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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

MO-FG-BRA-03: A Monte-Carlo Study of Cellular Dosimetry of Radioactive Gold-Palladium Nanoparticles

Purpose: Radioactive gold-palladium nanoparticles ({sup 103}Pd:Pd@Au NPs) are being developed for prostate cancer brachytherapy. Photons emitted by the radioisotope palladium (photon energy: 20.1 and 23.0 keV), interacting with gold-coating of NPs, lead to enhanced energy distribution in nucleus. Here, a simple cellular model was studied using detailed track-structure method. Methods: Geant4-DNA was used with auger electrons enabled. Biological cell was modeled as a sphere of radius r=5 µm that were immersed in a fluid containing large number of NPs at different concentrations (S=1, 2.15, 5.1, 17.2 mg-Au/g-H2O). Nucleus was modeled as a concentric sphere (r=3µm). Thickness of gold-coating on {sup 103}Pd core was 15nm, 20nm and 25nm, respectively. A scenario of NP diffusion was investigated, where S=5.1 mg-Au/g-H2O outside cell and S=1 mg-Au/g-H2O in cytoplasm. 10{sup 10} {sup 103}Pd decays were simulated for each combination of NP concentration and gold-coating. Results: A uniform increase in energy deposition (Edep) is observed in cell nucleus and the energy enhancement ratio (EER) is 1.16, 1.22 and 1.3 for 15nm, 20nm and 25nm of gold -coatings, respectively. Edep at the center of nucleus is increased by a factor of 1.47, 2.51 and 5.54 when the NP concentration in the cytoplasm increases from 1 mg-Au/g-H2O to 2.15, 5.10 and 17.2 mg-Au/g-H2O, respectively. When NPs diffuse into cytoplasm, the mean value of Edep in nucleus increases from 0.42 to 1.13 MeV per 10{sup 9} decays (GBq-Second) of {sup 103}Pd and the maximum value increases from 0.54 to 2.5 MeV per GBq-Second. Conclusion: These results suggest that {sup 103}Pd:Pd@Au NPs constitute a promising nanotherapeutic agent. Ongoing studies use transmission electron microscopy (TEM) images of prostate cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

XRN2 is required for the degradation of target RNAs by RNase H1-dependent antisense oligonucleotides

Antisense oligonucleotides (ASOs) can suppress the expression of a target gene by cleaving pre-mRNA and/or mature mRNA via RNase H1. Following the initial endonucleolytic cleavage by RNase H1, the target RNAs are degraded by a mechanism that is poorly understood. To better understand this degradation pathway, we depleted the expression of two major 5′ to 3′ exoribonucleases (XRNs), named XRN1 and XRN2, and analyzed the levels of 3′ fragments of the target RNAs in vitro. We found that the 3′ fragments of target pre-mRNA generated by ASO were almost completely degraded from their 5′ ends by nuclear XRN2 after RNase H1-mediated cleavage, whereas the 3′ fragments of mature mRNA were partially degraded by XRN2. In contrast to ASO, small interference RNA (siRNA) could reduce the expression level of only mature mRNA, and the 3′ fragment was degraded by cytoplasmic XRN1. Our findings indicate that the RNAs targeted by RNase H1-dependent ASO are rapidly degraded in the nucleus, contrary to the cytoplasmic degradation pathway mediated by siRNA. - Highlights: • We compared the degradation mechanism of the transcript targeted by ASO and siRNA. • We focused on two 5′ to 3′ exoribonucleases, cytoplasmic XRN1, and nuclear XRN2. • The 3′ fragment of target pre-mRNA generated by ASO was degraded by XRN2. • The 3′ fragment of target mRNA generated by ASO was partially degraded by XRN2. • XRN1 depletion promoted accumulation of the 3′ fragment of mRNA generated by siRNA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

TSG101 interacts with the androgen receptor and attenuates its expression through the endosome/lysosome pathway

Highlights: • TSG101interacts with AR and recruits AR to its associated late endosome structure. • TSG101 overexpression reduces AR protein level and its transactivation activity. • The downregulation of AR is mediated by TSG101 through lysosomal degradation. The androgen receptor (AR) signaling pathway plays a vital role in the normal development and function of the male reproductive organs. Dysregulation of the androgen-AR signaling pathway has been linked to prostate cancer. Here, we demonstrate that tumor susceptibility gene 101 (TSG101) regulates AR expression level via the endosome/lysosome degradation pathway. In LNCaP cells, TSG101 overexpression recruits the AR to TSG101-containing cytoplasmic vesicles resulting in reduced AR protein level and AR transactivation activity downregulation. Immunofluorescence microscopy demonstrated that TSG101-decorated cytoplasmic vesicles are associated with late endosomes/lysosomes and the AR could be found within the Lamp2 positive TSG101 vesicles upon lysosomal protease inhibitor treatment. Furthermore, chloroquine or bafilomycin A1 treatment was able to restore TSG101-mediated AR expression reduction. Based on these data, we conclude that the interaction of the AR and TSG101 leads to AR recruitment to TSG101-containing cytoplasmic vesicles and induces AR-attenuated expression through the late endosome/lysosome degradation pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Role of nucleocytoplasmic transport in interphase microtubule organization in fission yeast

The proper organization of microtubules is essential for many cellular functions. Microtubule organization and reorganization are highly regulated during the cell cycle, but the underlying mechanisms remain elusive. Here we characterized unusual interphase microtubule organization in fission yeast nuclear export mutant crm1-124. The mutant cells have an intranuclear microtubule bundle during interphase that pushes the nuclear envelope to assume a protruding morphology. We showed that the formation of this protruding microtubule bundle requires the nuclear accumulation of two microtubule-associated proteins (MAPs), Alp14/TOG and Mal3/EB1. Interestingly, the forced accumulation of Alp14 in the nucleus of wild type cells is sufficient to form the intranuclear microtubule bundle. Furthermore, the frequency of the intranuclear microtubule formation by Alp14 accumulated in the nucleus is prominently increased by a reduction in the nucleation activity of interphase cytoplasmic microtubules. We propose that properly regulated nucleocytoplasmic transport and maintained activity of cytoplasmic microtubule nucleation during interphase are important for the proper organization of interphase cytoplasmic microtubules.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells—a potential cause of neurodegeneration in AOA4 patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Epstein–Barr virus glycoprotein gM can interact with the cellular protein p32 and knockdown of p32 impairs virus

The Epstein–Barr virus glycoprotein complex gMgN has been implicated in assembly and release of fully enveloped virus, although the precise role that it plays has not been elucidated. We report here that the long predicted cytoplasmic tail of gM is not required for complex formation and that it interacts with the cellular protein p32, which has been reported to be involved in nuclear egress of human cytomegalovirus and herpes simplex virus. Although redistribution of p32 and colocalization with gM was not observed in virus infected cells, knockdown of p32 expression by siRNA or lentivirus-delivered shRNA recapitulated the phenotype of a virus lacking expression of gNgM. A proportion of virus released from cells sedimented with characteristics of virus lacking an intact envelope and there was an increase in virus trapped in nuclear condensed chromatin. The observations suggest the possibility that p32 may also be involved in nuclear egress of Epstein–Barr virus. - Highlights: • The predicted cytoplasmic tail of gM is not required to complex with gN. • Cellular p32 can interact with the predicted cytoplasmic tail of EBV gM. • Knockdown of p32 recapitulates the phenotype of virus lacking the gNgM complex.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The cytoskeletal inhibitors latrunculin A and blebbistatin exert antitumorigenic properties in human hepatocellular carcinoma cells by interfering with intracellular HuR trafficking

The impact of the RNA-binding protein HuR for the post-transcriptional deregulation of tumor-relevant genes is well established. Despite of elevations in HuR expression levels, an increase in cytoplasmic HuR abundance in many cases correlates with a high grade of malignancy. Here, we demonstrated that administration of the actin-depolymerizing macrolide latrunculin A, or blebbistatin, an inhibitor of myosin II ATPase activity, caused a dose- and time-dependent reduction in the high cytoplasmic HuR content of HepG2 and Huh7 hepatocellular carcinoma (HCC) cells. Subcellular fractionation revealed that in addition, both inhibitors strongly attenuated cytoskeletal and membrane-bound HuR abundance and conversely increased the HuR amount in nuclear cell fractions. Concomitant with changes in intracellular HuR localization, both cytoskeletal inhibitors markedly decreased the half-lives of cyclooxygenase-2 (COX-2), cyclin A and cyclin D{sub 1} encoding mRNAs resulting in a significant reduction in their expression levels in HepG2 cells. Importantly, a similar reduction in the expression of these HuR targets was achieved by a RNA interference (RNAi)-mediated knockdown of either HuR or nonmuscle myoin IIA. Using polysomal fractionation, we further demonstrate that the decrease in cytoplasmic HuR by latrunculin A or blebbistatin is accompanied by a marked change in the allocation of HuR and its mRNA cargo from polysomes to ribonucleoprotein (RNP) particles. Functionally, the basal migration and prostaglandin E{sub 2} synthesis are similarly impaired in inhibitor-treated and stable HuR-knockdown HepG2 cells. Our data demonstrate that interfering with the actomyosin-dependent HuR trafficking may comprise a valid therapeutic option for antagonizing pathologic posttranscriptional gene expression by HuR and furthermore emphasize the potential benefit of HuR inhibitory strategies for treatment of HCC. - Highlights: • We tested the effects of latrunculin A and blebbistatin on different HuR activities. • Both cytoskeletal inhibitors disturbed the RNP-polysome HuR allocation in HepG2 cells. • Accordingly, both inhibitors reduced the stability and levels of HuR controlled mRNAs. • Functionally, important HuR-triggered cell functions were impaired by both compounds. • Targeting of HuR trafficking implies a useful approach for novel antitumor therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

6-Shogaol induces caspase-independent paraptosis in cancer cells via proteasomal inhibition

Highlights: • 6-Shogaol induced cytoplasmic vacuolation and death in breast and lung cancer cells. • Absence of caspase cleavage and DNA fragmentation proves its non-apoptotic nature. • Persistence of death in presence of autophagic inhibitors certifies it to be non-autophagic cell death. • It is found to inhibit the proteasome by binding to the β5 chymotrypsin subunit. • 6-Shogaol increases level of ER stress markers like Bip and CHOP in treated cancer cells. An α, β-unsaturated carbonyl compound of ginger, 6-Shogaol (6S), induced extensive cytoplasmic vacuolation and cell death in breast cancer cell (MDA-MB-231) and non-small lung cancer (A549) cells. In the presence of autophagic inhibitors the cells continued to exhibit cytoplasmic vacuolation and cell death clearly distinguishing it from the classic autophagic process. 6S induced death did not exhibit the characteristic apoptotic features like caspase cleavage, phosphatidyl serine exposure and DNA fragmentation. The immunofluorescence with the Endoplasmic Reticulum (ER) resident protein, calreticulin indicated that the vacuoles were of ER origin, typical of paraptosis. This was supported by the increase in level of microtubule associated protein light chain 3B (LC3 I and LC3 II) and polyubiquitin binding protein, p62. The level of ER stress markers like polyubiquitinated proteins, Bip and CHOP also consistently increased. We have found that 6S inhibits the 26S proteasome. The proteasomal inhibitory activity was elucidated by a) molecular docking of 6S onto the active site of β5 subunit and b) reduced fluorescence by the fluorogenic substrate of the chymotrypsin-like subunit. In conclusion these studies demonstrate for the first time that proteasomal inhibition by 6S induces cell death via paraptosis. So 6-shogaol may act as a template for anti-cancer lead discovery against the apoptosis resistant cancer cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Nuclear speed and cycle length co-vary with local density during syncytial blastoderm formation in a cricket

Abstract The blastoderm is a broadly conserved stage of early animal development, wherein cells form a layer at the embryo’s periphery. The cellular behaviors underlying blastoderm formation are varied and poorly understood. In most insects, the pre-blastoderm embryo is a syncytium: nuclei divide and move throughout the shared cytoplasm, ultimately reaching the cortex. In Drosophila melanogaster , some early nuclear movements result from pulsed cytoplasmic flows that are coupled to synchronous divisions. Here, we show that the cricket Gryllus bimaculatus has a different solution to the problem of creating a blastoderm. We quantified nuclear dynamics during blastoderm formation in G. bimaculatus embryos, finding that: (1) cytoplasmic flows are unimportant for nuclear movement, and (2) division cycles, nuclear speeds, and the directions of nuclear movement are not synchronized, instead being heterogeneous in space and time. Moreover, nuclear divisions and movements co-vary with local nuclear density. We show that several previously proposed models for nuclear movements in D. melanogaster cannot explain the dynamics of G. bimaculatus nuclei. We introduce a geometric model based on asymmetric pulling forces on nuclei, which recapitulates the patterns of nuclear speeds and orientations of both unperturbed G. bimaculatus embryos, and of embryos physically manipulated to have atypical nuclear densities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization

Although as many as half of all proteins are thought to require a metal cofactor, the metalloproteomes of microorganisms remain relatively unexplored. Microorganisms from different environments are likely to vary greatly in the metals that they assimilate, not just among the metals with well-characterized roles but also those lacking any known function. Herein we investigated the metal utilization of two microorganisms that were isolated from very similar environments and are of interest because of potential roles in the immobilization of heavy metals, such as uranium and chromium. The metals assimilated and their concentrations in the cytoplasm of Desulfovibrio vulgaris strain Hildenborough (DvH) and Enterobacter cloacae strain Hanford (EcH) varied dramatically, with a larger number of metals present in Enterobacter. For example, a total of 9 and 19 metals were assimilated into their cytoplasmic fractions, respectively, and DvH did not assimilate significant amounts of zinc or copper whereas EcH assimilated both. However, bioinformatic analysis of their genome sequences revealed a comparable number of predicted metalloproteins, 813 in DvH and 953 in EcH. These allowed some rationalization of the types of metal assimilated in some cases (Fe, Cu, Mo, W, V) but not in others (Zn, Nd, Ce, Pr, Dy, Hf and Th). It was also shown that U binds an unknown soluble protein in EcH but this incorporation was the result of extracellular U binding to cytoplasmic components after cell lysis.

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

Membrane permeabilization by conjugated oligoelectrolytes accelerates whole-cell catalysis

Conjugated oligoelectrolytes (COEs) boost the electrical performance of a wide range of bioelectrochemical systems, yet their mechanism of action remains incompletely understood. One possible mode of action is that COEs permeabilize the cell envelope. We thus examined the effect of tetracationic COE, DSSN+, on the permeability of the inner and outer membrane of Escherichia coli by detecting extracellular activity of normally periplasmic and cytoplasmic enzymes. DSSN+ increases the release of the periplasmic enzyme alkaline phosphatase (ALP) up to 20-fold, but does not significantly change the release of the cytoplasmic enzyme β-galactosidase. Additionally, DSSN+ caused a 2-fold increase in the turnover of a cytoplasmic substrate. These studies present a more complete understanding of the mechanism of action in bioelectrochemical systems and pivot future applications of COEs towards a method for improving whole-cell catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Harnessing the periplasm of bacterial cells to develop biocatalysts for the biosynthesis of highly pure chemicals

ABSTRACT Although biocatalytic transformation has shown great promise in chemical synthesis, there remain significant challenges in controlling high selectivity without the formation of undesirable by-products. For instance, few attempts to construct biocatalysts for de novo synthesis of pure flavin mononucleotide (FMN) have been successful, due to riboflavin (RF) accumulating in the cytoplasm and being secreted with FMN. To address this problem, we show here a novel biosynthesis strategy, compartmentalizing the final FMN biosynthesis step in the periplasm of an engineered Escherichia coli strain. This construct is able to overproduce FMN with high specificity (92.4% of total excreted flavins). Such a biosynthesis approach allows isolation of the final biosynthesis step from the cytoplasm to eliminate undesirable byproducts, providing a new route to develop biocatalysts for the synthesis of highpurity chemicals. IMPORTANCE The periplasm of Gram-negative bacterial hosts is engineered to compartmentalize the final biosynthesis step from the cytoplasm. This strategy is promising for the overproduction of high-value products with high specificity. We demonstrate the successful implementation of this strategy in microbial production of highly pure FMN.

Yang, Yun↗
DOE OSTI2016

13 C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13 C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%.

-omics data↗
DOE OSTI2017

Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123

Kap123, a major karyopherin protein of budding yeast, recognizes the nuclear localization signals (NLSs) of cytoplasmic histones H3 and H4 and translocates them into the nucleus during DNA replication. Mechanistic questions include H3- and H4-NLS redundancy toward Kap123 and the role of the conserved diacetylation of cytoplasmic H4 (K5ac and K12ac) in Kap123-mediated histone nuclear translocation. Here, we report crystal structures of full-length Kluyveromyces lactis Kap123 alone and in complex with H3- and H4-NLSs. Structures reveal the unique feature of Kap123 that possesses two discrete lysine-binding pockets for NLS recognition. Structural comparison illustrates that H3- and H4-NLSs share at least one of two lysine-binding pockets, suggesting that H3- and H4-NLSs are mutually exclusive. Additionally, acetylation of key lysine residues at NLS, particularly H4-NLS diacetylation, weakens the interaction with Kap123. These data support that cytoplasmic histone H4 diacetylation weakens the Kap123-H4-NLS interaction thereby facilitating histone Kap123-H3-dependent H3:H4/Asf1 complex nuclear translocation.

An, Sojin↗
NASA NTRS1984

Influence of clinostat rotation on fertilized amphibian egg pattern specification

Pattern specification in fertile Xenopus eggs rotated on horizontal clinostats was monitored with respect to primary embryonic axis formation, subsequent morphogenesis, and compartmentalization of the cytoplasm. At the speeds of 1 to 24 rpm (which are believed to simulate microgravity) a large percentage of eggs developed normal axial structures. Eggs clinostated at 12 rpm showed a randomization of dorsal/ventral polarity. The cytoplasmic compartments showed some clinostat effects but no abnormal mixing, disruption or dislocation of compartments. It is predicted that Xenopus eggs fertilized and allowed to develop in space will retain normal cytoplasmic density compartments, establish primary axes and undergo normal morphogenesis in space. Their dorsal/ventral polarity may not, however, be determined by the sperm entrance site (as is the case for 1 g eggs).

Neff, A. W.↗
NASA NTRS1986

Distribution of calmodulin in corn seedlings - Immunocytochemical localization in coleoptiles and root apices

Immunofluorescence techniques have been used to study the distribution of calmodulin in several tissues in etiolated corn (Zea mays, var. Bear Hybrid) seedlings. Uniform staining was seen in the background cytoplasm of most cell types. Cell walls and vacuoles were not stained. In coleoptile mesophyll cells the nucleoplasm of most nuclei was stained as was the stroma of most amyloplasts. The lumen border of mature tracheary elements in coleoptiles also stained. In the rootcap the most intensely stained regions were the cytoplasms of columella cells and of the outermost cells enmeshed in the layer of secreted slime. Nuclei in the rootcap cells did not stain distinctly, but those in all cell types of the root meristem did. Also in the root meristem, the cytoplasm of metaxylem elements stained brightly. These results are compared and contrasted with previous data on the localization of calmodulin in pea root apices and epicotyls and discussed in relation to current hypotheses on mechanisms of gravitropism.

Dauwalder, M.↗