@article{GrohDiamantopoulosDuanetal.2022, author = {Groh, Jannis and Diamantopoulos, Efstathios and Duan, Xiaohong and Ewert, Frank and Heinlein, Florian and Herbst, Michael and Holbak, Maja and Kamali, Bahareh and Kersebaum, Kurt-Christian and Kuhnert, Matthias and Nendel, Claas and Priesack, Eckart and Steidl, J{\"o}rg and Sommer, Michael and P{\"u}tz, Thomas and Vanderborght, Jan and Vereecken, Harry and Wallor, Evelyn and Weber, Tobias K. D. and Wegehenkel, Martin and Weiherm{\"u}ller, Lutz and Gerke, Horst H.}, title = {Same soil, different climate: Crop model intercomparison on translocated lysimeters}, series = {Vadose zone journal}, volume = {21}, journal = {Vadose zone journal}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1539-1663}, doi = {10.1002/vzj2.20202}, pages = {25}, year = {2022}, abstract = {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.}, language = {en} } @article{DunkerBoydDurkaetal.2022, author = {Dunker, Susanne and Boyd, Matthew and Durka, Walter and Erler, Silvio and Harpole, W. Stanley and Henning, Silvia and Herzschuh, Ulrike and Hornick, Thomas and Knight, Tiffany and Lips, Stefan and M{\"a}der, Patrick and Švara, Elena Motivans and Mozarowski, Steven and Rakosy, Demetra and R{\"o}mermann, Christine and Schmitt-Jansen, Mechthild and Stoof-Leichsenring, Kathleen and Stratmann, Frank and Treudler, Regina and Virtanen, Risto and Wendt-Potthoff, Katrin and Wilhelm, Christian}, title = {The potential of multispectral imaging flow cytometry for environmental monitoring}, series = {Cytometry part A}, volume = {101}, journal = {Cytometry part A}, number = {9}, publisher = {Wiley}, address = {Hoboken}, issn = {1552-4922}, doi = {10.1002/cyto.a.24658}, pages = {782 -- 799}, year = {2022}, abstract = {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.}, language = {en} } @article{CaoChenTianetal.2022, author = {Cao, Xianyong and Chen, Jianhui and Tian, Fang and Xu, Qinghai and Herzschuh, Ulrike and Telford, Richard and Huang, Xiaozhong and Zheng, Zhuo and Shen, Caiming and Li, Wenjia}, title = {Long-distance modern analogues bias results of pollen-based precipitation reconstructions}, series = {Science bulletin}, volume = {67}, journal = {Science bulletin}, number = {11}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2095-9273}, doi = {10.1016/j.scib.2022.01.003}, pages = {1115 -- 1117}, year = {2022}, language = {en} } @article{SchulteMeucciStoofLeichsenringetal.2022, author = {Schulte, Luise and Meucci, Stefano and Stoof-Leichsenring, Kathleen R. and Heitkam, Tony and Schmidt, Nicola and von Hippel, Barbara and Andreev, Andrei A. and Diekmann, Bernhard and Biskaborn, Boris and Wagner, Bernd and Melles, Martin and Pestryakova, Lyudmila A. and Alsos, Inger G. and Clarke, Charlotte and Krutovsky, Konstantin and Herzschuh, Ulrike}, title = {Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA}, series = {Communications biology}, volume = {5}, journal = {Communications biology}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2399-3642}, doi = {10.1038/s42003-022-03455-0}, pages = {11}, year = {2022}, abstract = {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.}, language = {en} } @article{CaoTianHerzschuhetal.2022, author = {Cao, Xianyong and Tian, Fang and Herzschuh, Ulrike and Ni, Jian and Xu, Qinghai and Li, Wenjia and Zhang, Yanrong and Luo, Mingyu and Chen, Fahu}, title = {Human activities have reduced plant diversity in eastern China over the last two millennia}, series = {Global change biology}, volume = {28}, journal = {Global change biology}, number = {16}, publisher = {Wiley}, address = {Hoboken}, issn = {1354-1013}, doi = {10.1111/gcb.16274}, pages = {4962 -- 4976}, year = {2022}, abstract = {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.}, language = {en} } @article{ZielhoferSchmidtReicheetal.2022, author = {Zielhofer, Christoph and Schmidt, Johannes and Reiche, Niklas and Tautenhahn, Marie and Ballasus, Helen and Burkart, Michael and Linst{\"a}dter, Anja and Dietze, Elisabeth and Kaiser, Knut and Mehler, Natascha}, title = {The lower Havel River Region (Brandenburg, Germany)}, series = {Water}, volume = {14}, journal = {Water}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2073-4441}, doi = {10.3390/w14030480}, pages = {23}, year = {2022}, abstract = {Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30\% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas.}, language = {en} } @article{KamaliJahanbakhshiDogaruetal.2022, author = {Kamali, Bahareh and Jahanbakhshi, Farshid and Dogaru, Diana and Dietrich, J{\"o}rg and Nendel, Claas and AghaKouchak, Amir}, title = {Probabilistic modeling of crop-yield loss risk under drought: a spatial showcase for sub-Saharan Africa}, series = {Environmental research letters}, volume = {17}, journal = {Environmental research letters}, number = {2}, publisher = {IOP Publishing}, address = {Bristol}, issn = {1748-9326}, doi = {10.1088/1748-9326/ac4ec1}, pages = {15}, year = {2022}, abstract = {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.}, language = {en} } @article{HoangGryzikHoppeetal.2022, author = {Hoang, Yen and Gryzik, Stefanie and Hoppe, Ines and Rybak, Alexander and Sch{\"a}dlich, Martin and Kadner, Isabelle and Walther, Dirk and Vera, Julio and Radbruch, Andreas and Groth, Detlef and Baumgart, Sabine and Baumgrass, Ria}, title = {PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments}, series = {Frontiers in immunology}, volume = {13}, journal = {Frontiers in immunology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-3224}, doi = {10.3389/fimmu.2022.849329}, pages = {9}, year = {2022}, abstract = {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.}, language = {en} } @article{EsmaeilishirazifardUsherTrimetal.2022, author = {Esmaeilishirazifard, Elham and Usher, Louise and Trim, Carol and Denise, Hubert and Sangal, Vartul and Tyson, Gregory H. and Barlow, Axel and Redway, Keith F. and Taylor, John D. and Kremyda-Vlachou, Myrto and Davies, Sam and Loftus, Teresa D. and Lock, Mikaella M. G. and Wright, Kstir and Dalby, Andrew and Snyder, Lori A. S. and Wuster, Wolfgang and Trim, Steve and Moschos, Sterghios A.}, title = {Bacterial adaptation to venom in snakes and arachnida}, series = {Microbiology spectrum}, volume = {10}, journal = {Microbiology spectrum}, number = {3}, publisher = {American Society for Microbiology}, address = {Birmingham, Ala.}, issn = {2165-0497}, doi = {10.1128/spectrum.02408-21}, pages = {16}, year = {2022}, abstract = {Notwithstanding their 3 to 5\% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75\% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5\% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75\% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections.}, language = {en} } @article{VencesKoehlerCrottinietal.2022, author = {Vences, Miguel and K{\"o}hler, J{\"o}rn and Crottini, Angelica and Hofreiter, Michael and Hutter, Carl R. and du Preez, Louis and Preick, Michaela and Rakotoarison, Andolalao and Rancilhac, Lo{\"i}s and Raselimanana, Achille P. and Rosa, Gon{\c{c}}alo M. and Scherz, Mark D. and Glaw, Frank}, title = {An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar}, series = {Vertebrate zoology}, volume = {72}, journal = {Vertebrate zoology}, publisher = {Senckenberg Gesellschaft f{\"u}r Naturforschung}, address = {Frankfurt am Main}, issn = {1864-5755}, doi = {10.3897/vz.72.e78830}, pages = {271 -- 309}, year = {2022}, abstract = {The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4\% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy.}, language = {en} } @article{SporbertJakubkaBucheretal.2022, author = {Sporbert, Maria and Jakubka, Desiree and Bucher, Solveig Franziska and Hensen, Isabell and Freiberg, Martin and Heubach, Katja and K{\"o}nig, Andreas and Nordt, Birgit and Plos, Carolin and Blinova, Ilona and Bonn, Aletta and Knickmann, Barbara and Koubek, Tom{\´a}š and Linst{\"a}dter, Anja and Maškov{\´a}, Tereza and Primack, Richard B. and Rosche, Christoph and Shah, Manzoor A. and Stevens, Albert-Dieter and Tielb{\"o}rger, Katja and Tr{\"a}ger, Sabrina and Wirth, Christian and R{\"o}mermann, Christine}, title = {Functional traits influence patterns in vegetative and reproductive plant phenology - a multi-botanical garden study}, series = {New phytologist}, volume = {235}, journal = {New phytologist}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.18345}, pages = {2199 -- 2210}, year = {2022}, abstract = {Phenology has emerged as key indicator of the biological impacts of climate change, yet the role of functional traits constraining variation in herbaceous species' phenology has received little attention. Botanical gardens are ideal places in which to investigate large numbers of species growing under common climate conditions. We ask whether interspecific variation in plant phenology is influenced by differences in functional traits. We recorded onset, end, duration and intensity of initial growth, leafing out, leaf senescence, flowering and fruiting for 212 species across five botanical gardens in Germany. We measured functional traits, including plant height, absolute and specific leaf area, leaf dry matter content, leaf carbon and nitrogen content and seed mass and accounted for species' relatedness. Closely related species showed greater similarities in timing of phenological events than expected by chance, but species' traits had a high degree of explanatory power, pointing to paramount importance of species' life-history strategies. Taller plants showed later timing of initial growth, and flowered, fruited and underwent leaf senescence later. Large-leaved species had shorter flowering and fruiting durations. Taller, large-leaved species differ in their phenology and are more competitive than smaller, small-leaved species. We assume climate warming will change plant communities' competitive hierarchies with consequences for biodiversity.}, language = {en} } @article{DerežaninBlažytėDobryninetal.2022, author = {Derežanin, Lorena and Blažytė, Asta and Dobrynin, Pavel and Duch{\^e}ne, David A. and Grau, Jos{\´e} Horacio and Jeon, Sungwon and Kliver, Sergei and Koepfli, Klaus-Peter and Meneghini, Dorina and Preick, Michaela and Tomarovsky, Andrey and Totikov, Azamat and Fickel, J{\"o}rns and F{\"o}rster, Daniel W.}, title = {Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae}, series = {Molecular ecology}, volume = {31}, journal = {Molecular ecology}, number = {10}, publisher = {Wiley}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.16443}, pages = {2898 -- 2919}, year = {2022}, abstract = {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.}, language = {en} } @article{GarbulowskiSmolinskaCabuketal.2022, author = {Garbulowski, Mateusz and Smolinska, Karolina and {\c{C}}abuk, Uğur and Yones, Sara A. and Celli, Ludovica and Yaz, Esma Nur and Barrenas, Fredrik and Diamanti, Klev and Wadelius, Claes and Komorowski, Jan}, title = {Machine learning-based analysis of glioma grades reveals co-enrichment}, series = {Cancers}, volume = {14}, journal = {Cancers}, number = {4}, publisher = {MDPI}, address = {Basel}, issn = {2072-6694}, doi = {10.3390/cancers14041014}, pages = {19}, year = {2022}, abstract = {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.}, language = {en} } @article{PotenteLeveilleBourretYousefietal.2022, author = {Potente, Giacomo and L{\´e}veill{\´e}-Bourret, {\´E}tienne and Yousefi, Narjes and Choudhury, Rimjhim Roy and Keller, Barbara and Diop, Seydina Issa and Duijsings, Dani{\"e}l and Pirovano, Walter and Lenhard, Michael and Sz{\"o}v{\´e}nyi, P{\´e}ter and Conti, Elena}, title = {Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism}, series = {Molecular biology and evolution : MBE}, volume = {39}, journal = {Molecular biology and evolution : MBE}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msac035}, pages = {16}, year = {2022}, abstract = {Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?}, language = {en} } @misc{HuuPlaschilHimmelbachetal.2022, author = {Huu, Cuong Nguyen and Plaschil, Sylvia and Himmelbach, Axel and Kappel, Christian and Lenhard, Michael}, title = {Female self-incompatibility type in heterostylous Primula is determined by the brassinosteroid-inactivating cytochrome P450 CYP734A50}, series = {Current biology}, volume = {32}, journal = {Current biology}, number = {3}, publisher = {Cell Press}, address = {Cambridge, Mass.}, issn = {0960-9822}, doi = {10.1016/j.cub.2021.11.046}, pages = {671 -- 676, E1-E5}, year = {2022}, abstract = {Most flowering plants are hermaphrodites, with flowers having both male and female reproductive organs. One widespread adaptation to limit self-fertilization is self-incompatibility (SI), where self-pollen fails to fertilize ovules.(1,2) In homomorphic SI, many morphologically indistinguishable mating types are found, although in heteromorphic SI, the two or three mating types are associated with different floral morphologies.(3-6) In heterostylous Primula, a hemizygous supergene determines a short-styled S-morph and a long-styled L-morph, corresponding to two different mating types, and full seed set only results from inter morph crosses.(7-9) Style length is controlled by the brassinosteroid (BR)-inactivating cytochrome P450 CYP734A50,(10) yet it remains unclear what defines the male and female incompatibility types. Here, we show that CYP734A50 also determines the female incompatibility type. Inactivating CYP734A50 converts short S-morph styles into long styles with the same incompatibility behavior as L-morph styles, and this effect can be mimicked by exogenous BR treatment. In vitro responses of S-and L-morph pollen grains and pollen tubes to increasing BR levels could only partly explain their different in vivo behavior, suggesting both direct and indirect effects of the different BR levels in S-versus L-morph stigmas and styles in controlling pollen performance. This BR-mediated SI provides a novel mechanism for preventing self-fertilization. The joint control of morphology and SI by CYP734A50 has important implications for the evolutionary buildup of the heterostylous syndrome and provides a straightforward explanation for why essentially all of the derived self-compatible homostylous Primula species are long homostyles.(11)}, subject = {heteromorphic self-incompatibility}, language = {en} } @article{OberkoflerBaeurle2022, author = {Oberkofler, Vicky and B{\"a}urle, Isabel}, title = {Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {189}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {Oxford University Press}, address = {Oxford}, issn = {0032-0889}, doi = {10.1093/plphys/kiac113}, pages = {703 -- 714}, year = {2022}, abstract = {A temperature-inducible epigenome editing system to knock down histone methylation can be used to study the role of histone H3K4 methylation during heat stress memory in Arabidopsis.
Histone modifications play a crucial role in the integration of environmental signals to mediate gene expression outcomes. However, genetic and pharmacological interference often causes pleiotropic effects, creating the urgent need for methods that allow locus-specific manipulation of histone modifications, preferably in an inducible manner. Here, we report an inducible system for epigenome editing in Arabidopsis (Arabidopsis thaliana) using a heat-inducible dCas9 to target a JUMONJI (JMJ) histone H3 lysine 4 (H3K4) demethylase domain to a locus of interest. As a model locus, we target the ASCORBATE PEROXIDASE2 (APX2) gene that shows transcriptional memory after heat stress (HS), correlating with H3K4 hyper-methylation. We show that dCas9-JMJ is targeted in a HS-dependent manner to APX2 and that the HS-induced overaccumulation of H3K4 trimethylation (H3K4me3) decreases when dCas9-JMJ binds to the locus. This results in reduced HS-mediated transcriptional memory at the APX2 locus. Targeting an enzymatically inactive JMJ protein in an analogous manner affected transcriptional memory less than the active JMJ protein; however, we still observed a decrease in H3K4 methylation levels. Thus, the inducible targeting of dCas9-JMJ to APX2 was effective in reducing H3K4 methylation levels. As the effect was not fully dependent on enzyme activity of the eraser domain, the dCas9-JMJ fusion protein may act in part independently of its demethylase activity. This underlines the need for caution in the design and interpretation of epigenome editing studies. We expect our versatile inducible epigenome editing system to be especially useful for studying temporal dynamics of chromatin modifications.}, language = {en} } @article{MitzscherlingMacLeanLipusetal.2022, author = {Mitzscherling, Julia and MacLean, Joana and Lipus, Daniel and Bartholom{\"a}us, Alexander and Mangelsdorf, Kai and Lipski, Andr{\´e} and Roddatis, Vladimir and Liebner, Susanne and Wagner, Dirk}, title = {Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste}, series = {International journal of systematic and evolutionary microbiology}, volume = {72}, journal = {International journal of systematic and evolutionary microbiology}, number = {4}, publisher = {Microbiology Society}, address = {London}, issn = {1466-5026}, doi = {10.1099/ijsem.0.005319}, pages = {11}, year = {2022}, abstract = {Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1\% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6\%) and Nocardioides dubius KSL-104(T) (98.3\%). The genomic DNA G+C content of strain NGK65(T) was 68.2\%. Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9\% as well as digital DNA-DNA hybridization values between 22.5 and 19.7\%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).}, language = {en} } @article{HagemannConejeroStillfriedetal.2022, author = {Hagemann, Justus and Conejero, Carles and Stillfried, Milena and Mentaberre, Gregorio and Castillo-Contreras, Raquel and Fickel, J{\"o}rns and Lopez-Olvera, Jorge Ram{\´o}n}, title = {Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {833}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.155126}, pages = {10}, year = {2022}, abstract = {Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.}, language = {en} } @article{HanniganNendelKrull2022, author = {Hannigan, Sara and Nendel, Claas and Krull, Marcos}, title = {Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius}, series = {Journal of pest science}, journal = {Journal of pest science}, publisher = {Springer}, address = {Heidelberg}, issn = {1612-4758}, doi = {10.1007/s10340-022-01510-7}, pages = {389 -- 402}, year = {2022}, abstract = {Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread.}, language = {en} } @article{LiAbdulkadirSchattenbergetal.2022, author = {Li, Shuang and Abdulkadir, Nafi'u and Schattenberg, Florian and da Rocha, Ulisses Nunes and Grimm, Volker and M{\"u}ller, Susann and Liu, Zishu}, title = {Stabilizing microbial communities by looped mass transfer}, series = {Proceedings of the National Academy of Sciences of the United States of America : PNAS}, volume = {119}, journal = {Proceedings of the National Academy of Sciences of the United States of America : PNAS}, number = {17}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {1091-6490}, doi = {10.1073/pnas.2117814119}, pages = {11}, year = {2022}, abstract = {Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates mu'. Subsets of cells that did not show net growth mu'SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.}, language = {en} }