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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Development of dual‐inducible duet‐expression vectors for tunable gene expression control and CRISPR interference‐based gene repression in Pseudomonas putida KT2440

Summary The development of P. putida as an industrial host requires a sophisticated molecular toolbox for strain improvement, including vectors for gene expression and repression. To augment existing expression plasmids for metabolic engineering, we developed a series of dual‐inducible duet‐expression vectors for P. putida KT2440. A number of inducible promoters (P lac , P tac , P tetR/tetA and P bad ) were used in different combinations to differentially regulate the expression of individual genes. Protein expression was evaluated by measuring the fluorescence of reporter proteins (GFP and RFP). Our experiments demonstrated the use of compatible plasmids, a useful approach to coexpress multiple genes in P. putida KT2440. These duet vectors were modified to generate a fully inducible CRISPR interference system using two catalytically inactive Cas9 variants from S. pasteurianus (dCas9) and S. pyogenes (spdCas9). The utility of developed CRISPRi system(s) was demonstrated by repressing the expression of nine conditionally essential genes, resulting in growth impairment and prolonged lag phase for P. putida KT2440 growth on glucose. Furthermore, the system was shown to be tightly regulated, tunable and to provide a simple way to identify essential genes with an observable phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Kindlin-3 mutation in mesenchymal stem cells results in enhanced chondrogenesis

Identifying patient mutations driving skeletal development disorders has driven our understanding of bone development. Integrin adhesion deficiency disease is caused by a Kindlin-3 (fermitin family member 3) mutation, and its inactivation results in bleeding disorders and osteopenia. In this study, we uncover a role for Kindlin-3 in the differentiation of bone marrow mesenchymal stem cells (BMSCs) down the chondrogenic lineage. Kindlin-3 expression increased with chondrogenic differentiation, similar to RUNX2. BMSCs isolated from a Kindlin-3 deficient patient expressed chondrocyte markers, including SOX9, under basal conditions, which were further enhanced with chondrogenic differentiation. Rescue of integrin activation by a constitutively activated β{sub 3} integrin construct increased adhesion to multiple extracellular matrices and reduced SOX9 expression to basal levels. Growth plates from mice expressing a mutated Kindlin-3 with the integrin binding site ablated demonstrated alterations in chondrocyte maturation similar to that seen with the human Kindlin-3 deficient BMSCs. These findings suggest that Kindlin-3 expression mirrors RUNX2 during chondrogenesis.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1985

Second-order Compton-Getting effect on arbitrary intensity distribution

Theoretical studies of energetic particles in space are often referred to a special frame of reference. To compare theory with experiment, one has to transform the particle distribution from the special frame to the observer's frame, or vice versa. Various methods have been derived to obtain the directional distribution in the comoving frame from the directional fluxes measured on a spacecraft. These methods have become progressively complicated as increasingly detailed directional particle data become available. A set of 2nd order correct formulae for the transformation of an arbitrary differential intensity distribution, expressed as a series of spherical harmonics, between any two frames in constant relative motion is presented. These formulae greatly simplify the complicated procedures currently in use for the determination of the differential intensity distribution in a comoving frame.

Ng, C. K.↗
NASA NTRS1991

A unified approach to the helioseismic forward and inverse problems of differential rotation

A general, degenerate perturbation theoretic treatment of the helioseismic forward and inverse problem for solar differential rotation is presented. For the forward problem, differential rotation is represented as the axisymmetric component of a general toroidal flow field using velocity spherical harmonics. This approach allows each degree of differential rotation to be estimated independently from all other degrees. In the inverse problem, the splitting caused by differential rotation is expressed as an expansion in a set of orthonormal polynomials that are intimately related to the solution of the forward problem. The combined use of vector spherical harmonics as basis functions for differential ratio and the Clebsch-Gordon coefficients to represent splitting provides a unified approach to the forward and inverse problems of differential rotation which greatly simplify inversion.

Ritzwoller, Michael H.↗
NASA NTRS1960

Slow-Neutron Scattering by Rotators. II

The methods developed in a previous paper for extending the neutron scattering formalism of Zemach and Glauber to any type of molecular rotator have been employed to derive generalized forms generalized forms of the differential cross sections for rotator scattering. A mass-ratio expansion for the treatment of the high-energy limit is illustrated on the classical cross section and then employed in the treatment of the more general quantum-mechanical expression for the differential cross section. The results apply to an arbitrarily asymmetric rotator. The very low energy approximation is carried out for the symmetric rotator, and the procedure is compared with the explicit summing of the partial cross sections for individual rotational transitions. The inelastic correction to the static approximation for interference scattering is calculated to an accuracy of first order in the mass ratios for the case of the symmetric rotator.

Volkin, Howard C.↗
NASA NTRS2002

Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon

The low-shear environment of optimized rotation suspension culture allows both eukaryotic and prokaryotic cells to assume physiologically relevant phenotypes that have led to significant advances in fundamental investigations of medical and biological importance. This culture environment has also been used to model microgravity for ground-based studies regarding the impact of space flight on eukaryotic and prokaryotic physiology. We have previously demonstrated that low-shear modeled microgravity (LSMMG) under optimized rotation suspension culture is a novel environmental signal that regulates the virulence, stress resistance, and protein expression levels of Salmonella enterica serovar Typhimurium. However, the mechanisms used by the cells of any species, including Salmonella, to sense and respond to LSMMG and identities of the genes involved are unknown. In this study, we used DNA microarrays to elucidate the global transcriptional response of Salmonella to LSMMG. When compared with identical growth conditions under normal gravity (1 x g), LSMMG differentially regulated the expression of 163 genes distributed throughout the chromosome, representing functionally diverse groups including transcriptional regulators, virulence factors, lipopolysaccharide biosynthetic enzymes, iron-utilization enzymes, and proteins of unknown function. Many of the LSMMG-regulated genes were organized in clusters or operons. The microarray results were further validated by RT-PCR and phenotypic analyses, and they indicate that the ferric uptake regulator is involved in the LSMMG response. The results provide important insight about the Salmonella LSMMG response and could provide clues for the functioning of known Salmonella virulence systems or the identification of uncharacterized bacterial virulence strategies.

Non-NASA Center↗
DOE OSTI2024

Heterologous expression of Arabidopsis laccase2, laccase4 and peroxidase52 driven under developing xylem specific promoter DX15 improves saccharification in populus

Secondary cell wall holds considerable potential as it has gained immense momentum to replace the lignocellulosic feedstock into fuels. Lignin one of the components of secondary cell wall tightly holds the polysaccharides thereby enhancing the recalcitrance and complexity in the biomass. Laccases (LAC) and peroxidases (PRX) are the major phenyl-oxidases playing key functions during the polymerization of monolignols into lignin. Yet, the functions of laccase and peroxidases gene families remained largely unknown. Hence, the objective of this conducted study is to understand the role of specific LAC and PRX in Populus wood formation and to further investigate how the altered Lac and Prx expression affects biomass recalcitrance and plant growth. This study of heterologous expression of Arabidopsis Lac and Prx genes was conducted in poplar to avoid any otherwise occurring co-suppression mechanism during the homologous overexpression of highly expressed native genes. In the pursuit of optimizing lignocellulosic biomass for biofuel production, the present study focuses on harnessing the enzymatic potential of Arabidopsis thaliana Laccase2, Laccase4, and Peroxidase52 through heterologous expression. We overexpressed selected Arabidopsis laccase2 (AtLac2), laccase4 (AtLac4), and peroxidase52 (AtPrx52) genes, based on their high transcript expression respective to the differentiating xylem tissues in the stem, in hybrid poplar (cv. 717) expressed under the developing xylem tissue-specific promoter, DX15 characterized the transgenic populus for the investigation of growth phenotypes and recalcitrance efficiency. Bioinformatics analyses conducted on AtLac2 and AtLac4 and AtPrx52, revealed the evolutionary relationship between the laccase gene and peroxidase gene homologs, respectively. Transgenic poplar plant lines overexpressing the AtLac2 gene (AtLac2-OE) showed an increase in plant height without a change in biomass yield as compared to the controls; whereas AtLac4-OE and AtPrx52-OE transgenic lines did not show any such observable growth phenotypes compared to their respective controls. The changes in the levels of lignin content and S/G ratios in the transgenic poplar resulted in a significant increase in the saccharification efficiency as compared to the control plants. Overall, saccharification efficiency was increased by 35–50%, 21–42%, and 8–39% in AtLac2-OE, AtLac4-OE, and AtPrx52-OE transgenic poplar lines, respectively, as compared to their controls. Moreover, the bioengineered plants maintained normal growth and development, underscoring the feasibility of this approach for biomass improvement without compromising overall plant fitness. This study also sheds light on the potential of exploiting regulatory elements of DX15 to drive targeted expression of lignin-modifying enzymes, thereby providing a promising avenue for tailoring biomass for improved biofuel production. These findings contribute to the growing body of knowledge in synthetic biology and plant biotechnology, offering a sustainable solution to address the challenges associated with lignocellulosic biomass recalcitrance.

09 BIOMASS FUELS↗
NASA NTRS2003

Inhibition of HSP70 and a Collagen-Specific Molecular Chaperone (HSP47) Expression in Rat Osteoblasts by Microgravity

Rat osteoblasts were cultured aboard a space shuttle for 4 or 5 days. Cells were exposed to 1alpha, 25 dihydroxyvitamin D(3) during the last 20 h and then solubilized by guanidine solution. The mRNA levels for molecular chaperones were analyzed by semi-quantitative RT-PCR. ELISA was used to quantify TGF-beta1 in the conditioned medium. The HSP70 mRNA levels in the flight cultures were almost completely suppressed, as compared to the ground (1 x g) controls. The inducible HSP70 is known as the major heat shock protein that prevents stress-induced apoptosis. The mean mRNA levels for the constitutive HSC73 in the flight cultures were reduced to 69%, approximately 60% of the ground controls. HSC73 is reported to prevent the pathological state that is induced by disruption of microtubule network. The mean HSP47 mRNA levels in the flight cultures were decreased to 50% and 19% of the ground controls on the 4th and 5th days. Concomitantly, the concentration of TGF-beta1 in the conditioned medium of the flight cultures was reduced to 37% and 19% of the ground controls on the 4th and 5th days. HSP47 is the collagen-specific molecular chaperone that controls collagen processing and quality and is regulated by TGF-beta1. Microgravity differentially modulated the expression of molecular chaperones in osteoblasts, which might be involved in induction and/or prevention of osteopenia in space.

Animals↗
NASA NTRS2002

Fluid flow increases mineralized matrix deposition in 3D perfusion culture of marrow stromal osteoblasts in a dose-dependent manner

Bone is a complex highly structured mechanically active 3D tissue composed of cellular and matrix elements. The true biological environment of a bone cell is thus derived from a dynamic interaction between responsively active cells experiencing mechanical forces and a continuously changing 3D matrix architecture. To investigate this phenomenon in vitro, marrow stromal osteoblasts were cultured on 3D scaffolds under flow perfusion with different rates of flow for an extended period to permit osteoblast differentiation and significant matrix production and mineralization. With all flow conditions, mineralized matrix production was dramatically increased over statically cultured constructs with the total calcium content of the cultured scaffolds increasing with increasing flow rate. Flow perfusion induced de novo tissue modeling with the formation of pore-like structures in the scaffolds and enhanced the distribution of cells and matrix throughout the scaffolds. These results represent reporting of the long-term effects of fluid flow on primary differentiating osteoblasts and indicate that fluid flow has far-reaching effects on osteoblast differentiation and phenotypic expression in vitro. Flow perfusion culture permits the generation and study of a 3D, actively modeled, mineralized matrix and can therefore be a valuable tool for both bone biology and tissue engineering.

Non-NASA Center↗
NASA NTRS2019

Gravity as a Continuum: Effects of Altered Gravity on Drosophila Melanogaster Immunity

The impact of spaceflight on immune function is undoubtedly a critical focus in the area of space biology and human health research. Heat shock proteins (Hsp) are an evolutionarily conserved family of proteins that are expressed in response to cellular and physiological stressors, experienced during radiation exposure, confinement, circadian rhythm disruption, and altered gravity (hypergravity experienced at launch/landing and microgravity experienced in-flight). In particular, Hsp70 aids in the folding of proteins, facilitates the movement of proteins across the membranes during signal transductions and can stimulate innate immunity. Since Hsp70 is induced during cellular stress, and can act as a stimulator for innate immunity, we sought to address how a loss of Hsp70 affects immunity, under the stress-inducing model of acute and chronic hypergravity. Moreover, the effects of gravity as a continuum on the induction of Hsps and key immune genes were also assessed to determine if increased cellular stress, via increased gravity (g)-force, contributes to immune dysfunctions. For this, wildtype (W1118) and Hsp70 deficient (Hsp70null) Drosophila melanogaster were subjected to simulated hypergravity at increasing levels of g-force (1.2g, 3g, and 5g) for acute (1hr) and chronic (7-day) timepoints and were compared to 0g 'non-hypergravity' controls. Following simulation, whole bodies were sex-segregated, RNA was isolated and quantitative (q)PCR was performed to determine differential immune gene expression profiles. Further, functional output of hemocytes were assessed by a phagocytosis assay. Collectively, these studies evaluated the effects of Hsp70 in the context of immunity during acute and chronic hypergravity. Indeed, relevance for this work can directly translate to acute effects of launch/landing gravitational forces upon liftoff (~1.7g) and entry (~3.4g) that astronauts experience. In addition, the effects of chronic cellular stress is directly relevant to the immune health of astronauts on long duration missions, as well. Thus, as we approach the goal of returning to the Moon and landing the first humans on Mars, an evaluation of gravity as a continuum and the stress-inducing effects of altered gravity experienced during spaceflight on astronaut immunity and health are necessary.

Olivieri, Joe↗
DOE OSTI2022

Photoproduction of pion pairs at high energy and small angles

Here, we explore the photoproduction mechanisms for charged and neutral pion pairs off a heavy nucleus at threshold. We calculate the production of charged pairs in the Coulomb field of the nucleus in the Born approximation using explicit expressions for the differential cross sections and their connection with the total cross section σ(γγ→π + π - ). The production of σ mesons at threshold and their subsequent decay into pions is an important mechanism and is investigated quantitatively in a framework that can be used for both charged and neutral pions. σ mesons can be produced via electromagnetic (photon exchange) or strong (ω exchange) interactions. For neutral pions, another production mechanism consists of the two-step process where charged pions are produced first and then charge exchange into two neutral pions. Differential and total cross sections are computed for each production mechanism.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Chromatin structures from integrated AI and polymer physics model

The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Incorporating physical constraints into Gaussian process surrogate models (LDRD Project Summary)

This report summarizes work done under the Laboratory Directed Research and Development (LDRD) project titled "Incorporating physical constraints into Gaussian process surrogate models?' In this project, we explored a variety of strategies for constraint implementations. We considered bound constraints, monotonicity and related convexity constraints, Gaussian processes which are constrained to satisfy linear operator constraints which represent physical laws expressed as partial differential equations, and intrinsic boundary condition constraints. We wrote three papers and are currently finishing two others. We developed initial software implementations for some approaches. This report summarizes the work done under this LDRD.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Assessing Critical Conditions for Scour Near Obstructions using Bed Shear, Particle Onset of Motion Balances, and CFD-DEM Modeling of Granular Beds

Computational Fluid Dynamics combined with a Discrete Element Method is one of the computational methods that can be used to model multiphase flows. In this method various phases, gas and liquid or solid, are present in the same computational domain. The local averaged Navier–Stokes equations determine the flow of the continuous phase fluid and are solved using the traditional CFD finite volume approach. DEM is based on a Lagrangian formulation, which solves the equations of motion, expressed in ordinary differential equations, for representative particles as they move in space and time. The interactions between the continuous fluid phase and discrete solid phase are modeled with the use of Newton’s laws of motion via drag force. The particles interact with each other and with the boundaries of the fluid continuum, and the resulting contact forces are included in the equations of motion. The properties of solid particles and boundaries are treated as elastic bodies, with specified density, elastic modulus, and Poisson’s ratio. Particle shapes may vary from single spherical particles to more complex-shaped composite particles. The particles may be introduced into the domain by random or structured injection at a point, surface, or volume, depending on the application. More details on the formulation can be found in the Simcenter STAR-CCM+ User’s Manual and OpenFOAM website.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1972

Canonical fluid thermodynamics

The space-time integral of the thermodynamic pressure plays the role of the thermodynamic potential for compressible, adiabatic flow in the sense that the pressure integral for stable flow is less than for all slightly different flows. This stability criterion can be converted into a variational minimum principle by requiring the molar free-enthalpy and the temperature, which are the arguments of the pressure function, to be generalized velocities, that is, the proper-time derivatives of scalar spare-time functions which are generalized coordinates in the canonical formalism. In a fluid context, proper-time differentiation must be expressed in terms of three independent quantities that specify the fluid velocity. This can be done in several ways, all of which lead to different variants (canonical transformations) of the same constraint-free action integral whose Euler-Lagrange equations are just the well-known equations of motion for adiabatic compressible flow.

Schmid, L. A.↗
NASA NTRS1983

Large space structure model reduction and control system design based upon actuator and sensor influence functions

A model reduction procedure based on aggregation with respect to sensor and actuator influences rather than modes is presented for large systems of coupled second-order differential equations. Perturbation expressions which can predict the effects of spillover on both the aggregated and residual states are derived. These expressions lead to the development of control system design constraints which are sufficient to guarantee, to within the validity of the perturbations, that the residual states are not destabilized by control systems designed from the reduced model. A numerical example is provided to illustrate the application of the aggregation and control system design method.

Yam, Y.↗