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At least 991 records · Page 55

Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

Genome-scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling and pairing product formation with substrate utilization and can improve strain performance beyond levels typically accessible using traditional strain engineering approaches. However, sustainable feedstocks pose a challenge due to incomplete high-resolution metabolic data for non-canonical carbon sources required to curate GSMM and identify implementable designs. Here we address a four-gene deletion design in the Pseudomonas putida KT2440 strain for the lignin-derived non-sugar carbon source, p-coumarate (p-CA), that proved challenging to implement. We examine the performance of the fully implemented design for p-coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product that is commonly used to colorimetrically quantify glutamine concentration. Through proteomics, promoter-variation, and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism in the completed design is rate-limited by fumarase hydratase (FUM) enzyme activity in the citrate cycle and requires careful optimization of another fumarate hydratase protein (PP_0897) expression to achieve growth and production. A double sensitivity analysis also confirmed a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. Metabolic cross-feeding experiments were used to examine the impact of complete removal of the fumarase hydratase reaction and revealed an unanticipated nutrient requirement, suggesting additional functions for this enzyme. While a complete implementation of the design was achieved, this study highlights the challenge of completely inactivating metabolic reactions encoded by under-characterized proteins, especially in the context of multi-gene edits.

59 BASIC BIOLOGICAL SCIENCES↗

Grain reorientation and stress-state evolution during cyclic loading of an α -Ti alloy below the elastic limit

Here, high-energy synchrotron x-rays are used to track grain-averaged lattice reorientation and stress-state evolution in Ti–7Al as it is cyclically loaded to 90% of its macroscopic yield stress. This evolution provides clear indication of accumulating plastic strain even though the sample never exceeded the elastic limit. The largest changes in lattice orientation and stress state are observed following the first cycle then evolution continues at a lower rate with subsequent cycles. Variation of the axes about which lattice reorientation occurs is found to be highly dependent on the maximum resolved shear stress and corresponding activation of various families of slip systems.

36 MATERIALS SCIENCE↗

Rating of a Pitch Bearing for a 1.5-Megawatt Wind Turbine

Slew ring or "pitch" bearings are used in wind turbines to connect the blade root to the hub. They support the resulting simultaneous radial, axial, and overturning moment loads while allowing relative rotation of the blade with respect to the hub. NREL has recently begun a research program related to pitch bearing reliability, recognizing its growing importance for wind turbines. The purpose of this first paper is to describe the rating analysis for a reference pitch bearing representative of that used a 1.5-megawatt (MW) wind turbine. The analysis will serve as a baseline for future finite-element analyses and strain and deflection measurements of an installed pitch bearing. If successful, this work will enable the design and specification of more reliable pitch bearings, a key concern in the long-term operation of land-based wind turbines and new development of offshore wind turbines.

17 WIND ENERGY↗

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo

The 2014–2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was mined to identify emerging mutations and trends in mutations as the outbreak progressed over time. Information on transmission dynamics, prevalence, and persistence of intra-host mutants, and the position of a mutation on a protein were then used to prioritize 544 reported mutations based on their ability to impact ZIKV phenotype. Using this criteria, six mutants (representing naturally occurring mutations) were generated as synthetic infectious clones using a 2015 Puerto Rican epidemic strain PRVABC59 as the parental backbone. The phenotypes of these naturally occurring variants were examined using both cell culture and murine model systems. Mutants had distinct phenotypes, including changes in replication rate, embryo death, and decreased head size. In particular, a NS2B mutant previously detected during in vivo studies in rhesus macaques was found to cause lethal infections in adult mice, abortions in pregnant females, and increased viral genome copies in both brain tissue and blood of female mice. Additionally, mutants with changes in the region of NS3 that interfaces with NS5 during replication displayed reduced replication in the blood of adult mice. This analytical pathway, integrating both bioinformatic and wet lab experiments, provides a foundation for understanding how naturally occurring single mutations affect disease outcome and can be used to predict the of severity of future ZIKV outbreaks. To determine if naturally occurring individual mutations in the Zika virus epidemic genotype affect viral virulence or replication rate in vitro or in vivo, we generated an infectious clone representing the epidemic genotype of stain Puerto Rico, 2015. Using this clone, six mutants were created by changing nucleotides in the genome to cause one to two amino acid substitutions in the encoded proteins. The six mutants we generated represent mutations that differentiated the early epidemic genotype from genotypes that were either ancestral or that occurred later in the epidemic. We assayed each mutant for changes in growth rate, and for virulence in adult mice and pregnant mice. Three of the mutants caused catastrophic embryo effects including increased embryonic death or significant decrease in head diameter. Three other mutants that had mutations in a genome region associated with replication resulted in changes in in vitro and in vivo replication rates. These results illustrate the potential impact of individual mutations in viral phenotype.

59 BASIC BIOLOGICAL SCIENCES↗

TiO2 Nanocrystal-Framed Li 2 TiSiO 5 Platelets for Low-Voltage Lithium Battery Anode

Titanium-based anode materials are attracting considerable attention for use in high-performance lithium-ion batteries, but the compromised energy density caused by high voltage plateaus and unsatisfactory capacities severely retards their practical applications. Herein, a molten-salt synthesis of Li 2 TiSiO 5 crystalline platelets and a subsequent selective facet modification by in situ growth of TiO 2 nanocrystal frames are facilely achieved. The discharge voltage plateau at around 0.5 V renders the Li 2 TiSiO 5 anode safe compared with graphite and confers a high energy density compared with zero-strain Li 4 Ti 5 O 12 anode. With the optimized size, structure, and content of modified TiO2 nanocrystals associated with the exposed (001) plane of Li 2 TiSiO 5 , the Li 2 TiSiO 5 -based anodes can deliver a capacity of above 300 mAh g -1 , enhanced rate performance, and a capacity retention of 66% after 10 000 cycles. In situ X-ray diffraction and ex situ transmission electron microscopy have demonstrated the structural stability of the anodes upon charge/discharge. Further theoretical calculation reveals 3D migration paths of Li + ions in Li 2 TiSiO 5 . The selective modification of in situ grown TiO2 nanocrystals on certain facets of crystallites opens a new door for the development of electrode materials possessing superior electrochemical properties.

anodes↗

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

Biological production of 5‐aminolevulinic acid (5‐ALA) has received growing attentionover theyears.However, thereis 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 28mg/L to 120‐, 150‐, and 300mg/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 510mg/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.

Bioproducts↗

Crystal dissolution by particle detachment

Crystal dissolution, which is a fundamental process in both natural and technological settings, has been predominately viewed as a process of ion-by-ion detachment into a surrounding solvent. Here we report a mechanism of dissolution by particle detachment (DPD) that dominates in mesocrystals formed via crystallization by particle attachment (CPA). Using liquid phase electron microscopy to directly observe dissolution of hematite crystals — both compact rhombohedra and mesocrystals of coaligned nanoparticles — we find that the mesocrystals evolve into branched structures, which disintegrate as individual sub-particles detach. The resulting dissolution rates far exceed those for equivalent masses of compact single crystals. Applying a numerical generalization of the Gibbs-Thomson effect, we show that the physical drivers of DPD are curvature and strain inherently tied to the original CPA process. Based on the generality of the model, we anticipate that DPD is widespread for both natural minerals and synthetic crystals formed via CPA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genome reduction improves octanoic acid production in scale down bioreactors

Microorganisms in large-scale bioreactors are exposed to heterogeneous environmental conditions due to physical mixing constraints. Nutritional gradients can lead to transient expression of energetically wasteful stress responses and as a result, can reduce the titres, rates and yields of a bioprocess at larger scales. To what extent these process parameters are impacted is often unknown and therefore bioprocess scale-up comes with major risk. Designing platform strains to account for these intermittent stresses before introducing synthesis pathways is one strategy for de-risking bioprocess development. For example, Escherichia coli strain RM214 is a derivative of wild-type MG1655 that has had several genes and whole operons removed from its genome based on their metabolic cost. In this study, we engineered E. coli strain RM214 (referred to as WG02) to produce octanoic acid from glycerol in batch-flask and fed-batch bioreactor cultivations and compared it to an octanoic acid-producing E. coli MG1655 (WG01). In batch flask cultivations, the two strains performed similarly. However, in carbon limited fed-batch bioreactor cultivations, WG02 provided a greater than 22% boost to biomass compared to WG01 while maintaining similar titres of octanoic acid. Reducing the biomass accumulation of WG02 with nitrogen limited fed-batch cultivation resulted in a 16% improvement in octanoic acid titre over WG01. Finally, in a scale-down system consisting of a stirred tank reactor (representing a well-mixed zone) and plug flow reactor (representing an intermittent carbon starvation zone), WG02 again improved octanoic acid titre by almost 18% while maintaining similar biomass concentrations as WG01.

59 BASIC BIOLOGICAL SCIENCES↗

Zinc(II) Monomeric, Dimeric, and Trimeric Photosensitizers with Microsecond‐Lived Intra‐ligand Charge Transfer Excited States Investigated through Time‐Resolved Optical and X‐Ray Spectroscopy

Zn II photosensitizers relative to Cu I complexes have received less attention due to their energetically higher metal‐to‐ligand charge transfer states. Three Zn II complexes, namely a Monomer, a bimetallic helicate, and a trimetallic helicate, bearing phenanthroline ligands are hereby studied through time‐resolved X‐ray absorption (tr‐XAS) and femto‐microsecond optical transient absorption spectroscopy (OTA). The formation of intraligand singlet charge transfer ( I ILCT) excited states is achieved within femtoseconds, followed by intersystem crossing (ISC) in nanoseconds to generate microsecond‐lived triplet ( 3 ILCT) states. Femtosecond OTA shows that the 1 ILCT states in the Monomer, Dimer, and Trimer occur within 235 fs, 683 fs, and 730 fs, respectively, while nano‐microsecond OTA and tr‐XAS show their 3 ILCT states to decay within 1.00 µs, 1.48 µs, and 1.51 µs. The ISC from the 1 ILCT to the 3 ILCT state for the Trimer is 42.8 ns compared to the Monomer and Dimer with ISC rates of less than 13 ns. These differences arise due to the stabilization by π‐π and CH‐π noncovalent interactions of the phenanthroline ligands. The dihedral and torsional angles indicate stronger ligand strains in the excited states of the Dimer and Trimer versus the Monomer. DFT calculations for the electrochemical oxidation potentials further highlight their capability in inducing photoredox processes.

earth-abundant Zn-based photosensitizers↗

Water-Weakening and Time-Dependent Deformation of Organic-Rich Chalks

Abstract The Ghareb Formation is a shallowly buried porous chalk in southern Israel that is being considered as a host rock for a geologic nuclear waste repository. Setup and operation of a repository will induce significant mechanical, hydrological and chemical perturbations in the Ghareb. Developing a secure repository requires careful characterization of the rock behavior to different loads. To characterize hydromechanical behavior of the Ghareb, several short- and long-term deformation experiments were conducted. Hydrostatic loading tests were conducted both dry and water-saturated, using different setups to measure elastic properties, time-dependent behavior, and permeability. A set of triaxial tests were conducted to measure the elastic properties and rock strength under differential loading at dry and water-saturated conditions. The hydrostatic tests showed the Ghareb began to deform inelastically around 12–15 MPa, a relatively low effective pressure. Long-term permeability measurements demonstrated that permeability declined with increasing effective pressure and was permanently reduced by ~ 1 order of magnitude after unloading pressure. Triaxial tests showed that water saturation significantly degrades the rock properties of the Ghareb, indicating water-weakening is a significant risk during repository operation. Time-dependent deformation is observed during hold periods of both the hydrostatic and triaxial tests, with deformation being primarily visco-plastic. The rate of deformation and permeability loss is strongly controlled by the effective pressure as well. Additionally, during holds of both hydrostatic and triaxial tests, it is observed that when water-saturated, radial strain surpassed axial strain when above effective pressures of 13–20 MPa. Thus, deformation anisotropy may occur in situ during operations even if the stress conditions are hydrostatic when above this pressure range.

58 GEOSCIENCES↗

A selection approach using high‑oxygen and pond-mimicking culture conditions increases biomass productivity in the industrially relevant diatom Nitzschia inconspicua str. hildebrandi

To meet the energy and food challenges of the 21st century, renewable and sustainable sources of fuel and nutrients are required. Microalgae offer promise in meeting these challenges but must achieve higher rates of areal productivity to compete with fully scaled, existing industries. In this study, we used selective O 2 pressure to attain a ~90% increase in areal biomass productivity relative to the parental strain in the diatom Nitzschia inconspicua str. hildebrandi under pond-mimicking conditions with high O 2 stress. The resulting strain (GAI-337) was tested further for dilution time, culture density, CO 2 supplementation, pH, temperature, and dissolved O 2 concentration under outdoor pond-mimicking conditions to improve areal productivities. These experiments yielded an optimum harvest and dilution time just after sunset, ~0.45 g AFDW L -1 initial culture density for maximal productivities, no requirement for CO 2 gas supplementation or pH control, maximal performance under a diel temperature curve going from 24 °C at night to 36 °C during the day, and benefits from some O 2 removal from the culture by bubbling with air. Using pond-mimicking laboratory bioreactors, N. inconspicua GAI-337 achieved ~42 g AFDW m -2 d -1 , placing it among the most productive microalgal strains tested to date. Nutrient limitation experiments resulted in a biomass composition with 36% of AFDW comprised of lipids (measured as FAMEs) that equated to ~160 Gallons of Gasoline Equivalent energy per ton AFDW, highlighting the potential of GAI337 as a promising renewable fuel feedstock strain.

09 BIOMASS FUELS↗

3D Simulations of gas injection on callovo-oxfordian claystone assuming spatial heterogeneity and anisotropy

A series of gas injection tests on Callovo-Oxfordian (COx) claystone from the Bure underground research laboratory (URL) in France were carried out at the British Geological Survey (BGS). The tests were performed using a triaxial apparatus specifically designed to capture small volumetric strains induced by the injected gas flow and consequent material dilatancy. The long-duration experiments were monitored throughout. Measurements also included pressure, stresses (axial and radial stresses prescribed for each test stage), rate of gas inflow, gas outflow volume as well as pore-pressures observed at various points of the sample. A coupled hydro-gas-mechanical 3D numerical model has been developed to simulate the tests. Initial permeability is assumed heterogeneous throughout the specimen and embedded fractures are incorporated in the formulation. Gas pressure-induced deformations during the test lead to variations of permeability due to changes in matrix porosity and, especially, fracture aperture as well as fracture orientation due to material anisotropy. A programme of sensitivity analyses involving the variation of different aspects and parameters of the model contributes to a better understanding of the phenomena and highlights its complexity. The model is able to reproduce the observed behaviour of the tests.

58 GEOSCIENCES↗

Controlling Metal–Organic Framework/ZnO Heterostructure Kinetics through Selective Ligand Binding to ZnO Surface Steps

Metal–organic framework (MOF) heterostructures exhibit unique properties beyond those of individual components, but their design requires an understanding of energetic and kinetic controls at MOF–substrate interfaces. Although the structural relationship has been widely used in heterostructure design, it overlooks the interplay between the organic ligand and the substrate which controls the kinetics and energetics of growth of the final structure. In this study, we used zeolitic imidazolate frameworks (ZIF-8) on ZnO as a model system to evaluate this interplay via in situ monitoring and simulations. Our results demonstrate multiple roles of the 2-methyl-imidazole (2-MIM) ligand as “dissolution-promoter”, “step-pinner”, and “terrace-binder” on the ZnO (001) face and “dissolution-promoter” and “terrace-binder” on the ZnO (100) face. Through these multiple face-specific roles, 2-MIM modulates ZnO dissolution kinetics and, hence, the Zn 2+ release rate, tuning local supersaturations that dictating the characteristic ZIF-8 crystallization kinetics on different substrate faces. The critical thickness for transition from 2D to 3D growth is dictated by competition between interfacial and strain energies. The atomic-scale mechanism of the coupled substrate dissolution and MOF growth, mediated by selective linker–substrate binding, furnishes a new synthesis pathway for other complex heterostructures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Blade-Type Reaction Front in Micrometer-Sized Germanium Particles during Lithiation

To investigate the lithium transport mechanism in micrometer-sized germanium (Ge) particles, in situ focused ion beam-scanning electron microscopy was used to monitor the structural evolution of individual Ge particles during lithiation. Our results show that there are two types of reaction fronts during lithiation, representing the differences of reactions on the surface and in bulk. Further, the cross-sectional SEM images and transmission electron microscopy characterizations show that the interface between amorphous Li x Ge and Ge has a wedge shape because of the higher Li transport rate on the surface of the particle. The blade-type reaction front is formed at the interface of the amorphous Li x Ge and crystalline Ge and is attributed to the large strain at the interface.

25 ENERGY STORAGE↗

Accelerated Self-Healing and Property Recovery in Brush Particle Solids Featuring Brush Dispersity

Brush particles, hybrid materials consisting of polymer chains tethered to particle surfaces, offer tunable properties that make them promising candidates for advanced functional materials. This study investigated the role of chain dispersity in the viscoelastic self-healing of poly (methyl acrylate) (PMA)-based brush particle solids. Increasing the molecular weight dispersity of grafted chains significantly enhanced both strain-to-fracture and toughness of brush particle solids, while the elastic modulus and glass transition temperature were independent of chain dispersity. Cut-and-adhere testing revealed a significant acceleration of the rate of toughness recovery in high-dispersity systems as compared to low-dispersity analogs for which toughness recovery markedly lagged the recovery of Young’s modulus. The results suggest that structure and property recovery in brush particle solids are sensitive to the dynamical heterogeneity of brush canopies and highlight the role of molecular weight dispersity as a design parameter to enable hybrid materials with advanced self-healing ability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanical rolling and annealing of wire-arc additively manufactured stainless steel plates

Thin walls of 304L stainless steel were fabricated by wire-arc additive manufacturing (WAAM) followed by post build thermomechanical processing to modify the as built microstructure and properties. The walls were made using a high-deposition-rate robotically controlled gas-metal arc welding system and were characterized using optical microscopy and tensile tested for mechanical properties. Post processing consisted of mechanical rolling the walls to 25% and 40% strains, followed by annealing at 1050°C to demonstrate a wide range of properties. Results show that WAAM can be used to build custom sized semi-finished parts or blanks that can later be thermomechanically processed to increase strength and ductility through recrystallization of the as built microstructure, and/or processed into desired shapes with improved mechanical properties.

304L stainless steel↗

Sequential formulation of all‐way coupled finite strain thermoporomechanics for largely deformable gas hydrate deposits

We develop a numerically stable sequential formulation of thermoporomechanics for largely deformable gas hydrate deposits, extended from the fixed stress split of infinitesimal transformation. Constitutive equations are based on the total Lagrangian approach for both flow and geomechanics, including dynamic full tensor permeability and thermal conductivity updated from the deformation gradient. For space discretization, we take the cell-centered finite volume and node-based finite element method for flow and geomechanics, respectively. Then, we propose a sequential implicit method for all-way coupled thermoporomechanics, where the nonisothermal multiphase flow problem of gas hydrates is solved implicitly first and then the geomechanics problem is solved implicitly at the next step. During solution of the flow problem, we fix the rate of first Pioal total stress for numerical stability as well as apply porosity correction and entropy correction to account for geomechanical effects. We test numerical examples where flow and geomechanics parameters are based on deep oceanic gas hydrate deposits. When applying depressurization, even though the results between the infinitesimal transformation and finite strain geomechanics are similar in the early stages due to small deformation, we find differences between them in the late times as deformation becomes large. Accordingly, permeability and thermal conductivity tensors become nonisotropic full tensors although they are initially isotropic. Furthermore, we identify numerical stability of the developed sequential method from the test cases that exhibit the highly complex coupled gas hydrate systems with large deformation. Thus, the proposed sequential formulation can be applied in largely deformable gas hydrate systems.

42 ENGINEERING↗

Engineering improved ethylene production: Leveraging systems biology and adaptive laboratory evolution

Ethylene is a small hydrocarbon gas widely used in the chemical industry. Annual worldwide production currently exceeds 150 million tons, producing considerable amounts of CO 2 contributing to climate change. The need for a sustainable alternative is therefore imperative. Ethylene is natively produced by several different microorganisms, including Pseudomonas syringae pv. phaseolicola via a process catalyzed by the ethylene forming enzyme (EFE), subsequent heterologous expression of EFE has led to ethylene production in non-native bacterial hosts including E. coli and cyanobacteria. However, solubility of EFE and substrate availability remain rate limiting steps in biological ethylene production. We employed a combination of genome scale metabolic modelling, continuous fermentation, and protein evolution to enable the accelerated development of a high efficiency ethylene producing E. coli strain, yielding a 49-fold increase in production, the most significant improvement reported to date. Furthermore, we have clearly demonstrated that this increased yield resulted from metabolic adaptations that were uniquely linked to the EFE enzyme (WT vs mutant). Our findings provide a novel solution to deregulate metabolic bottlenecks in key pathways, which can be readily applied to address other engineering challenges.

59 BASIC BIOLOGICAL SCIENCES↗