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At least 109 records · Page 6

Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5–Aminolevulinic Acid Production

Biological production of 5-aminolevulinic acid (5-ALA) has received growing attention over the years. However, there is the tradeoff between 5-ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5-ALA. To address this limitation, we engineered an acid-tolerant yeast, Issatchenkia orientalis SD108, for 5-ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5-ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5-ALA was improved from 28 mg/L to 120-, 150-, and 300 mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5-ALA to 510 mg/L, a 13-fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid-tolerant I. orientalis SD108ΔPDC has a high potential for 5-ALA production at a large scale in the future.

59 BASIC BIOLOGICAL SCIENCES↗

Divergent Responses of Carbon Nitride Dot‐Based Amorphous Species and Small Molecule Hybrids to Trace Level Analytes

Bottom-up synthesis of carbon nitride dots (CNDs) offers a versatile platform for the creation of diverse nanomaterials with tunable properties. Here, we report a facile hydrothermal approach using citric acid (CA) and urea (U) as precursors to synthesize CNDs with varying degrees of condensation and crystallinity. By carefully controlling reaction conditions and post-synthetic treatments, we obtained two distinct fractions: a polycrystalline fraction composed of small-molecule hybrids and an amorphous fraction containing CNDs. We then sought to understand how the dominant species in these fractions impact sensing abilities using trace-level explosive exemplars. In conclusion, the results have important implications for sensing and related applications where understanding the complex interplay between synthetic conditions and post-synthetic processing play vital roles in determining the final properties of CND materials.

carbon nitride dots↗

In silico evaluation of plant nitrification suppression effects on agroecosystem nitrogen loss

Abstract Nitrification regulates the potential for nitrogen (N) loss from ecosystems because it converts ammonium to nitrate, which is susceptible to leaching and gaseous emissions. Crops can suppress the microbes that perform nitrification by exuding nitrification‐inhibiting compounds from their roots and taking up available ammonium. However, the effect of nitrification suppression on agroecosystem N losses remains poorly characterized, and a lack of temporal synchrony between nitrification, N losses, and nitrification suppression by plants could limit the effect of nitrification suppression. We used the DayCent‐CABBI model to evaluate the effectiveness of the suppression of nitrification by sorghum to reduce N 2 O emissions and nitrate leaching in an energy sorghum/soybean rotation at the Energy Farm in Urbana‐Champaign, IL. We simulated nitrification suppression at the measured levels (MeasNS) and at the maximum measured level applied to the entire growing season (MaxNS), and we also explored ways to better utilize nitrification suppression by altering the timing of urea–ammonium–nitrate fertilizer applications. Model experiments showed that most nitrification occurred immediately after fertilizer was applied, whereas nitrification suppression began to ramp up more than a month after planting. On an annual basis, MeasNS experiments showed a 1%–2% reduction in annual N 2 O emissions relative to no nitrification suppression (NoNS), and MaxNS experiments showed a 4%–9% reduction in annual N 2 O emissions relative to NoNS. Both nitrification suppression levels showed <1% reduction in nitrate leaching. Altering the timing of fertilizer applications to better synchronize nitrification suppression with high soil ammonium levels had mixed effects on annual N 2 O emissions and nitrate leaching and sometimes resulted in increased N losses. The timing of simulated N 2 O emissions shifted with the timing of fertilization, and N 2 O emissions from denitrification increased when N 2 O emissions from nitrification decreased. Increasing N retention during the non‐growing season may be more effective than growing‐season nitrification suppression for reducing annual N losses in the rainfed Midwest.

60 APPLIED LIFE SCIENCES↗

Hydrogen Bond Benchmark: Focal‐Point Analysis and Assessment of DFT Functionals

We performed a hierarchical, convergent ab initio benchmark study and systematically analyzed the performance of density functional approximations for describing hydrogen bonds in small neutral, cationic, and anionic complexes, as well as in larger systems involving amide, urea, deltamide, and squaramide moieties. Focal point analyses (FPA), extrapolating to the ab initio limit, were carried out using correlated wave function methods up to CCSDT(Q) for the small complexes and CCSD(T) for the larger systems, together with correlation-consistent Gaussian basis sets up to the complete basis set limit. Optimized geometries and vibrational frequencies were obtained at the CCSD(T) level. The resulting FPA hydrogen-bond energies converge within a few tenths of a kcal mol −1 . These reference data were used to evaluate 60 density functionals (including 12 dispersion-corrected), spanning the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. Overall, the meta-hybrid M06-2X provides the best performance for both hydrogen bond energies and geometries, while the dispersion-corrected GGAs BLYP-D3(BJ) and BLYP-D4 also yield accurate hydrogen-bond data and can serve as cost-effective options for studying large and complex systems.

coupled cluster theory↗

Ionic Liquid Aided [ 11 C]CO Fixation for Synthesis of 11 C‐carbonyls

Tributyl(ethyl)phosphonium oxopentenolate ([P 4442 ][Pen]) is an ionic liquid developed to capture CO and has shown ability to catalyze carbonylation reactions in organic chemistry. Carbon-11 ( 11 C, t 1/2 =20.4 min) labeled CO is a highly versatile building block for the synthesis of positron emission tomography (PET) radiotracers that are applied for medical imaging. The use of [ 11 C]CO is limited by its low solubility in organic solvents. Herein, we report a proof-of-concept study evaluating a new method to prepare 11 C-labeled amides, ureas and carbamates via reaction of [ 11 C]CO in [P 4442 ][Pen] and applied for fully automated radiosyntheses of Bruton's tyrosine kinase inhibitors, [ 11 C]evobrutinib and [ 11 C]ibrutinib.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The denatured state of HIV ‐1 protease under native conditions

Abstract The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.

60 APPLIED LIFE SCIENCES↗

Photocatalytic Hydrogen Evolution Using Mesoporous Honeycomb Iron Titanate

Mesoporous honeycomb iron titanate using a sol-gel, evaporation-induced self-assembly method is synthesized. A triblock copolymer, F127, serves as a structure-directing agents, with iron chloride and titanium (IV) isopropoxide as inorganic precursors. The strong intermolecular force of attraction among urea, metal precursors, and polymer led to the formation of the mesoporous honeycomb structure. The study of physicochemical properties using different techniques reveals the formation of microstructures with a remarkable degree of porosity. The amorphous iron titanate outperforms the photochemical generation of H 2 due to its disorderly structural arrangement and incomplete crystal formation. The randomness on the structure provides more area for catalytic reaction by providing more contact with the reactant and superior light absorption capability. The high amount of hydrogen gas, 40.66 mmolg -1 h -1 , is observed in the investigation over 3 h of activity for the iron titanate honeycomb sample. This yield is a more significant amount compared to the obtained for the commercially available TiO 2 (23.78 mmolg -1 h -1 ). The iron titanate materials synthesized with low-cost materials and methods are very effective and have the potential for hydrogen generation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The Epidermal Microbiome Within an Aggregation of Leopard Sharks ( Triakis semifasciata ) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points

The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray–Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray–Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.

59 BASIC BIOLOGICAL SCIENCES↗

Beyond the Surface: Non-Invasive Low-Field NMR Analysis of Microbially-Induced Calcium Carbonate Precipitation in Shale Fractures

Microbially-induced calcium carbonate precipitation (MICP) is a biological process in which microbially-produced urease enzymes convert urea and calcium into solid calcium carbonate (CaCO 3 ) deposits. MICP has been demonstrated to reduce permeability in shale fractures under elevated pressures, raising the possibility of applying this technology to enhance shale reservoir storage safety. For this and other applications to become a reality, non-invasive tools are needed to determine how effectively MICP seals shale fractures at subsurface temperatures. In this study, two different MICP strategies were tested on 2.54 cm diameter and 5.08 cm long shale cores with a single fracture at 60 °C. Flow-through, pulsed-flow MICP-treatment was repeatedly applied to Marcellus shale fractures with and without sand (“proppant”) until reaching approximately four orders of magnitude reduction in apparent permeability, while a single application of polymer-based “immersion” MICP-treatment was applied to an Eagle Ford shale fracture with proppant. Low-field nuclear magnetic resonance (LF-NMR) and X-Ray computed microtomography (micro-CT) techniques were used to assess the degree of biomineralization. With the flow-through approach, these tools revealed that while CaCO 3 precipitation occurred throughout the fracture, there was preferential precipitation around proppant. Without proppant, the same approach led to premature sealing at the inlet side of the core. In contrast, immersion MICP-treatment sealed off the fracture edges and showed less mineral precipitation overall. This study highlights the use of LF-NMR relaxometry in characterizing fracture sealing and can help guide NMR logging tools in subsurface remediation efforts.

MICP↗

Differential DNA methylation and metabolite profiling of Atlantic killifish (Fundulus heteroclitus) from the New Bedford Harbor Superfund site

Atlantic killifish (Fundulus heteroclitus) is a valuable model in evolutionary toxicology to study how the interactions between genetic and environmental factors serve the adaptive ability of organisms to resist chemical pollution. Killifish populations inhabiting environmental toxicant-contaminated New Bedford Harbor (NBH) show phenotypes tolerant to polychlorinated biphenyls (PCBs) and differences at the transcriptional and genomic levels. However, limited research has explored epigenetic alterations and metabolic effects in NBH killifish. To identify the involvement of epigenetic and metabolic regulation in the adaptive response of killifish, we investigated tissue- and sex-specific differences in global DNA methylation and metabolomic profiles of NBH killifish populations, compared to sensitive populations from a non-polluted site, Scorton Creek (SC). The results revealed that liver-specific global DNA hypomethylation and differential metabolites were evident in fish from NBH compared with those from SC. The sex-specific differences were not greater than the tissue-specific differences. We demonstrated liver-specific enriched metabolic pathways (e.g., amino acid metabolic pathways converged into the urea cycle and glutathione metabolism), suggesting possible crosstalk between differential metabolites and DNA hypomethylation in the livers of NBH killifish. Additional investigation of methylated gene regions is necessary to understand the functional role of DNA hypomethylation in the regulation of enzyme-encoding genes associated with metabolic processes and physiological changes in NBH populations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Use of a Pressurized Water Treatment to Prevent Cracking of Internal Gelation Sol-Gel Microspheres

Pressurized water treatments were investigated as a means to prevent cracking of internal gelation sol-gel microspheres upon drying and heating. A batch of gelled cerium oxide microspheres was prepared, split into two samples that were processed with and without a pressurized water treatment, and dried in air at room temperature. Thermal gravimetric analysis was used to compare the mass loss profiles between the two samples and to understand volatile emissions from cerium oxide microspheres during heat treatments up to 600 °C. Microspheres that were processed without a pressurized water treatment lost approximately 4.6 times more mass upon heating than microspheres that were subjected to a pressurized water treatment. Comparison of the cracking behavior of microspheres prepared with and without a pressurized water treatment indicated that microspheres subjected to a pressurized water treatment were virtually crack-free after heat treatments. Conversely, microspheres processed without a pressurized water treatment, which is typical of traditional washing processes, exhibited extensive cracking. Analysis of residues dried from pressurized water treatment effluents indicated that hexamethylenetetramine and urea, which are excess reactants from the internal gelation process, were removed from gelled microspheres during the pressurized water treatment step. Traditional processing methods for preparing internal gelation microspheres use specific feed solution and gelation parameters to reduce subsequent cracking upon drying and heating. Results from this study indicate that more aggressive gel-forming conditions may be used to produce crack-free microspheres, if a pressurized water treatment step is included after washing and before air-drying.

cerium oxide, internal gelation, microsphere, TRIS↗

Towards an Integrated Process for CO 2 Capture and Utilization: Cultivation of Scenedesmus acutus Using Gaseous CO 2 and NH 3

Integrating CO 2 scrubbing from flue gas with its utilization in algae cultivation represents a potential means of lowering the cost of CO 2 capture. Towards this goal, this study sought to assess the feasibility of using gaseous a CO 2 /NH 3 stream, derived from CO 2 capture using aqueous ammonia, as a C- and N-source for algae cultivation. Scenedesmus acutus was cultured in 800 mL photobioreactors using gaseous CO 2 /NH 3 in mole ratios varying from 7 to 18. Excellent growth of Scenedesmus acutus was observed, the average growth rate for CO 2 /NH 3 = 10 of 0.171 ± 0.015 g/L·day exceeding that obtained using 1% CO 2 /N 2 and urea as the N-source (0.099 ± 0.28 g/L·day). Under optimal growth conditions (CO 2 /NH 3 mole ratio of 10), CO 2 utilization ranged from 57% to 72%, while the NH 3 utilization was >90%. The CO 2 /NH 3 feed rate was also found to exert a significant effect on algae productivity, excessive feed rates leading to accumulation of NH 3 in the culture at concentrations that were toxic to the algae. Consequently, to avoid the toxic effects of high NH 3 concentrations (>2.0 mM), it proved necessary to balance the NH 3 supply with the algae growth rate so that excessive NH 3 accumulation was prevented. This indicates that for practical applications, a CO 2 /NH 3 feed control strategy would be required that takes into account the ammonium ion concentration in solution and the pH so as to avoid significant concentrations of free NH 3 . Furthermore, analysis of the harvested biomass revealed a high protein (≥ 47 wt%) and a low ash content (< 3.6 wt%), suggesting it would be well suited for use as animal feed or as a feedstock for the production of bioplastics.

03 NATURAL GAS↗

Splitting tensile strength of shale cores: intact versus fractured and sealed with ureolysis-induced calcium carbonate precipitation (UICP)

Ureolysis-induced calcium carbonate precipitation (UICP) is a biomineral solution where the urease enzyme converts urea and calcium into calcium carbonate. The resulting biomineral can bridge gaps in fractured shale, reduce undesired fluid flow, limit fracture propagation, better store carbon dioxide, and potentially enhance well efficiency. The mechanical properties of shale cores were investigated using a modified Brazilian indirect tensile strength test. An investigation of intact shale using Eagle Ford and Wolfcamp cores was conducted at varying temperatures. Results show no significant difference between shale types (average tensile strength = 6.19 MPa). Eagle Ford displayed higher strength at elevated temperature, but temperature did not influence Wolfcamp. Comparatively, cores with a single, lengthwise heterogeneous fracture were sealed with UICP and further tested for tensile strength. UICP was delivered via a flow-through method which injected 20–30 sequential patterns of ureolytic microorganisms and UICP-promoting fluids into the fracture until permeability reduced by three orders of magnitude or with an immersion method which placed cores treated with guar gum and UICP-promoting fluids into a batch reactor, demonstrating that guar gum is a suitable inclusion and may reduce the number of flow-through injections required. Tensile results for both delivery methods were variable (0.15–8 MPa), and in some cores the biomineralized fracture split apart, possibly due to insufficient sealing and/or heterogeneity in the composite UICP-shale cores. Notably in other cores the biomineralized fracture remained intact, demonstrating more cohesion than the surrounding shale, indicating that UICP may produce a strong seal for subsurface application.

58 GEOSCIENCES↗

Co nanoclusters derived from zinc-trimesic acid fiber for efficient levulinic acid hydrogenation

The hydrogenation of levulinic acid (LA) to γ-valerolactone (GVL) is significant for producing chemicals and fuels from renewable resources, a promising direction in biomass refining. Currently, non-precious metal catalysts suffer from low activity due to a single electronic structure, which is incapable of effectively activating both CO in LA and H 2 . Herein we report in situ fabricated Co nanoclusters within positive and metallic Co sites on N-doped carbon, which can simultaneously activate LA's CO and H 2 , enhancing the activity and selectivity for GVL production. Urea-assisted Co dispersion coupled with variation of pyrolysis temperature, Co nanoclusters were formed via direct conversion of Co-containing zinc trimesic acid fibers. The resulting Co nanoclusters possess dual active sites of Co-N x and metallic Co, with adjustable electronic structures. Under the reaction conditions of 200 °C and 4.5 MPa H 2 for 4 h, LA was completely converted, achieving 95 % yield of GVL. The outstanding catalytic activity is attributed to the Co-N x and metallic Co active sites, which facilitate the activation of CO and H 2 , respectively. In conclusion, this research provides a new concept for converting N-free metal-organic frameworks into non-precious metal nanoclusters, offering valuable insights for designing high-performance non-precious metal catalysts for biomass-derived chemical and fuel production.

Co nanoclusters↗

Addressing wellbore integrity and thief zone permeability using microbially-induced calcium carbonate precipitation (MICP): A field demonstration

Microbially-induced calcium carbonate precipitation (MICP) is an emerging biotechnology for wellbore integrity applications including sealing defects in wellbore cement and modifying the permeability of rock formations. The goal of this field demonstration was to characterize a failed waterflood injection well and provide proof of principle that MICP can reduce permeability in the presence of oil using conventional oilfield fluid delivery methods. Here we compared well logs performed at the time the well was drilled with ultrasonic logs, sonic cement evaluation, and temperature logs conducted after the well failed. Analysis of these logs suggested that, rather than entering the target waterflood formation, injectate was traveling through defects in the well cement to a higher permeability sandstone layer above the target formation. Sporosarcina pasteurii cultures and urea-calcium media were delivered 2290 ft (698 m) below ground surface using a 3.75 gal (14.2 L) slickline dump bailer to promote mineralization in the undesired flow paths. By Day 6 and after 25 inoculum and 49 calcium media injections, the injectivity [gpm/psi] had decreased by approximately 70%. This demonstration shows that 1) common well logs can be used to identify scenarios where MICP can be employed to reduce system permeability, remediate leakage pathways, and improve waterflood efficiency, and 2) MICP can occur in the presence of hydrocarbons.

42 ENGINEERING↗

Formation and energetics of amorphous rare earth (RE) carbonates in the RE 2 O 3 –CO 2 –H 2 O system

Amorphous materials are of interest in the genesis of crystalline solids. They are often the first to precipitate from supersaturated solutions and are in the nanometer size range, transforming into a nanocrystalline metastable phase, and then to thermodynamically stable phases. One must seek knowledge of the composition, structure, thermodynamics, kinetics, and reaction pathways that relate the amorphous and crystalline phases. The subject of this study is the amorphous phases in the system RE 2 O 3 -CO 2 –H 2 O (RE- La, Nd, Dy,Yb). They were synthesized via direct precipitation and urea hydrolysis, and characterized by powder XRD, DTA with mass spectrometric analysis of the evolved gases. Phases have the non-stoichiometric composition RE 2 O 3 ·xCO 2 ·yH 2 O (1 < x < 3, 3 < y <7), which is different from that of crystalline simple carbonates and hydroxycarbonates. Thus we consider them to be amorphous precursors, rather than amorphous carbonates. High temperature oxide melt solution calorimetry in molten sodium molybdate solvent was used to derive their enthalpies of formation from oxides and elements. Increase of energetic stability per mole of RE 2 O 3 compounds occurs in the order: RE 2 O 3 → 2RE(OH)3→ 2REO(OH) → RE 2 O 2 CO 3 → Amorphous precursor → 2(REOHCO 3 ) → RE 2 (CO 3 ) 3 ·yH 2 O. We calculated the enthalpies of possible transformations of amorphous precursors to crystalline phases and conclude that thermodynamics determines the dependence of the crystallizing products on the temperature and partial pressure of CO 2 and H 2 O. Amorphous precursors are clearly intermediate in the synthesis, and ternary phases containing both H 2 O and CO 2 compete with each other in terms of thermodynamic stability. The energy landscape obtained here will allow one to directly synthesize specific products and control their functionality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lithium-ion hopping weakens thermal stability of LiPF 6 carbonate electrolytes

Lithium hexafluorophosphate (LiPF 6 )-based carbonate electrolytes are widely used in commercial lithium-ion batteries (LIBs), but their thermal instability limits the cycle life and safety of LIBs at elevated temperatures. Few studies have yielded insight into the initial PF 6 — decomposition reaction that promotes thermal instability of LiPF6-based electrolytes. Here, we find that lithium-ion hopping assisted by the overall reorientational motion of propylene carbonate molecules facilitates PF 6 — decomposition at elevated temperatures in 1 M LiPF 6 /propylene carbonate electrolyte. Further, we demonstrate that urea additives, by preventing lithium-ion hopping, suppress the initial LiPF 6 decomposition reaction and enhance the thermal stability of the electrolyte. LIB cell tests with LiNi 0.6 Mn 0.2 Co 0.2 O 2 ||Li 4 Ti 5 O 12 show improved LIB performance at elevated temperatures with the thermally stabilized electrolyte. This study provides key insights into the design of thermally stable LiPF 6 -based carbonate electrolytes for improving the cycle life, calendar life, and safety of LIBs in elevated-temperature applications.

25 ENERGY STORAGE↗