Dataset Search

Honey bee (apis mellifera) MERFISH data set prepared by the Han lab, from brains collected by the Robinson lab at UIUC. Dataset is comprised of ~22 thousand cells and 130 genes with x,y locations for each cell. Jupyter notebook file is included as an example to load the data using Scanpy.

Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metabolize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endogenous PDCs will eliminate ethanol production, but the resulting strain suffers from C2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product without the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae expressing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L−1 from the 12 g L−1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.

Data was generated from a field and lab study to determine the influence of thermal variation in livewells on largemouth bass recovery from angling tournaments. The field study data includes temperature data from inside angler livewells during a tournament day. This was collected across four tournaments. The laboratory data was generated from a series of experiments simulating tournament practices and trends in thermal variation within livewells observed in the field proponent. Following simulation, blood was collected to determine levels of analytes consistent with primary, secondary, and tertiary stress response in largemouth bass. Reflex impairment was also included.

This repository includes scripts and datasets for the paper, "Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy" submitted to Bioinformatics.

Steady-state and dynamic gas exchange data for maize (B73), sugarcane (CP88-1762) and sorghum (Tx430)

Dataset includes temperature data (local average April daily temperatures), first egg dates and reproductive output of Prothonotary Warblers breeding in southernmost Illinois, USA. Also included are arrival dates for warblers returning to breeding grounds from wintering grounds, and global temperature anomaly data for comparison with local temperatures. These data were used in the manuscript entitled "Warmer April Temperatures on Breeding Grounds Promote Earlier Nesting in a Long-Distance Migratory Bird, the Prothonotary Warbler" published in Frontiers in Ecology and Evolution. A rich text file is included with explanations of each variable in the dataset.

This dataset includes supporting data for our article 'Assessing long-term impacts of cover crops on soil organic carbon in the central U.S. Midwestern agroecosystems'. The dataset contains carbon fluxes and SOC benefits from cover crops at six cover crop experiment sites in Illinois with three rotation systems: (1) without-cover-crop (maize-soybean rotations), (2) non-legume-preceding-maize (maize-annual ryegrass-soybean-annual ryegrass rotations), and (3) legume-preceding-maize (maize-cereal rye-soybean-hairy vetch rotations). <b>*NOTE:</b> there should be 13 files + 1 readme file, instead of 15 files as mentioned in readme.

Femoral skeletal traits (cross-sectional properties, maximum distal metaphyseal breadth of the femur, and maximum superior/inferior femoral head diameter) of 219 Taiwanese subadult individuals (aged 0 to 17) as used in the manuscript "Allometric scaling and growth: evaluation and applications in subadult body mass estimation."

This data set documents bat activity (counts per detector-night per phonic group) and bat diversity (number of bat species per detector-night) in relation to distance to the nearest forested corridor in a row crop agriculture dominated landscape and in relation to relative crop pest abundance. This data set was used to assess if bats were homogeneously distributed over a near-uninterrupted agricultural landscape and to assess the importance of forested corridors and the presence of pest species on their distribution across the landscape. Data was collected with 50 AudioMoth bat detectors along 10 transects, with each transect having 5 detectors. The transects started at a forest corridor and extended out for 4 km into uninterrupted row crop agriculture. Pest abundance was extrapolated from data collected in the same county during the same time as the study. Potentially important weather covariates were extracted from the nearest operational weather station.

This dataset contains the amino acid and nucleotide alignments corresponding to the phylogenetic analyses of South et al. 2020 in Systematic Entomology. This dataset also includes the gene trees that were used as input for coalescent analysis in ASTRAL.

The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".

This dataset contains raw data of plasma glucose, insulin, c-peptide, GLP-1, and FGF21 collected as part of a study aimed to study alcohol pharmacokinetics in women who underwent metabolic surgery.

This is the dataset used in the BioScience publication of the same name. More information about this dataset: Interested parties can request data from the Critical Trends Assessment Program, which was the source for the data on natural areas in this study. More information on the program and data requests can be obtained by visiting the program webpage. Critical Trends Assessment Program, Illinois Natural History Survey. http://wwx.inhs.illinois.edu/research/ctap/ These spatial datasets were used for analyses: Illinois Natural History Survey. 2003. Illinois GAP analysis land cover classification 1999-2000, 1:100 000 Scale, Raster Digital Data, Version 2.0. Champaign, IL, USA. Illinois State Geological Survey. 1995. Illinois Landcover Thematic Map Coverage Map 1991-1995. Champaign, IL, USA. Illinois State Geological Survey. 2001. Illinois Landcover Thematic Map Coverage Map 1999-2000. Champaign, IL, USA. USDA National Agricultural Statistics Service Cropland Data Layer. 1999-2015. Published crop-specific data layer [Online]. Available at https://nassgeodata.gmu.edu/CropScape/. USDA-NASS, Washington, DC. Information on agricultural practices and landcover changes were derived from the following U.S. Department of Agriculture (USDA) resources: USDA Economic Research Service. 2016. Adoption of Genetically Engineered Crops in the U.S. Available at http://www.ers.usda.gov/data-products/. USDA-ERS, Washington, DC. USDA Natural Resources Conservation Service. 2015. Summary Report: 2012 National Resources Inventory. https://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/nrcseprd396218.pdf. USDA-NRCS, Washington, DC, and Center for Survey Statistics and Methodology, Iowa State University, Ames, Iowa.

High-speed X-ray videos of four E. abruptus specimens recorded at the Advanced Photron Source (Argonne National lab) in the Summer of 2018 and corresponding position data of landmarks tracked during the motion. See readme file for more details.

Data from census of peer-reviewed papers discussing nosZ and published from 2013 to 2019. These data were reported in the manuscript titled, "Beyond denitrification: the role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions" published in Global Change Biology as an Invited Report.

The data file contains a list of included studies with their detailed metadata, taken from Cochrane reviews which were used in a project associated with the manuscript "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

Video footage of an Eastern Box Turtle (Terrapene carolina carolina) partially predating a Field Sparrow nest (Spizella pusilla) at 0845 h on the 31 of May 2020. Please note that the date on the video footage is incorrect due to user error, but the time is correct.

A mechanistic functional structural plant model. The .gsz file includes a parameterised maize and soybean to be used in GRoIMP software https://grogra.de/. The current model is parameterised to maize cultivar DKC63-21RIB and soybean cultivar AG36X6 for the 2019 growing season in Champaign, IL USA.

Perennial crops have been the focus of bioenergy research and development for their sustainability benefits associated with high soil carbon (C) and reduced nitrogen (N) requirements. However, perennial crops mature over several years and their sustainability benefits can be negated through land reversion. A photoperiod‐sensitive energy sorghum (Sorghum bicolor) may provide an annual crop alternative more ecologically sustainable than maize (Zea mays) that can more easily integrate into crop rotations than perennials, such as miscanthus (Miscanthus × giganteus). This study presents an ecosystem‐scale comparison of C, N, water and energy fluxes from energy sorghum, maize and miscanthus during a typical growing season in the Midwest United States. Gross primary productivity (GPP) was highest for maize during the peak growing season at 21.83 g C m−2 day−1, followed by energy sorghum (17.04 g C m−2 day−1) and miscanthus (15.57 g C m−2 day−1). Maize also had the highest peak growing season evapotranspiration at 5.39 mm day−1, with energy sorghum and miscanthus at 3.81 and 3.61 mm day−1, respectively. Energy sorghum was the most efficient water user (WUE), while maize and miscanthus were comparatively similar (3.04, 1.75 and 1.89 g C mm−1 H2O, respectively). Maize albedo was lower than energy sorghum and miscanthus (0.19, 0.26 and 0.24, respectively), but energy sorghum had a Bowen ratio closer to maize than miscanthus (0.12, 0.13 and 0.21, respectively). Nitrous oxide (N2O) flux was higher from maize and energy sorghum (8.86 and 12.04 kg N ha−1, respectively) compared with miscanthus (0.51 kg N ha−1), indicative of their different agronomic management. These results are an important first look at how energy sorghum compares to maize and miscanthus grown in the Midwest United States. This quantitative assessment is a critical component for calibrating biogeochemical and ecological models used to forecast bioenergy crop growth, productivity and sustainability.

Raw data of Auchenorrhyncha (Hemiptera) species presence and abundance from samples collected as part of Morgan Brown's M.S. thesis entitled "Investigating changes in Auchenorrhyncha (Hemiptera) communities in Illinois prairies over 25 years." Collection_Events_MBrown.pdf contains information that corresponds to each collection event code listed in the raw data files, including coordinates, date of collection, collection method, and name of collector. Each CSV file contains Auchenorrhyncha species presence and abundance data from each sampling area in Illinois: Route 45 Railroad Prairie, Richardson Wildlife Foundation, Mason County nature preserves, and Twelve Mile Prairie. Variables included in the CSV files include: Family: Taxonomic family to which each species belongs Subfamily: Taxonomic subfamily to which each species belongs Tribe: Taxonomic tribe to which each species belongs Species: Lowest taxonomic level to which individuals were identified The first row of column 5 to the end are collection event codes which correspond to each code listed in the PDF * New in V2: The CSV files originally uploaded in V1 contained outdated species names. V2 provides updated CSV files with the corrected names. * New in V3: There were some inconsistencies in the collection event codes listed in the PDF and CSV files uploaded in V1 and V2. V3 provides updated PDF and CSV files with the corrected codes. File update status: Collection_Events_MBrown_V2.pdf -> updated in this V3 (in V2 it remained the same as in V1 but now is updated in V3) MasonCounty_RawData_V3.csv -> updated in this V3 RichardsonWildlifeFoundation_RawData_V2.csv -> remains the same as in V2 Route45_RawData_V3.csv -> updated in this V3 TwelveMilePrairie_RawData_V3.csv -> updated in this V3

This is a general description of the datasets included in this upload; details of each dataset can be found in the individual README.txt in each compressed folder. We have: 1. ROSE-HF.tar.gz 2. ROSE-LF.tar.gz HF (high fragmentary): 50% of the sequences are made fragmentary, which have average lengths of 25% of the original lengths with a standard deviation of 60 bp. LF (low fragmentary): 25% of the sequences are made fragmentary, which have average lengths of 50% of the original lengths with a standard deviation of 60 bp. The seven ROSE datasets made fragmentary are: 1000L1, 1000L3, 1000L4, 1000M3, 1000S1, 1000S2 and 1000S4. "ROSE-HF.tar.gz" contains HF versions of the seven ROSE datasets. "ROSE-LF.tar.gz" contains LF versions of the seven ROSE datasets.

Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.

Data are from a long-term fire manipulation experiment in the Missouri Ozarks, USA. Data include the raw, annual ring-width increment (rwl), basal area increment (BAI), population-level annual growth resistance (Drs) and resilience (Drl) to drought, intrinsic water use efficiency values (WUEi) and oxygen isotopic composition of individual radial growth rings (δ18O) from southern red oak (Quercus falcata) and post oak (Q. stellata) trees. ---------------------- TITLE: Data for "Sixty-five years of fire manipulation reveals climate and fire interact to determine growth rates of Quercus spp." ---------------------- FILE OVERVIEW: This dataset contains four (4) CSV files as described below: Refsland_et_al_ECS20-0465_BAI.csv: annual basal area increment between 1948-2015 for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_DroughtIndices.csv: population-level drought resistance and resilience of trees during each target drought period Refsland_et_al_ECS20-0465_WUEi.csv: carbon isotope indicators of drought stress for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_d18Or.csv: oxygen isotope indicators of drought stress for trees across the fire manipulation experiment ---------------------- VARIABLE EXPLANATION: All the variables in those four files are explained as below: treeID: unique character string that identifies subject tree block: integer (1, 2) that identifies the study block plot: integer (1-12) that identifies the plot nested within each study block trt: character string (Annual, Control, Periodic) that identifies the fire treatment of a given plot species: character string (Quercus falcata, Quercus stellata) that identifies species of subject tree year: integer (1948-2015) that identifies the dated year of each tree ring rwl_mm: numerical value representing the annual tree ring-width, in mm bai_cm2: numerical value representing the annual basal area increment, in cm2 timeperiod: integer value (1953, 1964, 2007, 2012) representing the periods encompassing target dry and wet years Drs_2yr: numerical value representing the drought resistance, defined as the population-level annual growth of trees during drought years relative to pre-drought years for a given time period Drl_2yr: numerical value representing the drought resilience, defined as the population-level annual growth of trees following drought years relative to pre-drought years for a given time period stand_ba_m2ha: numerical value representing the total basal area of a given plot, in m2 per ha stand_density_stems_ha: numerical value representing the total stem density of a given plot, in stems per ha pool: numerical value (1-40) identifying the set of tree ring samples pooled for analysis. Samples were pooled by block, plot, year and species period: integer value (1953, 1964, 1980, 2007, 2012) representing the periods encompassing target dry and wet years type: character string (Dry, Wet) indicating the water availability of a given year d13C: numerical value representing the carbon isotopic composition of radial growth rings within a given sample pool, in per mil WUEi: numerical value representing the annual intrinsic water use efficiency of radial growth rings within a given sample pool d18O: numerical value representing the oxygen isotopic composition of radial growth rings within a given sample pool, in per mil

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ∼0.6 to ∼1.5 kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. An excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.