Dataset Search

This dataset contains the data used for the publication “Aboveground rather than belowground productivity drives variability in Miscanthus x giganteus net primary productivity”. This dataset contains Miscanthus x giganteus biomass, carbon, and nitrogen tissue data for aboveground and belowground plant parts collected in 2021 for three different sites in Iowa with three different nitrogen application rates. Data at the Iowa sites were collected via biometric hand harvesting, belowground excavations, and soil coring both in-clump and beside-clump. Data were collected at two collection timepoints to calculate the contributions of belowground parts to Miscanthus x giganteus net primary productivity. This dataset also includes Miscanthus x giganteus and Switchgrass soil coring and excavation data collected in 2012 at the University of Illinois Urbana Champaign Energy Farm.

2′-Fucosyllactose (2′-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Bacillus subtilis have been engineered to produce 2′-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2′-FL, but accumulation of by-products due to overflow metabolism of glucose hampered efficient production of 2′-FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidative metabolism, for the production of 2′-FL by engineered yeast. Specifically, we modified an engineered S. cerevisiae strain capable of assimilating xylose to produce 2′-FL from a mixture of xylose and lactose. First, a lactose transporter (Lac12) from Kluyveromyces lactis was introduced. Second, a heterologous 2′-FL biosynthetic pathway consisting of enzymes Gmd, WcaG, and WbgL from E. coli was introduced. Third, we adjusted expression levels of the heterologous genes to maximize 2′-FL production. The resulting engineered yeast produced 25.5 g/L of 2′-FL with a volumetric productivity of 0.35 g/L∙h in a fed-batch fermentation with lactose and xylose feeding to mitigate the glucose repression. Interestingly, the major location of produced 2′-FL by the engineered yeast can be changed using different culture media. While 72% of the produced 2′-FL was secreted when a complex medium was used, 82% of the produced 2′-FL remained inside the cells when a minimal medium was used. As yeast extract is already used as food and animal feed ingredients, 2′-FL enriched yeast extract can be produced cost-effectively using the 2′-FL-accumulating yeast cells.

This dataset includes images and annotated counts for 150 airborne pollen samples from the Center for Tropical Forest Science 50 ha forest dynamics plot on Barro Colorado Island, Panama. Samples were collected once a year from April 1994 to June 2010.

Dataset associated with Jones and Ward BEAS-D-21-00106R2 submission: Parasitic cowbird development up to fledging and subsequent post-fledging survival reflect life history variation found across host species. Excel CSV files and .inp file with data used in nest survival and Brown-headed Cowbird post-fledging analyses and file with descriptions of each column. The CSV file is setup for logistic exposure models in SAS or R and the .inp file is setup to be uploaded into program MARK for multi-state recaptures only analysis. Species included in the analyses: American Robin, Blue Grosbeak, Brown Thrasher, Blue-winged Warbler, Carolina Chickadee, Chipping Sparrow, Common Yellowthroat, Dickcissel, Eastern Bluebird, Eastern Phoebe, Eastern Towhee, Field Sparrow, Gray Catbird, House Wren, Indigo Bunting, Northern Cardinal, Red-winged Blackbird, Tree Swallow, Yellow-breasted Chat, and Yellow Warbler.

This dataset includes the gas exchange and TDL (tunable diode laser) files between 4 accessions of Glycine soja and 1 elite accession of Glycine max (soybean) during light induction. In this V2, code files for Matlab and R are also included to calculate mesophyll conductance and calculate the limitation on photosynthesis, respectively.

Multiple sequence alignments from concatenated nuclear and mitochondrial genes and resulting phylogenetic tree files of fruit doves and their close relatives. Files include: BEAST input XML file (fruit_dove_beast_input.xml); a maximum clade credibility tree from a BEAST analysis (fruit_dove_beast_mcc.tre); concatenated multiple sequence alignment NEXUS files for the novel dataset (fruit_dove_concatenated_alignment.nex, 76 taxa, 4,277 characters) and the dataset with additional sequences (fruit_dove_plus_cibois_data_concatenated_alignment.nex, 204 taxa, 4,277 characters), both of which contain a MrBayes block including partition information; and 50% majority-rule consensus trees generated from MrBayes analyses, using the NEXUS alignment files as inputs (fruit_dove_mrbayes_consensus.tre, fruit_dove_plus_cibois_data_mrbayes_consensus.tre).

This dynamic photosynthesis model of soybean canopy is developed by Yu Wang (yuwangcn@illinois.edu), IGB, University of Illinois. If you want to know more details, please check the following publication Yu Wang, Steven J. Burgess, Elsa de Becker, Stephen P. Long. Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity? The Plant Journal.

This dataset contains transcribed entries from the "Prairie Directory of North America" (Adelman and Schwartz 2013) for the Tallgrass, Mixed Grass, and Shortgrass prairie regions of the united states. We identified the historical spatial extent of the Tallgrass, Mixed Grass, and Shortgrass prairie regions using Ricketts et al. (1999), Olson et al. (2001), and Dixon et al. (2014) and selected the counties entirely or partially within these boundaries from the USDA Forest Service (2022) file. The resulting lists of counties are included as separate files. The dataset contains information on publicly accessible grasslands and prairies in these regions including acreage and amenities like hunting access, restrooms, parking, and trails.

Data files associated with the assembly of mitochondrial minicircles from five species of parasitic lice. This includes data from four species in the genus Columbicola and from the human louse (Pediculus humanus). The files include FASTA sequences for all five species, reference sequences for read mapping approaches, resulting contigs produced by various assembly approaches, and alignments of human louse minicircles mapped to published sequences of the same species.

These are the data sets associated with our publication "Field borders provide winter refuge for beneficial predators and parasitoids: a case study on organic farms." For this project, we compared the communities of overwintering arthropod natural enemies in organic cultivated fields and wildflower-strip field borders at five different sites in central Illinois. Abstract: Semi-natural field borders are frequently used in midwestern U.S. sustainable agriculture. These habitats are meant to help diversify otherwise monocultural landscapes and provision them with ecosystem services, including biological control. Predatory and parasitic arthropods (i.e., potential natural enemies) often flourish in these habitats and may move into crops to help control pests. However, detailed information on the capacity of semi-natural field borders for providing overwintering refuge for these arthropods is poorly understood. In this study, we used soil emergence tents to characterize potential natural enemy communities (i.e., predacious beetles, wasps, spiders, and other arthropods) overwintering in cultivated organic crop fields and adjacent field borders. We found a greater abundance, species richness, and unique community composition of predatory and parasitic arthropods in field borders compared to arable crop fields, which were generally poorly suited as overwintering habitat. Furthermore, potential natural enemies tended to be positively associated with forb cover and negatively associated with grass cover, suggesting that grassy field borders with less forb cover are less well-suited as winter refugia. These results demonstrate that semi-natural habitats like field borders may act as a source for many natural enemies on a year-to-year basis and are important for conserving arthropod diversity in agricultural landscapes.

The Allan Lab has published a Fluidigm pipeline online. This is the url: https://github.com/HPCBio/allan-fluidigm-pipeline. This url includes a tutorial for running the pipeline. However it does not have test datasets yet. This tarball hosted at the Illinois Data Bank is the dataset that completes the github tutorial. It includes inputs (custom database of tick pathogens and fluidigm raw reads) and output files (tables of samples with taxonomic classifications).

Automatic and manual counts of black flies captured in Illinois.

This is the data set from the published manuscript 'Vertebrate scavenger guild composition and utilization of carrion in an East Asian temperate forest' by Inagaki et al.

Data extracted from Text, Tables and Figures of publications in summarizing crop responses to Free-Air CO2 Elevation (FACE)

This is the 5 states 5000 cells synthetic expression file we used for validation of SimiC, a single cell gene regulatory network inference method with similarity constraints. Ground truth GRNs are stored in Numpy array format, and expression profiles of all states combined are stored in Pandas DataFrame in format of Pickle files.

This data describes habitat use, availability, landscape level influences, and daily movement of dabbling ducks in the Wabash River Valley of southeastern Illinois and southwestern Indiana. It contains triangulated locations of individual ducks, associated habitat assignments of those locations, flood survey data to determine water availability, and randomly generated points to assess landscape level questions.

Dataset associated with Hoover et al AUK-19-093 submission: Local conspecific density does not influence reproductive output in a secondary cavity-nesting songbird. Excel CSV with all of the data used in analyses. Description of variables YEARS: year ORDINAL_DATE: number for what day of the year it is with 1 January = 1,……30 December = 365 SITE: acronym for each study site BOX: unique nest box identifier on each study site TREAT: designates whether nest box was in a high- or low- nest box density area within each study site ACTUAL_NO_NEIGHBORS: number of pairs of warblers using a nest box within 200 m of a given pair’s nest box CLUTCH_SIZE: number of warbler eggs in nest at the onset of incubation PROWN: number of warbler nestlings once eggs have hatched PROWF: number of warbler nestlings that fledged out of the nest box HATCH_SUCCESS: proportion of eggs in the nest that hatched FLEDG_SUCCESS: proportion of the nestlings that fledged from the nest box HATCH_SUCCESS2: binary category where “0” indicates there was some, and “1” indicates there was no hatching failure FLEDG_SUCCESS2: binary category where “0” indicates there was some, and “1” indicates there was no nestling failure (i.e. nestling death) BHCO_PARASIT2: binary category where “0” indicates no cowbird parasitism, and “1” indicates there was cowbird parasitism BHCOE: number of cowbird eggs in clutch BHCOF: number of cowbird nestlings that fledged from the nest PAIRID: unique number that identifies a male and female warbler that are together at a nest box and this number is the same in a subsequent nesting attempt or year if the same male and female are together again FEMALE_ID: unique identifier for each female which represents her leg band combination. Each letter represents a band with letters preceding the hyphen being on the right leg and after the hyphen the left leg FEM_AGE: binary category where “0” indicates a 1-year-old bird and “1” indicates a >1-year-old bird FEMALE_BREEDING_ATTEMPT: “1” indicates first, “2” indicates second,……..breeding attempt within a given year SECOND_ATTEMPT: for any female that fledged a brood in a given year, binary category where “0” represents that they did not, and “1” indicates that they did attempt a second brood that year F_TOT_PROWF: total reproductive output (number of warbler fledglings produced) for a given female in a given year MALE_ID: unique identifier for each male which represents his leg band combination. Each letter represents a band with letters preceding the hyphen being on the right leg and after the hyphen the left leg MALE_AGE2: binary category where “0” indicates a 1-year-old bird and “1” indicates a >1-year-old bird Provisioning_rate: total number of food provisions per nestling per hour by male and female warbler combined BROOD_MASS: average nestling mass (g) for the brood BROOD_TARSUS: average nestling tarsus length (mm) for the brood Brood_condition: unit-less index of nestling condition that uses the residuals of the BROOD_MASS/BROOD_TARSUS relationship A period (“.”) represents where data were not collected, not available, or because individual nest or female did not qualify for consideration of a category assignment. An empty cell represents no data available for this particular cell.

This dataset contains the protein sequences and trees used to compare Non-Ribosomal Peptide Synthetase (NRPS) condensation domains in the AMB gene cluster and was used to create figure S1 in Rojas et al. 2015. Instead of having to collect representative sequences independently, this set of condensation domain sequences may serve as a quick reference set for coarse classification of condensation domains.

The text file contains the original DNA nucleotide sequence data used in the phylogenetic analyses of Xue et al. (in review), comprising the 13 protein-coding genes and 2 ribosomal gene subunits of the mitochondrial genome. The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 30 taxa (species) and 13078 characters, indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes (version 3.2.6) beginning near the end of the file. The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the Methods section of the submitted manuscript. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the individual mitochondrial genes and for different codon positions of the protein-coding genes used for analyses in the programs MrBayes and IQ-Tree (version 1.6.8) (Table S2). Full citations for references listed in Table S1 can be found by searching GenBank using the corresponding accession number. The supplemental tables will also be linked to the article upon publication at the journal website.

This dataset includes microclimate species distribution models at a ~3 m2 spatial resolution and free-air temperature species distribution models at ~0.85 km2 spatial resolution for three plethodontid salamander species (Demognathus wrighti, Desmognathus ocoee, and Plethodon jordani) across Great Smoky Mountains National Park. We also include heatmaps representing the differences between microclimate and free-air species distribution models and polygon layers representing the fragmented habitat for each species' predicted range. All datasets include predictions for 2010, 2030, and 2050.

BAM files for evolved strains from migration rate selection experiments conducted in low viscosity (0.2% w/v) agar plates containing M63 minimal medium with 1mM of mannose, melibiose, N-acetylglucosamine or galactose

MATLAB files for the analysis of an ODE model for disease transmission. The codes may be used to find equilibrium points, study transient dynamics, evaluate the basic reproductive number (R0), and simulate the model when parameters depend on the independent variables. In addition, the codes may be used to perform local sensitivity analysis of R0 on the model parameters.

Data from a study on the behavior of blue-winged and golden-winged warblers. We were investigating vocalizations and how the species reconizes each other. There are banding, behavioral data from a playback study, and song data.

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.