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At least 127 records · Page 7

Improving the Methanol Tolerance of an Escherichia coli Methylotroph via Adaptive Laboratory Evolution Enhances Synthetic Methanol Utilization

There is great interest in developing synthetic methylotrophs that harbor methane and methanol utilization pathways in heterologous hosts such as Escherichia coli for industrial bioconversion of one-carbon compounds. While there are recent reports that describe the successful engineering of synthetic methylotrophs, additional efforts are required to achieve the robust methylotrophic phenotypes required for industrial realization. Here, we address an important issue of synthetic methylotrophy in E. coli : methanol toxicity. Both methanol, and its oxidation product, formaldehyde, are cytotoxic to cells. Methanol alters the fluidity and biological properties of cellular membranes while formaldehyde reacts readily with proteins and nucleic acids. Thus, efforts to enhance the methanol tolerance of synthetic methylotrophs are important. Here, adaptive laboratory evolution was performed to improve the methanol tolerance of several E. coli strains, both methylotrophic and non-methylotrophic. Serial batch passaging in rich medium containing toxic methanol concentrations yielded clones exhibiting improved methanol tolerance. In several cases, these evolved clones exhibited a > 50% improvement in growth rate and biomass yield in the presence of high methanol concentrations compared to the respective parental strains. Importantly, one evolved clone exhibited a two to threefold improvement in the methanol utilization phenotype, as determined via 13 C-labeling, at non-toxic, industrially relevant methanol concentrations compared to the respective parental strain. Whole genome sequencing was performed to identify causative mutations contributing to methanol tolerance. Common mutations were identified in 30S ribosomal subunit proteins, which increased translational accuracy and provided insight into a novel methanol tolerance mechanism. This study addresses an important issue of synthetic methylotrophy in E. coli and provides insight as to how methanol toxicity can be alleviated via enhancing methanol tolerance. Coupled improvement of methanol tolerance and synthetic methanol utilization is an important advancement for the field of synthetic methylotrophy.

Bennett, R. Kyle↗

Analytical model for balling defects in laser melting using rivulet theory and solidification

In laser welding and additive manufacturing communities, the balling (humping) defect is primarily attributed to the Plateau–Rayleigh fluid instability (PRI) with a few authors suggesting fluid jetting and volume conservation as alternative mechanisms. As analytical descriptions of these mechanisms are unavailable, combining them into a single formalism is unfeasible. We present a new model of PRI with higher accuracy, accounting for competition with solidification, to compare the expected behavior with known experimental trends when fluid jetting is neglected. We adapt a rivulet instability model from fluid physics to account for the stabilizing effects of the substrate, which the traditional cylindrical-jet geometry does not account for and estimate the instability growth rate. Our model yields a continuous transition from non-balling to balling hitherto lacking in current literature and predicts instability growth at higher wavelengths with strong sensitivity to the solidification front curvature. While the fluid surface is most unstable for shallow melt pools, the absolute magnitude of balling relevant to printing defects scales with melt pool depth and has a maximum for a given melt pool geometry. Synchrotron-based x-ray radiography of thin samples indicates that PRI growth rates and solidification can be comparable in magnitude and thus compete, as we find in this work. We predict that deviations between model predictions and our experimental results demonstrate the importance of fluid flows and heat transport in the balling process. Our experiments further demonstrate at least one mechanism by which the melt pool length and the balling wavelength are not equivalent, as commonly claimed.

Taylor, Z. [Stanford Univ., CA (United States); SL↗

Synthesis of Narrow SnTe Nanowires Using Alloy Nanoparticles

Topological crystalline insulator tin telluride (SnTe) provides a rich playground to examine interactions of correlated electronic states, such as ferroelectricity, topological surface states, and superconductivity. The study of SnTe nanowires may lead to even richer physics owing to the one-dimensional (1D) confinement effect and an increased contribution from the topological surface states. Thus, for transport measurements, SnTe nanowires must be synthesized with reduced diameters and high crystalline quality to ensure 1D confinement and phase coherence of the topological surface electrons. Here, we report a facile growth method to produce narrow SnTe nanowires with a high yield using alloy nanoparticles as growth catalysts. The average diameter of the SnTe nanowires grown using alloy nanoparticles is 85 nm, nearly a factor of three reduction compared to the average diameter of 240 nm when using gold nanoparticles as growth catalysts. Transport measurements reveal the effect of the nanowire diameter on the residual resistance ratio and magnetoresistance. Particularly, the ferroelectric transition temperature for SnTe evolves systematically with the nanowire diameter. In situ cryogenic cooling of narrow SnTe nanowires in a transmission electron microscope directly reveals the cubic to rhombohedral structural transition, which is associated with the ferroelectric transition. Thus, these narrow SnTe nanowires represent a model system to study electronic states arising from 1D confinement, such as 1D topological superconductivity and potential multiband superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Growth-uncoupled propanediol production in a Thermoanaerobacterium thermosaccharolyticum strain engineered for high ethanol yield

Abstract Cocultures of engineered thermophilic bacteria can ferment lignocellulose without costly pretreatment or added enzymes, an ability that can be exploited for low cost biofuel production from renewable feedstocks. The hemicellulose-fermenting species Thermoanaerobacterium thermosaccharolyticum was engineered for high ethanol yield, but we found that the strains switched from growth-coupled production of ethanol to growth uncoupled production of acetate and 1,2-propanediol upon growth cessation, producing up to 6.7 g/L 1,2-propanediol from 60 g/L cellobiose. The unique capability of this species to make 1,2-propanediol from sugars was described decades ago, but the genes responsible were not identified. Here we deleted genes encoding methylglyoxal reductase, methylglyoxal synthase and glycerol dehydrogenase. Deletion of the latter two genes eliminated propanediol production. To understand how carbon flux is redirected in this species, we hypothesized that high ATP levels during growth cessation downregulate the activity of alcohol and aldehyde dehydrogenase activities. Measurements with cell free extracts show approximately twofold and tenfold inhibition of these activities by 10 mM ATP, supporting the hypothesized mechanism of metabolic redirection. This result may have implications for efforts to direct and maximize flux through alcohol dehydrogenase in other species.

09 BIOMASS FUELS↗

Microbial maintenance energy quantified and modeled with microcalorimetry

Refining the energetic costs of cellular maintenance is essential for predicting microbial growth and survival in the environment. In this work, we evaluate a simple batch culture method to quantify energy partitioning between growth and maintenance using microcalorimetry and thermodynamic modeling. The constants derived from the batch culture system were comparable to those that have been reported from meta-analyses of data derived from chemostat studies. The model accurately predicted temperature-dependent biomass yield and the upper temperature limit of growth for Desulfovibrio alaskensis G20, suggesting the method may have broad application. An Arrhenius temperature dependence for the specific energy consumption rate, inferred from substrate consumption and heat evolution, was observed over the entire viable temperature range. By combining this relationship for specific energy consumption rates and observed specific growth rates, the model describes an increase in nongrowth associated maintenance at higher temperatures and the corresponding decrease in energy available for growth. This analytical and thermodynamic formulation suggests that simply monitoring heat evolution in batch culture could be a useful complement to the recognized limitations of estimating maintenance using extrapolation to zero growth in chemostats.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive Laboratory Evolution for Enhanced Performance of Cupriavidus necator on Formic Acid

The need to decarbonize our economy is becoming ever more pressing. CO2, can be electrochemically reduced to formic acid, a soluble C1 molecule that can be used to store carbon and energy. Cupriavidus necator H16, a soil bacterium, capable of consuming and growing on formic acid as its sole carbon source, is well positioned to upgrade CO2-derived formic acid into value added chemicals such as sustainable aviation fuel. To improve the performance of C. necator on formic acid adaptive laboratory evolution (ALE), a proven tool for improving microbial fitness, has been conducted using continuous pH-stat bioreactors. The system works on the basis that consumption of formic acid raises the pH and triggers the addition of more formic acid to maintain the pH at 6.7, such that formic acid is provided at the same rate as it is consumed. This system has been coupled with level control to achieve continuous fermentation where cells acquiring mutations that improve growth on formic acid become more abundant in the population, from which they can be isolate and characterized. This configuration where the dilution rate is controlled by pH-stat has been found to seek out a dilution rate that matches the exponential growth rate of the organism. During developmental experiments it was discovered that formic acid accumulated to inhibitory levels. It was determined that the nitrogen source, ammonium hydroxide, must be tailored to the carbon consumption to avoid formic acid accumulation. ALE has run in three lineages for 2000+ hours and 300+ generations. Growth of evolved isolates derived from all lineages will be evaluated on formic acid and those with improved growth rates or biomass yield will be subjected to whole genome sequencing to identify potentially causative mutations. These mutations will be evaluated individually and in combination to identify those that improve growth on formic acid.

adaptive laboratory evolution↗

Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii

High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Furthermore, our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.

59 BASIC BIOLOGICAL SCIENCES↗

Transient electron scavengers modulate carrier density at a polar/nonpolar perovskite oxide heterojunction

Here, we show how transient electron scavengers can be utilized to control the carrier concentration at polar/non-polar perovskite interfaces. By combining quantitative synchrotron x-ray-based interface structure determination with ab initio modeling, we demonstrate that Nd vacancy formation and the resulting formation of Nd adatoms, stabilized by oxygen scavengers at the growth front, can quantitatively account for the decreased carrier concentration at the SrTiO 3 /n NdTiO 3 /SrTiO 3 (001) heterojunction for n = 1 unit cell. This study yields new insights into growth mechanisms and the effect of transient species and defects on the electronic properties of oxide heterojunctions.

36 MATERIALS SCIENCE↗

Growth Phenomena and Bandgap Shift in Melt-Grown β-(In x Ga 1- x ) 2 O 3 Alloys

β-Ga 2 O 3 is an emerging ultra-wide bandgap semiconductor with great promise for power electronics and optoelectronics. Alloys in the In 2 O 3 -Ga 2 O 3 system are interesting for optoelectronic applications, particularly where bandgap tuning is desirable. Herein, β-(In x Ga 1- x ) 2 O 3 alloys with target compositions x = 0.025 or 0.10 are grown from the melt using the Czochralski and vertical gradient freeze techniques. Growth with 10 mol% In yields only small, needle-like crystals, while 2.5 mol% In allows growth of centimeter-sized single crystals. A substantial degree of indium segregation is unveiled by spatial measurements of lattice parameters and the bandgap. The bandgap decreases by a maximum of 0.28 eV in the case of the highest In content crystals. Z-contrast transmission electron microscopy confirms a solely octahedral coordination of In in the β-Ga 2 O 3 lattice. With indium concentrations higher than 2.5 mol%, samples contain micron-scale voids that impart a dark coloration. All measured crystals are electrically conductive, with carrier concentrations varying 10 16 –10 17 cm -3 depending upon the location of the sample in the growth. Lastly, a unique luminescence with unknown origin centered around 2.0 eV is revealed by photoluminescence spectroscopy.

36 MATERIALS SCIENCE↗

Tropical Red Macroalgae Cultivation with a Focus on Compositional Analysis

To create carbon efficient sources of bioenergy feedstocks and feedstuff for aquaculture and terrestrial livestock, it is critical to develop and commercialize the most efficient seaweed cultivation approach with a sustainable nutrient input supply. Here, we present data for a novel, onshore tropical macroalgae cultivation system, based on influent deep seawater as the nutrient and carbon sources. Two red algal species were selected, Agardhiella subulata and Halymenia hawaiiana, as the basis for growth optimization. Highest productivity in small-scale cultivation was demonstrated with A. subulata in the 10% deep seawater (64.7 µg N L−1) treatment, growing at up to 26% specific growth rate day−1 with highest yields observed at 247.5 g m−2 day−1 fresh weight. The highest yields for H. hawaiiana were measured with the addition of 10% deep seawater up to 8.8% specific growth rate day−1 and yields at 63.3 g fresh weight m−2 day−1 equivalent. Biomass should be culled weekly or biweekly to avoid density limitations, which likely contributed to a decrease in SGR over time. With a measured 30–40% carbon content of the ash-free dry weight (20–30% of the dry weight) biomass, this translates to an almost 1:1 CO2 capture to biomass ratio. The compositional fingerprint of the high carbohydrate content of both Agardhiella and Halymenia makes for an attractive feedstock for downstream biorefinery applications. By focusing on scaling and optimizing seaweed farming technologies for large-scale onshore farms, the opportunities for yield potential, adaptability to cultivation conditions, and meeting global sustainability goals through novel, carbon-negative biomass sources such as seaweed can be realized.

09 BIOMASS FUELS↗

Geometry versus growth: Internal consistency of the flat ΛCDM model with KiDS-1000

Here, we carry out a multi-probe self-consistency test of the flat Lambda Cold Dark Matter (ΛCDM) model with the aim of exploring potential causes of the reported tensions between high- and low-redshift cosmological observations. We divide the model into two theory regimes determined by the smooth background (geometry) and the evolution of matter density fluctuations (growth), each governed by an independent set of ΛCDM cosmological parameters. This extended model is constrained by a combination of weak gravitational lensing measurements from the Kilo-Degree Survey, galaxy clustering signatures extracted from Sloan Digital Sky Survey campaigns and the Six-Degree Field Galaxy Survey, and the angular baryon acoustic scale and the primordial scalar fluctuation power spectrum measured in Planck cosmic microwave background (CMB) data. For both the weak lensing data set individually and the combined probes, we find strong consistency between the geometry and growth parameters, as well as with the posterior of standard ΛCDM analysis. In the non-split analysis, for which one single set of parameters was used, tension in the amplitude of matter density fluctuations as measured by the parameter S 8 persists at around 3σ, with a 1.5% constraint of S 8 = 0.776$_{–0.008}^{+0.016}$ for the combined probes. We also observe a less significant preference (at least 2σ) for higher values of the Hubble constant, H 0 = 70.5$_{–1.5}^{+0.7}$ km s –1 Mpc –1 , as well as for lower values of the total matter density parameter Ω m = 0.289$_{–0.005}^{+0.007}$ compared to the full Planck analysis. Including the subset of the CMB information in the probe combination enhances these differences rather than alleviate them, which we link to the discrepancy between low and high multipoles in Planck data. Our geometry versus growth analysis does not yet yield clear signs regarding whether the origin of the discrepancies lies in ΛCDM structure growth or expansion history but holds promise as an insightful test for forthcoming, more powerful data.

79 ASTRONOMY AND ASTROPHYSICS↗

BETO 2021 Peer Review - Improving Formate Upgrading by Cupriavidus Necator 2.3.2.111

Formate can be generated by electrocatalytic reduction of CO2 and has been proposed as a soluble intermediate for the storage of carbon and energy. Biological systems capable of assimilating formate could enable conversion of formate generated from low-cost renewable energy and waste CO2 to myriad fuels and chemicals. To that end, the goal of this project is to develop the natural formatotroph Cupriavidus necator as a robust microbial chassis for efficient conversion of formate to value-added products. Using a combination of laboratory evolution and rational engineering, we have identified mutations and genetic deletions that improve its growth rate and biomass yield on formate by 1.2X. Using RNA-seq transcriptomics, we are elucidating the mechanisms that underly these improvements and anticipate this will contribute to our understanding of formate conversion. We have also engineered C. necator to convert formate to the potential polymer precursor 2-hydroxymuconate semialdehyde (2HMS) by introducing an exogenous pathway and deleting competing pathways and demonstrated production and robust growth using a pH-stat bioreactor. Final techno-economic analysis and life-cycle assessment on biological production of 2HMS from formate will enable the DOE and other stake holders to evaluate the economic and environmental impact of this project and related technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Plant Cell Wall Loosening by Expansins

Expansins comprise an ancient group of cell wall proteins ubiquitous in land plants and their algal ancestors. During cell growth, they facilitate passive yielding of the wall's cellulose networks to turgor-generated tensile stresses, without evidence of enzymatic activity. Expansins are also implicated in fruit softening and other developmental processes and in adaptive responses to environmental stresses and pathogens. The major expansin families in plants include α-expansins (EXPAs), which act on cellulose-cellulose junctions, and β-expansins, which can act on xylans. EXPAs mediate acid growth, which contributes to wall enlargement by auxin and other growth agents. The genomes of diverse microbes, including many plant pathogens, also encode expansins designated expansin-like X. Expansins are proposed to disrupt noncovalent bonding between laterally aligned polysaccharides (notably cellulose), facilitating wall loosening for a variety of biological roles.

Cell Biology↗

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗

Power-Law Entanglement and Hilbert Space Fragmentation in Nonreciprocal Quantum Circuits

Quantum circuits utilizing measurement to evolve a quantum wave function offer a new and rich playground to engineer unconventional entanglement dynamics. Here, in this work, we introduce a hybrid, nonreciprocal setup featuring a quantum circuit, whose updates are conditioned on the state of a classical dynamical agent. In our example the circuit is represented by a Majorana quantum chain controlled by a classical N-state Potts chain undergoing pair flips. The local orientation of the classical spins controls whether randomly drawn local measurements on the quantum chain are allowed or not. This imposes a dynamical kinetic constraint on the entanglement growth, described by the transfer matrix of an N-colored loop model. It yields an equivalent description of the circuit by an SU(N)-symmetric Temperley-Lieb Hamiltonian or by a kinetically constrained surface growth model for an N-component height field. For N = 2, we find a diffusive growth of the half-chain entanglement toward a stationary profile S(L) ~ L 1/2 for L sites. For N ≥ 3, the kinetic constraints impose Hilbert space fragmentation, yielding subdiffusive growth toward S(L) ~ L 0.57 . This showcases how the control by a classical dynamical agent can enrich the entanglement dynamics in quantum circuits, paving a route toward novel entanglement dynamics in nonreciprocal hybrid circuit architectures.

1-dimensional spin chains↗

Ultrasmooth Epitaxial Pt Thin Films Grown by Pulsed Laser Deposition

Platinum (Pt) thin films are useful in applications requiring high-conductivity electrodes with excellent thermal and chemical stability. Ultrasmooth and epitaxial Pt thin films with single-crystalline domains have the added benefit of providing ideal templates for the subsequent growth of heteroepitaxial structures. Here, we grow epitaxial Pt (111) electrodes (ca. 30 nm thick) on sapphire (α-Al 2 O 3 (0001)) substrates with pulsed laser deposition. This versatile technique allows control of the growth process and fabrication of films with carefully tailored parameters. X-ray scattering, atomic-force microscopy, and electron microscopy provide structural characterization of the films. Various gaseous atmospheres and temperatures were explored to achieve epitaxial growth of films with low roughness. A two-step (500 °C/300 °C) growth process was developed, yielding films with improved epitaxy without compromising roughness. The resulting films possess ultrasmooth interfaces (<3 Å) and high electrical conductivity (6.9 × 10 6 S/m). Finally, Pt films were used as current collectors and templates to grow lithium manganese oxide (LiMn 2 O 4 (111)) epitaxial thin films, a cathode material used in Li-ion batteries. In conclusion, using a solid-state ionogel electrolyte, the films were highly stable when electrochemically cycled in the 3.5-4.3 V vs Li/Li + range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlled Spalling of 4H Silicon Carbide with Investigated Spin Coherence for Quantum Engineering Integration

We detail scientific and engineering advances which enable the controlled spalling and layer transfer of single crystal 4H silicon carbide (4H-SiC) from bulk substrates. 4HSiC’s properties, including high thermal conductivity and a wide bandgap, make it an ideal semiconductor for power electronics. Moreover, 4H-SiC is an excellent host of solid-state atomic defect qubits for quantum computing and quantum networking. Because 4H-SiC substrates are expensive (due to long growth times and limited yield), techniques for removal and transfer of bulk-quality films are desirable for substrate reuse and integration of the separated films. In this work, we utilize updated approaches for stressor layer thickness control and spalling crack initiation to demonstrate controlled spalling of 4H-SiC, the highest fracture toughness crystal spalled to date. We achieve coherent spin control of neutral divacancy (VV 0 ) qubit ensembles and measure a quasi-bulk spin T 2 of 79.7 μs in the spalled films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗