AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Detection of <i>Salmonella enterica </i>and <i>Listeria monocytogenes</i> in alternative irrigation water by culture and qPCR-based methods in the Mid-Atlantic U.S.

<p dir="ltr">Alternative irrigation waters (rivers, ponds, and reclaimed water) can harbor bacterial foodborne pathogens like <i>Salmonella enterica</i> and <i>Listeria monocytogenes</i>, potentially contaminating fruit and vegetable commodities. Detecting foodborne pathogens using qPCR-based methods may accelerate testing methods and procedures compared to culture-based methods. This study compared detection of <i>S. enterica</i> and <i>L. monocytogenes</i> by qPCR (real-time PCR) and culture methods in irrigation waters to determine the influence of water type (river, pond, and reclaimed water), season (winter, spring, summer, and fall), or volume (0.1, 1, and 10 L) on sensitivity, accuracy, specificity, and positive (PPV), and negative (NPV) predictive values of these methods. Water samples were collected by filtration through modified Moore swabs (MMS) over a 2-year period at 11 sites in the Mid-Atlantic U.S. on a bi-weekly or monthly schedule. For qPCR, bacterial DNA from culture-enriched samples (n = 1,990) was analyzed by multiplex qPCR specific for S. enterica and L. monocytogenes. For culture detection, enriched samples were selectively enriched, isolated, and PCR confirmed. PPVs for qPCR detection of <i>S. enterica</i> and <i>L. monocytogenes</i> were 68% and 67%, respectively. The NPV were 87% (S. enterica) and 85% (L. monocytogenes). Higher levels of qPCR/culture agreement were observed in spring and summer compared to fall and winter for <i>S. enterica</i>; for <i>L. monocytogenes</i>, lower levels of agreement were observed in winter compared to spring, summer, and fall. Reclaimed and pond water supported higher levels of qPCR/culture agreement compared to river water for both <i>S. enterica</i> and <i>L. monocytogenes</i>, indicating that water type may influence the agreement of these results.</p>

Tags: culture-based-methods, detection, irrigation, listeria-monocytogenes, qpcr, salmonella-enterica, water
Organization: Department of Agriculture
Data from: Perennial forages influence mineral and protein concentrations in annual wheat cropping systems

<p dir="ltr">Agricultural land management may influence crop nutritional quality. However, few studies have explored potential connections between crop quality with different land management strategies. We analyzed mineral and crude protein concentrations in spring wheat grain (Triticum aestivum L.) samples from a study in Mandan, ND conducted from 2006 to 2014. The study introduced a perennial forage phase into an annual spring wheat cropping system, in three to four replicates, and previously found yield benefits and enhanced soil parameters in the perennial forage treatments. We determined whether integrating a perennial forage phase into continuous wheat would also affect crop nutritional quality by measuring wheat grain mineral and protein concentrations. Crude protein concentration was greater (p < .05) when wheat followed alfalfa (Medicago sativa L.) and increased linearly after 2–5 yr of established alfalfa. We observed comparable wheat grain crude protein and mineral concentrations between continuous annually fertilized wheat and unfertilized wheat following perennial forages. Negative correlations (p < .001) were observed between wheat grain yield and crude protein, potassium (K), magnesium (Mg), nickel (Ni), phosphorus (P), sulfur (S), and zinc (Zn) concentrations. Discriminate multivariate analyses showed, with 96% predictive accuracy, that differences in crude protein and mineral concentration were largely driven by year of wheat harvest. Differences between harvest years were likely due to timely precipitation at critical Growth Stage 3, during spikelet development. Study outcomes highlighted the important role of perennial forages and environmental factors to influence protein and mineral concentration in spring wheat grain.</p>

Tags: perennials, spring-wheat, wheat-grain-quality
Organization: Department of Agriculture
An interspecific F1 mapping population to study grape powdery mildew resistance

<p dir="ltr">The mapping family was composed of F1 hybrids obtained by crossing the resistant female parent <i>Vitis amurensis Rupr.</i> “PI 588631” with the pollen donor <i>Vitis vinifera</i> “Valley Pearl.” This cross was performed in 2014, and the resulting hybrids were planted at the ARS San Joaquin Valley Agricultural Sciences Center (latitude 36°81′N, longitude 119°72′W). These F1 hybrids served as the basis for studying resistance to grape powdery mildew. The data set includes marker data that was used to develop genetic map and phenotype data generated from Blackbird microscopy robot analysis of grapevine powdery mildew (<i>Erysiphe necator</i>) severity.</p>

Tags: disease-resistance-loci, genetic-map, grapevine, leaf-disc-assay, powdery-mildew
Organization: Department of Agriculture
Data from: A variety-specific analysis of climate change effects on California winegrapes

<div>This folder, titled "Data," contains the MATLAB code, final products, tables, and figures used in Parker, L.E., Zhang, N., Abatzoglou, J.T. <em>et al.</em> A variety-specific analysis of climate change effects on California winegrapes. <em>Int J Biometeorol</em> <strong>68</strong>, 1559–1571 (2024). https://doi.org/10.1007/s00484-024-02684-8  </div>
<p><br></p>
<ul><li><strong>Data Collection:</strong> Climatological data (daily maximum and minimum temperatures, precipitation, and reference evapotranspiration) were obtained from the gridMET dataset for the contemporary period (1991-2020) and from 20 global climate models (GCMs) for the mid-21st century (2040-2069) under RCP 4.5.</li><li><strong>Phenology Modeling:</strong> Variety-specific phenology models were developed using published climatic thresholds to assess chill accumulation, budburst, flowering, veraison, and maturity stages for the six winegrape varieties.</li><li><strong>Agroclimatic Metrics:</strong> Fourteen viticulturally important agroclimatic metrics were calculated, including Growing Degree Days (GDD), Cold Hardiness, Chilling Degree Days (CDD), Frost Damage Days (FDD), and others.</li><li><strong>Analysis Tools:</strong> MATLAB was used for data processing, analysis, and visualization. The MATLAB code provided in this dataset includes scripts for analyzing climate data, running phenology models, and generating visualizations.</li></ul><ul><li><strong>MATLAB Code:</strong> Scripts and functions used for data analysis and modeling.</li><li><strong>Processed Data:</strong> Results from phenology and agroclimatic analyses, including the projected changes in phenological stages and climate metrics for the selected varieties and AVAs.</li><li><strong>Tables:</strong> Detailed results of phenological changes and climate metrics, presented in a clear and structured format.</li><li><strong>Figures:</strong> Visual representations of the data and results, including charts and maps illustrating the impacts of climate change on winegrape development stages and agroclimatic conditions.</li></ul>
<p><br></p>
<div><strong>Research Description:</strong> This study investigates the impacts of climate change on the phenology and agroclimatic metrics of six winegrape varieties (Cabernet Sauvignon, Chardonnay, Pinot Noir, Zinfandel, Pinot Gris, Sauvignon Blanc) across multiple California American Viticultural Areas (AVAs). Using climatological data and phenology models, the research quantifies changes in key development stages and viticulturally important climate metrics for the mid-21st century.</div>
<p><br></p>

Tags: agroclimatic-metrics, california, climate-change, crop-yield, phenology, winegrapes
Organization: Department of Agriculture
Data and code from: Avocado cultivar and tree-to-tree leaf compositional differences affect infestation severity of avocado lace bug, <i>Pseudocysta perseae</i> (Hemiptera: Tingidae)

<p dir="ltr">Datasets and R script used for article accepted to Environmental Entomology (June 5, 2024):"Avocado cultivar and tree-to-tree leaf compositional differences affect infestation severity of avocado lace bug, <i>Pseudocysta perseae</i> (Hemiptera: Tingidae)."<br>Authors: Bosch, Michael; Sun, Xiuxiu; Hall, Sierra; Love, Ken; Cox, David; Matsumoto, Tracie; Liang, Peishih; Follett, Peter; Stockton, Dara<br></p><p dir="ltr"><b>Rep_GLMM_UHKCES.csv</b>: Data used for repeated measures generalized linear mixed model for abundance surveys conducted at the University of Hawai'i Kona Cooperative Extension Service orchard.</p><p dir="ltr"><b>Rep_GLMM_CC.csv</b>: Data used for repeated measures generalized linear mixed model for abundance surveys conducted at the Captain Cook orchard.</p><p dir="ltr"><b>ALB_Honaunau.csv</b>: Data summarizing avocado lace bug abundance from leaves collected from the Honaunau orchard. Is to be used to perform generalized linear mixed models between lace bug abundance and sugars in corresponding avocado leaves.</p><p dir="ltr"><b>LeafTraits_Honaunau.csv</b>: Data for performing generalized linear mixed models between avocado lace bug abundance and several avocado leaf traits from leaves collected from the Honaunau orchard.</p><p dir="ltr"><b>Sugars_Honaunau.csv</b>: Data for performing generalized linear mixed models between avocado lace bug abundance and avocado leaf sugar content from leaves collected from the Honaunau orchard.</p><p dir="ltr"><b>Fig1_Average.csv</b>: Data averaging avocado lace bug abundance across trees surveyed at the University of Hawai'i Kona Cooperative Extension Service and Captain Cook orchards. To be used to generating figure 1 in manuscript.</p><p dir="ltr"><b>Fig1_Sites.csv</b>: Data on avocado lace bug abundance across trees surveyed at the University of Hawai'i Kona Cooperative Extension Service and Captain Cook orchards. To be used to generating figure 1 in manuscript.<br><br><b>LogOdds_USDAGermplasm.csv</b>: Data used for performing a repeated measures proportional odds logistic regression on avocado lace bug infestation category surveys conducted at the USDA Germplasm Repository.</p><p><br></p><p dir="ltr"><b>EE_Rscript.R</b>: R script used to run analyses conducted and construct figures presented in the corresponding manuscript. Required R packages include:</p><ul><li>tidyverse</li><li>reshape2</li><li>DHARMa</li><li>scales</li><li>glmmTMB</li><li>emmeans</li><li>cowplot</li><li>repolr</li></ul><p></p>

Tags: avocado, cultivar, hawaii, infestation, invasive
Organization: Department of Agriculture
ITSxpress: Software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing

<p dir="ltr">The ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions are commonly used to identify fungi and other eukaryotic taxa in amplicon sequencing. The highly conserved rRNA regions flanking the ITS need to be trimmed before being used for taxonomic assignment. The Python software package ITSxpress rapidly trims single-end or paired-end sequences in FASTQ format for use in amplicon sequence variant clustering methods like DADA2. This new major release of ITSxpress improves the paired-end merging method, simplifies installation of the QIIME 2 ITSxpress plugin, removes major dependencies, adds use cases, and is compatible with newer compression formats.  This paper discusses the modifications to ITSxpress that improve the output and user experience, leading to a major version increase.</p>

Tags: amplicon-sequencing, internal-transcribed-spacer-its-sequence, qiime-2
Organization: Department of Agriculture
Data from: Vulnerability of Early Life Stages of <i>Lygodium microphyllum</i> to the biological control agent <i>Floracarus perrepae</i>

<p dir="ltr">Data from the experimental investigation of the vulnerability of early life stages of the invasive fern <i>Lygodium microphyllum</i> to the biological control agent <i>Floracarus perrepae</i>. Five initial development stages were examined: gametophyte, sporophyte, true leaf, rachis node, and mature plants. The objectives of the research were to determine what earlier life stages of <i>L. microphyllum </i>are susceptible to attack by <i>F. perrepae</i>, if damage from <i>F. perrepae </i>increase mortality in earlier life stages, can <i>F. perrepae </i>damage alter above ground and/or below ground biomass in earlier life stages, and can <i>F. perrepae</i> reduce the number of rachis and the number of fiddleheads in the earlier life stages. Twice a week, plant measurements were taken, measurements included longest rachis length, number of rachises, and number of fiddleheads. Upon completion of the experiment, we harvested the above and below ground biomass.</p><p dir="ltr">Partially funded by the USDA through the Comprehensive Everglades Restoration Plan (CERP) (USDA agreement 58-6032-1-001) and through the Southwest Florida Water Management District (USDA agreement 58-6032-3-003).</p>

Tags: biological-control, ferns, floracarus-perrepae, galls, invasive-species, lygodium-microphyllum, mites, usda
Organization: Department of Agriculture
Data from:  Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota <i>in vitro</i>

<p dir="ltr">The SHIME® (Simulator of the Human Intestinal Microbial Ecology) was used for in vitro cultivation of the human gut microbiota (3 donors) with additions of either soluble or insoluble fractions from rice bran or no addition controls (n=3 treatments.) Data collected include 16S rRNA gene amplicon sequencing and short chain fatty acid (SCFA) concentrations. Raw sequencing data can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA1032541. Data here include sample metadata and SCFA concentrations. </p>

Tags: 16s-rrna-sequencing-data, ars, fiber, gut-microbiome, in-vitro-fermentation, np306, rice-bran, shime
Organization: Department of Agriculture
Data from: Rapid and cost-effective screening of genetic markers associated with pyrethroid resistance in <i>Musca domestica</i> using RNAse H2 PCR (rhPCR)

<p dir="ltr">Pyrethroid resistance, particularly knockdown resistance (<i>kdr</i>), is widespread in insect<i> </i>pest populations, but rarely has <i>kdr</i> been associated with field-level pest control failure. The prevailing understanding is that <i>kdr </i>contributes to a resistant phenotype, but this knowledge has remained largely an academic pursuit and has not translated to tools and strategies needed by agricultural producers to make rapid decisions for effective resistance management. As a first step in providing these operational tools, we developed robust assays using the high specificity of rhPCR to reduce <i>kdr</i> assessment time by approximately 80% and costs ~75% from the traditional Sanger based method used for <i>Musca domestica</i>. An important consideration for the use of an operational tool is the ability to get an accurate result on the first attempt, so we used Nanopore sequencing to confirm genotypes in a subset of samples and found the first pass genotyping accuracy of rhPCR method to be 75.0%, versus 41.2% with the traditional Sanger method. To demonstrate the broad applicability and comparability of screening for <i>kdr</i> SNPs using rhPCR, we conducted the largest assessment of <i>kdr</i> genotypes of <i>M. domestica</i> in United States dairy operations and found similar <i>kdr</i> patterns to other recent studies using traditional methods.</p>

Tags: genotyping, knockdown-resistance-kdr, musca-domestica-l, rhpcr, voltage-gated-sodium-channel
Organization: Department of Agriculture
Nanoencapsulated cinnamaldehyde β-cyclodextrin inclusion complexes as a sustained release strategy for postharvest rambutan preservation

<p>The nanoscale β-cyclodextrin encapsulated cinnamaldehyde inclusion complexes were fabricated by a nano spray dryer. The inclusion complexes' physical and chemical properties, encapsulation efficiency, Fourier transform infrared, release profile, particle diameter, antimicrobial and antioxidant activity, were included in this dataset. Also, its effects of postharvest preservation of rambutan, which contains fruit firmness, soluble solid content, titratable acid, sugar to acid ratio, weight loss, peel browning, and surface microbial population were recorded to develop a comprehensive dataset on nanoscale β-cyclodextrin encapsulated cinnamaldehyde inclusion complexes and preservation effects on postharvest rambutans.</p>

Tags: encapsulation, essential-oil, fruit-preservation, nano-spray-dry, rambutan
Organization: Department of Agriculture
Data from: Hairy vetch (Vicia villosa Roth) germplasm contains a cryptic second species (Vicia varia Host)

<p dir="ltr">In an effort to improve cover crop performance, we have been breeding improved strains of the cover crop hairy vetch.  Based on field data and molecular data, we realized that hairy vetch germplasm contains a genetically isolated subpopulation which can be reasonably considered a distinct species called smooth vetch (Vicia varia Host). These two species are visually quite similar, but have differences in agronomic performance (flowering time and winter survival). To provide a rapid, low cost method to screen individuals and determine their species, we collected single sequence repeat (SSR) marker data on a large number of individuals in the breeding program.  Using individuals with known species identities from next-gen sequencing, we built a model to discriminate between the two species of vetch using a linear discriminant model.  Properly identifying strains of cover crop vetch can improve agronomic outcomes and breeding progress.</p>

Tags: cover-crop, crop-adaptation, hairy-vetch, plant-breeding, smooth-vetch
Organization: Department of Agriculture
Powell FLU39 raw data.xlsx

<p>Interspecies human-to-swine IAV transmission occurs globally and contributes to increased IAV diversity in pig populations. We present data that a swine isolate from a 2018-2019 human-to-swine transmission event was shed for multiple days in challenged and contact pigs. By characterizing this introduction through bioinformatic, molecular, and animal experimental approaches, these findings better inform animal health practices and in vaccine decision-making. Since wholly human seasonal H3N2 viruses in the U.S. were not previously identified as being transmissible in pigs (i.e. reverse zoonosis), these findings reveal the interspecies barriers for transmission to pigs may not require significant changes to all human seasonal H3N2.</p>

Tags: 3c3a, h3n2, influenza, interspecies-transmission, swine
Organization: Department of Agriculture
Sequence Set Browser

This site is for browsing WGS (Whole Genome Shotgun) genomes, TSA (Transcriptome Shotgun Assemblies) and TLS (Targeted Locus Study) sets. WGS sequences are incomplete genomes that have been sequenced by a whole genome shotgun strategy. TSA sequences are transcript sequences that have been computationally assembled from primary RNA sequence data. TLS sequences are large-scale marker gene sequencing studies.

Please consult WGS Submission or TSA Submission pages for more details.
https://www.ncbi.nlm.nih.gov/genbank/wgs
https://www.ncbi.nlm.nih.gov/genbank/tsa

Tags: genomics, tools-utilities
Organization: U.S. Department of Health & Human Services
Data from: Host usage in <i>Aedes aegypti</i> collected from Houston, Texas and Phoenix, Arizona using whole mosquito third-generation sequencing blood meal analysis

<p dir="ltr"><i>Aedes aegypti</i> is the primary vector of several viruses of international public health concern, including Zika, dengue, yellow fever, and chikungunya. Their synanthropic ecology and establishment in tropical, sub-tropical, and temperate areas make <i>Ae. aegypti</i> one of the most medically relevant mosquito species in the world. While they have been reported to be highly anthropophilic, several studies indicate a broader host range. They are also reported to take multiple bloodmeals between gonotrophic cycles. This consumption of multiple bloodmeals makes determination of host usage difficult when using typical Sanger sequencing methods due to sequence overlap. In this study, we examined host usage of <i>Ae. aegypti </i>in Maricopa County, Arizona and Harris County, Texas, using a Nanopore-based third-generation sequencing protocol to alleviate this issue.</p><p dir="ltr">This repository contains files related to the methods described in this study, sequencing output metadata files, and the database files and the bioinformatic process used for the analysis of the sequencing data.</p>

Tags: aedes-aegypti, blood-meal-analysis, houston-texas, nanopore-sequencing, phoenix-arizona
Organization: Department of Agriculture
Evaluate means of integrating biological control into overall management strategies for <i>Lygodium microphyllum</i>

<p dir="ltr">In 2020, a field experiment was started to look at the combined impacts of biological control and herbicide on <i>Lygodium microphyllum</i>.<b> </b>At two heavily <i>L. microphyllum</i> invaded sites with high mite and moth activity, we established 5x5m plots (72 plots total) that received an herbicide treatment (no treatment, treat in Year 1, treat in Years 1 and 2; 2% Garlon 3A, active ingredient triclopyr) and a pesticide treatment (untreated or treated to exclude agents every 4-6 weeks; Bonide Systemic Insecticide, active ingredient acephate). 10 ft tall trellises simulating trees in the field to measure the ability of <i>L. microphyllum</i> to grow with and without agents. Permanent quadrats were also installed within the plots for monitoring <i>L. microphyllum</i> cover. Additionally, these quadrats were used to quantify <i>Neomusotima conspurcatalis</i> damage.</p><p dir="ltr">Partially funded by the USDA through the Comprehensive Everglades Restoration Plan (CERP) (USDA agreement 58-6032-1-001), through the Southwest Florida Water Management District (USDA agreement 58-6032-3-003), and through the Florida Fish and Wildlife Conservation Commission (USDA agreement 58-6032-9-008).</p><p dir="ltr"><br></p>

Tags: biological-control, ferns, floracarus-perrepae, galls, herbicide, integrated-weed-management, invasive-species, mites, moths, neomusotima-conspurcatalis, usda
Organization: Department of Agriculture
A regionally-adapted implementation of conservation agriculture delivers rapid improvements to soil properties associated with crop yield stability

<p>Maize and soybean yield data set for Precision Zonal Management (PZM) project from 2012-2015. Project compared chisel plow tillage against ridge tillage (PZM) systems, with and without winter cereal rye cover crops. Experimental sites in four US states: IL, MI, MN and PA. Data set provides plot-level yield data (kg/ha) for each site-year and for both crops.</p>
<p>File also contains data set of maize and soybean yield stability, with soil properties measured in 2015 (end of experimental period) and delta values (values in 2015 minus values prior to experiment establishment in 2011).  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data for: A regionally-adapted implementation of conservation agriculture delivers rapid improvements to soil properties associated with crop yield stability.</p> <p>File Name: PZM_yields_stability_soil.xlsx</p><p>Resource Description: Data files combined into a single excel document.</p></li><br><li><p>Resource Title: Data Dictionary.</p> <p>File Name: PZM_data_dictionary.csv</p></li><br><li><p>Resource Title: Yield data for: A regionally-adapted implementation of conservation agriculture delivers rapid improvements to soil properties associated with crop yield stability.</p> <p>File Name: PZM_Yields.csv</p></li><br><li><p>Resource Title: Stable Soil data for: A regionally-adapted implementation of conservation agriculture delivers rapid improvements to soil properties associated with crop yield stability.</p> <p>File Name: PZM_stable_soil.csv</p></li></ul><p></p>

Tags: ars, conservation-agriculture, cover-crops, data-gov, maize-yield-stability, reduced-tillage, soil-organic-matter, soybean-yield-stability
Organization: Department of Agriculture