The main purpose of the project was to reconstruct the conditions of rocks sedimentation (deposition) in the Lower Silurian (433-430 million years ago) in order to determine the causes of what is known as the Ireviken extinction, during which mainly deep-sea organisms, such as graptolites, conodonts, and trilobites became extinct. The causes are still widely debated in the scientific community. Funded within the framework of PRELUDIUM 7, the research project aimed to reconstruct the water column oxygenation levels that obtained before, during and after the Ireviken event. Its innovative character resided in the application of state-of-the-art methods of organic and inorganic geochemistry, such as gas chromatography coupled with mass spectrometry (GC-MS), total organic carbon concentration (TOC%) and measurements of microscopic framboidal pyrite diameters and trace elements content.

Three models of sedimentation conditions before – A, during – B and after – C the Ireviken event The results obtained with the above methods served as a basis for developing a conceptual model of the sedimentation environment before, during and after the Ireviken extinction (Fig. 1). The period leading up to the event was characterized by an absence of framboidal pyrites, low concentrations of trace elements (such as molybdenum) and low TOC%, which suggests stable oxygen conditions in the water column (Fig.1A). In contrast, fluctuations in the diameter of framboidal pyrites, trace elements concentrations and TOC% pointed to rapid changes in oxygenation and strong chemistry gradients in the water column (chemoclines) during the Ireviken event. These changes were likely to contribute to the extinction of Silurian organisms (Fig.1B). In the aftermath of the event, large quantities of small framboidal pyrites typical of anoxic environments appeared and TOC% increased; trace elements concentrations were not significantly elevated, which suggests that the seabed was occasionally ventilated, probably in connection with upwellings (sea currents that push cold deep sea water toward the ocean surface) (Fig.1C).

A detailed geochemical analysis of the sedimentation conditions of the Ireviken event allowed us to confirm its similarity to the earlier great Ordovician-Silurian extinction. Based on the identification of biomarkers characteristic for green sulphur bacteria, the project was also able to document the presence of an anoxic photic zone (layer of the water column that is accessible to sunlight) in the Lowest Silurian. This discovery helped to connect the Ireviken extinction to other biotic crises of the Phanerozoic (Ordovician, Devonian, Permian and Triassic). The project findings shed new light on the structure of the water column and the possible causes and consequences not only of the Ireviken event, but also the Ordovician-Silurian extinction. The aims of the project were accomplished and its results were published in prestigious JCR-listed journals and presented at international academic conferences.

Degenerative joint diseases, such as osteoarthritis, represent an increasingly serious problem for society, not only in elderly patients. Damage to tissue and its progressive degradation are a natural result of the ageing process, but other risk factors for the disease include lack of exercise, sedentary lifestyle, unhealthy diet and obesity. Because of its special structure, cartilage can regenerate only to a small extent. Despite significant advances in medicine, still the gold standard in severe osteoarthritis remains the total joint replacement with implant.

Prof. Dr hab. Aleksandra Czyrska-Filemonowicz and mgr inż. Joanna Karbowniczek with Titan Cubed G2 60-300 microscope (photo by Michał Łepecki) The primary objective of the research project was to develop innovative biomaterials (such as bioactive composite coatings and polymer nanofibre scaffolds) designed to significantly improve the treatment of bone loss and degenerative bone and cartilage lesions. This was achieved through interdisciplinary research in cutting-edge materials science and stem cell-based tissue engineering. Detailed project objectives included producing of novel biomaterials followed by detailed qualitative and quantitative characterization of their micro- and nanostructure as well as their micromechanical properties. Additionally coatings adhesion strength and surface topography were examined; finally their biocompatibility was studied. The project postulated that a microporous composite coating, like PEEK/Bioglass (fabricated through electrophoretic deposition), or TiO2/Ca-P and TiO2/HAp (produced by plasma electrolytic oxidation), would improve the quality of the interface between titanium alloys and bone tissue. To test this hypothesis, basic research was conducted to determine the impact of the micro- and nanostructure, phase composition and porosity of surface-modified biomaterials on their bioactivity and biocompatibility.

Titanium alloys are the most frequently used materials in implant elements that come into direct contact with bone tissue, because of their high corrosion resistance, excellent mechanical properties, as well as low density. In addition, titanium alloys often undergo surface modification in order to facilitate post-surgery implant stabilization. The very first results of our research on surface-modified titanium implants showed a pressing need to expand the scope of the project, which found its reflection in a PhD dissertation prepared by Joanna Karbowniczek, MSc. Its goal was to design, produce and comprehensively characterize coatings used to improve the bioactivity and biocompatibility of titanium alloys. The coatings were produced through micro-arc oxidation (MAO) and electrophoretic deposition; different parameters of these two processes were tested. Optimization of the MAO process parameters allowed to obtain coatings with high surface roughness, porosity, good adhesion strength and outer layer composed of crystalline hydroxyapatite. During in vitro tests good bioactivity and biocompatibility of the coatings was confirmed. Their properties were studied using advanced techniques of microscopy, spectroscopy, and electron tomography. The use of the latest-generation analytical electron microscope (S)TEM FEI Titan Cubed 60-300 and its unique equipment, available at the International Centre of Electron Microscopy for Materials Science (IC-EM), allowed the cutting-edge methods of electron microscopy to be harnessed for the study of the micro- and nanostructure of biomaterials down to the hitherto inaccessible atomic scale. In addition, the project conducted a pioneering 3D visualisation study of the interface between the cells and the coating with the use of a focused-ion beam (FIB) scanning electron microscope.

Interdisciplinary research, combined with the latest achievements in various disciplines (such as materials science, biotechnology, tissue engineering), cutting-edge technologies (fabrication of coatings and cell scaffolds) and advanced research methods allowed objectives and the tasks of the project to be successfully completed. Its results were presented at international scientific congresses and conferences, and published in JCR-listed journals. Another tangible outcome of the project is the doctoral dissertation by Dr inż. Joanna Karbowniczek entitled "Microstructure, cellular response and selected properties of titanium based biomaterials applied in regenerative medicine of bone tissue and joints” (currently in its final elaboration).

Funded within the framework of the HARMONIA 3 programme, the project served as an excellent platform to establish new or deepen already existing international research co-operation. It was conducted in co-operation with Professor F. Rustichelli from Università Politecnica delle Marche (Ancona, Italy), Professor Aldo R. Boccaccini from Friedrich-Alexander-Universität Erlangen-Nürnberg (Erlangen, Germany), and Professor E. Amler from the Institute of Experimental Medicine of the Czech Academy of Sciences (Prague, Czech Republic), as well as Professor H. Cimenoglu from the Istanbul Technical University (Istanbul, Turkey). An important factor that contributed to the successful accomplishment of project objectives was the vast research experience of project partners and the opportunity to use equipment available at foreign research institutions. The international experience gained by our research team made it possible to finally open a new Biomaterials Laboratory, which expanded the research and teaching offer of the Microscopy Centre and the Faculty of Metals Engineering and Industrial Computer Science of the AGH University of Science and Technology.

Team of International Centre of Electron Microscopy for Materials Science during the project OPTYMED realisation (photo by Stanisław Malik, 2015)

The research project investigated structural fire safety in building. The investigation based on an originally-developed integrated computing system that employs fire simulation results to analyse the thermo-mechanical response of the structure. The computing system has been designed to support structural designers in important design decisions.

fot. Michał Łepecki The cognitive value of the research project resides in its comprehensive view of fire phenomena. Fire safety was assessed based on simulations that relied on three coupled physical models: hydrodynamic, heat flow and structural mechanics. It is contrary to the traditional approach, in which fire safety assessments do not consider the actual impact of the fire, but instead relies on standardized relationship between fire gas temperature and time.

A main part of an integrated computing system is the heat flow model that coupled fire simulations and thermo-mechanical response analyses. The validity of the model was verified experimentally. Both numerical and experimental tests adopted an innovative approach to describing thermal impacts, which relied on the concept of adiabatic surface temperature. An analytical solution to the adiabatic surface thermal equilibrium equation allowed to determine the boundary conditions in thermal analysis and facilitated the correlation of experimental data with the theoretical model.

Applying the newly-developed computing system to the analysis of the mechanical response of an actual building allows to consider a number of physical phenomena that directly affect its condition and cause structural deformations, but which are not taken into account in the traditional approach. This helped boost the cognitive potential of the project and allowed for a more complete analysis, which in turn makes it possible to carry out more accurate safety level assessments.

­­­­­­­­­­­Against the masculinist landscape of the first decades of the 20th century, Polish military masculinity stands out not only for its special historical image, but also its political status. In the period leading up to the First World War, Polish culture did not employ the tripartite reference system state – nation – politics that had shaped western conceptions of "classical" militarism and masculinism. Polish military masculinity had to constitute itself in isolation from its own state structures, in the shadow of strong partitioning powers and their hegemonic masculinities, but continued a national heroic tradition and thus reflected the mental structures of long duration.

The objective of the research project carried out in 2014-2017 was to describe how Polish masculinity was constructed in the period leading up to the Great War, in the conditions of dependence from partitioning powers with their own consolidated military traditions and institutions, and to analyse the war experience of Polish soldiers from the perspective of the history of masculinity (taking into account, on the one hand, the "elitist" character of the Polish Legions, and on the other, the mass recruitment of soldiers to fight for the partitioning powers). The research project also investigated the role of military masculinity in the new state, both in the 1920s and during the remilitarization of Europe (in the following decade), which culminated in the outbreak of the Second World War. Cultural and political processes were discussed to contextualize a reflection on masculinity in the wartime constellation of power – body – emotions and an interpretation of literary works and selected pieces of visual art that manifested, and at the same time deconstructed, military masculinity. The methodology behind the interpretation treated cultural texts as sources of knowledge about gender constructions, archives attesting to the continuity of cultural myths, media "agents" participating in the discursive processes of the "formation" of military masculinity, but also as a platform where its patterns, norms and staging forms are critically analysed and deconstructed.

Photo by Michał Łepecki The project provided a comprehensive analysis of the phenomenon of soldiership in the context of the First World War, presented in a monograph entitled Habitus żołnierski w literaturze i kulturze polskiej w kontekście Wielkiej Wojny [The Soldier's Habitus in Polish Literature and Culture in the Context of the Great War] (Kraków: Universitas 2017) and ten articles in collective volumes and journals, mainly on the international forum. The imperatives of the national liberation struggle, which implied the need for military action and problematized pacifism, caused Polish literature to get "implicated in soldiership". However, it featured not only images of incontrovertible heroes, "mad patriots", but also images of active participation in the "craft" of killing, anti-heroism and oppression. A critical interpretation of the heroic paradigm and the inclusion of a broad spectrum of material allowed cultural texts to be probed for the aporias, conflicts and contradictions inherent in the construction of military masculinity, made up of actions and interactions, bodies and discourses, and constituted by media texts and images. The military habitus is strictly linked to the national habitus, creating an intersectional construction built from historical, geographical, mental, social, local and situational elements, a combination of factors supplied by culture, history, ideology and geography. A characteristic feature of Polish military masculinity, which resurges and regenerates over and over again due to anachronistic memorial discourses still preserved in the national imaginary and continues to influence the gender system, is  a specific meaning attributed todeath and sacrifice. The analysis of war and postwar culture leads to  the conclusion that patterns of military masculinity may be renegotiated in different historical situations. Narrations in which masculinity is functionalized, dehumanized or humiliated in a war or peace context cannot compete against the appeal of the figure of the soldier, the uniform and the military parade. Masculinist cultural norms display immense generative power, which is why knowing the history of Polish masculinity and its cultural representations allows us to better appreciate the importance of masculine patterns for Polish culture and mentality and to understand their contemporary emanations.

The purpose of the project was to study specific pathways along which viruses can quickly spread between cells. Viruses may infect susceptible cells from the outside, binding to their surface receptors and gradually penetrating into their interior. Inside the cell, these viral molecules fall apart and release genetic material (DNA or RNA), which is then replicated, followed by the synthesis of viral proteins; new viral molecules are then formed, which can travel out and infect more cells. However, some viruses are also able to penetrate neighbouring cells without being released into the extracellular environment. To do so, they use sites of direct contact between adjacent cells or various intercellular connections. This direct transmission pathway allows them to spread faster and avoid contact with antibodies and immune cells. For some enveloped viruses (e.g. HIV, measles, human leukaemia virus), cell-to-cell spread has been shown to account for perhaps more than 60% of all infections. Targeting the cell-to-cell transmission mechanism is thus being hailed as a promise of important new treatments, especially for neurological disorders.

Our project focuses primarily on herpesviruses, which persist in the host in latent form for a lifetime after primary infection and may reactivate multiple times, which means they must particularly good at evading the host’s immune response (at primary infection). Around 80% of the human population is chronically infected with at least two viruses from the family, such as the herpes virus (HSV-1) or the cytomegalovirus (CMV), although in most people the infection is latent and asymptomatic. Herpesvirus strains with an impaired ability to spread via the cell-to-cell pathway are not pathogenic and can be used as vaccines against animal herpesviruses. However, no similar strains have been obtained for human herpesviruses. Another research model we used was the hepatitis C virus (HCV), one of the most dangerous human pathogens, which is very difficult to cultivate in a lab and mutates quickly, which has stalled any efforts to create an effective vaccine thus far. Our knowledge of the process by which the HCV enters host cells has increased, but it is still far from fully understood. It is only recently that it was discovered that the virus is also able to spread directly from cell to cell without being released into the extracellular environment.

Our methodology involves producing virus mutants, modifying genes involved in cell-to-cell transmission, studying their purified products, and analysing their mutual interactions and important functional domains. In an important experiment, we were able to directly track the movements of viruses in live cells, using fluorescent-labelled, “glowing” specimens constructed in our labs. This allowed us to show, for instance, that herpesviruses can travel between distant cells via long and thin projections, known as tunnelling nanotubes, which serve as specialised bridges and were only identified in recent years. What is more, we managed to demonstrate that the presence of the virus stimulates the formation of such intercellular connections and one of the viral kinases is involved in the process. This was an important discovery because, until then, this pathway had only been observed for HIV and some RNA viruses. The findings of our study were published in the Journal of Virology (DOI: 10.1128/JVI.00090-18). 

We also identified a number of cell proteins that interact directly with glycoprotein gE, an envelope protein of an animal herpesvirus (BHV-1), which is essential for its rapid transmission, and developed new methods for measuring the speed of cell-to-cell spread. Our findings indicate that this pathway is frequently used in the course of natural infection.

Intercellular transport of fluorescent labelled particles of BHV-1 virus through tunnelling nanotubes. Green marker: GFP, fused to the capsid; red marker: mitochondria We are particularly interested in the still poorly-studied issue of how viruses are transported between cells of various lineages (e.g. epithelial cells that line the infected organs) and blood cells. Studying the molecular mechanisms that allow viruses to quickly spread between cells may be crucial for developing new methods to control viral infections. As a follow-up to this study, we are now planning to look into the cell-to-cell spread mechanisms of coronaviruses. To date, very few preliminary reports exist on this transmission pathway for viruses from this family. Considering how effective the SARS-CoV2 virus is at infecting a variety of organs (not only the lungs, but also the intestines, kidneys and heart), it may be assumed to rely on the same transmission mechanism. This is the subject of our next NCN project, which will be carried out under PRELUDIUM BIS. The project aims to identify the transport pathways of coronaviruses between nearby and distant cells, initially based on a murine model of MHV, with a focus on the transmission of the virus between different types of infected and non-infected cells via intercellular connections. Until now, we have managed to adapt our lab to meet the security standards for working with SARS-CoV2, which will allow us to experiment with human coronaviruses. Our research experience, as well as the methodology we developed in our MAESTRO project, are now being put to use in our research on the SARS-CoV2 virus.