71 Works

Data from: Birds with high lifetime reproductive success experience increased telomere loss

Joanna Sudyka, Aneta Arct, Szymon M. Drobniak, Lars Gustafsson & Mariusz Cichoń
Lifetime reproductive success (LRS) is what counts in terms of evolution, but investments in reproduction entail costs for an organism. The idea that telomere dynamics may be shaped in response to such costs is already established, however we still lack information if this relation translates to overall fitness. Here, we quantified lifetime reproductive success (number of fledged young) and longitudinal telomere dynamics of small passerine birds - the blue tits. We found that individual telomere...

Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs

Gordon Lax, Martin Kolisko, Yana Eglit, Won Je Lee, Naoji Yubuki, Anna Karnkowska, Leander Brian, Gertraud Burger, Patrick Keeling & Alastair Simpson
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many...

Plant herbivore interactions: Combined effect of ground water level, root vole grazing and sedge silicification

Zbigniew Borowski, Karol Zub, Marcin Sulwiński, Małgorzata Suska-Malawska & Marek Konarzewski
1. Accumulation of silica (Si) by plants can driven by (1) herbivore pressure (and therefore, plant-herbivore interactions) (2) geo-hydrological cycles or (3) a combination of (1) and (2), with (1-3) possibly affecting Si concentration with a 1-year delay. 2. To identify the relative significance of (1-3) we analysed the concentration of Si in fibrous tussock sedge (Carex appropinquata), the population density of the root vole (Microtus oeconomus) and the ground water level, over 11 years....

Supplementary Data for \"Molecular characterization of a DNA polymerase from Thermus thermophilus MAT72 phage vB_Tt72, a novel type-A family enzyme with strong proofreading activity\" by Dorawa S., Werbowy O., Plotka M., Kaczorowska A.-K., Makowska J., Kozlowski L.P., Fridjonsson O.H., Hreggvidsson G.O., Aevarsson A., Kaczorowski T.

Lukasz P. Kozlowski
Bioinformatics results related to the article "Molecular characterization of a DNA polymerase from Thermus thermophilus MAT72 phage vB_Tt72, a novel type-A family enzyme with strong proofreading activity".├── crude_refinment_models #models from GalaxyRefine│ ├── model_1.pdb│ ├── model_2.pdb│ ├── model_3.pdb│ ├── model_4.pdb│ └── model_5.pdb├── DNA_polymerase_phage_Tt72_model_after_refinement.pdb #final model - PDB format├── DNA_polymerase_phage_Tt72_model_after_refinement.png #final model - USCF Chimera v.1.15 session├── DNA_polymerase_phage_Tt72_model_after_refinement.py├── DNA_polymerase_phage_Tt72_model_after_refinement_section1.png ├── DNA_polymerase_phage_Tt72_model_after_refinement_section2.png├── DNA_polymerase_phage_Tt72_model_before_refinement.pdb├── DNA_polymerase_phage_Tt72_model_before_refinement.py├── Fig2A.odg├── Fig2A.png├── README.txt ├── Tt72_alignment.fas #alignment├── Tt72.avi #Tt72 model animation└── Tt72.fasta #protein sequence

Optical properties of biomass burning aerosol observed in 2013-2020 over Warsaw with a multiwavelength Raman polarization lidar

Łucja Janicka & Iwona Sylwia Stachlewska
The dataset comprises high-level data products obtained from measurements of the multiwavelength aerosol polarization Raman lidar (PollyXT-UW) during the period of 2013 – 2020 in Warsaw, Poland. It contains the set of mean optical properties (with associated uncertainties) of aerosol particles in 62 layers identified for 31 cases of observed biomass burning aerosols advection over Warsaw. The properties are divided into four groups according to the area of the aerosol origin (Western Europe, Eastern Europe,...

Data for: Realizing Persistent-Spin-Helix Lasing in the Regime of Rashba-Dresselhaus Spin-Orbit Coupling in a Dye-Filled Liquid-Crystal Optical Microcavity

Marcin Muszyński, Jacek Szczytko, Barbara Piętka, Mateusz Król, Katarzyna Rechcińska, Przemysław Oliwa, Mateusz Kędziora, Karolina Łempicka-Mirek, Rafał Mazur, Przemysław Morawiak, Wiktor Piecek, Przemysław Kula & Pavlos G. Lagoudakis
Experimental data from the article "Realizing Persistent-Spin-Helix Lasing in the Regime of Rashba-Dresselhaus Spin-Orbit Coupling in a Dye-Filled Liquid-Crystal Optical Microcavity" by Marcin Muszyński et. al. The article is available online in arXiv:2109.07338 [physics.optics] and in Physical Review Applied 17, 014041 (2022) (Fig.2, Fig.3, Fig.4 and Fig.5). The optical gain introduced into the liquid crystal optical microcavity system allowed to observe the lasing in the Rashba-Dresselhaus regime and the nonlinear optical persistent spin-helix effect at...

Data from: Recovery of large carnivores in Europe’s modern human-dominated landscapes

Guillaume Chapron, Petra Kaczensky, John D. C. Linnell, Manuela Von Arx, Djuro Huber, Henrik Andrén, José Vicente López-Bao, Michal Adamec, Francisco Álvares, Ole Anders, Linas Balčiauskas, Vaidas Balys, Péter Bedő, Ferdinand Bego, Juan Carlos Blanco, Urs Breitenmoser, Henrik Brøseth, Luděk Bufka, Raimonda Bunikyte, Paolo Ciucci, Alexander Dutsov, Thomas Engleder, Christian Fuxjäger, Claudio Groff, Katja Holmala … & Luigi Boitani
The conservation of large carnivores is a formidable challenge for biodiversity conservation. Using a data set on the past and current status of brown bears (Ursus arctos), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and wolverines (Gulo gulo) in European countries, we show that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records. The reasons for this overall conservation success...

Pottery assemblage from Chhim, Lebanon

Urszula Wicenciak-Núñez
This assemblage includes data on ceramic material presented in Urszula Wicenciak's book From Sacred to Everyday. Common Wares and Amphorae from Chhim in the Sidon Hinterland (see below). Data on each fragment of vessel illustrated in the volume has been compiled into an excel file, making it easily searchable and sortable. The document will be updated in the future as not all data is available at this stage of the research. The volume From Sacred...

Polskie Generalne Sondaże Społeczne 1992-2002

Bogdan Cichomski, Tomasz Jerzyński & Marcin Zieliński
Poruszana problematyka badawczaProblematyka PGSS obejmuje główne nurty zainteresowań polskiej i światowej czołówki badaczy z różnych dyscyplin empirycznych nauk społecznych: socjologii, psychologii społecznej, nauk politycznych i ekonomii. Jest również bliska zainteresowaniom praktyków śledzących procesy przekształceń systemowych w Polsce i analizujących ich skutki. W obrębie powtarzanej od 1992 roku problematyki, w PGSS znalazły się następujące bloki zagadnień:Charakterystyki społeczno-demograficzne badanych, obejmujące również ekologię społeczną i mobilność geograficzną, strukturę rodziny i małżeństwa. Do tej grupy należy zaliczyć także wskaźniki...

Polskie Generalne Sondaże Społeczne 1992-1999

Bogdan Cichomski, Tomasz Jerzyński & Marcin Zieliński
Poruszana problematyka badawczaProblematyka PGSS obejmuje główne nurty zainteresowań polskiej i światowej czołówki badaczy z różnych dyscyplin empirycznych nauk społecznych: socjologii, psychologii społecznej, nauk politycznych i ekonomii. Jest również bliska zainteresowaniom praktyków śledzących procesy przekształceń systemowych w Polsce i analizujących ich skutki. W obrębie powtarzanej od 1992 roku problematyki, w PGSS znalazły się następujące bloki zagadnień:Charakterystyki społeczno-demograficzne badanych, obejmujące również ekologię społeczną i mobilność geograficzną, strukturę rodziny i małżeństwa. Do tej grupy należy zaliczyć także wskaźniki...

Polskie Generalne Sondaże Społeczne 1992-2005

Bogdan Cichomski, Tomasz Jerzyński & Marcin Zieliński
Poruszana problematyka badawczaProblematyka PGSS obejmuje główne nurty zainteresowań polskiej i światowej czołówki badaczy z różnych dyscyplin empirycznych nauk społecznych: socjologii, psychologii społecznej, nauk politycznych i ekonomii. Jest również bliska zainteresowaniom praktyków śledzących procesy przekształceń systemowych w Polsce i analizujących ich skutki. W obrębie powtarzanej od 1992 roku problematyki, w PGSS znalazły się następujące bloki zagadnień:Charakterystyki społeczno-demograficzne badanych, obejmujące również ekologię społeczną i mobilność geograficzną, strukturę rodziny i małżeństwa. Do tej grupy należy zaliczyć także wskaźniki...

Proteome-pI 2.0 Isoelectric point for nr (NCBI) proteins

Lukasz P. Kozlowski
Predicted isoelectric point for nr (NCBI) proteins (406M sequences) done using 20 different algorithms (September 2021). Compressed with 7zip and zip.Methods:Bjellqvist, DTASelect, Dawson, EMBOSS, Grimsley, IPC2_peptide, IPC2_protein, IPC_peptide, IPC_protein, Lehninger, Nozaki, Patrickios, ProMoST, Rodwell, Sillero, Solomon, Thurlkill, Toseland, Wikipedia, IPC2.protein.svr19Primary references:Kozlowski LP. Proteome-pI 2.0: proteome isoelectric point database update. Nucleic Acids Res. 2021, doi: 10.1093/nar/gkab944WWW:http://isoelectricpointdb2.orghttp://isoelectricpointdb2.mimuw.edu.pl

Proteome-pI 2.0 Isoelectric point for SwissProt proteins

Lukasz P. Kozlowski
Predicted isoelectric point for SwissProt proteins (561k sequences) done using 20 different algorithms (September 2021). Compressed with 7zip and zip.Methods:Bjellqvist, DTASelect, Dawson, EMBOSS, Grimsley, IPC2_peptide, IPC2_protein, IPC_peptide, IPC_protein, Lehninger, Nozaki, Patrickios, ProMoST, Rodwell, Sillero, Solomon, Thurlkill, Toseland, Wikipedia, IPC2.protein.svr19Primary references:Kozlowski LP. Proteome-pI 2.0: proteome isoelectric point database update. Nucleic Acids Res. 2021, 10.1093/nar/gkab944WWW:http://isoelectricpointdb2.orghttp://isoelectricpointdb2.mimuw.edu.pl

Z4-symmetric perturbations to the XY model from functional renormalization

Andrzej Chlebicki, Carlos A. Sánchez-Villalobos, Paweł Jakubczyk & Nicolás Wschebor
The dataset contains the renormalization group flow equations used to acquire the results discussed in the linked article. Each of the 12 datafiles contains a complete set of equations valid in a specific approximation scheme.The presented flow equations describe the behaviour of the O(2) model with cubic (Z4-symmetric) perturbations. They are derived within the one-particle-irreducible variant of the nonperturbative renormalization group based on the Wetterich equation. We employ the derivative expansion at the leading and...

Data from: Phenotypic plasticity of senescence in Daphnia under predation impact: No ageing acceleration when the perceived risk decreases with age

Barbara Pietrzak, Max Rabus, Maciej Religa, Christian Laforsch & Maciej J. Dańko
Recognizing the nature of the predation risk, and responding to it accurately, is crucial to fitness. Yet, even the most accurate adaptive responses to predation risk usually entail costs, both immediate and lifelong. Rooting in life history theory, we hypothesize that an animal can perceive the nuances of prey size and age selectivity by the predator and modulate its life history accordingly. We test the prediction that – contrary to the faster or earlier senescence...

The expansion wave of an invasive predator leaves declining waterbird populations behind

Marcin Brzeziński, Michał Żmihorski, Marek Nieoczym, Piotr Wilniewczyc & Andrzej Zalewski
Aim: Theory predicts that the evolutionary adaptations of prey to reduce predator pressure often fail in confrontation with non-native predators; thus, their predation usually leads to sharp declines of prey populations. However, over time, prey can develop anti-predator adaptations, reduce predator impact and recover its population. We analyse the numerical response of multiple prey species to the impact of a non-native predator on a large spatiotemporal scale. Location: Poland Methods: Long-term population dynamics of 13...

Data from: Fungal disease incidence along tree diversity gradients depends on latitude in European forests

Diem Nguyen, Bastien Castagneyrol, Helge Bruelheide, Filippo Bussotti, Virginie Guyot, Hervé Jactel, Bogdan Jaroszewicz, Fernando Valladares, Jan Stenlid & Johanna Boberg
European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured...

Data from: Microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus)

Hanna Panagiotopoulou, James D. Austin, Katarzyna Zalewska, Magdalena Gonciarz, Kinga Czarnogórska, Jan Gawor, Piotr Weglenski & Danijela Popovic
Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13,228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3x10-4 per locus per generation (95%CI: 1.48x10-3, 4.15x10-4). Single-step mutations predominated and there were...

Data from: Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis

Aurélie Albert, Alistair G. Auffret, Eric Cosyns, Sara A. O. Cousins, Bram D'Hondt, Carsten Eichberg, Amy E. Eycott, Thilo Heinken, Maurice Hoffmann, Bogdan Jaroszewicz, Juan E. Malo, Anders Mårell, Maarten Mouissie, Robin J. Pakeman, Mélanie Picard, Jan Plue, Peter Poschlod, Sam Provoost, Kiowa Alraune Schulze & Christophe Baltzinger
Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter – which differentially affects individuals according to their characteristics and shapes species assemblages – and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal...

Data from: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Ortillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. De Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, Joseph Heitman, Cedar Hesse … & David S. Hibbett
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as...

Long-term shifts in the functional diversity of abandoned wet meadows – Impacts of historical disturbance and successional pathways

Patryk Czortek, Lidia Borkowska & Marlena Lembicz
Investigating the direction of changes in functional diversity involving successional pathways and historical disturbances may be a promising tool for predictions of the effectiveness of the semi-natural meadows conservation, with great emphasis on formulation of more cost-effective restoration strategies. The goal of this research was to assess the differences in long-term shifts in the functional diversity of plant species in semi-natural wet meadows unmanaged for the last 40 years, under the influence of different successional...

Disentangling effects of disturbance severity and frequency: does bioindication really work?

Remigiusz Pielech & Patryk Czortek
Ecological disturbances are recognized as a crucial factor influencing the attributes of ecological communities. Depending on the specific adaptation or life cycle, plant species show different responses to disturbances of different magnitudes. Herben et al. (2016) proposed disturbance indicator values (DIVs) that describe the niche of each Central-European plant species along gradients of disturbance frequency and severity. Here we ask if the DIVs can be used in community ecology for bioindication of disturbance regime? We...

Data from: Forest degradation limits the complementarity and quality of animal seed dispersal

Finn Rehling, Jan Schlautmann, Bogdan Jaroszewicz, Dana G. Schabo & Nina Farwig
Forest degradation changes the structural heterogeneity of forests and species communities, with potential consequences for ecosystem functions including seed dispersal by frugivorous animals. While the quantity of seed dispersal may be robust towards forest degradation, changes in the effectiveness of seed dispersal through qualitative changes are poorly understood. Here, we carried out extensive field sampling on the structure of forest microhabitats, seed deposition sites, and plant recruitment along three characteristics of forest microhabitats (canopy cover,...

Data from: The early composition and evolution of the turtle shell (Reptilia, Testudinata)

Tomasz Szczygielski & Tomasz Sulej
The shell of the oldest true turtle (Testudinata) branch (Proterochersidae) from the Late Triassic (Norian) of Poland and Germany was built in its anterior and posterior part from an osteodermal mosaic which developed several million years after the plastron, neurals, and costal bones. The most detailed description of the shell composition in proterochersids thus far is provided together with a review of the shell composition in other Triassic pantestudinates, the scenario of early evolution of...

Physiological responses of fen mosses along a nitrogen gradient point to competition restricting their fundamental niches

Izabela Jaszczuk, Wiktor Kotowski, Łukasz Kozub, Juergen Kreyling & Ewa Jabłońska
Nutrient availability determines vegetation patterns and ecological functioning of intact groundwater-fed peatlands (fens). Bryophytes, commonly referred to as ‘brown mosses’, dominate calcareous fens (rich fens), are an integral part of their unique biodiversity and contribute significantly to peat formation and carbon sequestration. Brown mosses are replaced by vascular plants as nutrient availability increases. The decline of brown mosses may either be due to their physiological intolerance of high nutrient levels or to them being outcompeted...

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