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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Comparative transcriptome analysis of rainbow trout gonadal cells (RTG-2) infected with U and J genogroup infectious hematopoietic necrosis virus

Infectious hematopoietic necrosis virus (IHNV) is the causative pathogen of infectious hematopoietic necrosis, outbreaks of which are responsible for significant losses in rainbow trout aquaculture. Strains of IHNV isolated worldwide have been classified into five major genogroups, J, E, L, M, and U. To date, comparative transcriptomic analysis has only been conducted individually for the J and M genogroups. In this study, we compared the transcriptome profiles in U genogroup and J genogroup IHNV-infected RTG-2 cells with mock-infected RTG-2 cells. The RNA-seq results revealed 17,064 new genes, of which 7,390 genes were functionally annotated. Differentially expressed gene (DEG) analysis between U and J IHNV-infected cells revealed 2,238 DEGs, including 1,011 downregulated genes and 1,227 upregulated genes. Among the 2,238 DEGs, 345 new genes were discovered. The DEGs related to immune responses, cellular signal transduction, and viral diseases were further analyzed. RT-qPCR validation confirmed that the changes in expression of the immune response-related genes trpm2 , sting , itgb7 , ripk2 , and irf1 , cellular signal transduction-related genes irl , cacnb2 , bmp2l , gadd45α , and plk2 , and viral disease-related genes mlf1, mtor, armc5 , pik3r1 , and c-myc were consistent with the results of transcriptome analysis. Taken together, our findings provide a comprehensive transcriptional analysis of the differential virulence of the U and J genogroups of IHNV, and shed new light on the pathogenic mechanisms of IHNV strains.

Zhao, Jing-Zhuang↗
NASA NTRS1994

ASTM E 1559 method for measuring material outgassing/deposition kinetics has applications to aerospace, electronics, and semiconductor industries

The American Society for Testing and Materials has published a new standard test method for characterizing time and temperature-dependence of material outgassing kinetics and the deposition kinetics of outgassed species on surfaces at various temperatures. This new ASTM standard, E 1559(1), uses the quartz crystal microbalance (QCM) collection measurement approach. The test method was originally developed under a program sponsored by the United States Air Force Materials Laboratory (AFML) to create a standard test method for obtaining outgassing and deposition kinetics data for spacecraft materials. Standardization by ASTM recognizes that the method has applications beyond aerospace. In particular, the method will provide data of use to the electronics, semiconductor, and high vacuum industries. In ASTM E 1559 the material sample is held in vacuum in a temperature-controlled effusion cell, while its outgassing flux impinges on several QCM's which view the orifice of the effusion cell. Sample isothermal total mass loss (TML) is measured as a function of time from the mass collected on one of the QCM's which is cooled by liquid nitrogen, and the view factor from this QCM to the cell. The amount of outgassed volatile condensable material (VCM) on surfaces at higher temperatures is measured as a function of time during the isothermal outgassing test by controlling the temperatures of the remaining QCM's to selected values. The VCM on surfaces at temperatures in between those of the collector QCM's is determined at the end of the isothermal test by heating the QCM's at a controlled rate and measuring the mass loss from the end of the QCM's as a function of time and temperature. This reevaporation of the deposit collected on the QCM's is referred to as QCM thermogravimetric analysis. Isothermal outgassing and deposition rates can be determined by differentiating the isothermal TML and VCM data, respectively, while the evaporation rates of the species can be obtained as a function of temperature by differentiating the QCM thermogravimetric analysis data.

Garrett, J. W.↗
DOE OSTI2025

Single cell RNA sequencing reveals shifts in cell maturity and function of endogenous and infiltrating cell types in response to acute intervertebral disc injury

Intervertebral disc (IVD) degeneration contributes to disabling back pain. Degeneration can be initiated by injury and progressively leads to an irreversible loss of cells and function. IVD function restoration through cell replacement therapies have had limited success due to knowledge gaps in the critical cell populations important for repair. Here, in this study, we used single cell RNA sequencing to identify the transcriptional changes of IVD resident and infiltrating cell populations from Control and Injured coccygeal IVDs extracted from 12-week-old female C57BL/6J mice 7 days post injury. Clustering, gene ontology, and pseudotime trajectory analyses determined transcriptomic divergences with injury, flow cytometry identified they types of infiltrating immune cells, and immunofluorescence was utilized to define mesenchymal stem cell (MSC) localization. We identified 11 distinct clusters that included IVD, immune, vascular cells, and MSCs. Differential gene expression analysis determined that Outer Annulus Fibrosus, Neutrophils, Saa2-High MSCs, Macrophages, and Krt18 + Nucleus Pulposus (NP) cells were the major drivers of transcriptomic differences between Control and Injured cells. Gene ontology revealed that the most upregulated biological pathways were angiogenesis and T cell-related while wound healing and ECM regulation were downregulated. Pseudotime trajectory analyses revealed that IVD injury directed cells towards increased differentiation in all clusters, except for Krt18 + NP cells which remained in a less mature cell state. Saa2-High and Grem1-High MSCs populations shifted towards more differentiated IVD cells profiles with injury and localized distinctly within the IVD. This study revealed novel MSC populations with the potential to be leveraged for future IVD repair studies.

Cartilage↗
NASA NTRS1987

Factorization and the synthesis of optimal feedback kernels for differential-delay systems

A combination of ideas from the theories of operator Riccati equations and Volterra factorizations leads to the derivation of a novel, relatively simple set of hyperbolic equations which characterize the optimal feedback kernel for the finite-time regulator problem for autonomous differential-delay systems. Analysis of these equations elucidates the underlying structure of the feedback kernel and leads to the development of fast and accurate numerical methods for its computation. Unlike traditional formulations based on the operator Riccati equation, the gain is characterized by means of classical solutions of the derived set of equations. This leads to the development of approximation schemes which are analogous to what has been accomplished for systems of ordinary differential equations with given initial conditions.

Milman, Mark M.↗
DOE OSTI2021

Deinococcus radiodurans UWO298 Dependence on Background Radiation for Optimal Growth

Ionizing radiation is a major environmental variable for cells on Earth, and so organisms have adapted to either prevent or to repair damages caused by it, primarily from the appearance and accumulation of reactive oxygen species (ROS). In this study, we measured the differential gene expression in Deinococcus radiodurans UWO298 cultures deprived of background ionizing radiation (IR) while growing 605 m underground at the Waste Isolation Pilot Plant (WIPP), reducing the dose rate from 72.1 to 0.9 nGy h –1 from control to treatment, respectively. This reduction in IR dose rate delayed the entry into the exponential phase of the IR-shielded cultures, resulting in a lower biomass accumulation for the duration of the experiment. The RNASeq-based transcriptome analysis showed the differential expression of 0.2 and 2.7% of the D. radiodurans genome after 24 and 34 h of growth in liquid culture, respectively. Gene expression regulation after 34 h was characterized by the downregulation of genes involved in folding newly synthesized and denatured/misfolded proteins, in the assimilation of nitrogen for amino acid synthesis and in the control of copper transport and homeostasis to prevent oxidative stress. We also observed the upregulation of genes coding for proteins with transport and cell wall assembly roles. These results show that D. radiodurans is sensitive to the absence of background levels of ionizing radiation and suggest that its transcriptional response is insufficient to maintain optimal growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infection

Influenza A virus (IAV) in the human and swine host infects epithelial cells lining the respiratory tract causing a necrotizing bronchitis and bronchiolitis. These epithelial surfaces are protected by large glycoproteins called mucins. Mucin 4 (MUC4) is a transmembrane mucin that consists of an alpha subunit responsible for surface protection and intracellular beta subunit involved in signal transduction which repress apoptosis and stimulate epithelial proliferation. This study was designed to determine the expression and potential role of MUC4 during IAV infection. We used immunohistochemistry in combination with machine learning image analysis to quantify differential protein expression of MUC4 subunits in IAV-infected and uninfected lung in a porcine model. MUC4 protein basal expression in control animals varied significantly by litter. MUC4 protein expression was significantly increased in bronchioles with necrotizing bronchiolitis compared to histologically normal bronchioles, likely representing a regenerative response to restore mucosal integrity of conducting airways. Understanding the impact of differential MUC4 expression among healthy individuals and during IAV infection will facilitate control strategies by elucidating mechanisms associated with susceptibility to IAV that can be therapeutically or genetically regulated and may be extended to other respiratory diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Design, execution, and interpretation of plant RNA-seq analyses

Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.

transcription start and end sites↗
DOE OSTI2026

Identifying Differential Equations in Fourier Domain (FourierIdent)

We investigate identifying differential equations in the frequency domain. Fourier analysis is an important tool in theoretical analysis and numerical solvers of differential equations, yet there is limited work in exploring this connection in the identification of differential equations. This paper aims to identify the underlying differential equation in the frequency domain, from a given single realization of the differential equation perturbed by noise. Such setting imposes difficulties which are different from other identification methods where computation is carried out in the physical domain. We propose several ways to mitigate the challenges arising from noise in data and large differences in the magnitudes of frequency responses. The main takeaways are that identifying differential equations solely in the frequency domain is challenging, the method we propose is based on a form of domain partitions in the frequency domain, and this method shows benefits for complex data even with high level of noise. We introduce a Fourier feature denoising, and define the meaningful data region and the core regions of features to reduce the effect of noise in the frequency domain and to enhance the accuracy in coefficient identification. The proposed method is tested on various differential equations with linear, nonlinear, and high-order derivative feature terms, and shows advantages on complex data with many frequency modes, even under high level of noise.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The oncogenic role of meiosis-specific Aurora kinase C in mitotic cells

Highlights: • AURKC is expressed in meiotic cells and some cancers. • AURKC expression increases cell migration and transformation of human mitotic cells. • Deletion of AURKC in U2OS cells decreases cell migration and soft agar growth. • Transcriptome analysis reveals that AURKC alters the extracellular matrix. Aberrant expression of meiosis-specific genes in cancer has recently emerged as a driver of some cancer formation. Aurora kinase C (AURKC) is a member of the Aurora kinase family of proteins known to regulate chromosome segregation during cell divisions. AURKC is normally expressed in meiotic cells; however, elevated levels of AURKC mRNA and protein are frequently measured in cancer cells. To understand the function of AURKC in cancer cells, expression was induced in noncancerous, human retina pigmented epithelial cells. While AURKC expression did not alter cell proliferation over 72 h, it did increase cell migration and anchorage independent growth in soft agar suggesting an oncogenic role in mitotically dividing cells. To evaluate AURKC as a potential therapeutic target, a frameshift mutation in the gene was introduced in U2OS osteosarcoma cells using CRISPR-Cas9 technology resulting in a premature stop codon. Cancer cells lacking AURKC displayed no change in cell proliferation over 72 h but did migrate less and formed fewer colonies in soft agar. Whole transcriptome sequencing analysis uncovered over 400 differentially expressed genes in U2OS cells with and without AURKC. GO analysis revealed alterations in proteinaceous extracellular matrix genes including COL1A1. These data indicate that therapeutics targeting AURKC could decrease cancer cell metastasis and disease progression. Because AURKC is transcriptionally silenced in normal mitotic cells, its disruption could specifically target cancer cells limiting the toxic side effects associated with current therapeutics.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1984

Communications-imposed pilot workload - A comparison of sixteen estimation techniques

Sixteen potential metrics of mental workload were investigated in regard to their relative sensitivity to communications load and their differential intrusion on primary task performance. A moving-base flight simulator was used to present three cross-country flights to each of 30 subject pilots, each flight varying only in the difficulty of the inherent communications requirements. With the exception of the rating scale measures, which were obtained immediately post-flight, all measures were taken over a seven minute segment of the flight task. The results indicated that both the Modified Cooper-Harper and the workload Multi-descriptor rating scales were reliably sensitive to changes in communications load. Also, the secondary task measure of time estimation and the physiological measure of pupil diameter yielded sensitivity. As expected, those primary task measures which were direct measures of communicative performance were also sensitive to load, while aircraft control primary task measures were not, attesting to the task-specificity of such measures. Finally, the intrusion analysis revealed no differential interference between workload measures.

Casali, J. G.↗
DOE OSTI2023

Semiclassical theory and the Koopman-van Hove equation *

Abstract The phase space Koopman-van Hove (KvH) equation can be derived from the asymptotic semiclassical analysis of partial differential equations. Semiclassical theory yields the Hamilton–Jacobi equation for the complex phase factor and the transport equation for the amplitude. These two equations can be combined to form a nonlinear semiclassical version of the KvH equation in configuration space. There is a natural injection of configuration space solutions into phase space and a natural projection of phase space solutions onto configuration space. Hence, every solution of the configuration space KvH equation satisfies both the semiclassical phase space KvH equation and the Hamilton–Jacobi constraint. For configuration space solutions, this constraint resolves the paradox that there are two different conserved densities in phase space. For integrable systems, the KvH spectrum is the Cartesian product of a classical and a semiclassical spectrum. If the classical spectrum is eliminated, then, with the correct choice of Jeffreys–Wentzel–Kramers–Brillouin (JWKB) matching conditions, the semiclassical spectrum satisfies the Einstein–Brillouin–Keller quantization conditions which include the correction due to the Maslov index. However, semiclassical analysis uses different choices for boundary conditions, continuity requirements, and the domain of definition. For example, use of the complex JWKB method allows for the treatment of tunneling through the complexification of phase space. Finally, although KvH wavefunctions include the possibility of interference effects, interference is not observable when all observables are approximated as local operators on phase space. Observing interference effects requires consideration of nonlocal operations, e.g. through higher orders in the asymptotic theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Conversion of (NH 4 ) 2 [ReF 6 ] into ReO 2 mixed phases: A thermal analysis study

We report the thermal behavior of (NH 4 ) 2 [ReF 6 ] was evaluated in an alumina crucible using simultaneous thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) in an argon atmosphere. The TGA of (NH 4 ) 2 [ReF 6 ] is characterized by a single step decomposition while the DSC exhibits two exothermic peaks. Powder X-ray diffraction (PXRD) analyses of the decomposition products show the presence of a mixed ReO 2 phase. The formation of ReO2 is driven by the reaction of (NH 4 ) 2 [ReF 6 ] with Al 2 O 3 at the grain boundary of the alumina crucible. XRD peak broadenings due to the combined effect of crystallite size and lattice strain were evaluated using both Scherrer and Williamson-Hall methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1969

Rapid and precise analysis for calcium in blood serum

Differential absorption spectrophotometric technique, using murexide, gives a highly precise analysis of calcium in volumes of blood serum as small as 0.01 ml. The method of additions and proper timing allows compensation to be made for fading, variation in type of serum or plasma, and aging of the specimen.

Holtzman, R. B.↗
DOE OSTI2020

Kinetics of TATB and LX-17 Decomposition by Thermal Analysis

The kinetics of TATB decomposition have been investigated by thermal analysis (thermogravimetric analysis, TGA, and differential scanning calorimetry, DSC) at both LLNL and the University of Alabama Birmingham. This report summarizes progress in understanding from those results within the context of identifying the global reaction mechanism, i.e., sequential, autocatalytic, competitive, or some mixture thereof. A particularly important issue is how pressure affects both the reaction rate and enthalpy. The effect of pressure helps identify dominant mechanisms and construct and constrain a global mechanism that will work over a wide range of conditions. This memorandum is simply a snapshot of current progress and not a definitive interpretation. I have written it to organize work of others and my interpretations in a systematic manner with the intention of stimulating further advances in understanding. SDT data comes from Jen Montgomery at LLNL, and high-pressure DSC comes from Victoria Stanford and Sergey Vyazovkin at University of Alabama at Birmingham. Major observations and conclusions, some new and some not, are (1) outgassing below 150 °C prior to decomposition releases adsorbed water vapor, (2) outgassing between 150 and 250 °C may come primarily from intercalated water (3) initial thermal decomposition above 250 °C or so involves dehydration of TATB to create furazans, (4) quickly heating to higher temperatures in open pans with flowing gas leads primarily to TATB evaporation between 270 and 390 °C, (5) using a pinhole crucible at atmospheric pressure largely eliminates TATB sublimation, (6) at typical thermal analysis heat rates, the main stage of decomposition is described by a single mass loss process, and decomposition of residual material is spread over a wide range of thermal severity, (7) at typical thermal analysis heat rates and constant temperatures above 300 °C, heat release occurs in two overlapping peaks, with the first one a little faster than mass loss and the second on a little slower than mass loss, (8) total heat release increases significantly with heating rate and substantially with increased pressure, and (9) isothermal experiments at 340 °C indicate that the first exotherm increases by more with LX-17 than TATB, which suggests a possible chemical role of Kel-F decomposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1979

Stability of sequences generated by nonlinear differential systems

A local stability analysis is presented for both the analytic and numerical solutions of the initial value problem for a system of ordinary differential equations. It is shown that, using a proper choice of Liapunov function, a connected region of stable initial values of both the analytic solution and the one-leg k-step numerical solution can be approximated. Attention is given to the example of the two-dimensional problem involving the stability of the longitudinal equations of motion of a gliding jet aircraft.

Brown, R. L.↗