Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering
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59 BASIC BIOLOGICAL SCIENCES↗
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Results for “Strain engineering”
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Synthesis of High-Performance Lignin-Based Inverse Thermoplastic Vulcanizates with Tailored Morphology and Properties
In this work, we report synthesis of a high-strength renewable phenolic composition with linear large deformation strain without a thermoplastic-like yielding while retaining thermal processability. Small molecule carboxylic acid derivatives with varying molecular architectures act as esterifying crosslinkers in an equal mass mixture of lignin and acrylonitrile–butadiene copolymers in a highly scalable, solvent-free process. These “inverse thermoplastic vulcanizates” (iTPVs)—unique in their approach of crosslinking the rigid lignin phase rather than the soft phase—exhibit ordered self-assembly, tunable nanoscale morphology, and processability. The first of its kind iTPV compositions exhibit engineering stress–strain curves with two- to sixfold linear extensibility, a twofold rise in strength, and an order of magnitude enhanced modulus compared to a simple lignin-rubber blend. Viscoelastic properties correlate well with crosslinker architecture and the resulting morphology, allowing competing properties of toughness and stiffness to be tuned. This research finds a path for identifying the potential of lignin as a sustainable feedstock.
36 MATERIALS SCIENCE↗
Corrigendum to “High-fidelity micro-scale modeling of the thermo-visco-plastic behavior of carbon fiber polymer matrix composites” [Compos Struct 134 (2015) 132–141]
The authors would like to inform that one of the modifications proposed in the article “High-fidelity micro-scale modeling of the thermo-visco-plastic behavior of carbon fiber polymer matrix composites” [1] was found to be unnecessary: the paraboloid yield criterion is sufficient to describe the shear behavior of the epoxy matrix considered (Epoxy 3501-6). The authors recently noted that the experimental work [2] used to validate the pure matrix response considered engineering shear strain instead of its tensorial counter-part, which caused the apparent inconsistency with the paraboloid yield criterion. A recently proposed temperature dependency law for glassy polymers is evaluated herein, thus better agreement with the experimental results for this epoxy is observed.
36 MATERIALS SCIENCE↗
Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica
ABSTRACT Microbially derived lipids have recently attracted renewed interests due to their broad applications in production of green diesels, cosmetic additives, and oleochemicals. Metabolic engineering efforts have targeted a large portfolio of biosynthetic pathways to efficiently convert sugar to lipids in oleaginous yeast. In the engineered overproducing strains, endogenous cell metabolism typically generates harmful electrophilic molecules that compromise cell fitness and productivity. Lipids, particularly unsaturated fatty acids, are highly susceptible to oxygen radical attack and the resulting oxidative species are detrimental to cell metabolism and limit lipid productivity. In this study, we investigated cellular oxidative stress defense pathways in Yarrowia lipolytica to further improve the lipid titer, yield, and productivity. Specifically, we determined that coupling glutathione disulfide reductase and glucose‐6‐phosphate dehydrogenase along with aldehyde dehydrogenase are efficient solutions to combat reactive oxygen and aldehyde stress in Y. lipolytica . With the reported engineering strategies, we were able to synchronize cell growth and lipid production, improve cell fitness and morphology, and achieved industrially‐relevant level of lipid titer (72.7 g/L), oil content (81.4%) and productivity (0.97 g/L/h) in controlled bench‐top bioreactors. The strategies reported here represent viable steps in the development of sustainable biorefinery platforms that potentially upgrade low value carbons to high value oleochemicals and biofuels. Biotechnol. Bioeng. 2017;114: 1521–1530. © 2017 Wiley Periodicals, Inc.
Xu, Peng↗
CERES: CRISPR Engineering for the Rapid Enhancement of Strains
Previous strain development efforts for cyanobacteria have failed to achieve the necessary productivities needed to support economic biofuel production. We proposed to develop CRISPR Engineering for Rapid Enhancement of Strains (CERES). We developed genetic and computational tools to enable future high-throughput screening of CRISPR interference (CRISPRi) libraries in the cyanobacterium Synechococcus sp. PCC 7002, including: (1) Operon- SEQer: an ensemble of algorithms for predicting operon pairs using RNA-seq data, (2) experimental characterization and machine learning prediction of gRNA design rules for CRISPRi, and (3) a shuttle vector for gene expression. These tools lay the foundation for CRISPR library screening to develop cyanobacterial strains that are optimized for growth or metabolite production under a wide range of environmental conditions. The optimization of cyanobacterial strains will directly advance U.S. energy and climate security by enabling domestic biofuel production while simultaneously mitigating atmospheric greenhouse gases through photoautotrophic fixation of carbon dioxide.
09 BIOMASS FUELS↗
Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para -aminophenylalanine
Introducing heterologous pathways into host cells constitutes a promising strategy for synthesizing nonstandard amino acids (nsAAs) to enable the production of proteins with expanded chemistries. However, this strategy has proven challenging, as the expression of heterologous pathways can disrupt cellular homeostasis of the host cell. Here, we sought to optimize the heterologous production of the nsAA para -aminophenylalanine (pAF) in Escherichia coli . First, we incorporated a heterologous pAF biosynthesis pathway into a genome-scale model of E. coli metabolism and computationally identified metabolic interventions in the host’s native metabolism to improve pAF production. Next, we explored different approaches of imposing these flux interventions experimentally and found that the upregulation of flux in the chorismate biosynthesis pathway through the elimination of feedback inhibition mechanisms could significantly raise pAF titers (~20-fold) while maintaining a reasonable pAF production-growth rate trade-off. Overall, this study provides a promising strategy for the biosynthesis of nsAAs in engineered cells.
59 BASIC BIOLOGICAL SCIENCES↗
Expanding the Scope of Genomic Security: Targeted Genome Editing within Microbiomes through Designer Bacteriophage Vectors
The ability to engineer the genome of a bacterial strain, not as an isolate, but while present among other microbes in a microbiome, would open new technological possibilities in the areas of medicine, energy and biomanufacturing. Our approach is to develop sets of phages (bacterial viruses) active on the target strain and themselves engineered to act not as killers but as vectors for gene delivery. This approach is rooted in our bioinformatic tools that map prophages accurately within bacterial genomes. We present new bioinformatic results in cross-contig search, design of phage genome assemblies, satellites that embed within prophages, alignment of large numbers of biological sequences, and improvement of reference databases for prophage discovery. We targeted a Pseudomonas putida strain within a lignin-degrading microbiome, but were unable to obtain active phages, and turned toward a defined microbiome of the mouse gut.
59 BASIC BIOLOGICAL SCIENCES↗
In situ observation of atomic movement in a ferroelectric film under an external electric field and stress
Atomic movement under application of external stimuli (i.e., electric field or mechanical stress) in oxide materials has not been observed due to a lack of experimental methods but has been well known to determine the electric polarization. Here, we investigated atomic movement arising from the ferroelectric response of BiFeO 3 thin films under the effect of an electric field and stress in real time using a combination of switching spectroscopy, time-resolved X-ray microdiffraction, and in situ stress engineering. Under an electric field applied to a BiFeO 3 film, the hysteresis loop of the reflected X-ray intensity was found to result from the opposing directions of displaced atoms between the up and down polarization states. An additional shift of atoms arising from the linearly increased dielectric component of the polarization in BiFeO 3 was confirmed through gradual reduction of the diffracted X-ray intensity. The electric-fieldinduced displacement of oxygen atoms was found to be larger than that of Fe atom for both ferroelectric switching and increase of the polarization. In conclusion, the effect of external stress on the BiFeO 3 thin film, which was controlled by applying an electric field to the highly piezoelectric substrate, showed smaller atomic shifts than for the case of applying an electric field to the film, despite the similar tetragonality.
74 ATOMIC AND MOLECULAR PHYSICS↗
Local strain effect on the band gap engineering of graphene by a first-principles study
We have systematically investigated the effect of local strain on electronic properties of graphene by first-principles calculations. Two major types of local strain, oriented along the zigzag and the armchair directions, have been studied. We find that local strain with a proper range and strength along the zigzag direction results in opening of significant band gaps in graphene, on the order of 10{sup −1 }eV; whereas, local strain along the armchair direction cannot open a significant band gap in graphene. Our results show that appropriate local strain can effectively open and tune the band gap in graphene; therefore, the electronic and transport properties of graphene can also be modified.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Anisotropic Phonon Response of Few-Layer PdSe 2 under Uniaxial Strain
PdSe 2 , an emerging 2D material with a novel anisotropic puckered pentagonal structure, has attracted growing interest due to its layer-dependent electronic bandgap, high carrier mobility, and good air stability. In this work, a detailed Raman spectroscopic study of few-layer PdSe 2 (two to five layers) under the in-plane uniaxial tensile strain up to 3.33% is performed. Two of the prominent PdSe 2 Raman peaks are influenced differently depending on the direction of strain application. Additionally, the A g 1 mode redshifts more than the A g 3 mode when the strain is applied along the a -axis of the crystal, while the A g 3 mode redshifts more than the A g 1 mode when the strain is applied along the b -axis. Such an anisotropic phonon response to strain indicates directionally dependent mechanical and thermal properties of PdSe 2 and also allows the identification of the crystal axes. The results are further supported using first-principles density-functional theory. Interestingly, the near-zero Poisson’s ratios for few-layer PdSe 2 are found, suggesting that the uniaxial tensile strain can easily be applied to few-layer PdSe 2 without significantly altering their dimensions at the perpendicular directions, which is a major contributing factor to the observed distinct phonon behavior. The findings pave the way for further development of 2D PdSe 2 -based flexible electronics.
36 MATERIALS SCIENCE↗
Quantum Anomalies in Condensed Matter
Quantum materials provide a fertile ground in which to test and realize unusual phenomena such as quantum anomalies predicted by quantum field theory. There are three important symmetries that are broken when classical field theory is moved into the quantum regime, the scale anomaly, the axial (chiral) anomaly, and the parity anomaly. Several potential device applications may be realized by the discovery of quantum anomalies in condensed matter, enabled by the new physics they embody, including ultra‐sensitive dark matter detectors, far infrared optical modulators, micro‐bolometric detectors, low‐dissipation ballistic transporters, terahertz‐based qubits, terahertz polarization state controls, passive magnetic field sensors, stable topological superconductors that host Majorana fermions, and qubits topologically protected against decoherence. In this perspective article, the definition of these quantum anomalies is laid out, how little is known in the context of condensed matter, and how quantum anomalies are predicted to manifest as anomalous electronic, thermal, and magnetic behavior in experiments on topological quantum materials, including Weyl and Dirac semimetals. Furthermore, the importance that mechanical strain and defects will play in modifying signatures of quantum anomalies is discussed.
36 MATERIALS SCIENCE↗
Identification and analysis of sugar transporters capable of co–transporting glucose and xylose simultaneously
Simultaneous co-fermentation of glucose and xylose is a key desired trait of engineered Saccharomyces cerevisiae for efficient and rapid production of biofuels and chemicals. However, glucose strongly inhibits xylose transport by endogenous hexose transporters of S. cerevisiae. We identified structurally distant sugar transporters (Lipomyces starkeyi LST1_205437 and Arabidopsis thaliana AtSWEET7) capable of co-transporting glucose and xylose from previously unexplored oleaginous yeasts and plants. Kinetic analysis showed that LST1_205437 had lenient glucose inhibition on xylose transport and AtSWEET7 transported glucose and xylose simultaneously with no inhibition. Modelling studies of LST1_205437 revealed that Ala335 residue at sugar binding site can accommodates both glucose and xylose. Docking studies with AtSWEET7 revealed that Trp59, Trp183, Asn145, and Asn179 residues stabilized the interactions with sugars, allowing both xylose and glucose to be co-transported. In addition, we altered sugar preference of LST1_205437 by single amino acid mutation at Asn365. Furthermore, our findings provide a new mechanistic insight on glucose and xylose transport mechanism of sugar transporters and the identified sugar transporters can be employed to develop engineered yeast strains for producing cellulosic biofuels and chemicals.
59 BASIC BIOLOGICAL SCIENCES↗
Mechanical Behavior of Titanium-Based Layered Structures Fabricated Using Blended Elemental Powder Metallurgy
Mechanical behavior of bilayered structures composed of the layer of Ti-6Al-4 V (wt.%) (Ti-64) alloy and metal matrix composite (MMC) on the base of this alloy reinforced with 5 and 10% (vol.) of either TiB or TiC particles has been studied. Structures were fabricated using blended elemental powder metallurgy and studied by tensile and three-point flexural tests. Mechanical tests were performed on uniform single-layer samples of the alloy as well as individual MMCs. In addition, bilayered structures were also tested in three-point flexural experiment. Posttest fractographic inspections were made using the SEM. The deformation energy was measured based on engineering stress–strain curves obtained on tensile test. The results were compared with the data previously reported on Ti-64 alloy fabricated using cast and wrought technique. The presence of TiB and TiC reinforcement particles in the alloy causes substantial drop in strength and ductility of MMCs as compared to uniform sintered Ti-64 alloy, since those particles provide additional sites for the cracks and pores nucleation and promote the embrittlement of material. However, when MMC layers are used in bilayered structures with Ti-64 alloy layers, the three-point flexural test demonstrates significant increase in flexure stress compared to uniform Ti-64 alloy and uniform structures of MMCs. The suitability of studied structures for antiballistic impact application is discussed.
36 MATERIALS SCIENCE↗
Dynamic Tensile Characterization of Vascomax Maraging C250 and C300 Alloys.
Abstract not provided.
Song, Bo↗
Substantial tensile ductility in sputtered Zr-Ni-Al nano-sized metallic glass
Abstract not provided
Liontas, Rachel↗
Rapid Annotation of Photosynthetic Systems (RAPS): automated algorithm to generate genome-scale metabolic networks from algal genomes
Algae have mounting potential to serve as platform strains for engineering efforts, but tools for these species lag behind traditional model systems like E. coli and yeast. Metabolic models are one such tool that would enhance our ability to rationally engineer algae but current automated algorithms to build models do not perform well for algal genomes. We introduce a novel software pipeline, Rapid Annotation of Photosynthetic Systems (RAPS), which leverages manual curation efforts of published models to create high quality first draft metabolic networks for new species. We compared models produced by our pipeline to published models and found that these models are able to capture more genes than the published models and are more predictive of experimentally determined growth rate. We used RAPS to automate the creation of 8 first draft metabolic models of new species to enable the further study of metabolism in these species.
09 BIOMASS FUELS↗
Synthetic methylotrophy: Strategies to assimilate methanol for growth and chemicals production
Methanol is an attractive and broadly available substrate for large-scale bioproduction of fuels and chemicals. It contains more energy and electrons per carbon than carbohydrates and can be cheaply produced from natural gas. Synthetic methylotrophy refers to the development of non-native methylotrophs such as Escherichia coli and Corynebacterium glutamicum to utilize methanol as a carbon source. Furthermore, we discuss recent advances in engineering these industrial hosts to assimilate methanol for growth and chemicals production through the introduction of the ribulose monophosphate (RuMP) cycle. In addition, we present novel strategies based on flux coupling and adaptive laboratory evolution to engineer new strains that can grow exclusively on methanol.
60 APPLIED LIFE SCIENCES↗
Characterization and comparative analysis of the tensile properties of five tempered martensitic steels and an oxide dispersion strengthened ferritic alloy irradiated at ≈295 °C to ≈6.5 dpa
Tensile test results at 25 and 300 °C on five 9-12Cr tempered martensitic steels and one 14Cr oxide dispersion strengthened alloy, that were side-by side irradiated to 6.5 dpa at 295 °C in the Advanced Test Reactor (ATR), are reported. The engineering stress–strain curves are analyzed to provide true stress–strain constitutive σ(ε) laws for all of these alloys. In the irradiated condition, the σ(ε) fall into categories of: strain softening, nearly perfectly plastic and strain hardening. Increases in yield stress (Δσ y ) and reductions in uniform strain ductility (e u ) are observed, where as the latter can be understood in terms of the alloy's σ(ε) behavior. Increases in the average σ(ε) in the range of 0–10% strain are smaller than the corresponding Δσ y , and vary more from alloy to alloy. The data are analyzed to establish relations between Δσ y and coupled changes in the ultimate stresses as well as the effects of both test temperature and the unirradiated yield stress (σ yu ). The latter shows that higher σ yu correlates with lower Δσ y . In five out of six cases the effects of irradiation are generally consistent with previous observations on these alloys. However, the particular heat of the 12Cr HT-9 tempered martensitic steel in this study has a much higher e u than observed for earlier heats. The reasons for this improved behavior are not understood and may be microstructural in origin. However, it is noted that the new heat of HT-9, which was procured under modern quality assurance standards, has lower interstitial nitrogen than previous heats. As a result, notably lower interstitial solute contents correlate with improved ductility and homogenous deformation in broadly similar steels.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗