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Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production
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Issatchenkia orientalis as a platform organism for cost-effective production of organic acids
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Structure and Kinetics of Organic Acid Radicals Formed in Reaction with • OH Radicals
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Renewables-Driven Production of Organic Acids from Industrial CO2
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Production of organic acids from Aspergillus cis-aconitic acid decarboxylase (cadA) deletion strains
This application provides recombinant Aspergillus fungi having an endogenous cis-aconitic acid decarboxylase (cadA) gene genetically inactivated, which allows aconitic acid production by the recombinant fungi. Such recombinant fungi can further include an exogenous nucleic acid molecule encoding aspartate decarboxylase (panD), an exogenous nucleic acid molecule encoding β-alanine-pyruvate aminotransferase (BAPAT), and an exogenous nucleic acid molecule encoding 3-hydroxypropionate dehydrogenase (HPDH). Kits including these fungi, and methods of using these fungi to produce aconitic acid and 3-hydroxypropionic acid (3-HP) are also provided.
Imaging plant metabolism in situ
Abstract Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.
Kinetically Controlled Linker Binding in Rare Earth-2,5-Dihydroxyterepthalic Acid Metal–Organic Frameworks and Its Predicted Effects on Acid Gas Adsorption
In the pursuit of highly stable and selective metal–organic frameworks (MOFs) for the adsorption of caustic acid gas species, an entire series of rare earth MOFs have been explored. Each of the MOFs in this series (RE-DOBDC; RE = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu; DOBDC = 2,5-dihydroxyterepthalic acid) was synthesized in the tetragonal space group I4/m. Crystallized MOF samples, specifically Eu-DOBDC, were seen to have a combination of monodentate and bidentate binding when synthesized under typical reaction conditions, resulting in a contortion of the structure. However, extended crystallization times determined that this binding is kinetically controlled and that the monodentate binding option was crystallographically eliminated by extended reaction times at higher temperatures. Furthermore, this series allows for the direct study of the effect of the metal center on the structure of the of the MOF; herein, the lanthanide metal ionic radii contraction across the periodic table results in a reduction of the MOF pore size and lattice parameters. Scanning electron microscopy–energy-dispersive spectroscopy was used to investigate the stages of crystal growth for these RE-DOBDC MOFs. All MOFs, except Er-DOBDC had a minimum of two stages of growth. These analogues were demonstrated by analysis of neutron diffraction (PND) to exhibit a cooperative rotational distortion of the secondary building unit, resulting in two crystallographically distinct linker sublattices. Computational modeling efforts were used to show distinct differences on acid gas (NO 2 and SO 2 ) binding energies for RE-DOBDC MOFs when comparing the monodentate/bidentate combined linker with the bidentate-only linker crystal structures.
Organic Acid-Assisted Thermal Dehalogenation of Halide Salt Nuclear Wastes: From Waste Salts to Borosilicate Glass
Only a handful of high-halide salt waste forms have been demonstrated for vitrification-based immobilization strategies for halide-salt nuclear waste streams (e.g., pyroprocessing wastes, molten salt reactor wastes) and they all have low waste loading potential and most have low chemical durabilities for high-alkali streams. An alternative approach to direct salt immobilization is salt partitioning prior to waste form fabrication and one option for partitioning is halide removal (called dehalogenation). Removing the halogen fraction through dehalogenation can significantly reduce the waste volume required for disposal in the primary waste form. Furthermore, when dehalogenation is performed using organic acids, the dehalogenation reagent can decompose during high-temperature vitrification, reducing waste loading limitations in the waste form. In the current work, different organic acids (i.e., oxalic, formic, acetic, oxamic, and citric) were evaluated for dehalogenation efficiency of a simple chloride salt simulant (7.19% LaCl 3 , 53.77% LiCl, and 39.04% KCl, by mole) and a more complex chloride salt simulant called ERV3 (electrorefiner version 3) at 150 °C–300 °C and using H + /Cl – molar ratios of 1:1, 2:1, and 3:1. Additionally, a borosilicate glass waste form called TARS (or the average of refined specifications) was formulated, produced, and characterized for dehalogenated ERV3.
Can Isoprene Oxidation Explain High Concentrations of Atmospheric Formic and Acetic Acid over Forests?
Formic and acetic acid concentrations are particularly high over forested areas of the world. However, the gas-phase mechanisms for producing these acids are poorly understood even for isoprene, the globally dominant biogenic hydrocarbon. We quantified formic and acetic acid production from reactions of hydroxyl radical (OH) (between high and low ranges of nitric oxide (NO) levels) with isoprene, methacrolein (MACR), isoprene epoxydiol (IEPOX), isoprene hydroxy hydroperoxide (ISOPOOH), and α-pinene from the focused isoprene experiments at California Institute of Technology (FIXCIT) laboratory chamber study. We find that (i) OH oxidation of MACR, IEPOX, and ISOPOOH are sources of formic acid, (ii) isoprene peroxy radical isomerization and associated photolysis oxidation products are potentially important sources of organic acids, and (iii) high levels of NO generally suppress organic acid formation from OH oxidation of isoprene. We modified existing chemical mechanisms for isoprene oxidation to account for organic acid production pathways observed in the FIXCIT study. We simulated organic acid production during the Southeastern Oxidant and Aerosol Study using the updated chemical mechanisms and represented acetic acid within a factor of 2 but still underpredicted formic acid by a factor of 6. While we cannot explain ambient formic acid with explicit chemical mechanisms, the FIXCIT results suggest that the oxidation of isoprene could account for as much as 70% of the global annual production of formic acid from gas-phase reactions.
A Novel Continuous Ultrasound-Assisted Leaching Process for Rare Earth Element Extraction: Environmental and Economic Assessment
Rare earth elements (REEs) make up integral components in personal electronics, healthcare instrumentation, and modern energy technologies. REE leaching with organic acids is an environmentally friendly alternative to traditional extraction methods. Our previous study demonstrated that batch ultrasound-assisted organic acid leaching of REEs can significantly decrease environmental impacts compared to traditional bioleaching. The batch method is limited to small volumes and is unsuitable for industrial implementation. This study proposes a novel approach to increase reaction volume using a continuous ultrasound-assisted organic acid leaching method. Laboratory experiments showed that continuous ultrasound-assisted leaching increased the leaching rate (µg/h) 11.3–24.5 times compared to our previously reported batch method. Techno-economic analysis estimates the cost of the continuous approach using commercially purchased organic acids is $\$$9465/kg of extracted REEs and $\$$4325/kg of extracted REEs, using gluconic acid and citric acid, respectively. The sensitivity analysis reveals that substituting commercially purchased organic acids with microbially produced biolixiviant can reduce the process cost by approximately 99% while minimally increasing energy consumption. Environmental assessment shows that most of the emissions stemmed from the energy required to power the ultrasound reactor. We concluded that increased leaching capacity using a continuous ultrasound-assisted approach is feasible, but process modifications are needed to reduce the environmental impact.
Root exudates shift how N mineralization and N fixation contribute to the plant-available N supply in low fertility soils
Nitrogen (N) availability is a primary constraint to plant productivity, especially in marginal lands with inherently low fertility. Root exudates change with plant nutrient status, and are expected to affect the microbially-mediated N transformations (gross N mineralization vs N fixation) in low fertility soil (low soil organic matter). To explore this possibility, we sampled soils from two monoculture switchgrass (var. Cave-In-Rock) plot with and without N addition at two marginal land sites in Michigan, USA. In a two-week lab incubation, we quantified the effect of different root exudates on gross N mineralization and N fixation by adding simulated root exudates (carbohydrates, organic acids) at a rate of 100 μg C g –1 day –1 . On average, adding carbohydrates to low fertility soil increased the soil respiration by 254%, the dissolved organic carbon (DOC) by 366% and reduced dissolved organic N (DON) by 40%. In contrast, soils receiving organic acids had 159% more soil respiration, 163% higher DOC concentration and the DON concentration increased by 49%. Analysis of the C recovery in measured pools revealed that root exudates C inputs were nearly equivalent to the DOC, microbial biomass carbon (MBC), and soil respiration in sandy soil, but only 45–74% of the root exudate C was recovered in these pools in the sandy loam soil. This suggests that root exudate C may be adsorbed to mineral particles in the sandy loam soil. Soil treated with organic acids had higher gross N mineralization and N immobilization rates than soil with carbohydrates addition. Adding carbohydrates significantly increased the free-living N fixation rates, compared to organic acid addition. Changes in soil pH, and DON induced by root exudate addition had strong association with N transformation rates and N availability. Gross N mineralization produced more plant-available N than N fixation, as evidenced by higher inorganic N concentration in soils receiving organic acids than carbohydrates. Here, by quantifying how different root exudates affect the contribution of N mineralization and N fixation to the plant-available N pool in low fertility soils, this study enhances our understanding of the “C for N” exchange in the plant rhizosphere.
X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction
Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. Here, to better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ~13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe–Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO 3 ) and K-citrate [K 3 (C 6 H 5 O 7 )·H 2 O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO 3 has both the lowest and highest lying energy features, and K 3 (C 6 H 5 O 7 )·H 2 O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.
Concepts for Actinide Recovery from TRISO Used Nuclear Fuel
The work described in this report has developed a preliminary conceptual flowsheet based on limited published literature for the head-end of a TRISO oxycarbide UNF reprocessing plant. The essential function of the head-end is to prepare the UNF for subsequent separation of actinides. The main steps of the conceptual TRISO UNF head-end reprocessing flowsheet are: 1. Fragmentation of the graphite moderator to expose the fuel particles. 2. Separation of fuel particles from fragmented graphite moderator by sieving and fluidization. 3. Fragmentation of the fuel particles to expose the fuel kernel. 4. Dissolution of the fuel kernel in nitric acid. Noteworthy at this step is the formation of organic acids (mainly oxalic and mellitic acids) from the carbon associated with the fuel and TRISO coatings. These acids can interfere with actinide separations and solvent extraction hydraulic performance and carbon dioxide gas generation. 5. Clarification of the dissolved fuel solution to separate the coating fragments. 6. Dissolver off-gas treatment with specific emphasis on managing generation of carbon dioxide gas containing carbon-14. The quantity of carbon dioxide is projected to be 100 to 1000 times greater than that arising from dissolving LWR UNF. Pre or post treatment of the exposed fuel kernels could be undertaken to mitigate the formation of organic acids but there still exists a significant off-gas treatment challenge. The literature on reprocessing uranium nitride UNF was reviewed but a flowsheet was not specifically developed since its scope and uncertainties are expected to be encompassed by the oxycarbide flowsheet. Overall, the predominant feature of processing TRISO UNF is carbon management to reduce waste volume and mitigate the formation of carbon dioxide and organic acids. This report recommends broad areas of research that will help to further define the head-end flowsheet.
Prediction of Hydroxymethylfurfural Yield in Glucose Conversion through Investigation of Lewis Acid and Organic Solvent Effects
Hydroxymethylfurfural (HMF) is one of the important renewable platform compounds that can be obtained from biomass feedstocks through glucose conversion catalyzed by Brønsted and Lewis acids. However, it is challenging to enhance the HMF yield due to side reactions. In this study, a systematic approach combining theory and experiment was performed to investigate the influence of Lewis acids and organic solvents on the HMF yield. For the Lewis acid effect, a relationship between chemical hardness and experimental HMF yields was found in the rate-limiting step of glucose-to-fructose isomerization for six metal chlorides; HMF production was promoted when the metal chloride and a substrate had a similar chemical hardness. To study the organic solvent effect, a multivariate model was developed based on the insights gained from the mechanistic study of fructose dehydration, to predict HMF yields in a given water-organic cosolvent system. It showed a reliable accuracy in evaluating HMF yields with a mean absolute error (MAE) of 3.0% with respect to experimental HMF yields for 13 solvents, and also predicted HMF yields with a MAE of 10.7% for four new solvents. Chemical interpretation of the model revealed that it is desirable to use a solvent capable of stabilizing the carbocation intermediates with low proton transfer activity and high hydrogen bond basicity, to maximize the HMF yield. This multivariate model informs experimentalists about rational selection of solvents with very low computational costs needed to calculate only six variables for each solvent. It can be expanded to other catalytic systems such as heterogeneous Brønsted–Lewis bifunctional catalysts and enables optimization of reaction conditions to obtain other useful platform molecules through biomass conversion.
A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains
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.
Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains
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.