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245 results for “Rust”
White Pine Blister Rust (WPBR) Plot Data from the Western United States
As one of North America’s most damaging tree diseases, white pine blister rust (WPBR) is expected to continue to affect high-elevation five-needle (High-5) pine species in the near future. In order to better understand and estimate the risk it poses to white pines, data was compiled from independent studies across the Western U.S. from 1983-2025. This WPBR disease occurrence data includes nearly 6700 points, which were classified into two epidemic types: established or invading, based on the disease intensity value and the amount of time the disease had been present in the area.
RustMapper: White Pine Blister Rust Risk in the Western United States, 1980-2023
White pine blister rust (WPBR) is a highly destructive disease threatening high-elevation five-needle white pines across North America. To better understand risk patterns, we analyzed data from independent studies conducted across the western U.S. between 1995 and 2020. Using this data, we assessed WPBR risk for high-elevation five-needle pine species (High-5) from 1980 to 2023, integrating the results into the adaptive management tool "RustMapper." These projections estimate the annual probability of WPBR occurrence, providing valuable insights for monitoring and management. Risk ranges from 0 to 1, and values closer to 1 indicate a higher likelihood of disease occurrence based on conditions.
RustMapper: White Pine Blister Rust Risk in the Western United States, 2030-2099
White pine blister rust (WPBR) is a highly destructive disease threatening high-elevation five-needle white pines across North America. To better understand risk patterns, we analyzed data from independent studies conducted across the western U.S. between 1995 and 2020. Using this data, we assessed WPBR risk for high-elevation five-needle pine species (High-5) from 2030 to 2099, integrating the results into the adaptive management tool "RustMapper." These projections estimate the annual probability of WPBR occurrence, providing valuable insights for monitoring and management. Risk ranges from 0 to 1, and values closer to 1 indicate a higher likelihood of disease occurrence based on conditions.
Targeted Re-sequencing Identifies Candidate Fusiform Rust Resistance Genes in Loblolly Pine
<p>A fasta file containing the subset of the v2.01 Pita genome in addition to the novel NLR genes that were targeted by hybridization probes. </p> <p>A bed file describing the intervals targeted by the hybridization probes.</p> <p>Trinity assemblies of the 30 RNAseq libraries along with predictions by transdecoder of CDS and peptide sequences from those trinity assemblies. </p>
A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix
<p>Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen <em>Hemileia vastatrix,</em> have constrained the sustainable production of Arabica coffee for over 150 years. The ability of <em>H. vastatrix </em>to overcome resistance in coffee cultivars and evolve new races is inexplicable for a pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between <em>H. vastatrix</em> and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for <em>H. vastatrix</em> that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for <em>H. vastatrix </em>strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization. Citation: https://doi.org/10.1101/2022.07.29.502101</p>
Genomes of tropical rust fungi (Araucariomyces, Coleosporium, Hamaspora, Puccinia paululla, Skierka, and Sphaerophragmium)
<p>Hi, </p> <p>Everyone is welcome to use the assemblies shared here.</p> <p>The catch is they are not perfect. The DNA was extracted from environmental samples and has contaminant contigs from hosts, bacteria and endophytic or saprophytic fungi. I've run Kraken2 to remove most host and bacterial contigs, but there are no doubt some remaining. The genomes were sequenced in the same run and the mitochondrion of <em>Sphaerophragmium</em> is present in all genomes.</p> <p>The taxa are selected for their evolutionary relationships in the Pucciniales (see Aime and McTaggart 2021, A familial rank classification of rust fungi, with notes on genera). More about each taxon is available below.<br> <em>Araucariomyces fragiforme</em>: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/aecidiumfragiforme.html<br> <em>Coleosporium plumeriae</em>: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/coleosporiumplumeriae.html<br> <em>Hamaspora acutissima</em>: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/hamasporaacutissima.html<br> <em>Puccinia paullula</em>: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/pucciniapaullula.html<br> <em>Skierka agallocha</em>: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/skierkaagallocha.html<br> <em>Sphaerophragmium acaciae</em>: https://collections.daff.qld.gov.au/web/key/rustfungi/Media/Html/sphaerophragmiumacaciae.html</p> <p>The raw sequencing data are available either in this Google Drive folder https://drive.google.com/drive/folders/1nDRWYLEO80R6CCxdnMzkaFY3DqUKn6Vo?usp=sharing, or contact me (alistair.mctaggart@gmail.com) if you need another option.</p> <p>If you have the fortitude to clean up these genomes, let's get them on to GenBank. I'd be delighted to collaborate on anything and currently am working on mating genes and mitochondria.</p> <p>All genomes were assembled with the below commands for Supernova. The assembly reports have also been provided.</p> <p>supernova run --id RustName --accept-extreme-coverage --localmem 350 --fastqs=$PATH/reads --maxreads=2140000000<br> supernova mkoutput --style=megabubbles --asmdir=$PATH/RustName/outs/assembly --outprefix=RustName_mkoutput</p> <p>There are more raw sequencing data for <em>Uromycladium</em> and <em>Ravenelia</em>, but nothing assembled from these yet. You're welcome to use them if you need.</p> <p>You could do me a solid and cite: McTaggart et al. (2022) Sexual reproduction is the null hypothesis in life cycles of rust fungi. PLoS Pathogens 18(5):e1010439. DOI: 10.1371/journal.ppat.1010439. We released the MAT loci based on the genomes in there, more work on RNAi pathway genes coming that can be cited as an alternative to reference these assemblies when published.</p> <p>Enjoy and keep smiling,<br> Alistair</p>
Charles Rust (r2487)
<b>-- <a href="https://doi.org/10.5281/zenodo.11582199">Documentation</a> --</b><br><br><u>Name</u>: Charles Rust<br><u>musiXplora-ID</u>: r2487<br><u>musiXplora-URI</u>: <a href="https://musixplora.de/mxp/r2487">https://musixplora.de/mxp/r2487</a><br><u>Gender</u>: m<br><u>Date of Birth</u>: 1775<br><u>Place of Birth</u>: Undefined<br><u>Date of Death</u>: 1821<br><u>Place of Death</u>: Undefined<br><u>First Mentioned</u>: 1805<br><u>Sectors</u>: Instrumentenbau<br><u>Professions (Musical)</u>: Holzblasinstrumentenbauer<br><u>Other Places of Activity</u>: Lyon<br><br><br><u>Institutionen:</u><br><table><tbody><tr><th>Role</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>Rust & Dubois</td><td><a href="https://musixplora.de/mxp/3030950">3030950</a></td></tr><tr><td>Related</td><td>Forschungssammlung Hichwa-Rachor</td><td><a href="https://musixplora.de/mxp/3080536">3080536</a></td></tr></tbody></table><br><u>Titel/Medien:</u><br><table><tbody><tr><th>Role</th><th>Sigel</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>New Langwill Index 1993</td><td>The New Langwill Index. A Dictionary of Musical Wind-Instrument Makers and Inventors. NLI</td><td><a href="https://musixplora.de/mxp/5001112">5001112</a></td></tr></tbody></table><br><br><u>Changelog</u>:<br> - v0.0.1: Initial Upload.<br>
Watkins natural accessions yellow rust disease resistant scores
<p>The file contains the phenotypic information from field trails conducted in Kenya at the Kenya Agriculture and Livestock Research Organisation (KALRO) and the Ethiopian Institute of Agricultural Research (EIAR). Data are separated into the three rusts (yellow rust (Yr), stem rust (Sr) and leaf rust (Lr)), although data is not complete at all locations. When possible both seedling and adult plant data is provided. Adult scores include several observation across the growing season. For scoring rust severity, the modified Cobb scale (Peterson et al. 1948) was used to determine the percentage of tissue infected (0-100%) with rust and infection response (S, MS, MR and R, corresponding to susceptible, moderately susceptible, moderately resistant and resistant). </p> <p>Accession codes relate to Watkins landraces and their country of origin and accession names are indicated. Locations, dates and disease scores are indicated. Missing data is indicated as "-". </p> <p>For more detailed passport data and access to germplasm visit the John Innes Centre Germplasm Resources Unit (<a href="https://www.seedstor.ac.uk/search-browseaccessions.php?idCollection=39">SeedStor</a>). Additional germplasm resources and populations developed from the Watkins accessions can be found here: <a href="https://wisplandracepillar.jic.ac.uk/">https://wisplandracepillar.jic.ac.uk/</a> </p> <p> </p>
A Study of Undefined Behavior Across Foreign Function Boundaries in Rust Libraries
<p>Developers rely on the static safety guarantees of the Rust programming language to write secure and performant applications. However, Rust is frequently used to interoperate with other languages which allow design patterns that conflict with Rust’s evolving aliasing models. Miri is currently the only dynamic analysis tool that can validate applications against these models, but it does not support finding bugs in foreign functions, indicating that there may be a critical correctness gap across the Rust ecosystem. We conducted a large-scale evaluation of Rust libraries that call foreign functions to determine whether Miri’s dynamic analyses remain useful in this context. We used Miri and an LLVM interpreter to jointly execute applications that call foreign functions, where we found 46 instances of undefined or undesired behavior in 37 libraries. Three bugs were found in libraries that had more than 10,000 daily downloads on average during our observation period, and one was found in a library maintained by the Rust Project. Many of these bugs were violations of Rust’s aliasing models, but the latest Tree Borrows model was significantly more permissive than the earlier Stacked Borrows model. The Rust community must invest in new, production-ready tooling for multi-language applications to ensure that developers can detect these errors.</p>
Unpublished data on leaf rust infection and herbivory in willow plantations
<p>The data were collected during 2015 and 2018 within ~20 willow plantations in the Uppsala area, Sweden. I neither found the time nor research funding to use the data in a scientific publication or otherwise.</p> <p>The data from 2015 also offer canopy openness and vegetation cover within the willow short rotation plantations. The data from 2018 also included the establishment of plots for measuring stem diameter that were intended to be measures again.</p> <p>An associated data set (10.5281/zenodo.6995718) consist of similar estimation on willow bushes in Europe.</p>
Unpublished data on leaf rust infection, leaf galls, and herbivory on willow in Europe
<p>The data were collected between 2016 and 2022 in sites between southern Germany and Middle Sweden. I neither found the time nor research funding to use the data in a scientific publication or otherwise.</p> <p>In total 654 samples are available that record the occurrence of leaf rust, leaf galls, percent herbivory, and plant size.</p> <p>An associated data set (10.5281/zenodo.6992488) consist of similar estimation on willow bushes in willow plantations in the Uppsala area, Sweden.</p>
Fig. 1 in A new species of rust fungi from the middle Eocene Sakhalinian amber
Fig. 1. Rust fungus Nyssopsora eocaenica Tykhonenko and Hayova sp. nov., holotype PIN 3387/147 Starodubskoye, Sakhalin, Russia; middle Eocene Sakhalinian amber, Naibuchi Formation. General view of teliospores and part of the holotype of chironomid dipteran Heterotrissocladius naibuchi Baranov, Andersen, and Perkovsky, 2015 (A 1), teliospores with appendages (A 2, A 3, A 4).
Figure 4 in Within-plant distribution and rapid assessment of sugarcane rust mite population on sugarcane canopy
Figure 4 Relationship between sugarcane rust mite density and counting speed of the imprinting technique.
Figure 3 in Within-plant distribution and rapid assessment of sugarcane rust mite population on sugarcane canopy
Figure 3 Within-plant distribution of sugarcane rust mite population based on the imprinting tech- nique (mean ± SEM). The numbers within brackets are the proportions of mite populations within plants. Means across leaves with the same capital letters are not significantly different and means with the same lower letters on a given leaf position are not significantly different (Tukey,P <0.05).
Figure 5 in Within-plant distribution and rapid assessment of sugarcane rust mite population on sugarcane canopy
Figure 5 Physiological parameters of sugarcane canopy (mean±SEM).A=photosynthetic rate, gsw =stomatal conductance,Ci =intercellular CO2, E=transpiration, WUE=water use efficiency.
FIG. 1 in Species of Puccinia Pers. nom. sanct. (rust fungi) on Bambusoideae in Belgium and in Europe
FIG. 1. — Puccinia longicornis Pat. & Har.: A, teleutosores in February (AF 3760); B, teleutosores in May (covered with a layer of basidia and basidiospores) with an erumpent uredosore (AF 3739). – Puccinia deutziae (Dietel) Fraiture & Vanderweyen, comb. nov. (AF 3738): C, teleutosore and uredosore – Puccinia phyllostachydis Kusano (AF 3761); D, teleutosore growing from the centre of an uredosore. – Puccinia deutziae (AF 3738): E, uredosores parasitized by Sphaerellopsis filum (Biv.) Sutton (pycnidia and cirrhi); F, basidium with a basidiospore; G, conidia of Sphaerellopsis filum. Scale bars: A-E, 500 µm; F, 20 µm; G, 10 µm.
FIG. 2 in Species of Puccinia Pers. nom. sanct. (rust fungi) on Bambusoideae in Belgium and in Europe
FIG. 2. — Puccinia deutziae (Dietel) Fraiture & Vanderweyen, comb. nov. (AF 3738): A, teleutospores; B, basidiospores. – Puccinia longicornis Pat. & Har. (AF 3739): C, basidiospores; D, teleutospores; E, paraphyses. – Puccinia phyllostachydis Kusano: F, teleutospores (AF 3743); G, paraphyses (AF 3749). Scale bars: B, C, 10 µm; A, D-G, 20 µm.
A pathogen's spatial range is not constrained by geographical features in the flax rust pathosystem
<p>In this study, we performed several transect surveys over the course of the 2021 summer field season to assess potential ecogeographical range determinants for Lewis flax (<em>Linum</em> <em>lewisii</em>) and its pathogen, flax rust (<em>Melamspora</em> <em>lini</em>), in the area surrounding the Rocky Mountain Biological Laboratory in Gothic, Colorado. Additionally, we used generalized additive models to examine the effects of host population density and metapopulation structure on disease presence and prevalence.</p>
A pathogen’s spatial range is not constrained by geographical features in the flax rust pathosystem
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Evolution of morphological but not aggressiveness‐related traits following a major resistance breakdown in the poplar rust fungus, Melampsora larici‐populina
<p>Crop varieties carrying qualitative resistance to targeted pathogens lead to strong selection pressure on parasites, often resulting in resistance breakdown. It is well known that qualitative resistance breakdowns modify pathogen population structure but few studies have analysed the consequences on their quantitative aggressiveness-related traits. The aim of this study was to characterize the evolution of these traits following a resistance breakdown in the poplar rust fungus, <i>Melampsora larici-populina</i>. We based our experiment on three temporal populations sampled just before the breakdown event, immediately after and four years later. First, we quantified phenotypic differences among populations for a set of aggressiveness traits on a universally susceptible cultivar (infection efficiency, latent period, lesion size, mycelium quantity, and sporulation rate) and one morphological trait (mean spore volume). Then we estimated heritability to establish which traits could be subjected to adaptive evolution, and tested for evidence of selection. Our results revealed significant changes in the morphological trait but no variation in aggressiveness traits. By contrast, recent works have demonstrated that quantitative resistance (initially assumed more durable) could be eroded and lead to increased aggressiveness. Hence, this study is one example suggesting that the use of qualitative resistance may be revealed to be less detrimental to long term sustainable crop production.</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.
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.
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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.
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