionary process that fundamentally couples few major driving events (point mutations, rearrangements) with a complex flux of minor aberrations, many of which are epigenetic. We believe that these minor events are critical factors in the emergence of the cancer phenotype, and that understanding them is essential to the characterization of the disease. In particular, we hypothesize that a quantitative and principled evolutionary model for carcinogenesis is imperative for understanding the heterogeneity within tumor cell populations and predicting the effects of cancer therapies. We will therefore develop an interdisciplinary scheme that combines theoretical models of cancer evolution with in vitro evolutionary experiments and new methods for assaying the population heterogeneity of epigenomic organization. By developing techniques to interrogate DNA methylation and its interaction with other key epigenetic marks at the single-cell level, we will allow quantitative theoretical predictions to be scrutinized and refined. By combining models describing epigenetic aberrations with direct measurements of chromatin organization using Hi-C and 4C-seq, we shall revisit fundamental questions on the causative nature of epigenetic changes during carcinogenesis. Ultimately, we will apply both theoretical and experimental methodologies to assay and characterize the evolutionary histories of tumor cell populations from multiple mouse models and clinical patient samples.

1 499 998 €

Start date: 2012-12-01, End date: 2017-11-30

Volcanic eruptions occur with a frequency that is inversely proportional to their magnitude. Datasets of natural volcanic events, currently used to determine the recurrence rate of volcanic eruptions are intrinsically biased. Combining physical modelling of processes with detailed statistical analysis has been demonstrated essential for assessing reliably the recurrence rate of natural hazards, such as floods and earthquakes. This would be the first attempt to apply a similar, integrated approach to explosive volcanic eruptions. The high-gain final target of FEVER is to produce a physically based statistical model able to ForEcast the recurrence rate of Volcanic Eruptions both at regional and global scale. This is the first project of this kind and consequently involves a significant risk. Because 500 million people live in proximity of volcanoes and eruptions have a significant social and economical impact, forecasting the recurrence rate of volcanic eruption remains a great challenge in Science. This project builds on two main directions of my research: a) Thermo-mechanical and statistical modelling targeting the identification of the main physical factors controlling the recurrence rate of volcanic eruptions. We showed that the flux of magma from depth directly controls the magnitude of the largest possible eruptions. Thus, b) we developed a novel method to determine such magma fluxes. These two lines of research combine perfectly in FEVER and will be integrated to answer questions such as: What is the probability of an eruption similar to the Tambora 1815 to occur in the next 100 years on Earth or in Europe? What is the largest physically possible eruption that can occur in Europe? The high-gain target of FEVER is to mitigate the impact of volcanic eruptions on our society, by producing research of interest for governmental agencies dealing with location of strategic infrastructures, and for businesses such as aviation.

1 458 192 €

Start date: 2016-04-01, End date: 2021-03-31

In eukaryotes, silencing small (s)RNAs, including micro (mi)RNAs and small interfering (si)RNAs, regulate many aspects of biology, including cell differentiation, development, hormonal responses, or defense. In particular, many plant and metazoan miRNAs play crucial roles in embryonic/post-embryonic development; the precise timing and localization of their expression is thus crucial to their action. Hence, specific miRNA repertoires underlie specific cell identities, and deviations from such repertoires often have deleterious consequences such as cancer. Many miRNAs also help organisms to adapt to stress, thus, given their importance in virtually all aspects of biology, understanding how, when and where miRNAs exert their actions is of paramount importance. To date, however, the few approaches to miRNA-mediated silencing in whole organisms have not taken into account the exquisite definition, in space and time, of their biogenesis and action, leading to an inaccurate view of the biology of these molecules at the systems level. Using the root system of the model plant Arabidopsis thaliana, we propose to explore, at single-cell and subcellular resolution levels, the biology of the main miRNA effector protein, ARGONAUTE 1 (AGO1) in intact tissues. Using a combination of state-of the-art technologies for single-cell forward genetics, protein purification and RNA/polysome profiling, we will establish a functional spatiotemporal map of the root AGO1-sRNAome and identify cell-specific modifiers of sRNA biogenesis and action. As a complement to the above approaches, chemical genetics will isolate small molecules allowing direct and specific manipulation of AGO1-dependent sRNA pathways in planta. RNA silencing modifier compounds will also accelerate forward and reverse approaches of RNA silencing in plants with sensitized genetic backgrounds, and uncover novel connections between miRNA/siRNA and physiological or metabolic pathways.

2 251 600 €

Start date: 2013-07-01, End date: 2018-06-30

DNA methylation, the covalent binding of a methyl group (CH3) to cytosine base, regulates the genome activity and plays a fundamental developmental role in eukaryotes. Its epigenetic characteristics of regulating transcription without changing the genetic code together with the ability to be transmitted through DNA replication allow organisms to memorize cellular events for many generations. DNA methylation is mostly known for its role in transcriptional silencing; however, its functional output is more complex and is influenced in part by its DNA context. Recent genomic studies, have found DNA methylation to be targeted inside sequences of actively transcribed genes, thus termed gene body methylation. Despite being an evolutionary conserved and a robust methylation pathway targeted to thousands of genes in animal and plant genomes, the function of gene body methylation is still poorly understood at both the molecular and functional level. Similar to the chicken and egg conundrum, because we do not know what gene body methylation does, therefore scientists could not apply its function to discover its regulators either. Gene body methylation is targeted to a very specific subset and subregions of genes, thus we strongly believe that specific factors exist and are missing simply because that no one has ever searched for them before. Hence, to make major breakthroughs in the field, our approach is to artificially generate gene-body-specific hypomethylated plants that together with customized genetic and biochemical systems will allow us to discover regulators and interpreters of gene body methylation. Using these unique genetic tools and novel molecular factors, we will be able to ultimately explore the particular biological roles of gene body methylation. These findings will fill the gap towards a full comprehension of the entire functional array of DNA methylation, and to its more precise exploitation in yielding better crops and in treating human diseases.

1 500 000 €

Start date: 2016-10-01, End date: 2021-09-30

For decades the Holocene has been considered a flat and “boring” epoch from the standpoint of paleomagnetism, mainly due to insufficient resolution of the available paleomagnetic data. However, recent archaeomagnetic data have revealed that the Holocene geomagnetic field is anything but stable – presenting puzzling intervals of extreme decadal-scale fluctuations and unexpected departures from a simple dipolar field structure. This new information introduced an entirely new paradigm to the study of the geomagnetic field and to a wide range of research areas relying on paleomagnetic data, such as geochronology, climate research, and geodynamo exploration. This proposal aims at breaking the resolution limits in paleomagnetism, and providing a continuous time series of the geomagnetic field vector throughout the Holocene at decadal resolution and unprecedented accuracy. To this end I will use an innovative assemblage of data sources, jointly unique to the Levant, including rare archaeological finds, annual laminated stalagmites, varved sediments, and arid playa deposits. Together, these sources can provide unprecedented yearly resolution, whereby the “absolute” archaeomagnetic data can calibrate “relative” terrestrial data. The geomagnetic data will define an innovative absolute geomagnetic chronology that will be used to synchronize cosmogenic 10Be data and an extensive body of paleo-climatic indicators. With these in hand, I will address four ground-breaking problems: I) Chronology: Developing dating technique for resolving critical controversies in Levantine archaeology and Quaternary geology. II) Geophysics: Exploring fine-scale geodynamo features in Earth’s core from new generations of global geomagnetic models. III) Cosmogenics: Correlating fast geomagnetic variations with cosmogenic isotope production rate. IV) Climate: Testing one of the most challenging controversial questions in geomagnetism: “Does the Earth's magnetic field play a role in climate changes?”

1 786 381 €

Start date: 2018-11-01, End date: 2023-10-31

Hematopoiesis is an important model for stem cell differentiation with great medical significance. Heterogeneity within hematopoietic progenitor populations has considerably limited characterization and molecular understanding of lineage commitment in both health and disease. Advances in single-cell genomic technologies provide an extraordinary opportunity for unbiased and high resolution mapping of biological function and regulation. Recently we have developed an experimental and analytical method, termed massively parallel single-cell RNA-Seq (MARS-Seq), for unbiased classification of individual cells from their native context and successfully applied it for characterization of immune and hematopoietic progenitors. Here, we propose to uncover the hierarchy and regulatory mechanisms controlling hematopoiesis by combining comprehensive single-cell RNA-Seq analyses, modelling approaches, advanced functional assays, single-cell CRISPR screens, knockout models and epigenetic profiling. Exciting preliminary result show that indeed our approach is starting to uncover the complexity of hematopoietic progenitors and the regulatory circuits driving hematopoietic decisions. We will pursue the following aims: (i) Generate a refined model of hematopoiesis by comprehensive single-cell RNA-Seq profiling of hematopoietic progenitors, (ii) validate the predicted model by in vivo functional developmental assays and then (iii) test candidate transcription and chromatin factors uncovered by our model for their role in controlling progression towards various lineages using single-cell measurements combined with CRISPR screens. Together, our study is expected to generate a revised and high-resolution hematopoietic model and decipher the regulatory networks that control hematopoiesis. Our methods and models may provide a platform for future medical advancements including a large-scale European collaborative project to discover a comprehensive human hematopoietic tree.

2 000 000 €

Start date: 2017-10-01, End date: 2022-09-30

HYDROCARB is motivated by the enormous potential that stable hydrogen isotope ratios (δ2H values) in plant compounds have as hydrological proxy, but in particular as new proxy for the carbon metabolism in plants. Current conceptual models suggest that δ2H values in plant organic compounds are composed of (i) hydrological and (ii) metabolic signals. The hydrological information that is contained in δ2H values of plant material is now well understood and is often applied in (paleo-) hydrological research. In contrast, the metabolic information that is contained in plant δ2H values is mostly unknown. Intriguing recent research suggests, however, that metabolic signals in the δ2H values of plant organic compounds reflect the balance of autotrophic and heterotrophic processes in plants. This suggests that exciting and previously unknown opportunities exist to exploit δ2H values in plant compounds for information on the carbohydrate metabolism of plants, which would be relevant for a broad range of biological and biogeochemical disciplines. The goal of HYDROCARB is to perform the experimental work that is now needed to identify the key biochemical and physiological processes that determine the metabolic information that is recorded in the δ2H values of plant organic compounds such as leaf wax lipids, lignin and cellulose. With this HYDROCARB will provide the basis for semi-mechanistic models that will allow (i) disentangling hydrological from metabolic signals in plant δ2H values and (ii) identifying the precise physiological processes with respect to a plants carbohydrate metabolism that can be deducted from the δ2H values of different plant compounds. If successful, HYDROCARB will establish with this research δ2H values in plant organic compounds as a powerful new proxy that will allow ground-breaking and innovative research on plant and ecosystem carbon cycling, which has implications for plant biology, biogeochemistry and the earth system sciences.

1 999 941 €

Start date: 2017-11-01, End date: 2022-10-31

IRMIDYN will study the dynamics of redox-driven iron mineral transformation processes in soils and sediments and impacts on nutrient and trace element behavior using a novel approach based on enriched stable isotopes (e.g., 57Fe, 33S, 67Zn, 113Cd, 198Hg) in combination with innovative experiments and cutting-edge analytical techniques, most importantly 57Fe Mössbauer and Raman micro-spectroscopy and imaging. The thermodynamic stability and occurrence of iron minerals in sufficiently stable Earth surface environments is fairly well understood and supported by field observations. However, the kinetics of iron mineral recrystallization and transformation processes under rapidly changing redox conditions is far less understood, and has to date mostly been studied in in mixed reactors with pure minerals or sediment slurries, but rarely in-situ in complex soils and sediments. Thus, we do not know if and how fast certain iron mineral recrystallization and transformation processes observed in the laboratory actually occur in soils and sediments, and which environmental factors control the transformation rates and products. Redox-driven iron mineral recrystallization and transformation processes are key to understanding the biogeochemical cycles of C, N, P, S, and many trace elements (e.g., As, Zn, Cd, Hg, U). In face of current global challenges caused by massive anthropogenic changes in biogeochemical cycles of nutrients and toxic elements, it is paramount that we begin to understand and quantify the dynamics of these processes in-situ and learn how we can apply our mechanistic (but often reductionist) knowledge to the natural environment. This project will take a large step toward a better understanding of iron mineral dynamics in redox-affected Earth surface environments, with wide implications in biogeochemistry and other fields including environmental engineering, corrosion sciences, archaeology and cultural heritage sciences, and planetary sciences.

3 154 658 €

Start date: 2018-11-01, End date: 2023-10-31

Within a decade, advances in single-cell genomics would allow humanity to embark on a coordinated international effort to discover the human cell lineage tree. The goal of LineageDiscovery is to lay the biological, computational and architectural foundations for this envisioned project and demonstrate its feasibility and value. An organismal cell lineage tree is a rooted, labelled binary tree where nodes represent organism cells, edges represent progeny relations and labels capture cell state. The tree of an adult human has about 100 trillion nodes. Many fundamental open questions in biology and medicine are about the structure, dynamics and variance of the human cell lineage tree in development, health, ageing and disease. E.g., which cancer cells give rise to metastases? Do beta cells renew? Which progeny do brain stem cells produce in development, maintenance and ageing? LineageDiscovery is based on a decade of research on this challenge by Shapiro’s lab and others. It will develop an efficient biological-computational cell lineage discovery workflow that starts with sampled cells and ends with knowledge of their cell lineage tree; and a scalable architecture for the collaborative development and the distributed deployment of this workflow. The workflow will be based on emerging single-cell technologies and will include novel algorithms to analyse single-cell data, to reconstruct cell lineage trees, and to infer ancestral cell type and state dynamics. A programmable meta-system will be developed and used for workflow optimization and evaluation. The workflow and architecture will be deployed and tested in a broad range of proof-of-concept human cell lineage discovery experiments with self-funded collaborators. Successful execution of this research plan coupled with expected advances in single-cell genomics would establish both the feasibility and the value of the envisioned large-scale human cell lineage discovery project, ideally leading to its launch.

2 250 000 €

Start date: 2015-09-01, End date: 2020-07-31

The mammalian liver is a heterogeneous, yet highly structured organ, which performs diverse functions to maintain organismal homeostasis. Hepatocytes operate in repeating hexagonally shaped units termed lobules that are polarized by centripetal blood flow and morphogens. This polarized microenvironment facilitates optimal function by localizing specific processes to distinct lobule layers, a phenomenon known as ‘liver zonation’. While zonation of some key liver functions has been known for years, using spatially resolved single cell transcriptomics, we recently discovered that about 50% of liver genes are zonated. This surprisingly broad spatial heterogeneity raises a fundamental question - do hepatocytes form a uniform population that differs due to spatially graded inputs or are hepatocytes at different zones in fact distinct cell types? In this proposal we will tackle this question by developing techniques for sorting massive amounts of hepatocytes from defined tissue coordinates at high spatial resolution using zonated surface markers, new zonated reporter mouse models and mRNA content. We will perform a deep and comprehensive profiling of the hepatocyte genome, methylome, epigenome, transcriptome, proteome and metabolome at each zone to characterize liver zonation at all relevant cellular scales. We will also develop an ex-vivo system to functionally characterize the response of hepatocytes from distinct zones to identical input stimuli and the ability of hepatocytes to inter-convert to hepatocytes with differing zonal identities. These experiments will be performed in different metabolic states and along a high fat diet. This project will uncover new features of liver zonation in health and disease and redefine the hepatocyte cell state. Our approach for spatially refined tissue omics can be extended to other structured mammalian organs, thus opening new avenues of research in Systems Biology of mammalian tissues.

2 000 000 €

Start date: 2018-11-01, End date: 2023-10-31

"A key to understanding the processes operating in the outer part of the Earth is to look at the metamorphic rocks produced in orogenic belts. These rocks now exhumed to the Earth’s surface provide a record of what they experienced, if only they can be correctly interpreted. The recent use of high resolution devices has revealed the three-dimensional size, shape, composition and distribution of microstructural features in metamorphic rocks down to the nanometre-scale. The new observations show that mechanically maintained pressure variations can be significant (~1 GPa) even on a micro-scale. However, there is currently no satisfactory thermodynamic methodology for a quantitative interpretation of systems with such pressure variations in metamorphic rocks. Ignoring such pressure variations in petrological analysis can lead to errors in depth estimates that are comparable to the typical thickness of the whole continental crust. Such an error may then significantly influence the quality of geodynamic reconstructions. Here, I propose to develop a revolutionary theoretical and computational method to understand microstructures that reflect pressure variations, based on the chemical and mechanical properties of their constituent minerals. Using the novel theoretical approach, I and my team will perform 3D numerical simulations and give the criteria to correctly understand the key microstructures. This emerging multi-disciplinary research will provide a quantitative and physically-based framework for interpreting common microstructures in metamorphic rocks. Furthermore, the new approach will not only make a critical contribution to understanding the interplay between metamorphic processes and deformation on the grain scale, but it will also form the basis for a new generation of models for application to large-scale geological scenarios. The results of the project will thus significantly increase our understanding of key processes in the Earth’s lithosphere."

1 499 820 €

Start date: 2013-10-01, End date: 2018-09-30

There is a need for a radically new laboratory experimental approach for studying the interaction of seismic waves with the complex media of the Earth’s subsurface. We present here a fundamental new approach to seismic wave experimentation that involves fully immersing a physical seismic experiment within a virtual numerical environment. This enormously challenging endeavour, which is relevant to many outstanding issues in seismology, has not been previously attempted. By continuously varying the output of numerous transponders closely spaced around the physical domain using a control algorithm that takes advantage of measurements made by a scanning Laser-Doppler Vibrometer and a novel theory of exact boundary conditions, waves travelling between the physical and numerical domains will seamlessly propagate back and forth between the two domains without being affected by reflections at the boundaries between the two domains. This will allow us to investigate diverse types of Earth materials using frequencies that are much closer to those of seismic waves propagating through the Earth than previously possible. The novel laboratory enables experimentation under highly controlled conditions. A broad range of long-standing problems in wave propagation and imaging that have eluded Earth scientists and physicists for decades will be addressed. Fine scale heterogeneity, porosity and fluid saturation in real Earth media result in complex frequency-dependent amplitude and phase responses that we can characterize in the laboratory. Synthetically produced complex models can be used in wavefield-focussing experiments and to achieve complete elastic time-reversal for the first time ever. We will study coda waves that can be indicative of slight changes in stress fields before catastrophic fracturing and that might provide pre-cursory signs of earthquakes. Finally, the laboratory is highly relevant to applications such as non-destructive testing, medical imaging and lithotripsy.

3 498 330 €

Start date: 2016-12-01, End date: 2021-11-30

Tumor development emerges from an accumulation of somatic alterations that together enable malignant growth. These alterations are immensely diverse and the fate of a cell acquiring an alteration may depend on other alterations already present. Despite our progress in mapping the cancer genetic landscape and an expanding catalogue of cancer genes, a need arises to establish how alterations in cancer genes interact to transform healthy cells into cancer cells. Many fundamental questions regarding genomic interactions remain open. For example, we do not know which proteins make up signaling pathway hubs and in which genetic contexts, how genetic alterations interact functionally, how cancer genetic alterations influence the interaction with T cells and how these affect patient response to therapy. The recent growth in the number of genomics data sets gives rise to a parallel increase in statistical power to detect more complex associations allowing robust analyses of complex interrelated genomic networks. In this proposal we suggest to employ our expertise and unique toolsets, to shed new light on the complex interrelated networks formed in melanoma. We propose to combine state-of-the art high content tools with mechanistic studies to discover the structure of signaling-hub organization in melanoma (Aim 1), functionally characterize the complex genetic interactions within the melanoma genome using genome engineering approaches (Aim 2), and to decipher the immuno-genetic interactions between melanoma and T cells (Aim 3). Importantly, we will try to bridge the knowledge gap in deciphering melanoma-specific gene interactions, protein interactions and interactions with T cells by creating new tools and experimental models. Our findings should make an important step towards an unprecedented, thorough and multifaceted understanding of melanoma biology. More broadly, we believe these approaches provide a paradigm for addressing similarly complex questions in other cancers.

2 000 000 €

Start date: 2018-10-01, End date: 2023-09-30

About one-third of annual methane (CH4) emissions to the atmosphere originate from natural, nonanthropogenic sources. However, if all the naturally produced methane actually did reach the atmosphere, its levels would increase by an order of magnitude, dwarfing anthropogenic CO2 emissions. Fortunately, natural scavengers of this methane near its production zone limit its release. One of these scavengers, iron (Fe) oxide, can become a major sink for methane when sulfate concentrations are low. Methane-iron couplings in established sediments, however, are poorly understood. Specifically, significant iron oxide reduction has been observed in many aquatic sediments at depths well below its expected redox zone, where methane is produced by methanogenesis, often accompanied by decreases in methane concentrations. These observations challenge our understandings of iron-methane couplings and microbial players in the deep methanogenic zone and their impacts on the carbon, iron and other cycles. I aim in the proposed research to elucidate the unexplored mechanisms of methane-related iron reduction (MERIR) in the methanogenic zone of established sedimentary profiles under various environmental conditions and their impact on global biogeochemical cycles. I will resolve two striking yet unexplained phenomena: (1) the active involvement of aerobic methanotrophs in iron-coupled anaerobic oxidation of methane (AOM), and (2) the unusual reactivity of iron minerals toward reduction that is accompanied by intensive authigenic magnetite precipitation, and the effects of this mineralogy change on sedimentary magnetism. My expertise will enable me to achieve the objectives of this interdisciplinary proposed work using novel approaches from different fields. The project will likely lead to breakthroughs in our understanding of microbial survival strategies, reveal novel pathways for aerobic methanotrophs, and change our perspectives on iron mineral reactivities and sedimentary magnetism.

2 000 000 €

Start date: 2019-04-01, End date: 2024-03-31

MicroRNAs (miRNAs) are a novel class of genes, accounting for >1% of genes in a typical animal genome. They constitute an important layer of gene regulation that affects diverse processes such as cell differentiation, apoptosis, and metabolism. Despite such critical roles, deciphering the mechanism of action of miRNAs has been difficult, leading to multiple, partially contradictory, models of miRNA activity. Moreover, adding an additional layer of complexity, it is now emerging that miRNA activity is regulated by various mechanisms that we are only beginning to identify. Our objective is to understand how miRNAs are regulated under physiological conditions, in the roundworm Caenorhabditis elegans. We will focus on pathways of miRNA turnover, an issue of fundamental importance that has received little attention because miRNAs are widely held to be highly stable molecules. However, miRNA over-accumulation causes aberrant development and disease, prompting us to test rigorously whether degradation can antagonize miRNA activity and either identify the machinery involved, or confirm the dominance of other regulatory modalities, whose components we will identify. C. elegans is the organism in which miRNAs and many components of the miRNA machinery were discovered. However, previous studies emphasized genetics and cell biology approaches, limiting the degree of mechanistic insight that could be obtained. In addition to exploiting the traditional strengths of C. elegans, we will therefore develop and apply biochemical and genomic techniques to obtain a comprehensive understanding of miRNA regulation, enabling us to demonstrate both molecular mechanisms and physiological relevance. Given the importance of miRNAs in development and disease, identifying the regulators of these tiny gene regulators will be both of scientific interest and biomedical relevance.

1 782 200 €

Start date: 2010-05-01, End date: 2015-04-30

In eukaryotic cells, the higher-order organization of genomes is functionally important to ensure correct execution of gene expression programs. For instance, as cells differentiate into specialized cell types, chromosomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. However, how this process is achieved is still poorly understood. The elucidation of the mechanisms that control the spatial architecture of the genome and its contribution to gene regulation is a key open issue in molecular biology, relevant for physiological and pathological processes. Increasing evidence indicated that large-scale folding of chromatin may affect gene expression by locating genes to specific nuclear subcompartments that are either stimulatory or inhibitory to transcription. Nuclear periphery (NP) and nucleolus are two important nuclear landmarks where repressive chromatin domains are often located. The interaction of chromosomes with NP and nucleolus is thought to contribute to a basal chromosome architecture and genome function. However, while the role of NP in genome organization has been well documented, the function of the nucleolus remains yet elusive. To fully understand how genome organization regulates chromatin and gene expression states, it is necessary to obtain a comprehensive functional map of genome compartmentalization. However, so far, only domains associating with NP (LADs) have been identified and characterized while nucleolar-associated domains (NADs) remained under-investigated. The aim of this project is to fill this gap by developing methods to identify and characterize NADs and analyse the role of the nucleolus in genome organization, moving toward the obtainment of a comprehensive functional map of genome compartmentalization for each cell state and providing novel insights into basic principles of genome organization and its role in gene expression and cell function that yet remain elusive.

2 500 000 €

Start date: 2018-09-01, End date: 2023-08-31

Peptide-mediated protein interactions are emerging as key regulators of many important regulatory processes in the cell. Short motifs, usually embedded into disordered regions of the protein, interact with specific sets of protein partners in a transient way and allow efficient and malleable propagation of signals towards their targets. While regular protein interactions have been intensively studied, many aspects of peptide-mediated interactions have not yet been elucidated. The aim of this proposal is to improve our understanding of the basic strategies that are employed by peptide-mediated interactions to achieve different types of outcomes in different settings, and how the context of the peptide influences this outcome. Towards this aim, we will establish two complementary strategies, namely (1) a significant extension of our modeling tools for peptide-protein complex structures that will allow modeling of effects of the surrounding flexible linker, and (2) the establishment of an experimental lab that will allow us to independently validate and complement our modeling results. Targeted modulation of peptide affinity, specificity, and linker length and sequence, using both computational design as well as experimental in vitro evolution, will dissect different contributions to the functional outcome of a peptide-mediated interaction within its context. We can thus study in detail the interplay of the interaction with additional features in the linker sequence, such as posttranslational modification sites, as well as additional peptide binding motifs and interactions. Interactions mediated by intrinsically disordered regions are omnipresent. Their accurate characterization, modeling and manipulation holds therefore many promises towards applications for the development of better drugs and basic insights for better fundamental understanding of the underlying basis of regulatory interactions.

1 499 808 €

Start date: 2012-12-01, End date: 2017-11-30

Climatic variations at decadal scales, such as phases of accelerated warming, weak monsoons, or widespread subtropical drought, have profound effects on society and the economy. Understanding such variations requires insights from the past. However, no data sets of past climate are available to study decadal variability of large-scale climate with state-of-the-art diagnostic methods. Currently available data sets are limited to statistical reconstructions of local or regional surface climate. The PALAEO-RA project will produce the first ever comprehensive, 3-dimensional, physically consistent reconstruction of the global climate system at a monthly scale for the past six centuries. This palaeoreanalysis is based on combining information from early instrumental measurements, historical documents (e.g., capitalizing on large amounts of newly available data from China), and proxies (e.g., tree rings) with a large ensemble of climate model simulations. To achieve this novel combination, a completely new data assimilation system for palaeoclimatological data will be developed. The unique data sets produced in this project will become reference data sets for studying past climatic variations (i) for diagnostic studies of interannual-to-decadal variability, (ii) as a benchmark for model simulations and (iii) for climate impact studies. Using the data produced, the project will analyse episodes of slowed or accelerated global warming, decadal subtropical drought periods, episodes of expanding or contracting tropics, slowed or strengthened monsoons, changes in storm tracks, blocking and associated weather extremes, and links between Arctic and midlatitude climate. The analyses will provide new insights into the processes governing decadal variability of weather and climate.

2 499 975 €

Start date: 2018-10-01, End date: 2023-09-30

Cells process information using biochemical circuits of interacting proteins and genes. We wish to define principles guiding the design of those circuits. The interplay between variability and robustness is of key interest to us. Bio-molecular processes are stochastic, environmental conditions fluctuate, and sequence polymorphisms are abundant. How is variability buffered to maintain reproducible outcomes? Can variability enhance computational abilities? What is the impact of variability on bio-molecular circuit design? We will explore those fundamental questions in three contexts: Source of variability in Gene expression: We previously examined the mechanistic basis of expression variability, defining promoter structures associated with low vs. high variability. We will now address the more challenging question: what evolutionary pressures shape the expression program? On the network level, we will define mutual effects of selection for increased expression and for optimal growth. On the metabolic level, we will define which aspect of the expression process is limiting and the genomic consequences of this limitation. Role of expression variability in Nutrient homeostasis: We recently reported that repression of high affinity transporter in rich nutrient (the ‘dual-transporter’ motif) enables advanced preparation to nutrient depletion. We will now validate an additional predicted property of this motif: cells become committed to the starvation program, escaping it due to expression noise only. To this end, we will introduce a novel method for modulating expression noise while maintaining mean abundance. Buffering variability in Embryonic patterning: Buffering fluctuations is essential in embryonic patterning. We previously established that the embryonic DV axis of Drosophila is robustly patterned through the newly defined shuttling mechanism. We will quantify the ability of this system to buffer size variations (scaling), and reveal the underlying scaling mechanism.

2 311 000 €

Start date: 2014-02-01, End date: 2019-01-31

Deciphering the interactions within and between the three major components of living organisms, DNA, RNA and Protein, is at the heart of biological research. New large-scale experimental methods have dramatically advanced genome-wide detection of protein-protein, protein-DNA, protein-RNA and protein-mediated RNA-RNA interactions. However, at present there is no large-scale method that could detect all RNA-RNA interactions independent of a mediator protein, or when the mediator protein is unknown. Attaining such a method is of utmost importance and is very timely, as it is now evident that RNA-RNA interactions play central roles in cellular life. In particular, hundreds of expressed small RNA (sRNA) molecules were discovered in both pro- and eukaryotes, many of which act as posttranscriptional regulators of gene expression by base-pairing with their mRNA targets. It seems that in many organisms the layer of posttranscriptional regulation is as widespread as transcription regulation, presenting a major challenge towards achieving functional and mechanistic understanding of this regulation level. Here we propose to develop an innovative methodology for genome-wide detection of the sRNA targetome, all mRNA targets of cellular sRNAs. This new methodology combines in vivo structural probing with deep sequencing and is independent of protein considerations. We will apply this method to deciper the sRNA targetome of the model organism Escherichia coli, which encodes over 100 sRNAs. We will use the sRNA targetome data as the foundation for a systematic ‘bottom-up’ computational analysis of multifaceted aspects of sRNA-mediated posttranscriptional regulation, encompassing the basic underlying rules of sRNA-mRNA target recognition, the design principles of the posttranscriptional regulatory network and its integration with the transcriptional and metabolic networks, and the evolution of posttranscriptional regulation.

2 329 360 €

Start date: 2013-02-01, End date: 2019-01-31

"In the proposed research we will explore the functional proteomic diversity of histologically-defined regions within human breast tumors, aiming to identify novel protein biomarkers of tumor aggressiveness. Once identified, these proteins will serve as potent diagnostic markers and therapeutic targets. Towards this aim we will perform genome-scale proteomic profiling on tumor regions displaying diverse histopathology. This will be followed by functional investigation of these cancer cell sub-populations to determine their tumorigenic potential, and search for microparticle-based proteomic biomarkers from serum samples towards identification of cancer aggressiveness in blood tests. Analysis of the proteomic diversity holds a promise to reveal yet unidentified regulators of the tumorigenic phenotype as quantitative protein profiling is expected to most faithfully predict cellular phenotypes. This will be accomplished using the 'super-SILAC' technology, which I developed during my post-doctoral research. Using this technology, we identified over 12,000 proteins in formalin-fixed paraffin embedded breast cancer tumors. In the current project we will take one large step further, namely, microdissect and analyze selected regions in breast tumors based on local histopathological characteristics, such as the expression of known markers, cancer cell density, the vicinity to blood vessels and to the tumor invasive front. This ""topological map"" of the proteome will be followed by functional in vitro and in vivo studies, directly probing the aggressiveness of these cell populations, manifested by an accelerated proliferation and invasive/metastatic capacity. Finally, proteins associated with tumor aggressiveness will serve as blood-based biomarkers for predicting the tumorigenic phenotype using non-invasive tests. This work will set the basis for quantitative probing of tumor heterogeneity, which is crucial for accurate diagnosis and effective therapy. "

1 699 261 €

Start date: 2015-07-01, End date: 2020-06-30

Elements operating in the context of a system generate results that are different from the simple addition of the results of each element. This notion is one of the basic tenants of systems science. In systems biology/medicine complex (disease) phenotypes arise from multiple interacting factors, specifically proteins. Yet, the biochemical and mechanistic base of complex phenotypes remain elusive. An array of powerful genomic technologies including GWAS, WGS, transcriptomics, epigenetic analyses and proteomics have identified numerous factors that contribute to complex phenotypes. It can be expected that over the next few years, genetic factors contributing to specific complex phenotypes will be comprehensively identified, while their interactions will remain elusive. The project “Proteomics 4D: The proteome in context “explores the concept, that complex phenotypes arise from the perturbation of modules of interacting proteins and that these modules integrate seemingly independent genomic variants into a single biochemical response. We will develop and apply a generic technology to directly measure the composition, topology and structure of wild type and genetically perturbed protein modules and relate structural changes to their functional output. This will be achieved by a the integration of quantitative proteomic and phosphoproteomic technologies determining molecular phenotypes, and hybrid structural methods consisting of chemical cross-linking and mass spectrometry, cryoEM and computational data integration to probe structural perturbations. The project will focus initially on the structural and functional effects of cancer associated mutations in protein kinase modules and then generalize to study perturbed modules in any tissue and disease state. The resources supporting this technology will be disseminated to catalyze a broad transformation of biology and molecular medicine towards the analysis of the proteome as a modular entity, the proteome in context.

2 208 150 €

Start date: 2015-09-01, End date: 2020-08-31

Lack of replicability of scientific discoveries has surfaced too often in recent years, and even reached the attention of the general public. An ignored cause is the inappropriate statistical treatment of two statistical problems: (1) selective inference, manifested in selecting few promising leads following the statistical analysis of the potential many, where ignoring the selection process on estimates, confidence intervals and observed significance; (2) using too optimistic a yardstick of variation with which confidence intervals set and statistical significance of the potential discovery is judged, as a result of ignoring the variability between laboratories and subjects. The first problem becomes more serious as the pool of potential discoveries increases, the second paradoxically becomes more serious as measuring ability improves, which explain why the two problems are more prominent in recent years. Both problems have statistical solutions, but the solutions are not practical as they burden the analysis to a point where the power to discover new findings is exceedingly low. Therefore, unless required by regulating agencies, scientists tend to avoid using these solutions. I propose to develop methods that address such replicablity problems specific to medical research, epidemiology, genomics, brain research, and behavioral neuroscience. The methods include (a) new hierarchical weighted procedures, and model selection methods, that control the false discovery rate in testing; (b) shorter confidence intervals that offer false coverage-statement rate for the selected, both addressing the concern about selective inference; and (c) a compromise between using random effects models for the laboratories and subjects and treating them as fixed, to be aided by multiple laboratory database in behavior genetics and neuroscience. By serving the exact needs of scientists, while avoiding excessive protection, I expect the offered methodologies to become widely adapted.

1 933 200 €

Start date: 2012-03-01, End date: 2018-02-28

The research proposed uses an integrated data-modelling approach to elucidate the role that debris-covered glaciers play in the water cycle of High Mountain Asia (HMA) and establish how future HMA glacier and runoff will evolve. Debris-covered glaciers are of great significance for the hydrology of HMA, with large contributions to headwater streamflow. Despite this, their mass balance, hydrological role and future changes are poorly constrained, challenging model predictions of future water resources. Debris mantles insulate the ice and reduce ablation, but large-scale research indicates that HMA debris-covered glaciers are losing mass at rates similar to debris-free glaciers. This anomalous behaviour has profound implications for future glacier mass balance and runoff, but has not been reproduced with models, a fundamental limitation to a global assessment. I aim to establish that: 1) supraglacial cliffs and ponds are responsible for higher than expected mass losses of HMA debris-covered glaciers, because they act as windows of energy transfer through the debris; and that 2) their inclusion into models of glacier evolution will provide essential new estimates of glacier changes and future water availability in HMA. RAVEN will achieve these aims through combination of high-resolution satellite observations, field data and physically-based models in four sites along the Himalayan arc. This unprecedented setup captures the variety of climate and glaciers across HMA. Using satellite images I will investigate the spatial distribution and temporal evolution of cliffs and ponds; the insights will be used to develop physically-based models of cliff and pond ablation, which will be included in a glacio-hydrological model. Future glacier and runoff response will be projected using downscaled climate scenarios, allowing new estimates of glacier changes and future runoff for a data-starved region where millions of people depend on the water resources from glaciers and snow.

2 000 000 €

Start date: 2018-05-01, End date: 2023-04-30

Reconstruction of methane flux from lakes: development and application of a new approach

1 554 000 €

Start date: 2009-12-01, End date: 2014-11-30

The precise regulation of gene expression has been the subject of extensive scrutiny. Nonetheless, there is a big gap between genomic characterization of transcriptional responses and our predictions based on known molecular mechanisms and networks and of transcription regulation. In this proposal I argue for an approach to bridge this gap by using a novel experimental strategy that exploits the recent maturation of two technologies: the use of fluorescence reporter techniques to monitor promoter activity and high-throughput genetic manipulations for the construction of combinatorial genetic perturbations. By combining these, we will screen for genes that modulate the transcriptional response of target promoters, use genetic interactions between them to better resolve their functional dependencies, and build detailed quantitative models of transcriptional processes. We will use the budding yeast model organism, which allows for efficient manipulations, to dissect two transcriptional responses that are prototypical of many regulatory networks in living cells: [1] The early response to osmotic stress, which is mediated by at least two signaling pathways and multiple transcription factors, and [2] the central carbon metabolism response to shifts in carbon source, which involves multiple sensing and signaling pathways to maintain homeostasis. Our approach will elucidate mechanisms that are opaque to classical screens and facilitate building detailed predictive models of these responses. These results will lead to understanding of general principles that govern transcriptional networks. This is the first approach to comprehensively characterize the molecular mechanisms that modulate a transcriptional response, and arrange them in a coherent network. It will open many questions for detailed biochemical investigations, as well as set the stage to extend these ideas to use more detailed phenotypic assays and in more complex organisms.

2 199 899 €

Start date: 2009-01-01, End date: 2013-12-31

The proposal hinges on the noteworthy scientific perspectives provided by ecohydrological studies of river basins,seen as a natural laboratory for complex system perspectives integrating hydrologic, ecological and geomorphological dynamics. Moving from morphological and functional analyses of dendritic geometries observed in Nature over a wide range of scales,my claim is that essential processes sustaining human life and societies taking place along dendritic structures can be predicted. Population migrations and human settlements historically proceeded along river networks to follow water supply routes. Riparian systems,critically important ecosystems positioned along streams and rivers, play crucial roles in their watersheds,including nutrient filtering, biogeochemical processing,shade and resource provisioning, and stream bank stabilization. Devastating water-borne disease,such as cholera, and invading foreign species spread through water bodies linked by river networks. Although the dynamics of such systems has been extensively studied, existing approaches were mostly within the framework of mean-field or two-dimensional landscapes that ignore directionality of dispersal implied by the network acting as environmental matrix. How does connectivity within a a river network affect the emergent spreading of water-borne infections? Does the river basin act as a template for biodiversity? Are there hydrologic controls on the spreading of water-borne disease? To answer such questions, the present proposal addresses the study of biodiversity in the river basin (freshwater fish and riparian vegetation); cholera dynamics and zebra mussel invasions along river networks. Observational data and theoretical models, in a comparative mode,will be analyzed within a unified theoretical framework.This is intended to prove of crucial interest for understanding the functioning of river basins as a whole,including its ecosystem structure and function.

1 146 200 €

Start date: 2009-01-01, End date: 2013-12-31

RNA interference (RNAi) is a highly conserved, sequence-specific gene regulatory mechanism among eukaryotes. It is critical for a variety of important biological functions and is being pursued as a promising new tool for the treatment of a variety of human maladies. A surprising link between heterochromatin and the RNAi pathway was discovered a few years ago in fission yeast and plants, and similar mechanisms have more recently been described in various eukaryotes. However, to what extent the mechanisms we have been studying in yeast are conserved up to humans remains unknown. The goal of this proposal is to further our understanding of RNAi-mediated heterochromatin assembly by using fission yeast as a model organism, but also to investigate to role of RNAi in the nucleus of human cells. My proposal consists of three major aims. In aim 1 I propose to combine light and electron microscopy to address important and largely unanswered questions such as subcellular localization and temporal regulation of the RNAi pathway. Aim 2 builds on our recent discovery that RNAi factors physically associate with chromatin to control genome activity also outside constitutive heterochromatin. I am proposing experiments in fission yeast that aim at understanding the biological role of this new mode of genome regulation and its mechanistic dissection . However, we will also extend our analysis to human cells which will shed new light on the role of the RNAi pathway in the nucleus of higher eukaryotes. Finally, we are aiming at identifying the features a target locus in the S. pombe genome must have to become susceptible to RNAi-mediated silencing at the level of chromatin. Thus, the outcome of these experiments may substantially influence the developments of siRNA-based therapeutics.

1 599 992 €

Start date: 2012-01-01, End date: 2016-12-31

Robust and flexible tissue- and cell-type specific gene regulation is a definitive prerequisite for complex function in any multi-cellular organism. Modern genomics and epigenomics provide us with catalogues of gene regulatory elements and maps illustrating their activity in different tissues. Nevertheless, we are far from being able to explain emergence and maintenance of cellular states from such data, partly because we so far lacked characterization of individual molecular states and genome control mechanisms at their native resolution - the single cell. Recently, new approaches developed by the single cell genomics community, with several contributions from our group, allow massive acquisition of data on the transcriptional, epigenomic and chromosomal conformation states in large cohorts of single cells. In this research program, we aim to move forward rapidly to bridge a major gap between these experimental breakthroughs and models of genome regulation in complex tissues. We will develop algorithms and models for representing data the transcriptional profiles, DNA methylation landscapes and Hi-C maps of literally millions of cells. Our tools will be designed specifically to leverage on new single cell RNA-seq, single cell Hi-C, single cell capture-pBat and higher order 4C-seq that we will continue to develop experimentally. Furthermore, we shall enhance and optimize our interdisciplinary framework hand in hand with a working model aiming at unprecedentedly comprehensive single cell analysis of E8-E10 mouse embryos. This will provide us with hundreds of worked-out cases of tissue specific gene regulation. The techniques and insights from these studies will then be used to characterize cell type aberrations and epigenetic reprogramming in tumors. The open algorithms, techniques and methodology we shall develop can accelerate research in multiple groups that will utilize single cell genomics to study numerous questions on gene regulation in the coming years.

2 437 500 €

Start date: 2017-12-01, End date: 2022-11-30

The overall concept of this proposal is to investigate the main biogeochemical processes modulating spatial and temporal changes in marine export productivity, and assess their role in regulating atmospheric carbon dioxide (CO2) concentrations, both under present conditions and in the geological past. The exchange of CO2 between the atmosphere and ocean interior mediated by the oceanic ecosystem is a pivotal mechanism modulating the global carbon cycle, and thus, a substantial driver of the Earth’s climatic evolution. The overarching objective of this research proposal is to develop a novel proxy to trace changes in the global strength of the marine biological carbon pump (BCP) based on stable Chromium (Cr) isotopes. Despite its significance for the global carbon cycle, the BCP is still poorly constrained. This project will explore a tracer that has recently been developed to investigate the rise of atmospheric oxygen in the early history of the Earth and develop it thoroughly through a comprehensive, multidisciplinary calibration program and apply it to the much more subtle redox variations associated with organic matter remineralization in the ocean. The proposed approach includes phytoplankton culture experiments, water-column investigations and sedimentary analysis and will aim at elucidating the mechanisms governing the reduction of Cr and its associated isotopic fractionation. The proxy will subsequently be used to reconstruct export production variability in the past and assess its role in modulating glacial/interglacial climate oscillations. These past changes tended to be much slower than the current, anthropogenic change. Nonetheless, they can help to appraise sensitivities and point toward potentially dominant mechanisms of change. The observations gathered within the framework of this research program will enable refining the evolution of the marine carbon cycle and the rapidly declining buffering capacity of the ocean.

1 997 625 €

Start date: 2019-05-01, End date: 2024-04-30

Tumor metastases, relapse, and resistance to therapy are the main causes of death in cancer patients. Cancer stem cells (CSCs) drive cancer growth, are likely responsible for cancer reoccurrence, and provide the potential to colonize a metastatic site. A cell plasticity process called epithelial-mesenchymal transition (EMT) generates CSCs from epithelial cancer cells and simultaneously equips these cells with motility and invasiveness, features prerequisite for metastasis. Consequently, therapeutic strategies that target EMT and CSC signaling networks are highly attractive. However, the properties of these signaling networks and their dependency on the tumor microenvironment and cancer genotypes are poorly understood. Here we propose to generate quantitative, time-resolved biomarker signatures and network models of EMT stages and CSCs on the single-cell level and to define their dependency on breast cancer tumor microenvironments and genotypes. Using mass cytometry, a technology able to quantify up to 100 proteins and phosphorylation sites simultaneously in a single-cell, the signaling network structure of EMT and CSC state will be gauged by modulation of cancer-related and signaling genes. These data will be used to infer mathematical signaling network descriptions of EMT and the CSC states, and to determine their master regulators and regulatory sub-networks. By extending mass cytometry to spatially resolved measurements, the EMT/CSC network states and their microenvironment will be analyzed in three dimensions in patient samples, and data will be correlated with associated genomic and clinical information. Based on these in vivo data, follow-up experiments in mouse models will be performed to validate the identified network states and cell-to-cell interaction as therapeutic targets. Finally, the in vivo dataset and its correlation with genomic and clinical information will be used to identify biomarkers for personalized medicine approaches.

1 500 000 €

Start date: 2014-03-01, End date: 2019-02-28

"Terrestrial Reference Frames (TRFs) are the basis to which all positions on the Earth’s surface and all satellite orbits in the near Earth space have to refer to. The changes in the Earth's shape, rotation, and gravity field, the so-called ""three pillars"" of geodesy, provide the conceptual and observational basis for the TRFs. For today’s TRF realizations, four space geodetic techniques are combined and linked by co-location sites on the Earth’s surface (“Earth’s shape”) and by common Earth orientation parameters (“Earth rotation”). The third pillar (“Earth’s gravity field”) is today only contributing to the TRF determination via its associated center-of-mass. In SPACE TIE we will pave the way to unify the “three pillars” of Geodesy in future TRF realizations. We propose to use two satellite geodetic techniques, namely Global Navigation Satellite Systems (GNSS) and Satellite Laser Ranging (SLR), to connect them by co-location sites in space. These so-called space ties shall be realized on satellites of the currently existing space infrastructure, as well as on satellites due for launch in the near future. This includes the Medium Earth Orbits (MEO) of the GNSS satellites and, in particular, all satellites in Low Earth Orbits (LEO) with GNSS and SLR co-located on-board. To maximize the sensitivity to the Earth’s gravity field, the ultra-precise inter-satellite ranging between LEO satellites of dedicated gravity missions shall be added as a third satellite geodetic technique. One and the same state-of-the-art space geodetic software package will be used to ensure that standards, background models, and processing strategies are consistently applied across all co-location satellites and measurement techniques. The outcome of SPACE TIE will allow it to assess the geometric and gravimetric impact of mass transport in the atmosphere, oceans, and ice caps in a most consistent way to globally quantify the mass exchange between the different components of the system Earth."

1 999 563 €

Start date: 2019-05-01, End date: 2024-04-30

Carbon fixation is the main pathway for storing energy and accumulating biomass in the living world. It is also the principal reason for humanity s utilization of land and water. Under human cultivation, carbon fixation significantly limits growth. Hence increasing carbon fixation rate is of major importance towards agricultural and energetic sustainability. Are there limits on the rate of such central metabolic pathways? Attempts to improve the rate of Rubisco, the key enzyme in the Calvin-Benson cycle, have achieved very limited success. In this proposal we try to overcome this bottleneck by systematically exploring the space of carbon fixation pathways that can be assembled from all ~4000 metabolic enzymes known in nature. We computationally compare all possible pathways based on kinetics, energetics and topology. Our initial analysis suggests a new family of synthetic carbon fixation pathways utilizing the most effective carboxylating enzyme, PEPC. We propose to experimentally test these cycles in the most genetically tractable context by constructing an E. coli strain that will depend on carbon fixation as its sole carbon input. Energy will be supplied by compounds that cannot be used as carbon source. Initially, we will devise an autotrophic E. coli strain to use the Calvin-Benson Cycle; in the next stage, we will implement the most promising synthetic cycles. Systematic in vivo comparison will guide the future implementation in natural photosynthetic organisms. At the basic science level, this proposal revisits and challenges our understanding of central carbon metabolism and growth. Concomitantly, it is an evolutionary experiment on integration of a biological novelty. It will serve as a model for significantly adapting a central metabolic pathway.

1 498 792 €

Start date: 2011-01-01, End date: 2015-12-31

The complex functions of a living cell are carried out through the coordinated activity of many genes. Since transcription is a key step in establishing such coordinated activity, much effort was devoted to its study, and tremendous progress was made in identifying many of the transcription factors and regulatory DNA elements involved in the regulation of specific systems. However, very few attempts were made at going beyond these phenomenological and qualitative descriptions. Consequently, we are far from a quantitative and predictive understanding of transcriptional regulation. Through this program, I aim to develop a mechanistic understanding of transcriptional regulation, and for the first time model the entire process. We wish to go much beyond identifying and qualitatively describing the involved components, and arrive at a quantitative understanding of how transcriptional programs are encoded in the DNA sequences. To this end, my team and I will first work to mechanistically understand various building blocks of the transcriptional system, including: mechanisms of activation and repression; binding cooperativity; binding competition; transcription factors and chromatin interplay; architectural features of promoters that are important for its function; and the transcription functions “computed” by promoters. Since existing data are clearly insufficient for addressing such questions, I have opened an experimental lab and began to assemble a multidisciplinary team of scientists whose expertise span the experimental biology, computer science, physics, statistics, and mathematics disciplines, that will work synergistically to generate the appropriate data, analyze it, and use it to construct and experimentally validate models for the above transcriptional building blocks. We will then integrate all the insights gained into unified and quantitative models that should significantly enhance our understanding of the mechanistic workings of transcriptional regulation.

1 005 600 €

Start date: 2008-07-01, End date: 2013-06-30