DNA has a huge potential for the long-term storage of large amounts of data. However, writing, editing, and reading DNA-based data is expensive and inefficient with current technologies. Our vision is to develop a low-cost, energy-efficient, and fast data drive that is able to write, edit, store, and retrieve DNA-based data. The data drive is based on simple and easily available hardware components plus bacterial cells. The proposed technological solution enables the short-, medium-, and long-term storage of DNA-based data. To achieve this vision, we will exploit bacterial genetic mechanisms that were evolutionarily optimized for billions of years, such as colour-sensitive genetic switches and DNA exchange processes. We have defined two specific objectives to achieve our goal. As a proof-of-concept, we will store a large trajectory file of a molecular dynamics simulation encoded on DNA. Our consortium has six partners from four European countries. One research organisation, two university, and two SMEs will work together to achieve the outlined vision.

The World Health Organization has emphasized the importance of early and accurate diagnosis of bacterial infections. An ideal diagnostic tool would possess high speed, high throughput, accuracy, low cost and simplicity of use for the clinical laboratory or bed-side applications. Diagnostic tools that possess all these properties currently do not exist. To address this knowledge gap, in the BUG-ID consortium, seven European universities, one research institute, one hospital and six private companies have teamed up. Our consortium will train 15 doctoral candidates with skills in interdisciplinary research, spanning from nanotechnology and materials science to molecular microbiology, biochemistry, infection medicine to AI-based data analysis. Private sector participants will bring their full capacity to bear on intersectoral training, allowing doctoral students to forge links between science and innovation. At the core of the BUG-ID concept is the 2D nanomaterial graphene. Versatile surface chemistry, sensing capacity and possibility of integration with electronic and optical devices will be the key properties of graphene exploited by our consortium. Scientific challenges we will tackle will include the identification of suitable biomarkers for infection in complex environments (background of bacterial commensals), structural engineering of appropriate receptors for identified biomarkers, functionalization of graphene sensors with the receptors and their integration into functional sensors, miniaturization of sensor technology and optimization of complex signal readouts using machine learning techniques and explainable AI. To pave the way for building such game-changing technology, BUG-ID doctoral students will have to work together as a team, drawing competence from distant scientific disciplines, and moving across sectoral boundaries. In doing so, they will receive training that empowers them to become future leaders in science and innovation.

Phytoplasmas (genus Candidatus Phytoplasma) are wall-less bacteria from the class Mollicutes that affect numerous plant species worldwide causing significant economic losses. They have a unique life-style inhabiting plant phloem and insect cells and needing both hosts for survival in nature. Their genomes are repeat-rich yet relatively small and reduced missing many basic metabolic pathways. Phytoplasma axenic cultivation is still challenging. Nevertheless, 4 phytoplasma genomes have been sequenced and annotated with several genome drafts also available. However, the understanding of all mechanisms underlying phytoplasma pathogenicity is far from complete. First molecular evidence for the phytoplasma presence in Croatia has been given in late 1990’s on grapevine. Since then, the number of discovered phytoplasma species, insect vectors and affected plant hosts is rising with grapevine and fruit trees’ phytoplasma pathosystems being well characterized. The main objective of this project would be sequencing of ‘Ca. P. solani’, the most widespread phytoplasma in Croatia, with generation and comparative analysis of genome draft or fully assembled genome. Obtained results would give new data on candidate virulence effectors and other factors involved in interactions with hosts and adaptation to different environments. Another goal would be genotyping of new and already available isolates by multilocus sequence typing (MLST) analyses of house-keeping and specific variable genes. New genotyping tools for improved diagnostics and molecular epidemiology studies with implications in risk assessment would also be developed. Functional studies would focus on surface variable membrane proteins involved in interactions with insect hosts and transmissibility. Moreover, this would be the first sequencing project of a bacterial plant pathogen genome in Croatia. The establishment of this project would open a new field of molecular plant pathology and genomics in Croatian science.

The project aims at advancing our knowledge on effects of multiple stressors on: I) freshwater biodiversity, and on II) ecosystem functioning and aquatic-terrestrial habitat linkage (ATHL). These objectives will be approached by combining field-based research (in situ) and laboratory (mesocosm) experiments. More specifically, we aim at providing novel insights into species- and lineage-specific responses to environmental stressors through application of the DNA barcoding. This approach provides estimation of evolutionary lineage diversity in macroinvertebrate indicator taxa in multiple stressor environment (e.g. toxicants & climate change). Furthermore, we will measure transfer of emerging contaminants (ECs: PhACs, EDCs, antibiotics) through the ATHL in order to provide essential links necessary for evaluation of routes and mechanisms of ECs transfer through food webs and ecosystems. These are essential for development of more realistic biomagnification scenarios of ECs within a multiple stressor environment.

The goal of the project is the formation of a new research group around a new research direction. It is meant as an interplay of areas of the team members: we plan to relate the qualitative theory of dynamical systems with the theory of complex dimensions of fractal sets, through fractal analysis of orbits. By fractal properties of orbits, we mean their box dimension and generalizations. We are motivated by the ‘inverse question’: can we extract information on the behavior of a system by fractal analysis of a single trajectory? The complex dimensions of fractal sets generalize the notion of their box dimension and reveal the geometrical structure more precisely. Analysing complex dimensions of orbits seems to be well-adaptedto measuring the complexity of the system. The theory of complex dimensionsis based on the analysis of singularities of complex functions (fractal zeta functions introduced by Lapidus). It is a very interesting field in itself, related to spectral theory, mathematical physics and number theory (the well-known Riemann hypothesis).We plan to apply this theory to important questions in discrete dynamical systems, such as their classifications. In short, key points of the research are: classifications (formal and analytic) of 1-dim discrete systems through complex dimension analysis of attached orbits, and understanding their bifurcations by the set of complex dimensions of attached orbits. Our aim is also to promote the field of dynamical systems in Croatia by organizing a workshop and mini-courses. We plan to expand our small group by engaging a new PhD student and a postdoc. In Croatia, there is only a small group of researchers in dynamical systems, scattered in different areas, which we intend to bring closer together. In the course of the project, we will put a particular effort in scientific growth of the new PhD student. We plan to provide her/him with the opportunity of international collaborations from the beginning of her/his career.