TY - JOUR A1 - Thirumalaikumar, Venkatesh P. A1 - Gorka, Michal A1 - Schulz, Karina A1 - Masclaux-Daubresse, Celine A1 - Sampathkumar, Arun A1 - Skirycz, Aleksandra A1 - Vierstra, Richard D. A1 - Balazadeh, Salma T1 - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1 JF - Autophagy N2 - In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. KW - Arabidopsis thaliana KW - heat stress KW - HSFA2 KW - HSP90.1 KW - NBR1 KW - ROF1 KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2020 U6 - https://doi.org/10.1080/15548627.2020.1820778 SN - 1554-8635 VL - 17 IS - 9 SP - 2184 EP - 2199 PB - Taylor & Francis CY - Abingdon ER - TY - JOUR A1 - Friedrich, Thomas A1 - Oberkofler, Vicky A1 - Trindade, Inês A1 - Altmann, Simone A1 - Brzezinka, Krzysztof A1 - Lämke, Jörn S. A1 - Gorka, Michal A1 - Kappel, Christian A1 - Sokolowska, Ewelina A1 - Skirycz, Aleksandra A1 - Graf, Alexander A1 - Bäurle, Isabel T1 - Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis JF - Nature Communications N2 - Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory. Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation. Y1 - 2021 U6 - https://doi.org/10.1038/s41467-021-23786-6 SN - 2041-1723 VL - 12 IS - 1 PB - Nature Publishing Group UK CY - [London] ER - TY - JOUR A1 - Carpio Arias, Tannia Valeria A1 - Arias Mogrovejo, Diana Carolina A1 - Nicolalde Cifuentes, Tomás Marcelo A1 - Tapia Veloz, Estephany Carolina A1 - Zeeuw, Chris I. de A1 - Vinueza Veloz, Maria Fernanda T1 - Sleep quality does not mediate the negative effects of chronodisruption on body composition and metabolic syndrome in healthcare workers in Ecuador JF - Diabetes & metabolic syndrome : clinical research & reviews ; the official journal of DiabetesIndia N2 - Background and aims: The objective of the present work was to determine to what extent sleep quality may mediate the association between chronodisruption (CD) and metabolic syndrome (MS), and between CD and body composition (BC). Methodology: Cross-sectional study which included 300 adult health workers, 150 of whom were night shift workers and thereby exposed to CD. Diagnosis of MS was made based on Adult Treatment Panel III criteria. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Body mass index (BMI), fat mass percentage, and visceral fat percentage were measured as indicators of body composition (BC). Data were analyzed using logistic, linear regression and structural equation models. Results: The odds of health workers exposed to CD to suffer MS was 22.13 (IC95 8.68-66.07) when the model was adjusted for age, gender, physical activity and energy consumption. CD was also significantly associated with an increase in fat mass and visceral fat percentages, but not to BMI. Surprisingly, there was not enough evidence supporting the hypothesis that sleep quality contributes to the association between CD and MS or between CD and BC. Conclusions: Sleep quality does not mediate the negative effects of CD on MS nor on BC. KW - Shift work KW - Metabolic syndrome KW - Sleep quality KW - Chronodisruption KW - Body composition Y1 - 2021 U6 - https://doi.org/10.1016/j.dsx.2021.01.017 SN - 1871-4021 SN - 1878-0334 VL - 15 IS - 1 SP - 397 EP - 402 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Huß, Sebastian A1 - Judd, Rika Siedah A1 - Koper, Kaan A1 - Maeda, Hiroshi A. A1 - Nikoloski, Zoran T1 - An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana JF - The plant journal N2 - Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks. KW - atom mapping KW - genome-scale metabolic model KW - isotopic labeling KW - metabolic KW - flux analysis KW - technical advance Y1 - 2022 U6 - https://doi.org/10.1111/tpj.15903 SN - 0960-7412 SN - 1365-313X VL - 111 IS - 5 SP - 1486 EP - 1500 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Ostermann-Miyashita, Emu-Felicitas A1 - König, Hannes J. A1 - Pernat, Nadja A1 - Bellingrath-Kimura, Sonoko Dorothea A1 - Hibler, Sophia A1 - Kiffner, Christian T1 - Knowledge of returning wildlife species and willingness to participate in citizen science projects among wildlife park visitors in Germany JF - People and nature N2 - Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe. While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts. Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts. To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany. Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities. Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower. Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge. However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities. Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation. Read the free Plain Language Summary for this article on the Journal blog. KW - environmental awareness KW - human-animal relationships KW - human-wildlife conflicts KW - social-ecological system KW - wildlife conservation KW - wildlife knowledge Y1 - 2022 U6 - https://doi.org/10.1002/pan3.10379 SN - 2575-8314 VL - 4 IS - 5 SP - 1201 EP - 1215 PB - British Ecological Society; Wiley CY - London; Hoboken, NJ ER - TY - JOUR A1 - Scharnweber, Inga Kristin A1 - Chaguaceda, Fernando A1 - Eklöv, Peter T1 - Fatty acid accumulation in feeding types of a natural freshwater fish population JF - Oecologia / in cooperation with the International Association for Ecology, Intecol N2 - Fatty acids are widely used to study trophic interactions in food web assemblages. Generally, it is assumed that there is a very small modification of fatty acids from one trophic step to another, making them suitable as trophic biomarkers. However, recent literature provides evidence that many fishes possess genes encoding enzymes with a role in bioconversion, thus the capability for bioconversion might be more widespread than previously assumed. Nonetheless, empirical evidence for biosynthesis occurring in natural populations remains scarce. In this study, we investigated different feeding types of perch (Perca fluviatilis) that are specialized on specific resources with different levels of highly unsaturated fatty acids (HUFAs), and analyzed the change between HUFA proportions in perch muscle tissue compared to their resources. Perch showed matching levels to their resources for EPA, but ARA and especially DHA were accumulated. Compound-specific stable isotope analyses helped us to identify the origin of HUFA carbon. Our results suggest that perch obtain a substantial amount of DHA via bioconversion when feeding on DHA-poor benthic resources. Thus, our data indicate the capability of bioconversion of HUFAs in a natural freshwater fish population. KW - Fatty acid conversion KW - Compound-specific stable isotope analysis KW - Docosahexaenoic acid KW - Bioconversion KW - Trophic upgrading Y1 - 2021 U6 - https://doi.org/10.1007/s00442-021-04913-y SN - 0029-8549 SN - 1432-1939 VL - 196 IS - 1 SP - 53 EP - 63 PB - Springer CY - Berlin ; Heidelberg [u.a.] ER - TY - JOUR A1 - Leins, Johannes A. A1 - Banitz, Thomas A1 - Grimm, Volker A1 - Drechsler, Martin T1 - High-resolution PVA along large environmental gradients to model the combined effects of climate change and land use timing BT - lessons from the large marsh grasshopper JF - Ecological modelling : international journal on ecological modelling and systems ecology N2 - Both climate change and land use regimes affect the viability of populations, but they are often studied separately. Moreover, population viability analyses (PVAs) often ignore the effects of large environmental gradients and use temporal resolutions that are too coarse to take into account that different stages of a population's life cycle may be affected differently by climate change. Here, we present the High-resolution Large Environmental Gradient (HiLEG) model and apply it in a PVA with daily resolution based on daily climate projections for Northwest Germany. We used the large marsh grasshopper (LMG) as the target species and investigated (1) the effects of climate change on the viability and spatial distribution of the species, (2) the influence of the timing of grassland mowing on the species and (3) the interaction between the effects of climate change and grassland mowing. The stageand cohort-based model was run for the spatially differentiated environmental conditions temperature and soil moisture across the whole study region. We implemented three climate change scenarios and analyzed the population dynamics for four consecutive 20-year periods. Climate change alone would lead to an expansion of the regions suitable for the LMG, as warming accelerates development and due to reduced drought stress. However, in combination with land use, the timing of mowing was crucial, as this disturbance causes a high mortality rate in the aboveground life stages. Assuming the same date of mowing throughout the region, the impact on viability varied greatly between regions due to the different climate conditions. The regional negative effects of the mowing date can be divided into five phases: (1) In early spring, the populations were largely unaffected in all the regions; (2) between late spring and early summer, they were severely affected only in warm regions; (3) in summer, all the populations were severely affected so that they could hardly survive; (4) between late summer and early autumn, they were severely affected in cold regions; and (5) in autumn, the populations were equally affected across all regions. The duration and start of each phase differed slightly depending on the climate change scenario and simulation period, but overall, they showed the same pattern. Our model can be used to identify regions of concern and devise management recommendations. The model can be adapted to the life cycle of different target species, climate projections and disturbance regimes. We show with our adaption of the HiLEG model that high-resolution PVAs and applications on large environmental gradients can be reconciled to develop conservation strategies capable of dealing with multiple stressors. KW - Climate change KW - Land use KW - Population viability analysis KW - Stage-based model KW - High resolution KW - Environmental gradients Y1 - 2020 U6 - https://doi.org/10.1016/j.ecolmodel.2020.109355 SN - 0304-3800 VL - 440 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Potente, Giacomo A1 - Léveillé-Bourret, Étienne A1 - Yousefi, Narjes A1 - Choudhury, Rimjhim Roy A1 - Keller, Barbara A1 - Diop, Seydina Issa A1 - Duijsings, Daniël A1 - Pirovano, Walter A1 - Lenhard, Michael A1 - Szövényi, Péter A1 - Conti, Elena T1 - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism JF - Molecular biology and evolution : MBE N2 - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula? KW - genome architecture KW - supergene KW - heterostyly KW - evolutionary genomics KW - chromosome-scale genome assembly KW - primula Y1 - 2022 U6 - https://doi.org/10.1093/molbev/msac035 SN - 0737-4038 SN - 1537-1719 VL - 39 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Lucena-Perez, María A1 - Bazzicalupo, Enrico A1 - Paijmans, Johanna A1 - Kleinman-Ruiz, Daniel A1 - Dalén, Love A1 - Hofreiter, Michael A1 - Delibes, Miguel A1 - Clavero, Miguel A1 - Godoy, José A. T1 - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past. Y1 - 2022 U6 - https://doi.org/10.1016/j.quascirev.2022.107518 SN - 0277-3791 SN - 1873-457X VL - 285 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Nwosu, Ebuka Canisius A1 - Roeser, Patricia Angelika A1 - Yang, Sizhong A1 - Pinkerneil, Sylvia A1 - Ganzert, Lars A1 - Dittmann, Elke A1 - Brauer, Achim A1 - Wagner, Dirk A1 - Liebner, Susanne T1 - Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics JF - Frontiers in microbiology N2 - Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes. KW - Cyanobium KW - picocyanobacteria diversity KW - amplicon sequencing KW - lake monitoring KW - ecological succession KW - lake stratification KW - psychrotolerant Y1 - 2021 U6 - https://doi.org/10.3389/fmicb.2021.761259 SN - 1664-302X VL - 12 PB - Frontiers Media CY - Lausanne ER -