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245 results for “rust”
Data from: The escalatory Red Queen: population extinction and replacement following arms-race dynamics in poplar rust
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Data from: Rust disease of eucalypts, caused by Puccinia psidii, did not originate via host jump from guava in Brazil
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Supplementary material 1 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Table S1
Supplementary material 2 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Table S2
Figure 5 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Figure 5 Micrographs of Celoporthe paradisiaca sp. nov. (holotype: PREM 63205, ex-holotype CBS 147169 = CMW38360) A culture morphology on 2% MEA at 25 °C and 30 °C at 8 and 34 days B conidiomata produced on Eucalytpus stem sections on water agar C, D vertical section of conidioma E inner wall of conidioma F conidiomatal walls (ps, pseudoparenchymatous inner wall; pr, prosenchymatous outer or interlocular wall) G conidiogenous cells H conidia. Scale bars: 1 mm (B); 100 µm (C, D); 10 µm (E–H).
Figure 4 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Figure 4 Micrographs of Celoporthe hawaiiensis sp. nov. (holotype: PREM 61307, ex-holotype CBS 140642 = CMW38610) A culture morphology on 2% MEA at 25 °C and 30 °C at 9 and 27 days B, C conidiomata produced on Eucalyptus stem sections on water agar D, E vertical section of conidioma F conidiomatal wall G, H conidiogenous cells I conidia. Scale bars: 1 mm (B, C); 100 µm (D, E); 10 µm (F, G); 5 µm (H, I).
Figure 3 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Figure 3 Micrographs of Celoporthe hauoliensis sp. nov. (holotype: PREM 61309; ex-holotype CBS 140640 = CMW38389) A culture morphology on 2% MEA at 25 °C and 30 °C at 9 and 27 days B conidiomata produced on Eucalyptus stem sections on water agar C, D vertical section of conidioma E inner fertile wall of conidioma F conidiomatal wall G conidiogenous cells H conidia. Scale bars: 1 mm (B); 100 µm (C, D); 10 µm (E–H).
Figure 2 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Figure 2 Phylogenetic trees, based on Maximum Likelihood (ML) analyses for species in CeloportheAITS region BBT1 gene region CTEF1 gene region D combined ITS, BT1 and TEF1 regions. Bootstrap values ≥ 70% for ML and MP (maximum parsimony) analyses are presented at branches as follows: ML/MP. Bootstrap values lower than 70% are marked with * and absent analysis values are marked with –. Isolates collected in this study are in boldface and blue. Holocryphia capensis (CMW37329 and CMW37887) was used as the outgroup taxon.
Figure 1 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Figure 1 Phylogenetic trees based on Maximum Likelihood (ML) analyses of a combined DNA sequence dataset of ITS and BT1 regions for various genera in the Diaporthales. Bootstrap values ≥ 70% for ML and MP (maximum parsimony) analyses are presented at branches as follows: ML/MP. Bootstrap values lower than 70% are marked with * and absent analysis values are marked with –. Isolates collected in this study are in boldface and blue. Diaporthe ambigua (CMW5287 and CMW5588) (Diaporthaceae) was used as the outgroup taxon.
Figure 6 from: Roux J, Kamgan Nkuekam G, Marincowitz S, van der Merwe NA, Uchida J, Wingfield MJ, Chen SF (2020) Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii. MycoKeys 76: 49-79. https://doi.org/10.3897/mycokeys.76.58406
Figure 6 Vertical bar chart showing results of inoculation trial (xylem lesion) with Cryphonectriaceae isolates from Hawaii on S. jambos trees. Means with similar letters are not statistically significant, while those with different letters are statistically significant (significance level = 0.05).
Phylogenetic relatedness among Cladosporium leaf endophytes predicts their ability to reduce the severity of a poplar leaf rust disease
<p>More closely related organisms are expected to function more similarly than distantly related organisms due to shared ancestry and functional trait heritability. However, there have been few tests of this hypothesis for fungal leaf endophytes, which can modify host plant disease severity by a variety of mechanisms. We tested whether phylogenetic relatedness within <i>Cladosporium</i>, a genus including many common fungal leaf endophyte species, predicts endophyte effects on cottonwood leaf rust disease severity caused by <i>Melampsora ×</i> <i>columbiana</i>. First, we used multilocus sequence typing to infer phylogenetic relationships among 96 <i>Cladosporium </i>isolates collected from wild cottonwood trees growing in Pacific Northwest of North America. Next, we conducted a double-inoculation leaf-disk assay (endophyte inoculated first, then rust pathogen) for a subset of 50 <i>Cladosporium </i>isolates to characterize disease modification for the endophyte isolates; data on endophytes parasitizing rust was collected simultaneously for each isolate. We used generalized linear models to link disease modification and mycoparisitic ability to endophyte phylogeny, while accounting for endophyte geographic origin. We recognized 17 distinct species of <i>Cladosporium</i>; all fifty isolates of <i>Cladosporium</i> reduced rust disease severity in our leaf disk assay (by as much as 79% and as little as 45%). <i>Cladosporium </i>phylogeny was a significant predictor of rust disease severity and was also correlated with mycoparasitism. The geographic origin of the isolates explained only a small amount of the overall variation in disease reduction. Our results demonstrate that fungal endophyte phylogenetic relatedness can help predict differences in endophyte function.</p>
Data from: 28 year temporal sequence of epidemic dynamics in a natural rust – host plant metapopulation
A long-term study of disease dynamics caused by the rust Uromyces valerianae in 31 discrete populations of Valeriana salina provides a rare opportunity to explore extended temporal patterns in the epidemiology of a natural host-pathogen metapopulation. Over a 28-year period, pathogen population dynamics varied across the metapopulation with disease incidence (presence/absence), prevalence (% plants infected) and severity (% leaf area covered by lesions) all showing strong population and year effects, indicative of heterogeneity among years and host populations in the suitability of conditions for the pathogen. Disease incidence within individual host populations was significantly affected by host population size, disease prevalence the previous year and the proximity of neighbouring populations infected in the current year. After accounting for these variables there was still a marked temporal component with winter sea level having a significant effect; as did summer rainfall in the second part of the study period (1997-2011). Disease prevalence was also effected by host population size and disease prevalence in the previous year. However, it was less affected by spatial aspects of disease spread than was disease incidence. Winter sea level and June rainfall significantly affected disease prevalence. Assessment of disease impact on plant performance found strong variation in disease severity associated with the aspect and positioning of host populations. Plants growing in lower disease environments produced significantly more seeds than those growing in high disease sites. Significant variation in reaction to infection by U. valerianae was detected among plants within four populations and between these different populations. Synthesis. The epidemiology of U. valerianae was highly influenced by host population size, previous disease and distance. After accounting for these factors, there was a clear temporal signal of change in disease incidence linked to winter sea level and summer rainfall. These patterns reinforce the importance of considering interactions in multiple populations over long periods of time in order to obtain a clear picture of the variability of disease-induced selection pressures across time and space. The behaviour of the pathogen fitted that predicted for a metapopulation with considerable asynchrony in epidemiological patterns among demes.
A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii
<p>The fungal plant pathogen <em>Austropuccinia psidii</em> is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. <em>A. psidii </em>is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of <em>A. psidii </em>and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype. Please cite the following manuscript: https://www.biorxiv.org/content/10.1101/2022.04.22.489119v1</p>
Supplementary material 2 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
The machine-readable text from the screenshot.
Supplementary material 1 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
A one-per-line UT8-encoded plain-text list of URLs of the 5816 source PDFs used in this research
Supplementary material 1 from: Martone M, Murray-Rust P, Molloy J, Arrow T, MacGillivray M, Kittel C, Kasberger S, Steel G, Oppenheim C, Ranganathan A, Tennant J, Udell J (2016) ContentMine/Hypothes.is Proposal. Research Ideas and Outcomes 2: e8424. https://doi.org/10.3897/rio.2.e8424
Video showing ContentMine software applied to EPMC papers mentioning Zika virus.
Figure 6 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 6 - The consensus supertree produced from an analysis of 924 source trees from the journal IJSEM.
Figure 1 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 1 - Overall workflow; from content acquisition to stripping figure images out of the PDF, to image filtering, image analysis and reconversion back into re-usable, machine-readable phylogenetic data.
Figure 4 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 4 - Output from image analysis of the input tree image in figure 1. All taxa and relationships are correctly reproduced, with branch lengths also preserved with high fidelity. (Note that the vertical ordering of the tips is not meaningful and is arbitrarily created by the display software.)
Figure 5 from: Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589
Figure 5 - Screenshot of exemplar machine-readable NeXML formatted data output from our automated analysis of the figure image from figure 1 of Park et al. 2008. Note that the genus, species, strain, and Genbank Accession numbers are semantically distinguished where detected. Heuristic post-OCR autocorrection processes are also noted where these have been applied (e.g. the conversion of a letter 'Z' to the number '2' in many Genbank Accession numbers). A machine-readable version of this file is supplied as supplementary material (Suppl. material 2).
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.