@article{HeringHauptfleischJagoetal.2022, author = {Hering, Robert and Hauptfleisch, Morgan and Jago, Mark and Smith, Taylor and Kramer-Schadt, Stephanie and Stiegler, Jonas and Blaum, Niels}, title = {Don't stop me now: Managed fence gaps could allow migratory ungulates to track dynamic resources and reduce fence related energy loss}, series = {Frontiers in Ecology and Evolution}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {2296-701X}, doi = {10.3389/fevo.2022.907079}, pages = {1 -- 18}, year = {2022}, abstract = {In semi-arid environments characterized by erratic rainfall and scattered primary production, migratory movements are a key survival strategy of large herbivores to track resources over vast areas. Veterinary Cordon Fences (VCFs), intended to reduce wildlife-livestock disease transmission, fragment large parts of southern Africa and have limited the movements of large wild mammals for over 60 years. Consequently, wildlife-fence interactions are frequent and often result in perforations of the fence, mainly caused by elephants. Yet, we lack knowledge about at which times fences act as barriers, how fences directly alter the energy expenditure of native herbivores, and what the consequences of impermeability are. We studied 2-year ungulate movements in three common antelopes (springbok, kudu, eland) across a perforated part of Namibia's VCF separating a wildlife reserve and Etosha National Park using GPS telemetry, accelerometer measurements, and satellite imagery. We identified 2905 fence interaction events which we used to evaluate critical times of encounters and direct fence effects on energy expenditure. Using vegetation type-specific greenness dynamics, we quantified what animals gained in terms of high quality food resources from crossing the VCF. Our results show that the perforation of the VCF sustains herbivore-vegetation interactions in the savanna with its scattered resources. Fence permeability led to peaks in crossing numbers during the first flush of woody plants before the rain started. Kudu and eland often showed increased energy expenditure when crossing the fence. Energy expenditure was lowered during the frequent interactions of ungulates standing at the fence. We found no alteration of energy expenditure when springbok immediately found and crossed fence breaches. Our results indicate that constantly open gaps did not affect energy expenditure, while gaps with obstacles increased motion. Closing gaps may have confused ungulates and modified their intended movements. While browsing, sedentary kudu's use of space was less affected by the VCF; migratory, mixed-feeding springbok, and eland benefited from gaps by gaining forage quality and quantity after crossing. This highlights the importance of access to vast areas to allow ungulates to track vital vegetation patches.}, language = {en} } @article{HeringHauptfleischKramerSchadtetal.2022, author = {Hering, Robert and Hauptfleisch, Morgan and Kramer-Schadt, Stephanie and Stiegler, Jonas and Blaum, Niels}, title = {Effects of fences and fence gaps on the movement behavior of three southern African antelope species}, series = {Frontiers in Conservation Science}, volume = {3}, journal = {Frontiers in Conservation Science}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {2673-611X}, doi = {10.3389/fcosc.2022.959423}, pages = {1 -- 19}, year = {2022}, abstract = {Globally, migratory ungulates are affected by fences. While field observational studies reveal the amount of animal-fence interactions across taxa, GPS tracking-based studies uncover fence effects on movement patterns and habitat selection. However, studies on the direct effects of fences and fence gaps on movement behavior, especially based on high-frequency tracking data, are scarce. We used GPS tracking on three common African antelopes (Tragelaphus strepsiceros, Antidorcas marsupialis, and T. oryx) with movement strategies ranging from range residency to nomadism in a semi-arid, Namibian savanna traversed by wildlife-proof fences that elephants have regularly breached. We classified major forms of ungulate-fence interaction types on a seasonal and a daily scale. Furthermore, we recorded the distances and times spent at fences regarding the total individual space use. Based on this, we analyzed the direct effects of fences and fence gaps on the animals' movement behavior for the previously defined types of animal-fence interactions. Antelope-fence interactions peaked during the early hours of the day and during seasonal transitions when the limiting resource changed between water and forage. Major types of ungulate-fence interactions were quick, trace-like, or marked by halts. We found that the amount of time spent at fences was highest for nomadic eland. Migratory springbok adjusted their space use concerning fence gap positions. If the small home ranges of sedentary kudu included a fence, they frequently interacted with this fence. For springbok and eland, distance traveled along a fence declined with increasing utilization of a fence gap. All species reduced their speed in the proximity of a fence but often increased their speed when encountering the fence. Crossing a fence led to increased speeds for all species. We demonstrate that fence effects mainly occur during crucial foraging times (seasonal scale) and during times of directed movements (daily scale). Importantly, we provide evidence that fences directly alter antelope movement behaviors with negative implications for energy budgets and that persistent fence gaps can reduce the intensity of such alterations. Our findings help to guide future animal-fence studies and provide insights for wildlife fencing and fence gap planning.}, language = {en} } @article{IrobBlaumBaldaufetal.2022, author = {Irob, Katja and Blaum, Niels and Baldauf, Selina and Kerger, Leon and Strohbach, Ben and Kanduvarisa, Angelina and Lohmann, Dirk and Tietjen, Britta}, title = {Browsing herbivores improve the state and functioning of savannas}, series = {Ecology and evolution}, volume = {12}, journal = {Ecology and evolution}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.8715}, pages = {19}, year = {2022}, abstract = {Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.}, 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{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{PeterWenderingSchlickeiseretal.2022, author = {Peter, Lena and Wendering, D{\´e}sir{\´e}e Jacqueline and Schlickeiser, Stephan and Hoffmann, Henrike and Noster, Rebecca and Wagner, Dimitrios Laurin and Zarrinrad, Ghazaleh and M{\"u}nch, Sandra and Picht, Samira and Schulenberg, Sarah and Moradian, Hanieh and Mashreghi, Mir-Farzin and Klein, Oliver and Gossen, Manfred and Roch, Toralf and Babel, Nina and Reinke, Petra and Volk, Hans-Dieter and Amini, Leila and Schmueck-Henneresse, Michael}, title = {Tacrolimus-resistant SARS-CoV-2-specific T cell products to prevent and treat severe COVID-19 in immunosuppressed patients}, series = {Molecular therapy methods and clinical development}, volume = {25}, journal = {Molecular therapy methods and clinical development}, publisher = {Cell Press}, address = {Cambridge}, issn = {2329-0501}, doi = {10.1016/j.omtm.2022.02.012}, pages = {52 -- 73}, year = {2022}, abstract = {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.}, language = {en} } @article{WelkeSperberBergmannetal.2022, author = {Welke, Robert-William and Sperber, Hannah Sabeth and Bergmann, Ronny and Koikkarah, Amit and Menke, Laura and Sieben, Christian and Kr{\"u}ger, Detlev H. and Chiantia, Salvatore and Herrmann, Andreas and Schwarzer, Roland}, title = {Characterization of hantavirus N protein intracellular dynamics and localization}, series = {Viruses}, volume = {14}, journal = {Viruses}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {1999-4915}, doi = {10.3390/v14030457}, pages = {14}, year = {2022}, abstract = {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.}, language = {en} }