TY - THES A1 - Hippel, Barbara von T1 - Long-term bacteria-fungi-plant associations in permafrost soils inferred from palaeometagenomics N2 - The arctic is warming 2 – 4 times faster than the global average, resulting in a strong feedback on northern ecosystems such as boreal forests, which cover a vast area of the high northern latitudes. With ongoing global warming, the treeline subsequently migrates northwards into tundra areas. The consequences of turning ecosystems are complex: on the one hand, boreal forests are storing large amounts of global terrestrial carbon and act as a carbon sink, dragging carbon dioxide out of the global carbon cycle, suggesting an enhanced carbon uptake with increased tree cover. On the other hand, with the establishment of trees, the albedo effect of tundra decreases, leading to enhanced soil warming. Meanwhile, permafrost thaws, releasing large amounts of previously stored carbon into the atmosphere. So far, mainly vegetation dynamics have been assessed when studying the impact of warming onto ecosystems. Most land plants are living in close symbiosis with bacterial and fungal communities, sustaining their growth in nutrient poor habitats. However, the impact of climate change on these subsoil communities alongside changing vegetation cover remains poorly understood. Therefore, a better understanding of soil community dynamics on multi millennial timescales is inevitable when addressing the development of entire ecosystems. Unravelling long-term cross-kingdom dependencies between plant, fungi, and bacteria is not only a milestone for the assessment of warming on boreal ecosystems. On top, it also is the basis for agriculture strategies to sustain society with sufficient food in a future warming world. The first objective of this thesis was to assess ancient DNA as a proxy for reconstructing the soil microbiome (Manuscripts I, II, III, IV). Research findings across these projects enable a comprehensive new insight into the relationships of soil microorganisms to the surrounding vegetation. First, this was achieved by establishing (Manuscript I) and applying (Manuscript II) a primer pair for the selective amplification of ancient fungal DNA from lake sediment samples with the metabarcoding approach. To assess fungal and plant co-variation, the selected primer combination (ITS67, 5.8S) amplifying the ITS1 region was applied on samples from five boreal and arctic lakes. The obtained data showed that the establishment of fungal communities is impacted by warming as the functional ecological groups are shifting. Yeast and saprotroph dominance during the Late Glacial declined with warming, while the abundance of mycorrhizae and parasites increased with warming. The overall species richness was also alternating. The results were compared to shotgun sequencing data reconstructing fungi and bacteria (Manuscripts III, IV), yielding overall comparable results to the metabarcoding approach. Nonetheless, the comparison also pointed out a bias in the metabarcoding, potentially due to varying ITS lengths or copy numbers per genome. The second objective was to trace fungus-plant interaction changes over time (Manuscripts II, III). To address this, metabarcoding targeting the ITS1 region for fungi and the chloroplast P6 loop for plants for the selective DNA amplification was applied (Manuscript II). Further, shotgun sequencing data was compared to the metabarcoding results (Manuscript III). Overall, the results between the metabarcoding and the shotgun approaches were comparable, though a bias in the metabarcoding was assumed. We demonstrated that fungal shifts were coinciding with changes in the vegetation. Yeast and lichen were mainly dominant during the Late Glacial with tundra vegetation, while warming in the Holocene lead to the expansion of boreal forests with increasing mycorrhizae and parasite abundance. Aside, we highlighted that Pinaceae establishment is dependent on mycorrhizal fungi such as Suillineae, Inocybaceae, or Hyaloscypha species also on long-term scales. The third objective of the thesis was to assess soil community development on a temporal gradient (Manuscripts III, IV). Shotgun sequencing was applied on sediment samples from the northern Siberian lake Lama and the soil microbial community dynamics compared to ecosystem turnover. Alongside, podzolization processes from basaltic bedrock were recovered (Manuscript III). Additionally, the recovered soil microbiome was compared to shotgun data from granite and sandstone catchments (Manuscript IV, Appendix). We assessed if the establishment of the soil microbiome is dependent on the plant taxon and as such comparable between multiple geographic locations or if the community establishment is driven by abiotic soil properties and as such the bedrock area. We showed that the development of soil communities is to a great extent driven by the vegetation changes and temperature variation, while time only plays a minor role. The analyses showed general ecological similarities especially between the granite and basalt locations, while the microbiome on species-level was rather site-specific. A greater number of correlated soil taxa was detected for deep-rooting boreal taxa in comparison to grasses with shallower roots. Additionally, differences between herbaceous taxa of the late Glacial compared to taxa of the Holocene were revealed. With this thesis, I demonstrate the necessity to investigate subsoil community dynamics on millennial time scales as it enables further understanding of long-term ecosystem as well as soil development processes and such plant establishment. Further, I trace long-term processes leading to podzolization which supports the development of applied carbon capture strategies under future global warming. N2 - Die Arktis erwärmt sich schneller als der weltweite Durschnitt, was die dortigen Ökosysteme wie die borealen Nadelwälder stark beeinflusst. Die Baumgrenze verschiebt sich durch veränderte Wachstumsbedingungen nach Norden und breitet sich in Tundra-Gegenden aus. Das führt zu komplexen Auswirkungen auf den Kohlenstoffkreislauf, da durch das Baumwachstum vermehrt CO2 im Boden gespeichert wird. Andererseits wird der Albedo-Effekt der Tundra verringert und der Boden erwärmt sich verstärkt. Das wiederum führt zum Tauen von Permafrost und setzt große Mengen an gespeichertem Kohlenstoff frei. Bislang wurde vor allem die Auswirkung der Erwärmung auf Vegetationsdynamiken untersucht. Für ein gesundes Pflanzenwachstum stehen die meisten Landpflanzen in engem Austausch mit einer Vielzahl an Bakterien und Pilzen. Es ist bislang wenig verstanden, wie diese Bodengemeinschaften durch den Klimawandel beeinflusst werden. Es ist deshalb notwendig, verstärkt auch die Langzeitabhängigkeiten der Pflanzen von Mikroorganismen zu betrachten. Dies ist nicht nur ein Meilenstein bei der Untersuchung des Klimawandels auf arktische Ökosysteme. Zudem wird so die Entwicklung angepasster Strategien im Bereich der Landwirtschaft ermöglicht, was die Grundlage dafür ist, die wachsende Bevölkerung auch in Zukunft mit ausreichend Nahrungsmitteln versorgen zu können. Im ersten Teil meiner Arbeit untersuche ich das Potential, die Dynamiken von Bodenmikroorganismen aus Seesedimenten zu rekonstruieren. Ich habe gezeigt, dass molekulargenetische Analysen das sowohl für Pilze als auch Bakterien auf großen Zeitskalen ermöglichen. Eine Zuweisung der Mikroorganismen zu ihren Funktionen im Ökosystem ermöglichte, Dynamiken in den Nährstoffkreisläufen sowie in Pilzökologien zu verstehen. Die Analyse der komplexen Assoziationen von Pilzen und Pflanzen bildete den zweiten Teil meiner Arbeit. Hier konnte ich zeigen, dass Pilze und Pflanzen spezifische Muster in ihren Vorkommen miteinander zeigen und dass die Vegetation das Pilzvorkommen auch auf großen Zeitskalen beeinflusst. Die Tundravegetation des Spätglazials war vor allem von Flechten und Hefevorkommen dominiert, während die Einwanderung von borealen Wäldern in die untersuchten Gebiete zu zunehmder Mykorrhiza- und Parasitenverbreitung führte. Ich habe auch gezeigt, dass die Etablierung von Pinaceen langfristig von spezifischen Mykorrhiza-Pilzen wie Suillineae, Inocybaceae oder Hyaloscypha-Arten abhängt. Das dritte Ziel meiner Arbeit war es, zeitliche Dynamiken in der Zusammensetzung von Bodenorganismen im Bezug zur Entstehung von Böden zu rekonstruieren. Mir gelang es, die Verwitterung von Basalt nachzuvollziehen und daraus die Entstehung von Podsol abzuleiten. Ein Vergleich zu Bodengesellschaften aus Granit- und Sandstein-Einzugsgebieten zeigte, dass sich die Granit- und Basalt-Bodeneigenschaften ähneln. Allerdings zeigten die Pflanzen an den Standorten ein sehr ortsspezifisches Mikrobiom und somit eine lokale Anpassung an die Wachstumsbedingungen. Ich konnte mit dieser Arbeit zeigen, dass die Rekonstruktion von Bodenmikroorganismen im Vergleich zur Vegetation einen Einblick in Ökosystemdynamiken unter Klimawandel ermöglicht. Dies ermöglicht ein besseres Verständnis von Bodenentstehungsprozessen und vereinfacht die Entwicklung angewandter carbon capture Strategien. KW - sedimentary ancient DNA KW - ecology KW - lake sediment KW - Arctic KW - ecosystem reconstruction KW - climate change KW - treeline dynamics KW - microbial soil communities KW - plant-microbe interactions KW - Arktis KW - Klimawandel KW - Ökologie KW - Ökosystem-Rekonstruktion KW - Seesediment KW - mikrobielle Bodengemeinschaften KW - Pflanzen-Mikroben-Interaktionen KW - sedimentary ancient DNA KW - Baumgrenzen-Dynamik Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-636009 ER - TY - JOUR A1 - Krebs, Simon K. A1 - Rakotoarinoro, Nathanael A1 - Stech, Marlitt A1 - Zemella, Anne A1 - Kubick, Stefan T1 - A CHO-based cell-free dual fluorescence reporter system for the straightforward assessment of amber suppression and scFv functionality JF - Frontiers in Bioengineering and Biotechnology N2 - Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs). KW - expanded genetic code KW - orthogonal system KW - noncanonical amino acid KW - unnatural amino acid KW - antibody KW - cell-free protein synthesis KW - mRFP1 KW - sfGFP Y1 - 2022 U6 - https://doi.org/10.3389/fbioe.2022.873906 SN - 2296-4185 VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Kühn, Elisabeth A1 - Becker, Marc A1 - Harpke, Alexander A1 - Kühn, Ingolf A1 - Kuhlicke, Christian A1 - Schmitt, Thomas A1 - Settele, Josef A1 - Musche, Martin T1 - The benefits of counting butterflies: recommendations for a successful citizen science project JF - Ecology and Society N2 - Citizen science (CS) projects, being popular across many fields of science, have recently also become a popular tool to collect biodiversity data. Although the benefits of such projects for science and policy making are well understood, relatively little is known about the benefits participants get from these projects as well as their personal backgrounds and motivations. Furthermore, very little is known about their expectations. We here examine these aspects, with the citizen science project "German Butterfly Monitoring" as an example. A questionnaire was sent to all participants of the project and the responses to the questionnaire indicated the following: center dot Most transect walkers do not have a professional background in this field, though they do have a high educational level, and are close to retirement, with a high number of females; center dot An important motivation to join the project is to preserve the natural environment and to contribute to scientific knowledge; center dot Participants benefit by enhancing their knowledge about butterflies and especially their ability to identify different species (taxonomic knowledge); center dot Participants do not have specific expectations regarding the project beyond proper management and coordination, but have an intrinsic sense of working for a greater good. The willingness to join a project is higher if the project contributes to the solution of a problem discussed in the media (here, insect decline). Based on our findings from the analysis of the questionnaire we can derive a set of recommendations for establishing a successful CS project. These include the importance of good communication, e.g., by explaining what the (scientific) purpose of the project is and what problems are to be solved with the help of the data collected in the project. The motivation to join a CS project is mostly intrinsic and CS is a good tool to engage people during difficult times such as the COVID-19 pandemic, giving participants the feeling of doing something useful. KW - COVID-19 pandemic KW - gender gap KW - insect decline KW - intrinsic motivation KW - monitoring Y1 - 2022 U6 - https://doi.org/10.5751/ES-12861-270238 SN - 1708-3087 VL - 27 IS - 2 PB - Resilience Alliance CY - Wolfville ER - TY - JOUR A1 - Nie, Yan A1 - Wang, Weiwei A1 - Xu, Xun A1 - Ma, Nan A1 - Lendlein, Andreas T1 - The response of human induced pluripotent stem cells to cyclic temperature changes explored by BIO-AFM JF - MRS advances : a journal of the Materials Research Society (MRS) N2 - Human induced pluripotent stem cells (hiPSCs) are highly sensitive to extrinsic physical and biochemical signals from their extracellular microenvironments. In this study, we analyzed the effect of cyclic temperature changes on hiPSCs behaviors, especially by means of scanning force microscopy (BIO-AFM). The alternation in cellular mechanics, as well as the secretion and pattern of deposition of extracellular matrix (ECM) protein in hiPSCs were evaluated. The arrangement of the actin cytoskeleton changed with the variation of the temperature. The rearranged cytoskeleton architecture led to the subsequent changes in cell mechanics (Young's modulus of hiPSCs). With the exposure to the cyclic cold stimuli, an increase in the average surface roughness (Ra) and roughness mean square (RMS) was detected. This observation might be at least in part due to the upregulated secretion of Laminin alpha 5 during repeated temporary cooling. The expression of pluripotent markers, NANOG and SOX2, was not impaired in hiPSCs, when exposed to the cyclic cold stimuli for 24 h. Our findings provide an insight into the effect of temperature on the hiPSC behaviors, which may contribute to a better understanding of the application of locally controlled therapeutic hypothermia. Y1 - 2021 U6 - https://doi.org/10.1557/s43580-021-00110-4 SN - 2059-8521 VL - 6 IS - 31 SP - 745 EP - 749 PB - Springer CY - Cham ER - TY - JOUR A1 - Lozano, Yudi M. A1 - Aguilar-Trigueros, Carlos A. A1 - Onandia, Gabriela A1 - Maaß, Stefanie A1 - Zhao, Tingting A1 - Rillig, Matthias C. T1 - Effects of microplastics and drought on soil ecosystem functions and multifunctionality JF - Journal of applied ecology : an official journal of the British Ecological Society N2 - 1. Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well-known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water conditions, affect ecosystem functions and multifunctionality. 2. To address this gap, we performed an experiment using grassland plant communities growing in microcosms. Microplastic fibres (absent, present) and soil water conditions (well-watered, drought) were applied in a fully factorial design. At harvest, we measured soil ecosystem functions related to nutrient cycling (beta-glucosaminidase, beta-D-cellobiosidase, phosphatase, beta-glucosidase enzymes), respiration, nutrient retention, pH, litter decomposition and soil aggregation (water stable aggregates). As terrestrial systems provide these functions simultaneously, we also assessed ecosystem multifunctionality, an index that encompasses the array of ecosystem functions measured here. 3. We found that the interaction between microplastic fibres and drought affected ecosystem functions and multifunctionality. Drought had negatively affected nutrient cycling by decreasing enzymatic activities by up to similar to 39%, while microplastics increased soil aggregation by similar to 18%, soil pH by similar to 4% and nutrient retention by up to similar to 70% by diminishing nutrient leaching. Microplastic fibres also impacted soil enzymes, respiration and ecosystem multifunctionality, but importantly, the direction of these effects depended on soil water status. That is, under well-watered conditions, these functions decreased with microplastic fibres by up to similar to 34% while under drought they had similar values irrespective of the microplastic presence, or tended to increase with microplastics. Litter decomposition had a contrary pattern increasing with microplastics by similar to 6% under well-watered conditions while decreasing to a similar percentage under drought. 4. Synthesis and applications. Single ecosystem functions can be positively or negatively affected by microplastics fibres depending on soil water status. However, our results suggest that microplastic fibres may cause negative effects on ecosystem soil multifunctionality of a similar magnitude as drought. Thus, strategies to counteract this new global change factor are necessary. KW - enzymatic activities KW - grasslands ecosystem KW - litter decomposition KW - nutrient cycling KW - nutrient leaching KW - soil aggregation KW - soil pH KW - soil respiration Y1 - 2021 U6 - https://doi.org/10.1111/1365-2664.13839 SN - 1365-2664 VL - 58 IS - 5 SP - 988 EP - 996 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Huang, Lixing A1 - Qiao, Ying A1 - Xu, Wei A1 - Gong, Linfeng A1 - He, Rongchao A1 - Qi, Weilu A1 - Gao, Qiancheng A1 - Cai, Hongyan A1 - Grossart, Hans-Peter A1 - Yan, Qingpi T1 - Full-length transcriptome BT - a reliable alternative for single-cell RNA-seq analysis in the spleen of teleost without reference genome JF - Frontiers in immunology N2 - Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available. KW - scRNA-seq KW - full-length transcriptome KW - immune cell population KW - teleost KW - infection Y1 - 2021 U6 - https://doi.org/10.3389/fimmu.2021.737332 SN - 1664-3224 VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Habel, Jan Christian A1 - Ulrich, Werner A1 - Eberle, Jonas A1 - Schmitt, Thomas T1 - Species community structures of Afrotropical butterflies differ depending on the monitoring method JF - Biodiversity and conservation N2 - Standardised biodiversity assessment is crucial to understand community structures and population dynamics of animals. There exist various methods to monitor biodiversity. Approaches differ depending on the target species group and the aim of study, and show advantages and disadvantages. The obtained data and results are influenced by local environmental conditions and seasonal variability. In a comparative approach, we studied butterfly diversity and community structure in the dryland savannah biome of south-eastern Kenya with two different methods, transect counts and bait trapping. We repeatedly collected data throughout the dry and rainy seasons, in both near natural and anthropogenically influenced landscapes. Significantly more species and individuals were recorded by transect counts than by bait trapping, though the larger and more mobile Nymphalid species (and in particular representatives of the genus Charaxes) were comparatively overrepresented in traps. The transect data revealed much more pronounced effects of land-use and seasonality than the trap data. These results show that the choice of data collection methods must depend on the general research question, habitat conditions and season. To study the relative variation of species diversity and abundance, the collection of a fraction of the total species diversity might be sufficient. However, if the focus is on a largely complete recording of species diversity, the use of various collection methods is essential. More specifically, our data clearly demonstrate that transect counts represent a reasonable method for assessing butterfly diversity for the African dryland savannah region, but fails to fully capture occurrences of all species. Bait trapping can be used only as a supplementary method for assessing some few highly mobile low-density species. KW - monitoring KW - transect count KW - bait trap KW - population dynamic KW - disturbance KW - seasonality Y1 - 2022 U6 - https://doi.org/10.1007/s10531-021-02332-2 SN - 0960-3115 SN - 1572-9710 VL - 31 IS - 1 SP - 245 EP - 259 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Mbebi, Alain J. A1 - Breitler, Jean-Christophe A1 - Bordeaux, M'elanie A1 - Sulpice, Ronan A1 - McHale, Marcus A1 - Tong, Hao A1 - Toniutti, Lucile A1 - Castillo, Jonny Alonso A1 - Bertrand, Benoit A1 - Nikoloski, Zoran T1 - A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids JF - G3: Genes, genomes, genetics N2 - Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops. KW - genomic prediction KW - phenomic prediction KW - 3-way coffee hybrids KW - chlorophyll a fluorescence KW - GenPred KW - Shared Data Resource Y1 - 2022 U6 - https://doi.org/10.1093/g3journal/jkac170 SN - 2160-1836 VL - 12 IS - 9 PB - Genetics Soc. of America CY - Pittsburgh, PA ER - TY - JOUR A1 - Heim, Birgit A1 - Lisovski, Simeon A1 - Wieczorek, Mareike A1 - Morgenstern, Anne A1 - Juhls, Bennet A1 - Shevtsova, Iuliia A1 - Kruse, Stefan A1 - Boike, Julia A1 - Fedorova, Irina A1 - Herzschuh, Ulrike T1 - Spring snow cover duration and tundra greenness in the Lena Delta, Siberia BT - two decades of MODIS satellite time series (2001-2021) JF - Environmental research letters N2 - The Lena Delta in Siberia is the largest delta in the Arctic and as a snow-dominated ecosystem particularly vulnerable to climate change. Using the two decades of MODerate resolution Imaging Spectroradiometer satellite acquisitions, this study investigates interannual and spatial variability of snow-cover duration and summer vegetation vitality in the Lena Delta. We approximated snow by the application of the normalized difference snow index and vegetation greenness by the normalized difference vegetation index (NDVI). We consolidated the analyses by integrating reanalysis products on air temperature from 2001 to 2021, and air temperature, ground temperature, and the date of snow-melt from time-lapse camera (TLC) observations from the Samoylov observatory located in the central delta. We extracted spring snow-cover duration determined by a latitudinal gradient. The 'regular year' snow-melt is transgressing from mid-May to late May within a time window of 10 days across the delta. We calculated yearly deviations per grid cell for two defined regions, one for the delta, and one focusing on the central delta. We identified an ensemble of early snow-melt years from 2012 to 2014, with snow-melt already starting in early May, and two late snow-melt years in 2004 and 2017, with snow-melt starting in June. In the times of TLC recording, the years of early and late snow-melt were confirmed. In the three summers after early snow-melt, summer vegetation greenness showed neither positive nor negative deviations. Whereas, vegetation greenness was reduced in 2004 after late snow-melt together with the lowest June monthly air temperature of the time series record. Since 2005, vegetation greenness is rising, with maxima in 2018 and 2021. The NDVI rise since 2018 is preceded by up to 4 degrees C warmer than average June air temperature. The ongoing operation of satellite missions allows to monitor a wide range of land surface properties and processes that will provide urgently needed data in times when logistical challenges lead to data gaps in land-based observations in the rapidly changing Arctic. KW - Arctic vegetation KW - tundra KW - snow cover duration KW - NDVI KW - NDSI KW - MODIS KW - Lena Delta Y1 - 2022 U6 - https://doi.org/10.1088/1748-9326/ac8066 SN - 1748-9326 VL - 17 IS - 8 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Montes-Osuna, Nuria A1 - Cernava, Tomislav A1 - Gomez-Lama Cabanas, Carmen A1 - Berg, Gabriele A1 - Mercado-Blanco, Jesus T1 - Identification of volatile organic compounds emitted by two beneficial endophytic pseudomonas strains from olive roots JF - Plants N2 - The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species. In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae. For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta. KW - biological control agents KW - olive rhizobacteria KW - Pseudomonas sp KW - PICF6 KW - Pseudomonas simiae PICF7 KW - root endophytes KW - Verticillium dahliae KW - volatilome Y1 - 2022 U6 - https://doi.org/10.3390/plants11030318 SN - 2223-7747 VL - 11 IS - 3 PB - MDPI CY - Basel ER - TY - JOUR A1 - Nwosu, Ebuka Canisius A1 - Brauer, Achim A1 - Kaiser, Jérôme A1 - Horn, Fabian A1 - Wagner, Dirk A1 - Liebner, Susanne T1 - Evaluating sedimentary DNA for tracing changes in cyanobacteria dynamics from sediments spanning the last 350 years of Lake Tiefer See, NE Germany JF - Journal of paleolimnology N2 - Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, delta C-13 data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years. KW - Late Holocene KW - Methylheptadecanes KW - Varves KW - Anthropocene KW - Sericytochromatia KW - Melainabacteria Y1 - 2021 U6 - https://doi.org/10.1007/s10933-021-00206-9 SN - 0921-2728 SN - 1573-0417 VL - 66 IS - 3 SP - 279 EP - 296 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Manna, Vincenzo A1 - Zoccarato, Luca A1 - Banchi, Elisa A1 - Arnosti, Carol A1 - Grossart, Hans-Peter A1 - Celussi, Mauro T1 - Linking lifestyle and foraging strategies of marine bacteria BT - selfish behaviour of particle-attached bacteria in the northern Adriatic Sea JF - Environmental microbiology reports N2 - Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers. Y1 - 2022 U6 - https://doi.org/10.1111/1758-2229.13059 SN - 1758-2229 VL - 14 IS - 4 SP - 549 EP - 558 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Minutillo, Serena A. A1 - Ruano-Rosa, David A1 - Abdelfattah, Ahmed A1 - Schena, Leonardo A1 - Malacrino, Antonino T1 - The fungal microbiome of wheat flour includes potential mycotoxin producers JF - Foods N2 - Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain. KW - Penicillium KW - Alternaria KW - post-harvest KW - metabarcoding Y1 - 2022 U6 - https://doi.org/10.3390/foods11050676 SN - 2304-8158 VL - 11 IS - 5 PB - MDPI CY - Basel ER - TY - JOUR A1 - Glückler, Ramesh A1 - Herzschuh, Ulrike A1 - Kruse, Stefan A1 - Andreev, Andrei A1 - Vyse, Stuart Andrew A1 - Winkler, Bettina A1 - Biskaborn, Boris A1 - Pestryakova, Luidmila Agafyevna A1 - Dietze, Elisabeth T1 - Wildfire history of the boreal forest of south-western Yakutia (Siberia) over the last two millennia documented by a lake-sediment charcoal record JF - Biogeosciences : BG / European Geosciences Union N2 - Wildfires, as a key disturbance in forest ecosystems, are shaping the world's boreal landscapes. Changes in fire regimes are closely linked to a wide array of environmental factors, such as vegetation composition, climate change, and human activity. Arctic and boreal regions and, in particular, Siberian boreal forests are experiencing rising air and ground temperatures with the subsequent degradation of permafrost soils leading to shifts in tree cover and species composition. Compared to the boreal zones of North America or Europe, little is known about how such environmental changes might influence long-term fire regimes in Russia. The larch-dominated eastern Siberian deciduous boreal forests differ markedly from the composition of other boreal forests, yet data about past fire regimes remain sparse. Here, we present a high-resolution macroscopic charcoal record from lacustrine sediments of Lake Khamra (southwest Yakutia, Siberia) spanning the last ca. 2200 years, including information about charcoal particle sizes and morphotypes. Our results reveal a phase of increased charcoal accumulation between 600 and 900 CE, indicative of relatively high amounts of burnt biomass and high fire frequencies. This is followed by an almost 900-year-long period of low charcoal accumulation without significant peaks likely corresponding to cooler climate conditions. After 1750 CE fire frequencies and the relative amount of biomass burnt start to increase again, coinciding with a warming climate and increased anthropogenic land development after Russian colonization. In the 20th century, total charcoal accumulation decreases again to very low levels despite higher fire frequency, potentially reflecting a change in fire management strategies and/or a shift of the fire regime towards more frequent but smaller fires. A similar pattern for different charcoal morphotypes and comparison to a pollen and non-pollen palynomorph (NPP) record from the same sediment core indicate that broad-scale changes in vegetation composition were probably not a major driver of recorded fire regime changes. Instead, the fire regime of the last two millennia at Lake Khamra seems to be controlled mainly by a combination of short-term climate variability and anthropogenic fire ignition and suppression. Y1 - 2021 U6 - https://doi.org/10.5194/bg-18-4185-2021 SN - 1726-4170 SN - 1726-4189 VL - 18 IS - 13 SP - 4185 EP - 4209 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Courtin, Jérémy A1 - Andreev, Andrei A1 - Raschke, Elena A1 - Bala, Sarah A1 - Biskaborn, Boris A1 - Liu, Sisi A1 - Zimmermann, Heike A1 - Diekmann, Bernhard A1 - Stoof-Leichsenring, Kathleen R. A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Vegetation changes in Southeastern Siberia during the late pleistocene and the holocene JF - Frontiers in Ecology and Evolution N2 - Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last similar to 35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake's vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the "keystone herbivore" hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene. KW - last glacial KW - Holocene KW - Lake Bolshoe Toko KW - paleoenvironments KW - sedimentary ancient DNA KW - metabarcoding KW - trnL KW - pollen Y1 - 2021 U6 - https://doi.org/10.3389/fevo.2021.625096 SN - 2296-701X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Wassermann, Birgit A1 - Abdelfattah, Ahmed A1 - Wicaksono, Wisnu Adi A1 - Kusstatscher, Peter A1 - Müller, Henry A1 - Cernava, Tomislav A1 - Goertz, Simon A1 - Rietz, Steffen A1 - Abbadi, Amine A1 - Berg, Gabriele T1 - The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines JF - Microbial biotechnology N2 - Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes. Y1 - 2022 U6 - https://doi.org/10.1111/1751-7915.14077 SN - 1751-7915 VL - 15 IS - 9 SP - 2379 EP - 2390 PB - Wiley CY - Hoboken ER - TY - THES A1 - Freimuth, Nina T1 - Elucidating the suppression of root hair formation by a member of a novel, short ENTH protein family in Arabidopsis thaliana T1 - Untersuchungen der Unterdrückung der Wurzelhaarbildung durch ein Mitglied einer neuen, kurzen ENTH-Proteinfamilie in Arabidopsis thaliana N2 - This work analyzed functional and regulatory aspects of the so far little characterized EPSIN N-terminal Homology (ENTH) domain-containing protein EPSINOID2 in Arabidopsis thaliana. ENTH domain proteins play accessory roles in the formation of clathrin-coated vesicles (CCVs) (Zouhar and Sauer 2014). Their ENTH domain interacts with membranes and their typically long, unstructured C-terminus contains binding motifs for adaptor protein complexes and clathrin itself. There are seven ENTH domain proteins in Arabidopsis. Four of them possess the canonical long C-terminus and participate in various, presumably CCV-related intracellular transport processes (Song et al. 2006; Lee et al. 2007; Sauer et al. 2013; Collins et al. 2020; Heinze et al. 2020; Mason et al. 2023). The remaining three ENTH domain proteins, however, have severely truncated C-termini and were termed EPSINOIDs (Zouhar and Sauer 2014; Freimuth 2015). Their functions are currently unclear. Preceding studies focusing on EPSINOID2 indicated a role in root hair formation: epsinoid2 T DNA mutants exhibited an increased root hair density and EPSINOID2-GFP was specifically located in non-hair cell files in the Arabidopsis root epidermis (Freimuth 2015, 2019). In this work, it was clearly shown that loss of EPSINOID2 leads to an increase in root hair density through analyses of three independent mutant alleles, including a newly generated CRISPR/Cas9 full deletion mutant. The ectopic root hairs emerging from non-hair positions in all epsinoid2 mutant alleles are most likely not a consequence of altered cell fate, because extensive genetic analyses placed EPSINOID2 downstream of the established epidermal patterning network. Thus, EPSINOID2 seems to act as a cell autonomous inhibitor of root hair formation. Attempts to confirm this hypothesis by ectopically overexpressing EPSINOID2 led to the discovery of post-transcriptional and -translational regulation through different mechanisms. One involves the little characterized miRNA844-3p. Interference with this pathway resulted in ectopic EPSINOID2 overexpression and decreased root hair density, confirming it as negative factor in root hair formation. A second mechanism likely involves proteasomal degradation. Treatment with proteasomal inhibitor MG132 led to EPSINOID2-GFP accumulation, and a KEN box degron motif was identified in the EPSINOID2 sequence associated with degradation through a ubiquitin/proteasome-dependent pathway. In line with a tight dose regulation, genetic analyses of all three mutant alleles indicate that EPSINOID2 is haploinsufficient. Lastly, it was revealed that, although EPSINOID2 promoter activity was found in all epidermal cells, protein accumulation was observed in N-cells only, hinting at yet another layer of regulation. N2 - In der vorliegenden Arbeit wurden funktionelle und regulatorische Aspekte des bisher wenig charakterisierten EPSIN N-Terminal Homology (ENTH)-Domäne-enthaltenden Proteins EPSINOID2 in Arabidopsis thaliana untersucht. ENTH-Domänen Proteine spielen akzessorische Rollen in der Bildung von Clathrin-umhüllten Vesikeln (CCVs) (Zouhar and Sauer 2014). Ihre ENTH-Domäne interagiert mit Membranen und ihr typischerweise langer, unstrukturierter C-Terminus enthält Bindungsmotive für Adapterproteinkomplexe und Clathrin selbst. In Arabidopsis gibt es sieben ENTH-Domänen Proteine. Vier von ihnen besitzen den langen C-Terminus und sind an verschiedenen, vermutlich CCV-bezogenen intrazellulären Transportprozessen beteiligt (Song et al. 2006; Lee et al. 2007; Sauer et al. 2013; Heinze et al. 2020; Collins et al. 2020; Mason et al. 2023). Die verbleibenden drei ENTH-Domänen Proteine haben jedoch stark verkürzte C-Termini und wurden als EPSINOIDe bezeichnet (Zouhar and Sauer 2014; Freimuth 2015). Ihre Funktion ist derzeit unklar. Vorangegangene Studien, die sich auf EPSINOID2 konzentrierten, deuteten auf eine Rolle bei der Wurzelhaarbildung hin: epsinoid2 T-DNA-Mutanten zeigten eine erhöhte Wurzelhaardichte und EPSINOID2-GFP war speziell in Nicht-Haarzellen in der Wurzelepidermis von Arabidopsis lokalisiert (Freimuth 2015, 2019). In dieser Arbeit wurde durch Analysen von drei unabhängigen mutierten Allelen, einschließlich einer neu generierten CRISPR/Cas9-Deletionsmutante, klar gezeigt, dass der Verlust von EPSINOID2 zu einer Erhöhung der Wurzelhaardichte führt. Die ektopischen Wurzelhaare, die in allen epsinoid2 Allelen aus Nicht-Haar-Positionen hervorgehen, sind höchstwahrscheinlich keine Folge eines veränderten Zellschicksals, da umfangreiche genetische Analysen EPSINOID2 dem etablierten Netzwerk zur Ausbildung der epidermalen Identität nachgeschaltet platziert haben. Somit scheint EPSINOID2 als zellautonomer Inhibitor der Wurzelhaarbildung zu wirken. Versuche, diese Hypothese durch ektopische Überexpression von EPSINOID2 zu bestätigen, führten zur Entdeckung einer post-transkriptionellen und translationalen Regulation durch verschiedene Mechanismen. Bei einem davon handelt es sich um die wenig charakterisierte miRNA844-3p. Eine Beeinträchtigung dieses Signalwegs führte zu einer ektopischen Überexpression von EPSINOID2 und einer verringerten Wurzelhaardichte, was bestätigt, dass es sich um einen negativen Faktor bei der Wurzelhaarbildung handelt. Ein zweiter Mechanismus beinhaltet wahrscheinlich den proteasomalen Abbau. Die Behandlung mit dem proteasomalen Inhibitor MG132 führte zur Akkumulation von EPSINOID2-GFP, und in der Sequenz von EPSINOID2 wurde ein KEN-Box Degron Motiv identifiziert, das mit dem Abbau über einen Ubiquitin/Proteasom-abhängigen Weg verbunden ist. Im Einklang mit einer strengen Dosisregulierung zeigten genetische Analysen aller drei mutierten Allele, dass EPSINOID2 haploinsuffizient ist. Abschließend wurde festgestellt, dass die Aktivität des EPSINOID2 Promotors zwar in allen Epidermiszellen zu finden war, eine Proteinakkumulation jedoch nur in Nicht-Haarzellen beobachtet wurde, was auf eine weitere Ebene der Regulation hindeutet. KW - ENTH domain proteins KW - ENTH-Domänen Proteine KW - root hair formation KW - Wurzelhaarbildung KW - miRNA regulation KW - miRNA Regulation Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-634994 ER - TY - JOUR A1 - Dreymann, Nico A1 - Wuensche, Julia A1 - Sabrowski, Wiebke A1 - Moeller, Anja A1 - Czepluch, Denise A1 - Vu Van, Dana A1 - Füssel, Susanne A1 - Menger, Marcus M. T1 - Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA JF - International journal of molecular sciences N2 - Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a K-D of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a K-D of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity. KW - biomarker KW - cancer KW - cancer therapy KW - DNA aptamer KW - microscale thermophoresis (MST) KW - SELEX KW - surface plasmon resonance spectroscopy (SPR) KW - uPA KW - uPAR KW - urokinase Y1 - 2022 U6 - https://doi.org/10.3390/ijms23094890 SN - 1661-6596 SN - 1422-0067 VL - 23 IS - 9 PB - MDPI CY - Basel ER - TY - JOUR A1 - Zhang, Kai A1 - Hu, Jiege A1 - Yang, Shuai A1 - Xu, Wei A1 - Wang, Zhichao A1 - Zhuang, Peiwen A1 - Grossart, Hans-Peter A1 - Luo, Zhuhua T1 - Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1 JF - Journal of hazardous materials N2 - Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling. KW - Impranil PU degradation KW - Lipase KW - Cutinase KW - HsbA KW - Fatty acid degradation Y1 - 2022 U6 - https://doi.org/10.1016/j.jhazmat.2022.129406 SN - 0304-3894 SN - 1873-3336 VL - 437 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Raffeiner, Margot A1 - Üstün, Suayib A1 - Guerra, Tiziana A1 - Spinti, Daniela A1 - Fitzner, Maria A1 - Sonnewald, Sophia A1 - Baldermann, Susanne A1 - Börnke, Frederik T1 - The Xanthomonas type-III effector XopS stabilizes CaWRKY40a to regulate defense responses and stomatal immunity in pepper (Capsicum annuum) JF - The plant cell N2 - As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation. Y1 - 2022 U6 - https://doi.org/10.1093/plcell/koac032 SN - 1040-4651 SN - 1532-298X VL - 34 IS - 5 SP - 1684 EP - 1708 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Hannigan, Sara A1 - Nendel, Claas A1 - Krull, Marcos T1 - Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius JF - Journal of pest science N2 - Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread. KW - Agricultural pests KW - Diffusion KW - Hidden Markov models KW - Movement ecology Y1 - 2022 U6 - https://doi.org/10.1007/s10340-022-01510-7 SN - 1612-4758 SN - 1612-4766 SP - 389 EP - 402 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Hilgers, Leon A1 - Hartmann, Stefanie A1 - Pfaender, Jobst A1 - Lentge-Maass, Nora A1 - Marwoto, Ristiyanti M. A1 - von Rintelen, Thomas A1 - Hofreiter, Michael T1 - Evolutionary divergence and radula diversification in two ecomorphs from an adaptive radiation of freshwater snails JF - Genes N2 - (1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin's finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups. KW - speciation KW - adaptive radiation KW - molluscs KW - RNAseq KW - regulatory evolution KW - trophic specialization Y1 - 2022 U6 - https://doi.org/10.3390/genes13061029 SN - 2073-4425 VL - 13 IS - 6 PB - MDPI CY - Basel ER - TY - THES A1 - Siebler, Lara T1 - Identifying novel regulators of heat stress memory in Arabidopsis thaliana T1 - Identifikation neuer Regulatoren des Hitzestressgedächtnisses in Arabidopsis thaliana N2 - Heat stress (HS) is a major abiotic stress that negatively affects plant growth and productivity. However, plants have developed various adaptive mechanisms to cope with HS, including the acquisition and maintenance of thermotolerance, which allows them to respond more effectively to subsequent stress episodes. HS memory includes type II transcriptional memory which is characterized by enhanced re-induction of a subset of HS memory genes upon recurrent HS. In this study, new regulators of HS memory in A. thaliana were identified through the characterization of rein mutants. The rein1 mutant carries a premature stop in CYCLIN-DEPENDENT-KINASE 8 (CDK8) which is part of the cyclin kinase module of the Mediator complex. Rein1 seedlings show impaired type II transcriptional memory in multiple heat-responsive genes upon re-exposure to HS. Additionally, the mutants exhibit a significant deficiency in HS memory at the physiological level. Interaction studies conducted in this work indicate that CDK8 associates with the memory HEAT SHOCK FACTORs HSAF2 and HSFA3. The results suggest that CDK8 plays a crucial role in HS memory in plants together with other memory HSFs, which may be potential targets of the CDK8 kinase function. Understanding the role and interaction network of the Mediator complex during HS-induced transcriptional memory will be an exciting aspect of future HS memory research. The second characterized mutant, rein2, was selected based on its strongly impaired pAPX2::LUC re-induction phenotype. In gene expression analysis, the mutant revealed additional defects in the initial induction of HS memory genes. Along with this observation, basal thermotolerance was impaired similarly as HS memory at the physiological level in rein2. Sequencing of backcrossed bulk segregants with subsequent fine mapping narrowed the location of REIN2 to a 1 Mb region on chromosome 1. This interval contains the At1g65440 gene, which encodes the histone chaperone SPT6L. SPT6L interacts with chromatin remodelers and bridges them to the transcription machinery to regulate nucleosome and Pol II occupancy around the transcriptional start site. The EMS-induced missense mutation in SPT6L may cause altered HS-induced gene expression in rein2, possibly triggered by changes in the chromatin environment resulting from altered histone chaperone function. Expanding research on screen-derived factors that modify type II transcriptional memory has the potential to enhance our understanding of HS memory in plants. Discovering connections between previously identified memory factors will help to elucidate the underlying network of HS memory. This knowledge can initiate new approaches to improve heat resilience in crops. N2 - Hitzestress ist ein abiotischer Stressfaktor, der Pflanzenwachstum und Ertragsfähigkeit negativ beeinflusst. Pflanzen haben Anpassungsmechanismen entwickelt, einschließlich des Erwerbs und der Aufrechterhaltung von Thermotoleranz, die es ihnen ermöglichen auf wiederholte Stressereignisse effektiver zu reagieren. Das Hitzestress-Gedächtnis umfasst unter anderem verstärkte Re-Induktion von Gedächtnisgenen nach wiederholter Exposition (Typ II). In dieser Arbeit wurden anhand der Charakterisierung von Re-Induktionsmutanten (rein Mutanten) neue Regulatoren des Typ II Hitzestress-Gedächtnisses in A. thaliana identifiziert. Die rein1 Mutante weist ein vorzeitiges Stoppcodon in CDK8 auf, einer Untereinheit im Kinasemodul des Mediator Komplexes. Rein1 Keimlinge zeigen ein beeinträchtigtes Hitzstress-Transkriptionsgedächtnis, sowie Defekte in der Aufrechterhaltung der Thermotoleranz auf physiologischer Ebene. Mittels Interaktionsstudien konnte gezeigt werden, dass CDK8 mit den im Hitzestress-Gedächtnis fungierenden Hitzeschockfaktoren HSAF2 und HSFA3 interagiert. Die Ergebnisse legen nahe, dass CDK8 zusammen mit HSFs eine Rolle bei der Aufrechterhaltung des Hitzestress-Gedächtnisses spielt, wobei letztere potenzielle Ziele der Kinasefunktion von CDK8 darstellen. Die Rolle und das Interaktionsnetzwerk des Mediatorkomplexes während der durch Hitzstress-induzierten transkriptionellen Gedächtnis-bildung und Aufrechterhaltung ist ein aufregender Aspekt zukünftiger Forschung. Die zweite rein Mutante (rein2) wurde aufgrund einer stark beeinträchtigten transkriptionellen Re-Induktion nach wiederholtem Hitzestress für weitere Charakterisierungen ausgewählt. Dabei wurden zusätzliche Defekte in der initialen Induktion von Hitzestress-Gedächtnisgenen festgestellt. Die basale Thermotoleranz in rein2 war in ähnlicher Weise beeinträchtigt wie das Hitzestress-Gedächtnis. Die Position von REIN2 wurde mithilfe von Sequenzierung und Feinkartierung auf eine 1 Mb große Region auf Chromosom 1 eingegrenzt. Dieses Intervall enthält das Gen At1g65440, das für Histon-Chaperon SPT6L kodiert. Die Missense-Mutation in SPT6L könnte die Ursache für das veränderte Hitzestress-induzierte Transkriptionsmuster in rein2 sein, möglicherweise aufgrund von einer abweichenden Chaperonfunktion und folglich Veränderung in der Chromatinumgebung. Die Ausweitung der Forschung zu den in diesem Screening ermittelten Faktoren, die das Typ II Transkriptionsgedächtnis beeinflussen, hat das Potenzial, unser derzeitiges Verständnis des Hitzestress-Gedächtnisses in Pflanzen zu verbessern und Verbindungen zwischen zuvor entdeckten Gedächtnisregulatoren herzustellen. Dieses Wissen kann dazu beitragen neue Ansätze zur Verbesserung der Hitzeresilienz bei Nutzpflanzen anzustoßen. KW - epigenetics KW - heat stress KW - molecular biology KW - genetic screen KW - Epigenetik KW - Hitzestress KW - Molekularbiologie KW - genetischer Screen Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-634477 ER - TY - GEN A1 - Hermanussen, Michael A1 - Scheffler, Christiane A1 - Pulungan, Aman B. A1 - Batubara, Jose R. L. A1 - Julia, Madarina A1 - Bogin, Barry T1 - Response to the correspondence referring to our article "Stunting is not a synonym of malnutrition" (2018EJCN0997RR) by Conny Tanjung, Titis Prawitasari, Damayanti Rusli Sjarif T2 - European journal of clinical nutrition Y1 - 2020 U6 - https://doi.org/10.1038/s41430-020-0571-1 SN - 0954-3007 SN - 1476-5640 VL - 74 IS - 3 SP - 529 EP - 531 PB - Nature Publ. Group CY - New York, NY ER - TY - JOUR A1 - Perkins, Anita K. A1 - Santos, Isaac R. A1 - Rose, Andrew L. A1 - Schulz, Kai G. A1 - Grossart, Hans-Peter A1 - Eyre, Bradley D. A1 - Kelaher, Brendan P. A1 - Oakes, Joanne M. T1 - Production of dissolved carbon and alkalinity during macroalgal wrack degradation on beaches BT - a mesocosm experiment with implications for blue carbon JF - Biogeochemistry N2 - Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration. KW - Tidal pumping KW - Organic matter degradation KW - Carbon cycle KW - Mineralisation KW - Porewater exchange KW - Submarine groundwater discharge Y1 - 2022 U6 - https://doi.org/10.1007/s10533-022-00946-4 SN - 0168-2563 SN - 1573-515X VL - 160 IS - 2 SP - 159 EP - 175 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Terao, Mineko A1 - Garattini, Enrico A1 - Romão, Maria João A1 - Leimkühler, Silke T1 - Evolution, expression, and substrate specificities of aldehyde oxidase enzymes in eukaryotes JF - The journal of biological chemistry N2 - Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles. KW - metalloenzyme KW - molybdenum KW - mouse KW - drug metabolism KW - flavoprotein KW - xenobiotic KW - oxidase KW - oxygen radicals KW - iron-sulfur protein KW - aldehyde oxidase (AOX) KW - enzyme evolution KW - metal-containing enzyme KW - molybdenum cofactor (Moco) KW - molybdo-flavoenzyme KW - 2Fe-2S cluster KW - flavin adenine dinucleotide (FAD) Y1 - 2020 U6 - https://doi.org/10.1074/jbc.REV119.007741 SN - 0021-9258 SN - 1083-351X VL - 295 IS - 16 SP - 5377 EP - 5389 PB - American Society for Biochemistry and Molecular Biology CY - Rockville ER - TY - JOUR A1 - Kunstmann, Ruth Sonja A1 - Engström, Olof A1 - Wehle, Marko A1 - Widmalm, Göran A1 - Santer, Mark A1 - Barbirz, Stefanie T1 - Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein JF - Chemistry – A European Journal N2 - Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design. KW - carbohydrates KW - molecular dynamics simulations KW - NMR spectroscopy KW - protein-carbohydrate interactions KW - surface plasmon resonance Y1 - 2020 U6 - https://doi.org/10.1002/chem.202000495 SN - 0947-6539 SN - 1521-3765 VL - 26 IS - 32 SP - 7263 EP - 7273 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Calderan-Rodrigues, Maria Juliana A1 - Luzarowski, Marcin A1 - Monte-Bello, Carolina Cassano A1 - Minen, Romina Ines A1 - Zühlke, Boris M. A1 - Nikoloski, Zoran A1 - Skirycz, Aleksandra A1 - Caldana, Camila T1 - Proteogenic dipeptides are characterized by diel fluctuations and target of rapamycin complex-signaling dependency in the model plant Arabidopsis thaliana JF - Frontiers in plant science : FPLS N2 - As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes. KW - dipeptide KW - diel cycle KW - metabolism KW - TOR signaling KW - protein-metabolite KW - interactions KW - carbon limitation KW - amino acid Y1 - 2021 U6 - https://doi.org/10.3389/fpls.2021.758933 SN - 1664-462X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Thirumalaikumar, Venkatesh P. A1 - Gorka, Michal A1 - Schulz, Karina A1 - Masclaux-Daubresse, Celine A1 - Sampathkumar, Arun A1 - Skirycz, Aleksandra A1 - Vierstra, Richard D. A1 - Balazadeh, Salma T1 - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1 JF - Autophagy N2 - In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. KW - Arabidopsis thaliana KW - heat stress KW - HSFA2 KW - HSP90.1 KW - NBR1 KW - ROF1 KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2020 U6 - https://doi.org/10.1080/15548627.2020.1820778 SN - 1554-8635 VL - 17 IS - 9 SP - 2184 EP - 2199 PB - Taylor & Francis CY - Abingdon ER - TY - JOUR A1 - Friedrich, Thomas A1 - Oberkofler, Vicky A1 - Trindade, Inês A1 - Altmann, Simone A1 - Brzezinka, Krzysztof A1 - Lämke, Jörn S. A1 - Gorka, Michal A1 - Kappel, Christian A1 - Sokolowska, Ewelina A1 - Skirycz, Aleksandra A1 - Graf, Alexander A1 - Bäurle, Isabel T1 - Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis JF - Nature Communications N2 - Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory. Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-23786-6 SN - 2041-1723 VL - 12 IS - 1 PB - Nature Publishing Group UK CY - [London] ER - TY - JOUR A1 - Carpio Arias, Tannia Valeria A1 - Arias Mogrovejo, Diana Carolina A1 - Nicolalde Cifuentes, Tomás Marcelo A1 - Tapia Veloz, Estephany Carolina A1 - Zeeuw, Chris I. de A1 - Vinueza Veloz, Maria Fernanda T1 - Sleep quality does not mediate the negative effects of chronodisruption on body composition and metabolic syndrome in healthcare workers in Ecuador JF - Diabetes & metabolic syndrome : clinical research & reviews ; the official journal of DiabetesIndia N2 - Background and aims: The objective of the present work was to determine to what extent sleep quality may mediate the association between chronodisruption (CD) and metabolic syndrome (MS), and between CD and body composition (BC). Methodology: Cross-sectional study which included 300 adult health workers, 150 of whom were night shift workers and thereby exposed to CD. Diagnosis of MS was made based on Adult Treatment Panel III criteria. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Body mass index (BMI), fat mass percentage, and visceral fat percentage were measured as indicators of body composition (BC). Data were analyzed using logistic, linear regression and structural equation models. Results: The odds of health workers exposed to CD to suffer MS was 22.13 (IC95 8.68-66.07) when the model was adjusted for age, gender, physical activity and energy consumption. CD was also significantly associated with an increase in fat mass and visceral fat percentages, but not to BMI. Surprisingly, there was not enough evidence supporting the hypothesis that sleep quality contributes to the association between CD and MS or between CD and BC. Conclusions: Sleep quality does not mediate the negative effects of CD on MS nor on BC. KW - Shift work KW - Metabolic syndrome KW - Sleep quality KW - Chronodisruption KW - Body composition Y1 - 2021 U6 - https://doi.org/10.1016/j.dsx.2021.01.017 SN - 1871-4021 SN - 1878-0334 VL - 15 IS - 1 SP - 397 EP - 402 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Huß, Sebastian A1 - Judd, Rika Siedah A1 - Koper, Kaan A1 - Maeda, Hiroshi A. A1 - Nikoloski, Zoran T1 - An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana JF - The plant journal N2 - Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks. KW - atom mapping KW - genome-scale metabolic model KW - isotopic labeling KW - metabolic KW - flux analysis KW - technical advance Y1 - 2022 U6 - https://doi.org/10.1111/tpj.15903 SN - 0960-7412 SN - 1365-313X VL - 111 IS - 5 SP - 1486 EP - 1500 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Ostermann-Miyashita, Emu-Felicitas A1 - König, Hannes J. A1 - Pernat, Nadja A1 - Bellingrath-Kimura, Sonoko Dorothea A1 - Hibler, Sophia A1 - Kiffner, Christian T1 - Knowledge of returning wildlife species and willingness to participate in citizen science projects among wildlife park visitors in Germany JF - People and nature N2 - Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe. While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts. Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts. To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany. Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities. Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower. Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge. However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities. Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation. Read the free Plain Language Summary for this article on the Journal blog. KW - environmental awareness KW - human-animal relationships KW - human-wildlife conflicts KW - social-ecological system KW - wildlife conservation KW - wildlife knowledge Y1 - 2022 U6 - https://doi.org/10.1002/pan3.10379 SN - 2575-8314 VL - 4 IS - 5 SP - 1201 EP - 1215 PB - British Ecological Society; Wiley CY - London; Hoboken, NJ ER - TY - JOUR A1 - Scharnweber, Inga Kristin A1 - Chaguaceda, Fernando A1 - Eklöv, Peter T1 - Fatty acid accumulation in feeding types of a natural freshwater fish population JF - Oecologia / in cooperation with the International Association for Ecology, Intecol N2 - Fatty acids are widely used to study trophic interactions in food web assemblages. Generally, it is assumed that there is a very small modification of fatty acids from one trophic step to another, making them suitable as trophic biomarkers. However, recent literature provides evidence that many fishes possess genes encoding enzymes with a role in bioconversion, thus the capability for bioconversion might be more widespread than previously assumed. Nonetheless, empirical evidence for biosynthesis occurring in natural populations remains scarce. In this study, we investigated different feeding types of perch (Perca fluviatilis) that are specialized on specific resources with different levels of highly unsaturated fatty acids (HUFAs), and analyzed the change between HUFA proportions in perch muscle tissue compared to their resources. Perch showed matching levels to their resources for EPA, but ARA and especially DHA were accumulated. Compound-specific stable isotope analyses helped us to identify the origin of HUFA carbon. Our results suggest that perch obtain a substantial amount of DHA via bioconversion when feeding on DHA-poor benthic resources. Thus, our data indicate the capability of bioconversion of HUFAs in a natural freshwater fish population. KW - Fatty acid conversion KW - Compound-specific stable isotope analysis KW - Docosahexaenoic acid KW - Bioconversion KW - Trophic upgrading Y1 - 2021 U6 - https://doi.org/10.1007/s00442-021-04913-y SN - 0029-8549 SN - 1432-1939 VL - 196 IS - 1 SP - 53 EP - 63 PB - Springer CY - Berlin ; Heidelberg [u.a.] ER - TY - JOUR A1 - Leins, Johannes A. A1 - Banitz, Thomas A1 - Grimm, Volker A1 - Drechsler, Martin T1 - High-resolution PVA along large environmental gradients to model the combined effects of climate change and land use timing BT - lessons from the large marsh grasshopper JF - Ecological modelling : international journal on ecological modelling and systems ecology N2 - Both climate change and land use regimes affect the viability of populations, but they are often studied separately. Moreover, population viability analyses (PVAs) often ignore the effects of large environmental gradients and use temporal resolutions that are too coarse to take into account that different stages of a population's life cycle may be affected differently by climate change. Here, we present the High-resolution Large Environmental Gradient (HiLEG) model and apply it in a PVA with daily resolution based on daily climate projections for Northwest Germany. We used the large marsh grasshopper (LMG) as the target species and investigated (1) the effects of climate change on the viability and spatial distribution of the species, (2) the influence of the timing of grassland mowing on the species and (3) the interaction between the effects of climate change and grassland mowing. The stageand cohort-based model was run for the spatially differentiated environmental conditions temperature and soil moisture across the whole study region. We implemented three climate change scenarios and analyzed the population dynamics for four consecutive 20-year periods. Climate change alone would lead to an expansion of the regions suitable for the LMG, as warming accelerates development and due to reduced drought stress. However, in combination with land use, the timing of mowing was crucial, as this disturbance causes a high mortality rate in the aboveground life stages. Assuming the same date of mowing throughout the region, the impact on viability varied greatly between regions due to the different climate conditions. The regional negative effects of the mowing date can be divided into five phases: (1) In early spring, the populations were largely unaffected in all the regions; (2) between late spring and early summer, they were severely affected only in warm regions; (3) in summer, all the populations were severely affected so that they could hardly survive; (4) between late summer and early autumn, they were severely affected in cold regions; and (5) in autumn, the populations were equally affected across all regions. The duration and start of each phase differed slightly depending on the climate change scenario and simulation period, but overall, they showed the same pattern. Our model can be used to identify regions of concern and devise management recommendations. The model can be adapted to the life cycle of different target species, climate projections and disturbance regimes. We show with our adaption of the HiLEG model that high-resolution PVAs and applications on large environmental gradients can be reconciled to develop conservation strategies capable of dealing with multiple stressors. KW - Climate change KW - Land use KW - Population viability analysis KW - Stage-based model KW - High resolution KW - Environmental gradients Y1 - 2020 U6 - https://doi.org/10.1016/j.ecolmodel.2020.109355 SN - 0304-3800 SN - 1872-7026 VL - 440 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Potente, Giacomo A1 - Léveillé-Bourret, Étienne A1 - Yousefi, Narjes A1 - Choudhury, Rimjhim Roy A1 - Keller, Barbara A1 - Diop, Seydina Issa A1 - Duijsings, Daniël A1 - Pirovano, Walter A1 - Lenhard, Michael A1 - Szövényi, Péter A1 - Conti, Elena T1 - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism JF - Molecular biology and evolution : MBE N2 - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula? KW - genome architecture KW - supergene KW - heterostyly KW - evolutionary genomics KW - chromosome-scale genome assembly KW - primula Y1 - 2022 U6 - https://doi.org/10.1093/molbev/msac035 SN - 0737-4038 SN - 1537-1719 VL - 39 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Lucena-Perez, María A1 - Bazzicalupo, Enrico A1 - Paijmans, Johanna A1 - Kleinman-Ruiz, Daniel A1 - Dalén, Love A1 - Hofreiter, Michael A1 - Delibes, Miguel A1 - Clavero, Miguel A1 - Godoy, José A. T1 - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past. Y1 - 2022 U6 - https://doi.org/10.1016/j.quascirev.2022.107518 SN - 0277-3791 SN - 1873-457X VL - 285 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Nwosu, Ebuka Canisius A1 - Roeser, Patricia Angelika A1 - Yang, Sizhong A1 - Pinkerneil, Sylvia A1 - Ganzert, Lars A1 - Dittmann, Elke A1 - Brauer, Achim A1 - Wagner, Dirk A1 - Liebner, Susanne T1 - Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics JF - Frontiers in microbiology N2 - Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes. KW - Cyanobium KW - picocyanobacteria diversity KW - amplicon sequencing KW - lake monitoring KW - ecological succession KW - lake stratification KW - psychrotolerant Y1 - 2021 U6 - https://doi.org/10.3389/fmicb.2021.761259 SN - 1664-302X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Escalante, Ignacio A1 - Dominguez, Marisol A1 - Gomez-Ruiz, Daisy Alejandra A1 - Machado, Glauco T1 - Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones) JF - Frontiers in ecology and evolution N2 - Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals. KW - alarm signals KW - aggregation size KW - autotomy KW - chemical defenses KW - dilution KW - effect KW - ectoparasitism KW - group living KW - roosting site Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2021.766323 SN - 2296-701X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Lozada-Gobilard, Sissi Donna A1 - Jeltsch, Florian A1 - Zhu, Jinlei T1 - High matrix vegetation decreases mean seed dispersal distance but increases long wind dispersal probability connecting local plant populations in agricultural landscapes JF - Agriculture, ecosystems & environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere N2 - Seed dispersal plays an important role in population dynamics in agricultural ecosystems, but the effects of surrounding vegetation height on seed dispersal and population connectivity on the landscape scale have rarely been studied. Understanding the effects of surrounding vegetation height on seed dispersal will provide important information for land-use management in agricultural landscapes to prevent the spread of undesired weeds or enhance functional connectivity. We used two model species, Phragmites australis and Typha latifolia, growing in small natural ponds known as kettle holes, in an agricultural landscape to evaluate the effects of surrounding vegetation height on wind dispersal and population connectivity between kettle holes. Seed dispersal distance and the probability of long-distance dispersal (LDD) were simulated with the mechanistic WALD model under three scenarios of "low", "dynamic" and "high" surrounding vegetation height. Connectivity between the origin and target kettle holes was quantified with a connectivity index adapted from Hanski and Thomas (1994). Our results show that mean seed dispersal distance decreases with the height of surrounding matrix vegetation, but the probability of long-distance dispersal (LDD) increases with vegetation height. This indicates an important vegetation-based trade-off between mean dispersal distance and LDD, which has an impact on connectivity. Matrix vegetation height has a negative effect on mean seed dispersal distance but a positive effect on the probability of LDD. This positive effect and its impact on connectivity provide novel insights into landscape level (meta-)population and community dynamics - a change in matrix vegetation height by land-use or climatic changes could strongly affect the spread and connectivity of wind-dispersed plants. The opposite effect of vegetation height on mean seed dispersal distance and the probability of LDD should therefore be considered in management and analyses of future land-use and climate change effects. KW - Seed dispersal by wind KW - Long-distance seed dispersal KW - Matrix vegetation KW - Kettle holes KW - Agricultural landscapes KW - Metapopulation dynamics Y1 - 2021 U6 - https://doi.org/10.1016/j.agee.2021.107678 SN - 0167-8809 SN - 1873-2305 VL - 322 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Krumbholz, Julia A1 - Ishida, Keishi A1 - Baunach, Martin A1 - Teikari, Jonna A1 - Rose, Magdalena M. A1 - Sasso, Severin A1 - Hertweck, Christian A1 - Dittmann, Elke T1 - Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition N2 - Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds. KW - Biosynthesis KW - Cyanobacteria KW - Genomic Mining KW - Quorum Sensing KW - Specialized KW - Metabolism Y1 - 2022 U6 - https://doi.org/10.1002/anie.202204545 SN - 1433-7851 SN - 1521-3773 PB - Wiley-VCH CY - Weinheim ER - TY - GEN A1 - Scheffler, Christiane A1 - Bogin, Barry A1 - Hermanussen, Michael T1 - Catch-up growth is a better indicator of undernutrition than thresholds for stunting T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Objective: Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition. Design: Cross-sectional study; breakpoint analysis. Setting: Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES). Participants: 1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children. Results: When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017. Conclusions: Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1350 KW - no threshold for stunting KW - catch-up growth KW - social-economic-political-emotional KW - (SEPE) factors Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-550495 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Chorus, Ingrid A1 - Spijkerman, Elly T1 - What Colin Reynolds could tell us about nutrient limitation, N:P ratios and eutrophication control T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Colin Reynolds exquisitely consolidated our understanding of driving forces shaping phytoplankton communities and those setting the upper limit to biomass yield, with limitation typically shifting from light in winter to phosphorus in spring. Nonetheless, co-limitation is frequently postulated from enhanced growth responses to enrichments with both N and P or from N:P ranging around the Redfield ratio, concluding a need to reduce both N and P in order to mitigate eutrophication. Here, we review the current understanding of limitation through N and P and of co-limitation. We conclude that Reynolds is still correct: (i) Liebig's law of the minimum holds and reducing P is sufficient, provided concentrations achieved are low enough; (ii) analyses of nutrient limitation need to exclude evidently non-limiting situations, i.e. where soluble P exceeds 3-10 mu g/l, dissolved N exceeds 100-130 mu g/l and total P and N support high biomass levels with self-shading causing light limitation; (iii) additionally decreasing N to limiting concentrations may be useful in specific situations (e.g. shallow waterbodies with high internal P and pronounced denitrification); (iv) management decisions require local, situation-specific assessments. The value of research on stoichiometry and co-limitation lies in promoting our understanding of phytoplankton ecophysiology and community ecology. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1344 KW - phytoplankton KW - nitrogen limitation KW - redfield ratio KW - co-limitation KW - enrichment experiments Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-541979 SN - 1866-8372 IS - 1 ER - TY - JOUR A1 - Scheffler, Christiane A1 - Bogin, Barry A1 - Hermanussen, Michael T1 - Catch-up growth is a better indicator of undernutrition than thresholds for stunting JF - Public health nutrition : PHN / The Nutrition Society N2 - Objective: Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition. Design: Cross-sectional study; breakpoint analysis. Setting: Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES). Participants: 1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children. Results: When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017. Conclusions: Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting. KW - no threshold for stunting KW - catch-up growth KW - social-economic-political-emotional KW - (SEPE) factors Y1 - 2020 U6 - https://doi.org/10.1017/S1368980020003067 SN - 1475-2727 SN - 1368-9800 VL - 24 IS - 1 SP - 52 EP - 61 PB - Cambridge University Press CY - Cambridge ; New York, NY ER - TY - JOUR A1 - Horn, Juliane A1 - Becher, Matthias A. A1 - Johst, Karin A1 - Kennedy, Peter J. A1 - Osborne, Juliet L. A1 - Radchuk, Viktoriia A1 - Grimm, Volker T1 - Honey bee colony performance affected by crop diversity and farmland structure BT - a modeling framework JF - Ecological applications N2 - Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps. KW - apis mellifera KW - BEEHAVE KW - colony viability KW - crop diversity KW - cropping system KW - decline KW - forage availability KW - forage gaps KW - honey bees KW - landscape generator KW - modeling Y1 - 2020 U6 - https://doi.org/10.1002/eap.2216 SN - 1939-5582 SN - 1051-0761 VL - 31 IS - 1 SP - 1 EP - 22 PB - Wiley Periodicals LLC CY - Washington DC ER - TY - GEN A1 - Horn, Juliane A1 - Becher, Matthias A. A1 - Johst, Karin A1 - Kennedy, Peter J. A1 - Osborne, Juliet L. A1 - Radchuk, Viktoriia A1 - Grimm, Volker T1 - Honey bee colony performance affected by crop diversity and farmland structure BT - a modeling framework T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1351 KW - apis mellifera KW - BEEHAVE KW - colony viability KW - crop diversity KW - cropping system KW - decline KW - forage availability KW - forage gaps KW - honey bees KW - landscape generator KW - modeling Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-556943 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Jannasch, Franziska A1 - Nickel, Daniela A1 - Schulze, Matthias Bernd T1 - The reliability and relative validity of predefined dietary patterns were higher than that of exploratory dietary patterns in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam population T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The aim of this study was to assess the ability of the FFQ to describe reliable and valid dietary pattern (DP) scores. In a total of 134 participants of the European Prospective Investigation into Cancer and Nutrition-Potsdam study aged 35-67 years, the FFQ was applied twice (baseline and after 1 year) to assess its reliability. Between November 1995 and March 1997, twelve 24-h dietary recalls (24HDR) as reference instrument were applied to assess the validity of the FFQ. Exploratory DP were derived by principal component analyses. Investigated predefined DP were the Alternative Healthy Eating Index (AHEI) and two Mediterranean diet indices. From dietary data of each FFQ, two exploratory DP were retained, but differed in highly loading food groups, resulting in moderate correlations (r 0 center dot 45-0 center dot 58). The predefined indices showed higher correlations between the FFQ (r(AHEI) 0 center dot 62, r(Mediterranean Diet Pyramid Index (MedPyr)) 0 center dot 62 and r(traditional Mediterranean Diet Score (tMDS)) 0 center dot 51). From 24HDR dietary data, one exploratory DP retained differed in composition to the first FFQ-based DP, but showed similarities to the second DP, reflected by a good correlation (r 0 center dot 70). The predefined DP correlated moderately (r 0 center dot 40-0 center dot 60). To conclude, long-term analyses on exploratory DP should be interpreted with caution, due to only moderate reliability. The validity differed extensively for the two exploratory DP. The investigated predefined DP showed a better reliability and a moderate validity, comparable to other studies. Within the two Mediterranean diet indices, the MedPyr performed better than the tMDs in this middle-aged, semi-urban German study population. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1349 KW - dietary patterns KW - reliability KW - validity Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-550030 SN - 1866-8372 VL - 125 IS - 11 ER - TY - JOUR A1 - Li, Chenzhi A1 - Postl, Alexander K. A1 - Böhmer, Thomas A1 - Cao, Xianyong A1 - Dolman, Andrew M. A1 - Herzschuh, Ulrike T1 - Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0) JF - Earth system science data : ESSD N2 - We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats. All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection. The most common control points for the chronologies are radiocarbon dates (86.1 %), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials). The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8% of records), reservoir effect (4.9 %), and sediment deposition discontinuity (4.4 %). Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4% of records could be improved according to our assessment. Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively. Y1 - 2022 U6 - https://doi.org/10.5194/essd-14-1331-2022 SN - 1866-3508 SN - 1866-3516 VL - 14 IS - 3 SP - 1331 EP - 1343 PB - Copernics Publications CY - Katlenburg-Lindau ER - TY - THES A1 - Kiss, Andrea T1 - Moss-associated bacterial and archaeal communities of northern peatlands: key taxa, environmental drivers and potential functions T1 - Moos-assoziierte bakterielle und archaelle Gemeinschaften nördlicher Moore: Schlüsselspezies, beeinflussende Umweltfaktoren und potentielle Funktionen N2 - Moss-microbe associations are often characterised by syntrophic interactions between the microorganisms and their hosts, but the structure of the microbial consortia and their role in peatland development remain unknown. In order to study microbial communities of dominant peatland mosses, Sphagnum and brown mosses, and the respective environmental drivers, four study sites representing different successional stages of natural northern peatlands were chosen on a large geographical scale: two brown moss-dominated, circumneutral peatlands from the Arctic and two Sphagnum-dominated, acidic peat bogs from subarctic and temperate zones. The family Acetobacteraceae represented the dominant bacterial taxon of Sphagnum mosses from various geographical origins and displayed an integral part of the moss core community. This core community was shared among all investigated bryophytes and consisted of few but highly abundant prokaryotes, of which many appear as endophytes of Sphagnum mosses. Moreover, brown mosses and Sphagnum mosses represent habitats for archaea which were not studied in association with peatland mosses so far. Euryarchaeota that are capable of methane production (methanogens) displayed the majority of the moss-associated archaeal communities. Moss-associated methanogenesis was detected for the first time, but it was mostly negligible under laboratory conditions. Contrarily, substantial moss-associated methane oxidation was measured on both, brown mosses and Sphagnum mosses, supporting that methanotrophic bacteria as part of the moss microbiome may contribute to the reduction of methane emissions from pristine and rewetted peatlands of the northern hemisphere. Among the investigated abiotic and biotic environmental parameters, the peatland type and the host moss taxon were identified to have a major impact on the structure of moss-associated bacterial communities, contrarily to archaeal communities whose structures were similar among the investigated bryophytes. For the first time it was shown that different bog development stages harbour distinct bacterial communities, while at the same time a small core community is shared among all investigated bryophytes independent of geography and peatland type. The present thesis displays the first large-scale, systematic assessment of bacterial and archaeal communities associated both with brown mosses and Sphagnum mosses. It suggests that some host-specific moss taxa have the potential to play a key role in host moss establishment and peatland development. N2 - Während die Beziehungen zwischen Moosen und den mit ihnen assoziierten Mikroorganismen oft durch syntrophische Wechselwirkungen charakterisiert sind, ist die Struktur der Moos-assoziierten mikrobiellen Gemeinschaften sowie deren Rolle bei der Entstehung von Mooren weitgehend unbekannt. Die vorliegende Arbeit befasst sich mit mikrobiellen Gemeinschaften, die mit Moosen nördlicher, naturnaher Moore assoziiert sind, sowie mit den Umweltfaktoren, die sie beeinflussen. Entlang eines groß angelegten geographischen Gradienten, der von der Hocharktis bis zur gemäßigten Klimazone reicht, wurden vier naturbelassene Moore als Probenstandorte ausgesucht, die stellvertretend für verschiedene Stadien der Moorentwicklung stehen: zwei Braunmoos-dominierte Niedermoore mit nahezu neutralem pH-Wert sowie zwei Sphagnum-dominierte Torfmoore mit saurem pH-Wert. Die Ergebnisse der vorliegenden Arbeit machen deutlich, dass die zu den Bakterien zählenden Acetobacteraceae das vorherrschende mikrobielle Taxon der Sphagnum-Moose gleich welchen geographischen Ursprungs darstellen und insbesondere innerhalb des Wirtsmoosgewebes dominieren. Gleichzeitig gehörten die Acetobacteraceae zum wesentlichen Bestandteil der mikrobiellen Kerngemeinschaft aller untersuchten Moose, die sich aus einigen wenigen Arten, dafür zahlreich vorkommenden Prokaryoten zusammensetzt. Die vorliegende Arbeit zeigt zudem erstmals, dass sowohl Braunmoose als auch Torfmoose ein Habitat für Archaeen darstellen. Die Mehrheit der Moos-assoziierten Archaeen gehörte dabei zu den methanbildenden Gruppen, wenngleich die metabolischen Aktivitätsraten unter Laborbedingungen meistens kaum messbar waren. Im Gegensatz hierzu konnte die Bakterien-vermittelte Methanoxidation sowohl an Braunmoosen als auch an Sphagnum-Moosen gemessen werden. Dies zeigt eindrucksvoll, dass Moos-assoziierte Bakterien potenziell zur Minderung von Methanemissionen aus nördlichen, aber auch wiedervernässten Mooren beitragen können. Ein weiteres wichtiges Resultat der vorliegenden Arbeit ist die Bedeutung des Moortyps (Niedermoor oder Torfmoor), aber auch der Wirtsmoosart selbst für die Struktur der Moos-assoziierten Bakteriengemeinschaften, während die archaeellen Gemeinschaftsstrukturen weder vom Moortyp noch von der Wirtsmoosart beeinflusst wurden und sich insgesamt deutlich ähnlicher waren als die der Bakterien. Darüber hinaus konnte erstmalig gezeigt werden, dass sich die bakteriellen Gemeinschaften innerhalb der unterschiedlichen Moorsukzessionsstadien zwar ganz erheblich voneinander unterscheiden, ein kleiner Teil der Bakterien dennoch Kerngemeinschaften bilden, die mit allen untersuchten Moosarten assoziiert waren. Bei der hier präsentierten Arbeit handelt es sich um die erste systematische Studie, die sich auf einer großen geographischen Skala mit den bakteriellen und archaeellen Gemeinschaften von Braunmoosen und Torfmoosen aus naturbelassenen nördlichen Mooren befasst. Die vorliegenden Ergebnisse machen deutlich, dass die untersuchten Moose ein ganz spezifisches mikrobielles Konsortium beherbergen, welches mutmaßlich eine Schlüsselrolle bei der Etablierung der Wirtspflanzen am Anfang der Moorentwicklung spielt und darüber hinaus das Potential hat, die charakteristischen Eigenschaften von Mooren sowie deren weitere Entwicklung zu prägen. KW - moss-microbe-interactions KW - moss-associated bacteria KW - moss-associated archaea KW - northern peatlands KW - peatland core microbiome KW - Acetobacteraceae KW - moss-associated methanotrophy KW - moss-associated methanogenesis KW - Sphagnum KW - Amblystegiaceae KW - endophytes KW - brown mosses KW - epiphytes KW - peatland development KW - bryophytes KW - host-specificity KW - large-scale study KW - methanotrophic bacteria KW - methanogenic archaea KW - Essigsäurebakterien KW - Amblystegiaceae KW - Torfmoose KW - Braunmoose KW - Bryophyten KW - Endophyten KW - Epiphyten KW - Wirtsspezifität KW - geographische Großstudie KW - methanproduzierende Archaeen KW - methanoxidierende Bakterien KW - Moos-assoziierte Methanproduktion KW - Moos-assoziierte Methanoxidation KW - Moos-Mikroben-Interaktion KW - nördliche Moore KW - mikrobielle Moor-Kerngemeinschaft KW - Moorsukzession Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-630641 ER - TY - THES A1 - Hammel, Alexander T1 - Establishing the red microalga Porphyridium purpureum as a novel platform for the production of recombinant proteins T1 - Die Etablierung der roten Mikroalge Porphyridium purpureum als neue Platform für die Herstellung rekombinanter Proteine N2 - Microalgae have been recognized as a promising green production platform for recombinant proteins. The majority of studies on recombinant protein expression have been conducted in the green microalga C. reinhardtii. While promising improvement regarding nuclear transgene expression in this alga has been made, it is still inefficient due to epigenetic silencing, often resulting in low yields that are not competitive with other expressor organisms. Other microalgal species might be better suited for high-level protein expression, but are limited in their availability of molecular tools. The red microalga Porphyridium purpureum recently emerged as candidate for the production of recombinant proteins. It is promising in that transformation vectors are episomally maintained as autonomously replicating plasmids in the nucleus at a high copy number, thus leading to high expression values in this red alga. In this work, we expand the genetic tools for P. purpureum and investigate parameters that govern efficient transgene expression. We provide an improved transformation protocol to streamline the generation of transgenic lines in this organism. After being able to efficiently generate transgenic lines, we showed that codon usage is a main determinant of high-level transgene expression, not only at the protein level but also at the level of mRNA accumulation. The optimized expression constructs resulted in YFP accumulation up to an unprecedented 5% of the total soluble protein. Furthermore, we designed new constructs conferring efficient transgene expression into the culture medium, simplifying purification and harvests of recombinant proteins. To further improve transgene expression, we tested endogenous promoters driving the most highly transcribed genes in P. purpureum and found minor increase of YFP accumulation. We employed the previous findings to express complex viral antigens from the hepatitis B virus and the hepatitis C virus in P. purpureum to demonstrate its feasibility as producer of biopharmaceuticals. The viral glycoproteins were successfully produced to high levels and could reach their native confirmation, indicating a functional glycosylation machinery and an appropriate folding environment in this red alga. We could successfully upscale the biomass production of transgenic lines and with that provide enough material for immunization trials in mice that were performed in collaboration. These trials showed no toxicity of neither the biomass nor the purified antigens, and, additionally, the algal-produced antigens were able to elicit a strong and specific immune response. The results presented in this work pave the way for P. purpureum as a new promising producer organism for biopharmaceuticals in the microalgal field. N2 - Biotechnologisch hergestellte Proteine (rekombinante Proteine), wie zum Beispiel monoklonale Antikörper, Insulin oder diverse Impfstoffe, spielen heutzutage eine immer wichtigere Rolle bei der Bekämpfung von Krankheiten. Diese werden hauptsächlich aus genetisch veränderten humanen Zelllinien hergestellt. Die Produktion ist allerdings sehr teuer, anfällig für Kontaminationen und nicht nachhaltig. Als Alternative dazu können Mikroalgen benutzt werden, die viel günstiger kultiviert werden können und viele Vorteile bezüglich des ökologischen Aspekts bieten. Die bisherige Forschung an Mikroalgen als Plattform für die Herstellung rekombinanter Proteine konzentriert sich vor allem auf die grüne Mikroalge Chlamydomonas reinhardtii. Doch vor allem die geringe Proteinausbeute macht diese Alge nicht zum idealen Expressionsorganismus. Kürzlich wurde die rote Mikroalge Porphyridium purpureum als vielversprechende Kandidatin für die Produktion rekombinanter Proteine identifiziert. Besonders interessant ist, dass diese Alge rekombinante Proteine in einem hohen Maß exprimiert. Diese Arbeit beschäftigt sich mit dem Potenzial von Porphyridium purpureum als relativ unerforschte Alge. Es wurden neue genetische Werkzeuge entwickelt und verschiedene Faktoren untersucht, die die Expression von eingebrachten Genen beeinflussen. Durch Optimierung dieser Parameter konnten wir die Proteinausbeute eines gelb fluoreszierenden Proteins auf 5% des löslichen Gesamtproteins steigern. Wir haben das gewonnene Wissen genutzt, um jeweils ein Oberflächenprotein vom Hepatitis B Virus und vom Hepatitis C Virus in dieser roten Mikroalge herzustellen. Diese können als möglicher zukünftiger Impfstoff benutzt werden. Wir konnten zeigen, dass beide Proteine korrekt und in hoher Menge in Porphyridium purpureum hergestellt werden. Anschließend wurden die hergestellten Proteine auf ihre Wirksamkeit und Verträglichkeit an Mäusen getestet. Dabei wurde gezeigt, dass (i) Porphyridium purpureum nicht giftig ist und auch keine giftigen Produkte produziert und (ii) die produzierten Proteine eine effektive Immunantwort gegen die Viren induzieren. Mit dieser Arbeit wurde das Fundament für die biotechnologische Anwendung dieser roten Mikroalge gelegt. Die Ergebnisse dieser Studie zeigen, dass P. purpureum eine vielversprechende Mikroalgenart für die Produktion von biopharmazeutischen Proteinen ist. KW - microalgae KW - biotechnology KW - subunit vaccine KW - Biotechnologie KW - Mikroalgen KW - Untereinheitenimpfstoff Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-632709 ER - TY - JOUR A1 - Omranian, Sara A1 - Angeleska, Angela A1 - Nikoloski, Zoran T1 - Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient JF - Computational and structural biotechnology journal N2 - Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficient of proteins in PPI networks. Through comparative analyses with gold standards and PPI networks from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we demonstrate that GCC-v outperforms twelve state-of-the-art approaches for identification of protein complexes with respect to twelve performance measures in at least 85.71% of scenarios. We also show that GCC-v results in the exact recovery of similar to 35% of protein complexes in a pan-plant PPI network and discover 144 new protein complexes in Arabidopsis thaliana, with high support from GO semantic similarity. Our results indicate that findings from GCC-v are robust to network perturbations, which has direct implications to assess the impact of the PPI network quality on the predicted protein complexes. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. KW - Protein complexes KW - Protein-protein interaction KW - Network clustering KW - Species comparison Y1 - 2021 U6 - https://doi.org/10.1016/j.csbj.2021.09.014 SN - 2001-0370 VL - 19 SP - 5255 EP - 5263 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Hampf, Anna A1 - Nendel, Claas A1 - Strey, Simone A1 - Strey, Robert T1 - Biotic yield losses in the Southern Amazon, Brazil BT - making use of smartphone-assisted plant disease diagnosis data JF - Frontiers in plant science : FPLS N2 - Pathogens and animal pests (P&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P&A, (2) map the spatial distribution of P&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P&A, whereas soybean is mainly affected by P&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them. KW - plant pathology KW - animal pests KW - pathogens KW - machine learning KW - digital KW - image processing KW - disease diagnosis KW - crowdsourcing KW - crop losses Y1 - 2021 U6 - https://doi.org/10.3389/fpls.2021.621168 SN - 1664-462X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Irob, Katja A1 - Blaum, Niels A1 - Baldauf, Selina A1 - Kerger, Leon A1 - Strohbach, Ben A1 - Kanduvarisa, Angelina A1 - Lohmann, Dirk A1 - Tietjen, Britta T1 - Browsing herbivores improve the state and functioning of savannas BT - A model assessment of alternative land-use strategies JF - Ecology and evolution N2 - Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services. KW - browsing KW - ecohydrology KW - land use KW - plant community KW - savanna KW - wildlife KW - management Y1 - 2022 U6 - https://doi.org/10.1002/ece3.8715 SN - 2045-7758 VL - 12 IS - 3 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ghafarian, Fatemeh A1 - Wieland, Ralf A1 - Lüttschwager, Dietmar A1 - Nendel, Claas T1 - Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data JF - Environmental modelling & software with environment data news N2 - Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests. We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features. The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions. We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression. After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model. The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests. KW - cooling effect KW - machine learning KW - ensemble method KW - ecosystem services Y1 - 2022 U6 - https://doi.org/10.1016/j.envsoft.2022.105466 SN - 1364-8152 SN - 1873-6726 VL - 156 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Caserta, Giorgio A1 - Zhang, Xiaorong A1 - Yarman, Aysu A1 - Supala, Eszter A1 - Wollenberger, Ulla A1 - Gyurcsányi, Róbert E. A1 - Zebger, Ingo A1 - Scheller, Frieder W. T1 - Insights in electrosynthesis, target binding, and stability of peptide-imprinted polymer nanofilms JF - Electrochimica acta : the journal of the International Society of Electrochemistry (ISE) N2 - Molecularly imprinted polymer (MIP) nanofilms have been successfully implemented for the recognition of different target molecules: however, the underlying mechanistic details remained vague. This paper provides new insights in the preparation and binding mechanism of electrosynthesized peptide-imprinted polymer nanofilms for selective recognition of the terminal pentapeptides of the beta-chains of human adult hemoglobin, HbA, and its glycated form HbA1c. To differentiate between peptides differing solely in a glucose adduct MIP nanofilms were prepared by a two-step hierarchical electrosynthesis that involves first the chemisorption of a cysteinyl derivative of the pentapeptide followed by electropolymerization of scopoletin. This approach was compared with a random single-step electrosynthesis using scopo-letin/pentapeptide mixtures. Electrochemical monitoring of the peptide binding to the MIP nanofilms by means of redox probe gating revealed a superior affinity of the hierarchical approach with a Kd value of 64.6 nM towards the related target. Changes in the electrosynthesized non-imprinted polymer and MIP nanofilms during chemical, electrochemical template removal and rebinding were substantiated in situ by monitoring the characteristic bands of both target peptides and polymer with surface enhanced infrared absorption spectroscopy. This rational approach led to MIPs with excellent selectivity and provided key mechanistic insights with respect to electrosynthesis, rebinding and stability of the formed MIPs. KW - SEIRA spectroelectrochemistry KW - peptide imprinting KW - electrosynthesis KW - MIP KW - glycated peptide Y1 - 2021 U6 - https://doi.org/10.1016/j.electacta.2021.138236 SN - 0013-4686 SN - 1873-3859 VL - 381 PB - Elsevier CY - New York, NY [u.a.] ER - TY - JOUR A1 - Mitzscherling, Julia A1 - MacLean, Joana A1 - Lipus, Daniel A1 - Bartholomäus, Alexander A1 - Mangelsdorf, Kai A1 - Lipski, André A1 - Roddatis, Vladimir A1 - Liebner, Susanne A1 - Wagner, Dirk T1 - Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste JF - International journal of systematic and evolutionary microbiology N2 - Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%). The genomic DNA G+C content of strain NGK65(T) was 68.2%. Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)). KW - Nocardioides alcanivorans KW - hexadecane KW - plastic degradation KW - terrestrial KW - plastisphere KW - bacteria Y1 - 2022 U6 - https://doi.org/10.1099/ijsem.0.005319 SN - 1466-5026 SN - 1466-5034 VL - 72 IS - 4 PB - Microbiology Society CY - London ER - TY - JOUR A1 - Hilt, Sabine A1 - Grossart, Hans-Peter A1 - McGinnis, Daniel F. A1 - Keppler, Frank T1 - Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems JF - Limnology and oceanography N2 - Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems. Y1 - 2022 U6 - https://doi.org/10.1002/lno.12095 SN - 0024-3590 SN - 1939-5590 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Yarman, Aysu A1 - Kurbanoğlu, Sevinç A1 - Zebger, Ingo A1 - Scheller, Frieder W. T1 - Simple and robust BT - the claims of protein sensing by molecularly imprinted polymers JF - Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers N2 - A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 % of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering. KW - Molecularly imprinted polymer KW - Plastibodies KW - Functional scaffolds KW - Biomimetic sensors KW - Proteins Y1 - 2021 U6 - https://doi.org/10.1016/j.snb.2020.129369 SN - 0925-4005 SN - 1873-3077 VL - 330 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Tran, V. Phuong A1 - Tamura, Yui A1 - Pham, Van-Cuong A1 - Elhussiny, Mohamed Z. A1 - Han, Guofeng A1 - Sur Chowdhury, Vishwajit A1 - Furuse, Mitsuhiro T1 - Neuropeptide Y modifies a part of diencephalic catecholamine but not indolamine metabolism in chicks depending on feeding status JF - Neuropeptides N2 - The role of the monoaminergic system in the feeding behavior of neonatal chicks has been reported, but the functional relationship between the metabolism of monoamines and appetite-related neuropeptides is still unclear. This study aimed to investigate the changes in catecholamine and indolamine metabolism in response to the central action of neuropeptide Y (NPY) in different feeding statuses and the underlying mechanisms. In Experiment 1, the diencephalic concentrations of amino acids and monoamines following the intracerebroventricular (ICV) injection of NPY (375 pmol/10 mu l/chick), saline solution under ad libitum, and fasting conditions for 30 min were determined. Central NPY significantly decreased L-tyrosine concentration, the precursor of catecholamines under feeding condition, but not under fasting condition. Central NPY significantly increased dopamine metabolites, including 3,4-dihydroxyphenylacetic acid and homovanillic acid (HVA). The concentration of 3-methoxy-4-hydroxyphenylglycol was significantly reduced under feeding condition, but did not change under fasting condition by NPY. However, no effects of NPY on indolamine metabolism were found in either feeding status. Therefore, the mechanism of action of catecholamines with central NPY under feeding condition was elucidated in Experiment 2. Central NPY significantly attenuated diencephalic gene expression of catecholaminergic synthetic enzymes, such as tyrosine hydroxylase, L-aromatic amino acid decarboxylase, and GTP cyclohydrolase I after 30 min of feeding. In Experiment 3, co-injection of alpha-methyl-L-tyrosine, an inhibitor of tyrosine hydroxylase with NPY, moderately attenuated the orexigenic effect of NPY, accompanied by a significant positive correlation between food intake and HVA levels. In Experiment 4, there was a significant interaction between NPY and clorgyline, an inhibitor of monoamine oxidase A with ICV co-injection which implies that co-existence of NPY and clorgyline enhances the orexigenic effect of NPY. In conclusion, central NPY modifies a part of catecholamine metabolism, which is illustrated by the involvement of dopamine transmission and metabolism under feeding but not fasting conditions. KW - Neuropeptide Y KW - Feeding behavior KW - Neonatal chick KW - CNS KW - Catecholamines Y1 - 2021 U6 - https://doi.org/10.1016/j.npep.2021.102169 SN - 0143-4179 SN - 1532-2785 VL - 89 PB - Elsevier CY - New York, NY ER - TY - JOUR A1 - Pan, Xuefeng A1 - Sarhan, Radwan Mohamed A1 - Kochovski, Zdravko A1 - Chen, Guosong A1 - Taubert, Andreas A1 - Mei, Shilin A1 - Lu, Yan T1 - Template synthesis of dual-functional porous MoS2 nanoparticles with photothermal conversion and catalytic properties JF - Nanoscale N2 - Advanced catalysis triggered by photothermal conversion effects has aroused increasing interest due to its huge potential in environmental purification. In this work, we developed a novel approach to the fast degradation of 4-nitrophenol (4-Nip) using porous MoS2 nanoparticles as catalysts, which integrate the intrinsic catalytic property of MoS2 with its photothermal conversion capability. Using assembled polystyrene-b-poly(2-vinylpyridine) block copolymers as soft templates, various MoS 2 particles were prepared, which exhibited tailored morphologies (e.g., pomegranate-like, hollow, and open porous structures). The photothermal conversion performance of these featured particles was compared under near-infrared (NIR) light irradiation. Intriguingly, when these porous MoS2 particles were further employed as catalysts for the reduction of 4-Nip, the reaction rate constant was increased by a factor of 1.5 under NIR illumination. We attribute this catalytic enhancement to the open porous architecture and light-to-heat conversion performance of the MoS2 particles. This contribution offers new opportunities for efficient photothermal-assisted catalysis. Y1 - 2022 U6 - https://doi.org/10.1039/d2nr01040b SN - 2040-3372 VL - 14 IS - 18 SP - 6888 EP - 6901 PB - RSC Publ. (Royal Society of Chemistry) CY - Cambridge ER - TY - JOUR A1 - Hagemann, Justus A1 - Conejero, Carles A1 - Stillfried, Milena A1 - Mentaberre, Gregorio A1 - Castillo-Contreras, Raquel A1 - Fickel, Jörns A1 - Lopez-Olvera, Jorge Ramón T1 - Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments. KW - gene flow KW - island population KW - population genetics KW - sus scrofa KW - synurbisation KW - urban ecology Y1 - 2022 U6 - https://doi.org/10.1016/j.scitotenv.2022.155126 SN - 0048-9697 SN - 1879-1026 VL - 833 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Ralevski, Alexandra A1 - Apelt, Federico A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Rugarli, Elena I. A1 - Kragler, Friedrich A1 - Horvath, Tamas L. T1 - Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice JF - Cellular and molecular life sciences N2 - Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals. KW - Arabidopsis thaliana KW - Mitochondria KW - FMT KW - Hyponasty KW - Mice KW - CLUH; KW - Locomotion Y1 - 2022 U6 - https://doi.org/10.1007/s00018-022-04382-3 SN - 1420-682X SN - 1420-9071 VL - 79 IS - 6 PB - Springer International Publishing AG CY - Cham (ZG) ER - TY - JOUR A1 - Witzel, Katja A1 - Abu Risha, Marua A1 - Albers, Philip A1 - Börnke, Frederik A1 - Hanschen, Franziska S. T1 - Corrigendum : Identification and characterization of three epithiospecifier protein isoforms in Brassica oleracea / Witzel, Katja; Abu Risha, Marua; Albers, Philip; Börnke, Frederike; Hanschen, Franziska S. - Lausanne: Frontiers Media, 2019. - Frontiers in plant science : FPLS. - 10 (2019) art. 1552. - doi: 10.3389/fpls.2019.01552 JF - Frontiers in plant science : FPLS KW - epithionitrile KW - expression profile KW - functional complementation KW - glucosinolate hydrolysis KW - nitrile KW - specifier proteins KW - tissue KW - specificity Y1 - 2020 U6 - https://doi.org/10.3389/fpls.2020.00523 SN - 1664-462X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - GEN A1 - Schorn, Sina A1 - Salman-Carvalho, Verena A1 - Littmann, Sten A1 - Ionescu, Danny A1 - Grossart, Hans-Peter A1 - Cypionka, Heribert T1 - Cell architecture of the giant sulfur bacterium achromatium oxaliferum BT - Extra-cytoplasmic localization of calcium carbonate bodies T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1356 KW - sulfur-bacteria KW - calcium carbonate inclusions KW - extra-cytoplasmic pockets KW - calcite Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549935 SN - 1866-8372 IS - 2 ER - TY - JOUR A1 - Schorn, Sina A1 - Salman-Carvalho, Verena A1 - Littmann, Sten A1 - Ionescu, Danny A1 - Grossart, Hans-Peter A1 - Cypionka, Heribert T1 - Cell architecture of the giant sulfur bacterium achromatium oxaliferum BT - Extra-cytoplasmic localization of calcium carbonate bodies JF - FEMS Microbiology Ecology N2 - Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes. KW - sulfur-bacteria KW - calcium carbonate inclusions KW - extra-cytoplasmic pockets KW - calcite Y1 - 2019 U6 - https://doi.org/10.1093/femsec/fiz200 SN - 1574-6941 VL - 96 IS - 2 SP - 1 EP - 8 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Kürschner, Tobias A1 - Scherer, Cédric A1 - Radchuk, Viktoriia A1 - Blaum, Niels A1 - Kramer-Schadt, Stephanie T1 - Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions JF - Ecology and evolution N2 - Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change. KW - classical swine fever KW - dynamic landscapes KW - global change KW - host– pathogen dynamics KW - individual‐ based model KW - movement ecology Y1 - 2021 U6 - https://doi.org/10.1002/ece3.7478 SN - 2045-7758 VL - 11 IS - 10 SP - 5728 EP - 5741 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Leins, Johannes A. A1 - Grimm, Volker A1 - Drechsler, Martin T1 - Large-scale PVA modeling of insects in cultivated grasslands BT - the role of dispersal in mitigating the effects of management schedules under climate change JF - Ecology and evolution N2 - In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle. KW - bilinear interpolation KW - climate change KW - dispersal success KW - land use KW - large marsh grasshopper KW - spatially explicit model Y1 - 2022 U6 - https://doi.org/10.1002/ece3.9063 SN - 2045-7758 VL - 12 IS - 7 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ghafarian, Fatemeh A1 - Wieland, Ralf A1 - Nendel, Claas T1 - Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy JF - Water N2 - Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth. KW - canopy cooling effects KW - shading cooling KW - canopy-air temperature KW - energy KW - balance KW - the Penman-Monteith equation Y1 - 2022 U6 - https://doi.org/10.3390/w14030319 SN - 2073-4441 VL - 14 IS - 3 PB - MDPI CY - Basel ER - TY - THES A1 - Cheng, Feng T1 - Evolution and ontogeny of electric organ discharge in African weakly electric fish genus Campylomormyrus: a genomic and transcriptomic perspective N2 - The African weakly electric fishes (Mormyridae) exhibit a remarkable adaptive radiation possibly due to their species-specific electric organ discharges (EODs). It is produced by a muscle-derived electric organ that is located in the caudal peduncle. Divergence in EODs acts as a pre-zygotic isolation mechanism to drive species radiations. However, the mechanism behind the EOD diversification are only partially understood. The aim of this study is to explore the genetic basis of EOD diversification from the gene expression level across Campylomormyrus species/hybrids and ontogeny. I firstly produced a high quality genome of the species C. compressirostris as a valuable resource to understand the electric fish evolution. The next study compared the gene expression pattern between electric organs and skeletal muscles in Campylomormyrus species/hybrids with different types of EOD duration. I identified several candidate genes with an electric organ-specific expression, e.g. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. The overall genes expression pattern exhibited a significant association with EOD duration in all analyzed species/hybrids. The expression of several candidate genes, e.g. KCNJ2, KLF5, KCNK6 and KCNQ5, possibly contribute to the regulation of EOD duration in Campylomormyrus due to their increasing or decreasing expression. Several potassium channel genes showed differential expression during ontogeny in species and hybrid with EOD alteration, e.g. KCNJ2. I next explored allele specific expression of intragenus hybrids by crossing the duration EOD species C. compressirostris with the medium duration EOD species C. tshokwe and the elongated duration EOD species C. rhynchophorus. The hybrids exhibited global expression dominance of the C. compressirostris allele in the adult skeletal muscle and electric organ, as well as in the juvenile electric organ. Only the gene KCNJ2 showed dominant expression of the allele from C. rhynchophorus, and this was increasingly dominant during ontogeny. It hence supported our hypothesis that KCNJ2 is a key gene of regulating EOD duration. Our results help us to understand, from a genetic perspective, how gene expression effect the EOD diversification in the African weakly electric fish. N2 - Die Mormyridae, eine Familie afrikanischer schwach elektrischer Süßwasserfische, zeigen eine außergewöhnliche adaptive Radiation. Eine Erklärung für die Diversifizierung dieser Gruppe stellen die artspezifischen elektrischen Organentladungen (EODs) dar. Diese werden von einem elektrischen Organ muskulären Ursprungs im Ansatz der Schwanzflosse erzeugt. Die verschiedenen EODs könnten als präzygotischer Isolationsmechanismus für die Radiation verantwortlich sein. Dennoch ist der Mechanismus hinter der EOD-Diversifizierung bisher nicht vollständig geklärt. Ziel dieser Studie ist es, die genetische Grundlage der EOD-Diversifizierung auf der Ebene der Genexpression bei verschiedenen Campylomormyrus-Arten bzw. -Hybriden und während der Ontogenese zu ermitteln. Zunächst wurde erstmals das Genom der Art C. compressirostris in hoher Qualität sequenziert. Dies bildet eine bedeutende Grundlage für das Verständnis der Evolution der elektrischen Fische. In der zweiten Studie wurden Genexpressionsmuster von elektrischen Organen und Skelettmuskeln bei Campylomormyrus-Arten bzw. -Hybriden mit unterschiedlicher EOD-Dauer verglichen. Dabei konnten mehrere Kandidatengene identifiziert werden, die potentiell Elektroorgan-spezifisch exprimiert sind, i.a. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. Bei allen untersuchten Arten/Hybriden wies das Genexpressionsmuster einen signifikanten Zusammenhang mit der EOD-Dauer auf. Die Expression mehrerer Kandidatengene, wie beispielsweise KCNJ2, KLF5, KCNK6 und KCNQ5, trägt möglicherweise zur Regulierung der EOD-Dauer bei Campylomormyrus bei. Bei Arten und Hybriden mit EOD-Unterschieden zeigten Kaliumkanal-Gene wie KCNJ2 eine unterschiedliche Expression während der Ontogenese. Zudem wurde die Allel-spezifische Expression bei Intragenus-Hybriden unter Verwendung der Arten C. compressirostris, C. tshokwe und C. rhynchophorus, die jeweils eine kurze, intermediäre bzw. lange EOD-Dauer aufweisen, untersucht. Die Hybriden wiesen eine generell dominante Expression der Allele von C. compressirostris in der adulten Skelettmuskulatur und im elektrischen Organ sowie im juvenilen elektrischen Organ auf. Einzig im Gen KCNJ2 dominierte das Allel von C. rhynchophorus, mit zunehmender Dominanz mit fortschreitender Ontogenese. Dies stützt unsere Hypothese einer Beteiligung des KCNJ2-Gens an der Regulation der EOD-Dauer. Unsere Ergebnisse stellen einen wesentlichen Beitrag zum Verständnis des Einflusses der Genexpression auf die EOD-Diversifizierung bei afrikanischen schwach elektrischen Fischen dar. KW - tropical freshwater fish KW - weakly electric fish KW - genomics KW - transcriptomics KW - Genomik KW - Transkriptomik KW - tropische Süßwasserfische KW - schwach elektrischer Fisch Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-630172 ER - TY - GEN A1 - Lenzner, Bernd A1 - Magallon, Susana A1 - Dawson, Wayne A1 - Kreft, Holger A1 - König, Christian A1 - Pergl, Jan A1 - Pysek, Petr A1 - Weigelt, Patrick A1 - van Kleunen, Mark A1 - Winter, Marten A1 - Dullinger, Stefan A1 - Essl, Franz T1 - Role of diversification rates and evolutionary history as a driver of plant naturalization success T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Human introductions of species beyond their natural ranges and their subsequent establishment are defining features of global environmental change. However, naturalized plants are not uniformly distributed across phylogenetic lineages, with some families contributing disproportionately more to the global alien species pool than others. Additionally, lineages differ in diversification rates, and high diversification rates have been associated with characteristics that increase species naturalization success. Here, we investigate the role of diversification rates in explaining the naturalization success of angiosperm plant families. We use five global data sets that include native and alien plant species distribution, horticultural use of plants, and a time-calibrated angiosperm phylogeny. Using phylogenetic generalized linear mixed models, we analysed the effect of diversification rate, different geographical range measures, and horticultural use on the naturalization success of plant families. We show that a family's naturalization success is positively associated with its evolutionary history, native range size, and economic use. Investigating interactive effects of these predictors shows that native range size and geographic distribution additionally affect naturalization success. High diversification rates and large ranges increase naturalization success, especially of temperate families. We suggest this may result from lower ecological specialization in temperate families with large ranges, compared with tropical families with smaller ranges. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1363 KW - alien species KW - evolution KW - geographic distribution KW - invasion success KW - plant naturalization KW - range size Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569996 SN - 1866-8372 IS - 5 ER - TY - GEN A1 - Romero-Munoz, Alfredo A1 - Fandos, Guillermo A1 - Benítez-López, Ana A1 - Kuemmerle, Tobias T1 - Habitat destruction and overexploitation drive widespread declines in all facets of mammalian diversity in the Gran Chaco T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57%, similar to 37%, and similar to 6% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23% of the Chaco would have to be protected to safeguard the top 17% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1370 KW - biodiversity facets KW - extinction drivers KW - functional diversity KW - functional richness KW - overhunting KW - phylogenetic diversity KW - taxonomic KW - diversity KW - traits Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-567696 SN - 1866-8372 IS - 4 ER - TY - THES A1 - Kersting, Katerina T1 - Development of a CRISPR/Cas gene editing technique for the coccolithophore Chrysotila carterae Y1 - 2024 ER - TY - JOUR A1 - Milles, Alexander Benedikt A1 - Dammhahn, Melanie A1 - Jeltsch, Florian A1 - Schlägel, Ulrike A1 - Grimm, Volker T1 - Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways. KW - pace-of-life syndrome KW - density dependence KW - life history KW - trait KW - variation KW - model KW - personality Y1 - 2022 U6 - https://doi.org/10.1086/718473 SN - 0003-0147 SN - 1537-5323 VL - 199 IS - 4 SP - E124 EP - E139 PB - Univ. of Chicago Press CY - Chicago ER - TY - GEN A1 - Eckert, Silvia A1 - Herden, Jasmin A1 - Stift, Marc A1 - Joshi, Jasmin Radha A1 - van Kleunen, Mark T1 - Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1378 KW - common‐garden experiment KW - epigenetic variation KW - microsatellites KW - Solidago canadensis KW - Solidago gigantea KW - zebularine Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569528 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Fichtner, Franziska A1 - Barbier, Francois F. A1 - Annunziata, Maria Grazia A1 - Feil, Regina A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Stitt, Mark A1 - Beveridge, Christine A. A1 - Lunn, John Edward T1 - Regulation of shoot branching in arabidopsis by trehalose 6-phosphate T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood. We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds. TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous Tre6P phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression of FLOWERING LOCUS T (FT) and upregulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching in branched1 but not in ft mutant backgrounds. These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1383 KW - Arabidopsis thaliana (arabidopsis) KW - axillary bud KW - branching KW - sucrose KW - sugar signalling KW - trehalose 6‐ phosphate (Tre6P) Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569564 SN - 1866-8372 IS - 4 ER - TY - GEN A1 - Zaplata, Markus Klemens A1 - Nhabanga, Abel A1 - Stalmans, Marc A1 - Volpers, Thomas A1 - Burkart, Michael A1 - Sperfeld, Erik T1 - Grasses cope with high-contrast ecosystem conditions in the large outflow of the Banhine wetlands, Mozambique T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Ecosystems with highly pulsed water supply must be better understood as climate change may increase frequency and severity of intense storms, droughts and floods. Here we collected data over 3 years (2016-2018) in the episodic wetland outflow channel (Aluize), Banhine National Park, in which the system state changed from dry to wet to dry. Field sampling included vegetation records, small-scale vegetation zoning, the seed bank and water and soil quality. The same main plant species were found in both dry and wet conditions across the riverbed of the outflow channel. We found only very few diaspores of plants in the soil after prolonged drought. In the subsequent flooded state, we examined very dense vegetation on the water surface, which was dominated by the gramineous species Paspalidium obtusifolium. This species formed a compact floating mat that was rooted to the riverbed. The Cyperaceae Bolboschoenus glaucus showed high clonal growth in the form of root tubers, which likely serve as important food reservoir during drought. Soil and water analyses do not indicate a limitation by nutrients. We outline how resident people may change the plant community structure with an increasing practice of setting fire to the meadows in the dried-up riverbed to facilitate plant regrowth as food for their livestock. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1386 KW - Aluize KW - biological soil crusts KW - Changane KW - droughts KW - floating mat KW - flooded grasslands KW - multi‐ year flooding cycle KW - plant clonality KW - seed bank KW - temporary wetland Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-573515 SN - 1866-8372 IS - 1 ER - TY - THES A1 - Stange, Maike T1 - A study on Coronin-A and Aip1 function in motility of Dictyostelium discoideum and on Aip1 interchangeability between Dictyostelium discoideum and Arabidopsis thaliana T1 - Studie über die Funktion von Coronin-A und Aip1 bei der Motilität von Dictyostelium discoideum und zur Aip1-Austauschbarkeit zwischen Dictyostelium discoideum und Arabidopsis thaliana N2 - Actin is one of the most highly conserved proteins in eukaryotes and distinct actin-related proteins with filament-forming properties are even found in prokaryotes. Due to these commonalities, actin-modulating proteins of many species share similar structural properties and proposed functions. The polymerization and depolymerization of actin are critical processes for a cell as they can contribute to shape changes to adapt to its environment and to move and distribute nutrients and cellular components within the cell. However, to what extent functions of actin-binding proteins are conserved between distantly related species, has only been addressed in a few cases. In this work, functions of Coronin-A (CorA) and Actin-interacting protein 1 (Aip1), two proteins involved in actin dynamics, were characterized. In addition, the interchangeability and function of Aip1 were investigated in two phylogenetically distant model organisms. The flowering plant Arabidopsis thaliana (encoding two homologs, AIP1-1 and AIP1-2) and in the amoeba Dictyostelium discoideum (encoding one homolog, DdAip1) were chosen because the functions of their actin cytoskeletons may differ in many aspects. Functional analyses between species were conducted for AIP1 homologs as flowering plants do not harbor a CorA gene. In the first part of the study, the effect of four different mutation methods on the function of Coronin-A protein and the resulting phenotype in D. discoideum was revealed in two genetic knockouts, one RNAi knockdown and a sudden loss-of-function mutant created by chemical-induced dislocation (CID). The advantages and disadvantages of the different mutation methods on the motility, appearance and development of the amoebae were investigated, and the results showed that not all observed properties were affected with the same intensity. Remarkably, a new combination of Selection-Linked Integration and CID could be established. In the second and third parts of the thesis, the exchange of Aip1 between plant and amoeba was carried out. For A. thaliana, the two homologs (AIP1-1 and AIP1-2) were analyzed for functionality as well as in D. discoideum. In the Aip1-deficient amoeba, rescue with AIP1-1 was more effective than with AIP1-2. The main results in the plant showed that in the aip1-2 mutant background, reintroduced AIP1-2 displayed the most efficient rescue and A. thaliana AIP1-1 rescued better than DdAip1. The choice of the tagging site was important for the function of Aip1 as steric hindrance is a problem. The DdAip1 was less effective when tagged at the C-terminus, while the plant AIP1s showed mixed results depending on the tag position. In conclusion, the foreign proteins partially rescued phenotypes of mutant plants and mutant amoebae, despite the organisms only being very distantly related in evolutionary terms. N2 - Actin ist eines der am stärksten konservierten Proteine in Eukaryoten und sogar Prokaryoten weisen Aktin-ähnliche Proteine mit filamentbildenden Eigenschaften auf. Aufgrund dieser Gemeinsamkeiten teilen Aktin-modulierte Proteine vieler Arten ähnliche strukturelle Eigenschaften und vermutlich auch Funktionen. Die Polymerisierung und Depolymerisation von Aktin sind kritische Prozesse für eine Zelle, da sie zu Zellformänderungen beitragen können, um sich an die Umgebung anzupassen und Nährstoffe sowie zelluläre Komponenten innerhalb der Zelle zu bewegen und zu verteilen. Inwieweit die Funktionen von Aktin-bindenden Proteinen zwischen entfernt verwandten Arten funktionell konserviert sind, wurde jedoch nur in wenigen Fällen untersucht. In dieser Arbeit wurden Funktionen von Coronin-A (CorA) und Actin-interagierendem Protein 1 (AIP1), zweier an der Aktindynamik beteiligter Proteine, charakterisiert. Darüber hinaus wurde die Austauschbarkeit und Funktion von AIP1 in zwei phylogenetisch entfernten Modellorganismen untersucht. Die Blütenpflanze Arabidopsis thaliana (kodiert für zwei Homologe: AIP1-1 und AIP1-2) und die Amöbe Dictyostelium discoideum (kodiert für ein Homolog: DdAip1) wurden ausgewählt, weil die Funktionen ihrer Aktin-Zytoskelette in mehreren Aspekten verschieden sein könnten. Funktionelle Analysen zwischen Arten wurden für AIP1-Homologe durchgeführt, da Blütenpflanzen kein CorA Gen tragen. Im ersten Teil der Arbeit wurde die Wirkung von vier verschiedenen Mutationsmethoden auf die Funktion des CorA-Proteins und des resultierenden Phänotyps in D. discoideum in zwei genetischen Knockouts, einem RNAi Knockdown und einem durch chemisch induzierte Delokalisierung (CID) erzeugten Mutanten geprüft. Die Vor- und Nachteile der Methoden zur Motilität, des Aussehens und der Entwicklung der Amöben wurden untersucht. Die Ergebnisse zeigten, dass nicht alle beobachteten Eigenschaften mit der gleichen Intensität beeinflusst wurden. Hierbei wurde eine neue Methodenkombination aus selektionsgebundener Integration und CID etabliert. Im zweiten und im dritten Teil der Arbeit wurde der Austausch von AIP1 zwischen Pflanze und Amöben durchgeführt. Die zwei A. thaliana-Homologe AIP1-1 und AIP1-2 wurden auf Funktionalität in D. discoideum geprüft. In Aip1-defizienten Amöben war die Rettung mit AIP1-1 effektiver als bei AIP1-2. Die Hauptergebnisse der Arbeit wiesen darauf hin, dass AIP1-2 im aip1.2-1 act7 Mutantenhintergrund die effizienteste Rettung zeigte, während A. thaliana AIP1-1 effizienter rettete als DdAip1. Die Auswahl der Tagging-Site war für die AIP1-Funktion bedeutend, da sterische Hinderung eine Rolle spielen könnte. DdAip1 war weniger effektiv, wenn es am C-Terminus fusioniert war, während die Proteinfusionen der A. thaliana AIP1s je nach Position der „tags“ unterschiedliche Ergebnisse zeigten. Zusammenfassend retteten die fremden Proteine teilweise Phänotypen von mutierten Pflanzen und mutierten Amöben, obwohl die Organismen evolutionär weit entfernt verwandt sind. KW - actin KW - cell motility KW - plant growth KW - selection-linked integration KW - chemically induced dislocation KW - interspecies interchange KW - Aktin KW - Zellmotilität KW - Pflanzenwachstum KW - Selection-Linked Integration KW - chemisch-induzierte Dislokation KW - Austausch zwischen zwei Spezies Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-628569 ER - TY - GEN A1 - Ehrlich, Elias A1 - Kath, Nadja Jeanette A1 - Gaedke, Ursula T1 - The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1390 KW - functional traits KW - community ecology KW - evolution KW - lake KW - mechanisms KW - diversity KW - plankton KW - fitness KW - maintenance KW - coexistence Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-513956 SN - 1866-8372 IS - 6 ER - TY - GEN A1 - Masigol, Hossein A1 - Khodaparast, Seyed Akbar A1 - Mostowfizadeh-Ghalamfarsa, Reza A1 - Rojas-Jimenez, Keilor A1 - Woodhouse, Jason Nicholas A1 - Neubauer, Darshan A1 - Grossart, Hans-Peter T1 - Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1395 KW - Achlya KW - Saprolegnia KW - aquatic ecosystems KW - carbon cycling KW - polymer degradation KW - Saprolegniaceae KW - Achlyaceae Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515820 SN - 1866-8372 IS - 1 ER - TY - JOUR A1 - Masigol, Hossein A1 - Khodaparast, Seyed Akbar A1 - Mostowfizadeh-Ghalamfarsa, Reza A1 - Rojas-Jimenez, Keilor A1 - Woodhouse, Jason Nicholas A1 - Neubauer, Darshan A1 - Grossart, Hans-Peter T1 - Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran JF - Aquatic Ecology N2 - Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems. KW - Achlya KW - Saprolegnia KW - aquatic ecosystems KW - carbon cycling KW - polymer degradation KW - Saprolegniaceae KW - Achlyaceae Y1 - 2020 U6 - https://doi.org/10.1007/s10452-019-09745-w SN - 1573-5125 SN - 1386-2588 VL - 54 IS - 1 SP - 323 EP - 336 PB - Springer Science CY - Dordrecht ER - TY - JOUR A1 - Stanke, Sandra A1 - Wenger, Christian A1 - Bier, Frank Fabian A1 - Hölzel, Ralph T1 - AC electrokinetic immobilization of influenza virus JF - Electrophoresis : microfluids & proteomics N2 - The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented. KW - AC electrokinetics KW - AC electroosmosis KW - dielectrophoresis KW - influenza virus KW - nanoelectrodes Y1 - 2022 U6 - https://doi.org/10.1002/elps.202100324 SN - 0173-0835 SN - 1522-2683 VL - 43 IS - 12 SP - 1309 EP - 1321 PB - Wiley-Blackwell CY - Weinheim ER - TY - JOUR A1 - Tong, Hao A1 - Nankar, Amol N. A1 - Liu, Jintao A1 - Todorova, Velichka A1 - Ganeva, Daniela A1 - Grozeva, Stanislava A1 - Tringovska, Ivanka A1 - Pasev, Gancho A1 - Radeva-Ivanova, Vesela A1 - Gechev, Tsanko A1 - Kostova, Dimitrina A1 - Nikoloski, Zoran T1 - Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits JF - Horticulture research N2 - Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding. Y1 - 2022 U6 - https://doi.org/10.1093/hr/uhac072 SN - 2052-7276 VL - 9 PB - Oxford Univ. Press CY - Cary ER - TY - GEN A1 - Crawford, Tim A1 - Karamat, Fazeelat A1 - Lehotai, Nóra A1 - Rentoft, Matilda A1 - Blomberg, Jeanette A1 - Strand, Åsa A1 - Björklund, Stefan T1 - Specific functions for mediator complex subunits from different modules in the transcriptional response of arabidopsis thaliana to abiotic stress T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1399 KW - regulate gene expression KW - signal transduction KW - circadian clock KW - plant Mediator KW - salicylic-acid KW - activation KW - jasmonate KW - network KW - defense KW - MED16 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-513666 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Moradian, Hanieh A1 - Roch, Toralf A1 - Lendlein, Andreas A1 - Gossen, Manfred T1 - mRNA transfection-induced activation of primary human monocytes and macrophages BT - Dependence on carrier system and nucleotide modifcation T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1403 KW - sirna transfection KW - mediated delivery KW - gene delivery KW - efficient KW - immunogenicity KW - lipoplexes KW - cells KW - therapeutics KW - polarization KW - pathways Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515694 SN - 1866-8372 IS - 1 ER - TY - JOUR A1 - Moradian, Hanieh A1 - Roch, Toralf A1 - Lendlein, Andreas A1 - Gossen, Manfred T1 - mRNA transfection-induced activation of primary human monocytes and macrophages BT - Dependence on carrier system and nucleotide modifcation JF - Scientific reports N2 - Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications. KW - sirna transfection KW - mediated delivery KW - gene delivery KW - efficient KW - immunogenicity KW - lipoplexes KW - cells KW - therapeutics KW - polarization KW - pathways Y1 - 2020 U6 - https://doi.org/10.1038/s41598-020-60506-4 SN - 2045-2322 VL - 10 IS - 1 SP - 1 EP - 15 PB - Springer Nature CY - London ER - TY - GEN A1 - Bäurle, Isabel A1 - Trindade, Inês T1 - Chromatin regulation of somatic abiotic stress memory T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1408 KW - abiotic stress KW - chromatin regulation KW - heat stress memory KW - histone modifications, priming KW - transcriptional memory KW - vernalization Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516668 SN - 1866-8372 IS - 17 ER - TY - GEN A1 - Obbard, Darren J. A1 - Shi, Mang A1 - Roberts, Katherine E. A1 - Longdon, Ben A1 - Dennis, Alice B. T1 - A new lineage of segmented RNA viruses infecting animals T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1411 KW - metagenome KW - RNA virus KW - dark virus KW - arthropod KW - RNA interference Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516040 SN - 1866-8372 IS - 1 ER - TY - JOUR A1 - Obbard, Darren J. A1 - Shi, Mang A1 - Roberts, Katherine E. A1 - Longdon, Ben A1 - Dennis, Alice B. T1 - A new lineage of segmented RNA viruses infecting animals JF - Virus Evolution N2 - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage. KW - metagenome KW - RNA virus KW - dark virus KW - arthropod KW - RNA interference Y1 - 2020 U6 - https://doi.org/10.1093/ve/vez061 SN - 2057-1577 VL - 6 IS - 1 SP - 1 EP - 10 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Zwaag, Jelle A1 - Horst, Rob ter A1 - Blaženović, Ivana A1 - Stößel, Daniel A1 - Ratter, Jacqueline A1 - Worseck, Josephine M. A1 - Schauer, Nicolas A1 - Stienstra, Rinke A1 - Netea, Mihai G. A1 - Jahn, Dieter A1 - Pickkers, Peter A1 - Kox, Matthijs T1 - Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system JF - Metabolites N2 - We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects. KW - metabolomics KW - LPS KW - endotoxin KW - pyruvate KW - lactate KW - cytokines KW - inflammation KW - human endotoxemia KW - cori cycle KW - warburg effect Y1 - 2020 U6 - https://doi.org/10.3390/metabo10040148 SN - 2218-1989 VL - 10 IS - 4 SP - 1 EP - 18 PB - MDPI CY - Basel ER - TY - GEN A1 - Zwaag, Jelle A1 - Horst, Rob ter A1 - Blaženović, Ivana A1 - Stößel, Daniel A1 - Ratter, Jacqueline A1 - Worseck, Josephine M. A1 - Schauer, Nicolas A1 - Stienstra, Rinke A1 - Netea, Mihai G. A1 - Jahn, Dieter A1 - Pickkers, Peter A1 - Kox, Matthijs T1 - Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1413 KW - metabolomics KW - LPS KW - endotoxin KW - pyruvate KW - lactate KW - cytokines KW - inflammation KW - human endotoxemia KW - cori cycle KW - warburg effect Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-517784 SN - 1866-8372 IS - 4 ER - TY - GEN A1 - Amen, Rahma A1 - Nagel, Rebecca A1 - Hedt, Maximilian A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1416 KW - ecological speciation KW - feeding behaviour KW - electric fish KW - trophic apparatus KW - evolutionary ecology Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-518714 SN - 1866-8372 IS - 3 ER - TY - JOUR A1 - Amen, Rahma A1 - Nagel, Rebecca A1 - Hedt, Maximilian A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences JF - Evolutionary Ecology N2 - Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated. KW - ecological speciation KW - feeding behaviour KW - electric fish KW - trophic apparatus KW - evolutionary ecology Y1 - 2020 U6 - https://doi.org/10.1007/s10682-020-10043-3 SN - 0269-7653 SN - 1573-8477 VL - 34 IS - 3 SP - 427 EP - 437 PB - Springer Science CY - Dordrecht ER - TY - JOUR A1 - Sabrowski, Wiebke A1 - Dreymann, Nico A1 - Möller, Anja A1 - Czepluch, Denise A1 - Albani, Patricia P. A1 - Theodoridis, Dimitrios A1 - Menger, Marcus M. T1 - The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer JF - Scientific reports N2 - The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-12062-2 SN - 2045-2322 VL - 12 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Moreno-Romero, Jordi A1 - Probst, Aline V. A1 - Trindade, Inês A1 - Kalyanikrishna, A1 - Engelhorn, Julia A1 - Farrona, Sara T1 - Looking At the Past and Heading to the Future BT - Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany JF - Frontiers in Plant Science N2 - In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop. KW - EWPC2019 KW - chromatin KW - epigenetics KW - transcription KW - nucleus Y1 - 2020 U6 - https://doi.org/10.3389/fpls.2019.01795 SN - 1664-462X VL - 10 IS - 1795 SP - 1 EP - 12 PB - Frontiers Media CY - Lausanne ER - TY - GEN A1 - Moreno-Romero, Jordi A1 - Probst, Aline V. A1 - Trindade, Inês A1 - Kalyanikrishna, A1 - Engelhorn, Julia A1 - Farrona, Sara T1 - Looking At the Past and Heading to the Future BT - Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1423 KW - EWPC2019 KW - chromatin KW - epigenetics KW - transcription KW - nucleus Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-511942 SN - 1866-8372 ER - TY - GEN A1 - Cao, Xianyong A1 - Tian, Fang A1 - Andreev, Andrei A1 - Anderson, Patricia M. A1 - Lozhkin, Anatoly V. A1 - Bezrukova, Elena A1 - Ni, Jian A1 - Rudaya, Natalia A1 - Stobbe, Astrid A1 - Wieczorek, Mareike A1 - Herzschuh, Ulrike T1 - A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1427 KW - Late Quaternary vegetation KW - Holocene environmental history KW - eastern continental Asia KW - plant macrofossil data KW - late pleistocene KW - paleoenvironmental records KW - Verkhoyansk mountains KW - climate dynamics KW - glacial maximum KW - Northern Asia Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-512438 SN - 1866-8372 IS - 1 ER - TY - JOUR A1 - Cao, Xianyong A1 - Tian, Fang A1 - Andreev, Andrei A1 - Anderson, Patricia M. A1 - Lozhkin, Anatoly V. A1 - Bezrukova, Elena A1 - Ni, Jian A1 - Rudaya, Natalia A1 - Stobbe, Astrid A1 - Wieczorek, Mareike A1 - Herzschuh, Ulrike T1 - A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr JF - Earth System Science Data N2 - Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa. KW - Late Quaternary vegetation KW - Holocene environmental history KW - eastern continental Asia KW - plant macrofossil data KW - late pleistocene KW - paleoenvironmental records KW - Verkhoyansk mountains KW - climate dynamics KW - glacial maximum KW - Northern Asia Y1 - 2020 U6 - https://doi.org/10.5194/essd-12-119-2020 SN - 1866-3508 SN - 1866-3516 VL - 12 IS - 1 SP - 119 EP - 135 PB - Copernics Publications CY - Katlenburg-Lindau ER - TY - JOUR A1 - Kaech, Heidi A1 - Dennis, Alice B. A1 - Vorburger, Christoph T1 - Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa JF - BMC genomics N2 - Background Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Results We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402. Conclusions Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola. KW - Aphis fabae KW - Buchnera KW - Cost of resistance KW - Hamiltonella KW - Host-symbiont interaction KW - RNA-Seq KW - Symbiosis Y1 - 2021 U6 - https://doi.org/10.1186/s12864-021-07742-8 SN - 1471-2164 VL - 22 IS - 1 PB - BioMed Central CY - London ER - TY - GEN A1 - Weyrich, Alexandra A1 - Yasar, Selma A1 - Lenz, Dorina A1 - Fickel, Jörns T1 - Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1431 KW - DNA methylation KW - gene-expression KW - CPG Islands KW - stress KW - hyperthermia KW - testis Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516525 SN - 1866-8372 IS - 5-6 ER - TY - GEN A1 - Fichtner, Franziska A1 - Olas, Justyna Jadwiga A1 - Feil, Regina A1 - Watanabe, Mutsumi A1 - Krause, Ursula A1 - Hoefgen, Rainer A1 - Stitt, Mark A1 - Lunn, John Edward T1 - Functional features of Trehalose-6-Phosphate Synthase 1 BT - an essential enzyme in Arabidopsis T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1432 KW - cyanobacterial sucrose-phosphatase KW - trehalose 6-phosphate KW - vegetative growth KW - crystal-structure KW - gene-expression KW - thaliana KW - metabolism KW - phosphorylation KW - reveals KW - proteins Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516532 SN - 1866-8372 IS - 6 ER -