Strong interactions are among the most important issues in contemporary physics. The strongest forces we know of to date, they occur between elementary particles such as quarks and gluons. In the world around us, quarks and gluons are normally trapped inside protons and neutrons, the components of atomic nuclei. fot. Michał Łepecki, prof. dr hab. Marek Gaździcki

It is commonly accepted, however, that at extremely high densities, much greater than those of atomic nuclei, matter can exist in a state known as quark-gluon plasma, in which quarks and gluons move around freely. Does plasma exist in nature? What are the features of the phase transition between low-density, strongly-interacting matter, where quarks and gluons are confined, and the state of quark-gluon plasma? Can the properties of strongly-interacting matter be studied in the lab?

The purpose of the project is to answer these questions by studying high-energy nucleus-nucleus collisions in cooperation with an international research team, NA61/SHINE. The team performs its measurements with the aid of the NA61/SHINE detector of the Super Proton Synchrotron (SPS) at the European Organization for Nuclear Research (CERN) in Geneva. The research project was started and is currently headed by Prof. Dr hab. Marek Gaździcki.

prof. dr hab. Marek Gaździcki przy pracy The project is divided into two parts:

1. Critical structures and protons. The analysis is focused on the production of protons in high-energy nucleus-nucleus collisions, based on unique data collected by the NA61/SHINE detector for different collision energies and mass numbers.

2. Critical structures and charms. This part is aimed at modernising the NA61/SHINE detector, by developing and constructing a new data collection system to record collisions at a much faster rate than before. Speeds of this magnitude are necessary if we want to measure rarely-produced particles that contain heavy charm quarks.

The first part of the project may directly allow us to discover the properties of transition between the confined state of quarks and gluons to the quark-gluon plasma. The second part paves the way for possible future discoveries, based on the systematic data on the production of charm quarks in collisions between heavy nuclei. The pioneering measurements carried out by NA61/SHINE will be later continued in two newly created labs: FAIR in Germany and J-PARC-HI in Japan.

Multiple studies have demonstrated that roasted coffee seeds contain not only bioactive substances with an overall positive effect on health, but also potentially harmful compounds, such as 5-Hydroxymethylfurfural (5-HMF) and acrylamide (AM). On the other hand, the polyphenols found in coffee considerably limit the pathogenesis of many modern chronic lifestyle diseases. The main goal of the project was to assess the health-boosting properties of coffee ingredients on physico-chemical and cell line models; the purpose was to determine their physiologically achievable levels and impact on selected signalling pathways and, subsequently, identify the specific coffee extracts and fractions that show the greatest beneficial health effects when digested and absorbed in the gastrointestinal system.

dr inż. Joanna Grzelczyk przy pracy, fot. Michał Łepecki In order to achieve that objective, we prepared green, light- and dark-roasted coffee seed extracts from the Arabica and Robusta species and isolated fractions containing different polyphenol groups, free or bound with Maillard reaction products (MRP), as well as selected low-molecular MRPs, including AM and 5-HMF. These extracts and fractions were then subjected to in vitro enzymatic digestion with or without selected strains of probiotic lactic acid bacteria. We measured the absorption of polyphenols from the extracts or fractions in question in a model system consisting of a single layer of enterocytes, followed by the molecular modelling of these compounds via docking and calorimetric simulations, using body enzymes and receptors. The results of the modelling experiments were compared with cellular model assessments in order to confirm the activation of selected metabolic pathways in a more complex biological system. We identified the extracts and fractions that showed the greatest beneficial effect on cells after digestion and absorption and determined their most beneficial physiological concentrations, corresponding to specific coffee intake levels.

dr inż. Joanna Grzelczyk przy pracy, fot. Michał Łepecki The concentration of free polyphenols was observed to rise as they broke away from more complex structures, mainly in the large intestine, during the digestion of coffee extracts/fractions in the simulated GI tract. The presence of probiotic bacteria contributed to an increase in the levels of free polyphenols derived from chlorogenic acids, with high activity observed in the lower sections of the GI tract. Docking simulation studies of interactions and affinities with selected body enzymes and receptors showed that the latter created stable complexes with bioactive coffee compounds, with coffee ingredients competitively binding to enzyme/receptor active sites. When coffee extracts and fractions were digested in vitro, their affinity with enzymes/receptors, as analysed with the ITC method, increased in comparison with undigested material. This suggests that, when consumed, coffee extracts and fractions may effectively inhibit the activity of enzymes such as: acetylcholinesterase, butyrylcholinesterase, monoaminoxidase A, and topoisomerase II, or regulate the activity of the PPAR receptor. Among the samples studied in our in vitro research on cell lines, the highest bioactivity levels were observed for green coffee extracts, including chlorogenic acid fractions, which exhibited cytoprotective properties, protecting our model enterocytes (Caco-2 and HT29), nerve cells (SH-SY5Y), and pancreatic cells (MIN6) against the induced oxidative stress that contributes to carcinogenesis. They reduced the activity of cellular β-secretase, which may prevent the formation of β-amyloid plaque that damages nerve cells. Coffee ingredients were also observed to reduce the release of pro-inflammatory cytokines by differentiated adipocytes (3T3-L1) and stimulate GSIS, which may contribute to the maintenance of metabolic homeostasis. At the same time, elevated coffee compound levels induced cell death via apoptosis, which confirmed their anti-cancer properties.

Qualitative research (case studies) and quantitative studies (surveys) have revealed the organisational and environmental factors that may have a strategic impact on power asymmetry between the two parties of a B2B relationship. Our research took the perspective of small and medium-sized enterprises working with large international entities and covered various sectors, characterised by different levels of internationalisation, including B2B transport providers, furniture manufacturers and material suppliers for national and international corporations. The international pandemic crisis that erupted during the project created an additional context for our conceptual and empirical investigations. fot. Michał Łepecki, prof. dr hab. Maciej Mitręga

fot. Michał Łepecki, prof. dr hab. Maciej Mitręga Our research suggests that SMEs can effectively boost their economic results in cooperation with larger strategic partners by relying on specific skills that can be developed in different management areas. On the one hand, as they enter into asymmetric power relations with large foreign buyers, SMEs should adapt to their requirements, because this is the only way to learn, i.e. shore up their skills and assets in the area of management and production technology. On the other, they should strive to strengthen their independent position within international supply chains, which requires the ability to diversify their buyer portfolio over time by actively searching for new partners and reassessing existing relationships. Our research suggests that this ability is severely limited in situations of market crisis, especially for service providers who have not yet built a recognisable brand. However, even then, their economic position vis-à-vis large players can still be enhanced via effective negotiation skills. Our research suggests that SMEs should develop different skillsets at different stages of their international market activities. Initially, their focus should be on meeting the requirements of strategic buyers; over time, however, they should move on to invest in their own brand and technology, which may gradually improve their position in international supply chains.

Funded by the National Science Centre under the SONATA 8 call, entitled “Tiwanaku: using genetic methods to explore the origin, characteristics and population changes of a pre-Columbian Lake Titicaca culture”, our project was carried out in 2015-2021 by a scientific consortium formed by the Museum and Institute of Zoology, PAS and the Department of History of the University of Warsaw. The project focused on the Tiwanaku Culture, which flourished in the Lake Titicaca basin in what is now Bolivia and Peru between the 5^th and 11^th centuries CE, ranking as one of the greatest pre-Incan civilisations of America. Unfortunately, because the culture did not develop writing and many centuries have passed since its disappearance, everything we know about the people who created it, their customs and beliefs, is based on what survives of Tiwanaku’s imposing buildings, ceramics and other artifacts, as well as on human and animal remains found at settlement sites. Even though we know quite a lot about the material culture of the Tiwanaku, information about their origin and diversity, as well as any population changes over time, is limited to guesswork, in accordance with the maxim that “pots are not people”, which highlights the fact that similarities and differences in material culture do not always go hand in hand with population stability or change. fot. Michał Łepecki, dr Martyna Molak-Tomsia

The purpose of the project was to collect high-resolution genetic information from individuals whose remains were excavated at Tiwanaku sites. To this end, we employed state-of-the-art lab analysis and bioinformatic methods normally used for scarce and degraded DNA from skeleton fossils. This allowed us to obtain genomic information from 13 individuals from sites associated with the Tiwanaku culture, including eight from its political and ceremonial centre, four from a remote residential enclave and one from a Tiwanaku colony, as well as, for comparative purposes, four from the Coropuna region. Our research suggests that the inhabitants of the Lake Titicaca basin were a genetically homogeneous group that did not undergo any significant population changes. In contrast, the ceremonial centre of the Tiwanaku seems to have attracted newcomers from remote regions, in some cases from as far as the Amazon. In contrast to other hypotheses, put forward based on the sacrificial remains found at the ceremonial centre, these visitors did not come there on a pilgrimage, nor were they forcibly brought as war captives. They came there to settle, as evidenced by the presence of mixed-ancestry remains, i.e. the descendants of locals and newcomers. fot. Michał Łepecki, dr Martyna Molak-Tomsia

However, human remains found on the Akapana ritual site, which date back to a later, final period, already show an entirely local genome, which suggests that the far-reaching influence of the Tiwanaku culture had waned in the run up to its ultimate disappearance. Research conducted within the framework of the project provides important insights into the organisation of complex primitive societies that formed out of scattered, independent settlements. While we may never know the processes that led to the formation of these complex societies in full, studying their earliest forms is one of the few ways we have at our disposal to better understand the very roots of civilisation.

Current debates on environmental protection and the treatment of high natural value forests in Europe often invoke the concept of a primeval forest. Different interpretations of this idea are frequently used to justify the intensive exploitation of areas that are not considered to be virgin, natural or primeval. Our contemporary idea of the primeval forest, however, is a product of several centuries of evolution, in which an important role was played by the interest taken by the European scientific and cultural community in the Białowieża Forest and the European bison in the 18^th century. fot. Michał Łepecki, dr hab. Tomasz Samojlik

The purpose of this international project (with principal investigators based in Poland and Lithuania, and contractors in France and Russia) was to chart the evolution of the idea of a primeval forest and trace the perception of the Białowieża Forest and the European bison in European culture and science in the 18^th and 19^th centuries. Archival and museum research, as well as literature surveys, carried out in Poland and beyond, allowed us to explore a variety of different sources (archival documents, research papers and popular science publications, hunting press releases, museum exhibits, publications, artworks).

The idea of a primeval or virgin forest dates back to a debate on the destruction of forests in the 18^th century in France. At the beginning of the 19^th century, the concept made it into the vocabulary of German Romanticism, which associated it with the roots of German exceptionalism. Concepts such as “primeval forest”, “virgin forest” and “natural forest”, however, long had no clear definition, let alone a designate. The designate only appeared later, following the “rediscovery” of Lithuanian forests, and especially the Białowieża Forest, at the end of the 18^th century. Targeted at scientists and the general public alike, descriptions of the Białowieża Forest either directly or indirectly referred to it as “primeval”, although it was not usually taken to mean it was completely untouched by man. The perception of Białowieża also changed over time; first dominated by folk beliefs, it was later supplemented by the reports of travellers who had traversed the “Lithuanian forests” (a shorthand for forests that were wild, vast and, most importantly, not exploited by man), only to become the subject of scientific research in the strict sense at the turn of the 18^th/19^th centuries. fot. Michał Łepecki, dr hab. Tomasz Samojlik

The Białowieża Forest largely owed its high-profile status to its last lowland population of the European bison. The recognition of the exceptional nature of this species was a complex process, which we traced on the basis of selected visual depictions created from the 16^th to the end of the 19^th century. The growing number of available illustrations of the European bison, the growth of our knowledge about the species and the wide distribution of bison exhibits in European museums all contributed to the success of the campaign to save this iconic species after its extinction in 1919.

Discussions about the primeval forest and the European bison also helped raise awareness of Polish and Lithuanian nature and culture in Western Europe. The debates were not limited to academic papers, but pervaded the culture at large, making appearances in literature, poetry, theatre, painting and later also in photography and film. The subject thus became an important element in the dissemination of natural knowledge among the general public throughout Europe.

In order to understand and describe the processes of change on our planet, we need to carry out relevant observations and situate them in time and space. Thanks to satellites, we can now learn much more about these phenomena in a continuous and global manner. Observing changes in sea level requires precise measurements, down to the last millimetre, since they occur at a rate of 3-4 mm/year. The same holds true for magnetic pole shifts, irregularities in the Earth’s rotation, the flattening of the Earth, and changes in its centre of mass; all these phenomena require millimetre-range precision. fot. M. Łepecki, prof. dr hab. Krzysztof Sośnica

Until now, observations from satellites at different orbits were all analysed separately. In our project, data from low-, medium-, and high-orbit satellites are integrated by ground-based laser stations that also carry out distance measurements. Low-orbit satellites monitor the level of seas and oceans (so-called altimetry satellites, such as, e.g. Jason-3, Sentinel-6), changes in the Earth’s gravitational field (gravimetry satellites, e.g. GRACE), space weather and the Earth’s magnetic field (SWARM satellites). Medium-orbit satellite geodesy allows us to locate the centre of the Earth, determine the gravitational constant and study relativistic effects (LAGEOS, LARES). Lastly, high-orbit satellites are used for the purposes of navigation and positioning, as well as for placing geodetic control networks (e.g. GPS and Galileo). Unfortunately, GPS satellites are fitted with laser measurement devices, in contrast to the Galileo system currently under construction in Europe, in which all satellites allow the combination of microwave and laser observations on board space ships. Because of their inconsistent reference system, analysing different satellite missions separately has often led to errors.

Laser measurements of distance to various satellites on orbits at different altitudes are integrated in an OPUS project entitled “Integrated terrestrial reference systems based on laser measurements of distance to geodetic, teledetection and GNSS satellites”. Laser measurements are carried out at ground-based stations, which send very short laser pulses to the satellite, which then bounce off and return to the detector. By measuring the time it takes for a pulse to make a round trip from the station to the satellite and back, it is possible to calculate the distance between them. Laser observations need to be corrected for measurement errors and beam refraction in the atmosphere, which is also addressed by the project. The project was the first to develop laser-based terrestrial reference systems to different satellites placed at different orbits. This has allowed us to create terrestrial reference systems necessary to study the terrestrial phenomena observed by satellites. fot. M. Łepecki, prof. dr hab. Krzysztof Sośnica

Another objective of the project is to conduct simulations of future satellite geodesy missions in order to answer the following question: Where should future satellites be placed to maximise the precision of their observations? At what altitude? At what angle relative to the plane of the Equator? On circular or elliptical orbits?

The project and its preliminary results have already attracted the attention of the European Space Agency (ESA). The ESA awarded the first prize to our presentation on integrated microwave and laser observations on board Galileo satellites during the International Colloquy on Scientific and Fundamental Aspects of GNSS. The preliminary results of our project will play a key role in future satellite missions, as they will help in the spatial localisation of all the terrestrial phenomena that require millimetre-range precision.

The project explores the relationships that hold between intense disturbances (such as hurricanes or woodworm invasions), natural forest regeneration and the browsing of young trees by wild ungulates. Explaining the impact of natural disturbances on the process of forest regeneration under strong herbivore pressure will make an important contribution to the theory of forest community dynamics. Since extreme weather events are likely to become more common due to global climate change, the frequency and intensity of natural disturbances in forest communities will probably increase as well. Such intense disturbances kill many large trees, increasing the availability of light, water and soil resources, which accelerates the growth of the young generation. Thanks to the greater availability of light, the density of young trees increases; they also produce more shoots, which means that ungulate populations in the area have more food at their disposal. fot. Michał Łepecki, prof. dr hab. Jerzy Szwagrzyk

Our assumption is that under conditions of greater resource availability, the growth of herbivore populations will be slower than the increase in the biomass of young trees. Because in the presence of ample light browsing pressure is distributed across a greater number of young trees and there are more opportunities for growth compensation, browsing does not stop the growth of the young generation. Consequently, even those species that would otherwise be strongly suppressed or eliminated by repeated browsing under abundant tree cover get a chance to grow into imposing trees in areas affected by natural disturbances. Our research covers four areas (the Tatra Mountains, Roztocze, Babia Góra, Puszcza Piska), where we have previously set up our outposts.

The goal of the project is to determine which environmental factors impact the spatial variation in ungulate browsing activity. The bulk of the project is carried out in Roztocze and the Tatra Mountains. The forests of the Tatras have experienced extensive natural disturbances in the past two decades, while the disturbances in Roztocze were few and far between and spatially limited. The species composition and forest regeneration dynamics in both areas show important similarities (a large proportion of beech and fir) and differences – spruce and rowan in the Tatras and hornbeam in Roztocze). Our research aims to estimate the number of shoots available to ungulates and analyse the intensity of browsing on young trees under different light conditions, ranging from compact forests to areas where the tree cover has been practically eliminated by hurricanes or woodworm invasions. We have fenced in 60 little research areas, where we measure the parameters of young trees (height, thickness, crown size) and record any damage caused by ungulate mammals. We also carry out parallel light intensity measurements and soil analyses. In order to determine which herbivore species feed in our area and when, we have set up automatic cameras to record animal presence and behaviour, which we hope will help us interpret the results of our measurements.

Preliminary project findings indicate that under conditions created by natural disturbances, species commonly considered as sensitive to herbivore pressure, such as sycamores and rowan trees, quickly grow to heights at which their crown tips are protected from browsing. With a lot of light available across extensive areas, they are able to successfully compete against shade-resistant species and account for a large percentage of the young tree generation. As a result, young forests growing in such areas show greater species diversity than older forest stands. The results of our research may serve as an argument to refrain from interference with natural forest regeneration processes after natural disturbances.

The climate crisis is one of the main global threats today. Climate change, however, often seems abstract as one cannot easily smell, touch or see it. In EmCliC we bring together natural sciences and social sciences to study how the changing climate affects people today. We study how the physical, weather and climate events are connected with people’s local knowledges and embodied experiences, to demonstrate how we already embody climate change.

Climate change means hotter, longer and more frequent heatwaves, also in Europe. Heat is exacerbated in cities and with increasing urbanization, heat stress severely affects people’s health and wellbeing. However, not all city inhabitants experience heat in the same way. Certain population groups, such as adults above the age of 65, are more vulnerable than others. EmCliC brings together methods and approaches from disciplines such as social anthropology, sociology, environmental physics, meteorology, climatology, and epidemiology to study the multiple dimensions of urban overheating. We focus on older adults living in two European locations, Warsaw and Madrid. We chose two cities which, due to their varied climates have historically and culturally experienced and adapted to hot temperatures very differently. fot. Zofia Bieńkowska

To understand older adults’ experiences of urban heat and their individual adaptation strategies we conducted extensive qualitative studies. This included focus groups in Warsaw with more than 80 participants. During the summers 2021 and 2022 we conducted ethnographic research with older adults living in Warsaw and Madrid, which consisted of participant observations, in-depth interviews, participants filling out diaries, drawing maps of their surroundings and bodies, and taking photographs. In Madrid, the participants’ narratives and their embodied experiences of heatwave were captured in an ethno-fiction film ‘The Wave’. Moreover, in both Warsaw and Madrid we conducted participatory workshops focused on the embodiment of heat. We also analysed public policy to see how public institutions approach and deal with urban heat.

Ethnographic research was combined with the use of wearable sensors, which measured temperature and humidity and were carried by the participants all the time. We also installed a static sensor at the participants’ homes collecting data about the indoor temperature. The goal of combining ethnographic research with the sensors is to understand individual experiences of thermal comfort and adaptation measures to urban heat, and how they are (dis)connected with the temperature measured by the sensors and the official meteorological information.

fot. Michał Łepecki, dr. Zofia Boni

During the summer 2022, we conducted a thermo-survey with around 1000 older adults in Warsaw and in Madrid. During face-to-face interviews we asked about individual health and daily routines, socioeconomic situation, social relationships and how these might change when temperatures get hot. Interviews were combined with temperature readings outside and inside respondents’ homes.

Moreover, we developed a framework combining high resolution climate projections with health and demographic data for mapping clusters of vulnerable groups within the city. The framework is designed to increase knowledge among local decision makers about particularly vulnerable areas, with the purpose of informing targeted adaptation measures.

EmCliC approaches climate change and urban heat as both a physical and social phenomenon. We combine natural and social sciences to better understand how urban heat affects people’s lives, how we can adapt to it, and how do we already embody climate change.

EmCliC Team

The team: Zosia Bieńkowska, Zofia Boni, Nuria Castell, Franciszek Chwałczyk, Amirhossein Hassani, Barbara Jancewicz, Iulia Marginean, Małgorzata Wrotek, Paloma Yáñez Serrano.

For more information see our website www.emclic.com and follow us on Twitter @EmCliC.

What is the secret behind the evolutionary explosion in the cognitive and computational capacity of the human brain? Astrocytes may hold the key to this fascinating riddle. Apart from their nutritive function, astrocytes also play a central role in the biogenesis and removal of synapses, i.e., two processes of key importance for neuroplasticity and, hence, learning.

In comparison with their counterparts in rodents or monkeys, human astrocytes show many unique morphological and functional properties. However, despite their important function, the structure and evolution of the regulatory network that coordinates the biology of these cells remain largely unknown. Our Dioscuri centre combines “omics” tools, CRISPR-Cas9, and stem cell and chimera models to uncover the genetic underpinnings of astrocyte function and evolution.

Isolating astrocytes from primate brains and growing them in a lab is very difficult, if not impossible. This is why our project focuses on using cutting-edge technologies to obtain astrocytes in vitro from induced pluripotent stem cells (iPS). This non-invasive approach allows to obtain any quantity of astrocytes for various mammalian species. Over the past three years, our lab has created a bank of iPS cells typical of humans, chimpanzees, macaques and mice; we have also implemented in vitro astrocyte differentiation and growing protocols.

fot. M. Łepecki, dr Aleksandra Pękowska

We employed molecular biology techniques to assess differences in gene expression patterns in human and monkey astrocytes. A gradual evolution of gene activity was observed. We identified more than a thousand loci, at which expression levels in humans were altered, as compared with chimpanzees and macaques. The list includes various factors related to brain disorders, such as multiple sclerosis or Alzheimer’s disease. We also identified a number of factors whose function is as yet unclear. Our data indicate that the evolution of astrocytes is associated with changes in the expression of many non-coding transcripts, which are particularly interesting, because the RNA molecules they produce can regulate the activity of other genes. At present, we are studying the implications of the most important of these factors, using the methods of genomic engineering and cell biology.

fot. M. Łepecki, dr Aleksandra Pękowska Gene expression is influenced by specific DNA sequences, known as regulatory elements. Enhancers act on promoters to increase their activity and, hence, boost gene expression. The role of insulators, on the other hand, is to inhibit enhancers. The evolution of gene expression levels is related to various changes in the sequences of enhancers, promoters and insulators, which may either increase or reduce their activity. By using molecular biology techniques and high-throughput sequencing methods (ATAC-seq and ChIP-seq), we obtained a map of regulatory elements active in the astrocyte genomes of humans, chimpanzees and macaques. This unique data set allowed us to correlate transcriptional and epigenetic changes and identify the mechanisms that may be involved in the evolution of gene expression in human astrocytes. At present, we are implementing a murine chimera model to explore the impact of these newly identified genes and regulatory elements on the biology of astrocytes and, more broadly, on brain activity. This research is funded from the Dioscuri grant and the EMBO Installation Grant awarded by the European Molecular Biology Organization.

Interlaminar astrocytes are a type of astrocytes found only in primates. Research on the brains of patients with Alzheimer’s disease suggests that interlaminar astrocytes dwindle in the most advanced forms of this devastating condition. However, their functions and epigenome have not yet been defined. Thanks to our research, funded under NCN’s OPUS 22 call, we will be able to study the molecular profile of interlaminar astrocytes and, in the future, hopefully understand the role of these unique cells in the development of neurodegenerative disorders.

Our research at the Dioscuri Centre for Chromatin Biology and Epigenomics also looks into the mechanisms behind the activity of DNA regulatory elements. Thanks to OPUS 17 and Sonata Bis grants, we have discovered surprisingly wide-ranging changes in the set of proteins that bind insulators during the differentiation of embryonic stem cells into nerve cells. We have demonstrated this new regulatory mechanism in mammalian development. We have also been able to implement new genome-mapping technologies. Our research lays the groundwork for a better understanding of the mechanism that regulates the specificity of regulatory elements. We are also members of the chrom_rare international research network (Maria Skłodowska Curie Actions), which aims to understand the molecular underpinnings of disorders associated with various mutations in chromatin activity regulators.

Lab website: https://pekowskalab.nencki.edu.pl

Selected Publications:

• Verkhratsky A., Arranz AM, Ciuba K, Pękowska A. Evolution of neuroglia. A.Ann N Y Acad Sci. 2022 Oct 26.
• Dehingia B., Milewska M., Janowski M. & Pękowska A. CTCF shapes chromatin structure and gene expression in health and disease. EMBO Reports (2022), e55146; https://doi.org/10.15252/embr.202255146.
• Janowski M., Milewska M., Zare P., & Pękowska A., Chromatin Alterations in Neurological Disorders and Strategies of (Epi) Genome Rescue. Pharmaceuticals 2021, 14(8), 765.
• Pękowska A.^, Klaus B, Xiang W., Severino J., Daigle N., Klein F.A., Oleś M., Casellas R., Ellenberg J., Steinmetz L.M.S., Bertone P.^, Huber W.^ Gain of CTCF-anchored chromatin loops marks the exit from naive pluripotency. Cell Systems Nov. 28; 7(5):482-495.
• Vian L.#, Pękowska A.#, Rao SSR.#, Kieffer-Kwon K-R#, Jung S#, Baranello L., Huang SC., El Khattabi L., Dose M., Pruett N., Sanborn AL., Canela A., Maman Y., Oksanen A., Resch W., Li X., Lee B., Kovalchuk AL., Tang Z., Nelson S., Di Pierro M., Cheng RR., Machol I., St Hilaire BG., Durand NC., Shamim MS., Stamenova EK., Onuchic JN., Ruan Y., Nussenzweig A., Levens D., Aiden EL., Casellas R. The energetics and physiological impact of cohesin extrusion. Cell 2018 May 17;173(5):1165-1178.e20.
• Schwarzer W.#, Abdennur N.#, Goloborodko A.#, Pękowska A., Fudenberg G., Loe-Mie Y., Fonseca N.A., Huber W, Haering C., Mirny L., Spitz F. Two independent modes of chromosome organization are revealed by cohesin removal. Nature 2017 Nov 2;551(7678):51-56
• Pękowska A.#, Benoukraf T.#, Zacarias-Cabeza J.#, Belhocine M., Koch F., Holota H., Imbert J. Andrau JC., Ferrier P., Spicuglia S. H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J. 2011;(July):1–13.
• Pękowska A., Benoukraf T., Ferrier P., Spicuglia S. A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Research, 2010 Nov; 20(11):1493–502.

Classically, dissolved organic matter (DOM) in sediment pore waters was assumed to be not available for microbial communities to consume. This assumption was based on the fact that DOM is accumulating with sediment depth, and the consumption rates within the sediments should be smaller than production rates of DOM. However, recently it was suggested that sediment pore waters might potentially serve a source of bioavailable DOM to the overlying near bottom water layer and water column. It was also hypothesized that DOM supplied by sediments might stimulate microbial activity in the near-bottom waters. dr. Alexandra Loginova, fot. M. Łepecki

dr. Alexandra Loginova, fot. Michał Łepecki DOMUSe project is determined to characterize microbial response to dissolved organic matter (DOM) supplied from the sediments to the near-bottom water of Baltic Sea Deeps. In DOMUSe, we will execute several studies, where part of the sediment and near-bottom waters will be enclosed in the anoxic atmosphere for a period of time. This way, we would like to assess the rates of microbial processes occurring in the near-bottom waters. We have chosen several proxies that will allow us to trace changes in quality and quantity of DOM, including chemical composition and optical DOM properties. We will use optical properties of DOM to assess changes in DOM quality. Optical properties of DOM, such as fluorescence, via statistical multivariate analyses, will allow to assess the DOM fractionation between humic-like (microbially reworked and mainly refractory) DOM and amino acid-like DOM, which is mainly associated to rapidly utilizable fresh DOM. We will use siderophores, ferric iron specific small organic molecules, as a proxy of microbial activity. Siderophores are small chained organic molecules, which are produced by microbes to assess ferric iron. Their production rates were previously shown to be affected by bioavailability of dissolved organic matter. Their production was previously associated to fresh labile organic matter sources, such as phytoplankton blooms, however, they were also found in the sediment pore waters. The measurements of microbial nutrient utilization will fulfil the measurements of the microbial response to DOM release from sediments pore waters. Bacterial abundance will be also measured overtime to access bacterial number increase associated to DOM supply by the sediments. Therefore, the measurements of DOM optical properties in conjunction with siderophores accumulation, microbial abundance, and nutrient consumption will provide critical insights on the ability of sediment released DOM to serve as a substrate for heterotrophic communities to grow on and function.