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Data associated with the manuscript "Stable isotopes and diet metabarcoding reveal trophic overlap between native and invasive Banded Killifish (Fundulus diaphanus) subspecies." by Jordan H. Hartman, Mark A. Davis, Nicholas J. Iacaruso, Jeremy S. Tiemann, Eric R. Larson. For this project, we sampled six locations in Michigan and Illinois for Eastern and Western Banded Killifish and primary consumers. Using stable isotope analysis we found that Eastern Banded Killifish had higher variance in littoral dependence and trophic position than Western Banded Killifish, but both stable isotope and gut content metabarcoding analyses revealed an overlap in the diet composition and trophic position between the subspecies. This dataset provides the sampling locations, accession numbers for gut content metabarcoding data from the National Center for Biotechnology Information Sequence Read Archive, the assignment of each family used in the gut content metabarcoding analysis as littoral, pelagic, terrestrial, or parasite. and the raw stable isotope data from University of California Davis.

Data characterize zooplankton in Shelbyville Reservoir, Illinois, United States of America. Zooplankton were sampled with a conical zooplankton net (0.5m diameter mouth) when water was deeper than 2 m and by grab sample when water was shallower. Zooplankton samples were concentrated and subsampled with a Hensen-Stempel pipette following protocols described in Detmer et al. (2019). Zooplankton were identified to the lowest feasible taxonomic unit according to Pennak (1989) and Thorp and Covich (2001) and were enumerated in a 1 mL Sedgewick-Rafter cell. Subsamples were analyzed until at least 200 individuals were enumerated from each site.were counted across for each of the three main taxonomic groups (cladocerans, copepods, and rotifers). Given the variation in zooplankton concentrations at each site, this process often lead to far more than 200 individuals being counted (x̄ = 269, min = 200, max = 487). A summary of the sample size from each site can be found in Supplementary Table S2. Abundances were corrected for volume of water filtered. For rare taxa (< 20 individuals per sample), all individuals were measured for length. For abundant taxa, length measurements were collected on the first 20 organisms of each abundant taxon encountered in a subsample. Dry mass was calculated from equations for microcrustaceans, rotifers, and Chaoborus sp. (Rosen ,1981; Botrell et al., 1976; Dumont and Balvay, 1979).

Raw data from a survey of para-veterinary workers in Pakistan regarding knowledge, attitudes, and practices around ticks and tick-borne diseases. Between March and August 2023, we conducted a web-based survey among para-veterinarians recruited via email, text message, and face-to-face conversations.

Glucose and xylose are the major sugars present in cellulosic hydrolysates. The cellulosic sugars can be used for the production of platform chemicals. In this study, productions of lipid and ethanol by yeasts were compared for concentrated bioenergy sorghum syrup. Bioenergy sorghum was hydrothermally pretreated at 50% w/w solids in a continuous industrial reactor and sequentially mechanically refined using a burr mill to improve biomass accessibility for hydrolysis. Fed-batch enzymatic hydrolysis was conducted with 50% w/v solids loading and cellulase cocktail (50 FPU/g biomass) to achieve 230 g/L sugar concentration. Various strains of Rhodosporidium toruloides were evaluated for converting sugars into lipids, and strain Y-6987 had the highest lipid titer (9.2 g/L). The lipid titer was improved to 19.0 g/L by implementing a two-stage culture scheme, where the first stage was optimized for yeast growth and the second for lipid production. For ethanol production, the engineered Saccharomyces cerevisiae SR8ΔADH6 was used to coferment glucose and xylose. Ethanol fermentation was optimized for media nutrients (YP, YNB/urea, and urea), cellulosic sugar concentration, and sulfite conditioning to maximize the ethanol concentration from sorghum syrups. Fermentation of 70% v/v concentrated hydrolysate conditioned with sulfite produces 50.1 g/L ethanol from 141 g/L of sugars.

This dataset is part of a genome annoucement. The main folder PROKKA_results contain nine Prokka v.1.14.6 annotation files from nine Clostridium scindens genome sequences. Each file provide 12 output files including predicted protein sequences (.faa), nucleotide sequences of the predicted coding regions (.ffn), nucleotide sequence of the genome (.fna and .fsa), annotated genome in GenBank format (.gbk), steps recording performed during the annotation process (.log), error messages or warnings (.err), annotations in Sequin format (.sqn), summary of the annotations in tabular (.tbl), tab-separated values (.tsv) and plain text (.txt) formats.

The International Registry of Reproductive Pathology Database is part of pioneering work done by Dr. Kenneth McEntee to comprehensively document thousands of disease cases studies. His large and comprehensive collection of case reports and physical samples was complimented by development of the International Registry of Reproductive Pathology Database in the 1980s. The original FoxPro Database files and a migrated access version were completed by the College of Veterinary Medicine in 2016. Access CSV files were completed by the University of Illinois Library in 2017.

This dataset includes data on soil nitrous oxide fluxes, soil properties, and climate presented in the manuscript, "A conceptual model explaining spatial variation in soil nitrous oxide emissions in agricultural fields," published in Commucations Earth & Environment. Please refer to that publication for details about methodologies used to generate these data and for the experimental design.

This supporting information file contains codes related to pending publication Ge et al. Proc. Nat. Acad. Sci. USA, (revisions in review). The contents include a Mathematica code that solves the Laplace transformed equations and generates figures from the paper. A python code is included for generation of Figure 5 in the main text.

Count histories from camera traps and remotely sensed covariate data used in N-mixture modeling to assess the site use intensity of raccoons in Illinois.

Includes two files (.csv) behind all analyses and results in the paper published with the same title. <b>1) 'sites.species.counts'</b> is the raw 2018-2022 data from Angella Moorehouse (Illinois Nature Preserves Commission) including her 456 identified pollinator species and her raw counts per site (there may be a few errors of identification or naming, and there will always be name changes over time). Headers in columns F through Q correspond to the remnant-site labels in Figure 1 and Table 1 of the paper. Columns R to AB are the “nonremnant” sites, which have not been uniquely labelled since the specific sites aren't referenced anywhere in the manuscript. <b>2) 'C.scores'</b> has the 265 species assigned empirical C values (empirical.C) along with the four sets of expert C values and their confidence ranks (low, medium, high), and the Illinois/Indiana conservation ranks (S-ranks), following the methods described in the paper. Other headers in these files: - taxa.code: four-letter abbreviation for genus and specific name - genus: genus name - species: specific epithet - common.name: English name - group: general pollinator taxa group - empirical.C: empirically estimated conservatism score - expert#.C: conservatism score assigned by each of four experts - expert#.conf: expert's confidence in their conservatism score Blank cells in the site-species abundance matrix indicates species absence (or non-detection) Blank cells in C.scores.csv indicates missing S-ranks and unassigned C-scores (with associated missing confidence ranks) where experts lacked knowledge or confidence

The dataset is for a study conducted to understand genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single nucleotide polymorphisms (SNPs).

This study advances the production of potassium sorbate (KS) from triacetic acid lactone (TAL) utilizing food-grade solvents, ethanol (EtOH) and isopropyl alcohol (IPA). We have previously demonstrated the route to produce KS from TAL in tetrahydrofuran (THF) as the main solvent, but the use of THF is associated with environmental and health risks especially for food applications. The process employs a catalytic approach in food-grade solvents and includes three main steps: hydrogenation, etherification and hydrolysis, and ring-opening hydrolysis to produce KS from TAL. In the synthesis of KS from TAL, the use of IPA leads to higher yields and reduced reaction times compared to EtOH. As a result, the overall reaction time in IPA was reduced to 35.7 h, compared to 42.1 h in our previous study using THF and EtOH, while achieving a comparable KS yield of 84% from TAL. The synthesized KS exhibits a trans-2, trans-4 geometrical configuration, identical to that of commercially available KS. Through techno-economic analysis (TEA) and life cycle assessment (LCA), we estimated full-scale production of KS from sugarcane with the developed process in IPA could achieve a minimum product selling price (MPSP) of $8.27 per kg with a range of $7.06–10.16 per kg [5th–95th percentiles from 6000 Monte Carlo simulations] and a carbon intensity (CI) of 13.7 [9.6–18.6] kg CO2-eq per kg. This study highlights the synthesis of KS from TAL using food-grade solvents, demonstrating improved economic viability and environmental sustainability compared to our previous research (MPSP of $9.68 per kg [$8.47–11.45 per kg] and CI of 16.2 [12.0–21.2] kg CO2-eq per kg), as the total required reaction decreases while achieving the comparable overall yield of KS from TAL.

Nucleotide sequences from wild parsnip CYP71AJ4 (angelic in synthase. <a href ="https://www.ncbi.nlm.nih.gov/nuccore/EF191021">Genbank EF191021</a>) were obtained by Sanger sequencing. Seeds from individual plants from different populations were harvested to obtain corresponding cDNA. The cDNA was cloned and directly sequenced. Aminoacid translations were obtained using standard codon usage. Alignments of CYP71AJ4 sequences (involved in angular furanocoumarin biosynthesis) with as the reference sequence. Consistent amino acid variabilities were found between some populations. The relationship between sequencing variability and selective pressure is not yet known.

This dataset contains nucleotide sequences of 16S rRNA gene from phytoplasmas and other bacteria detected in phloem-feeding insects (Hemiptera, Auchenorrhyncha). The datasets were used to compare traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas in insect DNA samples. The file “Trivellone_etal_SangerSequencing.fas”, comprising 1397 positions (the longest sequence), includes 35 not aligned bacterial 16S rRNA sequences (16 phytoplasmas and 19 other bacterial strains) yielded using Sanger sequencing. The file “Trivellone_etal_AHEmethod1.fas” includes 34 not aligned bacterial 16S rRNA sequences (28 phytoplasmas and 6 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled using assembled based on ABySS v2.1.0 pipeline. The file “Trivellone_etal_AHEmethod2.fas” includes 31 not aligned bacterial 16S rRNA sequences (27 phytoplasmas and 4 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled based on the HybPiper v2.0.1 pipeline . Additional details in the "read_me_trivellone.txt" file attached below.

Bioenergy sorghum (Sorghum bicolor L. Moench) is a promising crop for contributing to the United States bioenergy supply. However, the varying limitations of the marginal lands targeted for its cultivation present a management challenge. This two-year study aimed to investigate how the limitations associated with marginal cropland impact the effects of nitrogen fertilization on the yield of bioenergy sorghum and the uptake of 11 macro- (N, P, K, Ca, Mg, and S) and micronutrients (Fe, Mn, Zn, Cu, and B). The study contrasted prime cropland in central Illinois (Urbana) with three marginal cropland sites in southern (Ewing) and central Illinois (Fairbury and Pesotum). These marginal cropland sites are characterized by varying limitations, including low soil fertility (P and K limitations), leaching and erosion, and flooding, respectively. Four nitrogen rates (0, 56, 112, and 168 kg N ha−1) were tested under eight environments. The average yields and ranges of sorghum biomass were 20.2 (17.0–23.2) Mg ha−1 in Urbana, 18.1 (13.1–19.8) Mg ha−1 in Ewing, 13.8 (9.0–17.3) Mg ha−1 in Fairbury, and 23.3 (14.6–33.0) Mg ha−1 in Pesotum. Optimal N rates were 56 N in Pesotum and 112 N in Urbana, Ewing, and Fairbury. Tissue macronutrient contents in Urbana were generally higher than in the marginal croplands, while micronutrient contents did not show discernible trends. Increasing N rate generally correlated with the macronutrient removal except in Ewing. Comparable sorghum biomass yields were observed between prime and marginal croplands (averaging 18.3 Mg ha−1), but optimal N rates varied between 56 N and 112 N. This suggests that yield gaps can be narrowed by applying the optimal N rates for the respective locations. However, increased removals of macronutrients, especially P and K, with increasing yields indicate the need to revise fertilizer recommendations, particularly for soils deficient in these nutrients. Our study suggests that while sorghum production on marginal cropland is feasible, N management needs to be adapted to the unique limitations associated with various types of marginal cropland.

This dataset consists of the secondary ion mass spectrometry (SIMS) depth profiling data that was collected with a Cameca NanoSIMS 50 instrument from a 10 micron by 10 micron region on a Madin-Darby canine kidney (MDCK) cell that had been metabolically labeled so most of its sphingolipids and cholesterol contained the rare nitrogen-15 oxygen-18 isotopes, respectively.

This dataset is associated with the manuscript "Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment" This dataset includes 2 Excel files: 1) raw_data_bioassay.xlsx: this file contains the raw data for waxworm bioassay. There are 2 worksheets within this file: - LC50: raw data for measuring LC50 in the laboratory and field strain of Galleria mellonella. - RGR: Relative Growth Rate, raw data for measuring body weight of field strain of Galleria mellonella . 2) raw-data_RT-qPCR.xlsx: this file contains raw data (Ct value) of RT-qPCR.

Data sets from "Inferring Species Trees from Gene-Family with Duplication and Loss using Multi-Copy Gene-Family Tree Decomposition." It contains trees and sequences simulated with gene duplication and loss under a variety of different conditions. <b>Note:</b> - trees.tar.gz contains the simulated gene-family trees used in our experiments (both true trees from SimPhy as well as trees estimated from alignements). - sequences.tar.gz contains simulated sequence data used for estimating the gene-family trees as well as the concatenation analysis. - biological.tar.gz contains the gene trees used as inputs for the experiments we ran on empirical data sets as well as species trees outputted by the methods we tested on those data sets. - stats.txt list statistics (such as AD, MGTE, and average size) for our simulated model conditions.

This study evaluates the bioethanol potential in response to irrigation (IR) and non-irrigation (NIR) of oilcane (OC) during a seasonal drought prior harvest. The juice was extracted through mechanical pressing of stems and fermented by Ethanol Red® yeast to produce first-generation bioethanol. Hydrothermal pretreatment followed by enzymatic hydrolysis of bagasse was performed to produce monomeric sugars from structural carbohydrates. The hydrolysates were fermented with engineered yeast for second-generation bioethanol production. The irrigated oilcane juice (276.3 ± 8.9 g/L) constitutes higher sugar concentrations than non-irrigated oilcane juice (236.5 ± 2.2 g/L). The enzymatic hydrolysis of IR-OC and NIR-OC pretreated bagasse yielded similar concentrations of 247.5 ± 2.22 and 249.7 ± 4.98 g/L fermentable sugars. Industry-relevant bioethanol titers of ≥99 g/L and ≥75 g/L were achieved from juice and hydrolysates, respectively. Therefore, the non-irrigation regime did not impact the 1G and 2G bioethanol titers. However, the overall bioethanol yield can be lower due to the reduction of stem yield (8 %) per hectare.

This dataset includes neuronal development of the Caenorhabditis elegans dauer and adult.

In a set of field studies across four years, the effect of self-shading on photosynthetic performance in lower canopy sorghum leaves was studied at sites in Champaign County, IL. Photosynthetic parameters in upper and lower canopy leaves, carbon assimilation, electron transport, stomatal conductance, and activity of three C4-specific photosynthetic enzymes, were compared within a genetically diverse range of accessions varying widely in canopy architecture and thereby in the degree of self-shading. Accessions with erect leaves and high light transmission through the canopy are henceforth referred to as ‘erectophile’ and those with low leaf erectness, ‘planophile’. In the final year of the study, bundle sheath leakiness in erectophile and planophile accessions was also compared.

This dataset includes data on soil properties, soil N pools, and soil N fluxes presented in the manuscript, "Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes". Please refer to that publication for details about methodologies used to generate these data and for the experimental design. For this verison 2, we added specific gross nitrogen mineralization rates (ugN/gOM/d), microbial biomass carbon (ugC/gdw), microbial biomass nitrogen (ugN/gdw) and microbial biomass C:N ratios to the newest version of the data set. Additionally, we updated values for gross nitrogen mineralization, microbial NO3 assimilation and microbial NH4 assimilation to reflect slight changes in data processing. Those changes are reflected in "220829_All data_repository.csv". "220829_nitrogen_mineralization_readme.txt " is updated readme for the new file. The other 2 files begin with “220426_” are older version and same as in V1.

These data were used to make a predictive model of when ornate box turtles (Terrapene ornata) are likely to be above ground and at risk from fire. The data were generated using shell temperatures, soil temperatures at 0.35 m deep from known overwintering sites, and the spring and fall soil temperature inversion dates during 2019–2022 to infer if 26 individual radio-tracked turtles were above or below ground at three sites in Illinois.