ERC FUNDED PROJECTS

The objective of this project is to overcome current limitations for antibody production that are inherent to the extant immune system of vertebrates. This will be done by creating an all-in-one artificial/synthetic counterpart based exclusively on prokaryotic parts, devices and modules. To this end, ARISYS will exploit design concepts, construction hierarchies and standardization notions that stem from contemporary Synthetic Biology for the assembly and validation of (what we believe is) the most complex artificial biological system ventured thus far. This all-bacterial immune-like system will not only simplify and make affordable the manipulations necessary for antibody generation, but will also permit the application of such binders by themselves or displayed on bacterial cells to biotechnological challenges well beyond therapeutic and health-related uses. The work plan involves the assembly and validation of autonomous functional modules for [i] displaying antibody/affibody (AB) scaffolds attached to the surface of bacterial cells, [ii] conditional diversification of target-binding sequences of the ABs, [iii] contact-dependent activation of gene expression, [iv] reversible bi-stable switches, and [v] clonal selection and amplification of improved binders. These modules composed of stand-alone parts and bearing well defined input/output functions, will be assembled in the genomic chassis of streamlined Escherichia coli and Pseudomonas putida strains. The resulting molecular network will make the ABs expressed and displayed on the cell surface to proceed spontaneously (or at the user's decision) through subsequent cycles of affinity and specificity maturation towards antigens or other targets presented to the bacterial population. In this way, a single, easy-to-handle (albeit heavily engineered) strain will govern all operations that are typically scattered in a multitude of separate methods and apparatuses for AB production.

2 422 271 €

Start date: 2013-05-01, End date: 2019-04-30

The goal of ATOMICAR is to achieve the ultimate sensitivity limit in heterogeneous catalysis: Quantitative measurement of chemical turnover on a single catalytic nanoparticle. Most heterogeneous catalysis occurs on metal nanoparticle in the size range of 3 nm - 10 nm. Model studies have established that there is often a strong coupling between nanoparticle size & shape - and catalytic activity. The strong structure-activity coupling renders it probable that “super-active” nanoparticles exist. However, since there is no way to measure catalytic activity of less than ca 1 million nanoparticles at a time, any super-activity will always be hidden by “ensemble smearing” since one million nanoparticles of exactly identical size and shape cannot be made. The state-of-the-art in catalysis benchmarking is microfabricated flow reactors with mass-spectrometric detection, but the sensitivity of this approach cannot be incrementally improved by six orders of magnitude. This calls for a new measurement paradigm where the activity of a single nanoparticle can be benchmarked – the ultimate limit for catalytic measurement. A tiny batch reactor is the solution, but there are three key problems: How to seal it; how to track catalytic turnover inside it; and how to see the nanoparticle inside it? Graphene solves all three problems: A microfabricated cavity with a thin SixNy bottom window, a single catalytic nanoparticle inside, and a graphene seal forms a gas tight batch reactor since graphene has zero gas permeability. Catalysis is then tracked as an internal pressure change via the stress & deflection of the graphene seal. Crucially, the electron-transparency of graphene and SixNy enables subsequent transmission electron microscope access with atomic resolution so that active nanoparticles can be studied in full detail. ATOMICAR will re-define the experimental limits of catalyst benchmarking and lift the field of basic catalysis research into the single-nanoparticle age.

1 496 000 €

Start date: 2018-02-01, End date: 2023-01-31

Sustainable agriculture is an ambitious concept conceived to improve productivity but minimizing side effects. Why the efficiency of a biocontrol agent is so variable? How can different therapies be efficiently exploited in a combined way to combat microbial diseases? These are questions that need investigation to convey with criteria of sustainability. What I present is an integral proposal aim to study the microbial ecology and specifically bacterial biofilms as a central axis of two differential but likely interconnected scenarios in plant health: i) the beneficial interaction of the biocontrol agent (BCA) Bacillus subtilis, and ii) the non-conventional interaction of the food-borne pathogen Bacillus cereus. I will start working with B. subtilis, and reasons are: 1) Different isolates are promising BCAs and are commercialized for such purpose, 2) There exist vast information of the genetics circuitries that govern important aspects of B. subtilis physiology as antibiotic production, cell differentiation, and biofilm formation. In parallel I propose to study the way B. cereus, a food-borne pathogenic bacterium interacts with vegetables. I am planning to set up a multidisciplinary approach that will combine genetics, biochemistry, proteomics, cell biology and molecular biology to visualize how these bacterial population interacts, communicates with plants and other microorganisms, or how all these factors trigger or inhibit the developmental program ending in biofilm formation. I am also interested on knowing if structural components of the bacterial extracellular matrix (exopolysaccharides or amyloid proteins) are important for bacterial fitness. If this were the case, I will also investigate which external factors affect their expression and assembly in functional biofilms. The insights get on these studies are committed to impulse our knowledge on microbial ecology and their biotechnological applicability to sustainable agriculture and food safety.

1 453 563 €

Start date: 2015-03-01, End date: 2021-02-28

The use of renewable feedstocks by the chemical industry is fundamental due to both the depletion of fossil resources and the increasing pressure of environmental concerns. Biomass can act as a sustainable source of organic industrial chemicals; however, the establishment of a renewable chemical industry that is economically competitive with the present oil-based one requires the development of new processes to convert biomass-derived compounds into useful industrial materials following the principles of green chemistry. To achieve these goals, developments in several fields including heterogeneous catalysis are needed. One of the ways to accelerate the discovery of new potentially active, selective and stable catalysts is the massive use of computational chemistry. Recent advances have demonstrated that Density Functional Theory coupled to ab initio thermodynamics, transition state theory and microkinetic analysis can provide a full view of the catalytic phenomena. The aim of the present project is thus to employ these well-tested computational techniques to the development of a theoretical framework that can accelerate the identification of new catalysts for the conversion of biomass derived target compounds into useful chemicals. Since compared to petroleum-based materials-biomass derived ones are multifuncionalized, the search for new catalytic materials and processes has a strong requirement in the selectivity of the chemical transformations. The main challenges in the project are related to the high functionalization of the molecules, their liquid nature and the large number of potentially competitive reaction paths. The requirements of specificity and selectivity in the chemical transformations while keeping a reasonably flexible framework constitute a major objective. The work will be divided in three main work packages, one devoted to the properties of small molecules or fragments containing a single functional group; the second addresses competition in multiple functionalized molecules; and third is dedicated to the specific transformations of two molecules that have already been identified as potential platform generators. The goal is to identify suitable candidates that could be synthetized and tested in the Institute facilities.

1 496 200 €

Start date: 2010-10-01, End date: 2015-09-30