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At least 145 records · Page 8

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DOE OSTI2021

Species- and site-specific genome editing in complex bacterial communities

Knowledge of microbial gene functions comes from manipulating the DNA of individual strains in isolation from their natural communities. While this approach to microbial genetics has been foundational, its requirement for culturable microorganisms has left the majority of microbes and their interactions genetically unexplored. Here, we describe a generalizable strategy for editing the genomes of specific organisms within microbial communities. We identified genetically tractable bacteria within a community using Environmental Transformation Sequencing (ET-Seq), an approach in which non-targeted transposon integrations are mapped and quantified following community delivery. We next developed and used DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-Seq, enabling organism- and locus-specific genetic manipulation within the community context. To illustrate the utility of our approach, we selectively edited closely related strains, measured gene fitness, and enriched targeted members within soil and infant gut microbiota. These results establish a new paradigm for targeted community editing relevant to research and applications on medical, agricultural, and industrial microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

The Concept of Negative Capacitance in Ionically Conductive Van der Waals Ferroelectrics

Negative capacitance (NC) provides a path to overcome the Boltzmann limit that dictates operating voltages in transistors and, therefore, may open up a path to the challenging proposition of lowering energy consumption and waste heat in nanoelectronic integrated circuits. Typically, NC effects in ferroelectric materials are based on either stabilizing a zero-polarization state or slowing down ferroelectric switching in order to access NC regimes of the free-energy distribution. Here, a fundamentally different mechanism for NC, based on CuInP 2 S 6 , a van der Waals layered ferrielectric, is demonstrated. Using density functional theory and piezo-response force microscopy, it is shown that an unusual combination of high Cu-ion mobility and its crucial role in determining polarization magnitude and orientation (P) leads to a negative slope of the polarization versus the electric field E, dP/dE < 0, which is a requirement for NC. This mechanism for NC is likely to occur in a wide class of materials, offering new possibilities for NC-based devices. Finally, the nanoscale demonstration of this mechanism can be extended to the device-level by increasing the regions of homogeneous polarization and polarization switching, for example, through strain engineering and carefully selected electric field pulses.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Computational discovery of two-dimensional rare-earth iodides: promising ferrovalley materials for valleytronics

Two-dimensional Ferrovalley materials with intrinsic valley polarization are rare but highly promising for valley-based nonvolatile random access memory and valley filter devices. These ferromagnetic materials exhibit valleys at or near the Fermi level with intrinsic magnetism. The strong coupling between magnetism and spin–orbit coupling induces intrinsic valley polarization. Using Kinetically Limited Minimization, an unconstrained crystal structure prediction algorithm, and prototype sampling based on first-principles calculations, we have discovered new Ferrovalley materials, rare-earth iodides RI 2 , where R is a rare-earth element belonging to Sc, Y, or La-Lu, and I is Iodine. The rare-earth iodides are layered and demonstrate either 2H, 1T, or 1T d phase as the ground state in bulk, analogous to transition metal dichalcogenides (TMDCs). The calculated exfoliation energy of monolayers (MLs) is comparable to that of graphene and TMDCs, suggesting possible experimental synthesis. The MLs in the 2H phase exhibit ferromagnetism due to unpaired electrons in d and f orbitals. Throughout the rare-earth series, d bands have valley polarization at K and $\overline{K}$ points in the Brillouin zone in the vicinity of the Fermi level. Large intrinsic valley polarization in the range of 15–143 meV without external stimuli is observed in these Ferrovalley materials, which can be enhanced further by applying an in-plane bi-axial strain. These valleys can selectively be probed and manipulated for information storage and processing, potentially offering superior performance beyond conventional electronics and spintronics. Here we further show that the 2H ferromagnetic phase of RI 2 MLs possesses non-zero Berry curvature and exhibits anomalous valley Hall effect with considerable anomalous Hall conductivity. Our work will incite exploratory synthesis of the predicted Ferrovalley materials and their application in valleytronics and beyond.

2D materials↗

DOE OSTI2020

Evaluation of the recombinant proteins RlpB and VacJ as a vaccine for protection against Glaesserella parasuis in pigs

Abstract Background Glaesserella parasuis , the causative agent of Glӓsser’s disease, is widespread in swine globally resulting in significant economic losses to the swine industry. Prevention of Glӓsser’s disease in pigs has been plagued with an inability to design broadly protective vaccines, as many bacterin based platforms generate serovar or strain specific immunity. Subunit vaccines are of interest to provide protective immunity to multiple strains of G. parasuis . Selected proteins for subunit vaccination should be widespread, highly conserved, and surface exposed. Results Two candidate proteins for subunit vaccination (RlpB and VacJ) against G. parasuis were identified using random mutagenesis and an in vitro organ culture system. Pigs were vaccinated with recombinant RlpB and VacJ, outer membrane proteins with important contributions to cellular function and viability. Though high antibody titers to the recombinant proteins and increased interferon-γ producing cells were found in subunit vaccinated animals, the pigs were not protected from developing systemic disease. Conclusions It appears there may be insufficient RlpB and VacJ exposed on the bacterial surface for antibody to bind, preventing high RlpB and VacJ specific antibody titers from protecting animals from G. parasuis . Additionally, this work confirms the importance of utilizing the natural host species when assessing the efficacy of vaccine candidates.

Hau, Samantha J.↗

DOE OSTI2021

Recent Advances in Vertically Aligned Nanocomposites with Tunable Optical Anisotropy: Fundamentals and Beyond

Developing reliable and tunable metamaterials is fundamental to next-generation optical-based nanodevices and computing schemes. In this review, an overview of recent progress made with a unique group of ceramic-based functional nanocomposites, i.e., vertically aligned nanocomposites (VANs), is presented, with the focus on the tunable anisotropic optical properties. Using a self-assembling bottom-up deposition method, the as-grown VANs present great promise in terms of structural flexibility and property tunability. Such broad tunability of functionalities is achieved through VAN designs, material selection, growth control, and strain coupling. The as-grown multi-phase VAN films also present enormous advantages, including wafer scale integration, epitaxial quality, sharp atomic interface, as well as designable materials and geometries. This review also covers the research directions with practical device potentials, such as multiplex sensing, high-temperature plasmonics, magneto-optical switching, as well as photonic circuits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1972

Development and Design Application of Rigidized Surface Insulation Thermal Protection Systems, Volume 1

Materials and design technology of the all-silica LI-900 rigid surface insulation (RSI) thermal protection system (TPS) concept for the shuttle spacecraft is presented. All results of contract development efforts are documented. Engineering design and analysis of RSI strain arrestor plate material selections, sizing, and weight studies are reported. A shuttle prototype test panel was designed, analyzed, fabricated, and delivered. Thermophysical and mechanical properties of LI-900 were experimentally established and reported. Environmental tests, including simulations of shuttle loads represented by thermal response, turbulent duct, convective cycling, and chemical tolerance tests are described and results reported. Descriptions of material test samples and panels fabricated for testing are included. Descriptions of analytical sizing and design procedures are presented in a manner formulated to allow competent engineering organizations to perform rational design studies. Results of parametric studies involving material and system variables are reported. Material performance and design data are also delineated.

Source record↗

NASA NTRS1983

CLFE2D: A generalized plane strain finite element program laminated composites subject to mechanical and hygrothermal loading

CLFE2D is a two dimensional generalized plane strain finite element code, using a linear, four node, general quadrilateral, isoparametric element. The program is developed to calculate the displacements, strains, stresses, and strain energy densities in a finite width composite laminate. CLFE2D offers any combination of the following load types: nodal displacements, nodal forces, uniform normal strain, or hygrothermal. The program allows the user to input one set of three dimensional orthotropic material properties. The user can then specify the angle of material principal orientation for each element in the mesh. Output includes displacements, stresses, strains and strain densities at points selected by the user. An option is also available to plot the underformed and deformed finite element meshes.

Buczek, M. B.↗

NASA NTRS1988

Application of intelligent systems to wind tunnel test facilities

An approach to the application of intelligent-systems technology to the wind tunnel facilities at NASA Ames Research Center is outlined. To help fulfill the long-range goals of improving data quality and increasing personnel efficiency and management effectiveness, three major areas of intelligent systems application are recommended. The available state-of-the-art technology for developing the proposed systems is reviewed including the application of commercial software packages. The initial tasks and effort to develop these systems are recommended. A prototype expert system for selection of internal strain-gage balances has been built and is presented herein as an example model for the future systems.

Lo, Ching F.↗

NASA NTRS1999

Preliminary Statistical Analysis of the 1995 Evaluation by NASA LaRC of the IAI Automatic Balance Calibration Machine

The NASA Langley Research Center (LARC) participated in a national cooperative evaluation of the Israel Aircraft Industries (IAI) automatic balance calibration machine at Microcraft, San Diego in September 1995. A LaRC-designed six-component strain gauge balance was selected for test and calibration during LaRC's scheduled evaluation period. Eight calibrations were conducted using three selected experimental designs. Raw data were exported to LaRC facilities for reduction and statistical analysis using the techniques outlined in Tripp and Tcheng (1994). This report presents preliminary assessments of the results, and compares IAI calibration results with manual calibration results obtained at the Modern Machine and Tool Co., Inc. (MM & T). Newport News, VA. A more comprehensive report is forthcoming.

Tcheng, Ping↗

NASA NTRS2003

Apparatus and Method for Measuring Strain in Optical Fibers using Rayleigh Scatter

An apparatus and method for measuring strain in an optical fiber using the spectral shift of Rayleigh scattered light. The interference pattern produced by an air gap reflector and backscattered radiation is measured. Using Fourier Transforms, the spectrum of any section of fiber can be extracted. Cross correlation with an unstrained measurement produces a correlation peak. The location of the correlation peak indicates the strain level in the selected portion of optical fiber.

Froggatt, Mark E.↗

DOE OSTI2021

Multimodal imaging of oil-in-water bilgewater emulsion and biofilms

Bilgewater emulsions, consisting of oil and surfactant mixtures in water, affect many aquatic species. Thus development of methods and techniques to treat or mitigate the formation and undesired consequences of shipboard emulsions are urgently needed. This work presents new results of the evolution of the bilgewaer chemical and physical properties using in situ imaging. A Navy O/W emulsion consisting of three oils and a detergent mixture was used as the synthetic bilgewater model [1, 2]. Synthetic oil-in-water (O/W) emulsion droplets were seled in a vacuum compatible microfluidic sample holder and imaged using a suite of tools including scanning electron microscopy (SEM), time-of-flight secondary ion mass spectrometry (ToF-SIMS), confocal laser scanning microscopy, and optical microscopy, highlighting the advantage of multiscale analysis and its applications in waste reduction and treatment in the environment. The transferrable and vacuum compatible microfluidic interface, System for Analysis at the Liquid Vacuum Interface (SALVI), was used in this study. SALVI enabled surface analysis of liquids and liquid-solid interactions using ToF-SIMS and SEM [3, 4]. Its detection window is an aperture of 2 ?m in diameter open to vacuum, permitting direct detection of the liquid surface. Liquid is withheld by surface tension within the aperture. The interface is composed of a silicon nitride membrane and polydimethylsiloxane microchannel [3, 4]. A variety of samples including complex liquid mixtures, ionic liquids, single mammalian cells, live biofilms, and solid-electrolyte interface have been analyzed using in situ imaging [5, 6]. The feasibility of using SALVI for in situ SEM imaging of nanoparticles and colloids in liquid was recently demonstrated [7]. This paper shows new findings of multimodal imaging and analysis of synthesized emulsion particles in water. Figure 1 depicts a schematic of multimodal in situ imaging of bilgewater emulsion using SEM and ToF-SIMS. Furthermore, we study the interactions of microbes and bilgewater emulsion. Microbes play an important role in the ocean. We hypothesize that microbes release organics that can act as surfactants that affect bilgewater formation or weakening. We present the first systematic study of emulsions and biofilms and investigate the effects of biofilms on bilgewater emulsions. Pseudomonas was selected as a model strain. Biofilms were cultured in a microchannel to allow culture [8]. Once a thick layer of biofilms was formed, the medium solution was changed to a mixture consisting of 50 % bilgewater emulsion. Dispersed biofilms were collected at 24 hrs. and 48 hrs. after emulsions were introduced into the channel. Bilgewater emulsions, biofilms, and mixtures of bilgewater emulsions and biofilms were analyzed using multiple in situ and ex situ techniques as described earlier. Our findings indicate that biofilms change the chemical makeup of the emulsion surface compositions and emulsion droplet size distribution, confirming the hypothesis that extracellular polymeric substance (EPS) related components released from biofilms can function as surfactants and change the oil-in-water interfaces.

bilgewater, multimodal imaging, biofilms↗

NASA NTRS1993

Stress corrosion cracking properties of 15-5PH steel

Unexpected occurrence of failures, due to stress corrosion cracking (SCC) of structural components, indicate a need for improved characterization of materials and more advanced analytical procedures for reliably predicting structures performance. Accordingly, the purpose of this study was to determine the stress corrosion susceptibility of 15-5PH steel over a wide range of applied strain rates in a highly corrosive environment. The selected environment for this investigation was a highly acidified sodium chloride (NaCl) aqueous solution. The selected alloy for the study was a 15-5PH steel in the H900 condition. The slow strain rate technique was selected to test the metals specimens.

Rosa, Ferdinand↗

DOE OSTI2026

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↗

DOE OSTI2023

Comparison of phage-derived recombinases for genetic manipulation of Pseudomonas species

ABSTRACT Several strains in the Pseudomonas genus are categorized as plant growth-promoting rhizobacteria (PGPR). Although several of these strains are strong candidates for applications as biofertilizers or biopesticides, genome editing approaches are generally limited and require further development. Editing genomes in PGPR could enable more robust agricultural applications, persistence, and biosafety measures. In this study, we investigate the use of five phage-encoded recombinases to develop a recombineering workflow in three PGPR strains: Pseudomonas protegens Pf-5, Pseudomonas protegens CHA0, and Pseudomonas putida KT2440. Using point mutations in the rpoB gene, we reach maximum recombineering efficiencies of 1.5 × 10 −4 , 3 × 10 −4 , and 5 × 10 −5 , respectively, in these strains using λ-Red Beta recombinase from Escherichia coli . We further examine recombineering efficiencies across these strains as a function of selected mutation, editing template concentration, and phosphorothiolate bond protection. This work validates the use of these tools across several environmentally and biotechnologically relevant strains to expand the possibilities of genetic manipulation in the Pseudomonas genus. IMPORTANCE The Pseudomonas genus contains many members currently being investigated for applications in biodegradation, biopesticides, biocontrol, and synthetic biology. Though several strains have been identified with beneficial properties, chromosomal manipulations to further improve these strains for commercial applications have been limited due to the lack of efficient genetic tools that have been tested across this genus. Here, we test the recombineering efficiencies of five phage-derived recombinases across three biotechnologically relevant Pseudomonas strains: P. putida KT2440, P. protegens Pf-5, and P. protegens CHA0. These results demonstrate a method to generate targeted mutations quickly and efficiently across these strains, ideally introducing a method that can be implemented across the Pseudomonas genus and a strategy that may be applied to develop analogous systems in other nonmodel bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1995

Structurally altered capsular polysaccharides produced by mutant bacteria

Structurally altered capsular polysaccharides are produced by mutant bacteria. These polysaccharides are isolated by selecting a wild type bacterial strain and a phage producing degradative enzymes that have substrate specificity for the capsular polysaccharides produced by the wild type bacteria. Phage-resistant mutants producing capsular polysaccharides are selected and the structurally altered capsular polysaccharide is isolated therefrom.

Kern, Roger G.↗

NASA NTRS1994

Method for producing capsular polysaccharides

Kern, Roger G.↗

DOE OSTI2022

Controlling superconductivity of CeIrIn 5 microstructures by substrate selection

Superconductor/metal interfaces are usually fabricated in heterostructures that join these dissimilar materials. A conceptually different approach has recently exploited the strain sensitivity of heavy-fermion superconductors, selectively transforming regions of the crystal into the metallic state by strain gradients. The strain is generated by differential thermal contraction between the sample and the substrate. Here, we present an improved finite-element model that reliably predicts the superconducting transition temperature in CeIrIn 5 even in complex structures. Different substrates are employed to tailor the strain field into the desired shapes. Using this approach, both highly complex and strained as well as strain-free microstructures are fabricated to validate the model. This enables a high degree of control over the microscopic strain fields and forms the basis for more advanced structuring of superconductors as in Josephson junctions yet also finds natural use cases in any material class in which a modulation of the physical properties on a chip is desirable.

36 MATERIALS SCIENCE↗

NASA NTRS1991

A geometric nonlinear degenerated shell element using a mixed formulation with independently assumed strain fields

A mixed formulation is chosen to overcome deficiencies of the standard displacement-based shell model. Element development is traced from the incremental variational principle on through to the final set of equilibrium equations. Particular attention is paid to developing specific guidelines for selecting the optimal set of strain parameters. A discussion of constraint index concepts and their predictive capability related to locking is included. Performance characteristics of the elements are assessed in a wide variety of linear and nonlinear plate/shell problems. Despite limiting the study to geometric nonlinear analysis, a substantial amount of additional insight concerning the finite element modeling of thin plate/shell structures is provided. For example, in nonlinear analysis, given the same mesh and load step size, mixed elements converge in fewer iterations than equivalent displacement-based models. It is also demonstrated that, in mixed formulations, lower order elements are preferred. Additionally, meshes used to obtain accurate linear solutions do not necessarily converge to the correct nonlinear solution. Finally, a new form of locking was identified associated with employing elements designed for biaxial bending in uniaxial bending applications.

Graf, Wiley E.↗