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The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.

There is a growing interest in developing cooperative chemoenzymatic reactions to harness the reactivity of chemical catalysts and the selectivity of enzymes for the synthesis of nonracemic chiral compounds. However, existing chemoenzymatic systems with more than one chemical reaction and one enzymatic reaction working cooperatively are rare. Moreover, the application of oxidoreductases in cooperative chemoenzymatic reactions is limited by the necessity of using expensive and unstable redox equivalents such as nicotinamide cofactors. Here, we report a light-driven cooperative chemoenzymatic system comprised of a photoinduced electron transfer reaction (PET) and a photosensitized energy transfer reaction (PEnT) with an enzymatic reduction in one-pot to synthesize chiral building blocks of bioactive compounds. As a proof of concept, ene-reductase was directly regenerated by PET in the absence of external cofactors. Meanwhile, enzymatic reduction worked cooperatively with photocatalyst-catalyzed energy transfer that continuously replenished the reactive isomer from the less reactive one. The whole system stereoconvergently reduced E/Z mixtures of alkenes to the enantiopure products. Additionally, enantioselective enzymatic reduction worked competitively with photocatalyst-catalyzed racemic background reaction and side reactions to channel the overall electron flow to the single enantiopure product. Such a light-driven cooperative chemoenzymatic system holds great potential for asymmetric synthesis using inexpensive petroleum or biomass-derived alkenes.

The photosynthetic capacity or the CO2-saturated photosynthetic rate (Vmax), chlorophyll, and nitrogen are closely linked leaf traits that determine C4 crop photosynthesis and yield. Accurate, timely, rapid, and non-destructive approaches to predict leaf photosynthetic traits from hyperspectral reflectance are urgently needed for high-throughput crop monitoring to ensure food and bioenergy security. Therefore, this study thoroughly evaluated the state-of-the-art physically based radiative transfer models (RTMs), data-driven partial least squares regression (PLSR), and generalized PLSR (gPLSR) models to estimate leaf traits from leaf-clip hyperspectral reflectance, which was collected from maize (Zea mays L.) bioenergy plots with diverse genotypes, growth stages, treatments with nitrogen fertilizers, and ozone stresses in three growing seasons. The results show that leaf RTMs considering bidirectional effects can give accurate estimates of chlorophyll content (Pearson correlation r=0.95), while gPLSR enabled retrieval of leaf nitrogen concentration (r=0.85). Using PLSR with field measurements for training, the cross-validation indicates that Vmax can be well predicted from spectra (r=0.81). The integration of chlorophyll content (strongly related to visible spectra) and nitrogen concentration (linked to shortwave infrared signals) can provide better predictions of Vmax (r=0.71) than only using either chlorophyll or nitrogen individually. This study highlights that leaf chlorophyll content and nitrogen concentration have key and unique contributions to Vmax prediction.

Sugar alcohols are commonly used as low-calorie sweeteners and can serve as potential building blocks for bio-based chemicals. Previous work has shown that the oleaginous yeast Rhodosporidium toruloides IFO0880 can natively produce arabitol from xylose at relatively high titers, suggesting that it may be a useful host for sugar alcohol production. In this work, we explored whether R. toruloides can produce additional sugar alcohols. Rhodosporidium toruloides is able to produce galactitol from galactose. During growth in nitrogen-rich medium, R. toruloides produced 3.2 ± 0.6 g/L, and 8.4 ± 0.8 g/L galactitol from 20 to 40 g/L galactose, respectively. In addition, R. toruloides was able to produce galactitol from galactose at reduced titers during growth in nitrogen-poor medium, which also induces lipid production. These results suggest that R. toruloides can potentially be used for the co-production of lipids and galactitol from galactose. We further characterized the mechanism for galactitol production, including identifying and biochemically characterizing the critical aldose reductase. Intracellular metabolite analysis was also performed to further understand galactose metabolism. Rhodosporidium toruloides has traditionally been used for the production of lipids and lipid-based chemicals. Our work demonstrates that R. toruloides can also produce galactitol, which can be used to produce polymers with applications in medicine and as a precursor for anti-cancer drugs. Collectively, our results further establish that R. toruloides can produce multiple value-added chemicals from a wide range of sugars.

These data were used in the survival and cause-specific mortality analyses of translocated nuisance American black bear in Wisconsin published in Animal Conservation (Bauder, J.M., N.M. Roberts, D. Ruid, B. Kohn, and M.L. Allen. Accepted. Lower survival of nuisance American black bears (Ursus americanus) is not due to translocation. Animal Conservation). Included are CSV files including each bear's capture history and associated covariates and meta-data for each CSV file. Also included is an example R script of how to conduct the analyses (this R script is also included as supporting information with the published paper).

The PhytoplasmasRef_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the phylogenetic analyses of Trivellone et al. (Ecology and Evolution, in review). The 27 sequences (21 phytoplasma reference strains and 6 phytoplasmas strains from the present study) were aligned using the Muscle algorithm as implemented in MEGA 7.0 with default settings. The final dataset contains 952 positions of the F2n/R2 fragment of the 16S rRNA gene. The data analyses are further described in the cited original paper.

These data and code are associated with a study on differences in the rate of hatching failure of eggs across 14 free-living grassland and shrubland birds. We used a device to measure the embryonic heart rate of eggs and found there was variation across species related to factors such as nest type and nest safety. This work is to be published in Ornithology.

This dataset includes structural MRI head scans of 32 piglets, at 28 days of age, scanned at the University of Illinois. The dataset also includes manually drawn brain masks of each of the piglets. The dataset also includes brain masks that were generated automatically using Region-Based Convolutional Neural Networks (Mask R-CNN), trained on the manually drawn brain masks.

This data set describes temperature, dissolved oxygen, and secchi depth in 1-m interval profiles in the deepest point in 10 Illinois reservoirs between the years 1995 and 2016.

These are abundance dynamics data and simulations for the paper "Higher-order interaction between species inhibits bacterial invasion of a phototroph-predator microbial community". In this V2, data were converted in Python, in addition to MATLAB and more information on how to work with the data was included in the Readme.

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 images of a photoperiod sensitive sorghum accession population used for a GWAS/TWAS study of leaf traits related to water use efficiency in 2016 and 2017. *<b>Note:</b> new in this second version is that JPG images outputted from the nms files were added <b>Accessions_2016.zip</b> and <b>Accessions_2017.zip</b>: contain raw images produced by Optical Topometer (nms files) for all sorghum accessions. Images can be opened with Nanofocus μsurf analysis extended software (Oberhausen,Germany). <b>Accessions_2016_jpg.zip</b> and <b>Accessions_2017_jpg.zip</b>: contain jpg images outputted from the nms files and used in the machine learning phenotyping.

Ethanol and lactate are typical waste products of glucose fermentation. In mammals, glucose is catabolized by glycolysis into circulating lactate, which is broadly used throughout the body as a carbohydrate fuel. Individual cells can both uptake and excrete lactate, uncoupling glycolysis from glucose oxidation. Here we show that similar uncoupling occurs in budding yeast batch cultures of Saccharomyces cerevisiae and Issatchenkia orientalis. Even in fermenting S. cerevisiae that is net releasing ethanol, media 13C-ethanol rapidly enters and is oxidized to acetaldehyde and acetyl-CoA. This is evident in exogenous ethanol being a major source of both cytosolic and mitochondrial acetyl units. 2H-tracing reveals that ethanol is also a major source of both NADH and NADPH high-energy electrons, and this role is augmented under oxidative stress conditions. Thus, uncoupling of glycolysis from the oxidation of glucose-derived carbon via rapidly reversible reactions is a conserved feature of eukaryotic metabolism.

Gigatonne-scale atmospheric carbon dioxide removal (CDR), alongside deep emission cuts, is critical to stabilizing the climate. However, some of the most scalable CDR technologies are also the most land intensive. Here, we examine whether adequate land resources exist in the contiguous United States to meet CDR targets when prioritizing grid emissions reduction, food production, and the protection of sensitive ecosystems. We focus on biomass carbon removal and storage (BiCRS) and direct air capture and storage (DACS) and show that suitable lands exceed the expected needs: 37.6 million hectares of land are available for BiCRS, resulting in 0.26 GtCO2 of CDR/year, and 34 million hectares are suitable for wind- and solar-powered DACS, resulting in 4.8 GtCO2 of CDR/year if facilities are co-located with geologic CO2 storage. We identify biomass and energy supply hotspots to meet CDR targets while ensuring land protection and minimizing land competition.

This dataset contains 1) the cleaned version of 11 CRW datasets, 2) RNASim10k dataset in high fragmentation and 3) three CRW datasets (16S.3, 16S.T, 16S.B.ALL) in high fragmentation.

This dataset includes the RT-PCR results, RT-LAMP results, and the minutes to positive ROC curve calculations. This dataset includes data for the synthetic gBlock, cell culture, and clinical sample assays (nasal swabs and nasal wipes). Also included is a list of FDA approved point of care tests for influenza A virus to date (2-16-2024). MIQE guidelines are also included.

This dataset includes the RT-PCR shedding data and primers used for whole genome sequencing of Influenza A virus in swine. It also includes the GenBank accession numbers for all segments generated by Influenza A virus sequencing from nasal swab samples. Additionally, all nucleotide changes are listed by sample.

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, we herein report peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

Plant oils are increasingly in demand as renewable feedstocks for biodiesel and biochemicals. Currently, oilseeds are the primary source of plant oils. Although the vegetative tissues of plants express lipid metabolism pathways, they do not hyper-accumulate lipids. Elevated synthesis, storage, and accumulation of lipids in vegetative tissues have been achieved by metabolic engineering of sugarcane to produce “oilcane.” This study evaluates the potential of oilcane as a renewable feedstock for the co-production of lipids and fermentable sugars. Oilcane was grown under favorable climatic and field conditions in Florida (FLOC) as well as during an abbreviated growing season, outside its typical growing region, in Illinois (ILOC). The potential lipid yield of 0.35 tons/ha was projected from the hyperaccumulation of fatty acids in the stored vegetative biomass of FLOC, which is approaching the lipid yield of soybean (0.44 tons/ha). Processing of the vegetative tissues of oilcane recovered 0.20 tons/ha, which represents the recovery of 55% of the total lipids from FLOC. Chemical-free hydrothermal bioprocessing of ILOC and FLOC bagasse and leaves at 180 °C for 10 min prevented the degeneration of in situ plant lipids. This allowed the recovery of lipids at the end of the bioprocess with a major fraction of lipids remaining in the biomass residues after pretreatment and saccharification. Improvements through refined biomass processing, crop management, and metabolic engineering are expected to boost lipid yields and make oilcane a prime feedstock for the production of biodiesel.

This is a peptide imaging data obtained by mtarix assisted laser desoption ionization trapped ion mobility datasets from the central nervous sytem and select ganglion of aplysia Californica.

This dataset measurements for the following soil components from soil samples collected in northern Illinois between 2023 and 2024. Two file formats containing the same data are offered (Excel spreadsheet and CSV): 1. Soil clay minerals (illite, kaolinite, chlorite, and smectite) 2. pH 3. Other soil minerals: aluminum (Al), arsenic (As), barium (Ba), boron aluminide (Bal), calcium (Ca), cadmium (Cd), chloride (Cl), cobalt (Co), chromium (Cr), copper (Cu), iron (Fe), magnesium (Mg), manganese (Mn), mercury (Hg), molybdenum (Mo), nobium (Nb), nickel (Ni), potassium (K), phosphorous (P), lead (Pb), palladium (Pd), rubidium (Rb), silver (Ag), sulfur (S), thorium (Th), titanium (Ti), uranium (U), vanadium (V), yttrium (Y), zinc (Zn), and zirconium (Zr) Samples were collected on the side of public roads within the right of way. X-ray diffraction was used to quantify soil clay components, while other soil minerals were measured using a Niton XL5 Plus Analyzer. pH was measured using a Yinmik YK-S01 Digital Soil pH Tester. Samples were collected as part of a project funded by the United States Department of Agriculture Animal and Plant Inspection Service (USDA-APHIS) to examine the role of soil characteristics on chronic wasting disease (CWD) persistence in northern Illinois, USA.

Twenty-two genotypes of C4 species grown under ambient and elevated O3 concentration were studied at the SoyFACE (40°02’N, 88°14’W) in 2019. This dataset contains leaf morphology, photosynthesis and nutrient contents measured at three time points. The results of CO2 response curves are also included.

Storage lipids (mostly triacylglycerols, TAGs) serve as an important energy and carbon reserve in plants, and hyperaccumulation of TAG in vegetative tissues can have negative effects on plant growth. Purple acid phosphatase2 (PAP2) was previously shown to affect carbon metabolism and boost plant growth. However, the effects of PAP2 on lipid metabolism remain unknown. Here, we demonstrated that PAP2 can stimulate a futile cycle of fatty acid (FA) synthesis and degradation, and mitigate negative growth effects associated with high accumulation of TAG in vegetative tissues. Constitutive expression of PAP2 in Arabidopsis thaliana enhanced both lipid synthesis and degradation in leaves and led to a substantial increase in seed oil yield. Suppressing lipid degradation in a PAP2-overexpressing line by disrupting sugar-dependent1 (SDP1), a predominant TAG lipase, significantly elevated vegetative TAG content and improved plant growth. Diverting FAs from membrane lipids to TAGs in PAP2-overexpressing plants by constitutively expressing phospholipid:diacylglycerol acyltransferase1 (PDAT1) greatly increased TAG content in vegetative tissues without compromising biomass yield. These results highlight the potential of combining PAP2 with TAG-promoting factors to enhance carbon assimilation, FA synthesis and allocation to TAGs for optimized plant growth and storage lipid accumulation in vegetative tissues.

Dataset for F2F events of honeybees. F2F events are defined as face-to-face encounters of two honeybees that are close in distance and facing each other but not connected by the proboscis, thus not engaging in trophallaxis. The first and the second columns show the unique id's of honeybees participating in F2F events. The third column shows the time at which the F2F event started while the fourth column shows the time at which it ended. Each time is in the Unix epoch timestamp in milliseconds.

Please cite as: Menglin Liu and Benjamin M. Gramig. "Survey of Cover Crop, Conservation Tillage and Nutrient Management Practice Usage in Illinois and 2020 Fall Covers for Spring Savings Crop Insurance Discount Program Participation." Report to the Illinois Department of Agriculture and Fall Covers for Spring Savings working group. Center for the Economics of Sustainability and Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign. 2021. https://doi.org/10.13012/B2IDB-5222984_V1