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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Anthelmintic drug ivermectin inhibits angiogenesis, growth and survival of glioblastoma through inducing mitochondrial dysfunction and oxidative stress

Glioblastoma is one of the most vascular brain tumour and highly resistant to current therapy. Targeting both glioblastoma cells and angiogenesis may present an effective therapeutic strategy for glioblastoma. In our work, we show that an anthelmintic drug, ivermectin, is active against glioblastoma cells in vitro and in vivo, and also targets angiogenesis. Ivermectin significantly inhibits growth and anchorage-independent colony formation in U87 and T98G glioblastoma cells. It induces apoptosis in these cells through a caspase-dependent manner. Ivermectin significantly suppresses the growth of two independent glioblastoma xenograft mouse models. In addition, ivermectin effectively targets angiogenesis through inhibiting capillary network formation, proliferation and survival in human brain microvascular endothelial cell (HBMEC). Mechanistically, ivermectin decreases mitochondrial respiration, membrane potential, ATP levels and increases mitochondrial superoxide in U87, T98G and HBMEC cells exposed to ivermectin. The inhibitory effects of ivermectin are significantly reversed in mitochondria-deficient cells or cells treated with antioxidants, further confirming that ivermectin acts through mitochondrial respiration inhibition and induction of oxidative stress. Importantly, we show that ivermectin suppresses phosphorylation of Akt, mTOR and ribosomal S6 in glioblastoma and HBMEC cells, suggesting its inhibitory role in deactivating Akt/mTOR pathway. Altogether, our work demonstrates that ivermectin is a useful addition to the treatment armamentarium for glioblastoma. Our work also highlights the therapeutic value of targeting mitochondrial metabolism in glioblastoma. - Highlights: • Ivermectin is effective in glioblastoma cells in vitro and in vivo. • Ivermectin inhibits angiogenesis. • Ivermectin induces mitochondrial dysfunction and oxidative stress. • Ivermectin deactivates Akt/mTOR signaling pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Down-regulation of TRAF4 targeting RSK4 inhibits proliferation, invasion and metastasis in breast cancer xenografts

Highlights: • Knockdown of TRAF4 inhibited the growth of xenograft tumors in nude mice. • Knockdown of TRAF4 significantly decreased the lung and liver metastases. • There is a negative correlation between TRAF4 and RSK4 mRNA and proteins. TRAF4 is interacting with RSK4 possibly by the induction of AKT/NF-κB signal axis. Ribosomal S6 protein kinase 4 (RSK4) was known as a novel tumor suppressor gene, and the tumor necrosis factor receptor-associated factor 4 (TRAF4) was linked to carcinogenesis. The purpose of this study is to further investigate the effect of the TRAF4 gene on cell proliferation, invasion and metastasis in vivo and explore whether there is an interaction between TRAF4 and RSK4 in breast cancer. MDA-MB-231 cells were transfected with lentivirus TRAF4-shRNA to specifically block the expression of TRAF4, or transfected with lentivirus negative-shRNA as a negative control. Four-six weeks female BALB/c nude mice were randomly assigned to three groups (n = 14): TRAF4-shRNA, negative and control, and then inoculated subcutaneously with the corresponding cells. In-vivo metastasis model was constructed by injecting above cells into tail vein. Tumor proliferation was assessed in terms of the tumor growth curve, tumor size and weight. Invasion and metastasis were evaluated by the histopathologic examination in lung or/and liver tissues. Measurement of TRAF4 and RSK4 expression and their correlation factors (AKT, NF-κB, TGF-β1, TNF-α, MMP2 and MMP9) were performed by immunohistochemistry, western blot or fluorescence quantitative RT-PCR. We found that the size and weight of tumors in TRAF4-shRNA group was significantly smaller than the negative and blank group, and the number of the lung and liver metastases lesions was also fewer (P < 0.05). And TRAF4 and its correlation factors (P-AKT, P-NF-κB, TGF-β1, TNF-α, MMP2 and MMP9) in the TRAF4-shRNA group were significantly decreased compared with the negative and blank group. However, the expression of RSK4 mRNA and protein in TRAF4-shRNA group were significantly increased. Collectively, TRAF4 knockdown significantly inhibited proliferation, invasion and metastasis in the xenograft nude mouse model, possibly involving in the interaction with RSK4 through down-regulation of AKT signaling pathway and then inactivating NF-κB pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Involvement of TOR signaling motif in the regulation of plant autophagy

Highlights: • The plant TOS motif core sequence interacting with Raptor was identified in ATG13 as well as S6K1 of the Arabidopsis. • Autophagy response was observed when the plant TOS core sequence was deleted from AtATG13. • Phosphorylation of AtATG13 was reduced significantly when the plant TOS core sequence was deleted. In our previous studies, we have demonstrated that a stretch of amino-acid sequences identified from Arabidopsis ribosomal S6 kinase 1 (AtS6K1) provided a plant version of the TOS (TOR-signaling) motif, mediating the interaction with the Raptor protein in the TOR (Target of Rapamycin) kinase complex. Here we report the presence of same element in Arabidopsis Autophagy related-13 (AtATG13) protein, which is a key component of the plant autophagy response. Its composition is nearly identical to that found in the AtS6K1 in the five-amino-acid core sequence, and the presence of this five-amino-acid sequence was found to be essential for its interaction with the Raptor protein. A mutant AtATG13 protein lacking this five-amino-acid element conferred an elevated autophagy response and could not effectively phosphorylated by TOR kinase activity, demonstrating its role in mediating the TOR signaling to the components that carry it as a possible TOS motif. A ligand-binding simulation model using the MM-PBSA method indicates that both of the five-amino-acid sequence elements of AtS6K1 and AtATG13 have strong probability of making stable interface with the Raptor binding pocket, corroborating our proposition for this element as the plant TOS motif.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

PB1 and UBA domains of p62 are essential for aggresome-like induced structure formation

Highlights: • P62’s PB1 and UBA domains are required for the induction of ALIS. • YFP-tagged p62 is not a very mobile protein in ALIS. • P62 binds preferentially to K63-linked ubiquitin chains. ALIS are large, transient, cytosolic aggregates that serve as storage compartments for ubiquitin-tagged defective ribosomal products. We determined the importance of the protein p62 in the formation of ALIS and demonstrated that two domains of p62—PB1 and UBA—are essential for ALIS assembly. Those two major binding domains of p62, also known as sequestosome 1, were shown to play a critical role in the formation of autophagosomes or cytoplasmic aggregates. Specifically, the PB1 domain is essential for self-oligomerization, and the UBA domain allows p62 to bind to polyubiquitin chains or ubiquitinated proteins. After stimulation of RAW 264.7 macrophages with lipopolysaccharide, we observed a significant decrease in the number of cells with ALIS. Importantly, cells overexpressing either a PB1 mutant or UBA-deleted p62 construct also exhibited a substantially diminished number of cells containing ALIS. Since both p62 and ubiquitin are found in ALIS, we evaluated the dynamics of YFP-tagged p62 in ALIS. In contrast to the findings of a previous study that evaluated GFP-tagged ubiquitin motility in ALIS, we determined that YFP-tagged p62 has very limited mobility. Lastly, we determined that GST–tagged full-length p62 binds to Lys-63-linked polyubiquitin chains but not to Lys-48-linked chains. Overall, our findings provide insight on the essential role that p62, particularly its PB1 and UBA domains, has in the formation of ALIS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Efficient mRNA delivery system utilizing chimeric VSVG-L7Ae virus-like particles

Highlights: • Generation of chimeric virus-like particles by fusion of VSV-G and L7Ae proteins. • VSVG-L7Ae VLPs efficiently incorporate and deliver mRNA into various human cell lines. • Inclusion of mRNA is mediated by RNA binding domain of L7Ae. The delivery of mRNA is advantageous over DNA delivery as it is transient and does not carry the risk of genomic DNA integration. However, there are currently few efficient mRNA delivery options available, especially for hard-to-transfect cell types, and thus new delivery methods are needed. To this end, we have established a novel mRNA delivery system utilizing chimeric virus-like particles (VLPs). We generated a novel VLP by fusing protein G of Vesicular stomatitis virus (VSV-G) with a ribosomal protein L7Ae of Archeoglobus fulgidus. This system allowed the efficient delivery of EGFP mRNA which was independent from the presence of BoxC/D motif in the mRNA sequence. Our VSVG-L7Ae VLP system demonstrated high transduction efficacy in hard-to-transfect cell lines, such as human induced pluripotent stem cells (iPS cells) and monocytes. In summary, this platform may serve as an efficient and transient transgene delivery tool for an mRNA of interest.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Ferricrocin, the intracellular siderophore of Trichoderma virens, is involved in growth, conidiation, gliotoxin biosynthesis and induction of systemic resistance in maize

Highlights: • TvTex10 deletion increases fungal growth rate and sensitivity to oxidative stress. • Mutants demonstrate decreased conidiation and gliotoxin production. • Root colonization is increased in mutant treated plants. • Induced systemic resistance in treated plants is reduced compared to the wild type. Fungal siderophores are known to be involved in iron acquisition and storage, as well as pathogenicity of mammals and plants. As avirulent plant symbionts, Trichoderma spp. colonize roots and induce resistance responses both locally and systemically. To study the role of intracellular siderophore(s) in Trichoderma-plant interactions, we have obtained mutants in a non-ribosomal peptide synthetase, TvTex10, that was predicted to be involved in intracellular siderophore(s) biosynthesis. This gene has a detectable basal level of expression and is also upregulated under iron-deplete conditions. This is unlike two other siderophore-encoding genes, which are tightly regulated by iron. Disruption of tex10 gene using homologous recombination resulted in mutants with enhanced growth rate, reduced conidiation and hyper-sensitivity to oxidative stress as compared to wildtype strain. The mutants also produced reduced levels of gliotoxin and dimethyl gliotoxin but have enhanced ability to colonize maize seedling roots. The mutants were also impaired in induction of induced systemic resistance (ISR) in maize against the foliar pathogen Cochliobolus heterostrophus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols

Here, the terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. We report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Lipid Corona Formation from Nanoparticle Interactions with Bilayers

While mixing nanoparticles with certain biological molecules can result in coronas that afford some control over how engineered nanomaterials interact with living systems, corona formation mechanisms remain enigmatic. Here, we report spontaneous lipid corona formation, i.e. without active mixing, upon attachment to stationary lipid bilayer model membranes and bacterial cell envelopes, and present ribosome-specific outcomes for multi-cellular organisms. Experiments show that polycation-wrapped particles disrupt the tails of zwitterionic lipids, increase bilayer fluidity, and leave the membrane with reduced ?-potentials. Computer simulations suggest that the contact ion pairing between the lipid headgroups and the polycations' ammonium groups leads to the formation of stable, albeit fragmented, lipid bilayer coronas, while microscopy shows fragmented bilayers around nanoparticles after interacting with Shewanella oneidensis. Our mechanistic insight can be used to improve control over nano-bio interactions and to help understand why some nanomaterial/ligand combinations are detrimental to organisms, like Daphnia magna, while others are not.

Olenick, Laura L.↗
DOE OSTI2023

The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses

Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.50 years ago, "herpes-type" viral particles were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes, but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ~300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Simultaneous Targeting of RSK and AKT Efficiently Inhibits YB-1-Mediated Repair of Ionizing Radiation-Induced DNA Double-Strand Breaks in Breast Cancer Cells

Y-box binding protein 1 (YB-1) overexpression is associated with chemotherapy- and radiation therapy resistance. Ionizing radiation (IR), receptor tyrosine kinase ligands, and mutation in KRAS gene stimulate activation of YB-1. YB-1 accelerates the repair of IR-induced DNA double-strand breaks (DSBs). Ribosomal S6 kinase (RSK) is the main kinase inducing YB-1 phosphorylation. We investigated the impact of RSK targeting on DSB repair and radiosensitivity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection

Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed “discontinuous transcription” that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules

We describe a rapid and convenient method of growing streptavidin (SA) monolayer crystals directly on holey-carbon EM grids. As expected, these SA monolayer crystals retain their biotin-binding function and crystalline order through a cycle of embedding in trehalose and, later, its removal. This fact allows one to prepare, and store for later use, EM grids on which SA monolayer crystals serve as an affinity substrate for preparing specimens of biological macromolecules. In addition, we report that coating the lipid-tail side of trehalose-embedded monolayer crystals with evaporated carbon appears to improve the consistency with which well-ordered, single crystals are observed to span over entire, 2 μm holes of the support films. Randomly biotinylated 70S ribosomes are used as a test specimen to show that these support films can be used to obtain a high-resolution cryo-EM structure

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural and mechanistic basis for protein glutamylation by the kinase fold

The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here, in this work, we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation

RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here, we use cryoelectron microscopy (cryo-EM) to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Gene-specific factor TFIIIA interacts with DNA and acts as an adaptor for TFIIIC-promoter interactions. We also visualize DNA binding of TFIIIB subunits, Brf1 and TBP (TATA-box binding protein), which results in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA within the complex undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the transcription initiation complex assembly on the 5S rRNA promoter and allow us to directly compare Pol III and Pol II transcription adaptations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

From data to knowledge: The future of multi-omics data analysis for the rhizosphere

The rhizosphere is the interface between the root system of a plant and its surrounding soil. The microbiome of the rhizosphere, which is the totality of all microbes present there, represents a complex microbial ecosystem that nourishes the terrestrial biosphere. In order to untangle the complexity of the rhizosphere, and of the rhizospheric microbiome in particular, an integrated multi-omics approach can be applied to reveal the composition of the rhizospheric microbiome (through 16S ribosomal amplicons and metagenomics), the functional properties of the microbiome (through metatranscriptomics and metaproteomics), and the signaling network within the rhizosphere (through metametabolomics). The successful application of integrated multi-omics to rhizospheric science depends on the availability of rhizosphere-specific data and on the appropriate software used to analyze omics data from the rhizosphere. Here, we analyze the availability of software suites that are normally applied to surrogate disciplines (e.g., soil and plants) but which can be used for rhizospheric science. We also identify potential issues, challenges, and opportunities for rhizosphere science.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Molecular dynamics simulations of large macromolecular complexes

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. Finally, these examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Revising the dynamic energy budget theory with a new reserve mobilization rule and three example applications to bacterial growth

Dynamic energy budget (DEB) theory has been applied to model a wide range of organisms, including microbes. In the standard DEB model, biomass is partitioned into reserve and structural compartments, where reserve biomass is mobilized in a pseudolinear manner (while the reserve biomass density, defined as the ratio between reserve and structural biomass, decays linearly) to drive maintenance and the growth of structural biomass (and extracellular enzyme production if it is considered). However, the linear dynamics of the reserve biomass density makes the standard DEB model incapable of explaining the slowdown of microbial growth at high reserve density that is caused by macromolecular crowding effect which reduces biochemical reaction rates (a typical situation occurs when microbes are experiencing severe moisture stress) and is inconsistent with the observation that intracellular enzymatic reactions generally follow non-linear kinetics. By partitioning biomass into reserve, kinetic, and structural compartments, we show here that the Equilibrium Chemistry Approximation (ECA) kinetics can be used to represent enzymatically catalyzed reserve biomass mobilization that can then drive the kinetic and structural biomass synthesis. This revised DEB model better represents the tradeoff in ribosome allocation for structural growth and internal enzyme production, is structurally compatible with metabolic models of cell individuals, and includes the standard DEB model and the popular compromise model as special cases for representing population growth. We then applied the revised DEB model to interpret components of bacterial respiration, their dependence on substrate availability, and emergent microbial carbon use efficiency dynamics for an exponentially growing population. We found that the revised DEB model enables a better understanding of bacterial substrates use (carbon in our examples) than that can be derived from a few other models in the literature. In particular, the revised DEB model explains why carbon use efficiency may first increase, then plateau, and finally decrease with growth rate (and substrate uptake rate), as a function of proteomics. Additionally, the revised DEB model explains why the kinetic biomass compartment needs to be divided to reasonably incorporate proteomic control of microbial growth.

59 BASIC BIOLOGICAL SCIENCES↗