ERC FUNDED PROJECTS

"Given the alarming progression of chronic and relapsing infections in the last decades, and the even more alarming predictions for the upcoming years, it is urgent for chemists to be able to provide new molecular tools to study, and ultimately solve, these complex biological problems. Bacterial persisters are an elusive ""dormant"" phenotype that play a pivotal role in chronic infections, with mechanisms that remain to be fully unravelled. Current knowledge suggests that bacterial persisters are not genetically resistant to antibiotic treatment; they simply appear to shut down through a cascade of biochemical events called the stringent response (SR), becoming insensitive to current drugs. This subpopulation remains unaffected during the time of pharmacological treatment and represents a reservoir that sustains pathogen survival and resurgence. The goal of this project is to fill the knowledge gap between persisters formation and infection eradication, providing the community with potent and selective small molecular tools that can be used to challenge complementary survival mechanisms. I will adopt a combined approach targeting a specific cellular trigger of the persister phenotype with small molecules designed ad hoc in order to switch it off. The target is a bacterial protein involved in the SR cascade, whose activity is proposed to be allosterically regulated. Coordination propensity analysis of the dynamic behaviour of the target will highlight regulation sites exploitable to modulate and control the protein activity. Structure-based design, virtual fragment screening and chemical synthesis will operate in synergy. Experimental screening methodologies intrinsically rich in structural information, such as those based on NMR spectroscopy, will be privileged. The overarching goal is to identify molecules able to prevent the insurgence of the ""dormant"" drug-tolerant state and, possibly, revert the persisters already present to the ""awake"" drug-sensitive phenotype. "

1 500 000 €

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

This project aims to investigate the role of potassium (K+), protons (H+) and oxygen (O2) gradients in the extracellular space of tumour cells grown in 3D cultures by using a combination of imaging, cell biology and in silico analyses. By embedding ratiometric fluorescent particle-based sensors within 3D scaffolds, the changes in target analyte concentrations can be monitored and used to study the interactions between tumour cells and stromal cells in 3D tumoroids/scaffolds and to monitor response of the cells to drug treatments. I first demonstrated successful fabrication of barcoded capsules for multiplex sensing of H+, K+, and Na+ ions. Next, I demonstrated the use of pH-sensing capsules as valid real time optical reporter tools to sense and monitor intracellular acidification in living cells. Thus, I can fabricate capsule sensors for investigating the role of key analytes that are involved in regulation of crucial physiological mechanisms. In addition, I successfully integrated pH-sensing capsules within 3D nanofibrous matrices and demonstrated their operation under pH switches. INTERCELLMED will engineer 3D scaffolds that do not only sense extracellular pH but are also able to sense K+ and O2 changes. To this aim, a novel set of anisotropic analyte-sensitive ratiometric capsules will be developed and applied for generating robust and flexible capsules-embedded sensing scaffolds. To validate the functions of the 3D sensing platform, cocoltures of tumour cells and stromal cells will be grown and their interaction and response to drug treatments will be studied by mapping the K+/H+/O2 gradients in and around the cell aggregates. Finally, the 3D sensing platform will be adapted for growing tumour tissue-derived cells that will be tested ex-vivo with anticancer dugs. Specific mathematical models of cellular interactions will be developed to represent the biological processes occurring within the 3D sensing platform.

1 050 000 €

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

Engineers can actively contribute to fields thought to be out of their “comfort zones”. We can be leaders of discoveries that translate into advances in the understanding of disease and improving human health. Engineers might use different language and tools than Life Sciences Scientists but we find a common ground, as the laws of Thermodynamics, Physics, and Mathematics also apply to biological phenomena. The development of microbioreactors (μBRs) reconstructing biologically sound niches can revolutionize medical research. In our bodies cells reside in a complex milieu, the microenvironment (μEnv), regulating their fate and function. Most of this complexity is lacking in standard laboratory models, leading to readouts poorly predicting the in vivo situation. This is particularly felt in cancer research, as tumors are extremely heterogeneous and capable of conditioning both the local μEnv and distant organs. Neuroblastoma (NB) is the most common and difficult to cure pediatric malignant solid tumor. Secreted exosomes are means by which NBs reshape their μEnv and induce local and long-range changes in cells, regulating progression and prognosis. But the mechanisms involved are yet not completely understood. A major limitation is the difficulty to model in vitro the local in vivo dynamic μEnv. We hypothesize that μBRs exploiting classical engineering principles will solve the limitations of existing classical culture models. We propose to develop platforms and test their edge over classical approaches in decoding the role of exosomes and μEnv in NB. Our μBRs generate time and space-resolved concentration gradients, support fast dynamic changes and reconstruct complex interactions between cells and tissues while performing multifactorial and parallelized experiments. We expect that our technologies will bridge the gap between in vitro techniques and in vivo biological phenomena leading to significant and novel results, shedding light on previously unexplored scenarios.

1 446 250 €

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

Despite the fact that the catalyst structure has been an important factor in catalysis science since the discovery of structure sensitive reactions in single crystal studies, its effect on reactivity is neglected in state-of-the-art microkinetic modelling. In reality, the catalyst is dynamic by changing its structure, shape and size in response to the different conditions in the reactor. Thus, the inclusion of such effects within the framework of microkinetic modelling, albeit extremely complex, is of outmost importance in the quest of engineering the chemical transformation at the molecular level. This proposal aims to approach this grand challenge by developing a hierarchical multiscale methodology for the structure-dependent microkinetic modelling of catalytic processes in applied catalysis. In particular this challenging objective will be achieved by acting on two main fronts: i. development of a hierarchical multiscale methodology for the prediction of the structural changes of the catalyst material as a function of the operating conditions in the reactor and the analysis of the structure-activity relations through the development of structure-dependent microkinetic models; ii. show the applicability of the methodology by the assessment of the structure-activity relation in the context of relevant processes in energy applications such as the short-contact-time CH4 reforming with H2O and CO2 on supported-metal catalysts. The inherent complexity of the problem will be tackled by hierarchically combining novel methods at different levels of accuracy in a dual feed-back loop between theory and experiments. This will require interdisciplinary efforts in bridging among surface science, physical-chemistry and chemical engineering. The fundamental nature and impact of the methodology will be unprecedented and will pave the way toward the detailed analysis and design of the structure-activity relation by tuning shape and size to tailoring activity and selectivity.

1 496 250 €

Start date: 2016-05-01, End date: 2021-04-30