Dataset Search

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

This dataset contains all the raw data, figures, and Prism files corresponding to each experiment performed for the paper “Hippocampal ensembles regulate circuit-induced relapse of extinguished fear.”

This document contains the Supplemental Materials for Chapter 4: Climate Change Impacts on Agriculture from the report "An Assessment of the Impacts of Climate Change in Illinois" published in 2021.

Bigheaded carp were collected from the Illinois and Des Plaines Rivers, parts of the Illinois Waterway, from May to November 2018. A total of 93 fish were collected during sampling for a study comprised of 40 females, 41 males, and 12 unsexed fish. GC/MS metabolite profiling analysis detected 180 compounds. Livers from carp at the leading edge had differences in energy use and metabolism, and suppression of protective mechanisms relative to downstream fish; differences were consistent across time. This body of work provides evidence that water quality is linked to carp movement in the Illinois River. As water quality in this region continues to improve, consideration of this impact on carp spread is essential to protect the Great Lakes.

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ (R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides, providing a streamlined method for addressing genetic engineering challenges in the yeast.

This dataset includes data on soil properties, soil N pools, and soil N fluxes presented in the manuscript, "Effects of an invasive perennial forb on gross soil nitrogen cycling and nitrous oxide fluxes," submitted to Ecology for peer-reviewed publication. Please refer to that publication for details about methodologies used to generate these data and for the experimental design.

This dataset contains EEG and Temperature data acquired from inside the bore of an MRI scanner during scanning with two different types of fMRI sequences: single-band and and multi-band. The EEG data were acquired from the heads of adult humans undergoing scanning, and can be used to assess differences in EEG data quality due to sequence type. The temperature data were acquired from a watermelon phantom and can be used to assess heating differences due to sequence type.

This data set explores the effect of the cyanobacterial gene ictB on photosynthesis in sorghum, under both normal greenhouse growing temperatures (32 C / 25 C) and during and after an 8 day chilling stress (10 C / 5 C). IctB is a cyanobacterial gene of unknown function, which was initially thought to be involved in inorganic carbon transport into cells. While ictB is known now not to be an independently active carbon transporter in its own right, it may play a role in passive diffusion of metabolites. This transgene was introduced into sorghum by the lab of Thomas Clemente, through Agrobacterium mediated transformation, alone and in combination with the tomato sedoheptulose-1,7-bisphosphatase (SBPase) gene. Eleven events (six double construct and five single construct ictB) were involved in this study. SBPase was included because some previous experiments in C3 species and some previous modeling work, as well as its position at a metabolic branch point, indicates it plays a role as a control point for photosynthesis. A chilling treatment was included because chilling is one of the most serious ecological factors limiting the range of C4 species. Data includes gene expression, metabolomics (at normal growing temperature), SBPase enzyme activity, biomass and photosynthetic traits at both warm temperature and during and after chilling stress. ----------------- EXPLANATORY NOTES FOR ICTB/SBPASE SORGHUM MANUSCRIPT Data are organized into 10 worksheets, representing an expected 10 tables that will serve a supplementary role in the final publication. These include data on gene expression, metabolomics (at normal growing temperature), SBPase enzyme activity, biomass and photosynthetic traits at both warm temperature and during and after chilling stress. <i><b>Tables are as follows:</i></b> 1. Event_Code: for Table S1. Event codes for events and constructs. Two constructs were generated for this study, and numerous transgenic “events” (i.e. independent transformations) were carried out for each construct. A construct represents the actual vector which was introduced into the plants (complete with promoter, gene of interest, marker gene, etc.) while an event represents a single successful introduction of the transgene. Events are uniquely labeled with letter and number strings but also with a four-digit number for ease of reference, this table explains which event corresponds to each four-digit number. 2. Photosynthetic_Data: for Table S2. Photosynthetic data at greenhouse growing temperature, for ictB single construct, ictB/SBPase double construct, and wild type lines. Five ictB and six ictB/SBPase events were included. Greenhouse growing temperature was approximately 32 °C and 25 °C night. Photosynthetic parameters were measured using a Licor 6400-XT, and included parameters related to carbon dioxide uptake, water loss, and chlorophyll fluorescence. 3. Chilling_Treatment: for Table S3. Photosynthetic response to chilling treatment, for ictB single construct, and wild type lines. Four ictB events were included. Chilling treatment lasted approximately 8 days and began either 3.5 or 5.5 weeks after transplanting the plants (chilling was done in two batches). Chilling treatment involved temperatures of 10 °C day / 7 °C night in growth chambers. Photosynthetic parameters were measured at several time points during and after the chilling treatment, were measured using a Licor 6400-XT, and included parameters related to carbon dioxide uptake, water loss, and chlorophyll fluorescence. 4. SBPase_Activity: for Table S4. SBPase activity in double construct plants. These data measure in vitro substrate-saturated activity of SBPase in desalted extracts from leaf tissues, at 25 °C. Units are micromoles of SBP processed per second per m2 of leaf tissue. Five ictB/SBPase events were included. 5. 2014_gene_exp: for Table S5. Gene expression in 2014 experiment (units of cycle times). These data measure cycle times to threshold, relative to reference genes, for expression of ictB and SBPase. Six ictB single construct events and five ictB/SBPase double construct events were included. Cycle times to threshold relative to reference genes (ΔCT) are inversely related to number of transcripts relative to reference genes, as follows: ΔCT = -log2([NictB]/[Nreference])/[1 + log2b] where b = efficiency of replication. 6. 2016_gene_exp: for Table S5. Gene expression in 2016 experiment (units of cycle times). These data measure cycle times to threshold, relative to reference genes, for expression of ictB and SBPase. Six ictB single construct events and five ictB/SBPase double construct events were included. Cycle times to threshold relative to reference genes (ΔCT) are inversely related to number of transcripts relative to reference genes, as follows: ΔCT = -log2([NictB]/[Nreference])/[1 + log2b] where b = efficiency of replication. 7. Metabolites: for Table S7. Levels of 267 metabolites in leaf tissue. Four ictB single construct events and four ictB/SBPase double construct events were included in these analyses. Metabolites were measured in methanol-extracted samples, either by liquid chromatography / mass spectrometry or by gas chromatography / mass spectrometry, and were compared between events on a relative basis. As quantification was relative to wild type rather than on an absolute basis, no units are included. 8. Metabolite_F_values: for Table S8. F values for effects of ictB, SBPase (in cases where the model was better with a SBPase effect) and event. These analyses are done for each metabolite included in Table S7, and show effects of the explanatory variables ictB, SBPase, and individual event. 9. Biomass_2020: for Table S9. Biomass and grain yield at harvest, for ictB, ictB/SBPase and wild type sorghum plants in spring 2020. Four ictb/SBPase double construct and four ictB single construct events were included. 10. Biomass_2017: for Table S10. Biomass and grain yield at harvest, in chilled and non-chilled sorghum plants containing the ictB transgene (along with wild type controls) in fall 2017. Four ictB single construct events were included. Chilling treatment involved temperatures of 10 °C day / 7 °C night in growth chambers. <i><b>All the variables in the file are explained as below:</i></b> o Type (IctB-SBPase and IctB). This refers to whether a plant is wild type, single construct (contains only the ictB transgene) or double construct (contains both the ictB and SBPase transgenes). o Code: these codes are shorter labels to refer to each transgene event for the sake of convenience. o Alternate_Code: these codes are shorter labels to refer to each transgene event for the sake of convenience. o Event Number: these are unique labels for each transgenic events. o Construct Number: these are labels for each transgenic construct (either the ictB single construct or the ictB/SBPase double construct). o year (i): this refers to the year in which the study was conducted (2014, 2016, 2017, or 2020) o transgene or Transgenic: whether the transgene was present o construct or Type : whether the ictB or the ictB/SBPase construct was present (double, single, wildtype): o temp: leaf temperature during the measurement o A: carbon assimilation rate, in μmol m-2 s-1 o gs: stomatal conductance, in mol m-2 s-1 o CI: intercellular carbon dioxide concentration, in parts per million or μL L-1 o fvfm:FV’/FM’ (maximal potential photosystem II quantum yield under light adapted conditions), dimensionless ratio o phipsill: ΦPSII (maximal potential photosystem II quantum yield under light adapted conditions), dimensionless ratio o qP: photochemical quenching, i.e. ratio of ΦPSII to FV’/FM’ , dimensionless ratio o iwue: intrinsic water use efficiency, i.e. ratio of carbon assimilation rate to stomatal conductance, in units of μmol mol-1 o event: individual transgenic / transformation event o Vmax: substrate-saturated in vitro activity of the SBPase enzyme, in μmol m-2 s-1 o ID: identification number of sample o ΔCT1: difference in cycle times to threshold during gene expression (quantitative PCR) assay, between ictB and the reference gene GAPDH, in units of cycles o ΔCT2: cycle times to threshold during gene expression (quantitative PCR) assay, between SBPase and the reference gene GAPDH, in units of cycles o GAPDH: cycle times to threshold for the reference gene GAPDH (glyceraldehyde phosphate dehydrogenase) o IctB: cycle times to threshold for the gene of interest ictB o SBPase: cycle times to threshold for the gene of interest SBPase o v1 to v267 represent individual metabolite (see the heading immediately above the labels v1, v2, etc.). Variables v268-v272 refer to total (summed) metabolite levels for particular pathways of interest. o leaf: Leaf and stem dry biomass (in grams) o seed: Seedhead dry biomass (in grams) o biomass: Total (leaf, stem + seed head) dry biomass (in grams) o harvind: ratio of seed head dry biomass to total dry biomass o treatment (chilled and nonchilled): “Chilled” plants were grown under warm greenhouse conditions (32 °C day / 25 °C night) for 6 or 8 weeks, then switched to chilling temperatures under growth chamber conditions (10 °C / 7 °C night) for 8 days, and were then returned to greenhouse growing conditions. -----------------

This dataset contains the pregnancy status of wild, white-tailed deer (Odocoileus virginianus) from northern Illinois culled as part of the Illinois Department of Natural Resources' chronic wasting disease (CWD) surveillance program. Fiscal years 2005 through 2024 are included. A fiscal year is the time between July 1st of one calendar year and June 30th of the next. Variables in this dataset include the pregnancy status, CWD infection status, age, weight, and day of mortality for each female deer, as well as the deer land cover utility (LCU) score for the TRS, township, or county from which the deer was culled. The deer population density of the county is also included. Data have been anonymized for landowner privacy reasons so that the location and year are not identifiable, but will give the same modeling results by maintaining how the data are grouped. The R code used to conduct the regression modeling is also included.

An online knowledge, attitudes, and practices survey on ticks and tick-borne diseases was distributed to veterinary professionals in Southern and Central Illinois during summer and fall 2020. These are the raw data associated with that survey and the survey questions used. * NOTE: "age" and "gender" variables were removed from the data to protect participants.

This dataset includes the source data for Figures 1-4 and supplementary figures 1-10 for the manuscript "Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase".

This dataset contains: field study design parameters, plant performance metrics, and nitrogen cycling rates associated with a field experiment that compared nitrification rates between maize lines with and without nitrification inhibition loci nitrogen fixation rates with with and without a nitrogen fixing inoculant product. The overarching goal was to evaluate nitrogen fixation by a diazotroph inoculant and retention of nitrogen in the rhizosphere via a novel nitrification inhibition phenotype of maize.

UAV-based high-resolution multispectral time-series orthophotos utilized to understand the relation between growth dynamics, imagery temporal resolution, and end-of-season biomass productivity of biomass sorghum as bioenergy crop. Sensor utilized is a RedEdge Micasense flown at 40 meters above ground level at the Energy Farm- UIUC in 2019.

The Membracoidea_morph_data_Final.nex text file contains the original data used in the phylogenetic analyses of Dietrich et al. (Insect Systematics and Diversity, in review). 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 complete taxon names corresponding to the 131 genus names listed under “BEGIN TAXA” are listed in Table 1 in the included PDF file “Taxa_and_characters”; the 229 morphological characters (names abbreviated under under “BEGIN CHARACTERS” are fully explained in the list of character descriptions following Table 1 in the same PDF). The data matrix follows “MATRIX” and gives the numerical values of characters for each taxon. Question marks represent missing data. The lists of characters and taxa and details on the methods used for phylogenetic analysis are included in the submitted manuscript.

Dataset associated with Zenzal et al. Oikos submission: Retreat, detour, or advance? Understanding the movements of birds confronting the Gulf of Mexico. https://doi.org/10.1111/oik.07834 Four CSV files were used for analysis and are related to the following subsections under the “Statistics” heading in the “Materials and Methods” section of the journal article: 1. Departing the Edge = “AIC Analysis.csv” 2. Comparing Retreating to Advancing = “Advance and Retreat Analysis.csv” and “Wind Data at Departure.csv” 3. Food Abundance = “Fruit Data.csv” and “Arthropod Data.csv” <b>Description of variables:</b> Year: the year in which data were collected. Departure: the direction in which an individual departed the Bon Secour National Wildlife Refuge. “North” indicates an individual that departed ≥315° or <45°; “Circum” indicates an individual that departed east (45 – 134°) or west ( 225 – 314°); “Trans” indicates an individual that departed south (135 – 224°). Age: the age of an individual at capture. Individuals were aged as hatch year (HY) or after hatch year (AHY) according to Pyle (1997; see related article for full citation). Fat: the fat score of an individual at capture. Individuals were scored on a 6-point scale ranging from 0-5 following Helms and Drury (1960; see related article for full citation). Species: the standardized four letter alphabetic code used as an abbreviation for English common names of North American Birds. SWTH: Catharus ustulatus; REVI: Vireo olivaceus; INBU: Passerina cyanea; WOTH: Hylocichla mustelina; RTHU: Archilochus colubris. FTM_SD: stopover duration or number of days between first capture and departure from automated radio telemetry system coverage at the Bon Secour National Wildlife Refuge. TMB_SD: stopover duration or number of days between first and last detection from automated radio telemetry systems north of Mobile Bay, AL, USA. Mean speed north (km/hr): the northbound travel speed of individuals retreating from the Bon Secour National Wildlife Refuge by determining the time when the signal strength indicated the bird was directly east or west of the automated telemetry system and dividing the amount of time it took for an individual to move in an assumed straight path between the Refuge systems and those north of Mobile Bay, AL, USA. Mean speed south (km/hr): the southbound travel speed of individuals advancing from north of Mobile Bay, AL, USA by determining the time when the signal strength indicated the bird was directly east or west of the automated telemetry system and dividing the amount of time it took for an individual to move in an assumed straight path between the Refuge systems and those north of Mobile Bay, AL, USA. LN_FTM_DEP_TIME: the natural log of departure time from the Bon Secour National Wildlife Refuge. Departure time is defined as the number of hours before or after civil twilight. LN_TMB_DEP_TIME: the natural log of departure time from north of Mobile Bay, AL, USA. Departure time is defined as the number of hours before or after civil twilight. Paired_FTM_DEP_TIME: the departure time or number of hours before or after civil twilight from Bon Secour National Wildlife Refuge. Paired_TMB_DEP_TIME: the departure time or number of hours before or after civil twilight from north of Mobile Bay, AL, USA. Wind Direction: the direction from which the wind originated at the Bon Secour National Wildlife Refuge on nights when individuals were departing. “N” indicates winds from the north (≥315° or <45°); “E” indicates winds from the east (45 – 134°); “W” indicates winds from the west ( 225 – 314°); “S” indicates winds from the south (135 – 224°). Wind Speed (m/s): the wind speed on nights when individuals were departing the Bon Secour National Wildlife Refuge. Group: the direction the bird was traveling under specific wind conditions. Northbound individuals traveled north from Bon Secour National Wildlife Refuge. Southbound individuals traveled south from habitats north of Mobile Bay, AL, USA. Fruit: weekly mean number of ripe fruit per meter. Site: the site from which the data were collected. FTM is located within the Bon Secour National Wildlife Refuge. TMB is located within the Jacinto Port Wildlife Management Area. DOY: number indicating day of year (i.e., 1 January = 001….31 December = 365). Arthropod Biomass: estimated mean arthropod biomass from each sampling period. <b>Note:</b> Empty cells indicate unavailable data where applicable.

Since the discovery of Hofmann–Löffler–Freytag reaction more than 130 years ago, both the structure and reactivity of nitrogen-centred radicals have been widely studied. Nevertheless, catalytic enantioselective intermolecular radical hydroamination remains a challenge due to the existence of side reactions, the short lifetime of nitrogen-centred radicals and lack of understanding of the fundamental catalytic steps. In the laboratory, nitrogen-centred radicals are produced with radical initiators, photocatalysts or electrocatalysts. In contrast, their generation and reaction are unknown in nature. Here we report a pure biocatalytic system for the photoenzymatic production of nitrogen-centred radicals and enantioselective intermolecular radical hydroaminations by successfully repurposing an ene-reductase through directed evolution. These reactions progress efficiently at room temperature under visible light without any external photocatalysts and exhibit excellent enantioselectivities. A detailed mechanistic study reveals that the enantioselectivity originates from the radical-addition step while the reactivity originates from the ultrafast photoinduced electron transfer from reduced flavin mononucleotide to nitrogen-containing substrates.

Data sets from "Comparing Methods for Species Tree Estimation With Gene Duplication and Loss." It contains data simulated with gene duplication and loss under a variety of different conditions.

Dataset includes bee trait information and species abundance information for bees collected at 29 forests plots in southern Illinois, USA. Plots are located within three public land sites. Environmental data were also collected for each of the 29 plots.

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.