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At least 55 records · Page 3

A genetic toolbox for metabolic engineering of Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. Yet, 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 evidence of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray quantification of oxygen groups on diamond surfaces for quantum applications

Abstract Identifying the surface chemistry of diamond materials is increasingly important for device applications, especially quantum sensors. Oxygen-related termination species are widely used because they are naturally abundant, chemically stable, and compatible with stable nitrogen vacancy centres near the diamond surface. Diamond surfaces host a mixture of oxygen-related species, and the precise chemistry and relative coverage of different species can lead to dramatically different electronic properties, with direct consequences for near-surface quantum sensors. However, it is challenging to unambiguously identify the different groups or quantify the relative surface coverage. Here we show that a combination of x-ray absorption and photoelectron spectroscopies can be used to quantitatively identify the coverage of carbonyl functional groups on the { 100 } diamond surface. Using this method we reveal an unexpectedly high fraction of carbonyl groups ( > 9%) on a wide range of sample surfaces. Furthermore, through a combination of ab initio calculations and spectroscopic studies of engineered surfaces, we reveal unexpected complexities in the x-ray spectroscopy of oxygen terminated diamond surfaces. Of particular note, we find the binding energies of carbonyl-related groups on diamond differs significantly from other organic systems, likely resulting in previous misestimation of carbonyl fractions on diamond surfaces.

36 MATERIALS SCIENCE↗

Making Coal Relevant for Small Scale Applications: Modular Gasification for Syngas/Engine CHP Applications in Challenging Environments

The proposed project includes construction and operation of a power plant consisting of coal gasification facilities and engine generators which would produce electrical power and heat. The recovered heat and a portion of the carbon dioxide emissions from the engines would support an onsite greenhouse and other heat and power customers. The proposed project site is located on the Marathon North Pole Terminal property in North Pole, Alaska. Two gasifiers would convert the coal into syngas, which would be fed through a gas cleanup train and then combusted in six reciprocating engines driving electric generators. Heat recovery on the engine cooling loops and exhaust trains would provide heat to a glycol/water circulation system for use in the greenhouse, in the Marathon facilities and for other customers. Natural gas would fuel two additional engine generators and would also be available to supplement the syngas-fired engines.

01 COAL, LIGNITE, AND PEAT↗

MXenoids: Generalization of MXene-Inspired Covalent Surface Modifications Across Two-Dimensional Materials

The ability to perform versatile covalent surface modifications in two-dimensional (2D) inorganic materials marks a significant advance in the functionalization of this broad family of materials. One particularly successful example of 2D materials with chemically modifiable surfaces are 2D transition metal carbides and nitrides (MXenes). MXenes' strong in-plane metal-carbon bonds and labile surface metal-halide bonds create altogether unprecedented opportunities for versatile postsynthetic modifications and assembling complex materials, including various organic-inorganic hybrids. Here, we demonstrate the general applicability of this surface modification strategy to non-MXene halide-terminated 2D materials, termed MXenoids. These surface modifications enable compositional and electronic structure engineering, introduce chiral hybrid organic-inorganic structures, and photoluminescence ranging from near-IR to blue. This study highlights the avenue of surface chemistry-driven materials design, enhancing the functional capabilities of 2D materials.

Zhou, Chenkun [University of Chicago, IL (United S↗

Engineering an Extremely Hybrid PKS for Adipic Acid Production

Polyketide synthases (PKSs) are modular enzymes with exceptional potential as biocatalysts for producing non-native compounds. Here, we report the first PKS-based pathway for adipic acid (AA), an industrial monomer for nylon production, by engineering one of the most extensively hybridized PKS systems to date. Using a retrobiosynthetic approach, we identified EtnB, a succinyl-CoA-loading module that uniquely retains the terminal carboxyl group, enabling access to dicarboxylic polyketide products, rarely produced by canonical PKSs. EtnB was coupled to a fully reducing extension module through an engineered communication linker, which improved ACP–KS interactions, enhanced titers, and demonstrated selective succinyl-CoA loading in vivo . This construct integrates genes from five organisms─with domains from seven PKS modules joined across six non-natural junctions─and functions in both Escherichia coli and Pseudomonas putida . Additional engineering that included AT domain exchanges, optimization of extender unit supply, and host strain metabolic rewiring further increased AA production. Together, this work demonstrates that highly chimeric PKSs can be rendered functional through rational design, expands the PKS toolkit with a carboxyl-retaining loading module, and establishes a versatile platform for engineering diacids and other noncanonical products through PKS pathways.

biomanufacturing↗

Spatial Control of Substitutional Dopants in Hexagonal Monolayer WS 2 : The Effect of Edge Termination

The ability to control the density and spatial distribution of substitutional dopants in semiconductors is crucial for achieving desired physicochemical properties. Substitutional doping with adjustable doping levels has been previously demonstrated in 2D transition metal dichalcogenides (TMDs); however, the spatial control of dopant distribution remains an open field. In this work, edge termination is demonstrated as an important characteristic of 2D TMD monocrystals that affects the distribution of substitutional dopants. Particularly, in chemical vapor deposition (CVD)-grown monolayer WS 2 , it is found that a higher density of transition metal dopants is always incorporated in sulfur-terminated domains when compared to tungsten-terminated domains. Here two representative examples demonstrate this spatial distribution control, including hexagonal iron- and vanadium-doped WS 2 monolayers. Density functional theory (DFT) calculations are further performed, indicating that the edge-dependent dopant distribution is due to a strong binding of tungsten atoms at tungsten-zigzag edges, resulting in the formation of open sites at sulfur-zigzag edges that enable preferential dopant incorporation. Based on these results, it is envisioned that edge termination in crystalline TMD monolayers can be utilized as a novel and effective knob for engineering the spatial distribution of substitutional dopants, leading to in-plane hetero-/multi-junctions that display fascinating electronic, optoelectronic, and magnetic properties.

2D transition metal dichalcogenides↗

Plant‐produced SARS ‐ CoV ‐2 antibody engineered towards enhanced potency and in vivo efficacy

Summary Prevention of severe COVID‐19 disease by SARS‐CoV‐2 in high‐risk patients, such as immuno‐compromised individuals, can be achieved by administration of antibody prophylaxis, but producing antibodies can be costly. Plant expression platforms allow substantial lower production costs compared to traditional bio‐manufacturing platforms depending on mammalian cells in bioreactors. In this study, we describe the expression, production and purification of the originally human COVA2‐15 antibody in plants. Our plant‐produced mAbs demonstrated comparable neutralizing activity with COVA2‐15 produced in mammalian cells. Furthermore, they exhibited similar capacity to prevent SARS‐CoV‐2 infection in a hamster model. To further enhance these biosimilars, we performed three glyco‐ and protein engineering techniques. First, to increase antibody half‐life, we introduced YTE‐mutation in the Fc tail; second, optimization ofN‐linked glycosylation by the addition of a C‐terminal ER‐retention motif (HDEL), and finally; production of mAb in plant production lines lacking β‐1,2‐xylosyltransferase and α‐1,3‐fucosyltransferase activities (FX‐KO). These engineered biosimilars exhibited optimized glycosylation, enhanced phagocytosis and NK cell activation capacity compared to conventional plant‐produced S15 and M15 biosimilars, in some cases outperforming mammalian cell produced COVA2‐15. These engineered antibodies hold great potential for enhancingin vivoefficacy of mAb treatment against COVID‐19 and provide a platform for the development of antibodies against other emerging viruses in a cost‐effective manner.

Biotechnology & Applied Microbiology↗

Elastomeric vitrimers from designer polyhydroxyalkanoates with recyclability and biodegradability

Cross-linked elastomers are stretchable materials that typically are not recyclable or biodegradable. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are soft and ductile, making these bio-based polymers good candidates for biodegradable elastomers. Elasticity is commonly imparted by a cross-linked network structure, and covalent adaptable networks have emerged as a solution to prepare recyclable thermosets via triggered rearrangement of dynamic covalent bonds. Here, we develop biodegradable and recyclable elastomers by chemically installing the covalent adaptable network within biologically produced mcl-PHAs. Specifically, an engineered strain of Pseudomonas putida was used to produce mcl-PHAs containing pendent terminal alkenes as chemical handles for postfunctionalization. Thiol-ene chemistry was used to incorporate boronic ester (BE) cross-links, resulting in PHA-based vitrimers. mcl-PHAs cross-linked with BE at low density (<6 mole %) affords a soft, elastomeric material that demonstrates thermal reprocessability, biodegradability, and denetworking at end of life. The mechanical properties show potential for applications including adhesives and soft, biodegradable robotics and electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data for "Photoinduced Chemomimetic Biocatalysis for Enantioselective Intermolecular Radical Conjugate Addition"

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

Catalysis↗

Poly(oxymethylene) Ethers as a High Cetane, Low Sooting Biofuel Blendstock for Use in Medium to Heavy Duty Mixing Controlled Compression Ignition Engines

Compression ignition (CI) engines are currently the most common prime mover for medium and heavy duty vehicles; these engines contribute roughly a quarter of US greenhouse gas emissions from transportation, and even higher percentages of particulate and nitrogen oxide emissions. As a result, there have been significant efforts made to reduce these emissions, particularly through selection of low-emissions alternative fuels. Oxymethylene ethers (OMEs) are a class of molecule, typically structured R-O-(CH2O)n-R', which have been considered as a possible blendstock in CI fuels for the goal of soot reduction. Generally, past work has focused on methyl-terminated OMEs, CH3-O-(CH2O)n-CH3, which by virtue of containing no C--C bonds, produce negligible soot. These molecules show significant reductions in soot emission from engines when blended in moderate to high ratios with traditional diesels, however, they have been shown to have inferior physical properties and poor compatibility with some legacy systems. Recent theoretical work has shown that OMEs with non-methyl alkyl groups may have superior performance, albeit at the cost of increased soot formation. In this work, a variety of OMEs with terminating alkyl groups from methyl to butyl are considered for their suitability as CI fuels. The synthesis of these extended OMEs is studied, including formation of n=1 OMEs from common chemical sources, and extension of the chain length to heavier molecules, via reactions over acidic ion exchange resins. Following the synthesis, the properties of these OMEs are studied with respect to their engine applicability. It is found that heavier (propyl- and butyl-terminated) OMEs have superior properties for diesel compatibility, particularly in reactivity, volatility, and water solubility. Extended-alkyl OMEs are found to have higher soot production than methyl-terminated OMEs, but remain superior to diesel soot production on a per-unit-energy basis. A sample of a butyl-terminated OME mixture, n=2-4, is selected as the ideal OME blend for close compatibility with legacy diesel systems. This mixture is blended with certified diesel and tested for ASTM D975 compatibility, passing all required tests but lubricity; decreased heat of combustion is observed but not governed by the diesel standard. Fundamental combustion tests of various mid-weight OMEs are performed in a rapid compression machine, where it is shown that low-temperature chemistry causes a region of decreased dependence of ignition delay on temperature, consistent with methyl-terminated OME behavior. An isopropyl-terminated OME is observed to have low reactivity compared to other OMEs; this fuel is investigated via further rapid compression machine testing and CFR engine testing. It is found that this OME has strong negative-temperature-coefficient ignition behavior - a first for OMEs - and has reactivity lower than other OMEs, but insufficient for direct spark ignition engine testing.

09 BIOMASS FUELS↗

Interfacial Hydrogen-Bond Dynamics in Transition Metal Compounds

Understanding how water behaves when confined within atomic layers of active transition-metal carbides, nitrides, and carbonitrides is essential for uncovering the fundamental principles needed to engineer solid–liquid interfaces at the atomic scale. Yet, how lattice element chemistry and surface termination groups collectively regulate the structure and mobility of such interlayer water remains poorly understood. Here, we present a composition-controlled investigation of interlayer water dynamics in layered transition-metal nitride, carbide, and carbonitride systems using a systematic integration of quasi-elastic neutron scattering (QENS), ab initio molecular dynamics (AIMD) simulations, and density functional theory (DFT) calculations. QENS measurements show that nitride-rich systems host mobile, translationally diffusing water with thermally activated self-diffusion coefficients on the order of 10 –10 m 2 s –1 , whereas mixed C/N lattices confine water to localized, nontranslational motion that is insensitive to temperature. AIMD and DFT reveal that lattice C/N chemistry and surface functional group composition reshape the first hydration layer by modulating the surface electronic structure and termination-dependent hydrogen-bond networks, leading to pronounced differences in water ordering and thermal resilience. On the other hand, fully carbide systems exhibit intermediate behavior, highlighting that water mobility is not primarily controlled by the hydration level alone but by the coupling between lattice composition and surface chemistry. Overall, this study establishes how surface chemistry and lattice composition jointly control interfacial hydrogen bond dynamics, offering a mechanistic framework for designing transition-metal layered materials with tailored interfacial transport properties.

Hydration↗

Finding of No Adverse Effect for the Façade Alteration of Building 23-117, Administration Building, Mercury, Area 23, Nevada National Security Site, Nye County, Nevada

The U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) plans to update the façade of Building 23-117 in the town of Mercury (Nevada State Historic Preservation Office [SHPO] Resource No. B15256), which is on the Nevada National Security Site (NNSS) in Nye County, Nevada. The purpose of the undertaking is to incorporate Building 23-117 into the new Mercury campus in accordance with the master plan for the modernization of Mercury. The NNSA/NFO will implement this undertaking in accordance with the Programmatic Agreement between the National Nuclear Security Administration Nevada Field Office and the Nevada State Historic Preservation Officer Regarding Modernization and Operational Maintenance of the Nevada National Security Site, at Mercury in Nye County, Nevada, hereafter referred to as the Mercury PA. Building 23-117 was built in 1982 as the architect-engineer Administration Building1 for Holmes & Narver, a government contractor who helped design and engineer the town of Mercury and other areas on the NNSS from its inception until the termination of their contract in 1990. The building continued to be used by subsequent government contractors and is currently still in use by MSTS. The town of Mercury and the immediate surrounding area have been formally determined eligible for listing in the National Register of Historic Places (National Register, NRHP) as the Mercury Historic District (MHD, SHPO Resource No. D230) under Criteria A and C for its importance in supporting nuclear testing and scientific research from 1951 through 1992. Building 23-117 was identified as a contributing element to the MHD in a 2018 architectural survey of the district (Reno et al.) and recorded on a Nevada Architectural Resource Assessment (ARA) form (Reno et al. 2017). It is a historic property for the purposes of compliance with Section 106 of the National Historic Preservation Act (NHPA) and is subject to the stipulations of the Mercury PA. The NNSA/NFO requested that Desert Research Institute (DRI), cultural resource subject matter experts, analyze the effects of the proposed project on historic properties in the Area of Potential Effect (APE) and make a recommended finding for the undertaking in accordance with Section 106 of the NHPA and the Mercury PA. The purpose of this letter report is to submit documentation related to the mitigation of the façade alteration of Building 23-117 (Nevada State Historic Preservation Office [SHPO] Resource No. B15256) in the Mercury Historic District (MHD, SHPO Resource No. D230). This submission is intended to comply with the stipulations in the Programmatic Agreement between the National Nuclear Security Administration Nevada Field Office and the Nevada State Historic Preservation Officer Regarding Modernization and Operational Maintenance of the Nevada National Security Site at Mercury in Nye County, Nevada, hereafter referred to as the Mercury PA.

54 ENVIRONMENTAL SCIENCES↗

Surface-Functionalized, Two-Dimensional Polymer Electrochromic Layers as Ultrafast, Multi-State Infrared Optical Gates

Electrochromic devices have widespread application potential, but the currently available switching speeds limit broad real-world implementation of this technology. Here, we report surface-engineered two-dimensional polymers with ionophilic pores that offer unprecedented switching speeds in solid-state, two-terminal, electrochromic devices. In particular, we demonstrate that a crystalline donor–acceptor 2DP functionalized with ethylene glycol oligomers exhibits multistate infrared absorption that is 4× faster (t c = 320 ms) with 3× coloration efficiency (491 cm 2 C –1 ) compared to an alkyl functionalized 2DP constructed from the same chromophores. The functionalized nanoporous surfaces enable rapid switching in these materials under either oxidative or reductive conditions, allowing us to access a range of robust, stable optical responses in a single electrochromic layer. These attributes led us to leverage surface-functionalized 2DPs as multistate infrared logic gates. Collectively, this work demonstrates that surface engineering of nanoporous crystalline lattices is a promising approach to co-optimize the electronic and ionic conductivities required to achieve rapidly switchable electrochromic layers. Beyond speed and efficiency, the demonstration of multistate infrared characteristics shows that electrochromic frameworks are useful in integrated optoelectronic circuits. This positions surface-engineered 2DPs as improved electrochromic coatings and a new material platform for photonic information processing and adaptive devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chemistry and Interfacial Structure Promoting Quasi-van der Waals Epitaxial Growth of WS 2 Nanosheets on Sapphire for Prospective Application in Field-Effect Transistors

How do chemical and structural modifications to the supporting crystal surface affect the subsequent van der Waals (vdW) or quasi(Q)-vdW epitaxial growth of 2D nanocrystals? Developing an atomic-scale picture of such an interfacial system is crucial for understanding its impact on the physical and chemical properties of the supported 2D materials. The elucidation of the interfacial structure and chemistry needed to promote the Q-vdW epitaxial growth of 2D tungsten disulfide (WS 2 ) nanocrystals contributes to the growth mechanism understanding, thus pushing forward the integration of such atomically thin semiconductors toward real field-effect transistor applications. In addition to an atomic-force microscopy top view, we showcase a combination of X-ray techniques for a top-to-bottom investigation of the complexities of the buried interface structures. Furthermore, this approach uses X-ray photoelectron spectroscopy, X-ray standing wave excited X-ray fluorescence, and crystal truncation rod scattering to produce a highly resolved chemical-state-specific 3D atomic map for the extended interface structure of WS 2 /α-Al 2 O 3 (001). Employing these detailed analysis methods, along with density functional theory to further refine the picoscale structure, we demonstrate how two different types of interface engineering during the pregrowth stage lead to significant differences in the chemical and structural modifications to the terminal surface of c-face sapphire, which in turn leads to substantial differences in the submonolayer growth of supported WS 2 2D nanocrystals in terms of lateral domain sizes, epitaxial registry, vdW gaps, and stability.

36 MATERIALS SCIENCE↗

Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3′ Terminal Structures for Enzymatic De Novo DNA Synthesis

Enzymatic oligonucleotide synthesis methods based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) promise to enable the de novo synthesis of long oligonucleotides under mild, aqueous conditions. Intermediates with a 3′ terminal structure (hairpins) will inevitably arise during synthesis, but TdT has poor activity on these structured substrates, limiting its usefulness for oligonucleotide synthesis. Here, we described two parallel efforts to improve the activity of TdT on hairpins: (1) optimization of the concentrations of the divalent cation cofactors and (2) engineering TdT for enhanced thermostability, enabling reactions at elevated temperatures. By combining both of these improvements, we obtained a ~10-fold increase in the elongation rate of a guanine-cytosine hairpin.

59 BASIC BIOLOGICAL SCIENCES↗

A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗

Observation of formation and local structures of metal-organic layers via complementary electron microscopy techniques

Abstract Metal-organic layers (MOLs) are highly attractive for application in catalysis, separation, sensing and biomedicine, owing to their tunable framework structure. However, it is challenging to obtain comprehensive information about the formation and local structures of MOLs using standard electron microscopy methods due to serious damage under electron beam irradiation. Here, we investigate the growth processes and local structures of MOLs utilizing a combination of liquid-phase transmission electron microscopy, cryogenic electron microscopy and electron ptychography. Our results show a multistep formation process, where precursor clusters first form in solution, then they are complexed with ligands to form non-crystalline solids, followed by the arrangement of the cluster-ligand complex into crystalline sheets, with additional possible growth by the addition of clusters to surface edges. Moreover, high-resolution imaging allows us to identify missing clusters, dislocations, loop and flat surface terminations and ligand connectors in the MOLs. Our observations provide insights into controllable MOL crystal morphology, defect engineering, and surface modification, thus assisting novel MOL design and synthesis.

36 MATERIALS SCIENCE↗

Neutral Silicon Vacancy Centers in Undoped Diamond via Surface Control

Neutral silicon vacancy centers (SiV 0 ) in diamond are promising candidates for quantum applications; however, stabilizing SiV 0 requires high-purity, boron-doped diamond, which is not a readily available material. Here, we demonstrate an alternative approach via chemical control of the diamond surface. We use low-damage chemical processing and annealing in a hydrogen environment to realize reversible and highly stable charge state tuning in undoped diamond. The resulting SiV 0 centers display optically detected magnetic resonance and bulklike optical properties. Controlling the charge state tuning via surface termination offers a route for scalable technologies based on SiV 0 centers, as well as charge state engineering of other defects.

74 ATOMIC AND MOLECULAR PHYSICS↗