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Item Deep into the niche: Deciphering local endoderm-microenvironment interactions in development, homeostasis, and disease of pancreas and intestine(Wiley Periodicals LLC, 2023-03-04) Szlachcic, Wojciech J; Letai, Katherine C; Scavuzzo, Marissa; Borowiak, MałgorzataUnraveling molecular and functional heterogeneity of niche cells within the developing endoderm could resolve mechanisms of tissue formation and maturation. Here, we discuss current unknowns in molecular mechanisms underlying key developmental events in pancreatic islet and intestinal epithelial formation. Recent breakthroughs in single-cell and spatial transcriptomics, paralleled with functional studies in vitro, reveal that specialized mesenchymal subtypes drive the formation and maturation of pancreatic endocrine cells and islets via local interactions with epithelium, neurons and microvessels. Analogous to this, distinct intestinal niche cells regulate both epithelial development and homeostasis throughout life. We propose how this knowledge can be used to progress research in the human context using pluripotent stem cell-derived multilineage organoids. Overall, understanding the interactions between the multitude of microenvironmental cells and how they drive tissue development and function could help us make more therapeutically relevant in vitro models.Item Summer solstice orchestrates the subcontinental-scale synchrony of mast seeding(2023) Journé, Valentin; Szymkowiak, Jakub; Foest, Jessie; Hacket-Pain, Andrew; Kelly, Dave; Bogdziewicz, MichałHigh interannual variation in seed production in perennial plants can be synchronized at subcontinental scales with wide consequences for ecosystem functioning, but how such synchrony is generated is unclear. We investigated the factors contributing to masting synchrony in European beech, spanning an impressive 2000 km geographic range. Maximizing masting synchrony via spatial weather coordination, known as the Moran effect, requires distant populations to react simultaneously to weather conditions. A celestial cue that occurs simultaneously across the entire Hemisphere is the longest day (summer solstice). We show that European beech abruptly opens its temperature-sensing window on the solstice, hence widely separated populations all start responding to weather signals in the same week. This celestial "starting gun" generates ecological events with unparalleled spatial synchrony across the continent.Item Cyclic mismatch binding ligands interact with disease-associated CGG trinucleotide repeats in RNA and suppress their translation(Oxford University Press, 2021) Konieczny, Patryk; Mukherjee, Sanjukta; Stepniak-Konieczna, Ewa; Taylor, Katarzyna; Niewiadomska, Daria; Piasecka, Agnieszka; Walczak, Agnieszka; Baud, Anna; Dohno, Chikara; Nakatani, Kazuhiko; Sobczak, KrzysztofFragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder caused by a limited expansion of CGG repeats in the FMR1 gene. Degeneration of neurons in FXTAS cell models can be triggered by accumulation of polyglycine protein (FMRpolyG), a by-product of translation initiated upstream to the repeats. Specific aims of our work included testing if naphthyridine-based molecules could (1) block FMRpolyG synthesis by binding to CGG repeats in RNA, (2) reverse pathological alterations in affected cells and (3) preserve the content of FMRP, translated from the same FMR1 mRNA. We demonstrate that cyclic mismatch binding ligand CMBL4c binds to RNA structure formed by CGG repeats and attenuates translation of FMRpolyG and formation of nuclear inclusions in cells transfected with vectors expressing RNA with expanded CGG repeats. Moreover, our results indicate that CMBL4c delivery can reduce FMRpolyG-mediated cytotoxicity and apoptosis. Importantly, its therapeutic potential is also observed once the inclusions are already formed. We also show that CMBL4c-driven FMRpolyG loss is accompanied by partial FMRP reduction. As complete loss of FMRP induces FXS in children, future experiments should aim at evaluation of CMBL4c therapeutic intervention in differentiated tissues, in which FMRpolyG translation inhibition might outweigh adverse effects related to FMRP depletion.Item Partners in crime: proteins implicated in RNA repeat expansion diseases(Wiley, 2022) Baud, Anna; Derbis, Magdalena ; Tutak, Katarzyna ; Sobczak, KrzysztofShort tandem repeats are repetitive nucleotide sequences robustly distributed in the human genome. Their expansion underlies the pathogenesis of multiple neurological disorders, including Huntington's disease, amyotrophic lateral sclerosis, and frontotemporal dementia, fragile X-associated tremor/ ataxia syndrome, and myotonic dystrophies, known as repeat expansion disorders (REDs). Several molecular pathomechanisms associated with toxic RNA containing expanded repeats (RNAexp) are shared among REDs and contribute to disease progression, however, detailed mechanistic insight into those processes is limited. To deepen our understanding of the interplay between toxic RNAexp molecules and multiple protein partners, in this review, we discuss the roles of selected RNA-binding proteins (RBPs) that interact with RNAexp and thus act as “partners in crime” in the progression of REDs. We gather current findings concerning RBPs involved at different stages of the RNAexp life cycle, such as transcription, splicing, transport, and AUG-independent translation of expanded repeats. We argue that the activity of selected RBPs can be unique or common among REDs depending on the expanded repeat type. We also present proteins that are functionally depleted due to sequestration on RNAexp within nuclear foci and those which participate in RNAexp-dependent innate immunity activation.Item Measuring individual identity information in animal signals: Overview and performance of available identity metrics(2019) Linhart, Pavel; Osiejuk, Tomasz; Budka, Michal; Šálek, Martin; Špinka, Marek; Policht, Richard; Syrová, Michaela; Blumstein, Daniel T.Identity signals have been studied for over 50 years but, and somewhat remarkably, there is no consensus as to how to quantify individuality in animal signals. While there is a variety of different metrics to quantify individuality, these methods remain un‐validated and the relationships between them unclear. We contrasted three univariate and four multivariate identity metrics (and their different computational variants) and evaluated their performance on simulated and empirical datasets. Of the metrics examined, Beecher's information statistic (HS) performed closest to theoretical expectations and requirements for an ideal identity metric. It could be also easily and reliably converted into the commonly used discrimination score (and vice versa). Although Beecher's information statistic is not entirely independent of study sampling, this problem can be considerably lessened by reducing the number of parameters or by increasing the number of individuals in the analysis. Because it is easily calculated, has superior performance, can be used to quantify identity information in single variable or in a complete signal and because it indicates the number of individuals who can be discriminated given a set of measurements, we recommend that individuality should be quantified using Beecher's information statistic in future studies. Consistent use of Beecher's information statistic could enable meaningful comparisons and integration of results across different studies of individual identity signals.Item The influence of abiotic factors on the bloom-forming alga Ulva flexuosa (Ulvaceae, Chlorophyta): possibilities for the control of the green tides in freshwater ecosystems(Springer, 2017-11-07) Rybak, Andrzej; Gąbka, MaciejUlva species are characterised by the capacity to achieve rapid biomass increase, which results in the formation of “green tides”, particularly in nutrient-rich seawaters. Over the last decade, formation of large-scale Ulva mats has been increasingly observed in freshwater systems in Central Europe. Mass development of Ulva in freshwater ecosystems presents a growing burden in spite of its economic benefits. This study explores the formation dynamics of Ulva flexuosa mats with respect to habitat conditions, using the examples of a number of water systems located in Poland. Elevated water temperature, pH and high concentration of sulphates are among the most important factors affecting biometric parameters of Ulva blooms. An evident disparity was observed between lotic water ecosystems and lentic water ecosystems, which differed in terms of chemical characteristics of the habitat and mat structure properties. In flowing water, U. flexuosa displays a definitely higher potential for blooms. On the other hand, mass occurrence of U. flexuosa in freshwaters is caused by the inflow of fecund waters, especially following intense precipitation in summertime, as well as by periodic increases in salinity, pH and sulphate levels. The study suggests that potential U. flexuosa blooms in landlocked ecosystems may be controlled by means of reducing the inflow of particularly sulphate-rich waters.Item Kompleks TOB/SAM: kluczowa rola w biogenezie mitochondriów(2007) Kmita, Hanna; Wojtkowska, MałgorzataBiałka tworzące strukturę beczułki b występują w błonie zewnętrznej bakterii Gramujemnych oraz w błonie zewnętrznej organelli pochodzenia endosymbiotycznego, tj. mitochondriów i chloroplastów, gdzie mogą pełnić różne funkcje. Mitochondrialne białka o strukturze beczułki b biorą udział w imporcie białka, transporcie metabolitów oraz w regulacji morfologii i dystrybucji mitochondriów. Białka te uznaje siê takze za istotny element ewolucji mitochondriów. Mechanizm wbudowywania białek tworzących strukturę beczułki b w błone zewnętrzną mitochondriów i bakterii Gram-ujemnych został niedawno opisany. Co więcej, wykazano, iż uległ on utrwaleniu w toku ewolucji. W przypadku mitochondriów w procesie tym uczestniczy kompleks TOB/SAM (topogeneza białek zewnętrznej błony mitochondrialnej tworzących strukturę beczułki b/maszyneria sortowania i składania białek), tworzony przez trzy podstawowe białka: Tob55 (Sam50), Tob38 (Sam35) and Mas 37 (Sam37). Wyniki analizy filogenetycznej wskazują, iż białko Tob55 pochodzi od bakteryjnego białka Omp85, podczas gdy inne mitochondrialne białka o strukturze beczułki b nie mają homologów wśród białek bakteryjnych.Item Organizacja aparatu importu białka do mitochondriów – perspektywa filogenetyczna(2016) Kmita, Hanna; Wojtkowska, MałgorzataPrawidłowe funkcjonowanie mitochondriów, i w konsekwencji komórek eukariotycznych, wymaga bezwzględnie importu większości białek mitochondrialnych. Proces ten może przebiegać różnymi drogami, a w ich powstaniu uczestniczą złożone kompleksy białkowe, nazywane kompleksami importowymi, zlokalizowane we wszystkich przedziałach mitochondrialnych, w tym w obu błonach mitochondrialnych. Niniejsze opracowanie służy podsumowaniu aktualnego stanu wiedzy dotyczącego organizacji kompleksów importowych u przedstawicieli wyróżnianych obecnie różnych linii rozwojowych organizmów eukariotycznych. Wyłaniający się obraz, mimo braku wielu danych, wskazuje na zróżnicowanie organizacji tych kompleksów, szczególnie widoczne w przypadku kompleksu TOM, co może mieć istotne implikacje natury ewolucyjnej jak i aplikacyjnej.Item Phylogenetic analysis of mitochondrial outer membrane β-barrel channels(2012) Wojtkowska, Małgorzata; Jąkalski, Marcin; Pieńkowska, Joanna R.; Stobienia, Olgierd; Karachitos, Andonis; Przytycka, Teresa M.; Weiner, January; Kmita, Hanna; Makałowski, WojciechTransport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (voltage-dependent anion-selective channel, VDAC) as well as in import of proteins encoded by nuclear genes (Tom40 and Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome, and have β-barrel topology. We have compiled data sets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our data set and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial β-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista), they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases, they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane β-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta.Item AtDeg2 – a chloroplast protein with dual protease/chaperone activity(Polskie Towarzystwo Botaniczne, 2014-07-09) Jagodzik, Przemysław; Adamiec, Małgorzata; Jackowski, GrzegorzChloroplast protease AtDeg2 (an ATP-independent serine endopeptidase) is cytosolically synthesized as a precursor, which is imported into the chloroplast stroma and deprived of its transit peptide. Then the mature protein undergoes routing to its functional location at the stromal side of thylakoid membrane. In its linear structure AtDeg2 molecule contains the protease domain with catalytic triad (HDS) and two PDZ domains (PDZ1 and PDZ2). In vivo AtDeg2 most probably exists as a supposedly inactive haxamer, which may change its oligomeric stage to form active 12-mer, or 24-mer. AtDeg2 has recently been demonstrated to exhibit dual protease/chaperone function. This review is focused on the current awareness with regard to AtDeg2 structure and functional significance.Item Projekt badawczy w projekcie edukacyjnym(Instytut Badań Edukacyjnych, 2014) Rybska, ElizaW zależności od ujęcia projekt jest metodą lub strategią nauczania (Nowacki i wsp, 1999). W niektórych źródłach zaliczany do grupy metod nauczania przez dociekanie (ang. inquiry based learning) (Bransford i in., 2000). Metody nauczania oparte na dociekaniu zyskują coraz bardziej na popularności, także w dydaktyce akademickiej. W niniejszej pracy przedstawiono analizę jakościową 25 projektów zajęć dydaktycznych opracowanych przez doktorantów Wydziału Biologii UAM, w których projekt badawczy był składnikiem projektu edukacyjnego, a całość była propozycją zajęć dla studentów tegoż wydziału.Item Botanophila–Epichloe Interaction in a Wild Grass, Puccinellia distans, Lacks Dependence on the Fly Vector(2011) Górzyńska, Karolina; Lembicz, Marlena; Olszanowski, Ziemowit; Leuchtmann, AdrianIn grass-infecting Epichloe (Ascomycetes: Clavicipitaceae) fungi, the transfer of spermatia for fungal fertilization depends on an insect vector: flies of the genus Botanophila (Diptera: Anthomyiidae). The flies use the fungal stroma, a spore-producing fungal structure surrounding the grass inßorescence, for laying eggs and as a food source for both adults and larvae. This fly-fungus interaction is generally regarded as obligatory and mutualistic. Two Botanophila taxa were noted among four populations of the nonagricultural grass Puccinellia distans (L.) Parl. that were infected with the fungus Epichloe typhina (Pers.) Tul. However, during the 7 yr of field observations, Botanophila flies were present every year in only one population of P. distans. The number of eggs per stroma ranged from zero to four and differed with year and site. Overall, eggs (or larvae) were observed on only 132 (19.2%) of the 687 stromata examined during the survey, with one (13.8%), two (4.5%), or more than two (0.9%) per stroma. However, 90.8% of the examined stromata were fertilized and produced perithecia, suggesting that other mechanisms or vectors of spermatia were responsible for fertilization.Item The occurrence and preference of Botanophila flies (Diptera: Anthomyiidae) for particular species of Epichloë fungi infecting wild grasses(2013) Olszanowski, Ziemowit; Lembicz, Marlena; Górzyńska, Karolina; Michelsen, Verner; Leuchtmann, AdrianSpecific associations between species frequently occur in ecological interactions. The aim of this study was to determine the preferences of anthomyiid flies of the genus Botanophila for particular species of fungi as sites for laying eggs and as food for both larvae and adults. The associations of their eggs, larvae and flies with the stromata of different species of Epichloë fungi infecting 7 species of grass in Poland were analyzed. Scanning electron microscopy of the surface of their eggs and an analysis of the genetic sequences of their mitochondrial cytochrome oxidase (COII) were used to identify the taxa of the flies studied. Three types of eggs were distinguished based on their shape, colour and the presence of dorsal folds and sculpturing on the shells. Tentatively,these eggs were assigned to the following species: B. laterella, B. phrenione, B. dissecta and B. lobata. COII sequences obtained from larvae that hatched from two of the types of eggs formed three distinct clades associated with the reference sequences for Botanophila phrenione, B. lobata (new to the fauna of Poland) and a putative species, “Taxon 1”. Only one of these flies (B. lobata) was restricted to a single species of Epichloë (E. bromicola on Elymus repens); B. phrenione was recorded mainly from E. typhina infecting three different species of grass. The results of this study confirm that there is not a close species specific association between this fungus and this insect.Item It is raining mice and voles: which weather conditions influence the activity of Apodemus flavicollis and Myodes glareolus?(Springer, 2015-01) Wróbel, Aleksandra; Bogdziewicz, MichałRodents constitute a crucial part of food chains in many ecosystems; thus, changes in their activity might influence many other species in the community. Moreover, daily variations in activity appear to be an important adaptation, helping rodents to cope with fluctuating intensity of predation pressure and food availability. We investigated how the nightly activity of the yellow-necked mouse (Apodemus flavicollis) and the bank vole (Myodes glareolus) changes with weather conditions. Increased cloud cover enhanced activity of mice, but this effect tended to be weaker during the full moon. In turn, the activity of bank voles was positively influenced by moon phase regardless of cloud cover. Temperature had a negative effect on the activity of both species. Rainfall positively influenced A. flavicollis capture numbers, but tended to decrease the activity of M. glareolus. Therefore, while the activity of both mice and voles was under a strong influence of weather variables, their responses to weather were largely species specific.Item Sex differences in flea infections among rodent hosts: is there a male bias?(2015) Kowalski, Krzysztof; Bogdziewicz, Michał; Eichert, Urszula; Rychlik, LeszekRecognizing patterns of parasite distribution among wildlife hosts is of major importance due to growing risk of transmission of zoonotic diseases to humans. Thus, sex-dependent parasite distribution in higher vertebrates is extensively studied, and males are often found more parasit- ized than females. Male-biased parasitism may be the result of weaker immunocompetence of male hosts owing to the im- munosuppressive effect of androgens. Moreover, larger hosts (males) may demonstrate higher parasite infestation levels than smaller individuals (females), as they constitute a better nutritional resource for parasites and provide them with a greater variety of niches. In the present work, we investigated sex-dependent patterns of flea distribution among three com- mon rodent species (Apodemus agrarius, Apodemus flavicollis, and Myodes glareolus). We hypothesized that males have a higher flea infestation than females. We confirm male-biased parasitism in A. agrarius and M. glareolus, but not in A. flavicollis. Additionally, flea infestation increased with body mass in A. agrarius, but not in A. flavicollis and M. glareolus. The detected differences in parasite distribution among sexes are probably the result of immunosuppressive effects of androgens and spatial behavior of males.Item Fertility effects on Ulva thalli mass development in inland waters of Poland(2013) Messyasz, Beata; Rybak, Andrzej; Pikosz, Marta; Szendzina, LidiaThe genus Ulva (Ulvophyceae, Chlorophyta) consists of some 140 species which are present mainly in marine waters. Nine species occur in the inland waters in Poland (central Europe), of which U. flexuosa subsp. pilifera (Kützing) Bliding is the most widespread in the Wielkopolska region. The occurrence of Ulva species in any particular locality seems to be governed mainly by the availability of nutrients (N, P) than by the high levels of anthropogenic salinity in freshwaters. Freshwater Ulva can grow in different types of ecosystems from reservoir (Malta) through ponds (Tulce) or rivers (Nielba) and ending on drainage ditches. The main question addressed by this study was does the quantity and size of Ulva thalli increase together with the amount of nutrients in water? In addition, the aim of the study was to determine whether the development and the persistence for the long time of the big and dense Ulva patches exert influence for the aqueous ecosystem. We used freshwater Ulva as a model study species.Item Lata nasienne i gryzonie czyli o wpływie zwierząt na rozsiewanie nasion buka i dębu(2014) Bogdziewicz, MichałItem Ulva flexuosa subsp. pilifera (Chlorophyta, Ulvophyceae) from the Wielkopolska region (West Poland): a new observation of the ultrastructure of vegetative cells(Springer, 2013) Messyasz, Beata; Czerwik-Marcinkowska, Joanna; Uher, Bohuslav; Rybak, Andrzej; Szendzina, Lidia; Pikosz, MartaUlva flexuosa subsp. pilifera previously known from northern Poland, from the channel near Szczecin and ponds near Łódź, has recently been found in the Malta Reservoir in the Wielkopolska (West Poland) region. Specimens collected in the Wielkopolska region were examined in detail, also under a transmission electron microscope (TEM). The morphometric analysis of Ulva thalli (both young and mature specimens) was performed in order to study the differences in the ultrastructure of vegetative cells. Rectangular cells in young thalli measured from 32.21 - 55.81 μm to 20.24 – 35.12 μm, and they formed clear longitudinal rows, while cells in the mature specimens ranged from 25.09 – 47.66 μm to 18.90 – 31.56 μm. This study indicates that vegetative cells of the mature thalli show tendency towards distortions of both the longitudinal and transverse cells arrangement. This distortion is determined by the development of possible carbonate calcium crystals on the thalli surface. The ultrastructural analysis (TEM) confirmed that the structure and placement of thylakoids is genus/species specific.Item Morphological and ultrastructural studies on Ulva flexuosa subsp. pilifera (Chlorophyta) from Poland(2013) Messyasz, Beata; Czerwik-Marcinkowska, Joanna; Massalski, Andrzej; Uher, Bohuslav; Rybak, Andrzej; Szendzina, Lidia; Pikosz, MartaUlva flexuosa subsp. pilifera (Kütz.) M. J. Wynne 2005 (= Enteromorpha pilifera Kützing 1845) was previously found in Argentina, the Czech Republic, Germany, Hungary, Romania, Slovakia and Sweden, recently also in Poland. The genus Ulva was first time described as Enteromorpha. Interestingly, Enteromorpha is used nowadays as a synonym for Ulva, a development which is based on molecular data. The morphologies of both young and mature specimens were studied, and most life cycle stages could be observed. Further, the formation of calcium carbonate crystals on the surface of Ulva thalli seems to influence the arrangement of the cells. A detailed ultrastructural (TEM) analysis of cell walls is presented. The TEM reveals in great details highly complex, irregular structures with stratification lines.Item Biomasa alg słodkowodnych surowcem dla przemysłu i rolnictwa(2013) Schroeder, Grzegorz; Messyasz, Beata; Łęska, Bogusława; Fabrowska, Joanna; Pikosz, Marta; Rybak, AndrzejWykorzystując doniesienia literaturowe oraz wyniki badań własnych, przedstawiono występowanie, budowę chemiczną i morfologiczną alg słodkowodnych występujących także na terenie Polski oraz zastosowanie ich biomasy jako cennego surowca dla różnych gałęzi przemysłu i rolnictwa. Z powodu braku w Polsce systemu wykorzystywania biomasy alg do celów przemysłowych i rolniczych, zagospodarowanie tych surowców powstających na dużą skalę w zbiornikach wodnych stanowi duże wyzwanie i jest istotnym elementem gospodarki zrównoważonego rozwoju.