Dataset Search

Survey questions and data collected from Illinois land managers on practices and knowledge relating to impacts to wildlife. 0s indicated non-selection, 1s indicate selection of answer.

Simulation trajectory data and scripts for Nature manuscript "The structure and physical properties of a packaged bacteriophage particle" that reports the all-atom structure of a complete HK97 virion, including its entire 39,732 base pair genome, obtained through multi-resolution simulations.

This page contains the data for the publication "Revisiting bacterial cytolethal distending toxin structure and function" published in Frontiers in Cellular and Infection Microbiology in 2023.

This dataset contains all data and supplementary materials from "Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species". An Excel file a list of all QTLs and linkage group length (in cM) obtained with two different SNP-calling methods (Tassel-Uneak and Tassel-GBS), genetic map-construction method (linkage-only and reference order-corrected) and depth filters (12x, 20x, 30x and 40x) for genetic mapping of 18 biomass yield traits in a biparental Miscanthus sinensis population using RAD-Seq SNPs is provided as "Supplementary file 1". A Perl script with the code for filtering VCF and HapMap-formatted data files is provided as “Supplementary file 2”. Phenotype data used for QTL mapping is provided as “Supplementary File 3”. A Perl script with the code for the simulation study is provided as “Supplementary file 4”.

Enzymatic reduction of oxyanions such as sulfite (SO32−) requires the delivery of multiple electrons and protons, a feat accomplished by cofactors tailored for catalysis and electron transport. Replicating this strategy in protein scaffolds may expand the range of enzymes that can be designed de novo. Mirts et al. selected a scaffold protein containing a natural heme cofactor and then engineered a cavity suitable for binding a second cofactor—an iron-sulfur cluster (see the Perspective by Lancaster). The resulting designed enzyme was optimized through rational mutation into a catalyst with spectral characteristics and activity similar to that of natural sulfite reductases.

Bioenergy crops have potential for being a sustainable and renewable feedstock for biofuels and various value-added bioproducts. The study utilizes recently developed transgenic sugarcane (“oilcane”) bagasse for chemical-free coproduction of high-value bioproducts, i.e., furfurals, HMF, acetic acid, cellulosic sugars, and vegetative lipids. Hydrothermal pretreatment was optimized at 210 °C for 5 min to coproduce 6.91%, 2.67%, 5.07%, 2.42% and 37.82% (w/w) furfurals, HMF, acetic acid, vegetative lipids, and cellulosic sugars, respectively from lignocellulosic biomass. Additionally, nanofiltration system in-series was successfully established to recover sugars, furfurals, HMF, and acetic acid from the pretreatment liquor. 1st nanofiltration with Duracid NF membrane rejected ∼99% sugars. Concentrated sugars with significantly reduced inhibitory products were obtained in retentate for fermentation. 2nd nanofiltration with NF90 membrane used permeate of 1st nanofiltration as feed and rejected ∼ 86% furfurals. The work demonstrates the feasibility of coproducing and recovering multiple biochemicals from lignocellulosic biomass.

This dataset provides microhabitat and environmental variables collected in the habitat of the poison frog Mantella baroni from 155 1-meter square quadrats in Vohimana Reserve along forest valleys, on slopes, and on ridgelines. We also provide data from photographic capture-recapture surveys used for estimating abundance.

Over the past 15 years, soybean seed yield response to season-long elevated O3 concentrations [O3] and to year-to-year weather conditions was studied using free-air O3 concentration enrichment (O3-FACE) in the field at the SoyFACE facility in Central Illinois. Elevated [O3] significantly reduced seed yield across cultivars and years. However, our results quantitatively demonstrate that weather conditions, including soil water availability and air temperature, did not alter yield sensitivity to elevated [O3] in soybean.

Dataset associated with Jones and Ward JAE-2020-0031.R1 submission: Pre-to post-fledging carryover effects and the adaptive significance of variation in wing development for juvenile songbirds. Excel CSV files with data used in analyses and file with descriptions of each column. The flight ability variable in this dataset was derived from fledgling drop tests, examples of which can be found in the related dataset: Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2019): Flight Ability of Juvenile Songbirds at Fledgling: Examples of Fledgling Drop Tests. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2044905_V1.

Information on the location, dimensions, time of treefall or death, decay state, wood nutrient, wood pH and wood density data, and soil moisture, slope, distance from forest edge and soil nutrient data associated with the publication "Interspecific wood trait variation predicts decreased carbon residence time in changing forests" authored by Sierra Perez, Jennifer Fraterrigo, and James Dalling. ** <b>Note:</b> Blank cells indicate that no data were collected.

This data was collected between 2004 and 2010 at White River National Wildlife Refuge (WRNWR) and Saint Francis National Forest (SF). It was collected as part of two master’s and one PhD project at Arkansas State University USA studying Swainson’s Warbler habitat use, survival, and body condition.

Dataset for Food availability influences angling vulnerability in muskellunge

Dataset associated with Jones et al. ECY22-0118.R3 submission: Ontogenetic effects of brood parasitism by the Brown-headed Cowbird on host offspring. Excel CSV files with all of the data used in analyses and file with descriptions of each column.

Dataset associated with Merrill et al. ECE-2021-05-00793.R1 submission: Early life patterns of growth are linked to levels of phenotypic trait covariance and post-fledging mortality across avian species. Excel CSV files with all of the data used in analyses and file with descriptions of each column.

This dataset includes the original data (including photographs as .jpg files and sound recordings as .wav files) and detailed descriptions of workflows for analyses of acoustic and morphometric data for the Neoaliturus tenellus (beet leafhopper) species complex. Files needed for different parts of the two analytical workflows are included in the "Acoustics.zip" and "PCA.zip" archives. The "Folder Structure.png" file contains a diagram of the folder structure of the two archives. Each archive contains a "ReadMe" file with instructions for repeating the analyses. File and folder names including the two-letter abbreviations TB, TD, TN and TP refer to four different putative species (operational taxonomic units, or OTUs, of the Neoaliturus tenellus complex.

Rhodosporidium toruloides is an oleaginous yeast capable of producing a variety of biofuels and bioproducts from diverse carbon sources. Despite numerous studies showing its promise as a platform microorganism, little is known about its metabolism and physiology. In this work, we investigated the central carbon metabolism in R. toruloides IFO0880 using transcriptomics and metabolomics during growth on glucose, xylose, acetate, or soybean oil. These substrates were chosen because they can be derived from plants. Significant changes in gene expression and metabolite concentrations were observed during growth on these four substrates. We mapped these changes onto the governing metabolic pathways to better understand how R. toruloides reprograms its metabolism to enable growth on these substrates. One notable finding concerns xylose metabolism, where poor expression of xylulokinase induces a bypass leading to arabitol production. Collectively, these results further our understanding of central carbon metabolism in R. toruloides during growth on different substrates. They may also help guide the metabolic engineering and development of better models of metabolism for R. toruloides.

The dataset includes the survey results about farmers’ perceptions of marginal land availability and the likelihood of a land pixel being marginal based on a machine learning model trained from the survey. Two spreadsheet files are the farmer and farm characteristics (marginal_land_survey_data_shared.xlsx), and the existing land use of marginal lands (land_use_info_sharing.xlsx). <b>Note:</b> the blank cells in these two spreadsheets mean missing values in the survey response. The GeoTiff file includes two bands, one the marginal land likelihood in the Midwestern states (0-1), the other the dominant reason of land marginality (0-5; 0 for farm size, 1 for growing season precipitation, 2 for root zone soil water capacity, 3 for average slope, 4 for growing season mean temperature, and 5 for growing season diurnal range of temperature). To read the data, please use a GIS software such as ArcGIS or QGIS.

This dataset contains soil chemical properties used to variation in soil fungal communities beneath Oreomunnea mexicana trees in the manuscript "Watershed-scale variation in potential fungal community contributions to ectomycorrhizal biogeochemical syndromes"

Data in this publication were used to analyze the factors that influence the abundance of eastern whip-poor-wills in the Midwest and to describe the diet of this species. These data were collected in Illinois in 2019 and 2020. Procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 19006

Healthy mares were administered phenylephrine to induce transient polycythemia secondary to splenic contraction. Data was collected at baseline (T0), 5 minutes (T1) and 2 hours (T2) post-phenylephrine infusion. Collected data included baseline CBC, chemistry, fibrinogen, and serum amyloid A; at each time point viscoelastic coagulation profiles (VCM Vet), traditional in-vitro coagulation profiles, and ultrasonographic measurements of the spleen were obtained.

Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 °C and 180 °C for 10 minutes) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.

The data provided in this submission are the gene annotations for the Illinois EBP pilot project samples, as well as the predicted proteins for each sample in FASTA format.

L-malic acid is widely used in the food, chemical, and pharmaceutical industries. Here, we report on production of malic acid from xylose, the second most abundant sugar in lignocellulosic hydrolysates, by engineered Saccharomyces cerevisiae. To enable malic acid production in a xylose-assimilating S. cerevisiae, we overexpressed PYC1 and PYC2, coding for pyruvate carboxylases, a truncated MDH3 coding for malate dehydrogenase, and SpMAE1, coding for a Schizosaccharomyces pombe malate transporter. Additionally, both the ethanol- and glycerol-producing pathways were blocked to enhance malic acid production. The resulting strain produced malic acid from both glucose and xylose, but it produced much higher titers of malic acid from xylose than glucose. Interestingly, the engineered strain had higher malic acid yield from lower concentrations (10 g L‒1) of xylose, with no ethanol production, than from higher xylose concentrations (20 and 40 g L‒1). As such, a fed-batch culture maintaining xylose concentrations at low levels was conducted and 61.2 g L‒1 of malic acid was produced, with a productivity of 0.32 g L‒1 h. These results represent successful engineering of S. cerevisiae for the production of malic acid from xylose, confirming that that xylose offers the efficient production of various biofuels and chemicals by engineered S. cerevisiae.

Supplemental document corresponding to a submission to Physiological Genomics (Data supplements and source materials must now be deposited in a community-recognized data repository or to a generalist public access repository if no community resource is available. See "Author/Production Requirements" for more information.) https://pg.msubmit.net/