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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The global dynamic of DNA methylation in response to heat stress revealed epigenetic mechanism of heat acclimation in Saccharina japonica

Saccharina japonica is an ecologically and economically important kelp in cold‐temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica . We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non‐coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho = 0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome‐ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.

Liu, Fuli↗
DOE OSTI2012

Structural Insight into the Ion-Exchange Mechanism of the Sodium/Calcium Exchanger

Sodium/calcium (Na{sup +}/Ca{sup 2+}) exchangers (NCX) are membrane transporters that play an essential role in maintaining the homeostasis of cytosolic Ca{sup 2+} for cell signaling. We demonstrated the Na{sup +}/Ca{sup 2+}-exchange function of an NCX from Methanococcus jannaschii (NCX{_}Mj) and report its 1.9 angstrom crystal structure in an outward-facing conformation. Containing 10 transmembrane helices, the two halves of NCX{_}Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at the center of the protein: one specific for Ca{sup 2+} and three that likely bind Na{sup +}. Two passageways allow for Na{sup +} and Ca{sup 2+} access to the central ion-binding sites from the extracellular side. Based on the symmetry of NCX{_}Mj and its ability to catalyze bidirectional ion-exchange reactions, we propose a structure model for the inward-facing NCX{_}Mj.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Quorum sensing modulates microbial community structure through regulation of secondary metabolites

Bacteria are recognized for their diverse metabolic capabilities, yet the impact of microbe-microbe interactions on multispecies community structure and dynamics is poorly understood. Cell-to-cell signaling in the form of quorum sensing (QS) often regulates secondary metabolite production and microbial interactions. Here, we examine how acylhomoserine lactone (AHL)-mediated QS impacts microbial community structure in a 10-member synthetic community of isolates from Populus deltoides . To explore the role of QS in microbial community structure and dynamics, we disrupted AHL signaling by exogenous addition of AiiA-lactonase, an enzyme that cleaves the lactone ring. Microbial community structure resulting from signal inactivation, as measured by 16S rRNA amplicon sequencing and secondary metabolite production, was assessed after successive passaging of the community. Further, we investigated the impact of quorum quenching on specific microbe-microbe interactions using pairwise inhibition assays. Our results indicate that AHL inactivation alters the relative abundance of dominant community members at later passages but does not impact the overall membership in the community. Quorum quenching significantly alters the metabolic profile in lactonase-treated communities. This metabolic alteration impacts microbe-microbe interactions through decreased inhibition of other community members. Together, these results indicate that QS impacts microbial community structure through the regulation of secondary metabolites in dominant members and that the membership of microbial communities can be relatively stable despite changes in metabolic profiles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

mSystems: Learning To Love Systems

We want this journal to be a forum for publication of research, tools, and data sets that are advancing our understanding of, or ability to investigate or interpret, microbiology systems. For example, I hope that mSystems will be a venue for research that elucidates the metabolic and cell-cell signaling mechanisms that underpin observed successional dynamics in microbial ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR

Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology. A recent large-scale bioinformatics analysis reignited the debate as to the importance of fatty acids in Archaea by presenting genetic evidence for the presence of enzymes required for anabolic and catabolic fatty acid metabolism across the archaeal domain. Here, we present direct biochemical evidence from gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for the presence of fatty acids in two members of the Crenarchaeota, Sulfolobus solfataricus and Ignicoccus hospitalis . This is the first report providing biochemical data for the existence of fatty acids in these Crenarchaeota, opening new discussions on energy balance and the potential for the discovery of new thermostable enzymes for industry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes

Protein kinases catalyze the transfer of a phosphate moiety from a phosphate donor to the substrate molecule, thus playing critical roles in cell signaling and metabolism. Although plant genomes contain more than 1000 genes that encode kinases, knowledge is limited about the function of each of these kinases. A major obstacle that hinders progress towards kinase characterization is functional redundancy. To address this challenge, we previously developed the rice kinase database (RKD) that integrated omics-scale data within a phylogenetics context.

Agriculture↗
DOE OSTI2023

Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis

Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M . brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

A Genetic Screen Reveals Arabidopsis Stomatal and/or Apoplastic Defenses against Pseudomonas syringae pv. tomato DC3000

Bacterial infection of plants often begins with colonization of the plant surface, followed by entry into the plant through wounds and natural openings (such as stomata), multiplication in the intercellular space (apoplast) of the infected tissues, and dissemination of bacteria to other plants. Historically, most studies assess bacterial infection based on final outcomes of disease and/or pathogen growth using whole infected tissues; few studies have genetically distinguished the contribution of different host cell types in response to an infection. The phytotoxin coronatine (COR) is produced by several pathovars of Pseudomonas syringae. COR-deficient mutants of P. s. tomato (Pst) DC3000 are severely compromised in virulence, especially when inoculated onto the plant surface. We report here a genetic screen to identify Arabidopsis mutants that could rescue the virulence of COR-deficient mutant bacteria. Among the susceptible to coronatine-deficient Pst DC3000 (scord) mutants were two that were defective in stomatal closure response, two that were defective in apoplast defense, and four that were defective in both stomatal and apoplast defense. Isolation of these three classes of mutants suggests that stomatal and apoplastic defenses are integrated in plants, but are genetically separable, and that COR is important for Pst DC3000 to overcome both stomatal guard cell- and apoplastic mesophyll cell-based defenses. Of the six mutants defective in bacterium-triggered stomatal closure, three are defective in salicylic acid (SA)-induced stomatal closure, but exhibit normal stomatal closure in response to abscisic acid (ABA), and scord7 is compromised in both SA- and ABA-induced stomatal closure. We have cloned SCORD3, which is required for salicylic acid (SA) biosynthesis, and SCORD5, which encodes an ATP-binding cassette (ABC) protein, AtGCN20/AtABCF3, predicted to be involved in stress-associated protein translation control. Identification of SCORD5 begins to implicate an important role of stress-associated protein translation in stomatal guard cell signaling in response to microbe-associated molecular patterns and bacterial infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Engineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments

CAM provides an excellent opportunity to engineer enhanced photosynthetic performance and water-use efficiency (WUE) into bioenergy crops. Our vision was to understand the enzymatic and regulatory pathways required for CAM in order to engineer CAM photosynthetic machinery into Arabidopsis and Populus. Major advances were made in understanding the molecular “parts list” necessary for engineering CAM through the sequencing the genomes and transcriptomes of several model and agronomically important CAM species including Agave, Ananas, Clusia, Kalanchoe, Mesembryanthemum, and Opuntia. Comparison of diel co-expression network analyses in Agave, Ananas, and Kalanchoe with expression patterns in C 3 photosynthesis species revealed the rescheduling of gene expression associated with stomatal opening and closing and led to the identification of many candidate CAM-related genes for further functional testing. Both RNAi-mediated gene silencing and CRISPR/Cas genome editing for gene knockout were used to investigate over 70 CAM-related enzymes, regulatory kinases/phosphatases, and transporters and 25 transcription factors implicated in playing key regulatory roles in CAM. Knockdown of key C 4 cycle enzymes within the carboxylation and decarboxylation modules of CAM not only perturbed CAM itself, but also altered the expression of core circadian clock components demonstrating that loss of CAM function also perturbs the central circadian clock and alters the regulatory patterns of key guard cell signaling genes that are linked with the characteristic inverse pattern of stomatal opening and closing during CAM. An advanced system for joining D.AN fragments from a universal library was developed that automatically maintains open reading frames (ORFs) and does not require linkers, adaptors, regions of sequence homology, amplification (or mutation for domestication) of fragments to function systems for the construction of gene circuits. Alternatively, Gibson assembly was used to create gene circuits consisting of up to 15 unique gene expression cassettes expressing either the core C 4 cycle of CAM comprising carboxylation or decarboxylation modules or both modules together. The expression of each gene cassette was driven by a drought-stress inducible 5’ regulatory region or promoter (and cognate 3’ terminator region) from A. thaliana so that CAM gene expression would be enhanced under conditions of water-deficit stress. These gene circuits were introduced into the C 3 photosynthesis model species A. thaliana. Expression of the nocturnal carboxylation module resulted in increased biomass and seed yield arising from net CO 2 fixation at night and malate accumulation typical of a CAM plant along with daytime CO 2 fixation typical of a C 3 photosynthesis plant. To create a leaf anatomy suited for the optimal performance of CAM in a C 3 photosynthesis plant, increased tissue succulence was engineered in A. thaliana (and Nicotiana sylvestris), which also improved biomass and seed yield and drought attenuation and improved salinity tolerance. The basic CAM Biodesign principles described in this report can be extended to increase the productivity and WUE of food and bioenergy crops and are expected to have broad applicability and ensure sustainable biofuel feedstock production in the face of the global climate crisis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development and implementation of an in situ high-resolution isotopic microscope for measuring metabolic interactions in soil mesocosms (Final Report)

Many of our planet’s ecosystems rely on the activities of soil microbial communities. These microbes have significant and wide-ranging effects: they metabolize carbon and other nutrients, interact with plants and fungi, and perform other processes important to soil health. However, our ability to directly observe the enzymatic and metabolic activities of microbes within soil is currently limited, not only by the complexity of soil microbial communities themselves, but also by the lack of experimental tools to study them and their molecular interactions in situ. These challenges hinder our understanding of the life-sustaining processes of biomass decomposition and the manner in which it contributes to the movement of freed carbon within soil ecosystems. Here we aimed to develop a novel ultrahigh-resolution isotopic microscope that combines complementary imaging modalities to gain insights into metabolic cycling in soil. This final report covers both the portion of this work that was initially completed at the University of North Carolina at Chapel Hill from 2018 to 2019 (as award DE-SC0019012) and then from 2020 to 2022 (2023 in NCE) at the University of Massachusetts Chan Medical School. This goal was to build an integrated platform consisting of fluorescence microscopy, Raman microspectroscopy, and nanospray desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (nanoDESI-FTICR-MS) to directly investigate microbial activities and molecular transformations occurring in soil by exploiting the use of both fluorescent labels and stable isotope probing. Specifically, our instrument was conceived as integrating: (A) fluorescence detection to localize soil microbes, identify bacteria taking up polysaccharides, and monitor gene expression of enzymes involved in decomposition; (B) Raman microspectroscopy to determine which microbes incorporate decomposition products into their biomass, as well as which decomposers are metabolically active; and (C) nanoDESI-FTICR-MS imaging to spatially probe, in real-time, the metabolites in the surrounding area, which we expect will reveal the distributions of the products of the enzymatic breakdown of polysaccharides, as well as specialized metabolites acting as cell-cell signals between decomposers. To enable these measurements, we exploited fluorescence-based probes to map the microbes that are enzymatically active (per A) and utilized stable isotope-labeled substrates to visualize both the microbial and molecular fate of decomposed biomass (B and C, respectively). To accomplish our goal, we combined the expertise of a multidisciplinary group of scientists to pursue the construction of this microscope and to investigate scientific questions that would be facilitated by such a capability. We aimed to employ this spatially informative, high-resolution isotopic microscope to visualize the critical steps of biomass degradation and the molecular fate of other environmentally relevant substrates within soil mesocosms. Accordingly, this technology will enhance our understanding of the microbial and metabolic interactions occurring within soil communities that are relevant to carbon degradation and other soil processes. The instrument has been developed and housed at EMSL, where it will be available to the entire EMSL User Base, enabling a variety of related DOE-relevant systems to be interrogated in the future by diverse scientific research groups.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers

The p21-activated kinase (PAK) family plays a versatile role in cell signaling by forming a hub of interactions. PAKs bind the GTPases like RAC and CDC42. Their proline-rich motifs bind SH3 adaptor proteins such as PIX and NCK. PAKs display nuclear localization signal sites and a potential Integrin binding site. No fully complete structure of the PAKs has been published; partial 3D structures of the PAK family kinases include portions of the auto-inhibited PAK1, GTPase bound to small peptides from PAKs, and the kinase domains from PAK1 and PAK4–6 (with small ligands in a few cases). This review focuses on exploring the intermolecular interaction regions in these 3D structures and we offer insights on the missing regions in crystal structure of the auto-inhibited PAK1. Understanding and modulation of PAK intermolecular interactions can pave the way for PAK blockers and biosensors.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Analysis of the myosins encoded in the recently completed Arabidopsis thaliana genome sequence

BACKGROUND: Three types of molecular motors play an important role in the organization, dynamics and transport processes associated with the cytoskeleton. The myosin family of molecular motors move cargo on actin filaments, whereas kinesin and dynein motors move cargo along microtubules. These motors have been highly characterized in non-plant systems and information is becoming available about plant motors. The actin cytoskeleton in plants has been shown to be involved in processes such as transportation, signaling, cell division, cytoplasmic streaming and morphogenesis. The role of myosin in these processes has been established in a few cases but many questions remain to be answered about the number, types and roles of myosins in plants. RESULTS: Using the motor domain of an Arabidopsis myosin we identified 17 myosin sequences in the Arabidopsis genome. Phylogenetic analysis of the Arabidopsis myosins with non-plant and plant myosins revealed that all the Arabidopsis myosins and other plant myosins fall into two groups - class VIII and class XI. These groups contain exclusively plant or algal myosins with no animal or fungal myosins. Exon/intron data suggest that the myosins are highly conserved and that some may be a result of gene duplication. CONCLUSIONS: Plant myosins are unlike myosins from any other organisms except algae. As a percentage of the total gene number, the number of myosins is small overall in Arabidopsis compared with the other sequenced eukaryotic genomes. There are, however, a large number of class XI myosins. The function of each myosin has yet to be determined.

NASA Discipline Plant Biology↗
NASA NTRS2009

Bulk Current Injection Testing of Cable Noise Reduction Techniques, 50 kHz to 400 MHz

This paper presents empirical results of cable noise reduction techniques as demonstrated using bulk current injection (BCI) techniques with radiated fields from 50 kHz - 400 MHz. It is a follow up to the two-part paper series presented at the Asia Pacific EMC Conference that focused on TEM cell signal injection. This paper discusses the effects of cable types, shield connections, and chassis connections on cable noise. For each topic, well established theories are compared with data from a real-world physical system.

Bradley, Arthur T.↗
NASA NTRS2010

Interactions of Ku70/80 with Double-Strand DNA: Energetic, Dynamics, and Functional Implications

Space radiation is a proficient inducer of DNA damage leading to mutation, aberrant cell signaling, and cancer formation. Ku is among the first responding proteins in nucleus to recognize and bind the DNA double strand breaks (DSBs) whenever they are introduced. Once loaded Ku works as a scaffold to recruit other repair factors of non-homologous end joining and facilitates the following repair processes. The crystallographic study of the Ku70/80 heterodimer indicate the core structure of this protein shows virtually no conformational change after binding with DNA. To investigate the dynamical features as well as the energetic characteristics of Ku-DNA binding, we conduct multi-nanosecond molecular dynamics simulations of a modeled Ku70/80 structure and several complexes with two 24-bp DNA duplexes. Free energy calculations show significant energy differences between the complexes with Ku bound at DSBs and those with Ku associated at an internal site of a chromosome. The results also reveal detailed interactions between different nucleotides and the amino acids along the DNA-binding cradle of Ku, indicating subtle binding preference of Ku at specific DNA sequences. The covariance matrix analyses along the trajectories demonstrate the protein is stimulated to undergo correlated motions of different domains once bound to DNA ends. Additionally, principle component analyses identify these low frequency collective motions suitable for binding with and translocation along duplex DNA. It is proposed that the modification of dynamical properties of Ku upon binding with DSBs may provide a signal for the further recruitment of other repair factors such as DNA-PKcs, XLF, and XRCC4.

Hu, Shaowen↗
NASA NTRS2019

Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae

A combination of spaceflight-relevant factors (fluid-shift and radiation) created a different gene expression profile than either factor individually. Some gene pathways including reduced transcriptional machinery, increased neurogenesis and neuropeptide production, and dysregulated cell structure and cell signaling. Gene expression differences can persist for at least 4 months after a 21- day exposure to a combination of fluid-shift and radiation in the brain tissue of mice. Brain-related transcriptional changes are dynamic during readaptation phase from exposure to spaceflight-like conditions, which may lead to long-term neurological consequences.

Overbey, Eliah G.↗
DOE OSTI2012

Microfluidic devices for the controlled manipulation of small volumes

A method for conducting a broad range of biochemical analyses or manipulations on a series of nano- to subnanoliter reaction volumes and an apparatus for carrying out the same are disclosed. The invention is implemented on a fluidic microchip to provide high serial throughput. In particular, the disclosed device is a microfabricated channel device that can manipulate nanoliter or subnanoliter reaction volumes in a controlled manner to produce results at rates of 1 to 10 Hz per channel. The reaction volumes are manipulated in serial fashion analogous to a digital shift register. The invention has application to such problems as screening molecular or cellular targets using single beads from split-synthesis combinatorial libraries, screening single cells for RNA or protein expression, genetic diagnostic screening at the single cell level, or performing single cell signal transduction studies.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis

SUMMARY Bioenergy sorghum is a highly productive drought tolerant C 4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES ( SbLOB ), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM ( dw2 ) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non‐meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin‐dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

TRPV4 promotes the migration and invasion of glioma cells via AKT/Rac1 signaling

Highlights: • TRPV4 is upregulated in glioma, and high-level of TRPV4 indicates a worse prognosis. • TRPV4 activation enhances the cell migration and invasion of glioma. • TRPV4-induced cell motility via AKT/Rac1 signaling pathway. Experimental evidence indicates a critical role of TRPV4 (Transient Receptor Potential Vanilloid 4) in controlling the cell migratory activity of multiple tumors. However, the oncogenic role of TRPV4 in glioma still remains elusive. In this study, we tried to investigate the oncogenic role of TRPV4 in glioma. We found that the expression levels of TRPV4 were upregulated in glioma and the high levels of TRPV4 indicated a worse prognosis in patients with glioma. TRPV4 was critical for glioma migration and invasion: activating TRPV4 by agonist GSK1016790 A enhanced glioma migration and invasion, while, the specific TRPV4 antagonist HC-067047 suppressed glioma migration and invasion. Mechanically, activated TRPV4 promoted the activation of Rac1 (Ras-related C3 botulinum toxin substrate 1) by targeting the AKT for phosphorylation, then enhanced glioma migration and invasion. All these results suggested that TRPV4 accelerates glioma migration and invasion through the AKT/Rac1 signaling, and TRPV4 might be considered as a potential target for glioma therapy.

60 APPLIED LIFE SCIENCES↗