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Results for “differential expression”

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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Exosomes derived from thymic stromal lymphopoietin-treated dendritic cells regulate T helper 17/regulatory T cell differentiation via miR-21/Smad7 axis

Highlights: • Exosomes from TSLP-treated DCs promote Th17 differentiation. • Exosomes from TSLP-treated DCs inhibit Tregs differentiation. • MiR-21 is highly expressed in exosomes from TSLP-treated DCs. • Exosomal miR-21 regulates Th17/Treg differentiation by targeting Smad7. Thymic stromal lymphopoietin (TSLP) is associated with fungal keratitis. This work aims to investigate whether TSLP can regulate T helper (Th) 17 and regulatory T cell (Treg) differentiation. We separated dendritic cells (DCs) from peripheral blood of healthy volunteers. DCs were treated with TSLP to activate DCs, and exosomes were obtained. CD{sup +} T cells were incubated with exosomes from TSLP-treated DCs. We found that exosomes from TSLP-treated DCs notably promoted the proportions of Th17 cells and inhibited the proportions of Tregs in the CD4{sup +} T cells. Moreover, exosomes from TSLP-treated DCs enhanced the expression of retinoid-related orphan receptor γt (RORγt) and interleukin 17 (IL-17), and repressed the expression of forkhead box protein P3 (Foxp3) and interleukin 10 (IL-10) in the CD4{sup +} T cells. Furthermore, miR-21 was highly expressed in exosomes from TSLP-treated DCs. Exosomes from TSLP-treated miR-21-silenced DCs promoted Treg differentiation and suppressed Th17 differentiation. Smad7 up-regulation repressed Th17 differentiation and enhanced Treg differentiation, which was abolished by miR-21 overexpression. Smad7 overexpression rescued the effect of exosomes from TSLP-treated DCs on Th17/Treg differentiation. In conclusion, our article confirms that TSLP induces DCs to deliver miR-21 by secreting exosomes, and thus miR-21 regulates Th17/Treg differentiation by inhibiting Smad7. Thus, this work further reveals the biological role of miR-21 in fungal keratitis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Dual reporter transgene driven by 2.3Col1a1 promoter is active in differentiated osteoblasts

AIM: As quantitative and spatial analyses of promoter reporter constructs are not easily performed in intact bone, we designed a reporter gene specific to bone, which could be analyzed both visually and quantitatively by using chloramphenicol acetyltransferase (CAT) and a cyan version of green fluorescent protein (GFPcyan), driven by a 2.3-kb fragment of the rat collagen promoter (Col2.3). METHODS: The construct Col2.3CATiresGFPcyan was used for generating transgenic mice. Quantitative measurement of promoter activity was performed by CAT analysis of different tissues derived from transgenic animals; localization was performed by visualized GFP in frozen bone sections. To assess transgene expression during in vitro differentiation, marrow stromal cell and neonatal calvarial osteoblast cultures were analyzed for CAT and GFP activity. RESULTS: In mice, CAT activity was detected in the calvaria, long bone, teeth, and tendon, whereas histology showed that GFP expression was limited to osteoblasts and osteocytes. In cell culture, increased activity of CAT correlated with increased differentiation, and GFP activity was restricted to mineralized nodules. CONCLUSION: The concept of a dual reporter allows a simultaneous visual and quantitative analysis of transgene activity in bone.

Non-NASA Center↗
NASA NTRS2001

Airborne Differential Doppler Weather Radar

The Precipitation Radar aboard the Tropical Rain Measuring Mission (TRMM) Satellite has shown the potential for spaceborne sensing of snow and rain by means of an incoherent pulsed radar operating at 13.8 GHz. The primary advantage of radar relative to passive instruments arises from the fact that the radar can image the 3-dimensional structure of storms. As a consequence, the radar data can be used to determine the vertical rain structure, rain type (convective/stratiform) effective storm height, and location of the melting layer. The radar, moreover, can be used to detect snow and improve the estimation of rain rate over land. To move toward spaceborne weather radars that can be deployed routinely as part of an instrument set consisting of passive and active sensors will require the development of less expensive, lighter-weight radars that consume less power. At the same time, the addition of a second frequency and an upgrade to Doppler capability are features that are needed to retrieve information on the characteristics of the drop size distribution, vertical air motion and storm dynamics. One approach to the problem is to use a single broad-band transmitter-receiver and antenna where two narrow-band frequencies are spaced apart by 5% to 10% of the center frequency. Use of Ka-band frequencies (26.5 GHz - 40 GHz) affords two advantages: adequate spatial resolution can be attained with a relatively small antenna and the differential reflectivity and mean Doppler signals are directly related to the median mass diameter of the snow and raindrop size distributions. The differential mean Doppler signal has the additional property that this quantity depends only on that part of the radial speed of the hydrometeors that is drop-size dependent. In principle, the mean and differential mean Doppler from a near-nadir viewing radar can be used to retrieve vertical air motion as well as the total mean radial velocity. In the paper, we present theoretical calculations for the differential reflectivity and Doppler as functions of the center frequency, frequency difference, and median mass diameter. For a fixed pair of frequencies, the detectability of the differential signals can be expressed as the number of independent samples required to detect rain or snow with a particular median mass diameter. Because sampling numbers on the order of 1000 are needed to detect the differential signal over a range of size distributions, the instrument must be confined to a near-nadir, narrow swath. Radar measurements from a zenith directed radar operated at 9.1 GHz and 10 GHz are used to investigate the qualitative characteristics of the differential signals. Disdrometer and rain gauge data taken at the surface, just below the radar, are used to test whether the differential signals can be used to estimate characteristics of the raindrop size distribution.

Meneghini, R.↗
NASA NTRS2003

Effects of simulated microgravity on arterial nitric oxide synthase and nitrate and nitrite content

The aim of the present work was to investigate the alterations in nitric oxide synthase (NOS) expression and nitrate and nitrite (NOx) content of different arteries from simulated microgravity rats. Male Wistar rats were randomly assigned to either a control group or simulated microgravity group. For simulating microgravity, animals were subjected to hindlimb unweighting (HU) for 20 days. Different arterial tissues were removed for determination of NOS expression and NOx. Western blotting was used to measure endothelial NOS (eNOS) and inducible NOS (iNOS) protein content. Total concentrations of NOx, stable metabolites of nitric oxide, were determined by the chemiluminescence method. Compared with controls, isolated vessels from simulated microgravity rats showed a significant increase in both eNOS and iNOS expression in carotid arteries and thoracic aorta and a significant decrease in eNOS and iNOS expression of mesenteric arteries. The eNOS and iNOS content of cerebral arteries, as well as that of femoral arteries, showed no differences between the two groups. Concerning NOx, vessels from HU rats showed an increase in cerebral arteries, a decrease in mesenteric arteries, and no change in carotid artery, femoral artery and thoracic aorta. These data indicated that there were differential alterations in NOS expression and NOx of different arteries after hindlimb unweighting. We suggest that these changes might represent both localized adaptations to differential body fluid redistribution and other factors independent of hemodynamic shifts during simulated microgravity.

Non-NASA Center↗
DOE OSTI2022

The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes

The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ferredoxin reductase regulates proliferation, differentiation, cell cycle and lipogenesis but not apoptosis in SZ95 sebocytes

Highlights: • FDXR expression is increased in sebaceous cells of acne lesions. • FDXR may enhance sebocyte differentiation and lipogenesis via ROS production. • FDXR might inhibit proliferation through inducing G2/S blockade. • IGF-1 could facilitate sebaceous differentiation and lipogenesis via PI3K/Akt/FDXR pathway. Ferredoxin reductase (FDXR), a mitochondrial membrane-associated flavoprotein, is essential for electron transfer and modulates p53-dependent apoptosis in cancer cells.FDXR may be implicated in epidermal and sebocytic differentiation, but its explicit function in sebocytes remains to be elucidated. In the present study, immunohistochemistry revealed that FDXR expression was increased in sebaceous cells of acne lesions. FDXR, PPARγ, LXRα/β, SREBP1 and Sox9 expression was incremental during sebocyte differentiation. FDXR overexpression induced by Ad-GFP-FDXR infection enhanced differentiation, reactive oxygen species (ROS), lipogenesis and PPARγ expression, and consequnently inhibited proliferation in SZ95 sebocytes. Flow cytometry showed that FDXR overexpression induced significant blockade of G2/M phase but had no effect on sub-G1 (apoptotic) sebocytes. Insulin-like growth factor-1 (IGF-1)-induced FDXR and PPARγ expression and lipogenesis were abolished by pretreatment with PI3K inhibitor LY294002. These results suggest that FDXR overexpression might promote differentiation and lipogenesis via ROS production and suppress proliferation via G2/S blockade in SZ95 sebocytes. IGF-1 could facilitate differentiation and lipogenesis through PI3K/Akt/FDXR pathway. FDXR could serve as a potential marker of advanced sebaceous differentiation, and its overexpression may be involved in the development of acne lesions.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1973

Surface configuration as an explanation for lithology-related cross-polarized radar image anomalies

One problem that has persisted since the development of multipolarized radar is the cause or causes of differential depolarization which is expressed as tonal reversals between like- and cross-polarized images of certain outcrops. Rocks producing anomalously low returns on the cross-polarized image could be classed into three general types: (1) certain geologically recent lava flows (late Pleistocene and Holocene), (2) some tertiary volcanics and (3) certain massive sandstones. Differential depolarization has been produced by volcanic rocks of various compositions including rhyolite, rhyodacite, dacite, andesite, and basalt. This has led to the conclusion that differential depolarization is not directly caused by any compositional factor. However, the study of aerial photos and subsequent field observation have led to the conclusion that the weathering and other surface characteristics of the outcrops are responsible for their appearance on multipolarized imagery.

Mccauley, J. R.↗
DOE OSTI2020

The dual of non-extremal area: differential entropy in higher dimensions

The Ryu-Takayanagi formula relates entanglement entropy in a field theory to the area of extremal surfaces anchored to the boundary of a dual AdS space. It is interesting to ask if there is also an information theoretic interpretation of the areas of non-extremal surfaces that are not necessarily boundary-anchored. In general, the physics outside such surfaces is associated to observers restricted to a time-strip in the dual boundary field theory. When the latter is two-dimensional, it is known that the differential entropy associated to the strip computes the length of the dual bulk curve, and has an interpretation in terms of the information cost in Bell pairs of restoring correlations inaccessible to observers in the strip. A general realization of this formalism in higher dimensions is unknown. We first prove a no-go theorem eliminating candidate expressions for higher dimensional differential entropy based on entropic c-theorems. Then we propose a new formula in terms of an integral of shape derivatives of the entanglement entropy of ball shaped regions. Our proposal stems from the physical requirement that differential entropy must be locally finite and conformally invariant. Demanding cancelation of the well-known UV divergences of entanglement entropy in field theory guides us to our conjecture, which we test for surfaces in AdS 4 . Our results suggest a candidate c-function for field theories in arbitrary dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Detailed study of the eikonal reaction theory for the breakup of one-neutron halo nuclei

Background: One-neutron removal reactions are used to study the single-particle structure of unstable nuclei, and in particular the exotic halo nuclei. The eikonal reaction theory (ERT) has been developed by Yahiro, Ogata, and Minomo [Prog. Theor. Phys. 126, 167 (2011)] to include dynamical effects, which are missing in the usual eikonal description of these reactions. Encouraging results have been obtained for total breakup cross sections in comparison to more elaborate reaction models. Purpose: Here, we extend these comparisons to more differential breakup cross sections expressed as functions of the relative energy or parallel momentum between the core and halo neutron. Method: ERT predictions of these cross sections are compared to state-of-the-art calculations. Results: The hypotheses upon which the ERT is based are confirmed and their range of validity is made clearer. The actual ordering of the evolution operators affects ERT differential cross sections and a specific choice leads to excellent agreement with the reference calculation. Dynamical effects in the treatment of the neutron-target interaction can be significant in the parallel-momentum observable. Conclusions: The role of the different interactions in the dynamics of breakup reactions of one-neutron halo nuclei are better understood and improvements to the ERT are suggested.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation

Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats

Micron scale crystalline and fibrillar cellulose materials are “generally regarded as safe” (GRAS) as binders and thickeners in food products. Yet, partly due to a lack of relevant toxicological data, nanocellulose (NC) materials, which have unique properties that can be exploited to improve food quality and safety, have yet to receive FDA approval as food ingredients. Results of in vitro and in vivo toxicological studies of ingested NC, detailed in a recent companion report, revealed minimal acute in vitro cytotoxicity, and no toxicity in a subacute rat gavage model, suggesting that NC materials are non-hazardous. However, ingested materials may also modulate gut microbial populations, or alter aspects of intestinal function not evaluated in standard totoxicity testing, which could have important health implications. Here, we report the results of studies of the effects of ingested cellulose nanofibrils (CNF) on the fecal microbiome and metabolome, intestinal (ileal) epithelial cell mRNA expression of cell junction genes, and ileal cytokine production. Feces, plasma, and ileum samples were collected from Wistar Han rats before and after five weeks of biweekly gavages of water or cream, with or without 1% w/w CNF. Analysis of fecal microbial populations revealed that CNF caused changes in both genus and species diversity, with specific effects on species that produce short chain fatty acids, and that have been associated with increased IgA production and elevation of insulin levels. Fecal metabolomic analysis revealed relatively few effects of CNF, with significant changes in the levels of only ten metabolites out of 366 measured. Exposure to CNF also caused differential regulation of mRNA expression of several genes involved in epithelial cell junctions, and increased production of cytokines that both promote and inhibit proliferation of CD8 T cells. These perturbations in intestinal homeostasis contrast somewhat with the absence of in vitro and in vivo toxicity observed previously but would appear to represent minor effects. Additionally, the gut microbiome is highly sensitive to ingested substances, and such disturbances of the intestinal microbial ecosystem do not necessarily represent or predict meaningful pathology. Further studies, including chronic feeding studies, are needed to assess the real health implications, if any, of these changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The protective role of Ephrin-B2/EphB4 signaling in osteogenic differentiation under inflammatory environment

Highlights: • Ephrin-B2/EphB4 signaling alleviated the inhibited effect of inflammation on osteogenesis. • The effect of Ephrin-B2/EphB4 signaling might be related to the MAPK pathway. • In vivo application of Ephrin-B2-Fc resulted in less alveolar bone destruction. Inflammation and alveolar bone destruction constitute the main pathological process of periodontitis. However, the molecular mechanisms of bone destruction under the inflammation environment remain unclear. This study aims to explore the role of Ephrin-B2/EphB4 signaling in osteogenic differentiation under the inflammation environment. Mouse pre-osteoblasts MC3T3-E1 were pretreated with lipopolysaccharide of Porphyromonas gingivalis (Pg-LPS). The Ephrin-B2/EphB4 signaling was activated, and the osteogenic differentiation of cells was examined. The results showed that activation of Ephrin-B2/EphB4 signaling promoted the expression levels of osteogenic differentiation-related genes, and also relieved the inhibitory effect of Pg-LPS on osteogenesis. Noticeably, the effect of Ephrin-B2/EphB4 signaling might be related to the mitogen-activated protein kinase (MAPK) pathway. While applying Ephrin-B2-Fc and EphB4-Fc to periodontitis mice, we observed the reduction of alveolar crest destruction. The current study revealed the possible role of Ephrin-B2/EphB4 signaling in reducing bone destruction in periodontitis and suggested its potential values for further research.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1992

Comparison of level-1 and level-2 buckling and postbuckling solutions

The accuracy of the solutions obtained with the Level-1 computational modules of DISDECO (Delft Interactive Shell Design Code) are investigated by comparing them with solutions obtained with ANILISA, a Level-2 computational module. Whereas the Level-1 solutions are based on the use of trigonometric functions to represent the out-of-plane displacement W and involve Galerkin type approximations to reduce the governing partial differential equations to simple algebraic expressions, the Level-2 solutions employ a truncated Fourier expansion in the circumferential direction and solve the resulting ordinary differential equations forming a nonlinear eigenvalue problem by a Stodola like technique. This involves the numerical integration of the set of ordinary differential equations, which in turn makes it possible to satisfy the specified boundary conditions exactly. It is shown that in many applications the Level-1 predictions concerning the critical buckling load of the perfect structure and its imperfection sensitivity are quite accurate and reliable. For those cases where this is not true, it is shown how the pre and postprocessing facilities of DISDECO can be used efficiently to arrive at a reliable prediction. This involves always the use of the Level-2 computational module ANILISA with its rigorous prebuckling solution and its feature which makes it possible to satisfy the specified boundary conditions exactly.

Arbocz, J.↗
DOE OSTI2020

Master integrals for two-loop QCD corrections to quark quasi PDFs

We compute the master integrals for the two-loop QCD corrections to quark quasi parton distribution functions (PDFs) in the large momentum effective theory (LaMET). With a proper canonical basis, we derive the analytical results for the three families of master integrals using the method of differential equations. The final expressions for the master integrals are given in terms of Goncharov polylogarithms. These results allow us to extract the two-loop short-distant matching coefficients between quark quasi and lightcone PDFs in LaMET, and are valuable to improve the determination of the nucleon PDFs from first principles in future.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

DPM: A deep learning PDE augmentation method with application to large-eddy simulation

A framework is introduced that leverages known physics to reduce overfitting in machine learning for scientific applications. The partial differential equation (PDE) that expresses the physics is augmented with a neural network that uses available data to learn a description of the corresponding unknown or unrepresented physics. Training within this combined system corrects for missing, unknown, or erroneously represented physics, including discretization errors associated with the PDE's numerical solution. For optimization of the network within the PDE, an adjoint PDE is solved to provide high-dimensional gradients, and a stochastic adjoint method (SAM) further accelerates training. Additionally, the approach is demonstrated for large-eddy simulation (LES) of turbulence. High-fidelity direct numerical simulations (DNS) of decaying isotropic turbulence provide the training data used to learn sub-filter-scale closures for the filtered Navier–Stokes equations. Out-of-sample comparisons show that the deep learning PDE method outperforms widely-used models, even for filter sizes so large that they become qualitatively incorrect. It also significantly outperforms the same neural network when a priori trained based on simple data mismatch, not accounting for the full PDE. Measures of discretization errors, which are well-known to be consequential in LES, point to the importance of the unified training formulation's design, which without modification corrects for them. For comparable accuracy, simulation runtime is significantly reduced. A relaxation of the typical discrete enforcement of the divergence-free constraint in the solver is also successful, instead allowing the DPM to approximately enforce incompressibility physics. Since the training loss function is not restricted to correspond directly to the closure to be learned, training can incorporate diverse data, including experimental data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗