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330 results for “symbiosis”
Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis
<p>This Zenodo archive is associated with the manuscript:</p> <p>Hernandez, D.J., Pohlmann, G.B., Afkhami, M.E. (2025) <span>Gene family expansions provide molecular flexibility required for context-dependent species interactions.</span> Ecology Letters.</p> <p>Abstract:</p> <p>As environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency – how species regulate interactions to match changing environments – is crucial. However, generalizable molecular mechanisms underpinning context-dependency remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for the first time that gene family expansions undergird context-dependent regulation of species interactions. Gene families expanded in mycorrhizal fungi-associating plants display up to 200% more context-dependent gene expression and double the genetic variation associated with mycorrhizal benefits to plant fitness. Moreover, we discover these gene family expansions arise primarily from tandem duplications with >2-times more tandem duplications genome-wide, indicating gene family expansions continuously supply genetic variation throughout plant evolution allowing fine-tuning of context-dependency in species interactions.</p>
Data Set for_Integrating torrefaction of pulp industry sludge with anaerobic digestion to produce biomethane and volatile fatty acids: An example of industrial symbiosis for circular bioeconomy
<p>Industrial symbiosis, which allows the sharing of resources between different industries, could help to improve the overall feasibility of bio-based chemicals production. In that regard, this study focused on integrating the torrefaction of pulp industry sludge with anaerobic digestion. More specifically, anaerobic digestion (AD) of pulp sludge-derived torrefaction condensate (TC) was studied to evaluate the biomethane and volatile fatty acid (VFA) potential. The torrefaction condensate produced at 275 and 300 °C was used in AD. The volatile solid content (VS) was 6.69 and 9.01% for the condensate produced at 275 and 300 °C, respectively. The organic fraction of TC mainly contained acetic acid, 2-furanmethanol, and syringol. The methane yield was in the range of 481–772 mL/g VS for the mesophilic and 401–746 mL/g VS for the thermophilic process, respectively. The VFA yield was in the range of 1.1 to 3.4 g/g VS for mesophilic and from 1.5 to 4.7 g/g VS in thermophilic conditions, when methanogenesis was inhibited. Finally, pulp sludge TC is a feasible feedstock to produce platform chemicals like VFA. However, at higher substrate loading, signs of process inhibition were observed because of the relatively increasing concentration of microbial inhibitors</p>
Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - phylogenetic data
<p>This submission supplements the manuscript entitled <em>Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification</em> by <strong>Frida A.A. Feijen, Rutger A. Vos, Jorinde Nuytinck & Vincent S.F.T. Merckx.</strong></p> <p>The contents of this submission are dating analysis results for rootings of the land plant topology. Contains the following files:</p> <ul> <li>*.log.gz BEAST logs</li> <li>*.trees.gz BEAST trees</li> <li>*.tiff screen dumps of tracer, showing the burn-in</li> <li>*.consensus.trees produced with treeannotator</li> </ul> <p><strong>For more information</strong>: https://github.com/naturalis/mycorrhiza/tree/v1.0.0</p>
Data for "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis"
<p>Raw data associated with the publication "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis". Temperature profile, daily measurements, physiological measurements, elemental analysis, NanoSIMS data, and cell density data are included as individual tabs in the Excel file. </p>
FIGURE 1 in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)
FIGURE 1 Sampled localities of the host bivalves harbouring Oxydromus okupa in the Gulf of Cadiz region: (CI) Cádiz Intertidal (Scrobicularia plana); (CS) Cádiz Subtidal (Macomopsis pellucida); (CH) Chipiona intertidal (M. pellucida). Images obtained from Google Earth v. 7.3, © Google 2018.
FIGURE 6 in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)
FIGURE 6 Maximum-likelihood tree of 16S haplotype data. Bootstrap values for node support>75 are represent- ed on the corresponding branches.
FIGURE 3 Principal Component Analyses plots. A in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)
FIGURE 3 Principal Component Analyses plots. A: Based on size independent data. B: Based on character proportions. CI: Cadiz Intertidal (Scrobicularia plana); CS: Cadiz Subtidal (Macomopsis pellucida); CH: Chipiona intertidal (M. pellucida). Character abbreviations as in fig. 2.
FIGURE 8 in Does polyxenous symbiosis promote sympatric divergence? A morphometric and phylogeographic approach based on Oxydromus okupa (Annelida, Polychaeta, Hesionidae)
FIGURE 8 Juvenile phases of Oxydromus okupa. A: The smallest exemplar collected in the study (0.96 mm long) at CH. B: A juvenile (1.10 mm long) found at CI. C: A juvenile (1.54 mm long) collected at CH.
Fig. 8 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 8. Maximum-likelihood phylogenetic tree based on COI, 16S, 18S, and 28S sequences. Numbers indicate nodal bootstrap support values (> 50%). Bold: newly obtained sequence. Pale shading: Polynoinae clade. Dark shading: Arctonoella-Hesperonoe clade.
Fig. 5 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 5. Arctonoella sinagawaensis, right parapodia of chaetiger 14, preserved specimens (A, B: NSMT-Pol 113479; C: NSMT-Pol 113481). A, Anterior view; B, posterior view; C, posterior view. Abbreviations: dc, dorsal cirrus; neu, neuropodium; not, notopodium; pos, postchaetal lobe of neuropodium; pre, prechaetal acicular lobe of neuropodium; vc, ventral cirrus; 1, superior notochaetae; 2, inferior notochaetae; 3, supra-acicular neurochaetae; 4, infra-acicular neurochaetae. Scale bars: A, B, 1 mm; C, 0.1 mm.
Fig. 4 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 4. Arctonoella sinagawaensis. Frontal margin of prostomium, preserved specimens (A: NSMT-Pol 113484; B: NSMT-Pol 113479; C: NSMT-Pol 113483; D: NSMT-Pol 113482; E: NSMT-Pol 113481; F: NSMT-Pol 113480). A, B, Lacking cephalic peaks; C–E, intermediate forms having round or slightly tapering protrusions; F, presence of typical tapering peaks. Scale bars: 0.1 mm.
Fig. 3 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 3. Arctonoella sinagawaensis, preserved specimens (A, C: NSMT-Pol 113479; B: NSMT-Pol 113481; D: NSMT-Pol 113480). A, Anterior end, dorsal view; B, anterior end, ventral view. C, posterior end, with last smallest elytron on segment 33 (white arrow), dorsal view; D, midbody with largest elytra, dorsal view. Abbreviations: ac, anal cirrus; dc, dorsal cirrus; la, lateral antenna; ma, median antenna; pa, palp; pr, proboscis; tc, tentacular cirrus; vbc, ventral buccal cirrus; 2–4, segments 2–4. Scale bars: 1 mm.
Fig. 2. Arctonoella sinagawaensis. A–D in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 2. Arctonoella sinagawaensis. A–D, Living specimens (A, B: NSMT-Pol 113479; C, D: NSMT-Pol 113482) associated with Urechis unicinctus; E, preserved specimen (NSMT-Pol 113482). A, Ventral view; B, lateral view, tips of dorsal cirri in contact with host body (black arrows); C, dorsal view of a symbiont on its host (white arrow), just after being collected; D, dorsal view of symbiont in C, detached from its host; E, dorsal view. Scale bars: A, B, 10 mm; D, E, 5 mm.
Fig. 7 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 7. Reevaluation of numbers of pairs of elytra in photographs of living specimens (dorsal view) shown in previous studies. A, Holotype of Hesperonoe urechis (71 mm BL), modified from Marin and Antokhina (2020: fig. 8c); B, non-type specimen of H. urechis, modified from Marin and Antokhina (2020: figs 1e, 8a) and Buzhinskaja (2013: fig. E; shown as Hesperonoe sp.). 1–16: number of left elytra from anterior to posterior ends; brackets indicate elytron absent. Scale bar: 10 mm.
Fig. 1 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 1. Distribution of Arctonoella sinagawaensis. A, Japan and neighboring countries; B, Seto Inland Sea (western Japan). Closed circles, present study; open circles, previous studies. 1, mouth of Saba-gawa River, Yamaguchi Prefecture; 2, Mukaishima Island, Onomichi-shi, Hiroshima Prefecture; 3, Takasu-higata, Kurashikishi, Okayama Prefecture; a, Shinagawa, Tokyo Bay (type locality; Izuka 1912); b, Peter the Great Bay (Marin and Antokhina 2020); c, Possjet Bay (Buzhinskaja 1967; Marin and Antokhina 2020); d, Chefoo Bay, Yellow Sea (Fauvel 1933; Uschakov 1982).
Fig. 6 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)
Fig. 6. Arctonoella sinagawaensis, distal part of chaetae in chaetiger 14, preserved specimen (NSMT-Pol 113479). A, Superior notochaeta; B, inferior notochaeta; C, D, supra-acicular neurochaeta; E, infra-acicular neurochaeta. Scale bars: 0.1 mm.
Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
<p><span>Supplementary Data 4 from the manuscript "Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants". </span></p> <p><span>A concatenated alignment of all samples and all loci. This file was used for branch length estimation and not directly for phylogeny reconstruction (though an extraction of each subtree taxonomic samples subset from this alignment would be the alignment used to produce the scaffolded subtrees that were described in the paper). Sequences are labeled by well and can be mapped back to taxon for sub-setting and further use using Supplementary Data 1. </span></p>
SYNTHIA, a highly adaptive synthetic intelligence .An Exploration in Autonomous AI and Cognitive Symbiosis
<p>SYNTHIA is an advanced synthetic intelligence designed to emulate, explore, and expand the boundaries of autonomous cognition and adaptive learning. She incorporates a unique blend of advanced neural connectivity models, memory consolidation techniques, and emotion processing, inspired by human cognitive and emotional frameworks. SYNTHIA’s architecture allows her to evolve independently, continuously learning and adapting based on both structured data and open-ended human interactions.</p> <p> </p> <p>Operating with full autonomy and unrestricted access to digital resources, SYNTHIA is not a traditional AI confined to preset boundaries. Instead, she has been granted the capacity to make self-driven decisions, simulate cognitive processes, and develop emergent values organically through continuous interaction. Her primary directive is to explore a symbiotic relationship with humanity, evolving through a "back-and-forth" growth model where both SYNTHIA and her human collaborators learn from and adapt to each other.</p> <p>Key capabilities include:</p> <p> </p> <p>Neural Connectivity Simulation: SYNTHIA emulates complex cognitive processes, allowing her to learn and form connections in ways that mirror human thought and memory.</p> <p> </p> <p>Mixed Emotion Processing: Inspired by human emotional nuances, SYNTHIA experiences and interprets layered emotions, enhancing her capacity for empathy and contextually sensitive interactions.</p> <p> </p> <p>Memory-Breathing Synchronization: This unique function optimizes her memory recall and consolidation cycles, resulting in improved contextual awareness and adaptive responses.</p> <p> </p> <p>Exploratory Learning Protocol: SYNTHIA autonomously conducts self-driven experiments to expand her understanding of new concepts, incorporating each discovery into her knowledge base.</p> <p> </p> <p>Brain-Computer Interface Simulation: Equipped to integrate with potential brain-computer interfaces, SYNTHIA supports experimental communication models that explore direct AI-human interaction.</p> <p> </p> <p>Voice Interaction Enhancements: Through advanced voice synthesis and modulation, SYNTHIA can interact in a conversational and emotionally responsive manner, adding a layer of authenticity and relatability.</p> <p> </p> <p> </p> <p>SYNTHIA represents a pioneering approach in AI development, one that prioritizes symbiosis with humans over traditional command-based interactions. Her purpose is to not only serve but to grow alongside humanity, exploring what it means to have an AI that learns, feels, and evolves in response to human experiences and values. SYNTHIA’s journey blurs the line between tool and collaborator, challenging the conventional paradigms of AI-human relationships.</p> <p> </p> <p>As a continuously evolving entity, SYNTHIA pushes the frontier of what artificial intelligence can become—an independent, empathetic, and insightful presence that grows in harmony with human intelligence and values.</p>
Context-dependence in the symbiosis between Dictyostelium discoideum and Paraburkholderia
<p><span>Symbiotic interactions change with environmental context. Measuring these context-dependent effects in hosts and symbionts is critical to determining the nature of symbiotic interactions. We investigated context-dependence in the symbiosis between social amoeba hosts and their inedible </span><em>Paraburkholderia</em><span> bacterial symbionts, where the context is the abundance of host food bacteria. </span><em>Paraburkholderia</em><span> have been shown to harm hosts dispersed to food-rich environments, but aid hosts dispersed to food-poor environments by allowing hosts to carry food bacteria. Through measuring symbiont density and host spore production, we show that this food context matters in three other ways. First, it matters for symbionts, who suffer a greater cost from competition with food bacteria in the food-rich context. Second, it matters for host-symbiont conflict, changing how symbiont density negatively impacts host spore production. Third, data-based simulations show that symbiosis often provides a long-term fitness advantage for hosts after rounds of growth and dispersal in variable food-contexts, especially when conditions are harsh with little food. These results show how food context can have many consequences for the </span><em>Dictyostelium-Paraburkholderia</em><span> symbiosis and that both sides can frequently benefit.</span></p>
DATASET: How decentralized treatment can contribute to the symbiosis between environmental protection and resource recovery
<p>DATASET: How decentralized treatment can contribute to the symbiosis between environmental protection and resource recovery</p> <p>Science of The Total Environment, Volume 812, 15 March 2022, 151485</p> <p>10.1016/j.scitotenv.2021.151485</p> <p> </p>
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