Milk and its fermentation derivatives, yogurt and cheese, are globally consumed at rates of >750 million tonnes annually, and are responsible for ~10% of the protein consumption worldwide. In the process of yogurt and cheese production, starter cultures of lactic acid bacteria (LAB) are added to milk, leading to fermentative production of the end product. Optimal growth of the lactic acid bacteria within the milk is critical for high-quality fermentation in the manufacturing of such dairy products. During fermentation, growth of starter culture bacteria is frequently impaired by viruses (phages) that infect these bacteria. Phage infection of lactic acid bacteria fermentative cultures is the main cause for incomplete or delayed fermentation processes in the dairy industry, and it is estimated that 10% of dairy fermentation processes fail due to culture infection by phage. This puts an extensive financial burden on the yogurt and cheese industries, a market estimated at >$80B annually. There is therefore a strong need for tools that would protect lactic acid bacteria from phage infection during the fermentation process. In our ERC-funded project we discovered novel defense systems that confer strong resistance against multiple types of phages. We showed that our systems do not impair normal growth of bacteria, and provide efficient phage-resistance features, conferring protection against a broad range of phages. Within the current PoC project we will harness our discoveries to develop non-GMO prototype lactic acid bacteria that are strongly protected against phage infection. This prototype is expected to demonstrate highly resilient, enhanced starter culture bacteria that will have superior durability and resistance over currently available starter culture bacteria used in the market.

Trees play a major role in Earth’s water and carbon cycles. Climate change puts trees under a growing threat of drought-induced mortality. This already happens in Europe, where summers are becoming hotter and drier, and across global forest biomes. Due to their large size and long lifespan, trees need time to adapt and migrate, time they lack under the fast rate of global change. On the other hand, foersts are amog the most important ecosystems we simply cannot afford to lose. Loss of xylem hydraulic conductivity due to eruption of air bubbles is termed xylem embolism. Despite many years of studying tree responses to drought, it is still debated whether xylem embolism actually kills trees. Simultaneous processes like carbon starvation, leaf desiccation and heat damage make it harder to pinpoint the direct effects of drought on xylem enbolism. Further, while the extent of embolism avoidance has been characterized in many tree species, embolism tolerance has been rarely studied, and recovery processes are mostly unknown. Finally, a wide research gap exists between eco-physiological mechanisms at the tree scale and implications at the forest scale. This research proposal portrays a clear roadmap to resolving the open questions in tree hydraulic mechanisms under drought, and to integrating them at the forest scale. Increasing drought resilience in forests through eco-physiological mechanisms requires (1) in-situ field measurements, (2) controlled experiments to decipher tree mechanisms, and (3) advanced modeling to upscale tree-level measurements into the forest scale and support future forest management. We will combine novel techniques (custom-made micro-CT, field detection of xylem embolism and water potential, spatial mass spectrometry imaging, and more); field measurements and manipulations on mature trees; greenhouse experiments on diverse tree species; and computational modeling, to test new hypotheses aimed at increasing drought resilience of forests.

Immunotherapy, which has revolutionized cancer treatment, largely relies on the immune system’s recognition of neopeptides, degradation products of altered proteins specific to cancer cells presented on their surface. In particular, cancer vaccines targeting neopeptides have shown promising clinical results. Yet, to optimize their efficacy and broaden their application, we need to decipher the nature of the cancer peptide landscape (immunopeptidome) and delineate the neopeptide properties required to induce a potent immune response. The overarching goal of this proposal is to provide an unprecedented, thorough, multifaceted understanding of the mechanisms underlying aberrant peptide production, peptide-MHC presentation, and T-cell recognition in melanoma. We will do so by pursuing three key avenues: Systematic interrogation of the cancer immunopeptidome to identify novel canonical and non-canonical cancer antigens and quantify their presentation (Aim 1). Comprehensive functional assessment of the intrinsic qualities of actionable antigens by quantitatively charting the immunopeptidome in-vivo, while considering peptide presentation levels, clonality and cross-presentation; and delineating how these neoantigen qualities impact the immune response (Aim 2). Establish controlled in-vivo models to tease apart neoantigen qualities for the establishment of rational cancer vaccine modalities (Aim 3). In this effort, we will draw upon our pioneering tools and advanced mapping of the cancer peptidome in melanoma, which has already revealed novel antigenic sources. Our research approach combines comprehensive quantitative immunopeptidomics, novel imaging and computational approaches, advanced functional assays and novel mouse models. Our project will provide a fresh view of melanoma-immune interactions, new research tools and pipelines, cancer-specific antigen targets for immunotherapy and, more broadly, a paradigm for addressing similarly complex questions in other cancers.

Organisms form crystalline materials with superior structural and mechanical properties. This arises from the ability of functional macromolecules to create intricate architectures via a multi-step crystallization process. Current approaches to engineer bioinspired minerals focus on interactions between macromolecules and minerals in dilute aqueous environments, rarely considering the emergent properties of macromolecular condensates. However, we and others showed that macromolecular crowding is intimately associated with biomineral formation in vivo. In this project, we will develop a new type of chemistry—dense-phase mineralization—to unlock the pathways mastered by nature. Our hypothesis is that weak polymer-ion interactions within dense phases tune the chemical landscape, controlling the crystallization process and the properties of its products. Remarkably, our preliminary results using the calcium carbonate system show that molar-range polymer concentrations, four orders of magnitude denser than in previous works, result in intricate crystals with life-like properties. We will investigate dense-phase mineralization in both synthetic and living systems, relying on our unique expertise in cryo-electron and X-ray microscopies of hydrated biological samples. In Aim 1, we will grow crystals in a dense polymer phase and use the crowded environment to sculpt architectural motives. In Aim 2, we will investigate the challenging phase separation regime and transform inorganic condensates into transient precursors for mineralization. In Aim 3, we will elucidate how liquid-liquid phase separation evolved by mineralizing organisms to regulate inorganic condensate formation. This project will open an uncharted chemical landscape to form and control bioinspired minerals. The outcome will be a toolbox for process design that allows to optimize material properties - the highest gain we can ask for in bioinspired mineralization.

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.