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Chemical-free hydrothermal pretreatment of Miscanthus x giganteus (Mxg) at the lab scale using high liquid-to-solid ratios resulted in the recovery of anthocyanins and enhanced enzymatic digestibility of residual biomass. In this study, the process is scaled up by using a continuous hydrothermal pretreatment reactor operated at a low liquid-to-solid ratio (50 % w/w solids) as an important step towards commercialization. Anthocyanin yield was 70 % w/w at the pilot scale (50 kg of Mxg), compared to the 94 % w/w yield achieved at the lab scale (0.5 g of Mxg). The pretreated biomass was subsequently refined mechanically using a disc mill to increase the accessibility of cellulose by cellulases. Enzymatic saccharification of the pretreated and disc-milled residue yielded 238 g/L sugar concentration by operating in fed-batch mode at 50 % w/v solids content. Two strains of Rhodosporidium toruloides were evaluated for converting the hydrolysate sugars into microbial lipids, and strain Y-6987 had the highest lipid titer (11.0 g/L). Further, the residue left after enzymatic saccharification was determined to be enriched 1.7-fold in the lignin content. This lignin-rich residue has value as a feedstock for the production of sustainable aviation fuel precursors and other high-value lignin-based chemicals. Hence the proposed biorefinery based on Mxg creates an opportunity for generating revenue from multiple high-value products. As the demand for biofuels and biobased products is rising, the biorefinery products from Mxg would create a niche in the industrial sector.

Triacylglycerols (TAG), accumulate within lipid droplets (LD), predominantly surrounded by OLEOSINs (OLE), that protect TAG from hydrolysis. We tested the hypothesis that identifying and removing degradation signals from OLE would promote its abundance, preventing TAG degradation and enhancing TAG accumulation. We tested whether mutating potential ubiquitin-conjugation sites in a previously reported improved Sesamum indicum OLE (SiO) variant, o3-3 Cys-OLE (SiCO herein), would stabilize it and increase its lipogenic potential. SiCOv1 was created by replacing all five lysines in SiCO with arginines. Separately, six cysteine residues within SiCO were deleted to create SiCOv2. SiCOv1 and SiCOv2 mutations were combined to create SiCOv3. Transient expression of SiCOv3 in Nicotiana benthamiana increased TAG by two-fold relative to SiCO. Constitutive expression of SiCOv3 or SiCOv5, containing the five predominant TAG-increasing mutations from SiCOv3, in Arabidopsis along with mouse DGAT2 (mD) increased TAG accumulation by 54% in leaves and 13% in seeds compared with control lines coexpressing SiCO and mD. Lipid synthesis rates increased, consistent with an increase in lipid sink strength that sequesters newly synthesized TAG, thereby relieving the constitutive BADC-dependent inhibition of ACCase reported for WT Arabidopsis. These OLE variants represent novel factors for potentially increasing TAG accumulation in a variety of oil crops.

Cellulosic biomass-based sustainable aviation fuels (SAFs) can be produced from various feedstocks. The breakeven price and carbon intensity of these feedstock-to-SAF pathways are likely to differ across feedstocks and across spatial locations due to differences in feedstock attributes, productivity, opportunity costs of land for feedstock production, soil carbon effects, and feedstock composition. We integrate feedstock to fuel supply chain economics and life-cycle carbon accounting using the same system boundary to quantify and compare the spatially varying greenhouse gas (GHG) intensities and costs of GHG abatement with SAFs derived from four feedstocks (switchgrass, miscanthus, energy sorghum, and corn stover) at 4 km resolution across the U.S. rainfed region. We show that the optimal feedstock for each location differs depending on whether the incentive is to lower breakeven price, carbon intensity, or cost of carbon abatement with biomass or to have high biomass production per unit land. The cost of abating GHG emissions with SAF ranges from $181 Mg−1 CO2e to more than $444 Mg−1 CO2e and is lowest with miscanthus in the Midwest, switchgrass in the south, and energy sorghum in a relatively small region in the Great Plains. While corn stover-based SAF has the lowest breakeven price per gallon, it has the highest cost of abatement due to its relatively high GHG intensity. Our findings imply that different types of policies, such as volumetric targets, tax credits, and low carbon fuel standards, will differ in the mix of feedstocks they incentivize and locations where they are produced in the U.S. rainfed region. <b>Note: Column V in TableS7_DayCentSimulatedYield.csv should be labelled Corn Stover CoSo-NT-50% Max.</b>

Oxidative cleavage of carbon–carbon double bonds (C═C) in alkenes and fatty acids produces aldehydes and acids valued as chemical intermediates. Solid tungsten oxide catalysts are low cost, nontoxic, and selective for the oxidative cleavage of C═C bonds with hydrogen peroxide (H2O2) and are, therefore, a promising option for continuous processes. Despite the relevance of these materials, the elementary steps involved and their sensitivity to the form of W sites present on surfaces have not been described. Here, we combine in situ spectroscopy and rate measurements to identify significant steps in the reaction and the reactive species present on the catalysts and examine differences between the kinetics of this reaction on isolated W atoms grafted to alumina and on those exposed on crystalline WO3 nanoparticles. Raman spectroscopy shows that W–peroxo complexes (W–(η2-O2)) formed from H2O2 react with alkenes in a kinetically relevant step to produce epoxides, which undergo hydrolysis at protic surface sites. Subsequently, the CH3CN solvent deprotonates diols to form alpha-hydroxy ketones that react to form aldehydes and water following nucleophilic attack of H2O2. Turnover rates for oxidative cleavage, determined by in situ site titrations, on WOx–Al2O3 are 75% greater than those on WO3 at standard conditions. These differences reflect the activation enthalpies (ΔH‡) for the oxidative cleavage of 4-octene that are much lower than those for the isolated WOx sites (36 ± 3 and 60 ± 6 kJ·mol–1 for WOx–Al2O3 and WO3, respectively) and correlate strongly with the difference between the enthalpies of adsorption for epoxyoctane (ΔHads,epox), which resembles the transition state for epoxidation. The WOx–Al2O3 catalysts mediate oxidative cleavage of oleic acid with H2O2 following a mechanism comparable to that for the oxidative cleavage of 4-octene. The WO3 materials, however, form only the epoxide and do not cleave the C–C bond or produce aldehydes and acids. These differences reflect the distinct site requirements for these reaction pathways and indicate that acid sites required for diol formation are strongly inhibited by oleic acids and epoxides on WO3 whereas the Al2O3 support provides sites competent for this reaction and increase the yield of the oxidative cleavage products.

This study shows a new route to produce potassium sorbate (KS) from triacetic acid lactone (TAL), which is a chemical platform that can be biologically synthesized from natural sources. Sorbic acid and its potassium salt (KS) are widely used as preservatives in foods and pharmaceuticals. Three steps are used to produce KS from TAL: 1) hydrogenation of TAL into 4-hydroxy-6-methyltetrahydro-2-pyrone (HMP), 2) dehydration of HMP to parasorbic acid (PSA), and 3) ring-opening and hydrolysis of PSA to KS. TAL can be fully hydrogenated over Ni/SiO2 to give near quantitative yields of HMP. A three-step reaction kinetics model was developed for dehydration of HMP into PSA. This model was used to show that the highest PSA yield occurs at low temperatures. An experimental PSA yield of 84.2% with respect to TAL was obtained which agreed with the prediction of the reaction kinetics model. KOH was used as a coreactant for the ring-opening hydrolysis of PSA to produce >99.9% yield of KS from PSA. Tetrahydrofuran (THF) was used to purify the TAL derived-KS (TAL-KS). The TAL-KS had a KS purity of 95.5%. The overall yield of TAL-KS with respect to TAL was calculated to be 77.3%. TAL-KS produced in this study had similar antimicrobial activities as commercial KS.

Herein we report the production of high-pressure (19.3 bar), carbon-negative hydrogen (H2) from glycerol with a purity of 98.2 mol% H2, 1.8 mol% light hydrocarbons (mainly methane), and 400 ppm of CO. Aqueous phase reforming (APR) of 10 wt% glycerol solution was studied with a series of NiPt alumina bimetallic catalysts supported on alumina. The Ni8Pt1-450 catalyst had the highest hydrogen selectivity (95.6%) and the lowest alkanes selectivity (3.7%) of the tested catalysts. The hydrogen selectivity decreased in the order of Ni8Pt1-450 > Ni8Pt1-260 > Ni1Pt1-260 > Pt-260. The CO2 was sequestered with CaO adsorbent which formed CaCO3. We measured the adsorption capacity of the CaO adsorbent at different temperatures. Life cycle analysis showed that the APR of glycerol coupled with CO2 capture has net negative CO2 equivalent greenhouse gas emissions. The CO2 emissions are −9.9 kg CO2 eq./kg H2 and −50.1 kg CO2 eq./kg H2 when grid electricity and renewable electricity are used, respectively, and the CO2 is allocated respectively to the mass of products produced. The cost of this H2 (denoted as “green-emerald”) was estimated to be 2.4 USD per kg H2 when grid electricity is used and 2.7 USD per kg H2 when using renewable electricity. The cost of glycerol has the highest contribution of 1.71 USD per kg H2. Participation in the carbon credit markets can further decrease the price of the produced H2.

Living organisms rely on simultaneous reactions catalysed by mutually compatible and selective enzymes to synthesize complex natural products and other metabolites. To combine the advantages of these biological systems with the reactivity of artificial chemical catalysts, chemists have devised sequential, concurrent, and cooperative chemoenzymatic reactions that combine enzymatic and artificial catalysts. Cooperative chemoenzymatic reactions consist of interconnected processes that generate products in yields and selectivities that cannot be obtained when the two reactions are carried out sequentially with their respective substrates. However, such reactions are difficult to develop because chemical and enzymatic catalysts generally operate in different media at different temperatures and can deactivate each other. Owing to these constraints, the vast majority of cooperative chemoenzymatic processes that have been reported over the past 30 years can be divided into just two categories: chemoenzymatic dynamic kinetic resolutions of racemic alcohols and amines, and enzymatic reactions requiring the simultaneous regeneration of a cofactor. New approaches to the development of chemoenzymatic reactions are needed to enable valuable chemical transformations beyond this scope. Here we report a class of cooperative chemoenzymatic reaction that combines photocatalysts that isomerize alkenes with ene-reductases that reduce carbon–carbon double bonds to generate valuable enantioenriched products. This method enables the stereoconvergent reduction of E/Z mixtures of alkenes or reduction of the unreactive stereoisomers of alkenes in yields and enantiomeric excesses that match those obtained from the reduction of the pure, more reactive isomers. The system affords a range of enantioenriched precursors to biologically active compounds. More generally, these results show that the compatibility between photocatalysts and enzymes enables chemoenzymatic processes beyond cofactor regeneration and provides a general strategy for converting stereoselective enzymatic reactions into stereoconvergent ones.

This work evaluates the consistency and reliability of the title flag, i.e., retraction labeling that appears in the title of retracted publications, using 925 sampled retracted publications indexed in the Crossref only (Lee & Schneider, 2023), that are indexed in three other sources, Retraction Watch, Scopus, and Web of Science as of April 2023. We presume the retraction status of an item based on its title flag. For example, the flag "removal notice" is a retraction notice, and "retracted article" is a retracted paper. We compared the item's likely retraction status from the flag with the item's actual retraction status from the publisher's website.

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.

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus. This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus.

Lipids produced using oleaginous yeast cells are an emerging feedstock to manufacture commercially valuable oleochemicals ranging from pharmaceuticals to lipid-derived biofuels. Production of biofuels using oleaginous yeast is a multistep procedure that requires yeast cultivation and harvesting, lipid recovery, and conversion of the lipids to biofuels. The quantitative recovery of the total intracellular lipid from the yeast cells is a critical step during the development of a bioprocess. Their rigid cell walls often make them resistant to lysis. The existing methods include mechanical, chemical, biological and thermochemical lysis of yeast cell walls followed by solvent extraction. In this study, an aqueous thermal pretreatment was explored as a method for lysing the cell wall of the oleaginous yeast Rhodotorula toruloides for lipid recovery. Hydrothermal pretreatment for 60 min at 121 °C with a dry cell weight of 7% (w/v) in the yeast slurry led to a recovery of 84.6 ± 3.2% (w/w) of the total lipids when extracted with organic solvents. The conventional sonication and acid-assisted thermal cell lysis led to a lipid recovery yield of 99.8 ± 0.03% (w/w) and 109.5 ± 1.9% (w/w), respectively. The fatty acid profiles of the hydrothermally pretreated cells and freeze-dried control were similar, suggesting that the thermal lysis of the cells did not degrade the lipids. This work demonstrates that hydrothermal pretreatment of yeast cell slurry at 121 °C for 60 min is a robust and sustainable method for cell conditioning to extract intracellular microbial lipids for biofuel production and provides a baseline for further scale-up and process integration.

This dataset contains all raw data corresponding to the figures in the main text and appendices of the paper "Dispersion Engineering of Planar Sub-millimeter Wave Waveguides and Resonators with Low Radiation Loss."

Data for 'Atomic-scale imaging and charge state manipulation of NV centers by scanning tunneling microscopy' to be published in Nature Communications.

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 dataset contains the raw Florida bonneted bat echolocation calls recorded in southern Florida, USA from the years 2021 and 2022. This dataset also includes our artificial roost microclimate data (2021 only) and observations of bats recorded in our artificial roosts (2021 and 2022). Lastly, we include the R script required to analyze the Florida bonneted bat echolocation calls and the R script to produce the supplemental table and supplemental figure for our microclimate data.

Conversion of corn fiber to ethanol in the dry grind process can increase ethanol yields, improve coproduct quality and contribute to process sustainability. This work investigates the use of two physio-chemical pretreatments on corn fiber and effect of cellulase enzyme dosage to improve ethanol yields. Fiber separated after liquefaction of corn was pretreated using (1) hot water pretreatment (160°C for 5, 10 or 20 min); and (2) wet disk milling and converted to ethanol. The conversion efficiencies of hot water pretreated fiber were higher than untreated fiber, with highest increase in conversion (10.4%) achieved for 5-minute residence time at 160 °C. Disk milling was not effective in increasing conversion compared to other treatments. Hydrolysis and fermentation of untreated fiber with excess cellulase enzymes resulted in 33.3% higher conversion compared to untreated fiber. Note: in “Table1_Treatments.csv”, NA = Not applicable.

Datasheets relating to the article "Brachypodium SPEECHLESS2 promoter drives expression of a synthetic EPF to reduce stomatal density in sugarcane without pleiotropic effects" published in Plant Biotechnology Journal.

Curated networks and clustering output from the manuscript: Well-Connected Communities in Real-World Networks https://arxiv.org/abs/2303.02813

This dataset contains files and relevant metadata for real-world and synthetic LFR networks used in the manuscript "Well-Connectedness and Community Detection (2024) Park et al. presently under review at PLOS Complex Systems. The manuscript is an extended version of Park, M. et al. (2024). Identifying Well-Connected Communities in Real-World and Synthetic Networks. In Complex Networks & Their Applications XII. COMPLEX NETWORKS 2023. Studies in Computational Intelligence, vol 1142. Springer, Cham. https://doi.org/10.1007/978-3-031-53499-7_1. “The Overview of Real-World Networks image provides high-level information about the seven real-world networks. TSVs of the seven real-world networks are provided as [network-name]_cleaned to indicate that duplicated edges and self-loops were removed, where column 1 is source and column 2 is target. LFR datasets are contained within the zipped file. Real-world networks are labeled _cleaned_ to indicate that duplicate edges and self loops were removed. #LFR datasets for the Connectivity Modifier (CM) paper ### File organization Each directory `[network-name]_[resolution-value]_lfr` includes the following files: * `network.dat`: LFR network edge-list * `community.dat`: LFR ground-truth communities * `time_seed.dat`: time seed used in the LFR software * `statistics.dat`: statistics generated by the LFR software * `cmd.stat`: command used to run the LFR software as well as time and memory usage information

The increased awareness for eco-friendliness and sustainability has shifted the interest of stakeholders from synthetic colors to natural plant-based pigments. In this study, purple stemmed Miscanthus x giganteus was evaluated as a source of anthocyanins. Hydrothermal pretreatment was studied as a green, chemical-free process for recovering maximum anthocyanins in the pretreatment liquor. The highest recovery of 94.3 ± 1.5% w/w of the total anthocyanin concentration was obtained for a temperature and time combination of 170 °C and 10 min. The pretreatment also improved the enzymatic digestibility of the biomass and led to a 2.1-fold increase in the overall recovery of glucose (70.6 ± 0.5% w/w) at the end of 72 h. The sugar monomers obtained after the enzymatic hydrolysis of the pretreated biomass could be used for the production of biofuels or biochemicals in an integrated biorefinery based on purple-stemmed miscanthus. Overall, this study demonstrates that the clean pretreatment method developed could lead to an additional product stream (rich in anthocyanins) along with its effect in reducing the recalcitrance of miscanthus biomass.

This dataset consists of raw ADC readings from a 3 transmitter 4 receiver 77GHz FMCW radar, together with synchronized RGB camera and depth (active stereo) measurements. The data is grouped into 4 distinct radar configurations: - "indoor" configuration with range <14m - "30m" with range <38m - "50m" with range <63m - "high_res" with doppler resolution of 0.043m/s # Related code https://github.com/moodoki/radical_sdk # Hardware Project Page https://publish.illinois.edu/radicaldata

Please cite as: Wuebbles, D., J. Angel, K. Petersen, and A.M. Lemke, (Eds.), 2021: An Assessment of the Impacts of Climate Change in Illinois. The Nature Conservancy, Illinois, USA. https://doi.org/10.13012/B2IDB-1260194_V1 Climate change is a major environmental challenge that is likely to affect many aspects of life in Illinois, ranging from human and environmental health to the economy. Illinois is already experiencing impacts from the changing climate and, as climate change progresses and temperatures continue to rise, these impacts are expected to increase over time. This assessment takes an in-depth look at how the climate is changing now in Illinois, and how it is projected to change in the future, to provide greater clarity on how climate change could affect urban and rural communities in the state. Beyond providing an overview of anticipated climate changes, the report explores predicted effects on hydrology, agriculture, human health, and native ecosystems.

This dataset contains the following to replicate figures from "TChem-atm (v2.0.0): Scalable Performance-Portable Multiphase Atmospheric Chemistry" submitted to Geophysical Model Development (GMD). It contains (1) the simulation inputs, outputs and analysis notebook for recreating the PartMC-CAMP and PartMC-TChem-atm comparison and (2) scripts, timing results and analysis tools for recreating the performance evaluation. Users can either inspect the raw output to verify the results of the manuscript or rerun simulations using the provided inputs. Additionally, modifiying the inputs allows for for further exploration of both model simulation and performance characteristics.

The data within consist of compressed output files in the form of edgelists (*.edgelist.gz) and nodelists (*.aux.parquet) from large citation network simulations using an agent-based model. The code and instructions are available at: <a href="https://github.com/illinois-or-research-analytics/SASCA">https://github.com/illinois-or-research-analytics/SASCA</a>. In addition, we provide a distribution of citation frequencies drawn from a random sample of PubMed journal articles (pooled_50k_pubmed_unique.csv) and a table of recencies- the frequency with which citations are made to the previous year, the year before that and so on (recency_probs_percent_stahl_filled.csv). A manuscript describing the SASCA-s simulator has been submitted for review and will be referenced in a future version of this data repository if it is accepted. The prefixes sj and er refer to the real world and Erdos-Renyi random graph respectively that were used to initiate simulations. These 'seed' networks are available from the Github site referenced above.

Plant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae. The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an engineered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass.