Dataset Search Results

Respiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62 ± 0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.

Microbial fermentation provides a sustainable method of producing valuable chemicals. Adding dynamic control to fermentations can significantly improve titers, but most systems rely on transcriptional controls of metabolic enzymes, leaving existing intracellular enzymes unregulated. This limits the ability of transcriptional controls to switch off metabolic pathways, especially when metabolic enzymes have long half-lives. We developed a two-layer transcriptional/post-translational control system for yeast fermentations. Specifically, the system uses blue light to transcriptionally activate the major pyruvate decarboxylase PDC1, required for cell growth and concomitant ethanol production. Switching to darkness transcriptionally inactivates PDC1 and instead activates the anti-Pdc1p nanobody, NbJRI, to act as a genetically encoded inhibitor of Pdc1p accumulated during the growth phase. This dual transcriptional/post-translational control improves the production of 2,3-BDO and citramalate by up to 100 and 92% compared to using transcriptional controls alone in dynamic two-phase fermentations. This study establishes the NbJRI nanobody as an effective genetically encoded inhibitor of Pdc1p that can enhance the production of pyruvate-derived chemicals.

Microbial production of chemicals may suffer from inadequate cofactor provision, a challenge further exacerbated in yeasts due to compartmentalized cofactor metabolism. Here, we perform cofactor engineering through the decompartmentalization of mitochondrial metabolism to improve succinic acid (SA) production in Issatchenkia orientalis. We localize the reducing equivalents of mitochondrial NADH to the cytosol through cytosolic expression of its pyruvate dehydrogenase (PDH) complex and couple a reductive tricarboxylic acid pathway with a glyoxylate shunt, partially bypassing an NADH-dependent malate dehydrogenase to conserve NADH. Cytosolic SA production reaches a titer of 104 g/L and a yield of 0.85 g/g glucose, surpassing the yield of 0.66 g/g glucose constrained by cytosolic NADH availability. Additionally, expressing cytosolic PDH, we expand our I. orientalis platform to enhance acetyl-CoA-derived citramalic acid and triacetic acid lactone production by 1.22- and 4.35-fold, respectively. Our work establishes I. orientalis as a versatile platform to produce markedly reduced and acetyl-CoA-derived chemicals.

Data was generated from juvenile paddlefish acclimated to one of three different temperatures (13.0°C, 17.5°C, or 22.0°C) for two weeks. After which, fish were subjected to one of two experiments, one being simulated angling in which physiological parameters (stress hormones, lactate, glucose, ions, and oxygen transport parameters were evaluated in plasma or whole blood), the other experiment consisted of critical thermal maxima tests. Data set includes physiological parameters, water quality temperatures, and morphometric data generated from these experiments and fish.

Chemical-free pretreatments are attracting increased interest because they generate less inhibitor in hydrolysates. In this study, pilot-scaled continuous hydrothermal (PCH) pretreatment followed by disk refining was evaluated and compared to laboratory-scale batch hot water (LHW) pretreatment. Bioenergy sorghum bagasse (BSB) was pretreated at 160-190 °C for 10 min with and without subsequent disk milling. Hydrothermal pretreatment and disk milling synergistically improved glucose and xylose release by 10-20% compared to hydrothermal pretreatment alone. Maximum yields of glucose and xylose of 82.55% and 70.78%, respectively were achieved, when BSB was pretreated at 190 °C and 180 °C followed by disk milling. LHW pretreated BSB had 5-15% higher sugar yields compared to PCH for all pretreatment conditions. The surface area improvement was also performed. PCH pretreatment combined with disk milling increased BSB surface area by 31.80-106.93%, which was greater than observed using LHW pretreatment.

The oleaginous yeast Rhodosporidium toruloides is considered a promising candidate for production of chemicals and biofuels thanks to its ability to grow on lignocellulosic biomass, and its high production of lipids and carotenoids. However, efforts to engineer this organism are hindered by a lack of suitable genetic tools. Here we report the development of a CRISPR/Cas9 system for genome editing in R. toruloides based on a fusion 5S rRNA–tRNA promoter for guide RNA (gRNA) expression, capable of greater than 95% gene knockout for various genetic targets. Additionally, multiplexed double‐gene knockout mutants were obtained using this method with an efficiency of 78%. This tool can be used to accelerate future metabolic engineering work in this yeast.

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

Golden Gate assembly is one of the most widely used DNA assembly methods due to its robustness and modularity. However, despite its popularity, the need for BsaI-free parts, the introduction of scars between junctions, as well as the lack of a comprehensive study on the linkers hinders its more widespread use. Here, we first developed a novel sequencing scheme to test the efficiency and specificity of 96 linkers of 4-bp length and experimentally verified these linkers and their effects on Golden Gate assembly efficiency and specificity. We then used this sequencing data to generate 200 distinct linker sets that can be used by the community to perform efficient Golden Gate assemblies of different sizes and complexity. We also present a single-pot scarless Golden Gate assembly and BsaI removal scheme and its accompanying assembly design software to perform point mutations and Golden Gate assembly. This assembly scheme enables scarless assembly without compromising efficiency by choosing optimized linkers near assembly junctions.

Sugarcane, a tropical C4 grass in the genus Saccharum (Poaceae), accounts for nearly 80% of sugar produced worldwide and is also an important feedstock for biofuel production. Generating transgenic sugarcane with predictable and stable transgene expression is critical for crop improvement. In this study, we generated a highly expressed single copy locus as landing pad for transgene stacking. Transgenic sugarcane lines with stable integration of a single copy nptII expression cassette flanked by insulators supported higher transgene expression along with reduced line to line variation when compared to single copy events without insulators by NPTII ELISA analysis. Subsequently, the nptII selectable marker gene was efficiently excised from the sugarcane genome by the FLPe/FRT site-specific recombination system to create selectable marker free plants. This study provides valuable resources for future gene stacking using site-specific recombination or genome editing tools.

Data sets for material included in "A 13-year record indicates differences in the duration and depth of soil carbon accrual among potential bioenergy crops" by Kantola et al., 2025, in Global Change Biology Bioenergy. Data include soil organic carbon (SOC), carbon stable isotope ratios, annual belowground biomass, and annual post-harvest litter for four crops, maize/soybean, miscanthus, switchgrass, and prairie, between 2008 and 2021.

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780′, in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus, this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis. Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

Yarrowia lipolytica has been used to produce both citric acid and lipid-based bioproducts at high titers. In this study, we found that pH differentially affects citric acid and lipid production in Y. lipolytica W29, with citric acid production enhanced at more neutral pH’s and lipid production enhanced at more acid pH’s. To determine the mechanism governing this pH-dependent switch between citric acid and lipid production, we profiled gene expression at different pH’s and found that the relative expression of multiple transporters is increased at neutral pH. These results suggest that this pH-dependent switch is mediated at the level of citric acid transport rather than changes in the expression of the enzymes involved in citric acid and lipid metabolism. In further support of this mechanism, thermodynamic calculations suggest that citric acid secretion is more energetically favorable at neutral pH’s, assuming the fully protonated acid is the substrate for secretion. Collectively, these results provide new insights regarding citric acid and lipid production in Y. lipolytica and may offer new strategies for metabolic engineering and process design.

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.

Conversion of corn fiber to ethanol in the dry grind process could increase ethanol yields, reduce downstream processing costs and improve overall process profitability. This work investigates the in-situ conversion of corn fiber into ethanol (cellulase addition during simultaneous saccharification and fermentation) during dry grind process. Addition of 30 FPU/g fiber cellulase resulted in 4.6% increase in ethanol yield compared to the conventional process. Use of excess cellulase (120 FPU/g fiber) resulted in incomplete fermentation and lower ethanol yield compared to the conventional process. Multiple factors including high concentrations of ethanol and phenolic compounds were responsible for yeast stress and incomplete fermentation in excess cellulase experiments.

Most native producers of ribosomally synthesized and post-translationally modified peptides (RiPPs) utilize N-terminal leader peptides to avoid potential cytotoxicity of mature products to the hosts. Unfortunately, the native machinery of leader peptide removal is often difficult to reconstitute in heterologous hosts. Here we devised a general method to produce bioactive lanthipeptides, a major class of RiPP molecules, in Escherichia coli colonies using synthetic biology principles, where leader peptide removal is programmed temporally by protease compartmentalization and inducible cell autolysis. We demonstrated the method for producing two lantibiotics, haloduracin and lacticin 481, and performed analog screening for haloduracin. This method enables facile, high throughput discovery, characterization, and engineering of RiPPs.

This is the data set for the article entitled "Pollinator seed mixes are phenologically dissimilar to prairie remnants," a manuscript pending publication in Restoration Ecology. This represents the core phenology data of prairie remnant and pollinator seed mixes that were used for the main analyses. Note that additional data associated with the manuscript are intended to be published as a supplement in the journal. * In this V2, a second tab was added to the Rest.Ecol.data.xlsx file. This new sheet listed original data source citations that match the RELIX data base, a sister project.

Purpose-grown perennial herbaceous species are nonfood crops specifically cultivated for bioenergy production and have the potential to secure bioenergy feedstock resources while enhancing ecosystem services. This study assessed soil greenhouse gas emissions (CO2 and N2O), nitrate (NO3-N) leaching reduction potential, evapotranspiration (ET), and water-use efficiency (WUE) of bioenergy switchgrass (Panicum virgatum L.) in comparison to corn (Zea mays L.). The study was conducted on field-scale plots in Urbana, IL, during the 2020–2022 growing seasons. Switchgrass was established in 2020 and urea-fertilized at 56 kg N ha−1 year−1. Corn management followed best management practices for the US Midwest, including no-till and 202 kg N ha−1 year−1 fertilization, applied as urea–ammonium nitrate (32%). Our results showed lower direct N2O emissions in switchgrass compared to corn. Although soil CO2 emissions did not differ significantly during the establishment year, emissions in subsequent years were over 50% higher in switchgrass than in corn, likely due to increased belowground biomass, which was over five times higher in switchgrass. Nitrate-N leaching decreased as the switchgrass stand matured, reaching 80% lower than in corn by the third year. Differences in ET and WUE between corn and switchgrass were not significant; however, results indicate a trend toward reduced WUE in switchgrass under drought, driven by lower aboveground biomass production. Our study demonstrates that switchgrass can be implemented at a commercial scale without negatively impacting the hydrological cycle, while potentially reducing N losses through nitrate-N leaching and soil N2O emissions, and enhancing belowground C storage.

Miscanthus x giganteus (Mxg) is a promising perennial crop for producing natural colorants, renewable fuels, and bioproducts. However, natural recalcitrance and high pretreatment cost are major barriers to their complete conversion. In this study, a green processing method has been investigated for efficient recovery of natural pigments (anthocyanins), fermentable sugars, and pure lignin from Mxg genotypes using choline chloride-based natural deep eutectic solvents (NADES) systems. Interestingly, choline chloride: lactic acid (ChCl: LA) NADES-processed biomass resulted in 67.8 ± 2.1 μg g−1 of anthocyanins from dry biomass. A maximum of 87.4%–94.1% glucose yield was achieved after enzymatic saccharification. The effective extraction of lignin with high purity with higher β-aryl ether (βO4) bonds from advanced crops is crucial for lignin valorization. Notably, highly pure lignin (≈93.4% ± 1.4%) is achieved after low-temperature NADES pretreatment while retaining lignin’s native structure. 31P nuclear magnetic resonance demonstrated that total phenolics for ChCl: LA-lignin resulted in 1.20 mmol g−1 hydroxyls. The relative monolignol composition of syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H) is 19.0, 65.7, and 14.3%, respectively, as evidenced by heteronuclear single quantum coherence analysis. This study provides a novel approach for obtaining high-purity lignin for catalytic depolymerization for oligomers and bifunctional monoaromatics production and leverages current cellulosic biorefinery technologies.

Data from the 2025 publication in the Wilson Journal of Ornithology with the same name.

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.

Supplementary data and code associated with the Biogeosciences paper published by Cecilia Prada et al. "Soil and Biomass Carbon Storage is Much Higher in Central American than Andean Montane Forests". There are 16 files associated with this paper (1) AGB.csv providing the site, plot, treeID, mnemn, family, agb, and AGcarbon for each tree in the dataset. Column headings are described in the file AGB_metadata.csv (2) AGB_metadata.csv Metadata (column descriptions) for AGB.csv (3) CWD_D.csv Complete information on the downed coarse woody debris (CWD) measured in each plot (4) CWD_D_metadata.csv Metadata (column descriptions) for CWD_D.csv (5) CWD_S.csv Complete information on the standing coarse woody debris measured in each plot (6) CWD_S_metadata.csv Metadata (column descriptions) for CWD_S.csv (7) SoilC.csv Estimated soil carbon storage (Mg C) at each sampling location in each plot (8) SoilC_metadata.csv Metadata (column descriptions) for SoilC.csv (9) Table.csv Data source, soil carbon value (Mg C) and elevation from published data sources (10) Table_metadata.csv Metadata (column descriptions) for Table.csv (11) TableS1.csv Data source, above ground carbon value (Mg C) and elevation from published data sources (12) TableS1_metadata.csv Metadata (column descriptions) for TableS1.csv (13) RScript.R Annotated code for data analysis and figures (14)Full_dataset.csv Full set of environmental data and carbon data by plot (15) Full_dataset_metadata.csv Metadata (column descriptions) for Full_dataset.csv (16) Species list and species codes.csv Full family, genus and species names for the species codes (column mnemn in AGB.csv)

This dataset includes three data files for linking species' climate sensitivity, trait combinations, and listing status. It contains species occurrence data within Hydrologic Unit Code 12 (HUC12) watersheds, along with trait information and Rarity and Climate Sensitivity (RCS) index scores for lotic caddisflies, stoneflies, mussels, dragonflies, and crayfish across all Midwest Climate Adaptation Science Center states: Minnesota, Iowa, Missouri, Wisconsin, Illinois, Indiana, Michigan, and Ohio. For mussels, the geographic scope is expanded to include all Midwest Regional Species of Greatest Conservation Need (RSGCN) states—North Dakota, South Dakota, Nebraska, Kansas, and Kentucky. However, occurrence data for mussels is not included due to data-sharing agreements. Metadata are included with each data file. Please refer to the associated manuscript for original data sources, trait references, and details on the RCS index calculation.

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.

Chronic wasting disease (CWD) surveillance data from Illinois and Wisconsin, USA between the fiscal years 2003 and 2022 (calendar years 2002 and 2021). Data is reported at the township level as defined by the US Public Survey System. CWD cases, animals tested for CWD, and the apparent prevalence calculated from these values are given by township and fiscal year. Data has been anonymized by replacing original township names with identification numbers to maintain the privacy of landowners. Variables include Tests, Cases, and nonlinear transformations of Tests and Cases (inverse, square root, and log transformations).

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.