TY - JOUR A1 - Riemann, Lasse A1 - Rahav, Eyal A1 - Passow, Uta A1 - Grossart, Hans-Peter A1 - de Beer, Dirk A1 - Klawonn, Isabell A1 - Eichner, Meri A1 - Benavides, Mar A1 - Bar-Zeev, Edo T1 - Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens JF - Frontiers in microbiology N2 - Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments. KW - aggregates KW - nitrogen fixation KW - heterotrophic bacteria KW - marine KW - aquatic KW - NCDs Y1 - 2022 U6 - https://doi.org/10.3389/fmicb.2022.875050 SN - 1664-302X VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Schulte, Luise A1 - Meucci, Stefano A1 - Stoof-Leichsenring, Kathleen R. A1 - Heitkam, Tony A1 - Schmidt, Nicola A1 - von Hippel, Barbara A1 - Andreev, Andrei A. A1 - Diekmann, Bernhard A1 - Biskaborn, Boris A1 - Wagner, Bernd A1 - Melles, Martin A1 - Pestryakova, Lyudmila A. A1 - Alsos, Inger G. A1 - Clarke, Charlotte A1 - Krutovsky, Konstantin A1 - Herzschuh, Ulrike T1 - Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA JF - Communications biology N2 - Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03455-0 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - López-Sánchez, Aida A1 - Bareth, Georg A1 - Bolten, Andreas A1 - Rose, Laura E. A1 - Mansfeldt, Tim A1 - Sapp, Melanie A1 - Linstädter, Anja T1 - Effects of declining oak vitality on ecosystem multifunctionality BT - lessons from a Spanish oak woodland JF - Forest ecology and management N2 - Mediterranean oak woodlands are currently facing unprecedented degradation threats from oak decline. The Iberian oak decline "Seca", related to Phytophthora infection, causes crown defoliation that may adversely affect ecosystem services (ESs). We aim to improve our understanding of how Seca-induced declines in crown foliation affect the provision of multiple ecosystem services from understory vegetation. We selected holm (Quercus ilex) and cork oak (Q. suber) trees in a Spanish oak woodland and evaluated three proxies of canopy effects. One proxy (crown defoliation) solely captured Seca-dependent effects, one proxy solely captured Seca-independent effects (tree dimensions such as diameter and height), while the third proxy (tree vigor) captured overall canopy effects. We then used the best-performing proxies to assess canopy effects on key ecosystem services (ESs) such as aboveground net primary production (ANPP), grass and legume biomass, species diversity, litter decomposition rates, and a combined index of ecosystem multifunctionality.
We found that both types of canopy effects (i.e. Seca-dependent and Seca-independent effects) were related, indicating that ANPP was disproportionally more affected by Seca when defoliated trees were large. Responses of other ESs were mostly not significant, although lower species diversity was found under trees with intermediate vigor. Our results underline that a Seca-related decline in canopy density triggered a homogenization of ecosystem service delivery on the ecosystem scale. The ecosystem functions (EFs) under trees of low vigor are similar to that in adjacent open microsites indicating that the presence of vigorous (i.e. old and vital) trees is critical for maintaining EFs at a landscape level. Our results also highlight the importance of quantifying not only defoliation but also tree dimensions as both factors jointly and interactively modify canopy effects on ecosystem multifunctionality. KW - ANPP KW - Decomposition KW - Microsite degradation KW - Herb diversity KW - Seca Y1 - 2021 U6 - https://doi.org/10.1016/j.foreco.2021.118927 SN - 0378-1127 SN - 1872-7042 VL - 484 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Dunker, Susanne A1 - Boyd, Matthew A1 - Durka, Walter A1 - Erler, Silvio A1 - Harpole, W. Stanley A1 - Henning, Silvia A1 - Herzschuh, Ulrike A1 - Hornick, Thomas A1 - Knight, Tiffany A1 - Lips, Stefan A1 - Mäder, Patrick A1 - Švara, Elena Motivans A1 - Mozarowski, Steven A1 - Rakosy, Demetra A1 - Römermann, Christine A1 - Schmitt-Jansen, Mechthild A1 - Stoof-Leichsenring, Kathleen A1 - Stratmann, Frank A1 - Treudler, Regina A1 - Virtanen, Risto A1 - Wendt-Potthoff, Katrin A1 - Wilhelm, Christian T1 - The potential of multispectral imaging flow cytometry for environmental monitoring JF - Cytometry part A N2 - Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations. KW - environmental monitoring KW - imaging flow cytometry KW - plant traits Y1 - 2022 U6 - https://doi.org/10.1002/cyto.a.24658 SN - 1552-4922 SN - 1552-4930 VL - 101 IS - 9 SP - 782 EP - 799 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Groh, Jannis A1 - Diamantopoulos, Efstathios A1 - Duan, Xiaohong A1 - Ewert, Frank A1 - Heinlein, Florian A1 - Herbst, Michael A1 - Holbak, Maja A1 - Kamali, Bahareh A1 - Kersebaum, Kurt-Christian A1 - Kuhnert, Matthias A1 - Nendel, Claas A1 - Priesack, Eckart A1 - Steidl, Jörg A1 - Sommer, Michael A1 - Pütz, Thomas A1 - Vanderborght, Jan A1 - Vereecken, Harry A1 - Wallor, Evelyn A1 - Weber, Tobias K. D. A1 - Wegehenkel, Martin A1 - Weihermüller, Lutz A1 - Gerke, Horst H. T1 - Same soil, different climate: Crop model intercomparison on translocated lysimeters JF - Vadose zone journal N2 - Crop model intercomparison studies have mostly focused on the assessment of predictive capabilities for crop development using weather and basic soil data from the same location. Still challenging is the model performance when considering complex interrelations between soil and crop dynamics under a changing climate. The objective of this study was to test the agronomic crop and environmental flux-related performance of a set of crop models. The aim was to predict weighing lysimeter-based crop (i.e., agronomic) and water-related flux or state data (i.e., environmental) obtained for the same soil monoliths that were taken from their original environment and translocated to regions with different climatic conditions, after model calibration at the original site. Eleven models were deployed in the study. The lysimeter data (2014-2018) were from the Dedelow (Dd), Bad Lauchstadt (BL), and Selhausen (Se) sites of the TERENO (TERrestrial ENvironmental Observatories) SOILCan network. Soil monoliths from Dd were transferred to the drier and warmer BL site and the wetter and warmer Se site, which allowed a comparison of similar soil and crop under varying climatic conditions. The model parameters were calibrated using an identical set of crop- and soil-related data from Dd. Environmental fluxes and crop growth of Dd soil were predicted for conditions at BL and Se sites using the calibrated models. The comparison of predicted and measured data of Dd lysimeters at BL and Se revealed differences among models. At site BL, the crop models predicted agronomic and environmental components similarly well. Model performance values indicate that the environmental components at site Se were better predicted than agronomic ones. The multi-model mean was for most observations the better predictor compared with those of individual models. For Se site conditions, crop models failed to predict site-specific crop development indicating that climatic conditions (i.e., heat stress) were outside the range of variation in the data sets considered for model calibration. For improving predictive ability of crop models (i.e., productivity and fluxes), more attention should be paid to soil-related data (i.e., water fluxes and system states) when simulating soil-crop-climate interrelations in changing climatic conditions. Y1 - 2022 U6 - https://doi.org/10.1002/vzj2.20202 SN - 1539-1663 VL - 21 IS - 4 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Cao, Xianyong A1 - Chen, Jianhui A1 - Tian, Fang A1 - Xu, Qinghai A1 - Herzschuh, Ulrike A1 - Telford, Richard A1 - Huang, Xiaozhong A1 - Zheng, Zhuo A1 - Shen, Caiming A1 - Li, Wenjia T1 - Long-distance modern analogues bias results of pollen-based precipitation reconstructions JF - Science bulletin Y1 - 2022 U6 - https://doi.org/10.1016/j.scib.2022.01.003 SN - 2095-9273 SN - 2095-9281 VL - 67 IS - 11 SP - 1115 EP - 1117 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Sedaghatmehr, Mastoureh A1 - Thirumalaikumar, Venkatesh P. A1 - Kamranfar, Iman A1 - Schulz, Karina A1 - Müller-Röber, Bernd A1 - Sampathkumar, Arun A1 - Balazadeh, Salma T1 - Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery JF - The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology N2 - Moderate and temporary heat stresses prime plants to tolerate, and survive, a subsequent severe heat stress. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and can create a heat stress memory. We recently demonstrated that plastid-localized small heat shock protein 21 ( HSP21) is a key component of heat stress memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the heat stress recovery phase extends heat stress memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during heat stress recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with heat stress memory. ATI1 bodies co-localize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during heat stress recovery. Together, our results provide new insights into the module for control of the regulation of heat stress memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the heat stress effect at the cost of reducing the heat stress memory. KW - Arabidopsis thaliana KW - ATI1 KW - FtsH6 KW - heat stress KW - HSP21 KW - plastid KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2021 U6 - https://doi.org/10.1093/jxb/erab304 SN - 0022-0957 SN - 1460-2431 VL - 72 IS - 21 SP - 7498 EP - 7513 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Van den Wyngaert, Silke A1 - Ganzert, Lars A1 - Seto, Kensuke A1 - Rojas-Jimenez, Keilor A1 - Agha, Ramsy A1 - Berger, Stella A. A1 - Woodhouse, Jason A1 - Padisak, Judit A1 - Wurzbacher, Christian A1 - Kagami, Maiko A1 - Grossart, Hans-Peter T1 - Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits JF - ISME journal N2 - Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments. Y1 - 2022 U6 - https://doi.org/10.1038/s41396-022-01267-y SN - 1751-7362 SN - 1751-7370 VL - 16 IS - 9 SP - 2242 EP - 2254 PB - Springer Nature CY - London ER - TY - JOUR A1 - Gorin, Vladislav A. A1 - Scherz, Mark D. A1 - Korost, Dmitry V. A1 - Poyarkov, Nikolay A. T1 - Consequences of parallel miniaturisation in Microhylinae (Anura, Microhylidae), with the description of a new genus of diminutive South East Asian frogs JF - Zoosystematics and evolution : Mitteilungen aus dem Museum für Naturkunde in Berlin N2 - The genus Microhyla Tschudi, 1838 includes 52 species and is one of the most diverse genera of the family Microhylidae, being the most species-rich taxon of the Asian subfamily Microhylinae. The recent, rapid description of numerous new species of Microhyla with complex phylogenetic relationships has made the taxonomy of the group especially challenging. Several recent phylogenetic studies suggested paraphyly of Microhyla with respect to Glyphoglossus Gunther, 1869, and revealed three major phylogenetic lineages of mid-Eocene origin within this assemblage. However, comprehensive works assessing morphological variation among and within these lineages are absent. In the present study we investigate the generic taxonomy of Microhyla-Glyphoglossus assemblage based on a new phylogeny including 57 species, comparative morphological analysis of skeletons from cleared-and-stained specimens for 23 species, and detailed descriptions of generalized osteology based on volume-rendered micro-CT scans for five speciesal-together representing all major lineages within the group. The results confirm three highly divergent and well-supported clades that correspond with external and osteological morphological characteristics, as well as respective geographic distribution. Accordingly, acknowledging ancient divergence between these lineages and their significant morphological differentiation, we propose to consider these three lineages as distinct genera: Microhyla sensu stricto, Glyphoglossus, and a newly described genus, Nanohyla gen. nov. KW - Amphibians KW - integrative taxonomy KW - narrow-mouthed frogs KW - micro-computed tomography KW - Nanohyla gen. nov KW - osteology KW - sexual dimorphism KW - taxonomic revision Y1 - 2021 U6 - https://doi.org/10.3897/zse.97.57968 SN - 1860-0743 SN - 1435-1935 VL - 97 IS - 1 SP - 21 EP - 54 PB - Pensoft Publishers CY - Sofia ER - TY - JOUR A1 - Schmidt, Sabrina A1 - Reil, Daniela A1 - Jeske, Kathrin A1 - Drewes, Stephan A1 - Rosenfeld, Ulrike A1 - Fischer, Stefan A1 - Spierling, Nastasja G. A1 - Labutin, Anton A1 - Heckel, Gerald A1 - Jacob, Jens A1 - Ulrich, Rainer G. A1 - Imholt, Christian T1 - Spatial and temporal dynamics and molecular evolution of Tula orthohantavirus in German vole populations JF - Viruses / Molecular Diversity Preservation International (MDPI) N2 - Tula orthohantavirus (TULV) is a rodent-borne hantavirus with broad geographical distribution in Europe. Its major reservoir is the common vole (Microtus arvalis), but TULV has also been detected in closely related vole species. Given the large distributional range and high amplitude population dynamics of common voles, this host-pathogen complex presents an ideal system to study the complex mechanisms of pathogen transmission in a wild rodent reservoir. We investigated the dynamics of TULV prevalence and the subsequent potential effects on the molecular evolution of TULV in common voles of the Central evolutionary lineage. Rodents were trapped for three years in four regions of Germany and samples were analyzed for the presence of TULV-reactive antibodies and TULV RNA with subsequent sequence determination. The results show that individual (sex) and population-level factors (abundance) of hosts were significant predictors of local TULV dynamics. At the large geographic scale, different phylogenetic TULV clades and an overall isolation-by-distance pattern in virus sequences were detected, while at the small scale (<4 km) this depended on the study area. In combination with an overall delayed density dependence, our results highlight that frequent, localized bottleneck events for the common vole and TULV do occur and can be offset by local recolonization dynamics. KW - rodents KW - hantavirus KW - monitoring KW - population dynamics KW - common vole KW - field vole KW - water vole KW - phylogeny KW - molecular evolution Y1 - 2021 U6 - https://doi.org/10.3390/v13061132 SN - 1999-4915 VL - 13 IS - 6 PB - MDPI CY - Basel ER - TY - JOUR A1 - Belluardo, Francesco A1 - Scherz, Mark D. A1 - Santos, Barbara A1 - Andreone, Franco A1 - Antonelli, Alexandre A1 - Glaw, Frank A1 - Munoz-Pajares, A. Jesus A1 - Randrianirina, Jasmin E. A1 - Raselimanana, Achille P. A1 - Vences, Miguel A1 - Crottini, Angelica T1 - Molecular taxonomic identification and species-level phylogeny of the narrow-mouthed frogs of the genus Rhombophryne (Anura: Microhylidae: Cophylinae) from Madagascar JF - Systematics and biodiversity N2 - The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is probably large, calling for a revision of the taxonomic identification of published records and an update of the known distribution of each lineage. Here we generate DNA sequences of the mitochondrial 16S rRNA gene of all specimens available to us, revise the genetic data from public databases, and report all deeply divergent mitochondrial lineages of Rhombophryne identifiable from these data. We also generate a multi-locus dataset (including five mitochondrial and eight nuclear markers; 9844 bp) to infer a species-level phylogenetic hypothesis for the diversification of this genus and revise the distribution of each lineage. We recognize a total of 10 candidate species, two of which are identified here for the first time. The genus Rhombophryne is here proposed to be divided into six main species groups, and phylogenetic relationships among some of them are not fully resolved. These frogs are primarily distributed in northern Madagascar, and most species are known from only few localities. A previous record of this genus from the Tsingy de Bemaraha (western Madagascar) is interpreted as probably due to a mislabelling and should not be considered further unless confirmed by new data. By generating this phylogenetic hypothesis and providing an updated distribution of each lineage, our findings will facilitate future species descriptions, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of diamond frogs. KW - amphibians KW - candidate species KW - diamond frogs KW - mitochondrial lineages KW - northern Madagascar KW - species-identification KW - systematics Y1 - 2022 U6 - https://doi.org/10.1080/14772000.2022.2039320 SN - 1477-2000 SN - 1478-0933 VL - 20 IS - 1 SP - 1 EP - 13 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Garbulowski, Mateusz A1 - Smolinska, Karolina A1 - Çabuk, Uğur A1 - Yones, Sara A. A1 - Celli, Ludovica A1 - Yaz, Esma Nur A1 - Barrenas, Fredrik A1 - Diamanti, Klev A1 - Wadelius, Claes A1 - Komorowski, Jan T1 - Machine learning-based analysis of glioma grades reveals co-enrichment JF - Cancers N2 - Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment. KW - glioma KW - machine learning KW - batch effect KW - TCGA KW - co-enrichment KW - rough sets Y1 - 2022 U6 - https://doi.org/10.3390/cancers14041014 SN - 2072-6694 VL - 14 IS - 4 PB - MDPI CY - Basel ER - TY - JOUR A1 - Agarwal, Saloni A1 - Hamidizadeh, Mojdeh A1 - Bier, Frank Fabian T1 - Detection of reverse transcriptase LAMP-amplified nucleic acid from oropharyngeal viral swab samples using biotinylated DNA probes through a lateral flow assay JF - Biosensors : open access journal N2 - This study focuses on three key aspects: (a) crude throat swab samples in a viral transport medium (VTM) as templates for RT-LAMP reactions; (b) a biotinylated DNA probe with enhanced specificity for LFA readouts; and (c) a digital semi-quantification of LFA readouts. Throat swab samples from SARS-CoV-2 positive and negative patients were used in their crude (no cleaning or pre-treatment) forms for the RT-LAMP reaction. The samples were heat-inactivated but not treated for any kind of nucleic acid extraction or purification. The RT-LAMP (20 min processing time) product was read out by an LFA approach using two labels: FITC and biotin. FITC was enzymatically incorporated into the RT-LAMP amplicon with the LF-LAMP primer, and biotin was introduced using biotinylated DNA probes, specifically for the amplicon region after RT-LAMP amplification. This assay setup with biotinylated DNA probe-based LFA readouts of the RT-LAMP amplicon was 98.11% sensitive and 96.15% specific. The LFA result was further analysed by a smartphone-based IVD device, wherein the T-line intensity was recorded. The LFA T-line intensity was then correlated with the qRT-PCR Ct value of the positive swab samples. A digital semi-quantification of RT-LAMP-LFA was reported with a correlation coefficient of R2 = 0.702. The overall RT-LAMP-LFA assay time was recorded to be 35 min with a LoD of three RNA copies/µL (Ct-33). With these three advancements, the nucleic acid testing-point of care technique (NAT-POCT) is exemplified as a versatile biosensor platform with great potential and applicability for the detection of pathogens without the need for sample storage, transportation, or pre-processing. KW - RT-LAMP KW - LFA KW - NAAT-LFA KW - semi-quantitative KW - surveillance-based diagnostics Y1 - 2023 U6 - https://doi.org/10.3390/bios13110988 SN - 2079-6374 VL - 13 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Numberger, Daniela A1 - Zoccarato, Luca A1 - Woodhouse, Jason Nicholas A1 - Ganzert, Lars A1 - Sauer, Sascha A1 - García Márquez, Jaime Ricardo A1 - Domisch, Sami A1 - Grossart, Hans-Peter A1 - Greenwood, Alex T1 - Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urban-ization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sedi-ments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urban-ization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts. KW - Urbanization KW - Urban waters KW - Wastewater KW - Lakes KW - Microbial community KW - composition KW - Humanization KW - Full-length 16S rRNA PacBio sequencing Y1 - 2022 U6 - https://doi.org/10.1016/j.scitotenv.2022.157321 SN - 0048-9697 SN - 1879-1026 VL - 845 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Zavorka, Libor A1 - Blanco, Andreu A1 - Chaguaceda, Fernando A1 - Cucherousset, Julien A1 - Killen, Shaun S. A1 - Lienart, Camilla A1 - Mathieu-Resuge, Margaux A1 - Nemec, Pavel A1 - Pilecky, Matthias A1 - Scharnweber, Inga Kristin A1 - Twining, Cornelia W. A1 - Kainz, Martin J. T1 - The role of vital dietary biomolecules in eco-evo-devo dynamics JF - Trends in ecology and evolution N2 - The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization. Y1 - 2023 U6 - https://doi.org/10.1016/j.tree.2022.08.010 SN - 0169-5347 SN - 1872-8383 VL - 38 IS - 1 SP - 72 EP - 84 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Grdseloff, Nastasja A1 - Boulday, Gwenola A1 - Roedel, Claudia J. A1 - Otten, Cecile A1 - Vannier, Daphne Raphaelle A1 - Cardoso, Cecile A1 - Faurobert, Eva A1 - Dogra, Deepika A1 - Tournier-Lasserve, Elisabeth A1 - Abdelilah-Seyfried, Salim T1 - Impaired retinoic acid signaling in cerebral cavernous malformations JF - Scientific reports N2 - The capillary-venous pathology cerebral cavernous malformation (CCM) is caused by loss of CCM1/Krev interaction trapped protein 1 (KRIT1), CCM2/MGC4607, or CCM3/PDCD10 in some endothelial cells. Mutations of CCM genes within the brain vasculature can lead to recurrent cerebral hemorrhages. Pharmacological treatment options are urgently needed when lesions are located in deeply-seated and in-operable regions of the central nervous system. Previous pharmacological suppression screens in disease models of CCM led to the discovery that treatment with retinoic acid improved CCM phenotypes. This finding raised a need to investigate the involvement of retinoic acid in CCM and test whether it has a curative effect in preclinical mouse models. Here, we show that components of the retinoic acid synthesis and degradation pathway are transcriptionally misregulated across disease models of CCM. We complemented this analysis by pharmacologically modifying retinoic acid levels in zebrafish and human endothelial cell models of CCM, and in acute and chronic mouse models of CCM. Our pharmacological intervention studies in CCM2-depleted human umbilical vein endothelial cells (HUVECs) and krit1 mutant zebrafish showed positive effects when retinoic acid levels were increased. However, therapeutic approaches to prevent the development of vascular lesions in adult chronic murine models of CCM were drug regiment-sensitive, possibly due to adverse developmental effects of this hormone. A treatment with high doses of retinoic acid even worsened CCM lesions in an adult chronic murine model of CCM. This study provides evidence that retinoic acid signaling is impaired in the CCM pathophysiology and suggests that modification of retinoic acid levels can alleviate CCM phenotypes. KW - Developmental biology KW - Molecular medicine Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-31905-0 SN - 2045-2322 VL - 13 IS - 1 PB - Nature Portfolio CY - Berlin ER - TY - JOUR A1 - Stübler, Sabine A1 - Kloft, Charlotte A1 - Huisinga, Wilhelm T1 - Cell-level systems biology model to study inflammatory bowel diseases and their treatment options JF - CPT: pharmacometrics & systems pharmacology N2 - To help understand the complex and therapeutically challenging inflammatory bowel diseases (IBDs), we developed a systems biology model of the intestinal immune system that is able to describe main aspects of IBD and different treatment modalities thereof. The model, including key cell types and processes of the mucosal immune response, compiles a large amount of isolated experimental findings from literature into a larger context and allows for simulations of different inflammation scenarios based on the underlying data and assumptions. In the context of a large and diverse virtual IBD population, we characterized the patients based on their phenotype (in contrast to healthy individuals, they developed persistent inflammation after a trigger event) rather than on a priori assumptions on parameter differences to a healthy individual. This allowed to reproduce the enormous diversity of predispositions known to lead to IBD. Analyzing different treatment effects, the model provides insight into characteristics of individual drug therapy. We illustrate for anti-TNF-alpha therapy, how the model can be used (i) to decide for alternative treatments with best prospects in the case of nonresponse, and (ii) to identify promising combination therapies with other available treatment options. Y1 - 2023 U6 - https://doi.org/10.1002/psp4.12932 SN - 2163-8306 VL - 12 IS - 5 SP - 690 EP - 705 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Derežanin, Lorena A1 - Blažytė, Asta A1 - Dobrynin, Pavel A1 - Duchêne, David A. A1 - Grau, José Horacio A1 - Jeon, Sungwon A1 - Kliver, Sergei A1 - Koepfli, Klaus-Peter A1 - Meneghini, Dorina A1 - Preick, Michaela A1 - Tomarovsky, Andrey A1 - Totikov, Azamat A1 - Fickel, Jörns A1 - Förster, Daniel W. T1 - Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae JF - Molecular ecology N2 - Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance. KW - adaptation KW - gene family evolution KW - genomics KW - mustelids KW - positive KW - selection KW - structural variation Y1 - 2022 U6 - https://doi.org/10.1111/mec.16443 SN - 0962-1083 SN - 1365-294X VL - 31 IS - 10 SP - 2898 EP - 2919 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Abdelilah-Seyfried, Salim A1 - Iruela-Arispe, M. Luisa A1 - Penninger, Josef M. A1 - Tournier-Lasserve, Elisabeth A1 - Vikkula, Miikka A1 - Cleaver, Ondine T1 - Recalibrating vascular malformations and mechanotransduction by pharmacological intervention JF - Journal of clinical investigation Y1 - 2022 U6 - https://doi.org/10.1172/JCI160227 SN - 0021-9738 SN - 1558-8238 VL - 132 IS - 8 PB - American Society for Clinical Investigation CY - Ann Arbor ER - TY - JOUR A1 - Cao, Xianyong A1 - Tian, Fang A1 - Herzschuh, Ulrike A1 - Ni, Jian A1 - Xu, Qinghai A1 - Li, Wenjia A1 - Zhang, Yanrong A1 - Luo, Mingyu A1 - Chen, Fahu T1 - Human activities have reduced plant diversity in eastern China over the last two millennia JF - Global change biology N2 - Understanding the history and regional singularities of human impact on vegetation is key to developing strategies for sustainable ecosystem management. In this study, fossil and modern pollen datasets from China are employed to investigate temporal changes in pollen composition, analogue quality, and pollen diversity during the Holocene. Anthropogenic disturbance and vegetation's responses are also assessed. Results reveal that pollen assemblages from non-forest communities fail to provide evidence of human impact for the western part of China (annual precipitation less than 400 mm and/or elevation more than 3000 m.a.s.l.), as inferred from the stable quality of modern analogues, principal components, and diversity of species and communities throughout the Holocene. For the eastern part of China, the proportion of fossil pollen spectra with good modern analogues increases from ca. 50% to ca. 80% during the last 2 millennia, indicating an enhanced intensity of anthropogenic disturbance on vegetation. This disturbance has caused the pollen spectra to become taxonomically less diverse over space (reduced abundances of arboreal taxa and increased abundances of herbaceous taxa), highlighting a reduced south-north differentiation and divergence from past vegetation between regions in the eastern part of China. We recommend that care is taken in eastern China when basing the development of ecosystem management strategies on vegetation changes in the region during the last 2000 years, since humans have significantly disturbed the vegetation during this period. KW - analogue quality KW - human-vegetation interaction KW - land use KW - latitudinal KW - zonation KW - plant diversity KW - pollen Y1 - 2022 U6 - https://doi.org/10.1111/gcb.16274 SN - 1354-1013 SN - 1365-2486 VL - 28 IS - 16 SP - 4962 EP - 4976 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Córdoba, Sandra Correa A1 - Tong, Hao A1 - Burgos, Asdrubal A1 - Zhu, Feng A1 - Alseekh, Saleh A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism JF - Nature Communications N2 - The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism. Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism. KW - Biochemical networks KW - Biochemical reaction networks KW - Genetic models KW - Plant molecular biology Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40644-9 SN - 2041-1723 VL - 14 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Cheng, Feng A1 - Dennis, Alice B. A1 - Osuoha, Josephine Ijeoma A1 - Canitz, Julia A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha JF - BMC genomics N2 - Background Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular. Results A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. Conclusions We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species. KW - Campylomormyrus KW - Pacbio sequencing KW - Gene family KW - Osteoglossomorpha KW - Kv1 Y1 - 2023 U6 - https://doi.org/10.1186/s12864-023-09196-6 SN - 1471-2164 VL - 24 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Peter, Lena A1 - Wendering, Désirée Jacqueline A1 - Schlickeiser, Stephan A1 - Hoffmann, Henrike A1 - Noster, Rebecca A1 - Wagner, Dimitrios Laurin A1 - Zarrinrad, Ghazaleh A1 - Münch, Sandra A1 - Picht, Samira A1 - Schulenberg, Sarah A1 - Moradian, Hanieh A1 - Mashreghi, Mir-Farzin A1 - Klein, Oliver A1 - Gossen, Manfred A1 - Roch, Toralf A1 - Babel, Nina A1 - Reinke, Petra A1 - Volk, Hans-Dieter A1 - Amini, Leila A1 - Schmueck-Henneresse, Michael T1 - Tacrolimus-resistant SARS-CoV-2-specific T cell products to prevent and treat severe COVID-19 in immunosuppressed patients JF - Molecular therapy methods and clinical development N2 - Solid organ transplant (SOT) recipients receive therapeutic immunosuppression that compromises their immune response to infections and vaccines. For this reason, SOT patients have a high risk of developing severe coronavirus disease 2019 (COVID-19) and an increased risk of death from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Moreover, the efficiency of immunotherapies and vaccines is reduced due to the constant immunosuppression in this patient group. Here, we propose adoptive transfer of SARS-CoV-2-specific T cells made resistant to a common immunosuppressant, tacrolimus, for optimized performance in the immunosuppressed patient. Using a ribonucleoprotein approach of CRISPR-Cas9 technology, we have generated tacrolimus-resistant SARS-CoV-2-specific T cell products from convalescent donors and demonstrate their specificity and function through characterizations at the single-cell level, including flow cytometry, single-cell RNA (scRNA) Cellular Indexing of Transcriptomes and Epitopes (CITE), and T cell receptor (TCR) sequencing analyses. Based on the promising results, we aim for clinical validation of this approach in transplant recipients. Additionally, we propose a combinatory approach with tacrolimus, to prevent an overshooting immune response manifested as bystander T cell activation in the setting of severe COVID-19 immunopathology, and tacrolimus-resistant SARS-CoV-2-specific T cell products, allowing for efficient clearance of viral infection. Our strategy has the potential to prevent severe COVID-19 courses in SOT or autoimmunity settings and to prevent immunopathology while providing viral clearance in severe non-transplant COVID-19 cases. Y1 - 2022 U6 - https://doi.org/10.1016/j.omtm.2022.02.012 SN - 2329-0501 VL - 25 SP - 52 EP - 73 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Tomowski, Maxi A1 - Lozada-Gobilard, Sissi Donna A1 - Jeltsch, Florian A1 - Tiedemann, Ralph T1 - Recruitment and migration patterns reveal a key role for seed banks in the meta-population dynamics of an aquatic plant JF - Scientific reports N2 - Progressive habitat fragmentation threatens plant species with narrow habitat requirements. While local environmental conditions define population growth rates and recruitment success at the patch level, dispersal is critical for population viability at the landscape scale. Identifying the dynamics of plant meta-populations is often confounded by the uncertainty about soil-stored population compartments. We combined a landscape-scale assessment of an amphibious plant's population structure with measurements of dispersal complexity in time to track dispersal and putative shifts in functional connectivity. Using 13 microsatellite markers, we analyzed the genetic structure of extant Oenanthe aquatica populations and their soil seed banks in a kettle hole system to uncover hidden connectivity among populations in time and space. Considerable spatial genetic structure and isolation-by-distance suggest limited gene flow between sites. Spatial isolation and patch size showed minor effects on genetic diversity. Genetic similarity found among extant populations and their seed banks suggests increased local recruitment, despite some evidence of migration and recent colonization. Results indicate stepping-stone dispersal across adjacent populations. Among permanent and ephemeral demes the resulting meta-population demography could be determined by source-sink dynamics. Overall, these spatiotemporal connectivity patterns support mainland-island dynamics in our system, highlighting the importance of persistent seed banks as enduring sources of genetic diversity. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-37974-5 SN - 2045-2322 VL - 13 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Arend, Marius A1 - Zimmer, David A1 - Xu, Rudan A1 - Sommer, Frederik A1 - Mühlhaus, Timo A1 - Nikoloski, Zoran T1 - Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale JF - Nature Communications N2 - Metabolic engineering of microalgae offers a promising solution for sustainable biofuel production, and rational design of engineering strategies can be improved by employing metabolic models that integrate enzyme turnover numbers. However, the coverage of turnover numbers for Chlamydomonas reinhardtii, a model eukaryotic microalga accessible to metabolic engineering, is 17-fold smaller compared to the heterotrophic cell factory Saccharomyces cerevisiae. Here we generate quantitative protein abundance data of Chlamydomonas covering 2337 to 3708 proteins in various growth conditions to estimate in vivo maximum apparent turnover numbers. Using constrained-based modeling we provide proxies for in vivo turnover numbers of 568 reactions, representing a 10-fold increase over the in vitro data for Chlamydomonas. Integration of the in vivo estimates instead of in vitro values in a metabolic model of Chlamydomonas improved the accuracy of enzyme usage predictions. Our results help in extending the knowledge on uncharacterized enzymes and improve biotechnological applications of Chlamydomonas. KW - Computational models KW - Enzymes KW - Proteomics Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40498-1 SN - 2041-1723 VL - 14 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Ferreira, Clara Mendes A1 - Dammhahn, Melanie A1 - Eccard, Jana T1 - So many choices, so little time BT - food preference and movement vary with the landscape of fear JF - Ecology and evolution N2 - Spatial and temporal variation in perceived predation risk is an important determinant of movement and foraging activity of animals. Foraging in this landscape of fear, individuals need to decide where and when to move, and what resources to choose. Foraging theory predicts the outcome of these decisions based on energetic trade-offs, but complex interactions between perceived predation risk and preferences of foragers for certain functional traits of their resources are rarely considered. Here, we studied the interactive effects of perceived predation risk on food trait preferences and foraging behavior in bank voles (Myodes glareolus) in experimental landscapes. Individuals (n = 19) were subjected for periods of 24 h to two extreme, risk-uniform landscapes (either risky or safe), containing 25 discrete food patches, filled with seeds of four plant species in even amounts. Seeds varied in functional traits: size, nutrients, and shape. We evaluated whether and how risk modifies forager preference for functional traits. We also investigated whether perceived risk and distance from shelter affected giving-up density (GUD), time in patches, and number of patch visits. In safe landscapes, individuals increased time spent in patches, lowered GUD and visited distant patches more often compared to risky landscapes. Individuals preferred bigger seeds independent of risk, but in the safe treatment they preferred fat-rich over carb-rich seeds. Thus, higher densities of resource levels remained in risky landscapes, while in safe landscapes resource density was lower and less diverse due to selective foraging. Our results suggest that the interaction of perceived risk and dietary preference adds an additional layer to the cascading effects of a landscape of fear which affects biodiversity at resource level. KW - foraging behavior KW - functional traits KW - giving-up density KW - myodes glareolus KW - perceived predation risk KW - seed ecology Y1 - 2023 U6 - https://doi.org/10.1002/ece3.10330 SN - 2045-7758 VL - 13 IS - 7 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Petrich, Annett A1 - Aji, Amit Koikkarah A1 - Dunsing, Valentin A1 - Chiantia, Salvatore T1 - Benchmarking of novel green fluorescent proteins for the quantification of protein oligomerization in living cells JF - PLoS one N2 - Protein-protein-interactions play an important role in many cellular functions. Quantitative non-invasive techniques are applied in living cells to evaluate such interactions, thereby providing a broader understanding of complex biological processes. Fluorescence fluctuation spectroscopy describes a group of quantitative microscopy approaches for the characterization of molecular interactions at single cell resolution. Through the obtained molecular brightness, it is possible to determine the oligomeric state of proteins. This is usually achieved by fusing fluorescent proteins (FPs) to the protein of interest. Recently, the number of novel green FPs has increased, with consequent improvements to the quality of fluctuation-based measurements. The photophysical behavior of FPs is influenced by multiple factors (including photobleaching, protonation-induced "blinking" and long-lived dark states). Assessing these factors is critical for selecting the appropriate fluorescent tag for live cell imaging applications. In this work, we focus on novel green FPs that are extensively used in live cell imaging. A systematic performance comparison of several green FPs in living cells under different pH conditions using Number & Brightness (N & B) analysis and scanning fluorescence correlation spectroscopy was performed. Our results show that the new FP Gamillus exhibits higher brightness at the cost of lower photostability and fluorescence probability (pf), especially at lower pH. mGreenLantern, on the other hand, thanks to a very high pf, is best suited for multimerization quantification at neutral pH. At lower pH, mEGFP remains apparently the best choice for multimerization investigation. These guidelines provide the information needed to plan quantitative fluorescence microscopy involving these FPs, both for general imaging or for protein-protein-interactions quantification via fluorescence fluctuation-based methods. Y1 - 2023 U6 - https://doi.org/10.1371/journal.pone.0285486 SN - 1932-6203 VL - 18 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Xu, Huizhen A1 - Giannetti, Alessandro A1 - Sugiyama, Yuki A1 - Zheng, Wenna A1 - Schneider, René A1 - Watanabe, Yoichiro A1 - Oda, Yoshihisa A1 - Persson, Staffan T1 - Secondary cell wall patterning-connecting the dots, pits and helices JF - Open biology N2 - All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field. KW - plant cell wall KW - microtubules KW - xylem KW - cell wall patterning KW - cellulose Y1 - 2022 U6 - https://doi.org/10.1098/rsob.210208 SN - 2046-2441 VL - 12 IS - 5 PB - Royal Society CY - London ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Fettke, Jörg T1 - Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield JF - Frontiers in plant science N2 - The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches. KW - starch KW - oil yield KW - fruit development KW - gene expression KW - RNA-seq KW - and palm KW - oil KW - Elaeis guineensis Jacq Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1220237 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Berry, Paul E. A1 - Dammhahn, Melanie A1 - Blaum, Niels T1 - Keeping cool on hot days BT - activity responses of African antelope to heat extremes JF - Frontiers in ecology and evolution N2 - Long-lived organisms are likely to respond to a rapidly changing climate with behavioral flexibility. Animals inhabiting the arid parts of southern Africa face a particularly rapid rise in temperature which in combination with food and water scarcity places substantial constraints on the ability of animals to tolerate heat. We investigated how three species of African antelope-springbok Antidorcas marsupialis, kudu Tragelaphus strepsiceros and eland T. oryx-differing in body size, habitat preference and movement ecology, change their activity in response to extreme heat in an arid savanna. Serving as a proxy for activity, dynamic body acceleration data recorded every five minutes were analyzed for seven to eight individuals per species for the three hottest months of the year. Activity responses to heat during the hottest time of day (the afternoons) were investigated and diel activity patterns were compared between hot and cool days. Springbok, which prefer open habitat, are highly mobile and the smallest of the species studied, showed the greatest decrease in activity with rising temperature. Furthermore, springbok showed reduced mean activity over the 24 h cycle on hot days compared to cool days. Large-bodied eland seemed less affected by afternoon heat than springbok. While eland also reduced diurnal activity on hot days compared to cool days, they compensated for this by increasing nocturnal activity, possibly because their predation risk is lower. Kudu, which are comparatively sedentary and typically occupy shady habitat, seemed least affected during the hottest time of day and showed no appreciable difference in diel activity patterns between hot and cool days. The interplay between habitat preference, body size, movement patterns, and other factors seems complex and even sub-lethal levels of heat stress have been shown to impact an animal's long-term survival and reproduction. Thus, differing heat tolerances among species could result in a shift in the composition of African herbivore communities as temperatures continue to rise, with significant implications for economically important wildlife-based land use and conservation. KW - springbok KW - kudu KW - eland KW - dynamic body acceleration KW - tri-axial accelerometers KW - behavioral flexibility KW - climate change KW - savanna ecology Y1 - 2023 U6 - https://doi.org/10.3389/fevo.2023.1172303 SN - 2296-701X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Compart, Julia A1 - Singh, Aakanksha A1 - Fettke, Jörg A1 - Apriyanto, Ardha T1 - Customizing starch properties BT - a review of starch modifications and their applications JF - Polymers N2 - Starch has been a convenient, economically important polymer with substantial applications in the food and processing industry. However, native starches present restricted applications, which hinder their industrial usage. Therefore, modification of starch is carried out to augment the positive characteristics and eliminate the limitations of the native starches. Modifications of starch can result in generating novel polymers with numerous functional and value-added properties that suit the needs of the industry. Here, we summarize the possible starch modifications in planta and outside the plant system (physical, chemical, and enzymatic) and their corresponding applications. In addition, this review will highlight the implications of each starch property adjustment. KW - starch KW - starch modification KW - in planta modification KW - physical modification KW - chemical modification KW - enzymatic modification KW - starch application Y1 - 2023 U6 - https://doi.org/10.3390/polym15163491 SN - 2073-4360 VL - 15 IS - 16 PB - MDPI CY - Basel ER - TY - JOUR A1 - Kappel, Christian A1 - Friedrich, Thomas A1 - Oberkofler, Vicky A1 - Jiang, Li A1 - Crawford, Tim A1 - Lenhard, Michael A1 - Bäurle, Isabel T1 - Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis JF - Genome biology : biology for the post-genomic era N2 - Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior. KW - Transcriptional memory KW - Priming KW - Heat stress KW - HSFA2 KW - HSFA3 KW - Arabidopsis thaliana KW - Histone H3K4 trimethylation KW - ChIP-seq Y1 - 2023 U6 - https://doi.org/10.1186/s13059-023-02970-5 SN - 1474-760X VL - 24 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Tabatabaei, Iman A1 - Alseekh, Saleh A1 - Shahid, Mohammad A1 - Leniak, Ewa A1 - Wagner, Mateusz A1 - Mahmoudi, Henda A1 - Thushar, Sumitha A1 - Fernie, Alisdair R. A1 - Murphy, Kevin M. A1 - Schmöckel, Sandra M. A1 - Tester, Mark A1 - Müller-Röber, Bernd A1 - Skirycz, Aleksandra A1 - Balazadeh, Salma T1 - The diversity of quinoa morphological traits and seed metabolic composition JF - Scientific data N2 - Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa. Y1 - 2022 U6 - https://doi.org/10.1038/s41597-022-01399-y SN - 2052-4463 VL - 9 IS - 1 PB - Nature Research CY - Berlin ER - TY - JOUR A1 - Stiegler, Jonas A1 - Pahl, Janice A1 - Guillen, Rafael Arce A1 - Ullmann, Wiebke A1 - Blaum, Niels T1 - The heat is on BT - impacts of rising temperature on the activity of a common European mammal JF - Frontiers in Ecology and Evolution N2 - Climate conditions severely impact the activity and, consequently, the fitness of wildlife species across the globe. Wildlife can respond to new climatic conditions, but the pace of human-induced change limits opportunities for adaptation or migration. Thus, how these changes affect behavior, movement patterns, and activity levels remains unclear. In this study, we investigate how extreme weather conditions affect the activity of European hares (Lepus europaeus) during their peak reproduction period. When hares must additionally invest energy in mating, prevailing against competitors, or lactating, we investigated their sensitivities to rising temperatures, wind speed, and humidity. To quantify their activity, we used the overall dynamic body acceleration (ODBA) calculated from tri-axial acceleration measurements of 33 GPS-collared hares. Our analysis revealed that temperature, humidity, and wind speed are important in explaining changes in activity, with a strong response for high temperatures above 25 & DEG;C and the highest change in activity during temperature extremes of over 35 & DEG;C during their inactive period. Further, we found a non-linear relationship between temperature and activity and an interaction of activity changes between day and night. Activity increased at higher temperatures during the inactive period (day) and decreased during the active period (night). This decrease was strongest during hot tropical nights. At a stage of life when mammals such as hares must substantially invest in reproduction, the sensitivity of females to extreme temperatures was particularly pronounced. Similarly, both sexes increased their activity at high humidity levels during the day and low wind speeds, irrespective of the time of day, while the effect of humidity was stronger for males. Our findings highlight the importance of understanding the complex relationships between extreme weather conditions and mammal behavior, critical for conservation and management. With ongoing climate change, extreme weather events such as heat waves and heavy rainfall are predicted to occur more often and last longer. These events will directly impact the fitness of hares and other wildlife species and hence the population dynamics of already declining populations across Europe. KW - activity KW - ODBA KW - animal tracking KW - European hare KW - extreme weather events KW - climate change Y1 - 2023 U6 - https://doi.org/10.3389/fevo.2023.1193861 SN - 2296-701X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Schwieder, Marcel A1 - Wesemeyer, Maximilian A1 - Frantz, David A1 - Pfoch, Kira A1 - Erasmi, Stefan A1 - Pickert, Jürgen A1 - Nendel, Claas A1 - Hostert, Patrick T1 - Mapping grassland mowing events across Germany based on combined Sentinel-2 and Landsat 8 time series JF - Remote sensing of environment N2 - Spatially explicit knowledge on grassland extent and management is critical to understand and monitor the impact of grassland use intensity on ecosystem services and biodiversity. While regional studies allow detailed insights into land use and ecosystem service interactions, information on a national scale can aid biodiversity assessments. However, for most European countries this information is not yet widely available. We used an analysis-ready-data cube that contains dense time series of co-registered Sentinel-2 and Landsat 8 data, covering the extent of Germany. We propose an algorithm that detects mowing events in the time series based on residuals from an assumed undisturbed phenology, as an indicator of grassland use intensity. A self-adaptive ruleset enabled to account for regional variations in land surface phenology and non-stationary time series on a pixelbasis. We mapped mowing events for the years from 2017 to 2020 for permanent grassland areas in Germany. The results were validated on a pixel level in four of the main natural regions in Germany based on reported mowing events for a total of 92 (2018) and 78 (2019) grassland parcels. Results for 2020 were evaluated with combined time series of Landsat, Sentinel-2 and PlanetScope data. The mean absolute percentage error between detected and reported mowing events was on average 40% (2018), 36% (2019) and 35% (2020). Mowing events were on average detected 11 days (2018), 7 days (2019) and 6 days (2020) after the reported mowing. Performance measures varied between the different regions of Germany, and lower accuracies were found in areas that are revisited less frequently by Sentinel-2. Thus, we assessed the influence of data availability and found that the detection of mowing events was less influenced by data availability when at least 16 cloud-free observations were available in the grassland season. Still, the distribution of available observations throughout the season appeared to be critical. On a national scale our results revealed overall higher shares of less intensively mown grasslands and smaller shares of highly intensively managed grasslands. Hotspots of the latter were identified in the alpine foreland in Southern Germany as well as in the lowlands in the Northwest of Germany. While these patterns were stable throughout the years, the results revealed a tendency to lower management intensity in the extremely dry year 2018. Our results emphasize the ability of the approach to map the intensity of grassland management throughout large areas despite variations in data availability and environmental conditions. KW - Analysis-ready data KW - Big data KW - Large-area mapping KW - Germany KW - Common agricultural policy KW - Time series KW - Land use intensity KW - Optical remote sensing KW - Multi-spectral data KW - PlanetScope Y1 - 2022 U6 - https://doi.org/10.1016/j.rse.2021.112795 SN - 0034-4257 SN - 1879-0704 VL - 269 PB - Elsevier CY - New York ER - TY - JOUR A1 - Alshareef, Nouf Owdah A1 - Otterbach, Sophie L. A1 - Allu, Annapurna Devi A1 - Woo, Yong H. A1 - de Werk, Tobias A1 - Kamranfar, Iman A1 - Müller-Röber, Bernd A1 - Tester, Mark A1 - Balazadeh, Salma A1 - Schmöckel, Sandra M. T1 - NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis JF - Scientific reports N2 - Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-14429-x SN - 2045-2322 VL - 12 IS - 1 PB - Nature Research CY - Berlin ER - TY - JOUR A1 - Hoang, Yen A1 - Gryzik, Stefanie A1 - Hoppe, Ines A1 - Rybak, Alexander A1 - Schädlich, Martin A1 - Kadner, Isabelle A1 - Walther, Dirk A1 - Vera, Julio A1 - Radbruch, Andreas A1 - Groth, Detlef A1 - Baumgart, Sabine A1 - Baumgrass, Ria T1 - PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments JF - Frontiers in immunology N2 - Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm "pattern recognition of immune cells (PRI)" to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4(+)T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data. KW - multi-parametric analysis KW - re-analysis KW - combinatorial protein KW - expression KW - high-dimensional cytometry data KW - mass cytometry data KW - pattern perception Y1 - 2022 U6 - https://doi.org/10.3389/fimmu.2022.849329 SN - 1664-3224 VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Tian, Fang A1 - Qin, Wen A1 - Zhang, Ran A1 - Herzschuh, Ulrike A1 - Ni, Jian A1 - Zhang, Chengjun A1 - Mischke, Steffen A1 - Cao, Xianyong T1 - Palynological evidence for the temporal stability of the plant community in the Yellow River Source Area over the last 7,400 years JF - Vegetation history and archaeobotany N2 - The terrestrial ecosystem in the Yellow River Source Area (YRSA) is sensitive to climate change and human impacts, although past vegetation change and the degree of human disturbance are still largely unknown. A 170-cm-long sediment core covering the last 7,400 years was collected from Lake Xingxinghai (XXH) in the YRSA. Pollen, together with a series of other environmental proxies (including grain size, total organic carbon (TOC) and carbonate content), were analysed to explore past vegetation and environmental changes for the YRSA. Dominant and common pollen components-Cyperaceae, Poaceae, Artemisia, Chenopodiaceae and Asteraceae-are stable throughout the last 7,400 years. Slight vegetation change is inferred from an increasing trend of Cyperaceae and decreasing trend of Poaceae, suggesting that alpine steppe was replaced by alpine meadow at ca. 3.5 ka cal bp. The vegetation transformation indicates a generally wetter climate during the middle and late Holocene, which is supported by increased amounts of TOC and Pediastrum (representing high water-level) and is consistent with previous past climate records from the north-eastern Tibetan Plateau. Our results find no evidence of human impact on the regional vegetation surrounding XXH, hence we conclude the vegetation change likely reflects the regional climate signal. KW - Pollen KW - Lake Xingxinghai KW - Tibetan Plateau KW - Holocene KW - Vegetation change KW - Regional climate Y1 - 2022 U6 - https://doi.org/10.1007/s00334-022-00870-5 SN - 0939-6314 SN - 1617-6278 VL - 31 IS - 6 SP - 549 EP - 558 PB - Springer CY - New York ER - TY - JOUR A1 - Vatova, Mariyana A1 - Rubin, Conrad A1 - Grossart, Hans-Peter A1 - Goncalves, Susana C. A1 - Schmidt, Susanne I. A1 - Jarić, Ivan T1 - Aquatic fungi: largely neglected targets for conservation JF - Frontiers in ecology and the environment Y1 - 2022 U6 - https://doi.org/10.1002/fee.2495 SN - 1540-9295 SN - 1540-9309 VL - 20 IS - 4 SP - 207 EP - 209 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Glückler, Ramesh A1 - Geng, Rongwei A1 - Grimm, Lennart A1 - Baisheva, Izabella A1 - Herzschuh, Ulrike A1 - Stoof-Leichsenring, Kathleen R. A1 - Kruse, Stefan A1 - Andreev, Andrej Aleksandrovic A1 - Pestryakova, Luidmila A1 - Dietze, Elisabeth T1 - Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies JF - Frontiers in Ecology and Evolution N2 - Wildfires play an essential role in the ecology of boreal forests. In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation. However, long-term relationships between changes in fire regime and forest structure remain largely unknown. We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years. Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present. A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene. Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene. We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes. Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene. Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires. These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons. KW - fire KW - larch KW - boreal KW - forest KW - Russia KW - charcoal KW - pollen KW - ancient DNA Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.962906 SN - 2296-701X VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Welke, Robert-William A1 - Sperber, Hannah Sabeth A1 - Bergmann, Ronny A1 - Koikkarah, Amit A1 - Menke, Laura A1 - Sieben, Christian A1 - Krüger, Detlev H. A1 - Chiantia, Salvatore A1 - Herrmann, Andreas A1 - Schwarzer, Roland T1 - Characterization of hantavirus N protein intracellular dynamics and localization JF - Viruses N2 - Hantaviruses are enveloped viruses that possess a tri-segmented, negative-sense RNA genome. The viral S-segment encodes the multifunctional nucleocapsid protein (N), which is involved in genome packaging, intracellular protein transport, immunoregulation, and several other crucial processes during hantavirus infection. In this study, we generated fluorescently tagged N protein constructs derived from Puumalavirus (PUUV), the dominant hantavirus species in Central, Northern, and Eastern Europe. We comprehensively characterized this protein in the rodent cell line CHO-K1, monitoring the dynamics of N protein complex formation and investigating co-localization with host proteins as well as the viral glycoproteins Gc and Gn. We observed formation of large, fibrillar PUUV N protein aggregates, rapidly coalescing from early punctate and spike-like assemblies. Moreover, we found significant spatial correlation of N with vimentin, actin, and P-bodies but not with microtubules. N constructs also co-localized with Gn and Gc albeit not as strongly as the glycoproteins associated with each other. Finally, we assessed oligomerization of N constructs, observing efficient and concentration-dependent multimerization, with complexes comprising more than 10 individual proteins. KW - hantavirus KW - N protein KW - oligomerization KW - actin KW - P-bodies KW - vimentin KW - Number and Brightness KW - Puumalavirus KW - macromolecular assemblies Y1 - 2022 U6 - https://doi.org/10.3390/v14030457 SN - 1999-4915 VL - 14 IS - 3 PB - MDPI CY - Basel ER - TY - JOUR A1 - Kamali, Bahareh A1 - Jahanbakhshi, Farshid A1 - Dogaru, Diana A1 - Dietrich, Jörg A1 - Nendel, Claas A1 - AghaKouchak, Amir T1 - Probabilistic modeling of crop-yield loss risk under drought: a spatial showcase for sub-Saharan Africa JF - Environmental research letters N2 - Assessing the risk of yield loss in African drought-affected regions is key to identify feasible solutions for stable crop production. Recent studies have demonstrated that Copula-based probabilistic methods are well suited for such assessment owing to reasonably inferring important properties in terms of exceedance probability and joint dependence of different characterization. However, insufficient attention has been given to quantifying the probability of yield loss and determining the contribution of climatic factors. This study applies the Copula theory to describe the dependence between drought and crop yield anomalies for rainfed maize, millet, and sorghum crops in sub-Saharan Africa (SSA). The environmental policy integrated climate model, calibrated with Food and Agriculture Organization country-level yield data, was used to simulate yields across SSA (1980-2012). The results showed that the severity of yield loss due to drought had a higher magnitude than the severity of drought itself. Sensitivity analysis to identify factors contributing to drought and high-temperature stresses for all crops showed that the amount of precipitation during vegetation and grain filling was the main driver of crop yield loss, and the effect of temperature was stronger for sorghum than for maize and millet. The results demonstrate the added value of probabilistic methods for drought-impact assessment. For future studies, we recommend looking into factors influencing drought and high-temperature stresses as individual/concurrent climatic extremes. KW - Copula theory KW - crop model KW - drought stress KW - joint probability KW - risk Y1 - 2022 U6 - https://doi.org/10.1088/1748-9326/ac4ec1 SN - 1748-9326 VL - 17 IS - 2 PB - IOP Publishing CY - Bristol ER - TY - JOUR A1 - Kamali, Bahareh A1 - Lorite, Ignacio J. A1 - Webber, Heidi A. A1 - Rezaei, Ehsan Eyshi A1 - Gabaldon-Leal, Clara A1 - Nendel, Claas A1 - Siebert, Stefan A1 - Ramirez-Cuesta, Juan Miguel A1 - Ewert, Frank A1 - Ojeda, Jonathan J. T1 - Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain JF - Scientific reports N2 - This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability. Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields. The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017). By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66%). However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses. Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-08056-9 SN - 2045-2322 VL - 12 IS - 1 PB - Macmillan Publishers Limited, CY - London ER - TY - JOUR A1 - Tolomeev, Aleksandr P. A1 - Dubovskaya, Olga P. A1 - Kirillin, Georgiy A1 - Buseva, Zhanna A1 - Kolmakova, Olesya A1 - Grossart, Hans-Peter A1 - Tang, Kam W. A1 - Gladyšev, Michail I. T1 - Degradation of dead cladoceran zooplankton and their contribution to organic carbon cycling in stratified lakes BT - field observation and model prediction JF - Journal of plankton research N2 - The contribution of dead zooplankton biomass to carbon cycle in aquatic ecosystems is practically unknown. Using abundance data of zooplankton in water column and dead zooplankton in sediment traps in Lake Stechlin, an ecological-mathematical model was developed to simulate the abundance and sinking of zooplankton carcasses and predict the related release of labile organic matter (LOM) into the water column. We found species-specific differences in mortality rate of the dominant zooplankton: Daphnia cucullata, Bosmina coregoni and Diaphanosoma brachyurum (0.008, 0.129 and 0.020 day(-1), respectively) and differences in their carcass sinking velocities in metalimnion (and hypolimnion): 2.1 (7.64), 14.0 (19.5) and 1.1 (5.9) m day(-1), respectively. Our model simulating formation and degradation processes of dead zooplankton predicted a bimodal distribution of the released LOM: epilimnic and metalimnic peaks of comparable intensity, ca. 1 mg DW m(-3) day(-1). Maximum degradation of carcasses up to ca. 1.7 mg DW m(-3) day(-1) occurred in the density gradient zone of metalimnion. LOM released from zooplankton carcasses into the surrounding water may stimulate microbial activity and facilitate microbial degradation of more refractory organic matter; therefore, dead zooplankton are expected to be an integral part of water column carbon source/sink dynamics in stratified lakes. KW - zooplankton carcasses KW - non-predatory mortality KW - sinking velocities KW - microbial degradation KW - Lake Stechlin KW - simulation modeling Y1 - 2022 U6 - https://doi.org/10.1093/plankt/fbac023 SN - 0142-7873 SN - 1464-3774 VL - 44 IS - 3 SP - 386 EP - 400 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Leong, Jia Xuan A1 - Raffeiner, Margot A1 - Spinti, Daniela A1 - Langin, Gautier A1 - Franz-Wachtel, Mirita A1 - Guzman, Andrew R. A1 - Kim, Jung-Gun A1 - Pandey, Pooja A1 - Minina, Alyona E. A1 - Macek, Boris A1 - Hafren, Anders A1 - Bozkurt, Tolga O. A1 - Mudgett, Mary Beth A1 - Börnke, Frederik A1 - Hofius, Daniel A1 - Uestuen, Suayib T1 - A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component JF - The EMBO journal N2 - Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants. One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions. KW - autophagy KW - effectors KW - immunity KW - ubiquitination KW - xenophagy Y1 - 2022 U6 - https://doi.org/10.15252/embj.2021110352 SN - 1460-2075 VL - 41 IS - 13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Agne, Stefanie A1 - Naylor, Gavin J. P. A1 - Preick, Michaela A1 - Yang, Lei A1 - Thiel, Ralf A1 - Weigmann, Simon A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Hofreiter, Michael A1 - Straube, Nicolas T1 - Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes JF - Frontiers in Ecology and Evolution N2 - Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence. In contrast, DNA sequence information has rarely been used. Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions. The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far. However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data. Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals. Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species. Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research. KW - type specimens KW - Etmopterus litvinovi KW - Etmopterus pycnolepis KW - deep-sea KW - sharks KW - archival DNA Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.910009 SN - 2296-701X VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Havermann, Felix A1 - Ghirardo, Andrea A1 - Schnitzler, Jörg-Peter A1 - Nendel, Claas A1 - Hoffmann, Mathias A1 - Kraus, David A1 - Grote, Rüdiger T1 - Modeling intra- and interannual variability of BVOC emissions from maize, oil-seed rape, and ryegrass JF - Journal of advances in modeling earth systems N2 - Air chemistry is affected by the emission of biogenic volatile organic compounds (BVOCs), which originate from almost all plants in varying qualities and quantities. They also vary widely among different crops, an aspect that has been largely neglected in emission inventories. In particular, bioenergy-related species can emit mixtures of highly reactive compounds that have received little attention so far. For such species, long-term field observations of BVOC exchange from relevant crops covering different phenological phases are scarcely available. Therefore, we measured and modeled the emission of three prominent European bioenergy crops (maize, ryegrass, and oil-seed rape) for full rotations in north-eastern Germany. Using a proton transfer reaction-mass spectrometer combined with automatically moving large canopy chambers, we were able to quantify the characteristic seasonal BVOC flux dynamics of each crop species. The measured BVOC fluxes were used to parameterize and evaluate the BVOC emission module (JJv) of the physiology-oriented LandscapeDNDC model, which was enhanced to cover de novo emissions as well as those from plant storage pools. Parameters are defined for each compound individually. The model is used for simulating total compound-specific reactivity over several years and also to evaluate the importance of these emissions for air chemistry. We can demonstrate substantial differences between the investigated crops with oil-seed rape having 37-fold higher total annual emissions than maize. However, due to a higher chemical reactivity of the emitted blend in maize, potential impacts on atmospheric OH-chemistry are only 6-fold higher. KW - biogenic volatile organic compounds KW - process-based modeling KW - Zea mays KW - Brassica napus KW - Lolium multiflorum KW - plant ontogenetic stage Y1 - 2022 U6 - https://doi.org/10.1029/2021MS002683 SN - 1942-2466 VL - 14 IS - 3 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Rosso, Pablo A1 - Nendel, Claas A1 - Gilardi, Nicolas A1 - Udroiu, Cosmin A1 - Chlebowski, Florent T1 - Processing of remote sensing information to retrieve leaf area index in barley BT - a comparison of methods JF - Precision agriculture N2 - Leaf area index (LAI) is a key variable in understanding and modeling crop-environment interactions. With the advent of increasingly higher spatial resolution satellites and sensors mounted on remotely piloted aircrafts (RPAs), the use of remote sensing in precision agriculture is becoming more common. Since also the availability of methods to retrieve LAI from image data have also drastically expanded, it is necessary to test simultaneously as many methods as possible to understand the advantages and disadvantages of each approach. Ground-based LAI data from three years of barley experiments were related to remote sensing information using vegetation indices (VI), machine learning (ML) and radiative transfer models (RTM), to assess the relative accuracy and efficacy of these methods. The optimized soil adjusted vegetation index and a modified version of the Weighted Difference Vegetation Index performed slightly better than any other retrieval method. However, all methods yielded coefficients of determination of around 0.7 to 0.9. The best performing machine learning algorithms achieved higher accuracies when four Sentinel-2 bands instead of 12 were used. Also, the good performance of VIs and the satisfactory performance of the 4-band RTM, strongly support the synergistic use of satellites and RPAs in precision agriculture. One of the methods used, Sen2-Agri, an open source ML-RTM-based operational system, was also able to accurately retrieve LAI, although it is restricted to Sentinel-2 and Landsat data. This study shows the benefits of testing simultaneously a broad range of retrieval methods to monitor crops for precision agriculture. KW - leaf area index KW - vegetation indices KW - machine learning KW - radiative transfer models Y1 - 2022 U6 - https://doi.org/10.1007/s11119-022-09893-4 SN - 1385-2256 SN - 1573-1618 VL - 23 IS - 4 SP - 1449 EP - 1472 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Straube, Nicolas A1 - Preick, Michaela A1 - Naylor, Gavin J. P. A1 - Hofreiter, Michael T1 - Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae) JF - Royal Society Open Science N2 - After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy. KW - museum specimens KW - archival DNA KW - deep-sea sharks KW - Etmopterus pusillus KW - Etmopterus joungi KW - taxonomy Y1 - 2021 U6 - https://doi.org/10.1098/rsos.210474 SN - 2054-5703 VL - 8 IS - 9 PB - Royal Society CY - London ER - TY - JOUR A1 - Andreev, Andrei A1 - Raschke, Elena A1 - Biskaborn, Boris A1 - Vyse, Stuart Andrew A1 - Courtin, Jérémy A1 - Böhmer, Thomas A1 - Stoof-Leichsenring, Kathleen R. A1 - Kruse, Stefan A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Late Pleistocene to Holocene vegetation and climate changes in northwestern Chukotka (Far East Russia) deduced from lakes Ilirney and Rauchuagytgyn pollen records JF - Boreas : an international journal of quaternary research N2 - This paper presents two new pollen records and quantitative climate reconstructions from northern Chukotka documenting environmental changes over the last 27.9 ka. Open tundra- and steppe-like habitats dominated between 27.9 and 18.7 cal. ka BP. Betula and Alnus shrubs might have grown in sheltered microhabitats but disappeared after 18.7 cal. ka BP. Although the climate was rather harsh, local herb-dominated communities supported herbivores as is evident by the presence of coprophilous spores in the sediments. The increase in Salix and Cyperaceae similar to 16.1 cal. ka BP suggests climate amelioration. Shrub Betula appeared similar to 15.9 cal. ka BP, and became dominant after similar to 15.52 cal. ka BP, whilst typical steppe communities drastically reduced. Very high presence of Botryococcus in the Lateglacial sediments reflects widespread shallow habitats, probably due to lake level increase. Shrub Alnus became common after similar to 13 cal. ka BP reflecting further climate amelioration. Simultaneously, herb communities gradually decreased in the vegetation reaching a minimum similar to 11.8 cal. ka BP. A gradual decrease of algae remains suggests a reduction of shallow-water habitats. Shrubby and graminoid tundra was dominant similar to 11.8-11.1 cal. ka BP, later Salix stands significantly decreased. The forest-tundra ecotone established in the Early Holocene, shortly after 11.1 cal. ka BP. Low contents of green algae in the Early Holocene sediments likely reflect deeper aquatic conditions. The most favourable climate conditions were between similar to 10.6 and 7 cal. ka BP. Vegetation became similar to the modern after similar to 7 cal. ka BP but Pinus pumila came to the Ilirney area at about 1.2 cal. ka BP. It is important to emphasize that the study area provided refugia for Betula and Alnus during MIS 2. It is also notable that our records do not reflect evidence of Younger Dryas cooling, which is inconsistent with some regional environmental records but in good accordance with some others. Y1 - 2021 U6 - https://doi.org/10.1111/bor.12521 SN - 0300-9483 SN - 1502-3885 VL - 50 IS - 3 SP - 652 EP - 670 PB - Wiley-Blackwell CY - Oxford [u.a.] ER -