Illinois Data Bank Dataset Search Results
Results
published:
2024-04-11
Margenot, Andrew; Zhou, Shengnan; Xu, Suwei; Condron, Leo; Metson, Geneviève; Haygarth, Philip; Wade, Jordon; Agyeman, Price Chapman
(2024)
A defining feature of the Anthropocene is the distortion of the biosphere phosphorus (P) cycle. A relatively sudden acceleration of input fluxes without a concomitant increase in output fluxes has led to net accumulation of P in the terrestrial-aquatic continuum. Over the past century, P has been mined from geological deposits to produce crop fertilizers. When P inputs are not fully removed with harvest of crop biomass, the remaining P accumulates in soils. This residual P is a uniquely anthropogenic pool of P, and its management is critical for agronomic and environmental sustainability. This dataset includes data for us to quantify residual P from different long-term managed systems.
The following is the desccription of the dataset. There are 7 sheets in total.
1. P_balance: From Morrow Plots maize-maize rotaiton (1888-2021), L: Low estimation; M: medium estimation; H: high estimation;
2. M3P: From Morrow Plots selected plots (selected years), M3P_sur: Mehlich III P concentration in surface 17cm soils; M3P_sub: Mehlich III P concentration in 17-34cm subsoils; P_balance: the difference between P inputs and P outputs; TP_sur: total P stocks in surface 17cm soils; TP_sub: total P stocks in 17-34cm subsoils;
3. Morrow_Plot_P_pool_all: Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; Fertilized: P stocks in the fertilized plot; Unfertilized: P stocks in the unfertilized plot; F-U: difference between P stocks in ther fertilized and unfertilized plots; dif%: percent difference in total P;
4. Rothamsted_P_pool_all: Treatment: Unfertilized: no fertilization; FYM: farmyard manure; PK: synthetic P and K fertilizer; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P;
5. L'Acadie_P_pool_all: Treatment: MP_LowP: moldboard plow with low rate of P fertilizer; MP_HighP: moldboard plow with high rate of P fertilizer; NT_LowP: no till with low rate of P fertilizer; NT_HighP: no till with high rate of P fertilizer; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P;
6. Rothamsted_P_pool_duration: Treatment: Unfertilized: no fertilization; FYM: farmyard manure; PK: synthetic P and K fertilizer; Duration: from a year to another year; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P;
7. L'Acadie_P_pool_duration: Treatment: MP_LowP: moldboard plow with low rate of P fertilizer; MP_HighP: moldboard plow with high rate of P fertilizer; NT_LowP: no till with low rate of P fertilizer; NT_HighP: no till with high rate of P fertilizer; Duration: from a year to another year; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P;
keywords:
phosphate rock; biosphere; balances; soil test P; long-term experiment
published:
2025-12-02
Cheng, Ming-Hsun; Maitra, Shraddha; Carr Clennon, Aidan N.; Appell, Michael; Dien, Bruce; Singh, Vijay
(2025)
The recalcitrance of lignocellulosic biomass necessitates an efficient pretreatment protocol for operating a successful cellulosic biorefinery. It is critical to improve cellulose accessibility for hydrolysis and fermentation by altering the plant cell wall’s physical structure and chemical composition. Sequential hydrothermal-mechanical refining pretreatment (HMR) allows efficient recovery of cellulosic sugars without utilizing any hazardous chemicals. HMR has been successfully applied to Liberty switchgrass, a bioenergy cultivar released by the USDA, and now it is being applied to oilcane, a recently developed transgenic sugarcane variety engineered to accumulate lipids in its vegetative tissues. Sugar yields of oilcane bagasse (OCB) and switchgrass (SG) treated with HMR are 96.4% and 75.4%, respectively. This study sought to correlate cellulosic sugar yields with structural changes within the cell wall caused by HMR on two distinct bioenergy crops. Simon’s staining technique for the specific surface area analysis showed that HMR increased the specific surface area of pretreated biomass residues by 80-112%. In addition, ATR-FTIR was performed to determine the effects of HMR on physical structures based on the total crystallinity index (TCI) and hydrogen bonding intensity (HBI). Irrespective of biomass type, HMR decreased the initial crystalline cellulose contents of untreated biomass residues by 3.5% and reduced TCI and HBI by 7-13%. The study found that sugar yields were negatively correlated to reducing values of hydrogen bonding intensity, crystalline cellulose content, and total crystallinity index.
keywords:
Conversion;Biomass Analytics;Economics;Hydrolysate
published:
2025-12-18
Boob, Aashutosh; Zhang, Changyi; Pan, Yuwei; Zaidi, Airah; Whitaker, Rachel; Zhao, Huimin
(2025)
Sulfolobus islandicus, an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.
keywords:
AI/ML; gene editing; genome engineering; metabolic engineering
published:
2019-03-22
Jones, Todd M.; Benson, Thomas J.; Ward, Michael P.
(2019)
This data publication provides example video clips related to research on association among flight ability of juvenile songbirds at fledging and juvenile morphological traits (wing emergence, wing length, body condition, mass, and tarsus length. File names reflect the species dropped in each video. These videos are supplemental material for scientific publications by the authors and reflect an example subset of all videos collected form 2017-2018 as part of a larger study on the post-fledging ecology of grassland and shrubland birds in east-Central Illinois, USA. No birds were harmed/injured in the production of these videos and procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 18221. Individuals depicted in the videos have given consent for the videos to be shared (talent/model release form; <a href="https://publicaffairs.illinois.edu/resources/release/">https://publicaffairs.illinois.edu/resources/release/</a>)
keywords:
songbirds; flight ability; wing development; wing length; wing emergence; nestling development; post-fledging
published:
2025-08-20
Arshad, Muhammad Umer; Archer, David ; Wasonga, Daniel ; Namoi, Nictor; Boe, Arvid ; Rob , Mitchell; Heaton, Emily; Khanna, Madhu; Lee, DoKyoung
(2025)
The compiled datasets include detailed costs for switchgrass production, categorized into establishment, maintenance, and harvesting expenses, along with revenue calculations. Costs were gathered from multiple sources and adjusted for inflation, focusing on farm-gate profitability, excluding fixed costs and transportation. All financial data is provided per hectare. The dataset was used to evaluate the economic performance of forage- and bioenergy-type switchgrass cultivars and their response to nitrogen fertilization across diverse marginal environments in the U.S. Midwest. Data Envelopment Analysis (DEA) and cost-benefit analysis were employed to assess the efficiency and profitability of 23 different cultivar and fertilization rate combinations over five years.
published:
2025-11-25
The diel activity of study animals while feeding at their kills in the Santa Cruz Mountains of California
keywords:
Santa Cruz
published:
2026-01-08
Dibaeinia, Payam; Sinha, Saurabh
(2026)
CoNSEPT is a tool to predict gene expression in various cis and trans contexts. Inputs to CoNSEPT are enhancer sequence, transcription factor levels in one or many trans conditions, TF motifs (PWMs), and any prior knowledge of TF-TF interactions.
keywords:
software; gene expression
published:
2025-08-27
Jang, Chunhwa; Namoi, Nictor; Lee, Jung Woo; Becker, Talon; Rooney, William; Lee, DoKyoung
(2025)
Data were collected from agronomy fields in Urbana and Ewing, IL, during the 2022 and 2023 growing seasons. The dataset includes dry biomass yield, nitrogen, phosphorus, and potassium concentrations and removals, and chemical composition elements (cellulose, hemicellulose, lignin, and soluble fractions) for 13 high-biomass sorghum hybrids.
data_sharing.xlsx contains 20 columns and 104 rows. Below is the explanation of all variables in the file:
Year: 2022; 2023
Location: Urbana, IL; Ewing, IL
N rate (kg-N/ha): 0; 112
Hybrid #: H1-H13
Pedigree: Pedigree for 13 hybrids
Dry biomass yield (Mg/ha): Aboveground dry biomass yield
N (g/kg): Nitrogen concentration in plant tissue
P (g/kg): Phosphorus concentration in plant tissue
K (g/kg): Potassium concentration in plant tissue
N (kg/ha): Nitrogen removal by aboveground biomass
P (kg/ha): Phosphorus removal by aboveground biomass
K (kg/ha): Potassium removal by aboveground biomass
Cellulose (g/kg): Cellulose concentration in plant tissue
Hemicellulose (g/kg): Hemicellulose concentration in plant tissue
Lignin (g/kg): Lignin concentration in plant tissue
Soluble (g/kg): Soluble concentration in plant tissue
Cellulose (Mg/ha): Cellulose content in aboveground biomass
Hemicellulose (Mg/ha): Hemicellulose content in aboveground biomass
Lignin (Mg/ha): Lignin content in aboveground biomass
Soluble (Mg/ha): Soluble content in aboveground biomass
keywords:
high-biomass sorghum hybrids; yield potential; environmental adaptability; feedstock quality; nutrient removal; N fertilization
published:
2025-09-26
Arora, Amit; Singh, Vijay
(2025)
In this study, different process schemes were designed and evaluated for biodiesel production from engineered cane lipids with uncertain fatty acid compositions. Four different process schemes were compared under (i) thermal glycerolysis and (ii) enzymatic glycerolysis approaches. These schemes were based on the biodiesel yield and economic indicators such as the net present value (NPV) and the minimum selling price (MSP) of biodiesel. A scheme with polar lipid separation under thermal glycerolysis resulted in the maximum NPV ($96.5 million) and minimum MSP ($1107/ton biodiesel), respectively. Through local sensitivity analysis, it was concluded that the cane lipid percentage is the most significant factor influencing process economics. A conjoint analysis of the lipid procurement price and cane lipid percent suggested that 15% cane lipids with a low lipid procurement price ($0.536/kg) results in a positive NPV. When the cane lipid price is higher (>$0.80/kg), a 20% lipid content should be considered to achieve a positive NPV. At 20% cane lipids, the worst-case and best-case scenarios were evaluated by analyzing the interplay of the three most important parameters, The best-case scenario revealed that the minimum NPV under any process scheme could yield more than $100 million (or MSP: $0.80/L), and the worst-case analysis showed that losses incurred by the plant could be as high as $80 million (MSP: $1.36/L). A Monte Carlo simulation indicated that there is a 70% chance of the plant being profitable (NPV > 0).
keywords:
Conversion;Economics;Feedstock Bioprocessing;Modeling
published:
2025-10-21
Trieu, Anthony; Belaffif, Mohammad B.; Hirannaiah, Pradeepa; Manjunatha, Shilpa; Wood, Rebekah; Bathula, Yokshitha; Billingsley, Rebecca L.; Arpan, Anjali; Sacks, Erik; Clemente, Tom; Moose, Stephen; Reichert, Nancy A.; swaminathan, kankshita
(2025)
Miscanthus, a C4 member of the family Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies Miscanthus x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.
keywords:
Feedstock Production;Biomass Analytics;Genomics
published:
2023-07-14
Punyasena, Surangi W.; Urban, Michael A.; Adaime, Marc-Elie; Romero, Ingrid; Jaramillo, Carlos
(2023)
This dataset includes a total of 300 images of 45 extant species of Podocarpus (Podocarpaceae) and nine images of fossil specimens of the morphogenus Podocarpidites. The goal of this dataset is to capture the diversity of morphology within the genus and create an image database for training machine learning models.
The images were taken using Airyscan confocal superresolution microscopy at 630x magnification (63x/NA 1.4 oil DIC). The images are in the CZI file format. They can be opened using Zeiss propriety software (Zen, Zen lite) or open microscopy software, such as ImageJ. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/us/products/software/zeiss-zen/czi-image-file-format.html]
Please cite this dataset and listed publications when using these images.
keywords:
optical superresolution microscopy; Zeiss Airyscan; CZI images; conifer; saccate pollen; Podocarpus; Podocarpidites; Smithsonian Tropical Research Institute
published:
2022-07-19
Parmar, Dharmeshkumar; Jia, Jin; Shrout, Joshua; Sweedler, Jonathan; Bohn, Paul
(2022)
#### Details of Pseudomonas aeruginosa biofilm dataset ####
----------------*Folder Structure*-------------------------------------
This dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in "MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip", each folder contains 3 sub-folders as listed below.
1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]:
(1) Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h
2. StaticBiofilms [Static biofilms grown on mucin surface]:
(1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones
----------------*File name*----------------------------------------------
Sample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below.
*Example file name "Rep1-Stat-FRD1-mPat-48-FS"*
~ Each unit of information is separated by "-"
~Unit 1 - "Rep1" - Biological replicate ( Rep1, Rep2, and Rep3)
~Unit 2 - "Stat" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant)
~Unit 3 - "FRD1" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain)
~Unit 4 - "mPat" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface)
~Unit 5 - "48" - Sample time point (hours = 48, 72, 96)
~Unit 6 - "FS" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288))
----------------*File structure*------------------------------------------
All MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix.
----------------*End of Information*--------------------------------------
keywords:
mass spectrometry imaging (MSI); biofilm; antibiotic resistance; Pseudomonas aeruginosa; quorum sensing; rhamnolipids
published:
2024-08-19
Ward, Michael; Stewart, Sarah; Benson, Thomas
(2024)
Data on the nesting success and post-fledgling survival of Eastern Whip-poor-wills in central Illinois. Data was part of Sarah Stewart's MS project at the University of Illinois.
keywords:
bird nesting success; post-fledgling survival; eastern whip-poor-will
published:
2025-10-10
Field, John L.; Richard, Tom; Smithwick, Erica A. H.; Cai, Hao; Laser, Mark; LeBauer, David; Long, Stephen; Paustian, Keith; Qin, Zhangcai; Sheehan, John; Smith, Pete; Wang, Michael Q.; Lynd, Lee
(2025)
This zip file contains a UNIX-format DayCent model executable, input files, automation code, and associated directory structure necessary to re-produce the DayCent analysis underlying the manuscript. The main script “autodaycent.py” (written for Python 2.7) opens an interactive command line routine that facilitates: Calibrating the DayCent pine growth model; Initializing DayCent for a set of case studies sites; Executing an ensemble of model runs representing case study site reforestation, grassland restoration, or conversion to switchgrass cultivation; and Results analysis & generation of manuscript Fig. 3. Note that the interactive analysis code requires that all input files to be contained in the directory structure as uploaded, without modification. Executable versions of the DayCent model compatible with other operating systems are available upon request.
keywords:
Feedstock Production;Modeling
published:
2018-01-03
Sweet, Andrew; Bush, Sarah; Gustafsson, Daniel; Allen, Julie; DiBlasi, Emily; Skeen, Heather; Weckstein, Jason; Johnson, Kevin
(2018)
Concatenated sequence alignment, phylogenetic analysis files, and relevant software parameter files from a cophylogenetic study of Brueelia-complex lice and their avian hosts. The sequence alignment file includes a list of character blocks for each gene alignment and the parameters used for the MrBayes phylogenetic analysis.
1) Files from the MrBayes analyses:
a) a file with 100 random post-burnin trees (50% burnin) used in the cophylogenetic analysis - analysisrandom100_trees_brueelia.tre
b) a majority rule consensus tree - treeconsensus_tree_brueelia.tre
c) a maximum clade credibility tree - mcc_tree_brueelia.tre
The tree tips are labeled with louse voucher names, and can be referenced in Supplementary Table 1 of the associated publication.
2) Files related to a BEAST analysis with COI data:
a) the XML file used as input for the BEAST run, including model parameters, MCMC chain length, and priors - beast_parameters_coi_brueelia.xml
b) a file with 100 random post-burnin trees (10% burnin) from the BEAST posterior distribution of trees; used in OTU analysis - beast_100random_trees_brueelia.tre
c) an ultrametric maximum clade credibility tree - mcc_tree_beast_brueelia.tre
3) A maximum clade credibility tree of Brueelia-complex host species generated from a distribution of trees downloaded from https://birdtree.org/subsets/ - mcc_tree_brueelia_hosts.tre
4) Concatenated sequence alignment - concatenated_alignment_brueelia.nex
keywords:
bird lice; Brueelia-complex; passerines; multiple sequence alignment; phylogenetic tree; Bayesian phylogenetic analysis; MrBayes; BEAST
published:
2025-11-24
Dubinkina, Veronika; Bhogale, Shounak; Hsieh, Ping-Hung; Dibaeinia, Payam; Nambiar, Ananthan; Maslov, Sergei; Yoshikuni, Yasuo; Sinha, Saurabh
(2025)
Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.
keywords:
Conversion;Transcriptomics
published:
2024-02-21
Hartman, Jordan H; Corush, Joel B; Larson, Eric R; Tiemann, Jeremy S; Willink, Philip; Davis, Mark A
(2024)
Data associated with the manuscript "Niche conservatism and spread explain hybridization and introgression between native and invasive fish" by Jordan H. Hartman, Joel B. Corush, Eric R. Larson, Jeremy S. Tiemann, Philip Willink, and Mark A. Davis. For this project, we combined results of ecological niche models (ENMs) and next-generation restriction site-associated DNA sequencing (RADseq) to test theories of niche conservatism and biotic resistance on the success of invasion, hybridization, and extent of introgression between native Western Banded Killifish and non-native Eastern Banded Killifish. This dataset provides the sampling locations and number of Banded Killifish in each population, accession numbers for RADseq from the National Center for Biotechnology Information Sequence Read Archive and the assignment of each Banded Killifish, the habitat associations of each population from the ENMs, and the occurrence points used to build the ENMs.
keywords:
Banded Killifish; ecological niche model; Fundulus diaphanus; hybrid swarm; invasive species; Laurentian Great Lakes
published:
2025-11-06
Harrison, Wesley; Jiang, Guangde; Zhang, Zhengyi; Li, Maolin; Chen, Haoyu; Zhao, Huimin
(2025)
Chiral alkyl amines are common structural motifs in pharmaceuticals, natural products, synthetic intermediates, and bioactive molecules. An attractive method to prepare these molecules is the asymmetric radical hydroamination; however, this approach has not been explored with dialkyl amine-derived nitrogen-centered radicals since designing a catalytic system to generate the aminium radical cation, to suppress deleterious side reactions such as α-deprotonation and H atom abstraction, and to facilitate enantioselective hydrogen atom transfer is a formidable task. Herein, we describe the application of photoenzymatic catalysis to generate and harness the aminium radical cation for asymmetric intermolecular hydroamination. In this reaction, the flavin-dependent ene-reductase photocatalytically generates the aminium radical cation from the corresponding hydroxylamine and catalyzes the asymmetric intermolecular hydroamination to furnish the enantioenriched tertiary amine, whereby enantioinduction occurs through enzyme-mediated hydrogen atom transfer. This work highlights the use of photoenzymatic catalysis to generate and control highly reactive radical intermediates for asymmetric synthesis, addressing a long-standing challenge in chemical synthesis.
keywords:
Conversion;Bioproducts;Catalysis
published:
2018-10-17
Price, Edward; Spyreas, Greg; Matthews, Jeffrey
(2018)
This is the dataset used in the Ecological Applications publication of the same name. This dataset consists of the following files:
Internal.Community.Data.txt
Regional.Community.Data.txt
Site.Attributes.txt
Year.Of.Final.Bio.Monitoring.txt
Internal.Community.Data.txt is a site and plot by species matrix. Column labeled SITE consists of site IDs. Column labeled Plot consists of Plot numbers. All other columns represent species relative abundances per plot.
Regional.Community.Data.txt is a site by species matrix of relative abundances. Column labeled site consists of site IDs. All other columns represent species relative abundances per site.
Site.attributes.txt is a matrix of site attributes. Column labeled SITE consists of site IDs. Column labeled Long represents longitude in decimal degrees. Column labeled Lat represents latitude in decimal degrees. Column labeled Richness represents species richness of sites calculated from Regional Community Data. Column labeled NAT_COMP_REST represents designation as a randomly selected natural wetland (NAT), compensation wetland (COMP) or reference quality natural wetland (REF).
Column labeled HQ_LQ_COMP represents designation as high quality (HQ), low quality (LQ) or compensation wetland (COMP). Column labeled SAMPLING_YEAR_INTERNAL represents year data used for analysis of internal β-diversity was gathered. Column labeled SAMPLING_YEAR_REGIONAL represents year data used for analysis of regional β-diversity was gathered. Column labeled TRANSECT_LENGTH represents length in meters of initial sampling transect. INAI_GRADE represents Illinois Natural Areas Inventory grades assigned to each site. Grades range from A for highest quality natural areas to E for lowest quality natural areas.
Year.Of.Final.Bio.Monitoring.txt is a table representing years of final monitoring of compensation wetlands as mandated by the US Army Corps of Engineers. Column labeled Site consists of site IDs. Column labeled YR_FIN_BIO_MON consists of years of final monitoring. Entries of N/A represent dates that were unable to be located.
More information about this dataset: Interested parties can request data from the Critical Trends Assessment Program, which was the source for data on naturally occurring wetlands 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/
keywords:
biodiversity; wetlands; wetland mitigation; biotic homogenization; beta diversity
published:
2018-12-04
Wang, Yang; Dietrich, Christopher; Zhang, Yalin
(2018)
The text file contains the original data used in the phylogenetic analyses of Wang et al. (2017: Scientific Reports 7:45387). 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 81 taxa (species) and 2905 characters, indicate that the first 2805 characters are DNA sequence and the last 100 are morphological, that the data may be interleaved (with data for one species on multiple rows), that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The file contains aligned nucleotide sequence data for 5 gene regions and 100 morphological characters. The identity and positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes at 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 original publication. Descriptions of the morphological characters and more details on the species and specimens included in the dataset are provided in the supplementary document included as a separate pdf. The original raw DNA sequence data are available from NCBI GenBank under the accession numbers indicated in the supplementary file.
keywords:
phylogeny; DNA sequence; morphology; Insecta; Hemiptera; Cicadellidae; leafhopper; evolution; 28S rDNA; wingless; histone H3; cytochrome oxidase I; bayesian analysis
published:
2025-10-30
Cao, Dang Viet; Luo, Guangbin; Korynta, Shelby; Liu, Hui; Liang, Yuanxue; Shanklin, John; Altpeter, Fredy
(2025)
Metabolic engineering for hyperaccumulation of lipids in vegetative tissues is a novel strategy for enhancing energy density and biofuel production from biomass crops. Energycane is a prime feedstock for this approach due to its high biomass production and resilience under marginal conditions. DIACYLGLYCEROL ACYLTRANSFERASE (DGAT) catalyzes the last and only committed step in the biosynthesis of triacylglycerol (TAG) and can be a rate-limiting enzyme for the production of TAG. In this study, we explored the effect of intron-mediated enhancement (IME) on the expression of DGAT1 and resulting accumulation of TAG and total fatty acid (TFA) in leaf and stem tissues of energycane. To maximize lipid accumulation these evaluations were carried out by co-expressing the lipogenic transcription factor WRINKLED1 (WRI1) and the TAG protect factor oleosin (OLE1). Including an intron in the codon-optimized TmDGAT1 elevated the accumulation of its transcript in leaves by seven times on average based on 5 transgenic lines for each construct. Plants with WRI1 (W), DGAT1 with intron (Di), and OLE1 (O) expression (WDiO) accumulated TAG up to a 3.85% of leaf dry weight (DW), a 192-fold increase compared to non-modified energycane (WT) and a 3.8-fold increase compared to the highest accumulation under the intron-less gene combination (WDO). This corresponded to TFA accumulation of up to 8.4% of leaf dry weight, a 2.8-fold or 6.1-fold increase compared to WDO or WT, respectively. Co-expression of WDiO resulted in stem accumulations of TAG up to 1.14% of DW or TFA up to 2.08% of DW that exceeded WT by 57-fold or 12-fold and WDO more than twofold, respectively. Constitutive expression of these lipogenic “push pull and protect” factors correlated with biomass reduction. Intron-mediated enhancement (IME) of the expression of DGAT resulted in a step change in lipid accumulation of energycane and confirmed that under our experimental conditions it is rate limiting for lipid accumulation. IME should be applied to other lipogenic factors and metabolic engineering strategies. The findings from this study may be valuable in developing a high biomass feedstock for commercial production of lipids and advanced biofuels.
keywords:
Feedstock Production;Lipidomics;Metabolomics
published:
2025-11-19
Salesse-Smith, Coralie; Adar, Noga; Kannan, Baskaran; Nguyen, Thaibinhduong; Wei, Wei; Guo, Minghao; Ge, Zhengxiang; Altpeter, Fredy; Clemente, Tom; Long, Stephen
(2025)
This repository includes data sets and R scripts that were used to perform analysis and produce figures for the following publication: Salesse-Smith, C. E. et al. “Adapting C4 photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in sorghum and sugarcane.” Proceedings of the National Academy of Sciences 122, e2419943122 (2025) doi:10.1073/pnas.2419943122.
keywords:
Feedstock Production;Biomass Analytics;Sorghum;Sugarcane
published:
2017-12-22
Scheidler, Andrew; Kinnett-Hopkins, Dominique; Learmonth, Yvonne; Motl, Robert; Lopez-Ortiz, Citlali
(2017)
TBP assessment raw data files of pre- and post- motion capture velocity and center of pressure force plate data. Labels are self-explanatory. The .mat files refer to data exported from the force plate for the time-to-stabilization assessments while the .txt files are the data collected for smoothness of gait assessments. These files do not relate to one another and are from separate assessments. Version2's files are the result from using Python code Data_Bank_Cleaner.py on version1's. Please find more information in READ_ME_databank.txt.
keywords:
Multiple Sclerosis; Rehabilitation; Balance; Ataxia; Ballet; Dance; Targeted Ballet Program
published:
2025-12-15
Vector competence and survival data for Aedes albopictus mosquitoes exposed to Ross River virus
keywords:
Emerging viruses; vectorial capacity; vector competence; container-breeding mosquitoes; alphavirus; Culicidae
published:
2020-04-07
Larsen, Ryan; Charles, Hillman; Kramer, Arthur; Cohen, Neal; Barbey, Aron
(2020)
Baseline data from a multi-modal intervention study conducted at the University of Illinois at Urbana-Champaign. Data include results from a cardiorespiratory fitness assessment (maximal oxygen consumption, VO2max), a body composition assessment (Dual-Energy X-ray Absorptiometry, DXA), and Magnetic Resonance Spectroscopy Imaging. Data set includes data from 435 participants, ages 18-44 years.
keywords:
Magnetic Resonance Spectroscopy; N-acetyl aspartic acid (NAA); Body Mass Index; cardiorespiratory fitness; body composition