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462 results for “Mutualisms”
Integration of protein and coding sequences enables mutual augmentation of the language model
<p><strong>The file structure is as follows:</strong></p> <p>Project Root<br>├── TE_MRL<br>│ ├── MRL_dataset.zip<br>│ └── TE_dataset.zip<br>│<br>├── finetuned_model<br>│ ├── FoldP<br>│ ├── LocP<br>│ ├── SSP<br>│ └── SolP<br>│<br>├── tax_tsne<br>│ └── emb_3models.zip<br>│<br>└── training_data<br> ├── FoldP.csv<br> ├── LocP.csv<br> ├── SolP.csv<br> ├── SSP.pkl<br> └── pretrain_source_GCF.txt</p>
Bromus tectorum alters mycorrhizal fungal communities and disrupts mutualism
<p class="MsoNormal">Exotic plant invasions alter native plant productivity and ecosystem function. Mechanisms of plant invasions can include altered disturbance regimes or altered plant-soil feedbacks. Some important hypotheses regarding the invasion of cheatgrass in North America include pathogen spillover and mutualism disruption. Since an important mutualistic interaction in ecosystems is that of mycorrhizal fungi, here we test the mutualism disruption hypothesis by closely examining mycorrhizal allocation and community composition. We conducted a greenhouse study where we grew a native perennial grass in association with invaded and uninvaded soils. We found altered mycorrhizal communities and mycorrhizal allocation patterns associated with cheatgrass-invaded soils supporting the mutualism disruption hypothesis.</p>
Demo datasets for the protocol to identify shared transcriptional risks between diseases and compounds predicted to result in mutual benefit
<p>We present a computational protocol (https://github.com/ghbore/protocol-cancer-cvd-similarity), implemented as a Snakemake workflow, that was used in previous works (Gao et al., 2022; Baylis et al., 2023). This protocol allows researchers to identify shared transcriptional processes that drive disease and to screen existing compounds for mutual benefit. The protocol also includes a description of the pharmacovigilance study design used to validate the effect of novel compounds using electronic health records, where applicable. This repository bundles the datasets used in previous works as an example to run through the Snakemake workflow. These datasets include the TCGA cancer dataset, the STARNET and BiKE CVD datasets, and other dependent resources.</p>
More or less? The effect of symbiont density in protective mutualisms
<p><span><span>Symbionts can provide hosts with effective protection from natural enemies, but it can sometimes come at a cost. </span>It is unclear to what extent the density of symbionts modulates the cost and benefits of conferred protection. Here we use a meta-analysis of 103 effect sizes from a broad taxonomic range of protective symbioses, to show that the degree of both protection and cost afforded to hosts is a positive function of symbiont density. We found that the effects of symbiont density on protection and cost are robust across ecological contexts. Density-function relationships did not vary with host type, symbiont localization or transmission mode, nor the method of density manipulation. Together, our results suggest symbiont density can be a key variable determining the costs and benefits of a protective interaction. </span></p>
Data from: Mridha S and Kümmerli R (2022) Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa
<p><span>A common way for bacteria to cooperate is via the secretion of beneficial public goods (proteases, siderophores, biosurfactants) that can be shared among individuals in a group. Bacteria often simultaneously deploy multiple public goods with complementary functions. This raises the question whether natural selection could favour division of labour where subpopulations or species specialise in the production of a single public good, whilst sharing the complementary goods at the group level. Here we use an experimental system, where we mix engineered specialists of the bacterium <em>Pseudomonas aeruginosa</em> that can each only produce one of the two siderophores, pyochelin or pyoverdine, and explore the conditions under which specialization can lead to division of labour. When growing pyochelin and pyoverdine specialists at different mixing ratios under different levels of iron limitation, we found that specialists could only successfully complement each other in environments with moderate iron limitation and grow as good as the generalist wildtype but not better. Under more stringent iron limitation, the dynamics in specialist communities was characterized by mutual cheating and with higher proportions of pyochelin producers greatly compromising group productivity. Nonetheless, specialist communities remained stable through negative frequency-dependent selection. Our work shows that specialization in a bacterial community can be spurred by cheating and does not necessarily result in beneficial division of labour. We propose that natural selection might favour fine-tuned regulatory mechanisms in generalists over division of labour because the former enables generalists to remain flexible and adequately adjust public good investments in fluctuating environments. </span></p>
The evolution of antagonistic and mutualistic traits in the yucca-yucca moth obligate pollination mutualism
<p>Dataset used to analyze the rates of evolution of mouthparts used for pollination and egg-laying morphology in yucca moths. Dataset includes the morphological measurements, the phylogenetic tree, and the species means for the evolutionary rates test.</p>
Spectroscopy study of albumin interaction with negatively charged liposome membranes: Mutual structural effects of the protein and the bilayers
<p>Deconvolution of the signals of carbonyl groups in the ATR-FTIR spectra of lipids in the region 1700–1760 cm<sup>−1</sup> obtained during liposome incubation with albumin.</p>
Mutually dependent, yet highly asymmetric? Conversations about the relations and futures of Open Access academic publishing
<p>The research data in this dataset contains verbatim transcripts in PDF and ODT formats each (for reading and broader re-use purposes, respectively) as well as original audio recordings of two interviews. These semi-structured interviews form part of materials for a doctoral research project on recent developments in and possible implications of Open Access publishing models. Further information and full description of the research proposal are available online at http://hdl.handle.net/10760/29265</p>
Data for Fig 1C of PLOS Biology The Cybathlon BCI race: Successful longitudinal mutual learning with two tetraplegic users
<p>The mat file consists of the race completion time data of pilots P1 and P2 and the session date these races took place on.</p>
Data for S5 Fig of PLOS Biology The Cybathlon BCI race: Successful longitudinal mutual learning with two tetraplegic users
<p>The mat file consists of BCI discriminancy data after artifact removal for pilot P2 for three typical sessions of this user</p>
Mutual control of coherent spin waves and magnetic domain walls in a magnonic device
<p>Data shown in the main text and the supplementary materials of Mutual control of coherent spin waves and magnetic domain walls in a magnonic device.</p>
Data from: Harnessing ant defence at fruits reduces bruchid seed predation in a symbiotic ant-plant mutualism
In horizontally transmitted mutualisms, mutualists disperse separately and reassemble in each generation with partners genetically unrelated to those in the previous generation. Because of this, there should be no selection on either partner to enhance the other's reproductive output directly. In symbiotic ant–plant mutualisms, myrmecophytic plants host defensive ant colonies, and ants defend the plants from herbivores. Plants and ants disperse separately, and, although ant defence can indirectly increase plant reproduction by reducing folivory, it is unclear whether ants can also directly increase plant reproduction by defending seeds. The neotropical tree Cordia alliodora hosts colonies of Azteca pittieri ants. The trees produce domatia where ants nest at stem nodes and also at the node between the peduncle and the rachides of the infloresence. Unlike the stem domatia, these reproductive domatia senesce after the tree fruits each year. In this study, I show that the tree's resident ant colony moves into these ephemeral reproductive domatia, where they tend honeydew-producing scale insects and patrol the nearby developing fruits. The presence of ants significantly reduced pre-dispersal seed predation by Amblycerus bruchid beetles, thereby directly increasing plant reproductive output.
Data from: Mutualism effectiveness and vertical transmission of symbiotic fungal endophytes in response to host genetic background
Certain species of the Pooideae subfamily develop stress tolerance and herbivory resistance through symbiosis with vertically-transmitted, asexual fungi. This symbiosis is specific, and genetic factors modulate compatibility between partners. Although gene flow is clearly a fitness trait in allogamous grasses, since it injects hybrid vigor and raw material for evolution, it could reduce compatibility and thus, mutualism effectiveness. To explore the importance of host genetic background in modulating the performance of symbiosis, Lolium multiflorum plants, infected and non-infected with Neotyphodium occultans, were crossed with genetically distant plants of isolines (susceptible and resistant to diclofop-methyl herbicide) bred from two cultivars, and exposed to stress. The endophyte improved seedling survival in genotypes susceptible to herbicide, while it had a negative effect on one of the genetically resistant crosses. Mutualism provided resistance to herbivory independently of the host genotype, but this effect vanished under stress. While no endophyte effect was observed on host reproductive success, it was increased by inter-population plant crosses. Neither gene flow nor herbicide had an important impact on endophyte transmission. Host fitness improvements due to gene flow do not appear to result in direct conflict with mutualism while this seems to be an important mechanism for the ecological and contemporary evolution of the symbiotum.
Data from: A keystone mutualism underpins resilience of a coastal ecosystem to drought
Droughts are increasing in severity and frequency, yet the mechanisms that strengthen ecosystem resilience to this stress remain poorly understood. Here, we test whether positive interactions in the form of a mutualism between mussels and dominant cordgrass in salt marshes enhance ecosystem resistance to and recovery from drought. Surveys spanning 250 km of southeastern US coastline reveal spatially dispersed mussel mounds increased cordgrass survival during severe drought by 5- to 25-times. Surveys and mussel addition experiments indicate this positive effect of mussels on cordgrass was due to mounds enhancing water storage and reducing soil salinity stress. Observations and models then demonstrate that surviving cordgrass patches associated with mussels function as nuclei for vegetative re-growth and, despite covering only 0.1–12% of die-offs, markedly shorten marsh recovery periods. These results indicate that mutualisms, in supporting stress-resistant patches, can play a disproportionately large, keystone role in enhancing ecosystem resilience to climatic extremes.
Data from: Keystone mutualism strengthens top-down effects by recruiting large-bodied ants
Determining the impacts of mutualistic interactions and predator diversity on food webs are two important goals in community ecology. In this study, we examined how predator community variation mediates the strength of top–down effects in the presence and absence of mutualistic interactions. We examined the impacts of predatory ant species that simultaneously prey on leaf-chewing herbivores (Lepidoptera) and engage in food-for-protection mutualisms with sap-feeding herbivores (Hemiptera) in the lower canopy of Connecticut forests. In this 2-year study, we examined three hypothetical mechanisms by which mutualisms can alter the top–down effects of ants: (1) sap feeders increase ant abundance, thus strengthening predatory effects; (2) sap feeders increase the relative abundance of a species that has stronger predatory effects; and (3) changes to predator diversity (species richness) are caused by sap feeders mediating top–down effects of the ant community. Experiments revealed that host plants occupied by sap feeders favored large-bodied ant species in the genus Camponotus, but there were no changes to community-wide ant abundance or ant species richness. Fitting predictions of predation strength based on the functional trait of body size, large-bodied Camponotus suppressed caterpillars and reduced leaf herbivory. This work shows that the ant–hemipteran mutualism, which has been characterized as a keystone interaction, can generate strong top–down effects on leaf-chewing herbivores and herbivory via increasing the relative abundance of species with functional traits relevant to predation, such as body size. Therefore, the emergence of specific ants as keystone predators in a community can be contingent upon their mutualism with sap-feeding Hemiptera.
Data from: Limited gene dispersal and spatial genetic structure as stabilizing factors in an ant-plant mutualism
Comparative studies of the population genetics of closely associated species are necessary to properly understand the evolution of these relationships because gene flow between populations affects the partners' evolutionary potential at the local scale. As a consequence (at least for antagonistic interactions), asymmetries in the strength of the genetic structures of the partner populations can result in one partner having a co-evolutionary advantage. Here, we assess the population genetic structure of partners engaged in a species-specific and obligatory mutualism: the Neotropical ant-plant, Hirtella physophora, and its ant associate, Allomerus decemarticulatus. Although the ant cannot complete its life cycle elsewhere than on H. physophora and the plant cannot live for long without the protection provided by A. decemarticulatus, these species also have antagonistic interactions: the ants have been shown to benefit from castrating their host plant and the plant is able to retaliate against too virulent ant colonies. We found similar short dispersal distances for both partners, resulting in the local transmission of the association and, thus, inbred populations in which too virulent castrating ants face the risk of local extinction due to the absence of H. physophora offspring. On the other hand, we show that the plant populations probably experienced greater gene flow than did the ant populations, thus enhancing the evolutionary potential of the plants. We conclude that such levels of spatial structure in the partners' populations can increase the stability of the mutualistic relationship. Indeed, the local transmission of the association enables partial alignments of the partners' interests, and population connectivity allows the plant retaliation mechanisms to be locally adapted to the castration behaviour of their symbionts.
Data from: Nectar bacteria, but not yeast, weaken a plant-pollinator mutualism
Mutualistic interactions are often subject to exploitation by species that are not directly involved in the mutualism. Understanding which organisms act as such 'third-party' species and how they do so is a major challenge in the current study of mutualistic interactions. Here, we show that even species that appear ecologically similar can have contrasting effects as third-party species. We experimentally compared the effects of nectar-inhabiting bacteria and yeasts on the strength of a mutualism between a hummingbird-pollinated shrub, Mimulus aurantiacus, and its pollinators. We found that the common bacterium Gluconobacter sp., but not the common yeast Metschnikowia reukaufii, reduced pollination success, seed set and nectar consumption by pollinators, thereby weakening the plant–pollinator mutualism. We also found that the bacteria reduced nectar pH and total sugar concentration more greatly than the yeasts did and that the bacteria decreased glucose concentration and increased fructose concentration whereas the yeasts affected neither. These distinct changes to nectar chemistry may underlie the microbes' contrasting effects on the mutualism. Our results suggest that it is necessary to understand the determinants of microbial species composition in nectar and their differential modification of floral rewards to explain the mutual benefits that plants and pollinators gain from each other.
Data from: Geographically structured genetic variation in the Medicago lupulina – Ensifer mutualism
Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.
Mutual mate choice and assortative mating in relation to a carotenoid-based color trait in blue tits
<p>Choosing an appropriate partner is a critical decision for many animal species. However, many mechanisms involved in mate choice are still poorly understood. Do both males and females choose their sexual partners, do both sexes use the same criteria for choosing, and do their own phenotype influence the choices they make, are questions that need further investigation. Over two successive experiments conducted in captivity with hand-reared blue tits (Cyanistes caeruleus), we manipulated the color of the chest plumage, a secondary sexual trait that reflects an individual's condition, to create two different color morphs (one pale and one colored). We then tested whether both sexes express a preference, whether they are attracted to the same morphs, and if the subjects' own chest color influences the preference they show. Our data reveal that both sexes are choosy, with females tending to be slightly choosier than males. We also show that both sexes preferentially select individuals with a pale chest plumage over colorful individuals, and this was again more pronounced in females. Finally, paler individuals tend to be selected by birds that are themselves pale, even if this phenotype matching was not very robust. Such a preference for paler individuals is intriguing since mates are predicted to associate with individuals displaying higher, not lower, value of quality signals. It could result from adaptive mechanisms related to avoidance of aggressiveness in confined environment, avoidance of conflicting sexual signals within individuals, or from cultural mechanisms leading to preference for individuals that match its own phenotype.</p>
The joint role of coevolutionary selection and network structure in shaping trait matching in mutualisms
<p>Data used in the "The joint role of coevolutionary selection and network structure in shaping trait matching in mutualisms"</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.