Ján Turňa

Open Science infrastructure provides researchers with digital services, computational resources and data environments supporting the FAIR principles and enabling effective sharing and reuse of research outputs. This paper presents the development of Open Science infrastructure in Slovakia and demonstrates its application in the life sciences through pathogen genomics and antimicrobial resistance (AMR) surveillance. Particular attention is paid to the Slovak node of the European Open Science Cloud (EOSC), the NarCoS bioinformatics platform and their role in processing and analysing large-scale genomic datasets. The paper describes a federated approach to cross-border cooperation between the Slovak and Polish EOSC nodes, in which harmonised workflows enable analysis while sensitive data remain under local control. The presented use case demonstrates how federated Open Science infrastructure can support interoperable genomic analysis, strengthen data sovereignty and contribute to more effective cross-border surveillance of infectious pathogens and antimicrobial resistance.

The chapter examines the science and research ecosystem in Slovakia, including its constituent elements, actors, processes, and instruments, with particular emphasis on the organization of research information and research data management. Credibility and transparency constitute fundamental pillars of the contemporary scientific ecosystem. In a context where science increasingly depends on open data, interdisciplinary collaboration, and public funding, these principles acquire critical significance for the effective functioning of research and innovation. The first section explores national science policy and its key principles such as open science, research ethics, and gender equality in science and research. The second section focuses on the prerequisites for data-driven policymaking in the field of science and research. It addresses standards and models for data recording within information systems supporting scientific activity, the processing of research data, and the integration of such systems as essential conditions for producing high-quality and trustworthy data.

N-glycosylation of recombinant proteins using bacterial glycosylation system has proven to be a valuable although developing tool ultimately applicable to various industries. When used for enzyme engineering, it offers the possibility of increased stability or immobilization route and thus increasing effectiveness of e.g. biotransformation or other biocatalysis procedures. One such promising enzyme is alcohol dehydrogenase (ADH) for use in redox biotransformation reactions. Given the current possibilities of recombinant enzyme production, including major advances in glycoengineering and glycoprotein production in bacterial organisms, the aim of this work was the production of thermotolerant ADH from Rhodococcus ruber (RrADH) in glycosylated form in Escherichia coli. We have successfully developed a dual plasmid expression system enabling glycosylation of target proteins utilizing a glyco-tag approach. We were able to produce RrADH in soluble form and at the same time we detected a bacterial glycan conjugated to RrADH as well as the activity of the enzyme. The glycan bound to recombinant enzyme can be used for oriented covalent immobilization of the enzyme, which would increase the potential for its practical application in biotransformation of various compounds.

Tellurite resistance gene clusters have been identified in numerous pathogenic bacteria, including clinical isolates of Escherichia coli. The rareness of tellurium in host organisms and the noncontaminated environment raises a question about the true functionality of tellurite resistance gene clusters in pathogenesis and their possible contribution to bacterial fitness. The study aims to point out the beneficial effects of the tellurite resistance gene cluster of pathogenic bacteria to survive in ROS-rich environments. Here, we analysed the bacterial response to oxidative stress conditions with and without tellurite resistance gene clusters, which are composed of terWY1XY2Y3 and terZABCDEF genes. By measuring the levels of protein carbonylation, lipid peroxidation, and expression changes of oxidative stress genes upon oxidative stress, we propose a tellurite resistance gene cluster contribution to the elimination of oxidative damage, potentially increasing fitness and resistance to reactive oxygen species during macrophage attack. We have shown a different beneficial effect of various truncated versions of the tellurite resistance gene cluster on cell survival. The terBCDEF genes increased the survival of E. coli strain MC4100 by 13.21%, terW and terZABCDEF by 10.09%, and terWY1XY2Y3 and terZABCDEF by 25.57%, respectively. The ability to survive tellurite treatment is the most significant at 44.8% in wild clinical strain KL53 compared to laboratory strain E. coli MC4100 due to a complete wild-type plasmid presence.

Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage.

Cronobacter spp. are opportunistic pathogenic bacteria responsible for severe infections in neonates. Powdered infant formula has been confirmed to be the source of infection in some cases. Bacteriophages offer a safe means for eliminating this pathogen. In the present study, we characterized two closely related Cronobacter-specific bacteriophages of the proposed genus “GAP227virus”. The phages Dev-CD-23823 and Dev-CT57 possessed broad host specificity, as they infected 88% and 80% of the Cronobacter strains tested. Genome sequence comparisons of phages Dev-CD-23823 and Dev-CT57 showed different levels of similarity to the prototype GAP227 phage. The Dev-CT57 phage was highly similar, whereas the Dev-CD-23823 phage showed only 75% sequence identity. A phylogenic tree based on the RNA polymerase (RNAP) gene from selected representatives of the subfamily Autographivirinae confirmed the grouping of Dev-CD-23823, Dev-CT57 and GAP227 in one cluster together with phages PP2, Phi80-18 and PhiR8-01. A common conserved motif was also detected in the RNAP promoters of these phages. The functional activity of these RNAP promoters was confirmed experimentally using a promoter probe vector, and a phage-specific signal was observed; however, some cross-specificity of Dev-CD-23823 and Dev-CT57 promoters was also detected. These results will contribute to our understanding of the biology and evolution of Autographivirinae phages.

This paper deals with the surface temperature of rolls during hot rolling of seamless steel tubes in stretch reducing mill in Zeleziarne Podbrezova. The main goal of our work was to measure the temperature of the rolls and compare it with the results coming from numerical simulation of hot rolling process. In general, the temperature of the tubes after stretch reducing should be higher than A_r3 by 30 ÷ 50 °C. The surface temperature of selected roll (so called "B-roll") was measured by means of a contact thermocouple-based method. Boundary conditions for numerical simulation of hot rolling process was set up according to the actual process conditions during rolling.

This manuscript describes the enhanced functions and interoperability methods developed and implemented during the last year in National Telepresence Infrastructure. National telepresence infrastructure to support research, development and technology transfer in Slovakia (NTI) has been created as a project by Slovak Centre of Scientific and Technical Information to provide pilot services for high-quality video conferencing meetings with high efficiency, as well as the implementation of on-line broadcasts for the broad community and archive services for storing, sharing and distributing knowledge in form of multimedia content. Paper deals with enhanced solution design to increase the abilities of NTI in field of modern live streaming chain to providing secure and seamless broadcast, in field of interoperability of videoconferencing with mobile platforms, in field of improve web-based booking and archiving services or intelligent room controllers. The last section of paper contains usage experience of NTI during 33 month of pilot operations and real use cases of livestreaming and collaborative functions not only from standard conference venues but also for exposed locations such as for example large university sport event.

Innovation is a key determinant of sustainable growth. Biotechnology (BT) is one such industry that has witnessed a revolution in innovative ideas leading to the founding of many new companies based on providing products, solutions and services, stretching from the food industry to environmental remediation, and new medicines. BT holds much promise for the development of national and local economies, however, this requires a strategic approach involving actors within government, industry, and academia working in concert to maximize this potential. This first article reviews the current “state of play” in the field of BT within the Central Eastern European (CEE) countries. For the purposes of this article, CEE refers to the countries of Czech Republic, Hungary, Poland, and Slovakia (the so-called Visegrad – V4 countries). We examine the components that support the creation and development of a BT sector in CEE and also highlight the barriers to these objectives. Clearly setting priorities for the countries’ policy agenda, as well as the alignment of Smart Specialization Strategy will help to focus efforts. Recent investments in R&D infrastructure within CEE have been substantial, but conditions will need to be optimized to harness these largely European investments for effective use towards SME high-tech development.