Progesterone-Mediated Non-Classical Signaling.

PubMed

Garg, Deepika; Ng, Sinnie Sin Man; Baig, K Maravet; Driggers, Paul; Segars, James

2017-09-01

Progesterone is essential for pregnancy maintenance and menstrual cycle regulation. Hormone action has been primarily ascribed to the well-characterized classical signaling pathway involving ligand binding, activation of nuclear progesterone receptors (PRs), and subsequent activation of genes containing progesterone response elements (PREs). Recent studies have revealed progesterone actions via non-classical signaling pathways, often mediated by non-genomic signaling. Progesterone signaling, in conjunction with growth factor signaling, impacts on the function of growth factors and regulates important physiological actions such as cell growth and remodeling, as well as apoptosis. This review focuses on non-classical progesterone signaling pathways, both including and excluding PR, and highlights how research in this area will provide a better understanding of progesterone actions and may inform novel therapeutic strategies. Copyright © 2017. Published by Elsevier Ltd.

Nuclear delivery of a therapeutic peptide by long circulating pH-sensitive liposomes: benefits over classical vesicles.

PubMed

Ducat, E; Deprez, J; Gillet, A; Noël, A; Evrard, B; Peulen, O; Piel, G

2011-11-28

The purpose of this study is to propose a suitable vector combining increased circulation lifetime and intracellular delivery capacities for a therapeutic peptide. Long circulating classical liposomes [SPC:CHOL:PEG-750-DSPE (47:47:6 molar% ratio)] or pH-sensitive stealth liposomes [DOPE:CHEMS:CHOL:PEG(750)-DSPE (43:21:30:6 molar% ratio)] were used to deliver a therapeutic peptide to its nuclear site of action. The benefit of using stealth pH-sensitive liposomes was investigated and formulations were compared to classical liposomes in terms of size, shape, charge, encapsulation efficiency, stability and, most importantly, in terms of cellular uptake. Confocal microscopy and flow cytometry were used to evaluate the intracellular fate of liposomes themselves and of their hydrophilic encapsulated material. Cellular uptake of peptide-loaded liposomes was also investigated in three cell lines: Hs578t human epithelial cells from breast carcinoma, MDA-MB-231 human breast carcinoma cells and WI-26 human diploid lung fibroblast cells. The difference between formulations in terms of peptide delivery from the endosome to the cytoplasm and even to the nucleus was investigated as a function of time. Characterization studies showed that both formulations possess acceptable size, shape and encapsulation efficiency but cellular uptake studies showed the important benefit of the pH-sensitive formulation over the classical one, in spite of liposome PEGylation. Indeed, stealth pH-sensitive liposomes were able to deliver hydrophilic materials strongly to the cytoplasm. Most importantly, when encapsulated in pH-sensitive stealth liposomes, the peptide was able to reach the nucleus of tumorigenic and non tumorigenic breast cancer cells. Copyright © 2011 Elsevier B.V. All rights reserved.

The nuclear proteome of Trypanosoma brucei

PubMed Central

Goos, Carina; Dejung, Mario; Janzen, Christian J.; Butter, Falk

2017-01-01

Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes. PMID:28727848

G protein-coupled receptor 30 in tumor development.

PubMed

Wang, Dengfeng; Hu, Lina; Zhang, Guonan; Zhang, Lin; Chen, Chen

2010-08-01

Estrogen plays several important physiological and pathological functions in not only reproductive system but many other systems as well. Its transcriptional activation has been traditionally described as being mediated by classic nuclear estrogen receptors (ERs). It is however established recently that a novel functional estrogen transmembrane receptor, G protein-coupled receptor 30 (GPR30), modulates both rapid non-genomic events and genomic transcriptional events of estrogen. It has been demonstrated that GPR30 promotes the progress of estrogen-related tumors through mitogen-activated protein kinase (MAPK) signaling pathways. Effects mediated by GPR30 are maintained when classic ERs are absent or blocked. In addition, GPR30 is involved in drug resistance, which is often occurring during cancer treatments. All these new findings strongly imply that GPR30 may be an important therapeutic target for estrogen-related tumors. Simultaneously blocking both GPR30 and classic ERs may be a better strategy for the treatment of estrogen-related tumors.

Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence*

PubMed Central

Tsujii, Akira; Miyamoto, Yoichi; Moriyama, Tetsuji; Tsuchiya, Yuko; Obuse, Chikashi; Mizuguchi, Kenji; Oka, Masahiro; Yoneda, Yoshihiro

2015-01-01

Nucleocytoplasmic trafficking is a fundamental cellular process in eukaryotic cells. Here, we demonstrated that retinoblastoma-binding protein 4 (RBBP4) functions as a novel regulatory factor to increase the efficiency of importin α/β-mediated nuclear import. RBBP4 accelerates the release of importin β1 from importin α via competitive binding to the importin β-binding domain of importin α in the presence of RanGTP. Therefore, it facilitates importin α/β-mediated nuclear import. We showed that the importin α/β pathway is down-regulated in replicative senescent cells, concomitant with a decrease in RBBP4 level. Knockdown of RBBP4 caused both suppression of nuclear transport and induction of cellular senescence. This is the first report to identify a factor that competes with importin β1 to bind to importin α, and it demonstrates that the loss of this factor can trigger cellular senescence. PMID:26491019

Nuclear localisation of 53BP1 is regulated by phosphorylation of the nuclear localisation signal.

PubMed

von Morgen, Patrick; Lidak, Tomas; Horejsi, Zuzana; Macurek, Libor

2018-06-01

Repair of damaged DNA is essential for maintaining genomic stability. TP53-binding protein 1 (53BP1) plays an important role in repair of the DNA double-strand breaks. Nuclear localisation of 53BP1 depends on importin β and nucleoporin 153, but the type and location of 53BP1 nuclear localisation signal (NLS) have yet to be determined. Here, we show that nuclear import of 53BP1 depends on two basic regions, namely 1667-KRK-1669 and 1681-KRGRK-1685, which are both needed for importin binding. Lysine 1667 is essential for interaction with importin and its substitution to arginine reduced nuclear localisation of 53BP1. Furthermore, we have found that CDK1-dependent phosphorylation of 53BP1 at S1678 impairs importin binding during mitosis. Phosphorylation-mimicking mutant S1678D showed reduced nuclear localisation, suggesting that phosphorylation of the NLS interferes with nuclear import of the 53BP1 CONCLUSIONS: We show that 53BP1 contains a classical bipartite NLS 1666-GKRKLITSEEERSPAKRGRKS-1686, which enables the importin-mediated nuclear transport of 53BP1. Additionally, we found that posttranslational modification within the NLS region can regulate 53BP1 nuclear import. Our results indicate that integrity of the NLS is important for 53BP1 nuclear localisation. Precise mapping of the NLS will facilitate further studies on the effect of posttranslational modifications and somatic mutations on the nuclear localisation 53BP1 and DNA repair. © 2018 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kiriyama, Takao; Hirano, Makito; Asai, Hirohide

Triple A syndrome is an autosomal recessive neurological disease, mimicking motor neuron disease, and is caused by mutant ALADIN, a nuclear-pore complex component. We recently discovered that the pathogenesis involved impaired nuclear import of DNA repair proteins, including DNA ligase I and the cerebellar ataxia causative protein aprataxin. Such impairment was overcome by fusing classical nuclear localization signal (NLS) and 137-aa downstream sequence of XRCC1, designated stretched NLS (stNLS). We report here that the minimum essential sequence of stNLS (mstNLS) is residues 239-276, downsized by more than 100 aa. mstNLS enabled efficient nuclear import of DNA repair proteins in patientmore » fibroblasts, functioned under oxidative stress, and reduced oxidative-stress-induced cell death, more effectively than stNLS. The stress-tolerability of mstNLS was also exerted in control fibroblasts and neuroblastoma cells. These findings may help develop treatments for currently intractable triple A syndrome and other oxidative-stress-related neurological diseases, and contribute to nuclear compartmentalization study.« less

A Highly Organized Structure Mediating Nuclear Localization of a Myb2 Transcription Factor in the Protozoan Parasite Trichomonas vaginalis ▿ †

PubMed Central

Chu, Chien-Hsin; Chang, Lung-Chun; Hsu, Hong-Ming; Wei, Shu-Yi; Liu, Hsing-Wei; Lee, Yu; Kuo, Chung-Chi; Indra, Dharmu; Chen, Chinpan; Ong, Shiou-Jeng; Tai, Jung-Hsiang

2011-01-01

Nuclear proteins usually contain specific peptide sequences, referred to as nuclear localization signals (NLSs), for nuclear import. These signals remain unexplored in the protozoan pathogen, Trichomonas vaginalis. The nuclear import of a Myb2 transcription factor was studied here using immunodetection of a hemagglutinin-tagged Myb2 overexpressed in the parasite. The tagged Myb2 was localized to the nucleus as punctate signals. With mutations of its polybasic sequences, 48KKQK51 and 61KR62, Myb2 was localized to the nucleus, but the signal was diffusive. When fused to a C-terminal non-nuclear protein, the Myb2 sequence spanning amino acid (aa) residues 48 to 143, which is embedded within the R2R3 DNA-binding domain (aa 40 to 156), was essential and sufficient for efficient nuclear import of a bacterial tetracycline repressor (TetR), and yet the transport efficiency was reduced with an additional fusion of a firefly luciferase to TetR, while classical NLSs from the simian virus 40 T-antigen had no function in this assay system. Myb2 nuclear import and DNA-binding activity were substantially perturbed with mutation of a conserved isoleucine (I74) in helix 2 to proline that altered secondary structure and ternary folding of the R2R3 domain. Disruption of DNA-binding activity alone by point mutation of a lysine residue, K51, preceding the structural domain had little effect on Myb2 nuclear localization, suggesting that nuclear translocation of Myb2, which requires an ordered structural domain, is independent of its DNA binding activity. These findings provide useful information for testing whether myriad Mybs in the parasite use a common module to regulate nuclear import. PMID:22021237

Nuclear import of Nkx2-2 is mediated by multiple pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Wenbo; Xu, PengPeng; Guo, YingYing

Nkx2-2 homeoprotein is essential for the development of the central nervous system and pancreas. Although the nuclear localization signals of Nkx2-2 have been identified, the responsible transport receptor is still unknown. Here, we demonstrate that imp α1 not only interacts with Nkx2-2 but also transports it into the nucleus in vitro by acting together with imp β1. However, the nuclear import of Nkx2-2 in cells was not inhibited in response to knockdown expression of endogenous imp β1 or over-expression of Bimax2. Furthermore, imp β1 and imp 13, but not imp 4, directly interact with Nkx2-2 and are capable of transporting Nkx2-2more » in an in vitro import assay. By GST pull-down assay, we demonstrate that mutation of NLS1 or NLS2 has no effect on interaction with imp α1 or imp 13, but significantly reduced binding to imp β1. Thus, the nuclear import of Nkx2-2 is mediated not only by the classical import pathway but also directly by imp β1 or imp 13.« less

Baculovirus LEF-11 nuclear localization signal is important for viral DNA replication.

PubMed

Chen, Tingting; Dong, Zhanqi; Hu, Nan; Hu, Zhigang; Dong, Feifan; Jiang, Yaming; Li, Jun; Chen, Peng; Lu, Cheng; Pan, Minhui

2017-06-15

Baculovirus LEF-11 is a small nuclear protein that is involved in viral late gene transcription and DNA replication. However, the characteristics of its nuclear localization signal and its impact on viral DNA replication are unknown. In the present study, systemic bioinformatics analysis showed that the baculovirus LEF-11 contains monopartite and bipartite classical nuclear localization signal sequences (cNLSs), which were also detected in a few alphabaculovirus species. Localization of representative LEF-11 proteins of four baculovirus genera indicated that the nuclear localization characteristics of baculovirus LEF-11 coincided with the predicted results. Moreover, Bombyx mori nucleopolyhedrovirus (BmNPV) LEF-11 could be transported into the nucleus during viral infection in the absence of a cNLSs. Further investigations demonstrated that the NLS of BmNPV LEF-11 is important for viral DNA replication. The findings of the present study indicate that the characteristics of the baculovirus LEF-11 protein and the NLS is essential to virus DNA replication and nuclear transport mechanisms. Copyright © 2017 Elsevier B.V. All rights reserved.

Report on the Implementation of Homogeneous Nucleation Scheme in MARMOT-based Phase Field Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2013-09-30

In this report, we summarized our effort in developing mesoscale phase field models for predicting precipitation kinetics in alloys during thermal aging and/or under irradiation in nuclear reactors. The first part focused on developing a method to predict the thermodynamic properties of critical nuclei such as the sizes and concentration profiles of critical nuclei, and nucleation barrier. These properties are crucial for quantitative simulations of precipitate evolution kinetics with phase field models. Fe-Cr alloy was chosen as a model alloy because it has valid thermodynamic and kinetic data as well as it is an important structural material in nuclear reactors.more » A constrained shrinking dimer dynamics (CSDD) method was developed to search for the energy minimum path during nucleation. With the method we are able to predict the concentration profiles of the critical nuclei of Cr-rich precipitates and nucleation energy barriers. Simulations showed that Cr concentration distribution in the critical nucleus strongly depends on the overall Cr concentration as well as temperature. The Cr concentration inside the critical nucleus is much smaller than the equilibrium concentration calculated by the equilibrium phase diagram. This implies that a non-classical nucleation theory should be used to deal with the nucleation of Cr precipitates in Fe-Cr alloys. The growth kinetics of both classical and non-classical nuclei was investigated by the phase field approach. A number of interesting phenomena were observed from the simulations: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrated that it is critical to introduce the correct critical nuclei into phase field modeling in order to correctly capture the kinetics of precipitation. In most alloys the matrix phase and precipitate phase have different concentrations as well as different crystal structures. For example, Cu precipitates in FeCu alloys have fcc crystal structure while the matrix Fe-Cu solid solution has bcc structure at low temperature. The WBM model and KimS model, where both concentrations and order parameters are chosen to describe the microstructures, are commonly used to model precipitations in such alloys. The WBM and KimS models have not been implemented into Marmot yet. In the second part of this report, we focused on implementing the WBM and KimS models into Marmot. The Fe-Cu alloys, which are important structure materials in nuclear reactors, was taken as the model alloys to test the models.« less

Cell permeability and nuclear DNA staining by propidium iodide in basidiomycetous yeasts.

PubMed

Zhang, Ning; Fan, Yuxuan; Li, Chen; Wang, Qiming; Leksawasdi, Noppol; Li, Fuli; Wang, Shi'an

2018-05-01

Non-model yeasts within basidiomycetes have considerable importance in agriculture, industry, and environment, but they are not as well studied as ascomycetous yeasts. Serving as a basic technique, nuclear DNA staining is widely used in physiology, ecology, cell biology, and genetics. However, it is unclear whether the classical nuclear DNA staining method for ascomycetous yeasts is applicable to basidiomycetous yeasts. In this study, 5 yeasts ineffectively stained by the classical propidium iodide (PI) staining method were identified from 23 representative basidiomycetous yeasts. Pretreatment of cells using dimethyl sulfoxide (DMSO) or snailase markedly improved cell penetration to PI and thus enabled DNA content determination by flow cytometry on the recalcitrant yeasts. The pretreatments are efficient, simple, and fast, avoiding tedious mutagenesis or genetic engineering used in previous reports. The heterogeneity of cell penetration to PI among basidiomycetous yeasts was attributed to the discrepancy in cell wall polysaccharides instead of capsule or plasma membrane. This study also indicated that care must be taken in attributing PI-negative staining as viable cells when studying non-model microorganisms.

Entanglement in a solid-state spin ensemble.

PubMed

Simmons, Stephanie; Brown, Richard M; Riemann, Helge; Abrosimov, Nikolai V; Becker, Peter; Pohl, Hans-Joachim; Thewalt, Mike L W; Itoh, Kohei M; Morton, John J L

2011-02-03

Entanglement is the quintessential quantum phenomenon. It is a necessary ingredient in most emerging quantum technologies, including quantum repeaters, quantum information processing and the strongest forms of quantum cryptography. Spin ensembles, such as those used in liquid-state nuclear magnetic resonance, have been important for the development of quantum control methods. However, these demonstrations contain no entanglement and ultimately constitute classical simulations of quantum algorithms. Here we report the on-demand generation of entanglement between an ensemble of electron and nuclear spins in isotopically engineered, phosphorus-doped silicon. We combined high-field (3.4 T), low-temperature (2.9 K) electron spin resonance with hyperpolarization of the (31)P nuclear spin to obtain an initial state of sufficient purity to create a non-classical, inseparable state. The state was verified using density matrix tomography based on geometric phase gates, and had a fidelity of 98% relative to the ideal state at this field and temperature. The entanglement operation was performed simultaneously, with high fidelity, on 10(10) spin pairs; this fulfils one of the essential requirements for a silicon-based quantum information processor.

Identification of critical regions in human SAMHD1 required for nuclear localization and Vpx-mediated degradation.

PubMed

Guo, Haoran; Wei, Wei; Wei, Zhenhong; Liu, Xianjun; Evans, Sean L; Yang, Weiming; Wang, Hong; Guo, Ying; Zhao, Ke; Zhou, Jian-Ying; Yu, Xiao-Fang

2013-01-01

The sterile alpha motif (SAM) and HD domain-containing protein-1 (SAMHD1) inhibits the infection of resting CD4+ T cells and myeloid cells by human and related simian immunodeficiency viruses (HIV and SIV). Vpx inactivates SAMHD1 by promoting its proteasome-dependent degradation through an interaction with CRL4 (DCAF1) E3 ubiquitin ligase and the C-terminal region of SAMHD1. However, the determinants in SAMHD1 that are required for Vpx-mediated degradation have not been well characterized. SAMHD1 contains a classical nuclear localization signal (NLS), and NLS point mutants are cytoplasmic and resistant to Vpx-mediated degradation. Here, we demonstrate that NLS-mutant SAMHD1 K11A can be rescued by wild-type SAMHD1, restoring its nuclear localization; consequently, SAMHD1 K11A became sensitive to Vpx-mediated degradation in the presence of wild-type SAMHD1. Surprisingly, deletion of N-terminal regions of SAMHD1, including the classical NLS, generated mutant SAMHD1 proteins that were again sensitive to Vpx-mediated degradation. Unlike SAMHD1 K11A, these deletion mutants could be detected in the nucleus. Interestingly, NLS-defective SAMHD1 could still bind to karyopherin-β1 and other nuclear proteins. We also determined that the linker region between the SAM and HD domain and the HD domain itself is important for Vpx-mediated degradation but not Vpx interaction. Thus, SAMHD1 contains an additional nuclear targeting mechanism in addition to the classical NLS. Our data indicate that multiple regions in SAMHD1 are critical for Vpx-mediated nuclear degradation and that association with Vpx is not sufficient for Vpx-mediated degradation of SAMHD1. Since the linker region and HD domain may be involved in SAMHD1 multimerization, our results suggest that SAMHD1 multimerization may be required for Vpx-mediation degradation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klucevsek, K.; Daley, J.; Darshan, M.S.

We have investigated the nuclear import strategies of high-risk HPV18 L2 minor capsid protein. HPV18 L2 interacts with Kap {alpha}{sub 2} adapter, and Kap {beta}{sub 2} and Kap {beta}{sub 3} nuclear import receptors. Moreover, binding of RanGTP to either Kap {beta}{sub 2} or Kap {beta}{sub 3} inhibits their interaction with L2, suggesting that these Kap {beta}/L2 complexes are import competent. Mapping studies show that HPV18 L2 contains two NLSs: in the N-terminus (nNLS) and in the C-terminus (cNLS), both of which can independently mediate nuclear import. Both nNLS and cNLS form a complex with Kap {alpha}{sub 2}{beta}{sub 1} heterodimer andmore » mediate nuclear import via a classical pathway. The nNLS is also essential for the interaction of HPV18 L2 with Kap {beta}{sub 2} and Kap {beta}{sub 3}. Interestingly, both nNLS and cNLS interact with the viral DNA and this DNA binding occurs without nucleotide sequence specificity. Together, the data suggest that HPV18 L2 can interact via its NLSs with several Kaps and the viral DNA and may enter the nucleus via multiple import pathways mediated by Kap {alpha}{sub 2}{beta}{sub 1} heterodimers, Kap {beta}{sub 2} and Kap {beta}{sub 3}.« less

KPNB1 mediates PER/CRY nuclear translocation and circadian clock function.

PubMed

Lee, Yool; Jang, A Reum; Francey, Lauren J; Sehgal, Amita; Hogenesch, John B

2015-08-29

Regulated nuclear translocation of the PER/CRY repressor complex is critical for negative feedback regulation of the circadian clock of mammals. However, the precise molecular mechanism is not fully understood. Here, we report that KPNB1, an importin β component of the ncRNA repressor of nuclear factor of activated T cells (NRON) ribonucleoprotein complex, mediates nuclear translocation and repressor function of the PER/CRY complex. RNAi depletion of KPNB1 traps the PER/CRY complex in the cytoplasm by blocking nuclear entry of PER proteins in human cells. KPNB1 interacts mainly with PER proteins and directs PER/CRY nuclear transport in a circadian fashion. Interestingly, KPNB1 regulates the PER/CRY nuclear entry and repressor function, independently of importin α, its classical partner. Moreover, inducible inhibition of the conserved Drosophila importin β in lateral neurons abolishes behavioral rhythms in flies. Collectively, these data show that KPNB1 is required for timely nuclear import of PER/CRY in the negative feedback regulation of the circadian clock.

Regulation of Nuclear Import and Export of Negative Cofactor 2*S⃞

PubMed Central

Kahle, Joerg; Piaia, Elisa; Neimanis, Sonja; Meisterernst, Michael; Doenecke, Detlef

2009-01-01

The negative cofactor 2 (NC2) is a protein complex composed of two subunits, NC2α and NC2β, and plays a key role in transcription regulation. Here we investigate whether each subunit contains a nuclear localization signal (NLS) that permits individual crossing of the nuclear membrane or whether nuclear import of NC2α and NC2β depends on heterodimerization. Our results from in vitro binding studies and transfection experiments in cultured cells show that each subunit contains a classical NLS (cNLS) that is recognized by the importin α/β heterodimer. Regardless of the individual cNLSs the two NC2 subunits are translocated as a preassembled complex as co-transfection experiments with wild-type and cNLS-deficient NC2 subunits demonstrate. Ran-dependent binding of the nuclear export receptor Crm1/exportin 1 confirmed the presence of a leucine-rich nuclear export signal (NES) in NC2β. In contrast, NC2α does not exhibit a NES. Our results from interspecies heterokaryon assays suggest that heterodimerization with NC2α masks the NES in NC2β, which prevents nuclear export of the NC2 complex. A mutation in either one of the two cNLSs decreases the extent of importin α/β-mediated nuclear import of the NC2 complex. In addition, the NC2 complex can enter the nucleus via a second pathway, facilitated by importin 13. Because importin 13 binds exclusively to the NC2 complex but not to the individual subunits this alternative import pathway depends on sequence elements distributed among the two subunits. PMID:19204005

Nuclear Import of the Retrotransposon Tf1 Is Governed by a Nuclear Localization Signal That Possesses a Unique Requirement for the FXFG Nuclear Pore Factor Nup124p

PubMed Central

Dang, Van-Dinh; Levin, Henry L.

2000-01-01

Retroviruses, such as human immunodeficiency virus, that infect nondividing cells generate integration precursors that must cross the nuclear envelope to reach the host genome. As a model for retroviruses, we investigated the nuclear entry of Tf1, a long-terminal-repeat-containing retrotransposon of the fission yeast Schizosaccharomyces pombe. Because the nuclear envelope of yeasts remains intact throughout the cell cycle, components of Tf1 must be transported through the envelope before integration can occur. The nuclear localization of the Gag protein of Tf1 is different from that of other proteins tested in that it has a specific requirement for the FXFG nuclear pore factor, Nup124p. Using extensive mutagenesis, we found that Gag contained three nuclear localization signals (NLSs) which, when included individually in a heterologous protein, were sufficient to direct nuclear import. In the context of the intact transposon, mutations in the NLS that mapped to the first 10 amino acid residues of Gag significantly impaired Tf1 retrotransposition and abolished nuclear localization of Gag. Interestingly, this NLS activity in the heterologous protein was specifically dependent upon the presence of Nup124p. Deletion analysis of heterologous proteins revealed the surprising result that the residues in Gag with the NLS activity were independent from the residues that conveyed the requirement for Nup124p. In fact, a fragment of Gag that lacked NLS activity, residues 10 to 30, when fused to a heterologous protein, was sufficient to cause the classical NLS of simian virus 40 to require Nup124p for nuclear import. Within the context of the current understanding of nuclear import, these results represent the novel case of a short amino acid sequence that specifies the need for a particular nuclear pore complex protein. PMID:11003674

Nuclear import of the retrotransposon Tf1 is governed by a nuclear localization signal that possesses a unique requirement for the FXFG nuclear pore factor Nup124p.

PubMed

Dang, V D; Levin, H L

2000-10-01

Retroviruses, such as human immunodeficiency virus, that infect nondividing cells generate integration precursors that must cross the nuclear envelope to reach the host genome. As a model for retroviruses, we investigated the nuclear entry of Tf1, a long-terminal-repeat-containing retrotransposon of the fission yeast Schizosaccharomyces pombe. Because the nuclear envelope of yeasts remains intact throughout the cell cycle, components of Tf1 must be transported through the envelope before integration can occur. The nuclear localization of the Gag protein of Tf1 is different from that of other proteins tested in that it has a specific requirement for the FXFG nuclear pore factor, Nup124p. Using extensive mutagenesis, we found that Gag contained three nuclear localization signals (NLSs) which, when included individually in a heterologous protein, were sufficient to direct nuclear import. In the context of the intact transposon, mutations in the NLS that mapped to the first 10 amino acid residues of Gag significantly impaired Tf1 retrotransposition and abolished nuclear localization of Gag. Interestingly, this NLS activity in the heterologous protein was specifically dependent upon the presence of Nup124p. Deletion analysis of heterologous proteins revealed the surprising result that the residues in Gag with the NLS activity were independent from the residues that conveyed the requirement for Nup124p. In fact, a fragment of Gag that lacked NLS activity, residues 10 to 30, when fused to a heterologous protein, was sufficient to cause the classical NLS of simian virus 40 to require Nup124p for nuclear import. Within the context of the current understanding of nuclear import, these results represent the novel case of a short amino acid sequence that specifies the need for a particular nuclear pore complex protein.

Supernovae neutrino pasta interaction

NASA Astrophysics Data System (ADS)

Lin, Zidu; Horowitz, Charles; Caplan, Matthew; Berry, Donald; Roberts, Luke

2017-01-01

In core-collapse supernovae, the neutron rich matter is believed to have complex structures, such as spherical, slablike, and rodlike shapes. They are collectively called ``nuclear pasta''. Supernovae neutrinos may scatter coherently on the ``nuclear pasta'' since the wavelength of the supernovae neutrinos are comparable to the nuclear pasta scale. Consequently, the neutrino pasta scattering is important to understand the neutrino opacity in the supernovae. In this work we simulated the ``nuclear pasta'' at different temperatures and densities using our semi-classical molecular dynamics and calculated the corresponding static structure factor that describes ν-pasta scattering. We found the neutrino opacities are greatly modified when the ``pasta'' exist and may have influence on the supernovae neutrino flux and average energy. Our neutrino-pasta scattering effect can finally be involved in the current supernovae simulations and we present preliminary proto neutron star cooling simulations including our pasta opacities.

Quantum chaos in nuclear physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bunakov, V. E., E-mail: bunakov@VB13190.spb.edu

A definition of classical and quantum chaos on the basis of the Liouville–Arnold theorem is proposed. According to this definition, a chaotic quantum system that has N degrees of freedom should have M < N independent first integrals of motion (good quantum numbers) that are determined by the symmetry of the Hamiltonian for the system being considered. Quantitative measures of quantum chaos are established. In the classical limit, they go over to the Lyapunov exponent or the classical stability parameter. The use of quantum-chaos parameters in nuclear physics is demonstrated.

Many-body kinetics of dynamic nuclear polarization by the cross effect

NASA Astrophysics Data System (ADS)

Karabanov, A.; Wiśniewski, D.; Raimondi, F.; Lesanovsky, I.; Köckenberger, W.

2018-03-01

Dynamic nuclear polarization (DNP) is an out-of-equilibrium method for generating nonthermal spin polarization which provides large signal enhancements in modern diagnostic methods based on nuclear magnetic resonance. A particular instance is cross-effect DNP, which involves the interaction of two coupled electrons with the nuclear spin ensemble. Here we develop a theory for this important DNP mechanism and show that the nonequilibrium nuclear polarization buildup is effectively driven by three-body incoherent Markovian dissipative processes involving simultaneous state changes of two electrons and one nucleus. We identify different parameter regimes for effective polarization transfer and discuss under which conditions the polarization dynamics can be simulated by classical kinetic Monte Carlo methods. Our theoretical approach allows simulations of the polarization dynamics on an individual spin level for ensembles consisting of hundreds of nuclear spins. The insight obtained by these simulations can be used to find optimal experimental conditions for cross-effect DNP and to design tailored radical systems that provide optimal DNP efficiency.

RNA transcription modulates phase transition-driven nuclear body assembly

PubMed Central

Berry, Joel; Weber, Stephanie C.; Vaidya, Nilesh; Haataja, Mikko; Brangwynne, Clifford P.

2015-01-01

Nuclear bodies are RNA and protein-rich, membraneless organelles that play important roles in gene regulation. The largest and most well-known nuclear body is the nucleolus, an organelle whose primary function in ribosome biogenesis makes it key for cell growth and size homeostasis. The nucleolus and other nuclear bodies behave like liquid-phase droplets and appear to condense from the nucleoplasm by concentration-dependent phase separation. However, nucleoli actively consume chemical energy, and it is unclear how such nonequilibrium activity might impact classical liquid–liquid phase separation. Here, we combine in vivo and in vitro experiments with theory and simulation to characterize the assembly and disassembly dynamics of nucleoli in early Caenorhabditis elegans embryos. In addition to classical nucleoli that assemble at the transcriptionally active nucleolar organizing regions, we observe dozens of “extranucleolar droplets” (ENDs) that condense in the nucleoplasm in a transcription-independent manner. We show that growth of nucleoli and ENDs is consistent with a first-order phase transition in which late-stage coarsening dynamics are mediated by Brownian coalescence and, to a lesser degree, Ostwald ripening. By manipulating C. elegans cell size, we change nucleolar component concentration and confirm several key model predictions. Our results show that rRNA transcription and other nonequilibrium biological activity can modulate the effective thermodynamic parameters governing nucleolar and END assembly, but do not appear to fundamentally alter the passive phase separation mechanism. PMID:26351690

Region of Nipah virus C protein responsible for shuttling between the cytoplasm and nucleus.

PubMed

Horie, Ryo; Yoneda, Misako; Uchida, Shotaro; Sato, Hiroki; Kai, Chieko

2016-10-01

Nipah virus (NiV) causes severe encephalitis in humans, with high mortality. NiV nonstructural C protein (NiV-C) is essential for its pathogenicity, but its functions are unclear. In this study, we focused on NiV-C trafficking in cells and found that it localizes predominantly in the cytoplasm but partly in the nucleus. An analysis of NiV-C mutants showed that amino acids 2, 21-24 and 110-139 of NiV-C are important for its localization in the cytoplasm. Inhibitor treatment indicates that the nuclear export determinant is not a classical CRM1-dependent nuclear export signal. We also determined that amino acids 60-75 and 72-75 were important for nuclear localization of NiV-C. Furthermore, NiV-C mutants that had lost their capacity for nuclear localization inhibited the interferon (IFN) response more strongly than complete NiV-C. These results indicate that the IFN-antagonist activity of NiV-C occurs in the cytoplasm. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of the Human Herpesvirus 6 U69 Gene Product and Identification of Its Nuclear Localization Signal▿

PubMed Central

Isegawa, Yuji; Miyamoto, Yoichi; Yasuda, Yoshinari; Semi, Katsunori; Tsujimura, Kenji; Fukunaga, Rikiro; Ohshima, Atsushi; Horiguchi, Yasuhiro; Yoneda, Yoshihiro; Sugimoto, Nakaba

2008-01-01

To elucidate the function of the U69 protein kinase of human herpesvirus 6 (HHV-6) in vivo, we first analyzed its subcellular localization in HHV-6-infected Molt 3 cells by using polyclonal antibodies against the U69 protein. Immunofluorescence studies showed that the U69 signal localized to the nucleus in a mesh-like pattern in both HHV-6-infected and HHV6-transfected cells. A computer program predicted two overlapping classic nuclear localization signals (NLSs) in the N-terminal region of the protein; this NLS motif is highly conserved in the N-terminal region of most of the herpesvirus protein kinases examined to date. An N-terminal deletion mutant form of the protein failed to enter the nucleus, whereas a fusion protein of green fluorescent protein (GFP) and/or glutathione S-transferase (GST) and the U69 N-terminal region was transported into the nucleus, demonstrating that the predicted N-terminal NLSs of the protein actually function as NLSs. The nuclear transport of the GST-GFP fusion protein containing the N-terminal NLS of U69 was inhibited by wheat germ agglutinin and by the Q69L Ran-GTP mutant, indicating that the U69 protein is transported into the nucleus from the cytoplasm via classic nuclear transport machinery. A cell-free import assay showed that the nuclear transport of the U69 protein was mediated by importin α/β in conjunction with the small GTPase Ran. When the import assay was performed with a low concentration of each importin-α subtype, NPI2/importin-α7 elicited more efficient transport activity than did Rch1/importin-α1 or Qip1/importin-α3. These results suggest a relationship between the localization of NPI2/importin-α7 and the cell tropism of HHV-6. PMID:18003734

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agostini, Federica; Abedi, Ali; Suzuki, Yasumitsu

The decomposition of electronic and nuclear motion presented in Abedi et al. [Phys. Rev. Lett. 105, 123002 (2010)] yields a time-dependent potential that drives the nuclear motion and fully accounts for the coupling to the electronic subsystem. Here, we show that propagation of an ensemble of independent classical nuclear trajectories on this exact potential yields dynamics that are essentially indistinguishable from the exact quantum dynamics for a model non-adiabatic charge transfer problem. We point out the importance of step and bump features in the exact potential that are critical in obtaining the correct splitting of the quasiclassical nuclear wave packetmore » in space after it passes through an avoided crossing between two Born-Oppenheimer surfaces and analyze their structure. Finally, an analysis of the exact potentials in the context of trajectory surface hopping is presented, including preliminary investigations of velocity-adjustment and the force-induced decoherence effect.« less

The origin, composition and history of cometary ices from spectroscopic studies

NASA Technical Reports Server (NTRS)

Allamandola, L. J.

1989-01-01

The spectroscopic analysis of pristine cometary material provides a very important probe of the chemical identity of the material as well as of the physical and chemical conditions which prevailed during the comet's history. Concerning classical spectroscopy, the spectral regions which will most likely prove most useful are the infrared, the visible and ultraviolet. Newer spectroscopic techniques which have the potential to provide equally important information include nuclear magnetic resonance (NMR) and electron spin resonance (ESR). Each technique is summarized with emphasis placed on the kind of information which can be obtained.

Nuclear translocation of glutathione S-transferase {pi} is mediated by a non-classical localization signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawakatsu, Miho; Goto, Shinji, E-mail: sgoto@nagasaki-u.ac.jp; Yoshida, Takako

2011-08-12

Highlights: {yields} Nuclear translocation of GST{pi} is abrogated by the deletion of the last 16 amino acid residues in the carboxy-terminal region, indicating that residues 195-208 of GST{pi} are required for nuclear translocation. {yields} The lack of a contiguous stretch of positively charged amino acid residues within the carboxy-terminal region of GST{pi}, suggests that the nuclear translocation of GST{pi} is mediated by a non-classical nuclear localization signal. {yields} An in vitro transport assay shows that the nuclear translocation of GST{pi} is dependent on cytosolic factors and ATP. -- Abstract: Glutathione S-transferase {pi} (GST{pi}), a member of the GST family ofmore » multifunctional enzymes, is highly expressed in human placenta and involved in the protection of cellular components against electrophilic compounds or oxidative stress. We have recently found that GST{pi} is expressed in the cytoplasm, mitochondria, and nucleus in some cancer cells, and that the nuclear expression of GST{pi} appears to correlate with resistance to anti-cancer drugs. Although the mitochondrial targeting signal of GST{pi} was previously identified in the amino-terminal region, the mechanism of nuclear translocation remains completely unknown. In this study, we find that the region of GST{pi}195-208 is critical for nuclear translocation, which is mediated by a novel and non-classical nuclear localization signal. In addition, using an in vitro transport assay, we demonstrate that the nuclear translocation of GST{pi} depends on the cytosolic extract and ATP. Although further experiments are needed to understand in depth the precise mechanism of nuclear translocation of GST{pi}, our results may help to establish more efficient anti-cancer therapy, especially with respect to resistance to anti-cancer drugs.« less

Communication: Adiabatic and non-adiabatic electron-nuclear motion: Quantum and classical dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albert, Julian; Kaiser, Dustin; Engel, Volker

2016-05-07

Using a model for coupled electronic-nuclear motion we investigate the range from negligible to strong non-adiabatic coupling. In the adiabatic case, the quantum dynamics proceeds in a single electronic state, whereas for strong coupling a complete transition between two adiabatic electronic states takes place. It is shown that in all coupling regimes the short-time wave-packet dynamics can be described using ensembles of classical trajectories in the phase space spanned by electronic and nuclear degrees of freedom. We thus provide an example which documents that the quantum concept of non-adiabatic transitions is not necessarily needed if electronic and nuclear motion ismore » treated on the same footing.« less

An N-terminal nuclear localization sequence but not the calmodulin-binding domain mediates nuclear localization of nucleomorphin, a protein that regulates nuclear number in Dictyostelium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myre, Michael A.; O'Day, Danton H.

2005-06-24

Nucleomorphin is a novel nuclear calmodulin (CaM)-binding protein (CaMBP) containing an extensive DEED (glu/asp repeat) domain that regulates nuclear number. GFP-constructs of the 38 kDa NumA1 isoform localize as intranuclear patches adjacent to the inner nuclear membrane. The translocation of CaMBPs into nuclei has previously been shown by others to be mediated by both classic nuclear localization sequences (NLSs) and CaM-binding domains (CaMBDs). Here we show that NumA1 possesses a CaMBD ({sup 171}EDVSRFIKGKLLQKQQKIYKDLERF{sup 195}) containing both calcium-dependent-binding motifs and an IQ-like motif for calcium-independent binding. GFP-constructs containing only NumA1 residues 1-129, lacking the DEED and CaMBDs, still localized as patchesmore » at the internal periphery of nuclei thus ruling out a direct role for the CaMBD in nuclear import. These constructs contained the amino acid residues {sup 48}KKSYQDPEIIAHSRPRK{sup 64} that include both a putative bipartite and classical NLS. GFP-bipartite NLS constructs localized uniformly within nuclei but not as patches. As with previous work, removal of the DEED domain resulted in highly multinucleate cells. However as shown here, multinuclearity only occurred when the NLS was present allowing the protein to enter nuclei. Site-directed mutation analysis in which the NLS was changed to {sup 48}EF{sup 49} abolished the stability of the GFP fusion at the protein but not RNA level preventing subcellular analyses. Cells transfected with the {sup 48}EF{sup 49} construct exhibited slowed growth when compared to parental AX3 cells and other GFP-NumA1 deletion mutants. In addition to identifying an NLS that is sufficient for nuclear translocation of nucleomorphin and ruling out CaM-binding in this event, this work shows that the nuclear localization of NumA1 is crucial to its ability to regulate nuclear number in Dictyostelium.« less

Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus.

PubMed

Jang, A Reum; Moravcevic, Katarina; Saez, Lino; Young, Michael W; Sehgal, Amita

2015-02-01

Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, PERIOD (PER) and TIMELESS (TIM), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. We report here that nuclear entry of PER-TIM in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of PER-TIM require a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 can also drive rapid and efficient nuclear expression of TIM and PER in cultured cells, although the effect on PER is mediated by TIM. Mapping of interaction domains between IMPα1 and TIM/PER suggests that TIM is the primary cargo for the importin machinery. This is supported by attenuated interaction of IMPα1 with TIM carrying a mutation previously shown to prevent nuclear entry of TIM and PER. TIM is detected at the nuclear envelope, and computational modeling suggests that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for PER. These findings suggest that although PER is the major timekeeper of the clock, TIM is the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that TIM serves a karyopherin-like role for PER.

Nuclear ferritin: A new role for ferritin in cell biology.

PubMed

Alkhateeb, Ahmed A; Connor, James R

2010-08-01

Ferritin has been traditionally considered a cytoplasmic iron storage protein. However, several studies over the last two decades have reported the nuclear localization of ferritin, specifically H-ferritin, in developing neurons, hepatocytes, corneal epithelial cells, and some cancer cells. These observations encouraged a new perspective on ferritin beyond iron storage, such as a role in the regulation of iron accessibility to nuclear components, DNA protection from iron-induced oxidative damage, and transcriptional regulation. This review will address the translocation and functional significance of nuclear ferritin in the context of human development and disease. The nuclear translocation of ferritin is a selective energy-dependent process that does not seem to require a consensus nuclear localization signal. It is still unclear what regulates the nuclear import/export of ferritin. Some reports have implicated the phosphorylation and O-glycosylation of the ferritin protein in nuclear transport; others suggested the existence of a specific nuclear chaperone for ferritin. The data argue strongly for nuclear ferritin as a factor in human development and disease. Ferritin can bind and protect DNA from oxidative damage. It also has the potential of playing a regulatory role in transcription. Nuclear ferritin represents a novel new outlook on ferritin functionality beyond its classical role as an iron storage molecule. Copyright 2010 Elsevier B.V. All rights reserved.

Entangled trajectories Hamiltonian dynamics for treating quantum nuclear effects

NASA Astrophysics Data System (ADS)

Smith, Brendan; Akimov, Alexey V.

2018-04-01

A simple and robust methodology, dubbed Entangled Trajectories Hamiltonian Dynamics (ETHD), is developed to capture quantum nuclear effects such as tunneling and zero-point energy through the coupling of multiple classical trajectories. The approach reformulates the classically mapped second-order Quantized Hamiltonian Dynamics (QHD-2) in terms of coupled classical trajectories. The method partially enforces the uncertainty principle and facilitates tunneling. The applicability of the method is demonstrated by studying the dynamics in symmetric double well and cubic metastable state potentials. The methodology is validated using exact quantum simulations and is compared to QHD-2. We illustrate its relationship to the rigorous Bohmian quantum potential approach, from which ETHD can be derived. Our simulations show a remarkable agreement of the ETHD calculation with the quantum results, suggesting that ETHD may be a simple and inexpensive way of including quantum nuclear effects in molecular dynamics simulations.

DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway.

PubMed

de Barros, Andrea C; Takeda, Agnes A S; Dreyer, Thiago R; Velazquez-Campoy, Adrian; Kobe, Boštjan; Fontes, Marcos R M

2018-03-01

MLH1 and PMS2 proteins form the MutLα heterodimer, which plays a major role in DNA mismatch repair (MMR) in humans. Mutations in MMR-related proteins are associated with cancer, especially with colon cancer. The N-terminal region of MutLα comprises the N-termini of PMS2 and MLH1 and, similarly, the C-terminal region of MutLα is composed by the C-termini of PMS2 and MLH1, and the two are connected by linker region. The nuclear localization sequences (NLSs) necessary for the nuclear transport of the two proteins are found in this linker region. However, the exact NLS sequences have been controversial, with different sequences reported, particularly for MLH1. The individual components are not imported efficiently, presumably due to their C-termini masking their NLSs. In order to gain insights into the nuclear transport of these proteins, we solved the crystal structures of importin-α bound to peptides corresponding to the supposed NLSs of MLH1 and PMS2 and performed isothermal titration calorimetry to study their binding affinities. Both putative MLH1 and PMS2 NLSs can bind to importin-α as monopartite NLSs, which is in agreement with some previous studies. However, MLH1-NLS has the highest affinity measured by a natural NLS peptide, suggesting a major role of MLH1 protein in nuclear import compared to PMS2. Finally, the role of MLH1 and PMS2 in the nuclear transport of the MutLα heterodimer is discussed. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

The first dozen years of the history of ITEP Theoretical Physics Laboratory

NASA Astrophysics Data System (ADS)

Ioffe, B. L.

2013-01-01

The theoretical investigations at ITEP in the years 1945 - 1958 are reviewed. There are exposed the most important theoretical results, obtained in the following branches of physics: (1) the theory of nuclear reactors on thermal neutrons; (2) the hydrogen bomb project ("Tube" in USSR and "Classical Super" in USA); (3) radiation theory; (4) low temperature physics; (5) quantum electrodynamics and quantum field theories; (6) parity violation in weak interactions, the theory of β-decay and other weak processes; (7) strong interaction and nuclear physics. To the review are added the English translations of a few papers, originally published in Russian, but unknown (or almost unknown) to Western readers.

Nucleo-cytoplasmic shuttling of the endonuclease ankyrin repeats and LEM domain-containing protein 1 (Ankle1) is mediated by canonical nuclear export- and nuclear import signals.

PubMed

Zlopasa, Livija; Brachner, Andreas; Foisner, Roland

2016-06-01

Ankyrin repeats and LEM domain containing protein 1 (Ankle1) belongs to the LEM protein family, whose members share a chromatin-interacting LEM motif. Unlike most other LEM proteins, Ankle1 is not an integral protein of the inner nuclear membrane but shuttles between the nucleus and the cytoplasm. It contains a GIY-YIG-type nuclease domain, but its function is unknown. The mammalian genome encodes only one other GIY-YIG domain protein, termed Slx1. Slx1 has been described as a resolvase that processes Holliday junctions during homologous recombination-mediated DNA double strand break repair. Resolvase activity is regulated in a spatial and temporal manner during the cell cycle. We hypothesized that Ankle1 may have a similar function and its nucleo-cytoplasmic shuttling may contribute to the regulation of Ankle1 activity. Hence, we aimed at identifying the domains mediating Ankle1 shuttling and investigating whether cellular localization is affected during DNA damage response. Sequence analysis predicts the presence of two canonical nuclear import and export signals in Ankle1. Immunofluorescence microscopy of cells expressing wild-type and various mutated Ankle1-fusion proteins revealed a C-terminally located classical monopartite nuclear localization signal and a centrally located CRM1-dependent nuclear export signal that mediate nucleo-cytoplasmic shuttling of Ankle1. These sequences are also functional in heterologous proteins. The predominant localization of Ankle1 in the cytoplasm, however, does not change upon induction of several DNA damage response pathways throughout the cell cycle. We identified the domains mediating nuclear import and export of Ankle1. Ankle1's cellular localization was not affected following DNA damage.

FLIPing heterokaryons to analyze nucleo-cytoplasmic shuttling of yeast proteins.

PubMed

Belaya, Katsiaryna; Tollervey, David; Kos, Martin

2006-05-01

Nucleo-cytoplasmic shuttling is an important feature of proteins involved in nuclear export/import of RNAs, proteins, and also large ribonucleoprotein complexes such as ribosomes. The vast amount of proteomic data available shows that many of these processes are highly dynamic. Therefore, methods are needed to reliably assess whether a protein shuttles between nucleus and cytoplasm, and the kinetics with which it exchanges. Here we describe a combination of the classical heterokaryon assay with fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) techniques, which allows an assessment of the kinetics of protein shuttling in the yeast Saccharomyces cerevisiae.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Drosophila TIM Binds Importin α1, and Acts as an Adapter to Transport PER to the Nucleus

PubMed Central

Jang, A. Reum; Moravcevic, Katarina; Saez, Lino; Young, Michael W.; Sehgal, Amita

2015-01-01

Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, PERIOD (PER) and TIMELESS (TIM), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. We report here that nuclear entry of PER-TIM in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of PER-TIM require a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 can also drive rapid and efficient nuclear expression of TIM and PER in cultured cells, although the effect on PER is mediated by TIM. Mapping of interaction domains between IMPα1 and TIM/PER suggests that TIM is the primary cargo for the importin machinery. This is supported by attenuated interaction of IMPα1 with TIM carrying a mutation previously shown to prevent nuclear entry of TIM and PER. TIM is detected at the nuclear envelope, and computational modeling suggests that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for PER. These findings suggest that although PER is the major timekeeper of the clock, TIM is the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that TIM serves a karyopherin-like role for PER. PMID:25674790

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donangelo, R.J.

An integral representation for the classical limit of the quantum mechanical S-matrix is developed and applied to heavy-ion Coulomb excitation and Coulomb-nuclear interference. The method combines the quantum principle of superposition with exact classical dynamics to describe the projectile-target system. A detailed consideration of the classical trajectories and of the dimensionless parameters that characterize the system is carried out. The results are compared, where possible, to exact quantum mechanical calculations and to conventional semiclassical calculations. It is found that in the case of backscattering the classical limit S-matrix method is able to almost exactly reproduce the quantum-mechanical S-matrix elements, andmore » therefore the transition probabilities, even for projectiles as light as protons. The results also suggest that this approach should be a better approximation for heavy-ion multiple Coulomb excitation than earlier semiclassical methods, due to a more accurate description of the classical orbits in the electromagnetic field of the target nucleus. Calculations using this method indicate that the rotational excitation probabilities in the Coulomb-nuclear interference region should be very sensitive to the details of the potential at the surface of the nucleus, suggesting that heavy-ion rotational excitation could constitute a sensitive probe of the nuclear potential in this region. The application to other problems as well as the present limits of applicability of the formalism are also discussed.« less

Fine control of nuclear confinement identifies a threshold deformation leading to lamina rupture and induction of specific genes.

PubMed

Le Berre, Maël; Aubertin, Johannes; Piel, Matthieu

2012-11-01

The quest to understand how the mechanical and geometrical environment of cells impacts their behavior and fate has been a major force driving the recent development of new technologies in cell biology research. Despite rapid advances in this field, many challenges remain in order to bridge the gap between the classical and simple cell culture plate and the biological reality of actual tissue. In tissues, cells have their physical space constrained by neighboring cells and the extracellular matrix. Here, we propose a simple and versatile device to precisely and dynamically control this confinement parameter in cultured cells. We show that there is a precise threshold deformation above which the nuclear lamina breaks and reconstructs, whereas nuclear volume changes. We also show that different nuclear deformations correlate with the expression of specific sets of genes, including nuclear factors and classical mechanotransduction pathways. This versatile device thus enables the precise control of cell and nuclear deformation by confinement and the correlative study of the associated molecular events.

Identification of flat dysplastic aberrant crypt foci in the colon of azoxymethane-treated A/J mice.

PubMed

Paulsen, Jan Erik; Knutsen, Helle; Ølstørn, Hege Benedikte; Løberg, Else Marit; Alexander, Jan

2006-02-01

The role of aberrant crypt foci (ACF) as preneoplastic lesions in colon carcinogenesis is not clear. In Min/+ mice and their wild-type littermates treated with azoxymethane (AOM), we previously identified a subgroup of flat ACF that seem more immediate precursors of tumors than the classical elevated ACF. In the present study, we identified a similar subgroup of flat ACF in AOM-treated A/J mice and compared them with nascent tumors and classical elevated ACF. At week 1 and 2 after birth, A/J mice were injected subcutaneously with AOM (10 mg/kg bw/injection). At weeks 7-14, we examined the luminal surface of unsectioned colon preparations stained with methylene blue in the inverse light microscope. The lesions were also examined by histopathology and immunohistochemistry. Surface examination revealed flat ACF, classical elevated ACF and nascent tumors. Since flat ACF were not observed as elevated structures, their bright blue appearance and compressed pit pattern of crypt openings seen with transillumination were used as criteria for their identification. Flat ACF and nascent tumors displayed a uniform picture of severe dysplasia, compressed pit pattern, overexpression of cytoplasmic/nuclear beta-catenin and nuclear overexpression of cyclin D1. Apparently, flat ACF and tumors represented the same type of dysplastic lesions at different stages of crypt multiplication. In contrast, classical elevated ACF did not seem to be as clearly related to tumorigenesis. They infrequently (1/20) possessed severe dysplasia, overexpression of cytoplasmic/nuclear beta-catenin, or nuclear overexpression of cyclin D1, and they did not have compressed crypt openings. Furthermore, flat ACF grew significantly faster than classical elevated ACF. In conclusion, our data indicate a development from flat ACF to adenoma characterized by aberrant activation of the Wnt signaling pathway and fast crypt multiplication. Classical elevated ACF do not seem to be as closely related to tumorigenesis. Copyright 2005 Wiley-Liss, Inc.

A Class 1 Histone Deacetylase with Potential as an Antifungal Target

PubMed Central

Bauer, Ingo; Varadarajan, Divyavaradhi; Pidroni, Angelo; Gross, Silke; Vergeiner, Stefan; Faber, Birgit; Hermann, Martin; Tribus, Martin; Brosch, Gerald

2016-01-01

ABSTRACT Histone deacetylases (HDACs) remove acetyl moieties from lysine residues at histone tails and nuclear regulatory proteins and thus significantly impact chromatin remodeling and transcriptional regulation in eukaryotes. In recent years, HDACs of filamentous fungi were found to be decisive regulators of genes involved in pathogenicity and the production of important fungal metabolites such as antibiotics and toxins. Here we present proof that one of these enzymes, the class 1 type HDAC RpdA, is of vital importance for the opportunistic human pathogen Aspergillus fumigatus. Recombinant expression of inactivated RpdA shows that loss of catalytic activity is responsible for the lethal phenotype of Aspergillus RpdA null mutants. Furthermore, we demonstrate that a fungus-specific C-terminal region of only a few acidic amino acids is required for both the nuclear localization and catalytic activity of the enzyme in the model organism Aspergillus nidulans. Since strains with single or multiple deletions of other classical HDACs revealed no or only moderate growth deficiencies, it is highly probable that the significant delay of germination and the growth defects observed in strains growing under the HDAC inhibitor trichostatin A are caused primarily by inhibition of catalytic RpdA activity. Indeed, even at low nanomolar concentrations of the inhibitor, the catalytic activity of purified RpdA is considerably diminished. Considering these results, RpdA with its fungus-specific motif represents a promising target for novel HDAC inhibitors that, in addition to their increasing impact as anticancer drugs, might gain in importance as antifungals against life-threatening invasive infections, apart from or in combination with classical antifungal therapy regimes. PMID:27803184

Quantum factorization of 143 on a dipolar-coupling nuclear magnetic resonance system.

PubMed

Xu, Nanyang; Zhu, Jing; Lu, Dawei; Zhou, Xianyi; Peng, Xinhua; Du, Jiangfeng

2012-03-30

Quantum algorithms could be much faster than classical ones in solving the factoring problem. Adiabatic quantum computation for this is an alternative approach other than Shor's algorithm. Here we report an improved adiabatic factoring algorithm and its experimental realization to factor the number 143 on a liquid-crystal NMR quantum processor with dipole-dipole couplings. We believe this to be the largest number factored in quantum-computation realizations, which shows the practical importance of adiabatic quantum algorithms.

Experimental realization of Shor's quantum factoring algorithm using nuclear magnetic resonance.

PubMed

Vandersypen, L M; Steffen, M; Breyta, G; Yannoni, C S; Sherwood, M H; Chuang, I L

The number of steps any classical computer requires in order to find the prime factors of an l-digit integer N increases exponentially with l, at least using algorithms known at present. Factoring large integers is therefore conjectured to be intractable classically, an observation underlying the security of widely used cryptographic codes. Quantum computers, however, could factor integers in only polynomial time, using Shor's quantum factoring algorithm. Although important for the study of quantum computers, experimental demonstration of this algorithm has proved elusive. Here we report an implementation of the simplest instance of Shor's algorithm: factorization of N = 15 (whose prime factors are 3 and 5). We use seven spin-1/2 nuclei in a molecule as quantum bits, which can be manipulated with room temperature liquid-state nuclear magnetic resonance techniques. This method of using nuclei to store quantum information is in principle scalable to systems containing many quantum bits, but such scalability is not implied by the present work. The significance of our work lies in the demonstration of experimental and theoretical techniques for precise control and modelling of complex quantum computers. In particular, we present a simple, parameter-free but predictive model of decoherence effects in our system.

Experimental demonstration of information to energy conversion in a quantum system at the Landauer limit.

PubMed

Peterson, J P S; Sarthour, R S; Souza, A M; Oliveira, I S; Goold, J; Modi, K; Soares-Pinto, D O; Céleri, L C

2016-04-01

Landauer's principle sets fundamental thermodynamical constraints for classical and quantum information processing, thus affecting not only various branches of physics, but also of computer science and engineering. Despite its importance, this principle was only recently experimentally considered for classical systems. Here we employ a nuclear magnetic resonance set-up to experimentally address the information to energy conversion in a quantum system. Specifically, we consider a three nuclear spins [Formula: see text] (qubits) molecule-the system, the reservoir and the ancilla-to measure the heat dissipated during the implementation of a global system-reservoir unitary interaction that changes the information content of the system. By employing an interferometric technique, we were able to reconstruct the heat distribution associated with the unitary interaction. Then, through quantum state tomography, we measured the relative change in the entropy of the system. In this way, we were able to verify that an operation that changes the information content of the system must necessarily generate heat in the reservoir, exactly as predicted by Landauer's principle. The scheme presented here allows for the detailed study of irreversible entropy production in quantum information processors.

Yeast Nucleoporins Involved in Passive Nuclear Envelope Permeability

PubMed Central

Shulga, Nataliya; Mosammaparast, Nima; Wozniak, Richard; Goldfarb, David S.

2000-01-01

The vertebrate nuclear pore complex (NPC) harbors an ∼10-nm diameter diffusion channel that is large enough to admit 50-kD polypeptides. We have analyzed the permeability properties of the Saccharomyces cerevisiae nuclear envelope (NE) using import (NLS) and export (NES) signal-containing green fluorescent protein (GFP) reporters. Compared with wild-type, passive export rates of a classical karyopherin/importin (Kap) Kap60p/Kap95p-targeted NLS-GFP reporter (cNLS-GFP) were significantly faster in nup188-Δ and nup170-Δ cells. Similar results were obtained using two other NLS-GFP reporters, containing either the Kap104p-targeted Nab2p NLS (rgNLS) or the Kap121p-targeted Pho4p NLS (pNLS). Elevated levels of Hsp70 stimulated cNLS-GFP import, but had no effect on the import of rgNLS-GFP. Thus, the role of Hsp70 in NLS-directed import may be NLS- or targeting pathway-specific. Equilibrium sieving limits for the diffusion channel were assessed in vivo using NES-GFP reporters of 36–126 kD and were found to be greater than wild-type in nup188-Δ and nup170-Δ cells. We propose that Nup170p and Nup188p are involved in establishing the functional resting diameter of the NPC's central transport channel. PMID:10831607

Nuclear Ensemble Approach with Importance Sampling.

PubMed

Kossoski, Fábris; Barbatti, Mario

2018-06-12

We show that the importance sampling technique can effectively augment the range of problems where the nuclear ensemble approach can be applied. A sampling probability distribution function initially determines the collection of initial conditions for which calculations are performed, as usual. Then, results for a distinct target distribution are computed by introducing compensating importance sampling weights for each sampled point. This mapping between the two probability distributions can be performed whenever they are both explicitly constructed. Perhaps most notably, this procedure allows for the computation of temperature dependent observables. As a test case, we investigated the UV absorption spectra of phenol, which has been shown to have a marked temperature dependence. Application of the proposed technique to a range that covers 500 K provides results that converge to those obtained with conventional sampling. We further show that an overall improved rate of convergence is obtained when sampling is performed at intermediate temperatures. The comparison between calculated and the available measured cross sections is very satisfactory, as the main features of the spectra are correctly reproduced. As a second test case, one of Tully's classical models was revisited, and we show that the computation of dynamical observables also profits from the importance sampling technique. In summary, the strategy developed here can be employed to assess the role of temperature for any property calculated within the nuclear ensemble method, with the same computational cost as doing so for a single temperature.

Mechanism for G2 phase-specific nuclear export of the kinetochore protein CENP-F.

PubMed

Loftus, Kyle M; Cui, Heying; Coutavas, Elias; King, David S; Ceravolo, Amanda; Pereiras, Dylan; Solmaz, Sozanne R

2017-08-03

Centromere protein F (CENP-F) is a component of the kinetochore and a regulator of cell cycle progression. CENP-F recruits the dynein transport machinery and orchestrates several cell cycle-specific transport events, including transport of the nucleus, mitochondria and chromosomes. A key regulatory step for several of these functions is likely the G2 phase-specific export of CENP-F from the nucleus to the cytosol, where the cytoplasmic dynein transport machinery resides; however, the molecular mechanism of this process is elusive. Here, we have identified 3 phosphorylation sites within the bipartite classical nuclear localization signal (cNLS) of CENP-F. These sites are specific for cyclin-dependent kinase 1 (Cdk1), which is active in G2 phase. Phosphomimetic mutations of these residues strongly diminish the interaction of the CENP-F cNLS with its nuclear transport receptor karyopherin α. These mutations also diminish nuclear localization of the CENP-F cNLS in cells. Notably, the cNLS is phosphorylated in the -1 position, which is important to orient the adjacent major motif for binding into its pocket on karyopherin α. We propose that localization of CENP-F is regulated by a cNLS, and a nuclear export pathway, resulting in nuclear localization during most of interphase. In G2 phase, the cNLS is weakened by phosphorylation through Cdk1, likely resulting in nuclear export of CENP-F via the still active nuclear export pathway. Once CENP-F resides in the cytosol, it can engage in pathways that are important for cell cycle progression, kinetochore assembly and the faithful segregation of chromosomes into daughter cells.

Nuclear translocation of glutathione S-transferase π is mediated by a non-classical localization signal.

PubMed

Kawakatsu, Miho; Goto, Shinji; Yoshida, Takako; Urata, Yoshishige; Li, Tao-Sheng

2011-08-12

Glutathione S-transferase π (GSTπ), a member of the GST family of multifunctional enzymes, is highly expressed in human placenta and involved in the protection of cellular components against electrophilic compounds or oxidative stress. We have recently found that GSTπ is expressed in the cytoplasm, mitochondria, and nucleus in some cancer cells, and that the nuclear expression of GSTπ appears to correlate with resistance to anti-cancer drugs. Although the mitochondrial targeting signal of GSTπ was previously identified in the amino-terminal region, the mechanism of nuclear translocation remains completely unknown. In this study, we find that the region of GSTπ195-208 is critical for nuclear translocation, which is mediated by a novel and non-classical nuclear localization signal. In addition, using an in vitro transport assay, we demonstrate that the nuclear translocation of GSTπ depends on the cytosolic extract and ATP. Although further experiments are needed to understand in depth the precise mechanism of nuclear translocation of GSTπ, our results may help to establish more efficient anti-cancer therapy, especially with respect to resistance to anti-cancer drugs. Copyright © 2011 Elsevier Inc. All rights reserved.

Correlated electron-nuclear dissociation dynamics: classical versus quantum motion

NASA Astrophysics Data System (ADS)

Schaupp, Thomas; Albert, Julian; Engel, Volker

2017-01-01

We investigate the coupled electron-nuclear dynamics in a model system which undergoes dissociation. In choosing different initial conditions, the cases of adiabatic and non-adiabatic dissociation are realized. We treat the coupled electronic and nuclear motion in the complete configuration space so that classically, no surface hopping procedures have to be incorporated in the case that more than a single adiabatic electronic state is populated during the fragmentation. Due to the anharmonic interaction potential, it is expected that classical mechanics substantially deviate from quantum mechanics. However, we provide examples where the densities and fragmentation yields obtained from the two treatments are in astonishingly strong agreement in the case that one starts in the electronic ground state initially. As expected, larger deviations are found if one starts in electronically excited states where trajectories are sampled from the more spatially extended electronic wave function. In that case, higher initial energies are accessed, and the motion proceeds in regions with increasing degree of anharmonicity. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

Fish genome manipulation and directional breeding.

PubMed

Ye, Ding; Zhu, ZuoYan; Sun, YongHua

2015-02-01

Aquaculture is one of the fastest developing agricultural industries worldwide. One of the most important factors for sustainable aquaculture is the development of high performing culture strains. Genome manipulation offers a powerful method to achieve rapid and directional breeding in fish. We review the history of fish breeding methods based on classical genome manipulation, including polyploidy breeding and nuclear transfer. Then, we discuss the advances and applications of fish directional breeding based on transgenic technology and recently developed genome editing technologies. These methods offer increased efficiency, precision and predictability in genetic improvement over traditional methods.

Characterization of molecular determinants for nucleocytoplasmic shuttling of PRV UL54

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Meili; Wang Shuai; Cai Mingsheng

2011-09-01

The pseudorabies virus (PRV) early protein UL54 is a homologue of the herpes simplex virus 1 (HSV-1) immediate-early protein ICP27, which is a multifunctional protein and essential for HSV-1 infection. To determine if UL54 might shuttle between the nucleus and cytoplasm, as has been shown for its homologues in human herpesviruses, the molecular determinants for its nucleocytoplasmic shuttling were investigated. Heterokaryon assays demonstrated that UL54 was a nucleocytoplasmic shuttling protein and this property could not be blocked by leptomycin B, an inhibitor of chromosome region maintenance 1 (CRM1). However, TAP/NXF1 promoted the nuclear export of UL54 and interacted with UL54,more » suggesting that UL54 shuttles between the nucleus and the cytoplasm via a TAP/NXF1, but not CRM1, dependent nuclear export pathway. Furthermore, UL54 was demonstrated to target to the nucleus through a classic Ran-, importin {beta}1- and {alpha}5-dependent nuclear import mechanism.« less

Simple and Inexpensive Classroom Demonstrations of Nuclear Magnetic Resonance and Magnetic Resonance Imaging.

ERIC Educational Resources Information Center

Olson, Joel A.; Nordell, Karen J.; Chesnik, Marla A.; Landis, Clark R.; Ellis, Arthur B.; Rzchowski, M. S.; Condren, S. Michael; Lisensky, George C.

2000-01-01

Describes a set of simple, inexpensive, classical demonstrations of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) principles that illustrate the resonance condition associated with magnetic dipoles and the dependence of the resonance frequency on environment. (WRM)

Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics

NASA Astrophysics Data System (ADS)

Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.

2018-03-01

We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. We present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

PubMed

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

PubMed

Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas

2015-09-15

Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. Copyright © 2015 Elsevier Inc. All rights reserved.

Yrb4p, a yeast ran-GTP-binding protein involved in import of ribosomal protein L25 into the nucleus.

PubMed Central

Schlenstedt, G; Smirnova, E; Deane, R; Solsbacher, J; Kutay, U; Görlich, D; Ponstingl, H; Bischoff, F R

1997-01-01

Gsp1p, the essential yeast Ran homologue, is a key regulator of transport across the nuclear pore complex (NPC). We report the identification of Yrb4p, a novel Gsp1p binding protein. The 123 kDa protein was isolated from Saccharomyces cerevisiae cells and found to be related to importin-beta, the mediator of nuclear localization signal (NLS)-dependent import into the nucleus, and to Pse1p. Like importin-beta, Yrb4p and Pse1p specifically bind to Gsp1p-GTP, protecting it from GTP hydrolysis and nucleotide exchange. The GTPase block of Gsp1p complexed to Yrb4p or Pse1p is released by Yrb1p, which contains a Gsp1p binding domain distinct from that of Yrb4p. This might reflect an in vivo function for Yrb1p. Cells disrupted for YRB4 are defective in nuclear import of ribosomal protein L25, but show no defect in the import of proteins containing classical NLSs. Expression of a Yrb4p mutant deficient in Gsp1p-binding is dominant-lethal and blocks bidirectional traffic across the NPC in wild-type cells. L25 binds to Yrb4p and Pse1p and is released by Gsp1p-GTP. Consistent with its putative role as an import receptor for L25-like proteins, Yrb4p localizes to the cytoplasm, the nucleoplasm and the NPC. PMID:9321403

Busting Myths about Nuclear Deterrence

DTIC Science & Technology

2015-01-01

clearly showed Kim Jung Un’s in- tent to develop ballistic missiles capable of delivering a nuclear warhead against an Asian ally and possibly US...consequences of such aggression against the United States. Carl von Clausewitz ob- served in his classic work, On War, that when the potential exists for

Specific Armadillo Repeat Sequences Facilitate β-Catenin Nuclear Transport in Live Cells via Direct Binding to Nucleoporins Nup62, Nup153, and RanBP2/Nup358*

PubMed Central

Sharma, Manisha; Jamieson, Cara; Johnson, Michael; Molloy, Mark P.; Henderson, Beric R.

2012-01-01

β-Catenin transduces the Wnt signal from the membrane to nucleus, and certain gene mutations trigger its nuclear accumulation leading to cell transformation and cancer. β-Catenin shuttles between the nucleus and cytoplasm independent of classical Ran/transport receptor pathways, and this movement was previously hypothesized to involve the central Armadillo (Arm) domain. Fluorescence recovery after photobleaching (FRAP) assays were used to delineate functional transport regions of the Arm domain in living cells. The strongest nuclear import/export activity was mapped to Arm repeats R10–12 using both in vivo FRAP and in vitro export assays. By comparison, Arm repeats R3–8 of β-catenin were highly active for nuclear import but displayed a comparatively weak export activity. We show for the first time using purified components that specific Arm sequences of β-catenin interact directly in vitro with the FG repeats of the nuclear pore complex (NPC) components Nup62, Nup98, and Nup153, indicating an independent ability of β-catenin to traverse the NPC. Moreover, a proteomics screen identified RanBP2/Nup358 as a binding partner of Arm R10–12, and β-catenin was confirmed to interact with endogenous and ectopic forms of Nup358. We further demonstrate that knock-down of endogenous Nup358 and Nup62 impeded the rate of nuclear import/export of β-catenin to a greater extent than that of importin-β. The Arm R10–12 sequence facilitated transport even when β-catenin was bound to the Arm-binding partner LEF-1, and its activity was stimulated by phosphorylation at Tyr-654. These findings provide functional evidence that the Arm domain contributes to regulated β-catenin transport through direct interaction with the NPC. PMID:22110128

Nuclear transport of the Neurospora crassa NIT-2 transcription factor is mediated by importin-α.

PubMed

Bernardes, Natália E; Takeda, Agnes A S; Dreyer, Thiago R; Cupertino, Fernanda B; Virgilio, Stela; Pante, Nelly; Bertolini, Maria Célia; Fontes, Marcos R M

2017-12-06

The Neurospora crassa NIT-2 transcription factor belongs to the GATA transcription factor family and plays a fundamental role in the regulation of nitrogen metabolism. Because NIT-2 acts by accessing DNA inside the nucleus, understanding the nuclear import process of NIT-2 is necessary to characterize its function. Thus, in the present study, NIT-2 nuclear transport was investigated using a combination of biochemical, cellular, and biophysical methods. A complemented strain that produced an sfGFP-NIT-2 fusion protein was constructed, and nuclear localization assessments were made under conditions that favored protein translocation to the nucleus. Nuclear translocation was also investigated using HeLa cells, which showed that the putative NIT-2 nuclear localization sequence (NLS; 915 TISSKRQRRHSKS 927 ) was recognized by importin-α and that subsequent transport occurred via the classical import pathway. The interaction between the N. crassa importin-α (NcImpα) and the NIT-2 NLS was quantified with calorimetric assays, leading to the observation that the peptide bound to two sites with different affinities, which is typical of a monopartite NLS sequence. The crystal structure of the NcImpα/NIT-2 NLS complex was solved and revealed that the NIT-2 peptide binds to NcImpα with the major NLS-binding site playing a primary role. This result contrasts other recent studies that suggested a major role for the minor NLS-binding site in importin-α from the α2 family, indicating that both sites can be used for different cargo proteins according to specific metabolic requirements. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Quasi-classical approaches to vibronic spectra revisited

NASA Astrophysics Data System (ADS)

Karsten, Sven; Ivanov, Sergei D.; Bokarev, Sergey I.; Kühn, Oliver

2018-03-01

The framework to approach quasi-classical dynamics in the electronic ground state is well established and is based on the Kubo-transformed time correlation function (TCF), being the most classical-like quantum TCF. Here we discuss whether the choice of the Kubo-transformed TCF as a starting point for simulating vibronic spectra is as unambiguous as it is for vibrational ones. Employing imaginary-time path integral techniques in combination with the interaction representation allowed us to formulate a method for simulating vibronic spectra in the adiabatic regime that takes nuclear quantum effects and dynamics on multiple potential energy surfaces into account. Further, a generalized quantum TCF is proposed that contains many well-established TCFs, including the Kubo one, as particular cases. Importantly, it also provides a framework to construct new quantum TCFs. Applying the developed methodology to the generalized TCF leads to a plethora of simulation protocols, which are based on the well-known TCFs as well as on new ones. Their performance is investigated on 1D anharmonic model systems at finite temperatures. It is shown that the protocols based on the new TCFs may lead to superior results with respect to those based on the common ones. The strategies to find the optimal approach are discussed.

Classical molecular dynamics simulation of electronically non-adiabatic processes.

PubMed

Miller, William H; Cotton, Stephen J

2016-12-22

Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

The behavior and importance of lactic acid complexation in Talspeak extraction systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimes, Travis S.; Nilsson, Mikael; Nash, Kenneth L.

2008-07-01

Advanced partitioning of spent nuclear fuel in the UREX +la process relies on the TALSPEAK process for separation of fission-product lanthanides from trivalent actinides. The classic TALSPEAK utilizes an aqueous medium of both lactic acid and diethylenetriaminepentaacetic acid and the extraction reagent di(2-ethylhexyl)phosphoric acid in an aromatic diluent. In this study, the specific role of lactic acid and the complexes involved in the extraction of the trivalent actinides and lanthanides have been investigated using {sup 14}C-labeled lactic acid. Our results show that lactic acid partitions between the phases in a complex fashion. (authors)

Nuclear quantum dynamics in dense hydrogen

PubMed Central

Kang, Dongdong; Sun, Huayang; Dai, Jiayu; Chen, Wenbo; Zhao, Zengxiu; Hou, Yong; Zeng, Jiaolong; Yuan, Jianmin

2014-01-01

Nuclear dynamics in dense hydrogen, which is determined by the key physics of large-angle scattering or many-body collisions between particles, is crucial for the dynamics of planet's evolution and hydrodynamical processes in inertial confinement confusion. Here, using improved ab initio path-integral molecular dynamics simulations, we investigated the nuclear quantum dynamics regarding transport behaviors of dense hydrogen up to the temperatures of 1 eV. With the inclusion of nuclear quantum effects (NQEs), the ionic diffusions are largely higher than the classical treatment by the magnitude from 20% to 146% as the temperature is decreased from 1 eV to 0.3 eV at 10 g/cm3, meanwhile, electrical and thermal conductivities are significantly lowered. In particular, the ionic diffusion is found much larger than that without NQEs even when both the ionic distributions are the same at 1 eV. The significant quantum delocalization of ions introduces remarkably different scattering cross section between protons compared with classical particle treatments, which explains the large difference of transport properties induced by NQEs. The Stokes-Einstein relation, Wiedemann-Franz law, and isotope effects are re-examined, showing different behaviors in nuclear quantum dynamics. PMID:24968754

Research activities in nuclear astrophysics and related areas

NASA Technical Reports Server (NTRS)

1996-01-01

NASA/GRO grant NAG 5-2081, at the University of Chicago, has provided support for a broad program of theoretical research in nuclear astrophysics and related areas, with regard to gamma-ray and hard X-ray emission from classical nova explosions. This research emphasized the possible detection of 22Na gamma-ray line emission from nearby novae involving ONeMg white dwarfs, the detailed examination of 26Al production in novae, and the possible detection of the predicted early gamma ray emission from novae that arises from the decay of the short lived, positron emitting isotopes of CNO elements. Studies of nova related problems have consumed an increasing fraction of the Principal Investigator's research efforts over the past decade. Current research addresses problems associated with the standard model for the outbursts of the classical novae: the occurrence of thermonuclear runaways (TNR) in the accreted hydrogen rich envelopes on white dwarfs in close binary systems (see, e.g., the reviews by Truran 1982; and Shara 1989). Research in progress and planned for the next three years has three main objectives: (1) to gain an improved understanding of the early evolution of the light curves of, particularly, the fastest novae; (2) to gain an improved understanding of the relative importance of the various possible mechanisms of envelope hydrogen depletion (e.g. winds, common envelope driven mass loss, and nuclear burning) to the long term evolution of novae in outburst; and (3) to seek to provide a somewhat more definitive statement of the role of classical novae in nucleosynthesis. Our proposed 2-D studies of convection during the early phases of the TNR and our systematic attempt to incorporate an improved treatment of radiation hydrodynamics into the hydrodynamic code utilized in our calculations, are particularly relevant to the first of these objectives. Further 2-D studies of the effects of common envelope evolution are intended to provide more realistic constraints on the mass depletion mechanisms. Finally, detailed calculations of the thermonuclear history of the matter ejected in novae will be carried out for representative nova configurations involving both carbon-oxygen (CO) and oxygen-neon-magnesium (ONeMg) white dwarfs.

Resource Letter NSM-1: New insights into the nuclear shell model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dean, David Jarvis; Hamilton, J. H.

2011-01-01

This Resource Letter provides a guide to the literature on the spherical shell model as applied to nuclei. The nuclear shell model describes the structure of nuclei starting with a nuclear core developed by the classical neutron and proton magic numbers N,Z=2,8,20,28,50,82, 126, where gaps occur in the single-particle energies as a shell is filled, and the interactions of valence nucleons that reside beyond that core. Various modern extensions of this model for spherical nuclei are likewise described. Significant extensions of the nuclear shell model include new magic numbers for spherical nuclei and now for deformed nuclei as well. Whenmore » both protons and neutrons have shell gaps at the same spherical or deformed shapes, they can reinforce each other to give added stability to that shape and lead to new magic numbers. The vanishings of the classical spherical shell model energy gaps and magic numbers in new neutron-rich nuclei are described. Spherical and deformed shell gaps are seen to be critical for the existence of elements with Z > 100.« less

Quantum indistinguishability in chemical reactions.

PubMed

Fisher, Matthew P A; Radzihovsky, Leo

2018-05-15

Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high-temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent, and thus well approximated classically. We explore enzymatic chemical reactions involving small symmetric molecules and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "quantum dynamical selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally nonsymmetric molecular states. As we propose and discuss, the implications of the QDS rule include ( i ) a differential chemical reactivity of para- and orthohydrogen, ( ii ) a mechanism for inducing intermolecular quantum entanglement of nuclear spins, ( iii ) a mass-independent isotope fractionation mechanism, ( iv ) an explanation of the enhanced chemical activity of "reactive oxygen species", ( v ) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, and ( vi ) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.

Nuclear quantum effects on structure and transport properties of dense liquid helium

NASA Astrophysics Data System (ADS)

Kang, Dongdong; Dai, Jiayu; Yuan, Jianmin

2015-11-01

Transport properties of dense liquid helium under the conditions of planet's core and cool atmosphere of white dwarfs are important for determining the structure and evolution of these astrophysical objects. We have investigated these properties of dense liquid helium by using the improved centroid path-integral simulations combined with density functional theory. The results show that with the inclusion of nuclear quantum effects (NQEs), the self-diffusion is largely higher while the shear viscosity is notably lower than the results of without the inclusion of NQEs due to the lower collision cross sections even when the NQEs have little effects on the static structures. The potential surface of helium atom along the simulation trajectory is quite different between MD and PIMD simulations. We have shown that the quantum nuclear character induces complex behaviors for ionic transport properties of dense liquid helium. NQEs bring more fluctuations of local electronic density of states than the classical treatment. Therefore, in order to construct more reasonable structure and evolution model for the planets and WDs, NQEs must be reconsidered when calculating the transport properties at certain temperature and density conditions.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Initial angular momentum and flow in high energy nuclear collisions

NASA Astrophysics Data System (ADS)

Fries, Rainer J.; Chen, Guangyao; Somanathan, Sidharth

2018-03-01

We study the transfer of angular momentum in high energy nuclear collisions from the colliding nuclei to the region around midrapidity, using the classical approximation of the color glass condensate (CGC) picture. We find that the angular momentum shortly after the collision (up to times ˜1 /Qs , where Qs is the saturation scale) is carried by the "β -type" flow of the initial classical gluon field, introduced by some of us earlier. βi˜μ1∇iμ2-μ2∇iμ1 (i =1 ,2 ) describes the rapidity-odd transverse energy flow and emerges from Gauss's law for gluon fields. Here μ1 and μ2 are the averaged color charge fluctuation densities in the two nuclei, respectively. Interestingly, strong coupling calculations using anti-de Sitter/conformal field theory (AdS/CFT) techniques also find an energy flow term featuring this particular combination of nuclear densities. In classical CGC the order of magnitude of the initial angular momentum per rapidity in the reaction plane, at a time 1 /Qs , is |d L2/d η |≈ RAQs-3ɛ¯0/2 at midrapidity, where RA is the nuclear radius, and ɛ¯0 is the average initial energy density. This result emerges as a cancellation between a vortex of energy flow in the reaction plane aligned with the total angular momentum, and energy shear flow opposed to it. We discuss in detail the process of matching classical Yang-Mills results to fluid dynamics. We will argue that dissipative corrections should not be discarded to ensure that macroscopic conservation laws, e.g., for angular momentum, hold. Viscous fluid dynamics tends to dissipate the shear flow contribution that carries angular momentum in boost-invariant fluid systems. This leads to small residual angular momentum around midrapidity at late times for collisions at high energies.

Scaling relationships for nonadiabatic energy relaxation times in warm dense matter: toward understanding the equation of state.

PubMed

Pradhan, Ekadashi; Magyar, Rudolph J; Akimov, Alexey V

2016-11-30

Understanding the dynamics of electron-ion energy transfer in warm dense (WD) matter is important to the measurement of equation of state (EOS) properties and for understanding the energy balance in dynamic simulations. In this work, we present a comprehensive investigation of nonadiabatic electron relaxation and thermal excitation dynamics in aluminum under high pressure and temperature. Using quantum-classical trajectory surface hopping approaches, we examine the role of nonadiabatic couplings and electronic decoherence in electron-nuclear energy transfer in WD aluminum. The computed timescales range from 400 fs to 4.0 ps and are consistent with existing experimental studies. We have derived general scaling relationships between macroscopic parameters of WD systems such as temperature or mass density and the timescales of energy redistribution between quantum and classical degrees of freedom. The scaling laws are supported by computational results. We show that electronic decoherence plays essential role and can change the functional dependencies qualitatively. The established scaling relationships can be of use in modelling of WD matter.

Scale invariance in chaotic time series: Classical and quantum examples

NASA Astrophysics Data System (ADS)

Landa, Emmanuel; Morales, Irving O.; Stránský, Pavel; Fossion, Rubén; Velázquez, Victor; López Vieyra, J. C.; Frank, Alejandro

Important aspects of chaotic behavior appear in systems of low dimension, as illustrated by the Map Module 1. It is indeed a remarkable fact that all systems tha make a transition from order to disorder display common properties, irrespective of their exacta functional form. We discuss evidence for 1/f power spectra in the chaotic time series associated in classical and quantum examples, the one-dimensional map module 1 and the spectrum of 48Ca. A Detrended Fluctuation Analysis (DFA) method is applied to investigate the scaling properties of the energy fluctuations in the spectrum of 48Ca obtained with a large realistic shell model calculation (ANTOINE code) and with a random shell model (TBRE) calculation also in the time series obtained with the map mod 1. We compare the scale invariant properties of the 48Ca nuclear spectrum sith similar analyses applied to the RMT ensambles GOE and GDE. A comparison with the corresponding power spectra is made in both cases. The possible consequences of the results are discussed.

Structural and mechanistic insights into nuclear transport and delivery of the critical pluripotency factor Oct4 to DNA.

PubMed

Okuyama, Takahide; Yamagishi, Ryosuke; Shimada, Jiro; Ikeda, Masaaki; Maruoka, Yayoi; Kaneko, Hiroki

2018-02-01

Oct4 is a master regulator of the induction and maintenance of cellular pluripotency, and has crucial roles in early stages of differentiation. It is the only factor that cannot be substituted by other members of the same protein family to induce pluripotency. However, although Oct4 nuclear transport and delivery to target DNA are critical events for reprogramming to pluripotency, little is known about the molecular mechanism. Oct4 is imported to the nucleus by the classical nuclear transport mechanism, which requires importin α as an adaptor to bind the nuclear localization signal (NLS). Although there are structures of complexes of the NLS of transcription factors (TFs) in complex with importin α, there are no structures available for complexes involving intact TFs. We have therefore modeled the structure of the complex of the whole Oct4 POU domain and importin α2 using protein-protein docking and molecular dynamics. The model explains how the Ebola virus VP24 protein has a negative effect on the nuclear import of STAT1 by importin α but not on Oct4, and how Nup 50 facilitates cargo release from importin α. The model demonstrates the structural differences between the Oct4 importin α bound and DNA bound crystal states. We propose that the 'expanded linker' between the two DNA-binding domains of Oct4 is an intrinsically disordered region and that its conformational changes have a key role in the recognition/binding to both DNA and importin α. Moreover, we propose that this structural change enables efficient delivery to DNA after release from importin α.

Adrenocortical nuclear progesterone-binding protein: Identification by photoaffinity labeling and evidence for deoxyribonucleic acid binding and stimulation by adrenocorticotropin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demura, T.; Driscoll, W.J.; Lee, Y.C.

1991-01-01

Nuclei of the guinea pig adrenal cortex contain a protein that specifically binds progesterone and that, biochemically, is clearly distinct from the classical progesterone receptor. The adrenocortical nuclear progesterone-binding protein has now been purified more than 2000-fold by steroid-affinity chromatography with a 75% yield. The purified protein preparation demonstrated three major bands on sodium dodecyl sulfate-polyacrylamide gel of 79K, 74K, and 50K. To determine which of the three might represent the progesterone-binding protein, steroid photoaffinity labeling was performed which resulted in the specific and exclusive labeling of a 50K band. Thus, the adrenocortical nuclear progesterone-binding protein appears to be distinctmore » from the classical progesterone receptor not only biochemically, but also on the basis of molecular size. To test whether the adrenocortical nuclear progesterone-binding protein can be hormonally stimulated, guinea pigs were treated with ACTH. The chronic administration of ACTH caused a 4- to 6-fold increase in the specific progesterone binding capacity without a change in the binding affinity. There appeared to be no significant difference in nuclear progesterone binding between the zona fasciculata and zona reticularis. This finding suggests a mediating role for the progesterone-binding protein in ACTH action. In addition, the nuclear progesterone-binding protein bound to nonspecific DNA sequences, further suggesting a possible transcriptional regulatory role.« less

Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka, E-mail: kinjo@sci.hokudai.ac.jp

2015-07-31

Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS{sup SV40}) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesismore » takes place. GFP-NLS{sup SV40} in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS{sup SV40} formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS{sup SV40} likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS{sup SV40} can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. - Highlights: • Nuclear localization signal-tagged GFP (GFP-NLS) showed clear nuclear localization. • The GFP-NLS dynamically localized not only in the nucleoplasm, but also to the nucleolus. • The nuclear localization of GFP-NLS results from transient oligomerization mediated via RNA binding. • Our NLS-tagging procedure is ideal for use in artificial sequestration of proteins in the nucleus.« less

Hybrid Quantum-Classical Approach to Quantum Optimal Control.

PubMed

Li, Jun; Yang, Xiaodong; Peng, Xinhua; Sun, Chang-Pu

2017-04-14

A central challenge in quantum computing is to identify more computational problems for which utilization of quantum resources can offer significant speedup. Here, we propose a hybrid quantum-classical scheme to tackle the quantum optimal control problem. We show that the most computationally demanding part of gradient-based algorithms, namely, computing the fitness function and its gradient for a control input, can be accomplished by the process of evolution and measurement on a quantum simulator. By posing queries to and receiving answers from the quantum simulator, classical computing devices update the control parameters until an optimal control solution is found. To demonstrate the quantum-classical scheme in experiment, we use a seven-qubit nuclear magnetic resonance system, on which we have succeeded in optimizing state preparation without involving classical computation of the large Hilbert space evolution.

Quantum versus classical hyperfine-induced dynamics in a quantum dota)

NASA Astrophysics Data System (ADS)

Coish, W. A.; Loss, Daniel; Yuzbashyan, E. A.; Altshuler, B. L.

2007-04-01

In this article we analyze spin dynamics for electrons confined to semiconductor quantum dots due to the contact hyperfine interaction. We compare mean-field (classical) evolution of an electron spin in the presence of a nuclear field with the exact quantum evolution for the special case of uniform hyperfine coupling constants. We find that (in this special case) the zero-magnetic-field dynamics due to the mean-field approximation and quantum evolution are similar. However, in a finite magnetic field, the quantum and classical solutions agree only up to a certain time scale t <τc, after which they differ markedly.

A Transferrable Belief Model Representation for Physical Security of Nuclear Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

David Gerts

This work analyzed various probabilistic methods such as classic statistics, Bayesian inference, possibilistic theory, and Dempster-Shafer theory of belief functions for the potential insight offered into the physical security of nuclear materials as well as more broad application to nuclear non-proliferation automated decision making theory. A review of the fundamental heuristic and basic limitations of each of these methods suggested that the Dempster-Shafer theory of belief functions may offer significant capability. Further examination of the various interpretations of Dempster-Shafer theory, such as random set, generalized Bayesian, and upper/lower probability demonstrate some limitations. Compared to the other heuristics, the transferrable beliefmore » model (TBM), one of the leading interpretations of Dempster-Shafer theory, can improve the automated detection of the violation of physical security using sensors and human judgment. The improvement is shown to give a significant heuristic advantage over other probabilistic options by demonstrating significant successes for several classic gedanken experiments.« less

β Decay as a Probe of Explosive Nucleosynthesis in Classical Novae

NASA Astrophysics Data System (ADS)

Wrede, C.; Bennett, M. B.; Liddick, S. N.; Bardayan, D. W.; Bowe, A.; Brown, B. A.; Chen, A. A.; Chipps, K. A.; Cooper, N.; Fry, C.; Glassman, B.; Irvine, D.; José, J.; Langer, C.; Larson, N.; McNeice, E. I.; Meisel, Z.; Montes, F.; Naqvi, F.; Pain, S. D.; O'Malley, P.; Ortez, R.; Ong, W.; Pereira, J.; Pérez-Loureiro, D.; Prokop, C.; Quaglia, J.; Quinn, S.; Santia, M.; Schatz, H.; Schwartz, S. B.; Simon, A.; Shanab, S.; Spyrou, A.; Suchyta, S.; Thiagalingam, E.; Thompson, P.; Walters, M.

Classical novae are common thermonuclear explosions in the Milky Way galaxy, occurring on the surfaces of white-dwarf stars that are accreting hydrogen-rich material from companion stars. Nucleosynthesis in classical novae depends on radiative proton-capture reaction rates on radioactive nuclides. Many of these reactions cannot be measured directly at current accelerator facilities due to the lack of intense, high-quality, radioactive-ion beams at the relevant energies. Since most of these reactions proceed via resonant capture, their rates can be determined indirectly by measuring the properties of the resonances. At the National Superconducting Cyclotron Laboratory, we have used the β-delayed γ decays of 26P and 31Cl to populate resonances in 26Si and 31S and study the radiative proton captures on 25Al and 30P, respectively. These were two out of the three most important nuclear-physics uncertainties associated with the observable products of nova nucleosynthesis. The 26P experiment has enabled a more accurate estimate of the nova contribution to the long-lived Galactic 26Al detected with γ-ray telescopes. The 31Cl experiment, currently under analysis, will calibrate potential nova thermometers and mixing meters based on elemental abundance ratios, and facilitate the identification of pre-solar nova grain candidates found in primitive meteorites based on isotopic ratios.

Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

PubMed Central

Smirnov, Alexandre; Entelis, Nina; Martin, Robert P.; Tarassov, Ivan

2011-01-01

5S rRNA is an essential component of ribosomes of all living organisms, the only known exceptions being mitochondrial ribosomes of fungi, animals, and some protists. An intriguing situation distinguishes mammalian cells: Although the mitochondrial genome contains no 5S rRNA genes, abundant import of the nuclear DNA-encoded 5S rRNA into mitochondria was reported. Neither the detailed mechanism of this pathway nor its rationale was clarified to date. In this study, we describe an elegant molecular conveyor composed of a previously identified human 5S rRNA import factor, rhodanese, and mitochondrial ribosomal protein L18, thanks to which 5S rRNA molecules can be specifically withdrawn from the cytosolic pool and redirected to mitochondria, bypassing the classic nucleolar reimport pathway. Inside mitochondria, the cytosolic 5S rRNA is shown to be associated with mitochondrial ribosomes. PMID:21685364

Thin layer activation techniques at the U-120 cyclotron of Bucharest

NASA Astrophysics Data System (ADS)

Constantinescu, B.; Ivanov, E. A.; Pascovici, G.; Popa-Simil, L.; Racolta, P. M.

1994-05-01

The Thin Layer Activation (TLA) technique is a nuclear method especially used for different types of wear (or corrosion) investigations. Experimental results for selection criteria of nuclear reactions for various tribological studies, using the IPNE U-120 classical variable energy Cyclotron are presented. Measuring methods for the main types of wear phenomena and home made instrumentations dedicated for TLA industrial applications are also reported. Some typical TLA tribological applications, a nuclear scanning method to obtain wear profile of piston-rings are presented as well.

Proton relays in anomalous carbocations dictate spectroscopy, stability, and mechanisms: case studies on C2H5+ and C3H3.

PubMed

Sager, LeeAnn M; Iyengar, Srinivasan S

2017-10-18

We present a detailed analysis of the anomalous carbocations: C 2 H 5 + and C 3 H 3 + . This work involves (a) probing electronic structural properties, (b) ab initio dynamics simulations over a range of internal energies, (c) analysis of reduced dimensional potential surfaces directed along selected conformational transition pathways, (d) dynamically averaged vibrational spectra computed from ab initio dynamics trajectories, and (e) two-dimensional time-frequency analysis to probe conformational dynamics. Key findings are as follows: (i) as noted in our previous study on C 2 H 3 + , it appears that these non-classical carbocations are stabilized by delocalized nuclear frameworks and "proton shuttles". We analyze this nuclear delocalization and find critical parallels between conformational changes in C 2 H 3 + , C 2 H 5 + , and C 3 H 3 + . (ii) The vibrational signatures of C 2 H 5 + are dominated by the "bridge-proton" conformation, but also show critical contributions from the "classical" configuration, which is a transition state at almost all levels of theory. This result is further substantiated through two-dimensional time-frequency analysis and is at odds with earlier explanations of the experimental spectra, where frequencies close to the classical region were thought to arise from an impurity. While this is still possible, our results here indicate an additional (perhaps more likely) explanation that involves the "classical" isomer. (iii) Finally, in the case of C 3 H 3 + our explanation of the experimental result includes the presence of multiple, namely, "cyclic", "straight", and propargyl, configurations. Proton shuttles and nuclear delocalization, reminiscent of those seen in the case of C 2 H 3 + , were seen all through and have a critical role in all our observations.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

Nuclear reaction rate uncertainties and the 22Ne( p,gamma)23Na reaction: Classical novae and globular clusters

NASA Astrophysics Data System (ADS)

Kelly, Keegan John

The overall theme of this thesis is the advancement of nuclear astrophysics via the analysis of stellar processes in the presence of varying levels of precision in the available nuclear data. With regard to classical novae, the level of mixing that occurs between the outer layers of the white dwarf core and the solar accreted material in oxygen-neon novae is presently undetermined by stellar models, but the nuclear data relevant to these explosive phenomena are fairly precise. This precision allowed for the identification of a series of elemental ratios indicative of the level of mixing occurring in novae. Direct comparisons of the modelled elemental ratios to observations showed that there is likely to be much less of this mixing than was previously assumed. Thus, our understanding of classical novae was altered via the investigation of the nuclear reactions relevant to this phenomenon. However, this level of experimental precision is rare and large nuclear reaction uncertainties can hinder our understanding of certain astrophysical phenomena. For example, it is commonly believed that uncertainties in the 22Ne(p,g)23Na reaction rate at temperatures relevant to thermally-pulsing asymptotic giant branch stars are largely responsible for our inability to explain the observed sodium-oxygen anti-correlation in globular clusters. With this motivation, resonances in the 22Ne(p,g) 23Na reaction at E_{c.m.} = 458, 417, 178, and 151 keV were measured. The direct-capture contribution was also measured at E_{lab} = 425 keV. It was determined that the 22Ne(p,g)23Na reaction rate in the astrophysically relevant temperature range is dominated by the resonances at 178 and 151 keV and that the total reaction rate is greater than the previously assumed rate by a factor of approximately ˜40 at 0.15 GK. This increased reaction rate impacts the expected nucleosynthesis that occurs in these stars and will shed light onto the origin of this anti-correlation as it is incorporated into sophisticated stellar models in the future. In both of these cases the available nuclear data were used to probe stellar processes. This analysis of stellar processes through nuclear reactions is an extremely useful technique that is crucial for the advancement of astrophysics.

Nuclear quantum effects in electronically adiabatic quantum time correlation functions: Application to the absorption spectrum of a hydrated electron

NASA Astrophysics Data System (ADS)

Turi, László; Hantal, György; Rossky, Peter J.; Borgis, Daniel

2009-07-01

A general formalism for introducing nuclear quantum effects in the expression of the quantum time correlation function of an operator in a multilevel electronic system is presented in the adiabatic limit. The final formula includes the nuclear quantum time correlation functions of the operator matrix elements, of the energy gap, and their cross terms. These quantities can be inferred and evaluated from their classical analogs obtained by mixed quantum-classical molecular dynamics simulations. The formalism is applied to the absorption spectrum of a hydrated electron, expressed in terms of the time correlation function of the dipole operator in the ground electronic state. We find that both static and dynamic nuclear quantum effects distinctly influence the shape of the absorption spectrum, especially its high energy tail related to transitions to delocalized electron states. Their inclusion does improve significantly the agreement between theory and experiment for both the low and high frequency edges of the spectrum. It does not appear sufficient, however, to resolve persistent deviations in the slow Lorentzian-like decay part of the spectrum in the intermediate 2-3 eV region.

Exclusive nuclear location of estrogen receptors in Squalus testis.

PubMed Central

Callard, G V; Mak, P

1985-01-01

An estrogen (E)-binding molecule having both occupied and unoccupied sites is restricted to nuclear subfractions in the testis of the spiny dogfish (Squalus acanthias). We investigated the hypothesis that a species characterized by high body-fluid osmolarity (1010 mosM) has an estrogen receptor (ER) that binds to chromatin with high affinity and consequently resists redistribution during tissue processing. Although the steroid binding and sedimentation properties of the Squalus nuclear ER conformed to those of classical ER, its elution maximum from DNA-cellulose was unusually high (0.55 M NaCl). A tendency to adhere tightly to cell nuclei was reflected in the high salt concentration (0.43 M KCl) required to extract 50% of the receptors from the nuclear compartment during homogenization and in the stability of the nuclear ER population in the presence of high concentrations of a nonionic solute (urea) or increased buffer volume. Mixing and redistribution experiments showed that nuclear ER could be quantitatively and qualitatively measured in cytosolic extracts, ruling out the possibility that soluble receptors were being masked. Although Squalus oviduct ER was similar to that of testis, ER in the testis and liver of a related elasmobranch (Potamotrygon) that maintains osmotic equilibrium at 300 mosM more closely resembled mammalian ER in its elution maximum from DNA-cellulose (0.22 M NaCl) and cytosolic/nuclear ratios in low-salt buffers. We conclude that Squalus testis has a single ER pool located exclusively in the nuclear compartment. These observations support a revised concept of steroid action and further indicate that the chromatin affinity of the hormone-ER complex is an important factor in determining subfractional distribution during tissue processing. PMID:3856265

The Neutron's Discovery - 80 Years on

NASA Astrophysics Data System (ADS)

Rogers, John D.

A brief review is given of selected highlights in scientific developments from the birth of modern nuclear physics at the end of the 19th century to the discovery of the neutron in 1932. This is followed by some important milestones in neutron and reactor physics that have led to our current understanding and implementation of nuclear technologies. The beginnings can be traced back to the discovery of X-rays by Roentgen, the identification of natural radioactivity by Becquerel and the discovery of the electron by Thomson, towards the end of the 19th Century. Rutherford was a key figure in experimental physics who determined the structure of the atom and who inspired his students at McGill, Manchester and Cambridge Universities (many of whom would become Nobel laureates) in the pursuit of their physics research. One of Rutherford's students, James Chadwick, had studied the work carried out by Bothe and Becker on alpha particle-induced disintegration of light elements which had led to their observation of high energy penetrating radiation that neither they nor the Joliot-Curies could identify. Chadwick knew that the only possible explanation was the emission of a neutron in the nuclear reaction. He carried out tests in the Cavendish Laboratory and submitted his now classical paper identifying the neutron to the periodical Nature in 1932. The discovery of the neutron and of nuclear fission in 1939 opened up new areas for scientific investigation, in, for example, astrophysics, geology, neutron and nuclear physics. The prospects for nuclear power in particular appeared to be unlimited and both civil and military applications have been actively pursued. Many new experimental facilities have been designed and built to provide intense sources of neutrons for research purposes. Work carried out in such centres is included in the programme of the 7th International Topical Meeting on Neutron Radiography, an important forum for discussion of the latest research work of this ever-growing scientific community.

Nuclear physics: Macroscopic aspects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiatecki, W.J.

1993-12-01

A systematic macroscopic, leptodermous approach to nuclear statics and dynamics is described, based formally on the assumptions {h_bar} {yields} 0 and b/R << 1, where b is the surface diffuseness and R the nuclear radius. The resulting static model of shell-corrected nuclear binding energies and deformabilities is accurate to better than 1 part in a thousand and yields a firm determination of the principal properties of the nuclear fluid. As regards dynamics, the above approach suggests that nuclear shape evolutions will often be dominated by dissipation, but quantitative comparisons with experimental data are more difficult than in the case ofmore » statics. In its simplest liquid drop version the model exhibits interesting formal connections to the classic astronomical problem of rotating gravitating masses.« less

δ- and γ-tocotrienols induce classical ultrastructural apoptotic changes in human T lymphoblastic leukemic cells.

PubMed

Wong, Rebecca S Y; Radhakrishnan, Ammu K; Ibrahim, Tengku Azmi Tengku; Cheong, Soon-Keng

2012-06-01

Tocotrienols are isomers of the vitamin E family, which have been reported to exert cytotoxic effects in various cancer cells. Although there have been some reports on the effects of tocotrienols in leukemic cells, ultrastructural evidence of tocotrienol-induced apoptotic cell death in leukemic cells is lacking. The present study investigated the effects of three isomers of tocotrienols (alpha, delta, and gamma) on a human T lymphoblastic leukemic cell line (CEM-SS). Cell viability assays showed that all three isomers had cytotoxic effects (p < 0.05) on CEM-SS cells with delta-tocotrienol being the most potent. Transmission electron microscopy showed that the cytotoxic effects by delta- and gamma-tocotrienols were through the induction of an apoptotic pathway as demonstrated by the classical ultrastructural apoptotic changes characterized by peripheral nuclear chromatin condensation and nuclear fragmentation. These findings were confirmed biochemically by the demonstration of phosphatidylserine externalization via flow cytometry analysis. This is the first study showing classical ultrastructural apoptotic changes induced by delta- and gamma-tocotrienols in human T lymphoblastic leukemic cells.

Influence of collective nonideal shielding on fusion reaction in partially ionized classical nonideal plasmas

NASA Astrophysics Data System (ADS)

Lee, Myoung-Jae; Jung, Young-Dae

2017-04-01

The collective nonideal effects on the nuclear fusion reaction process are investigated in partially ionized classical nonideal hydrogen plasmas. The effective pseudopotential model taking into account the collective and plasma shielding effects is applied to describe the interaction potential in nonideal plasmas. The analytic expressions of the Sommerfeld parameter, the fusion penetration factor, and the cross section for the nuclear fusion reaction in nonideal plasmas are obtained as functions of the nonideality parameter, Debye length, and relative kinetic energy. It is found that the Sommerfeld parameter is suppressed due to the influence of collective nonideal shielding. However, the collective nonideal shielding is found to enhance the fusion penetration factor in partially ionized classical nonideal plasmas. It is also found that the fusion penetration factors in nonideal plasmas represented by the pseudopotential model are always greater than those in ideal plasmas represented by the Debye-Hückel model. In addition, it is shown that the collective nonideal shielding effect on the fusion penetration factor decreases with an increase of the kinetic energy.

Manifestations of classical physics in the quantum evolution of correlated spin states in pulsed NMR experiments.

PubMed

Ligare, Martin

2016-05-01

Multiple-pulse NMR experiments are a powerful tool for the investigation of molecules with coupled nuclear spins. The product operator formalism provides a way to understand the quantum evolution of an ensemble of weakly coupled spins in such experiments using some of the more intuitive concepts of classical physics and semi-classical vector representations. In this paper I present a new way in which to interpret the quantum evolution of an ensemble of spins. I recast the quantum problem in terms of mixtures of pure states of two spins whose expectation values evolve identically to those of classical moments. Pictorial representations of these classically evolving states provide a way to calculate the time evolution of ensembles of weakly coupled spins without the full machinery of quantum mechanics, offering insight to anyone who understands precession of magnetic moments in magnetic fields.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ciomperlik, Jessica J.; Basta, Holly A.; Palmenberg, Ann C., E-mail: acpalmen@wisc.edu

Cardiovirus infections inhibit nucleocytoplasmic trafficking by Leader protein-induced phosphorylation of Phe/Gly-containing nucleoporins (Nups). Recombinant Leader from encephalomyocarditis virus, Theiler's murine encephalomyelitis virus and Saffold virus target the same subset of Nups, including Nup62 and Nup98, but not Nup50. Reporter cell lines with fluorescence mCherry markers for M9, RS and classical SV40 import pathways, as well as the Crm1-mediated export pathway, all responded to transfection with the full panel of Leader proteins, showing consequent cessation of path-specific active import/export. For this to happen, the Nups had to be presented in the context of intact nuclear pores and exposed to cytoplasmic extracts.more » The Leader phosphorylation cascade was not effective against recombinant Nup proteins. The findings support a model of Leader-dependent Nup phosphorylation with the purpose of disrupting Nup-transportin interactions. - Highlights: • Nup98, but not Nup50 becomes phosphorylated by cardiovirus Leader protein-dependent mechanisms. • At least four independent nucleocytoplasmic trafficking pathways are inhibited by this process. • Nups must be presented in a nuclear pore context for Leader-directed phosphorylation. • Leader, by itself, does not cause activation of cellular kinases.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eich, F. G.; Agostini, Federica, E-mail: agostini@mpi-halle.mpg.de

We propose a procedure to analyze the relation between the exact factorization of the electron-nuclear wave function and the Born-Oppenheimer approximation. We define the adiabatic limit as the limit of infinite nuclear mass. To this end, we introduce a unit system that singles out the dependence on the electron-nuclear mass ratio of each term appearing in the equations of the exact factorization. We observe how non-adiabatic effects induced by the coupling to the nuclear motion affect electronic properties and we analyze the leading term, connecting it to the classical nuclear momentum. Its dependence on the mass ratio is tested numericallymore » on a model of proton-coupled electron transfer in different non-adiabatic regimes.« less

Pitfalls in classical nuclear medicine: myocardial perfusion imaging

NASA Astrophysics Data System (ADS)

Fragkaki, C.; Giannopoulou, Ch

2011-09-01

Scintigraphic imaging is a complex functional procedure subject to a variety of artefacts and pitfalls that may limit its clinical and diagnostic accuracy. It is important to be aware of and to recognize them when present and to eliminate them whenever possible. Pitfalls may occur at any stage of the imaging procedure and can be related with the γ-camera or other equipment, personnel handling, patient preparation, image processing or the procedure itself. Often, potential causes of artefacts and pitfalls may overlap. In this short review, special interest will be given to cardiac scintigraphic imaging. Most common causes of artefact in myocardial perfusion imaging are soft tissue attenuation as well as motion and gating errors. Additionally, clinical problems like cardiac abnormalities may cause interpretation pitfalls and nuclear medicine physicians should be familiar with these in order to ensure the correct evaluation of the study. Artefacts or suboptimal image quality can also result from infiltrated injections, misalignment in patient positioning, power instability or interruption, flood field non-uniformities, cracked crystal and several other technical reasons.

Educational activities with a tandem accelerator

NASA Astrophysics Data System (ADS)

Casolaro, P.; Campajola, L.; Balzano, E.; D'Ambrosio, E.; Figari, R.; Vardaci, E.; La Rana, G.

2018-05-01

Selected experiments in fundamental physics have been proposed for many years at the Tandem Accelerator of the University of Napoli ‘Federico II’s Department of Physics as a part of a one-semester laboratory course for graduate students. The aim of this paper is to highlight the educational value of the experimental realization of the nuclear reaction 19F(p,α)16O. With the purpose of verifying the mass-energy equivalence principle, different aspects of both classical and modern physics can be investigated, e.g. conservation laws, atomic models, nuclear physics applications to compositional analysis, nuclear cross-section, Q-value and nuclear spectroscopic analysis.

Classic Galaxy with Glamour

NASA Image and Video Library

2005-04-11

Young hot blue stars dominate the outer spiral arms of nearby galaxy NGC 300, while the older stars congregate in the nuclear regions which appear yellow-green in this image from NASA Galaxy Evolution Explorer.

Study of central light concentration in nearby galaxies

NASA Astrophysics Data System (ADS)

Aswathy, S.; Ravikumar, C. D.

2018-06-01

We propose a novel technique to estimate the masses of supermassive black holes (SMBHs) residing at the centres of massive galaxies in the nearby Universe using simple photometry. Aperture photometry using SEXTRACTOR is employed to determine the central intensity ratio (CIR) at the optical centre of the galaxy image for a sample of 49 nearby galaxies with SMBH mass estimations. We find that the CIR of ellipticals and classical bulges is strongly correlated with SMBH masses whereas pseudo-bulges and ongoing mergers show significant scatter. Also, the CIR of low-luminosity AGNs in the sample shows significant connection with the 5 GHz nuclear radio emission suggesting a stronger link between the former and the SMBH evolution in these galaxies. In addition, it is seen that various structural and dynamical properties of the SMBH host galaxies are correlated with the CIR making the latter an important parameter in galaxy evolution studies. Finally, we propose the CIR to be an efficient and simple tool not only to distinguish classical bulges from pseudo-bulges but also to estimate the mass of the central SMBH.

Signaling, physiological functions and clinical relevance of the G protein-coupled estrogen receptor GPER.

PubMed

Prossnitz, Eric R; Barton, Matthias

2009-09-01

GPR30, now named GPER1 (G protein-coupled estrogen receptor1) or GPER here, was first identified as an orphan 7-transmembrane G protein-coupled receptor by multiple laboratories using either homology cloning or differential expression and subsequently shown to be required for estrogen-mediated signaling in certain cancer cells. The actions of estrogen are extensive in the body and are thought to be mediated predominantly by classical nuclear estrogen receptors that act as transcription factors/regulators. Nevertheless, certain aspects of estrogen function remain incompatible with the generally accepted mechanisms of classical estrogen receptor action. Many recent studies have revealed that GPER contributes to some of the actions of estrogen, including rapid signaling events and rapid transcriptional activation. With the introduction of GPER-selective ligands and GPER knockout mice, the functions of GPER are becoming more clearly defined. In many cases, there appears to be a complex interplay between the two receptor systems, suggesting that estrogen-mediated physiological responses may be mediated by either receptor or a combination of both receptor types, with important medical implications.

GPR30: a novel therapeutic target in estrogen-related disease.

PubMed

Prossnitz, Eric R; Sklar, Larry A; Oprea, Tudor I; Arterburn, Jeffrey B

2008-03-01

Estrogen is a crucial hormone in human physiology that regulates a multitude of biological processes. It is also an important target in many diseases such as cancer and skeletal, neurological and immunological conditions. The actions of estrogen have traditionally been ascribed to one of two closely related classical nuclear hormone receptors, ERalpha and ERbeta, which are best characterized for regulating gene expression. Recent studies have revealed the contribution of a novel estrogen receptor GPR30, which belongs to the family of seven-transmembrane G-protein-coupled receptors, to many of the rapid biological responses to estrogen. Many drugs, such as tamoxifen and fulvestrant, which seem to selectively inhibit the activities of the classical estrogen receptors, are in widespread clinical use. However, recent results indicate that these same drugs activate multiple cellular-signaling pathways via GPR30. Unraveling the pharmacological profiles and specificities of ERalpha, ERbeta and GPR30 will be vital for understanding not only the physiological roles of each receptor but also for the development of the next generation of receptor-specific drugs.

Functional renal imaging: new trends in radiology and nuclear medicine.

PubMed

Durand, Emmanuel; Chaumet-Riffaud, Philippe; Grenier, Nicolas

2011-01-01

The objective of this work is to compare the characteristics of various techniques for functional renal imaging, with a focus on nuclear medicine and magnetic resonance imaging. Even with low spatial resolution and rather poor signal-to-noise ratio, classical nuclear medicine has the advantage of linearity and good sensitivity. It remains the gold standard technique for renal relative functional assessment. Technetium-99m ((99m)Tc)-labeled diethylenetriamine penta-acetate remains the reference glomerular tracer. Tubular tracers have been improved: (123)I- or (131)I-hippuran, (99m)Tc-MAG3 and, recently, (99m)Tc-nitrilotriacetic acid. However, advancement in molecular imaging has not produced a groundbreaking tracer. Renal magnetic resonance imaging with classical gadolinated tracers probably has potential in this domain but has a lack of linearity and, therefore, its value still needs evaluation. Moreover, the advent of nephrogenic systemic fibrosis has delayed its expansion. Other developments, such as diffusion or blood oxygen level-dependent imaging, may have a role in the future. The other modalities have a limited role in clinical practice for functional renal imaging. Copyright © 2011 Elsevier Inc. All rights reserved.

A Game Theoretic Model of Thermonuclear Cyberwar

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soper, Braden C.

In this paper we propose a formal game theoretic model of thermonuclear cyberwar based on ideas found in [1] and [2]. Our intention is that such a game will act as a first step toward building more complete formal models of Cross-Domain Deterrence (CDD). We believe the proposed thermonuclear cyberwar game is an ideal place to start on such an endeavor because the game can be fashioned in a way that is closely related to the classical models of nuclear deterrence [4–6], but with obvious modifications that will help to elucidate the complexities introduced by a second domain. We startmore » with the classical bimatrix nuclear deterrence game based on the game of chicken, but introduce uncertainty via a left-of-launch cyber capability that one or both players may possess.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirano, Hidemi; Matsuura, Yoshiyuki, E-mail: matsuura.yoshiyuki@d.mbox.nagoya-u.ac.jp

Highlights: {yields} MAL has a bipartite NLS that binds to Imp{alpha} in an extended conformation. {yields} Mutational analyses verified the functional significance of MAL-Imp{alpha} interactions. {yields} Induced folding and NLS-masking by G-actins inhibit nuclear import of MAL. -- Abstract: The coordination of cytoskeletal actin dynamics with gene expression reprogramming is emerging as a crucial mechanism to control diverse cellular processes, including cell migration, differentiation and neuronal circuit assembly. The actin-binding transcriptional coactivator MAL (also known as MRTF-A/MKL1/BSAC) senses G-actin concentration and transduces Rho GTPase signals to serum response factor (SRF). MAL rapidly shuttles between the cytoplasm and the nucleus inmore » unstimulated cells but Rho-induced depletion of G-actin leads to MAL nuclear accumulation and activation of transcription of SRF:MAL-target genes. Although the molecular and structural basis of actin-regulated nucleocytoplasmic shuttling of MAL is not understood fully, it is proposed that nuclear import of MAL is mediated by importin {alpha}/{beta} heterodimer, and that G-actin competes with importin {alpha}/{beta} for the binding to MAL. Here we present structural, biochemical and cell biological evidence that MAL has a classical bipartite nuclear localization signal (NLS) in the N-terminal 'RPEL' domain containing Arg-Pro-X-X-X-Glu-Leu (RPEL) motifs. The NLS residues of MAL adopt an extended conformation and bind along the surface groove of importin-{alpha}, interacting with the major- and minor-NLS binding sites. We also present a crystal structure of wild-type MAL RPEL domain in complex with five G-actins. Comparison of the importin-{alpha}- and actin-complexes revealed that the binding of G-actins to MAL is associated with folding of NLS residues into a helical conformation that is inappropriate for importin-{alpha} recognition.« less

Effects of the nuclear localization of the N(pro) protein of classical swine fever virus on its virulence in pigs.

PubMed

Li, Yongfeng; Shen, Liang; Sun, Yuan; Wang, Xiao; Li, Chao; Huang, Junhua; Chen, Jianing; Li, Lianfeng; Zhao, Bibo; Luo, Yuzi; Li, Su; Qiu, Hua-Ji

2014-12-05

The N(pro) protein of classical swine fever virus (CSFV) is localized in the cytoplasm and nucleus. However, it is unknown whether the nuclear localization of N(pro) correlates with the virulence of CSFV in the host. Previously, we showed that the N(pro) protein fused with interferon regulatory factor 3 (IRF3) was present only in the cytoplasm. Here, we generated and evaluated a recombinant CSFV vSM-IRF3 harboring the IRF3 gene inserted into the N(pro) gene of the highly virulent CSFV Shimen strain. Compared to the even nuclear and cytoplasmic distribution of the enhanced green fluorescent protein (EGFP)-N(pro) fusion expressed by the recombinant CSFV EGFP-CSFV, vSM-IRF3 expressed an IRF3-N(pro) fusion protein that only was localized in the cytoplasm. vSM-IRF3 was markedly attenuated in vitro and in vivo, and the inoculated pigs were completely protected from lethal CSFV challenge, whereas the parental virus as well as EGFP-CSFV exhibited a typical virulent phenotype. Taken together, the nuclear localization of N(pro) plays a significant role in the CSFV replication and virulence. Copyright © 2014 Elsevier B.V. All rights reserved.

TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-autonomously in Caenorhabditis elegans

PubMed Central

McCallum, Katie C.; Liu, Bin; Fierro-González, Juan Carlos; Swoboda, Peter; Arur, Swathi; Miranda-Vizuete, Antonio; Garsin, Danielle A.

2016-01-01

The Caenorhabditis elegans oxidative stress response transcription factor, SKN-1, is essential for the maintenance of redox homeostasis and is a functional ortholog of the Nrf family of transcription factors. The numerous levels of regulation that govern these transcription factors underscore their importance. Here, we add a thioredoxin, encoded by trx-1, to the expansive list of SKN-1 regulators. We report that loss of trx-1 promotes nuclear localization of intestinal SKN-1 in a redox-independent, cell non-autonomous fashion from the ASJ neurons. Furthermore, this regulation is not general to the thioredoxin family, as two other C. elegans thioredoxins, TRX-2 and TRX-3, do not play a role in this process. Moreover, TRX-1-dependent regulation requires signaling from the p38 MAPK-signaling pathway. However, while TRX-1 regulates SKN-1 nuclear localization, classical SKN-1 transcriptional activity associated with stress response remains largely unaffected. Interestingly, RNA-Seq analysis revealed that loss of trx-1 elicits a general, organism-wide down-regulation of several classes of genes; those encoding for collagens and lipid transport being most prevalent. Together, these results uncover a novel role for a thioredoxin in regulating intestinal SKN-1 nuclear localization in a cell non-autonomous manner, thereby contributing to the understanding of the processes involved in maintaining redox homeostasis throughout an organism. PMID:26920757

TRX-1 Regulates SKN-1 Nuclear Localization Cell Non-autonomously in Caenorhabditis elegans.

PubMed

McCallum, Katie C; Liu, Bin; Fierro-González, Juan Carlos; Swoboda, Peter; Arur, Swathi; Miranda-Vizuete, Antonio; Garsin, Danielle A

2016-05-01

The Caenorhabditis elegans oxidative stress response transcription factor, SKN-1, is essential for the maintenance of redox homeostasis and is a functional ortholog of the Nrf family of transcription factors. The numerous levels of regulation that govern these transcription factors underscore their importance. Here, we add a thioredoxin, encoded by trx-1, to the expansive list of SKN-1 regulators. We report that loss of trx-1 promotes nuclear localization of intestinal SKN-1 in a redox-independent, cell non-autonomous fashion from the ASJ neurons. Furthermore, this regulation is not general to the thioredoxin family, as two other C. elegans thioredoxins, TRX-2 and TRX-3, do not play a role in this process. Moreover, TRX-1-dependent regulation requires signaling from the p38 MAPK-signaling pathway. However, while TRX-1 regulates SKN-1 nuclear localization, classical SKN-1 transcriptional activity associated with stress response remains largely unaffected. Interestingly, RNA-Seq analysis revealed that loss of trx-1 elicits a general, organism-wide down-regulation of several classes of genes; those encoding for collagens and lipid transport being most prevalent. Together, these results uncover a novel role for a thioredoxin in regulating intestinal SKN-1 nuclear localization in a cell non-autonomous manner, thereby contributing to the understanding of the processes involved in maintaining redox homeostasis throughout an organism. Copyright © 2016 by the Genetics Society of America.

Ran-binding protein 5 (RanBP5) is related to the nuclear transport factor importin-beta but interacts differently with RanBP1.

PubMed Central

Deane, R; Schäfer, W; Zimmermann, H P; Mueller, L; Görlich, D; Prehn, S; Ponstingl, H; Bischoff, F R

1997-01-01

We report the identification and characterization of a novel 124-kDa Ran binding protein, RanBP5. This protein is related to importin-beta, the key mediator of nuclear localization signal (NLS)-dependent nuclear transport. RanBP5 was identified by two independent methods: it was isolated from HeLa cells by using its interaction with RanGTP in an overlay assay to monitor enrichment, and it was also found by the yeast two-hybrid selection method with RanBP1 as bait. RanBP5 binds to RanBP1 as part of a trimeric RanBP1-Ran-RanBP5 complex. Like importin-beta, RanBP5 strongly binds the GTP-bound form of Ran, stabilizing it against both intrinsic and RanGAP1-induced GTP hydrolysis and also against nucleotide exchange. The GAP resistance of the RanBP5-RanGTP complex can be relieved by RanBP1, which might reflect an in vivo role for RanBP1. RanBP5 is a predominantly cytoplasmic protein that can bind to nuclear pore complexes. We propose that RanBP5 is a mediator of a nucleocytoplasmic transport pathway that is distinct from the importin-alpha-dependent import of proteins with a classical NLS. PMID:9271386

One-Proton Breakup of 18F and the 17O(p,γ)18F Reaction in Classical Novae

NASA Astrophysics Data System (ADS)

Isherwood, Bryan; Banu, A.; E491 Collaboration

2013-10-01

Classical nova studies are of considerable interest for understanding the chemical evolution of the Galaxy. They have been proposed as the most significant source for the nucleosynthesis of the isotopes 13C, 15N, and 17O in the Universe. Novae are also likely to synthesize the short-lived radioisotope 18F (T1/2 = 110 min), which is expected to be the most important contributor to the observed emission of 511 keV gamma radiation by space-based γ-ray telescopes. This emission is produced by electron-positron annihilation following the beta + decay of radioactive nuclei. A detection of these gamma rays could significantly constrain the nova simulation models. 18F nucleosynthesis in classical novae strongly depends on the thermonuclear rate of the 17O(p,γ)18F reaction, which is part of the CNO cycle. This work presents preliminary results toward determination of the 17O(p,γ)18F reaction cross section, which was measured by the indirect method of one-proton nuclear breakup at intermediate energies. The experiment was carried out at GANIL using a beam of 18F at 40 MeV/u impinging on a carbon target. Longitudinal momentum distributions of the 17O breakup fragments were measured in coincidence with γ-rays emitted by 17O residues.

The role of nuclear localization signal in parvovirus life cycle.

PubMed

Liu, Peng; Chen, Shun; Wang, Mingshu; Cheng, Anchun

2017-04-14

Parvoviruses are small, non-enveloped viruses with an approximately 5.0 kb, single-stranded DNA genome. Usually, the parvovirus capsid gene contains one or more nuclear localization signals (NLSs), which are required for guiding the virus particle into the nucleus through the nuclear pore. However, several classical NLSs (cNLSs) and non-classical NLSs (ncNLSs) have been identified in non-structural genes, and the ncNLSs can also target non-structural proteins into the nucleus. In this review, we have summarized recent research findings on parvovirus NLSs. The capsid protein of the adeno-associated virus has four potential nuclear localization sequences, named basic region 1 (BR), BR2, BR3 and BR4. BR3 was identified as an NLS by fusing it with green fluorescent protein. Moreover, BR3 and BR4 are required for infectivity and virion assembly. In Protoparvovirus, the canine parvovirus has a common cNLS located in the VP1 unique region, similar to parvovirus minute virus of mice (MVM) and porcine parvovirus. Moreover, an ncNLS is found in the C-terminal region of MVM VP1/2. Parvovirus B19 also contains an ncNLS in the C-terminal region of VP1/2, which is essential for the nuclear transport of VP1/VP2. Approximately 1 or 2 cNLSs and 1 ncNLS have been reported in the non-structural protein of bocaviruses. Understanding the role of the NLS in the process of parvovirus infection and its mechanism of nuclear transport will contribute to the development of therapeutic vaccines and novel antiviral medicines.

Entangled γ-photons—classical laboratory exercise with modern detectors

NASA Astrophysics Data System (ADS)

Hetfleiš, Jakub; Lněnička, Jindřich; Šlégr, Jan

2018-03-01

This paper describes the application of modern semiconductor detectors of γ and β radiation, which can be used in undergraduate laboratory experiments and lecture demonstrations as a replacement for Geiger-Müller (GM) tubes. Unlike GM tubes, semiconductor detectors do not require a high voltage power source or shaping circuits. The principle of operation of semiconductor detectors is discussed briefly, and classical experiments from nuclear physics are described, ranging from the measurements of linear and mass attenuation coefficient to a demonstration of entangled γ-photons.

Nuclear Receptors in Neurodegenerative Diseases

PubMed Central

Skerrett, Rebecca; Malm, Tarja; Landreth, Gary

2014-01-01

Nuclear receptors have generated substantial interest in the past decade as potential therapeutic targets for the treatment of neurodegenerative disorders. Despite years of effort, effective treatments for progressive neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and ALS remain elusive, making non-classical drug targets such as nuclear receptors an attractive alternative. A substantial literature in mouse models of disease and several clinical trials have investigated the role of nuclear receptors in various neurodegenerative disorders, most prominently AD. These studies have met with mixed results, yet the majority of studies in mouse models report positive outcomes. The mechanisms by which nuclear receptor agonists affect disease pathology remain unclear. Deciphering the complex signaling underlying nuclear receptor action in neurodegenerative diseases is essential for understanding this variability in preclinical studies, and for the successful translation of nuclear receptor agonists into clinical therapies. PMID:24874548

Molecular Dynamics of Hot Dense Plasmas: New Horizons

NASA Astrophysics Data System (ADS)

Graziani, Frank

2011-10-01

We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. This work is performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

The importance of early investigation and publishing in an emergent health and environment crisis.

PubMed

Murase, Kaori

2016-10-01

To minimize the damage resulting from a long-term environmental disaster such as the 2011 Fukushima nuclear accident in Japan, early disclosure of research data by scientists and prompt decision making by government authorities are required in place of careful, time-consuming research and deliberation about the consequences and cause of the accident. A Bayesian approach with flexible statistical modeling helps scientists and encourages government authorities to make decisions based on environmental data available in the early stages of a disaster. It is evident from Fukushima and similar accidents that classical research methods involving statistical methodologies that require rigorous experimental design and complex data sets are too cumbersome and delay important actions that may be critical in the early stages of an environmental disaster. Integr Environ Assess Manag 2016;12:680-682. © 2016 SETAC. © 2016 SETAC.

Intestinal transport and metabolism of bile acids

PubMed Central

Dawson, Paul A.; Karpen, Saul J.

2015-01-01

In addition to their classical roles as detergents to aid in the process of digestion, bile acids have been identified as important signaling molecules that function through various nuclear and G protein-coupled receptors to regulate a myriad of cellular and molecular functions across both metabolic and nonmetabolic pathways. Signaling via these pathways will vary depending on the tissue and the concentration and chemical structure of the bile acid species. Important determinants of the size and composition of the bile acid pool are their efficient enterohepatic recirculation, their host and microbial metabolism, and the homeostatic feedback mechanisms connecting hepatocytes, enterocytes, and the luminal microbiota. This review focuses on the mammalian intestine, discussing the physiology of bile acid transport, the metabolism of bile acids in the gut, and new developments in our understanding of how intestinal metabolism, particularly by the gut microbiota, affects bile acid signaling. PMID:25210150

Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture

PubMed Central

Matharu, Navneet K.; Ahanger, Sajad H.

2015-01-01

The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. PMID:26340639

On the fly quantum dynamics of electronic and nuclear wave packets

NASA Astrophysics Data System (ADS)

Komarova, Ksenia G.; Remacle, F.; Levine, R. D.

2018-05-01

Multielectronic states quantum dynamics on a grid is described in a manner motivated by on the fly classical trajectory computations. Non stationary electronic states are prepared by a few cycle laser pulse. The nuclei respond and begin moving. We solve the time dependent Schrödinger equation for the electronic and nuclear dynamics for excitation from the ground electronic state. A satisfactory accuracy is possible using a localized description on a discrete grid. This enables computing on the fly for both the nuclear and electronic dynamics including non-adiabatic couplings. Attosecond dynamics in LiH is used as an example.

E. E. Just and Creativity in Science. The Importance of Diversity

PubMed Central

Byrnes, W. Malcolm

2015-01-01

Renowned biologist Ernest Everett Just (1883-1941) was an outspoken advocate for the classical embryologist’s view of the cell; he believed that all the parts of the cell, but especially the cytoplasm, have important roles to play in the process of development, whereby a one-celled zygote becomes a many-celled animal. In opposition to geneticist Thomas Hunt Morgan, Just formulated a hypothesis for how the cell works in development, one that gave a more dominant role to cytoplasmic (instead of nuclear) factors. This paper argues that, in creating his hypothesis, Just applied insights from the African American intellectual community in which he was immersed, much as Charles Darwin applied insights from British political economist Thomas R. Malthus in formulating his theory of evolution by natural selection. This in no way diminishes the scientific validity of Just’s (or Darwin’s) hypothesis. Rather, it highlights Just’s creativity and, as such, points to the importance of having diversity in science. PMID:26321893

Transfection of mitochondria: strategy towards a gene therapy of mitochondrial DNA diseases.

PubMed Central

Seibel, P; Trappe, J; Villani, G; Klopstock, T; Papa, S; Reichmann, H

1995-01-01

Successes in classical gene therapies have been achieved by placing a corrected copy of a defective nuclear gene in cells. A similar gene replacement approach for a mutant mitochondrial genome is invariably linked to the use of a yet unavailable mitochondrial transfection vector. Here we show that DNA coupled covalently to a short mitochondrial leader peptide (chimera) can enter mitochondria via the protein import pathway, opening a new way for gene-, antisense-RNA- or antisense-DNA-delivery in molecular therapies. The import behavior of the purified chimera, composed of the amino-terminal leader peptide of the rat ornithine transcarbamylase (OTC) and a double stranded DNA molecule (17 bp or 322 bp), was tested by incubating with coupled and 'energized' rat liver mitochondria in the presence of reticulocyte lysate. The chimera was translocated with a high efficiency into the matrix of mitochondria utilizing the protein import pathway, independent from the size of its passenger DNA. Images PMID:7870573

Work Domain Analysis Methodology for Development of Operational Concepts for Advanced Reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hugo, Jacques

2015-05-01

This report describes a methodology to conduct a Work Domain Analysis in preparation for the development of operational concepts for new plants. This method has been adapted from the classical method described in the literature in order to better deal with the uncertainty and incomplete information typical of first-of-a-kind designs. The report outlines the strategy for undertaking a Work Domain Analysis of a new nuclear power plant and the methods to be used in the development of the various phases of the analysis. Basic principles are described to the extent necessary to explain why and how the classical method wasmore » adapted to make it suitable as a tool for the preparation of operational concepts for a new nuclear power plant. Practical examples are provided of the systematic application of the method and the various presentation formats in the operational analysis of advanced reactors.« less

Deriving the exact nonadiabatic quantum propagator in the mapping variable representation.

PubMed

Hele, Timothy J H; Ananth, Nandini

2016-12-22

We derive an exact quantum propagator for nonadiabatic dynamics in multi-state systems using the mapping variable representation, where classical-like Cartesian variables are used to represent both continuous nuclear degrees of freedom and discrete electronic states. The resulting Liouvillian is a Moyal series that, when suitably approximated, can allow for the use of classical dynamics to efficiently model large systems. We demonstrate that different truncations of the exact Liouvillian lead to existing approximate semiclassical and mixed quantum-classical methods and we derive an associated error term for each method. Furthermore, by combining the imaginary-time path-integral representation of the Boltzmann operator with the exact Liouvillian, we obtain an analytic expression for thermal quantum real-time correlation functions. These results provide a rigorous theoretical foundation for the development of accurate and efficient classical-like dynamics to compute observables such as electron transfer reaction rates in complex quantized systems.

Classical electromagnetic fields from quantum sources in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Holliday, Robert; McCarty, Ryan; Peroutka, Balthazar; Tuchin, Kirill

2017-01-01

Electromagnetic fields are generated in high energy nuclear collisions by spectator valence protons. These fields are traditionally computed by integrating the Maxwell equations with point sources. One might expect that such an approach is valid at distances much larger than the proton size and thus such a classical approach should work well for almost the entire interaction region in the case of heavy nuclei. We argue that, in fact, the contrary is true: due to the quantum diffusion of the proton wave function, the classical approximation breaks down at distances of the order of the system size. We compute the electromagnetic field created by a charged particle described initially as a Gaussian wave packet of width 1 fm and evolving in vacuum according to the Klein-Gordon equation. We completely neglect the medium effects. We show that the dynamics, magnitude and even sign of the electromagnetic field created by classical and quantum sources are different.

The 21.5-kDa isoform of myelin basic protein has a non-traditional PY-nuclear-localization signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Graham S.T.; Seymour, Lauren V.; Boggs, Joan M.

2012-06-15

Highlights: Black-Right-Pointing-Pointer Full-length 21.5-kDa MBP isoform is translocated to the nucleus. Black-Right-Pointing-Pointer We hypothesized that the exon-II-encoded sequence contained the NLS. Black-Right-Pointing-Pointer We mutated this sequence in RFP-tagged constructs and transfected N19-cells. Black-Right-Pointing-Pointer Abolition of two key positively-charged residues resulted in loss of nuclear-trafficking. Black-Right-Pointing-Pointer The 21.5-kDa isoform of classic MBP contains a non-traditional PY-NLS. -- Abstract: The predominant 18.5-kDa classic myelin basic protein (MBP) is mainly responsible for compaction of the myelin sheath in the central nervous system, but is multifunctional, having numerous interactions with Ca{sup 2+}-calmodulin, actin, tubulin, and SH3-domains, and can tether these proteins to a lipidmore » membrane in vitro. The full-length 21.5-kDa MBP isoform has an additional 26 residues encoded by exon-II of the classic gene, which causes it to be trafficked to the nucleus of oligodendrocytes (OLGs). We have performed site-directed mutagenesis of selected residues within this segment in red fluorescent protein (RFP)-tagged constructs, which were then transfected into the immortalized N19-OLG cell line to view protein localization using epifluorescence microscopy. We found that 21.5-kDa MBP contains two non-traditional PY-nuclear-localization signals, and that arginine and lysine residues within these motifs were involved in subcellular trafficking of this protein to the nucleus, where it may have functional roles during myelinogenesis.« less

Membrane estrogen receptors - is it an alternative way of estrogen action?

PubMed

Soltysik, K; Czekaj, P

2013-04-01

The functions of estrogens are relatively well known, however the molecular mechanism of their action is not clear. The classical pathway of estrogen action is dependent on ERα and ERβ which act as transcription factors. The effects of this pathway occur within hours or days. In addition, so-called, non-classical mechanism of steroid action dependent on membrane estrogen receptors (mER) was described. In this mechanism the effects of estrogen action are observed in a much shorter time. Here we review the structure and cellular localization of mER, molecular basis of non-classical mER action, physiological role of mER as well as implications of mER action for cancer biology. Finally, some concerns about the new estrogen receptor - GPER and candidates for estrogen receptors - ER-X and ERx, are briefly discussed. It seems that mER is a complex containing signal proteins (signalosome), as IGF receptor, EGF receptor, Ras protein, adaptor protein Shc, non-receptor kinase c-Src and PI-3K, what rationalizes production of second messengers. Some features of membrane receptors are almost identical if compared to nuclear receptors. Probably, membrane and nuclear estrogen receptors are not separate units, but rather the components of a complex mechanism in which they both cooperate with each other. We conclude that the image of the estrogen receptor as a simple transcription factor is a far-reaching simplification. A better understanding of the mechanisms of estrogen action will help us to design more effective drugs affecting signal pathways depending on both membrane and nuclear receptors.

Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ.

PubMed

Desset, Sophie; Poulet, Axel; Tatout, Christophe

2018-01-01

Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context. Here, we describe a whole mount tissue preparation procedure coupled to DNA staining using the PicoGreen ® intercalating agent suitable for image analysis of the nucleus in living and fixed tissues. 3D Image analysis is then performed using NucleusJ, an open source ImageJ plugin, which allows for quantifying variations in nuclear morphology such as nuclear volume, sphericity, elongation, and flatness as well as in heterochromatin content and position in respect to the nuclear periphery.

Analysis of mouse brain peptides using mass spectrometry-based peptidomics: Implications for novel functions ranging from non-classical neuropeptides to microproteins

PubMed Central

Fricker, Lloyd D.

2010-01-01

Peptides are known to play many important physiological roles in signaling. A large number of peptides have been detected in mouse brain extracts using mass spectrometry-based peptidomics studies, and 850 peptides have been identified. Half of these peptides are derived from secretory pathway proteins and many are known bioactive neuropeptides which activate G protein-coupled receptors; these are termed “classical neuropeptides.” In addition, 427 peptides were identified that are derived from non-secretory pathway proteins; the majority are cystosolic, and the remainder are mitochondrial, nuclear, lysosomal, or membrane proteins. Many of these peptides represent the N- or C-terminus of the protein, rather than internal fragments, raising the possibility that they are formed by selective processing rather than protein degradation. In addition to consideration of the cleavage site required to generate the intracellular peptides, their potential functions are discussed. Several of the cytosolic peptides were previously found to interact with receptors and/or otherwise influence cellular activity; examples include hemophins, hemopressins, diazepam binding inhibitor, and hippocampal cholinergic neurostimulating peptide. The possibility that these peptides are secreted from cells and function in cell-cell signaling is discussed. If these intracellular peptides can be shown to be secreted in levels sufficient to produce a biological effect, they would appropriately be called “non-classical neuropeptides” by analogy with non-classical neurotransmitters such as nitric oxide and anandamide. It is also possible that intracellular peptides function as “microproteins” and modulate protein-protein interactions; evidence for this function is discussed, along with future directions that are needed to establish this and other possible functions for peptides. PMID:20428524

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rist, J.; Miteva, T.; Gaire, B.

In this paper we present a comprehensive and detailed study of Interatomic Coulombic Decay (ICD) occurring after irradiating argon dimers with XUV-synchrotron radiation. A manifold of different decay channels is observed and the corresponding initial and final states are assigned. Additionally, the effect of nuclear dynamics on the ICD electron spectrum is examined for one specific decay channel. The internuclear distance-dependent width Γ(R) of the decay is obtained from the measured kinetic energy release distribution of the ions employing a classical nuclear dynamics model.

Controlling Nuclear Jaks and Stats for Specific Gene Activation by Ifn γ and Other Cytokines: A Possible Steroid-like Connection

PubMed Central

Johnson, Howard M.; Noon-Song, Ezra; Ahmed, Chulbul M.

2011-01-01

The mechanism of specific gene activation by cytokines that use JAK/STAT signalling pathway is unknown. There are four different types of JAKs and seven different types of STATs. In the classical model of signaling, ligand interacts solely with the receptor extracellular domain, which triggers JAK activation at the receptor cytoplasmic domain. Activated STATs are then said to carry out nuclear events of specific gene activation, including associated epigenetic changes that cause heterochromatin destabilization. Ligand, receptor, and JAKs play no further role in the classical model. Given the limited number of STATs and the activation of the same STATs by cytokines with different functions, the mechanism of the specificity of their signalling is not obvious. Focusing on gamma interferon (IFNγ), we have shown that ligand, receptor, and activated JAKs are involved in nuclear events that are associated with specific gene activation. In this model, receptor subunit IFNGR1 functions as a transcription/cotranscription factor and the JAKs are involved in key epigenetic events that are required for specific gene activation. The model has implications for gene activation in cancer as well as stem cell differentiation. PMID:22924155

Controlling Nuclear Jaks and Stats for Specific Gene Activation by Ifn γ and Other Cytokines: A Possible Steroid-like Connection.

PubMed

Johnson, Howard M; Noon-Song, Ezra; Ahmed, Chulbul M

2011-09-03

The mechanism of specific gene activation by cytokines that use JAK/STAT signalling pathway is unknown. There are four different types of JAKs and seven different types of STATs. In the classical model of signaling, ligand interacts solely with the receptor extracellular domain, which triggers JAK activation at the receptor cytoplasmic domain. Activated STATs are then said to carry out nuclear events of specific gene activation, including associated epigenetic changes that cause heterochromatin destabilization. Ligand, receptor, and JAKs play no further role in the classical model. Given the limited number of STATs and the activation of the same STATs by cytokines with different functions, the mechanism of the specificity of their signalling is not obvious. Focusing on gamma interferon (IFNγ), we have shown that ligand, receptor, and activated JAKs are involved in nuclear events that are associated with specific gene activation. In this model, receptor subunit IFNGR1 functions as a transcription/cotranscription factor and the JAKs are involved in key epigenetic events that are required for specific gene activation. The model has implications for gene activation in cancer as well as stem cell differentiation.

Panning for SNuRMs: using cofactor profiling for the rational discovery of selective nuclear receptor modulators.

PubMed

Kremoser, Claus; Albers, Michael; Burris, Thomas P; Deuschle, Ulrich; Koegl, Manfred

2007-10-01

Drugs that target nuclear receptors are clinically, as well as commercially, successful. Their widespread use, however, is limited by an inherent propensity of nuclear receptors to trigger beneficial, as well as adverse, pharmacological effects upon drug activation. Hence, selective drugs that display reduced adverse effects, such as the selective estrogen receptor modulator (SERM) Raloxifene, have been developed by guidance through classical cell culture assays and animal trials. Full agonist and selective modulator nuclear receptor drugs, in general, differ by their ability to recruit certain cofactors to the receptor protein. Hence, systematic cofactor profiling is advancing into an approach for the rationally guided identification of selective NR modulators (SNuRMs) with improved therapeutic ratio.

Nucleoporin Nup98 associates with Trx/MLL and NSL histone-modifying complexes and regulates Hox gene expression.

PubMed

Pascual-Garcia, Pau; Jeong, Jieun; Capelson, Maya

2014-10-23

The nuclear pore complex is a transport channel embedded in the nuclear envelope and made up of 30 different components termed nucleoporins (Nups). In addition to their classical role in transport, a subset of Nups has a conserved role in the regulation of transcription via direct binding to chromatin. The molecular details of this function remain obscure, and it is unknown how metazoan Nups are recruited to their chromatin locations or what transcription steps they regulate. Here, we demonstrate genome-wide and physical association between Nup98 and histone-modifying complexes MBD-R2/NSL [corrected] and Trx/MLL. Importantly, we identify a requirement for MBD-R2 in recruitment of Nup98 to many of its genomic target sites. Consistent with its interaction with the Trx/MLL complex, Nup98 is shown to be necessary for Hox gene expression in developing fly tissues. These findings introduce roles of Nup98 in epigenetic regulation that may underlie the basis of oncogenicity of Nup98 fusions in leukemia.

Constitutive activation of alternative nuclear factor kappa B pathway in canine diffuse large B-cell lymphoma contributes to tumor cell survival and is a target of new adjuvant therapies.

PubMed

Seelig, Davis M; Ito, Daisuke; Forster, Colleen L; Yoon, Una A; Breen, Matthew; Burns, Linda J; Bachanova, Veronika; Lindblad-Toh, Kerstin; O'Brien, Timothy D; Schmechel, Stephen C; Rizzardi, Anthony E; Modiano, Jaime F; Linden, Michael A

2017-07-01

Activation of the classical nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway is a common molecular event observed in both human and canine diffuse large B-cell lymphoma (DLBCL). Although the oncogenic potential of the alternative NFκB pathway (ANFκBP) has also been recently identified in DLBCL, its precise role in tumor pathogenesis and potential as a treatment target is understudied. We hypothesized that up-regulation of the ANFκBP plays an important role in the proliferation and survival of canine DLBCL cells, and we demonstrate that the ANFκBP is constitutively active in primary canine DLBCL samples and a cell line (CLBL1). We further demonstrate that a small interfering RNA inhibits the activation of the NFκB pathway and induces apoptosis in canine DLBCL cells. In conclusion, the ANFκBP facilitates survival of canine DLBCL cells, and thus, dogs with spontaneous DLBCL can provide a useful large animal model to study therapies targeting the ANFκBP.

75 FR 53013 - Culturally Significant Objects Imported for Exhibition Determinations: “Chaos and Classicism: Art...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-30

... DEPARTMENT OF STATE [Public Notice 7137] Culturally Significant Objects Imported for Exhibition Determinations: ``Chaos and Classicism: Art in France, Italy, and Germany, 1918-1936'' SUMMARY: Notice is hereby... hereby determine that the objects to be included in the exhibition ``Chaos and Classicism: Art in France...

Classics. Essay on Teaching Able Students.

ERIC Educational Resources Information Center

Coffin, David D.

In a field as varied and as technical as the classical languages, the professional training of the teacher is of paramount importance. An undergraduate major and graduate school work in the field of classical languages give a general view of the field and show which writings are interesting or important and how difficult they are. A graduate…

New Frontiers in the Intrarenal Renin-Angiotensin System: A Critical Review of Classical and New Paradigms

PubMed Central

Zhuo, Jia L.; Ferrao, Fernanda M.; Zheng, Yun; Li, Xiao C.

2013-01-01

The renin-angiotensin system (RAS) is well-recognized as one of the oldest and most important regulators of arterial blood pressure, cardiovascular, and renal function. New frontiers have recently emerged in the RAS research well beyond its classic paradigm as a potent vasoconstrictor, an aldosterone release stimulator, or a sodium-retaining hormone. First, two new members of the RAS have been uncovered, which include the renin/(Pro)renin receptor (PRR) and angiotensin-converting enzyme 2 (ACE2). Recent studies suggest that prorenin may act on the PRR independent of the classical ACE/ANG II/AT1 receptor axis, whereas ACE2 may degrade ANG II to generate ANG (1–7), which activates the Mas receptor. Second, there is increasing evidence that ANG II may function as an intracellular peptide to activate intracellular and/or nuclear receptors. Third, currently there is a debate on the relative contribution of systemic versus intrarenal RAS to the physiological regulation of blood pressure and the development of hypertension. The objectives of this article are to review and discuss the new insights and perspectives derived from recent studies using novel transgenic mice that either overexpress or are deficient of one key enzyme, ANG peptide, or receptor of the RAS. This information may help us better understand how ANG II acts, both independently or through interactions with other members of the system, to regulate the kidney function and blood pressure in health and disease. PMID:24273531

A surprisingly simple correlation between the classical and quantum structural networks in liquid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamm, Peter; Fanourgakis, George S.; Xantheas, Sotiris S.

Nuclear quantum effects in liquid water have profound implications for several of its macroscopic properties related to structure, dynamics, spectroscopy and transport. Although several of water’s macroscopic properties can be reproduced by classical descriptions of the nuclei using potentials effectively parameterized for a narrow range of its phase diagram, a proper account of the nuclear quantum effects is required in order to ensure that the underlying molecular interactions are transferable across a wide temperature range covering different regions of that diagram. When performing an analysis of the hydrogen bonded structural networks in liquid water resulting from the classical (class.) andmore » quantum (q.m.) descriptions of the nuclei with the transferable, flexible, polarizable TTM3-F interaction potential, we found that the two results can be superimposed over the temperature range of T=270-350 K using a surprisingly simple, linear scaling of the two temperatures according to T(q.m.)=aT(class)- T , where a=1.2 and T=51 K. The linear scaling and constant shift of the temperature scale can be considered as a generalization of the previously reported temperature shifts (corresponding to structural changes and the melting T) induced by quantum effects in liquid water.« less

THE FIRST FERMI IN A HIGH ENERGY NUCLEAR COLLISION.

DOE Office of Scientific and Technical Information (OSTI.GOV)

KRASNITZ,A.

1999-08-09

At very high energies, weak coupling, non-perturbative methods can be used to study classical gluon production in nuclear collisions. One observes in numerical simulations that after an initial formation time, the produced partons are on shell, and their subsequent evolution can be studied using transport theory. At the initial formation time, a simple non-perturbative relation exists between the energy and number densities of the produced partons, and a scale determined by the saturated parton density in the nucleus.

9 CFR 94.25 - Restrictions on the importation of live swine, pork, or pork products from certain regions free...

Code of Federal Regulations, 2012 CFR

2012-01-01

... live swine, pork, or pork products from certain regions free of classical swine fever. 94.25 Section 94... DISEASE, EXOTIC NEWCASTLE DISEASE, AFRICAN SWINE FEVER, CLASSICAL SWINE FEVER, SWINE VESICULAR DISEASE... the importation of live swine, pork, or pork products from certain regions free of classical swine...

9 CFR 94.25 - Restrictions on the importation of live swine, pork, or pork products from certain regions free...

Code of Federal Regulations, 2013 CFR

2013-01-01

... live swine, pork, or pork products from certain regions free of classical swine fever. 94.25 Section 94... DISEASE, EXOTIC NEWCASTLE DISEASE, AFRICAN SWINE FEVER, CLASSICAL SWINE FEVER, SWINE VESICULAR DISEASE... the importation of live swine, pork, or pork products from certain regions free of classical swine...

Unified field theory from the classical wave equation: Preliminary application to atomic and nuclear structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Múnera, Héctor A., E-mail: hmunera@hotmail.com; Retired professor, Department of Physics, Universidad Nacional de Colombia, Bogotá, Colombia, South America

2016-07-07

It is postulated that there exists a fundamental energy-like fluid, which occupies the flat three-dimensional Euclidean space that contains our universe, and obeys the two basic laws of classical physics: conservation of linear momentum, and conservation of total energy; the fluid is described by the classical wave equation (CWE), which was Schrödinger’s first candidate to develop his quantum theory. Novel solutions for the CWE discovered twenty years ago are nonharmonic, inherently quantized, and universal in the sense of scale invariance, thus leading to quantization at all scales of the universe, from galactic clusters to the sub-quark world, and yielding amore » unified Lorentz-invariant quantum theory ab initio. Quingal solutions are isomorphic under both neo-Galilean and Lorentz transformations, and exhibit nother remarkable property: intrinsic unstability for large values of ℓ (a quantum number), thus limiting the size of each system at a given scale. Unstability and scale-invariance together lead to nested structures observed in our solar system; unstability may explain the small number of rows in the chemical periodic table, and nuclear unstability of nuclides beyond lead and bismuth. Quingal functions lend mathematical basis for Boscovich’s unified force (which is compatible with many pieces of evidence collected over the past century), and also yield a simple geometrical solution for the classical three-body problem, which is a useful model for electronic orbits in simple diatomic molecules. A testable prediction for the helicoidal-type force is suggested.« less

Mass stability in classical Stueckelberg-Horwitz-Piron electrodynamics

NASA Astrophysics Data System (ADS)

Land, Martin

2017-05-01

It is well-known that the 5D gauge structure of Stueckelberg-Horwitz-Piron (SHP) electrodynamics permits the exchange of mass between particles and the electromagnetic fields induced by their motion, even at the classical level. This phenomenon presents two closely related problems: (1) Under what circumstances can real particles evolve sufficiently off-shell to account for mass changing phenomena such as flavor-changing neutrino interactions and low energy nuclear reactions? (2) What accounts for the stability of the measured masses of the known particles? To approach these questions, we first propose a toy model in which a particle evolving through a complex charged environment can acquire a significant mass shift for a short time. We then consider a classical self-interaction that tends to restore on-shell propagation.

Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators.

PubMed

Mende, Susanne; Royer, Loic; Herr, Alexander; Schmiedel, Janet; Deschauer, Marcus; Klopstock, Thomas; Kostic, Vladimir S; Schroeder, Michael; Reichmann, Heinz; Storch, Alexander

2011-07-01

The heteroplasmic mitochondrial DNA (mtDNA) mutation A3243G causes the mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome as one of the most frequent mitochondrial diseases. The process of reconfiguration of nuclear gene expression profile to accommodate cellular processes to the functional status of mitochondria might be a key to MELAS disease manifestation and could contribute to its diverse phenotypic presentation. To determine master regulatory protein networks and disease-modifying genes in MELAS syndrome. Analyses of whole blood transcriptomes from 10 MELAS patients using a novel strategy by combining classic Affymetrix oligonucleotide microarray profiling with regulatory and protein interaction network analyses. Hierarchical cluster analysis elucidated that the relative abundance of mutant mtDNA molecules is decisive for the nuclear gene expression response. Further analyses confirmed not only transcription factors already known to be involved in mitochondrial diseases (such as TFAM), but also detected the hypoxia-inducible factor 1 complex, nuclear factor Y and cAMP responsive element-binding protein-related transcription factors as novel master regulators for reconfiguration of nuclear gene expression in response to the MELAS mutation. Correlation analyses of gene alterations and clinico-genetic data detected significant correlations between A3243G-induced nuclear gene expression changes and mutant mtDNA load as well as disease characteristics. These potential disease-modifying genes influencing the expression of the MELAS phenotype are mainly related to clusters primarily unrelated to cellular energy metabolism, but important for nucleic acid and protein metabolism, and signal transduction. Our data thus provide a framework to search for new pathogenetic concepts and potential therapeutic approaches to treat the MELAS syndrome.

Influence of nuclear exchange on nonadiabatic electron processes in H(+)+H2 collisions.

PubMed

Errea, L F; Illescas, Clara; Macías, A; Méndez, L; Pons, B; Rabadán, I; Riera, A

2010-12-28

H(+)+H(2) collisions are studied by means of a semiclassical approach that explicitly accounts for nuclear rearrangement channels in nonadiabatic electron processes. A set of classical trajectories is used to describe the nuclear motion, while the electronic degrees of freedom are treated quantum mechanically in terms of a three-state expansion of the collision wavefunction. We describe electron capture and vibrational excitation, which can also involve nuclear exchange and dissociation, in the E = 2-1000 eV impact energy range. We compare dynamical results obtained with two parametrizations of the potential energy surface of H(3)(+) ground electronic state. Total cross sections for E > 10 eV agree with previous results using a vibronic close-coupling expansion, and with experimental data for E < 10 eV. Additionally, some prototypical features of both nuclear and electron dynamics at low E are discussed.

Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model

NASA Astrophysics Data System (ADS)

Xu, Yang; Song, Kai; Shi, Qiang

2018-03-01

The hydride transfer reaction catalyzed by dihydrofolate reductase is studied using a recently developed mixed quantum-classical method to investigate the nuclear quantum effects on the reaction. Molecular dynamics simulation is first performed based on a two-state empirical valence bond potential to map the atomistic model to an effective double-well potential coupled to a harmonic bath. In the mixed quantum-classical simulation, the hydride degree of freedom is quantized, and the effective harmonic oscillator modes are treated classically. It is shown that the hydride transfer reaction rate using the mapped effective double-well/harmonic-bath model is dominated by the contribution from the ground vibrational state. Further comparison with the adiabatic reaction rate constant based on the Kramers theory confirms that the reaction is primarily vibrationally adiabatic, which agrees well with the high transmission coefficients found in previous theoretical studies. The calculated kinetic isotope effect is also consistent with the experimental and recent theoretical results.

Classical and Bayesian Seismic Yield Estimation: The 1998 Indian and Pakistani Tests

NASA Astrophysics Data System (ADS)

Shumway, R. H.

2001-10-01

- The nuclear tests in May, 1998, in India and Pakistan have stimulated a renewed interest in yield estimation, based on limited data from uncalibrated test sites. We study here the problem of estimating yields using classical and Bayesian methods developed by Shumway (1992), utilizing calibration data from the Semipalatinsk test site and measured magnitudes for the 1998 Indian and Pakistani tests given by Murphy (1998). Calibration is done using multivariate classical or Bayesian linear regression, depending on the availability of measured magnitude-yield data and prior information. Confidence intervals for the classical approach are derived applying an extension of Fieller's method suggested by Brown (1982). In the case where prior information is available, the posterior predictive magnitude densities are inverted to give posterior intervals for yield. Intervals obtained using the joint distribution of magnitudes are comparable to the single-magnitude estimates produced by Murphy (1998) and reinforce the conclusion that the announced yields of the Indian and Pakistani tests were too high.

Classical and Bayesian Seismic Yield Estimation: The 1998 Indian and Pakistani Tests

NASA Astrophysics Data System (ADS)

Shumway, R. H.

The nuclear tests in May, 1998, in India and Pakistan have stimulated a renewed interest in yield estimation, based on limited data from uncalibrated test sites. We study here the problem of estimating yields using classical and Bayesian methods developed by Shumway (1992), utilizing calibration data from the Semipalatinsk test site and measured magnitudes for the 1998 Indian and Pakistani tests given by Murphy (1998). Calibration is done using multivariate classical or Bayesian linear regression, depending on the availability of measured magnitude-yield data and prior information. Confidence intervals for the classical approach are derived applying an extension of Fieller's method suggested by Brown (1982). In the case where prior information is available, the posterior predictive magnitude densities are inverted to give posterior intervals for yield. Intervals obtained using the joint distribution of magnitudes are comparable to the single-magnitude estimates produced by Murphy (1998) and reinforce the conclusion that the announced yields of the Indian and Pakistani tests were too high.

Simulation of surface processes

PubMed Central

Jónsson, Hannes

2011-01-01

Computer simulations of surface processes can reveal unexpected insight regarding atomic-scale structure and transitions. Here, the strengths and weaknesses of some commonly used approaches are reviewed as well as promising avenues for improvements. The electronic degrees of freedom are usually described by gradient-dependent functionals within Kohn–Sham density functional theory. Although this level of theory has been remarkably successful in numerous studies, several important problems require a more accurate theoretical description. It is important to develop new tools to make it possible to study, for example, localized defect states and band gaps in large and complex systems. Preliminary results presented here show that orbital density-dependent functionals provide a promising avenue, but they require the development of new numerical methods and substantial changes to codes designed for Kohn–Sham density functional theory. The nuclear degrees of freedom can, in most cases, be described by the classical equations of motion; however, they still pose a significant challenge, because the time scale of interesting transitions, which typically involve substantial free energy barriers, is much longer than the time scale of vibrations—often 10 orders of magnitude. Therefore, simulation of diffusion, structural annealing, and chemical reactions cannot be achieved with direct simulation of the classical dynamics. Alternative approaches are needed. One such approach is transition state theory as implemented in the adaptive kinetic Monte Carlo algorithm, which, thus far, has relied on the harmonic approximation but could be extended and made applicable to systems with rougher energy landscape and transitions through quantum mechanical tunneling. PMID:21199939

Association of growth factors, HIF-1 and NF-κB expression with proteasomes in endometrial cancer.

PubMed

Spirina, Ludmila V; Yunusova, Nataliya V; Kondakova, Irina V; Kolomiets, Larisa A; Koval, Valeriya D; Chernyshova, Alena L; Shpileva, Olga V

2012-09-01

Insulin-like growth factors (IGFs), vascular endothelial growth factor (VEGF), hypoxia-inducible factor-1 (HIF-1), and nuclear factor kappa-B (NF-κB) are known to play an important role in endometrial cancer pathogenesis. However, the proteolytic regulation of these factors is still poorly understood. We studied the correlation between chymotrypsin-like activity of proteasomes and IGF-I, IGF-II, VEGF, HIF-1, and NF-κB levels in endometrial cancer tissues. It was shown that the total activity of proteasomes and the activity of the 20S and 26S proteasomes in malignant tumors were significantly higher than those observed in the normal endometrium. Negative relationships between the proteasome activity and IGF-I, HIF-1, and NF-κB p50 expressions were found. High 20S proteasome activity was associated with increase of HIF-1 level. Positive relationships between IGF-I expression and two classic forms of NF-κB p50 and p65 in endometrial cancer were revealed. The data obtained indicate the possible proteasomal regulation of growth and transcription factors. The major pool of IGF-I is located in the extracellular space, and it is likely that extracellular proteasomes also take part in the regulation of the IGF-I content. The present data show the evidence of proteasome regulation of growth and nuclear factors that can play an important role in cancer pathogenesis.

Nonadiabatic nuclear dynamics of the ammonia cation studied by surface hopping classical trajectory calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belyaev, Andrey K., E-mail: belyaev@herzen.spb.ru; Domcke, Wolfgang, E-mail: wolfgang.domcke@ch.tum.de; Lasser, Caroline, E-mail: classer@ma.tum.de

The Landau–Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected formore » the nuclear dynamics: Ultrafast Jahn–Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.« less

Dynamic Oligomerization of Integrase Orchestrates HIV Nuclear Entry.

PubMed

Borrenberghs, Doortje; Dirix, Lieve; De Wit, Flore; Rocha, Susana; Blokken, Jolien; De Houwer, Stéphanie; Gijsbers, Rik; Christ, Frauke; Hofkens, Johan; Hendrix, Jelle; Debyser, Zeger

2016-11-10

Nuclear entry is a selective, dynamic process granting the HIV-1 pre-integration complex (PIC) access to the chromatin. Classical analysis of nuclear entry of heterogeneous viral particles only yields averaged information. We now have employed single-virus fluorescence methods to follow the fate of single viral pre-integration complexes (PICs) during infection by visualizing HIV-1 integrase (IN). Nuclear entry is associated with a reduction in the number of IN molecules in the complexes while the interaction with LEDGF/p75 enhances IN oligomerization in the nucleus. Addition of LEDGINs, small molecule inhibitors of the IN-LEDGF/p75 interaction, during virus production, prematurely stabilizes a higher-order IN multimeric state, resulting in stable IN multimers resistant to a reduction in IN content and defective for nuclear entry. This suggests that a stringent size restriction determines nuclear pore entry. Taken together, this work demonstrates the power of single-virus imaging providing crucial insights in HIV replication and enabling mechanism-of-action studies.

Blood volume analysis: a new technique and new clinical interest reinvigorate a classic study.

PubMed

Manzone, Timothy A; Dam, Hung Q; Soltis, Daniel; Sagar, Vidya V

2007-06-01

Blood volume studies using the indicator dilution technique and radioactive tracers have been performed in nuclear medicine departments for over 50 y. A nuclear medicine study is the gold standard for blood volume measurement, but the classic dual-isotope blood volume study is time-consuming and can be prone to technical errors. Moreover, a lack of normal values and a rubric for interpretation made volume status measurement of limited interest to most clinicians other than some hematologists. A new semiautomated system for blood volume analysis is now available and provides highly accurate results for blood volume analysis within only 90 min. The availability of rapid, accurate blood volume analysis has brought about a surge of clinical interest in using blood volume data for clinical management. Blood volume analysis, long a low-volume nuclear medicine study all but abandoned in some laboratories, is poised to enter the clinical mainstream. This article will first present the fundamental principles of fluid balance and the clinical means of volume status assessment. We will then review the indicator dilution technique and how it is used in nuclear medicine blood volume studies. We will present an overview of the new semiautomated blood volume analysis technique, showing how the study is done, how it works, what results are provided, and how those results are interpreted. Finally, we will look at some of the emerging areas in which data from blood volume analysis can improve patient care. The reader will gain an understanding of the principles underlying blood volume assessment, know how current nuclear medicine blood volume analysis studies are performed, and appreciate their potential clinical impact.

A putative N-terminal nuclear export sequence is sufficient for Mps1 nuclear exclusion during interphase.

PubMed

Jia, Haiwei; Zhang, Xiaojuan; Wang, Wenjun; Bai, Yuanyuan; Ling, Youguo; Cao, Cheng; Ma, Runlin Z; Zhong, Hui; Wang, Xue; Xu, Quanbin

2015-02-27

Mps1, an essential component of the mitotic checkpoint, is also an important interphase regulator and has roles in DNA damage response, cytokinesis and centrosome duplication. Mps1 predominantly resides in the cytoplasm and relocates into the nucleus at the late G2 phase. So far, the mechanism underlying the Mps1 translocation between the cytoplasm and nucleus has been unclear. In this work, a dynamic export process of Mps1 from the nucleus to cytoplasm in interphase was revealed- a process blocked by the Crm1 inhibitor, Leptomycin B, suggesting that export of Mps1 is Crm1 dependent. Consistent with this speculation, a direct association between Mps1 and Crm1 was found. Furthermore, a putative nuclear export sequence (pNES) motif at the N-terminal of Mps1 was identified by analyzing the motif of Mps1. This motif shows a high sequence similarity to the classic NES, a fusion of this motif with EGFP results in dramatic exclusion of the fusion protein from the nucleus. Additionally, Mps1 mutant loss of pNES integrity was shown by replacing leucine with alanine which produced a diffused subcellular distribution, compared to the wild type protein which resides predominantly in cytoplasm. Taken these findings together, it was concluded that the pNES sequence is sufficient for the Mps1 export from nucleus during interphase.

"Talking Together, Learning Together": The Story of English PGCE Student Teachers' Adventures in Classics

ERIC Educational Resources Information Center

Smith, Lorna; Foley, Joan

2015-01-01

This article reports on the first two phases of a project to promote the classics through English at Key Stage 3, a scion of the Cambridge Schools Classics Project. We discuss the primary importance of speaking and listening in the English classroom both for the individual and the collective, and reflect on the power and importance of using…

BULGES OF NEARBY GALAXIES WITH SPITZER: THE GROWTH OF PSEUDOBULGES IN DISK GALAXIES AND ITS CONNECTION TO OUTER DISKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisher, David B.; Drory, Niv; Fabricius, Maximilian H.

2009-05-20

We study star formation rates (SFRs) and stellar masses in bulges of nearby disk galaxies. For this we construct a new SFR indicator that linearly combines data from the Spitzer Space Telescope and the Galaxy Evolution Explorer. All bulges are found to be forming stars irrespective of bulge type (pseudobulge or classical bulge). At present-day SFR the median pseudobulge could have grown the present-day stellar mass in 8 Gyr. Classical bulges have the lowest specific SFR implying a growth times that are longer than a Hubble time, and thus the present-day SFR does not likely play a major role inmore » the evolution of classical bulges. In almost all galaxies in our sample the specific SFR (SFR per unit stellar mass) of the bulge is higher than that of the outer disk. This suggests that almost all galaxies are increasing their B/T through internal star formation. The SFR in pseudobulges correlates with their structure. More massive pseudobulges have higher SFR density, this is consistent with that stellar mass being formed by moderate, extended star formation. Bulges in late-type galaxies have similar SFRs as pseudobulges in intermediate-type galaxies, and are similar in radial size. However, they are deficient in mass; thus, they have much shorter growth times, {approx}2 Gyr. We identify a class of bulges that have nuclear morphology similar to pseudobulges, significantly lower specific SFR than pseudobulges, and are closer to classical bulges in structural parameter correlations. These are possibly composite objects, evolved pseudobulges or classical bulges experiencing transient, enhanced nuclear star formation. Our results are consistent with a scenario in which bulge growth via internal star formation is a natural, and near ubiquitous phenomenon in disk galaxies. Those galaxies with large classical bulges are not affected by the in situ bulge growth, likely because the majority of their stellar mass comes from some other phenomenon. Yet, those galaxies without a classical bulge, over long periods of extended star formation are able to growth a pseudobulge. Though cold accretion is not ruled out, for pseudobulge galaxies an addition of stellar mass from mergers or accretion is not required to explain the bulge mass. In this sense, galaxies with pseudobulges may very well be bulgeless (or 'quasi-bulgeless') galaxies, and galaxies with classical bulges are galaxies in which both internal evolution and hierarchical merging are responsible for the bulge mass by fractions that vary from galaxy to galaxy.« less

Multimodality Imaging in Cardiooncology

PubMed Central

Pizzino, Fausto; Vizzari, Giampiero; Qamar, Rubina; Bomzer, Charles; Carerj, Scipione; Khandheria, Bijoy K.

2015-01-01

Cardiotoxicity represents a rising problem influencing prognosis and quality of life of chemotherapy-treated patients. Anthracyclines and trastuzumab are the drugs most commonly associated with development of a cardiotoxic effect. Heart failure, myocardial ischemia, hypertension, myocarditis, and thrombosis are typical manifestation of cardiotoxicity by chemotherapeutic agents. Diagnosis and monitoring of cardiac side-effects of cancer treatment is of paramount importance. Echocardiography and nuclear medicine methods are widely used in clinical practice and left ventricular ejection fraction is the most important parameter to asses myocardial damage secondary to chemotherapy. However, left ventricular ejection decrease is a delayed phenomenon, occurring after a long stage of silent myocardial damage that classic imaging methods are not able to detect. New imaging techniques including three-dimensional echocardiography, speckle tracking echocardiography, and cardiac magnetic resonance have demonstrated high sensitivity in detecting the earliest alteration of left ventricular function associated with future development of chemotherapy-induced cardiomyopathy. Early diagnosis of cardiac involvement in cancer patients can allow for timely and adequate treatment management and the introduction of cardioprotective strategies. PMID:26300915

The Wigner distribution and 2D classical maps

NASA Astrophysics Data System (ADS)

Sakhr, Jamal

2017-07-01

The Wigner spacing distribution has a long and illustrious history in nuclear physics and in the quantum mechanics of classically chaotic systems. In this paper, a novel connection between the Wigner distribution and 2D classical mechanics is introduced. Based on a well-known correspondence between the Wigner distribution and the 2D Poisson point process, the hypothesis that typical pseudo-trajectories of a 2D ergodic map have a Wignerian nearest-neighbor spacing distribution (NNSD) is put forward and numerically tested. The standard Euclidean metric is used to compute the interpoint spacings. In all test cases, the hypothesis is upheld, and the range of validity of the hypothesis appears to be robust in the sense that it is not affected by the presence or absence of: (i) mixing; (ii) time-reversal symmetry; and/or (iii) dissipation.

Nucleation and growth of lead oxide particles in liquid lead-bismuth eutectic.

PubMed

Gladinez, Kristof; Rosseel, Kris; Lim, Jun; Marino, Alessandro; Heynderickx, Geraldine; Aerts, Alexander

2017-10-18

Liquid lead-bismuth eutectic (LBE) is an important candidate to become the primary coolant of future, generation IV, nuclear fast reactors and Accelerator Driven System (ADS) concepts. One of the main challenges with the use of LBE as a coolant is to avoid its oxidation which results in solid lead oxide (PbO) precipitation. The chemical equilibria governing PbO formation are well understood. However, insufficient kinetic information is currently available for the development of LBE-based nuclear technology. Here, we report the results of experiments in which the nucleation, growth and dissolution of PbO in LBE during temperature cycling are measured by monitoring dissolved oxygen using potentiometric oxygen sensors. The metastable region, above which PbO nucleation can occur, has been determined under conditions relevant for the operation of LBE cooled nuclear systems and was found to be independent of setup geometry and thus thought to be widely applicable. A kinetic model to describe formation and dissolution of PbO particles in LBE is proposed, based on Classical Nucleation Theory (CNT) combined with mass transfer limited growth and dissolution. This model can accurately predict the experimentally observed changes in oxygen concentration due to nucleation, growth and dissolution of PbO, using the effective interfacial energy of a PbO nucleus in LBE as a fitting parameter. The results are invaluable to evaluate the consequences of oxygen ingress in LBE cooled nuclear systems under normal operating and accidental conditions and form the basis for the development of cold trap technology to avoid PbO formation in the primary reactor circuit.

Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.

PubMed

Lin, Jhih-Rong; Liu, Zhonghao; Hu, Jianjun

2014-10-01

The binding affinity between a nuclear localization signal (NLS) and its import receptor is closely related to corresponding nuclear import activity. PTM-based modulation of the NLS binding affinity to the import receptor is one of the most understood mechanisms to regulate nuclear import of proteins. However, identification of such regulation mechanisms is challenging due to the difficulty of assessing the impact of PTM on corresponding nuclear import activities. In this study we proposed NIpredict, an effective algorithm to predict nuclear import activity given its NLS, in which molecular interaction energy components (MIECs) were used to characterize the NLS-import receptor interaction, and the support vector regression machine (SVR) was used to learn the relationship between the characterized NLS-import receptor interaction and the corresponding nuclear import activity. Our experiments showed that nuclear import activity change due to NLS change could be accurately predicted by the NIpredict algorithm. Based on NIpredict, we developed a systematic framework to identify potential PTM-based nuclear import regulations for human and yeast nuclear proteins. Application of this approach has identified the potential nuclear import regulation mechanisms by phosphorylation of two nuclear proteins including SF1 and ORC6. © 2014 Wiley Periodicals, Inc.

Implementation of Quantum Private Queries Using Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Wang, Chuan; Hao, Liang; Zhao, Lian-Jie

2011-08-01

We present a modified protocol for the realization of a quantum private query process on a classical database. Using one-qubit query and CNOT operation, the query process can be realized in a two-mode database. In the query process, the data privacy is preserved as the sender would not reveal any information about the database besides her query information, and the database provider cannot retain any information about the query. We implement the quantum private query protocol in a nuclear magnetic resonance system. The density matrix of the memory registers are constructed.

Dissociative Recombination without a Curve Crossing

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1994-01-01

Ab initio calculations show that a curve crossing is not always needed for a high dissociative- recombination cross section. For HeH(+), in which no neutral states cross the ion potential curve, dissociative recombination is driven by the nuclear kinetic-energy operator on adiabatic potential curves. The kinetic-energy derivative operator allows for capture into repulsive curves that are outside of the classical turning points for the nuclear motion. The dominant dissociative route is the C (2)Sigma(+) state leading to H(n = 2) atoms. An analogous mechanism is proposed for the dissociative recombination of H3(+).

First-principles calculation of photo-induced electron transfer rate constants in phthalocyanine-C60 organic photovoltaic materials: Beyond Marcus theory

NASA Astrophysics Data System (ADS)

Lee, Myeong H.; Dunietz, Barry D.; Geva, Eitan

2014-03-01

Classical Marcus theory is commonly adopted in solvent-mediated charge transfer (CT) process to obtain the CT rate constant, but it can become questionable when the intramolecular vibrational modes dominate the CT process as in OPV devices because Marcus theory treats these modes classically and therefore nuclear tunneling is not accounted for. We present a computational scheme to obtain the electron transfer rate constant beyond classical Marcus theory. Within this approach, the nuclear vibrational modes are treated quantum-mechanically and a short-time approximation is avoided. Ab initio calculations are used to obtain the basic parameters needed for calculating the electron transfer rate constant. We apply our methodology to phthalocyanine(H2PC)-C60 organic photovoltaic system where one C60 acceptor and one or two H2PC donors are included to model the donor-acceptor interface configuration. We obtain the electron transfer and recombination rate constants for all accessible charge transfer (CT) states, from which the CT exciton dynamics is determined by employing a master equation. The role of higher lying excited states in CT exciton dynamics is discussed. This work is pursued as part of the Center for Solar and Thermal Energy Conversion, an Energy Frontier Research Center funded by the US Department of Energy Office of Science, Office of Basic Energy Sciences under 390 Award No. DE-SC0000957.

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David E.; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.« less

The TIC complex uncovered: The alternative view on the molecular mechanism of protein translocation across the inner envelope membrane of chloroplasts.

PubMed

Nakai, Masato

2015-09-01

Chloroplasts must import thousands of nuclear-encoded preproteins synthesized in the cytosol through two successive protein translocons at the outer and inner envelope membranes, termed TOC and TIC, respectively, to fulfill their complex physiological roles. The molecular identity of the TIC translocon had long remained controversial; two proteins, namely Tic20 and Tic110, had been proposed to be central to protein translocation across the inner envelope membrane. Tic40 also had long been considered to be another central player in this process. However, recently, a novel 1-megadalton complex consisting of Tic20, Tic56, Tic100, and Tic214 was identified at the chloroplast inner membrane of Arabidopsis and was demonstrated to constitute a general TIC translocon which functions in concert with the well-characterized TOC translocon. On the other hand, direct interaction between this novel TIC transport system and Tic110 or Tic40 was hardly observed. Consequently, the molecular model for protein translocation across the inner envelope membrane of chloroplasts might need to be extensively revised. In this review article, I intend to propose such alternative view regarding the TIC transport system in contradistinction to the classical view. I also would emphasize importance of reevaluation of previous works in terms of with what methods these classical Tic proteins such as Tic110 or Tic40 were picked up as TIC constituents at the very beginning as well as what actual evidence there were to support their direct and specific involvement in chloroplast protein import. This article is part of a Special Issue entitled: Chloroplast Biogenesis. Copyright © 2014 Elsevier B.V. All rights reserved.

Fragmentation of Thin Wires under High Voltage Pulses and Bipolar Fusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Papageorgiou, C. D.; Raptis, T. E.

2010-01-21

In this article we present an alternative explanation of the phenomenon of wire fragmentation under high transient currents based on classical electromagnetism. We also explain how this phenomenon can be utilized as a primitive example of low energy-high power disruptive phenomena that can affect even nuclear matter.

Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase.

PubMed

Engel, Hamutal; Doron, Dvir; Kohen, Amnon; Major, Dan Thomas

2012-04-10

The inclusion of nuclear quantum effects such as zero-point energy and tunneling is of great importance in studying condensed phase chemical reactions involving the transfer of protons, hydrogen atoms, and hydride ions. In the current work, we derive an efficient quantum simulation approach for the computation of the momentum distribution in condensed phase chemical reactions. The method is based on a quantum-classical approach wherein quantum and classical simulations are performed separately. The classical simulations use standard sampling techniques, whereas the quantum simulations employ an open polymer chain path integral formulation which is computed using an efficient Monte Carlo staging algorithm. The approach is validated by applying it to a one-dimensional harmonic oscillator and symmetric double-well potential. Subsequently, the method is applied to the dihydrofolate reductase (DHFR) catalyzed reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to yield S-5,6,7,8-tetrahydrofolate and NADP(+). The key chemical step in the catalytic cycle of DHFR involves a stereospecific hydride transfer. In order to estimate the amount of quantum delocalization, we compute the position and momentum distributions for the transferring hydride ion in the reactant state (RS) and transition state (TS) using a recently developed hybrid semiempirical quantum mechanics-molecular mechanics potential energy surface. Additionally, we examine the effect of compression of the donor-acceptor distance (DAD) in the TS on the momentum distribution. The present results suggest differential quantum delocalization in the RS and TS, as well as reduced tunneling upon DAD compression.

Benzothiadiazole Derivatives as Fluorescence Imaging Probes: Beyond Classical Scaffolds.

PubMed

Neto, Brenno A D; Carvalho, Pedro H P R; Correa, Jose R

2015-06-16

This Account describes the origins, features, importance, and trends of the use of fluorescent small-molecule 2,1,3-benzothiadiazole (BTD) derivatives as a new class of bioprobes applied to bioimaging analyses of several (live and fixed) cell types. BTDs have been successfully used as probes for a plethora of biological analyses for only a few years, and the impressive responses obtained by using this important class of heterocycle are fostering the development of new fluorescent BTDs and expanding the biological applications of such derivatives. The first use of a fluorescent small-molecule BTD derivative as a selective cellular probe dates back to 2010, and since then impressive advances have been described by us and others. The well-known limitations of classical scaffolds urged the development of new classes of bioprobes. Although great developments have been achieved by using classical scaffolds such as coumarins, BODIPYs, fluoresceins, rhodamines, cyanines, and phenoxazines, there is still much to be done, and BTDs aim to succeed where these dyes have shown their limitations. Important organelles and cell components such as nuclear DNA, mitochondria, lipid droplets, and others have already been successfully labeled by fluorescent small-molecule BTD derivatives. New technological systems that use BTDs as the fluorophores for bioimaging experiments have been described in recent scientific literature. The successful application of BTDs as selective bioprobes has led some groups to explore their potential for use in studying membrane pores or tumor cells under hypoxic conditions. Finally, BTDs have also been used as fluorescent tags to investigate the action mechanism of some antitumor compounds. The attractive photophysical data typically observed for π-extended BTD derivatives is fostering interest in the use of this new class of bioprobes. Large Stokes shifts, large molar extinction coefficients, high quantum yields, high stability when stored in solution or as pure solids, no fading even after long periods of irradiation, bright emissions with no blinking, good signal-to-noise ratios, efficiency to transpose the cell membrane, and irradiation preferentially in the visible-light region are just some features noted by using BTDs. As the pioneering group in the use of fluorescent small-molecule BTDs for bioimaging purposes, we feel pleased to share our experience, results, advances, and personal perspectives with the readers of this Account. The readers will clearly note the huge advantages of using fluorescent BTDs over classical scaffolds, and hopefully they will be inspired and motivated to further BTD technology in the fields of molecular and cellular biology.

Range parameters of slow gold ions implanted into light targets

NASA Astrophysics Data System (ADS)

Kuzmin, V.

2009-08-01

Interatomic potentials for Au-C, Au-B, Au-N and Au-Si systems, calculated with density-functional theory (DFT) methods, have been used to evaluate the range parameters of gold in B, Si, BN and SiC films at energies of about 10-400 keV. The potentials have been employed to describe scattering angles of a projectile and to calculate the nuclear stopping powers and the higher moments of the energy, transferred in single collisions. Utilizing these findings the range parameters have been obtained by the standard transport theory and by Monte-Carlo simulations. A velocity proportional electronic stopping was included into the consideration. The approach developed corresponds completely to the standard classical scheme of the calculation of range parameters. Good agreement between the computed range parameters and available experimental data allow us to conclude that correlation effects between the nuclear and electronic stopping can be neglected in the energy range in question. Moreover, it is proven for the first time that the model by Grande, et al. [P.L. Grande, F.C. Zawislak, D. Fink, M. Behar, Nucl. Instr. and Meth. B 61 (1991) 282], which relies on the importance of correlation effects, contains inherent contradictions.

Nuclear Quantum Effects on Aqueous Electron Attachment and Redox Properties.

PubMed

Rybkin, Vladimir V; VandeVondele, Joost

2017-04-06

Nuclear quantum effects (NQEs) on the reduction and oxidation properties of small aqueous species (CO 2 , HO 2 , and O 2 ) are quantified and rationalized by first-principles molecular dynamics and thermodynamic integration. Vertical electron attachment, or electron affinity, and detachment energies (VEA and VDE) are strongly affected by NQEs, decreasing in absolute value by 0.3 eV going from a classical to a quantum description of the nuclei. The effect is attributed to NQEs that lessen the solvent response upon oxidation/reduction. The reduction of solvent reorganization energy is expected to be general for small solutes in water. In the thermodynamic integral that yields the free energy of oxidation/reduction, these large changes enter with opposite sign, and only a small net effect (0.1 eV) remains. This is not obvious for CO 2 , where the integrand is strongly influenced by NQEs due to the onset of interaction of the reduced orbital with the conduction band of the liquid during thermodynamic integration. We conclude that NQEs might not have to be included in the computation of redox potentials, unless high accuracy is needed, but are important for VEA and VDE calculations.

Phospholipid Regulation of the Nuclear Receptor Superfamily

PubMed Central

Crowder, Mark K.; Seacrist, Corey D.; Blind, Raymond D.

2016-01-01

Nuclear receptors are ligand-activated transcription factors whose diverse biological functions are classically regulated by cholesterol-based small molecules. Over the past few decades, a growing body of evidence has demonstrated that phospholipids and other similar amphipathic molecules can also specifically bind and functionally regulate the activity of certain nuclear receptors, suggesting a critical role for these non-cholesterol-based molecules in transcriptional regulation. Phosphatidylcholines, phosphoinositides and sphingolipids are a few of the many phospholipid like molecules shown to quite specifically regulate nuclear receptors in mouse models, cell lines and in vitro. More recent evidence has also shown that certain nuclear receptors can “present” a bound phospholipid headgroup to key lipid signaling enzymes, which can then modify the phospholipid headgroup with very unique kinetic properties. Here, we review the broad array of phospholipid / nuclear receptor interactions, from the perspective of the chemical nature of the phospholipid, and the cellular abundance of the phospholipid. We also view the data in the light of well established paradigms for phospholipid mediated transcriptional regulation, as well as newer models of how phospholipids might effect transcription in the acute regulation of complex nuclear signaling pathways. Thus, this review provides novel insight into the new, non-membrane associated roles nuclear phospholipids play in regulating complex nuclear events, centered on the nuclear receptor superfamily of transcription factors. PMID:27838257

Outer crust of nonaccreting cold neutron stars

NASA Astrophysics Data System (ADS)

Rüster, Stefan B.; Hempel, Matthias; Schaffner-Bielich, Jürgen

2006-03-01

The properties of the outer crust of nonaccreting cold neutron stars are studied by using modern nuclear data and theoretical mass tables, updating in particular the classic work of Baym, Pethick, and Sutherland. Experimental data from the atomic mass table from Audi, Wapstra, and Thibault of 2003 are used and a thorough comparison of many modern theoretical nuclear models, both relativistic and nonrelativistic, is performed for the first time. In addition, the influences of pairing and deformation are investigated. State-of-the-art theoretical nuclear mass tables are compared to check their differences concerning the neutron drip line, magic neutron numbers, the equation of state, and the sequence of neutron-rich nuclei up to the drip line in the outer crust of nonaccreting cold neutron stars.

Theory of time-resolved x-ray photoelectron diffraction from transient conformational molecules

NASA Astrophysics Data System (ADS)

Tsuru, Shota; Sako, Tokuei; Fujikawa, Takashi; Yagishita, Akira

2017-04-01

We formulate x-ray photoelectron diffraction (XPD) from molecules undergoing photochemical reactions induced by optical laser pulses, and then apply the formula to the simulation of time-dependent XPD profiles from both dissociating I2 molecules and bending C S2 molecules. The dependence of nuclear wave-packet motions on the intensity and shape of the optical laser pulses is examined. As a result, the XPD simulations based on such nuclear wave-packet calculations are observed to exhibit characteristic features, which are compared with the XPD profiles due to classical trajectories of nuclear motions. The present study provides a methodology toward creating "molecular movies" of ultrafast photochemical reactions by means of femtosecond XPD with x-ray free-electron lasers.

GPR30: A G protein-coupled receptor for estrogen.

PubMed

Prossnitz, Eric R; Arterburn, Jeffrey B; Sklar, Larry A

2007-02-01

Estrogen is a critical steroid in human physiology exerting its effect both at the transcriptional level as well as at the level of rapid intracellular signaling through second messengers. Many of estrogen's transcriptional effects have long been known to be mediated through classical nuclear steroid receptors but recent studies also demonstrate the existence of a 7-transmembrane G protein-coupled receptor, GPR30 that responds to estrogen with rapid cellular signaling. There is currently controversy over the ability of classical estrogen receptors to recapitulate GPR30-mediated signaling mechanisms and vice versa. This article will summarize recent literature and address the relationship between GPR30 and conventional estrogen receptor signaling.

Influence of acute promyelocytic leukemia therapeutic drugs on nuclear pore complex density and integrity.

PubMed

Lång, Anna; Øye, Alexander; Eriksson, Jens; Rowe, Alexander D; Lång, Emma; Bøe, Stig Ove

2018-05-15

During cell division, a large number of nuclear proteins are released into the cytoplasm due to nuclear envelope breakdown. Timely nuclear import of these proteins following exit from mitosis is critical for establishment of the G1 nuclear environment. Dysregulation of post-mitotic nuclear import may affect the fate of newly divided stem or progenitor cells and may lead to cancer. Acute promyelocytic leukemia (APL) is a malignant disorder that involves a defect in blood cell differentiation at the promyelocytic stage. Recent studies suggest that pharmacological concentrations of the APL therapeutic drugs, all-trans retinoic acid (ATRA) and arsenic trioxide (ATO), affect post-mitotic nuclear import of the APL-associated oncoprotein PML/RARA. In the present study, we have investigated the possibility that ATRA and ATO affect post-mitotic nuclear import through interference with components of the nuclear import machinery. We observe reduced density and impaired integrity of nuclear pore complexes after ATRA and/or ATO exposure. Using a post-mitotic nuclear import assay, we demonstrate distinct import kinetics among different nuclear import pathways while nuclear import rates were similar in the presence or absence of APL therapeutic drugs. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

78 FR 14183 - Import Restrictions Imposed on Certain Archaeological Material From Belize

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-05

... Post-Classic Periods of the Pre-Columbian era through the Early and Late Colonial Periods. A list of...- Classic, Classic, and Post-Classic Periods of the Pre- Columbian era through the Early and Late Colonial... to 250 years old representing the Pre-Columbian era through the Early and Late Colonial Periods (19 U...

DNA damage talks to inflammation.

PubMed

Cohen, Idan

2017-02-01

Interleukin-1 alpha (IL-1α) and beta (IL-1β) are pleiotropic cytokines affecting multiple cells and regulating many immune and inflammatory responses. The recent finding that nuclear IL-1α is recruited to sites of DNA damage, and its ability to actively sense and report genotoxic stress to the surrounding tissue, dramatically alters the way we view IL-1 biology. This discovery add a new face to the classical "danger theory" and show that danger signaling is not strictly limited to passive release or dying cells. Most importantly, as now physiological stresses are linked to the release or secretion of IL-1α, chronic danger signaling and the alarmin inhibition should be considered as a new therapeutic approach for many diseases that are characterized by ongoing DNA damage, stress signaling and inflammation. Copyright © 2016. Published by Elsevier Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, J. B.; Hamilton, J. H.

The change in the structure of the collective levels with spin angular momentum in atomic nuclei is often expressed in terms of the classical concepts of the kinematic and the dynamic moments of inertia varying with spin. For the well deformed even-even nuclei the kinematic moment of inertia increases with spin up to 10%-20%, at say I{sup {pi}} = 12{sup +}. However, for the shape transitional nuclei, or almost spherical nuclei, it increases with spin much faster. The pitfalls of using the rotor model form of kinematic moment of inertia in such cases are pointed out here. Alternative methods ofmore » extracting the nuclear structure information are explored. The important role of the ground state deformation is illustrated. The use of the power index formula for evaluating the effective moment of inertia, free from the assumption of the rotor model, is described.« less

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.

2017-12-01

Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

A new symmetrical quasi-classical model for electronically non-adiabatic processes: Application to the case of weak non-adiabatic coupling

DOE PAGES

Cotton, Stephen J.; Miller, William H.

2016-10-14

Previous work has shown how a symmetrical quasi-classical (SQC) windowing procedure can be used to quantize the initial and final electronic degrees of freedom in the Meyer-Miller (MM) classical vibronic (i.e, nuclear + electronic) Hamiltonian, and that the approach provides a very good description of electronically non-adiabatic processes within a standard classical molecular dynamics framework for a number of benchmark problems. This study explores application of the SQC/MM approach to the case of very weak non-adiabatic coupling between the electronic states, showing (as anticipated) how the standard SQC/MM approach used to date fails in this limit, and then devises amore » new SQC windowing scheme to deal with it. Finally, application of this new SQC model to a variety of realistic benchmark systems shows that the new model not only treats the weak coupling case extremely well, but it is also seen to describe the “normal” regime (of electronic transition probabilities ≳ 0.1) even more accurately than the previous “standard” model.« less

A new symmetrical quasi-classical model for electronically non-adiabatic processes: Application to the case of weak non-adiabatic coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cotton, Stephen J.; Miller, William H.

Previous work has shown how a symmetrical quasi-classical (SQC) windowing procedure can be used to quantize the initial and final electronic degrees of freedom in the Meyer-Miller (MM) classical vibronic (i.e, nuclear + electronic) Hamiltonian, and that the approach provides a very good description of electronically non-adiabatic processes within a standard classical molecular dynamics framework for a number of benchmark problems. This study explores application of the SQC/MM approach to the case of very weak non-adiabatic coupling between the electronic states, showing (as anticipated) how the standard SQC/MM approach used to date fails in this limit, and then devises amore » new SQC windowing scheme to deal with it. Finally, application of this new SQC model to a variety of realistic benchmark systems shows that the new model not only treats the weak coupling case extremely well, but it is also seen to describe the “normal” regime (of electronic transition probabilities ≳ 0.1) even more accurately than the previous “standard” model.« less

Substituent Effects on Keto-Enol Equilibria Using NMR Spectroscopy

ERIC Educational Resources Information Center

Manbeck, Kimberly A.; Boaz, Nicholas C.; Bair, Nathaniel C.; Sanders, Allix M. S.; Marsh, Anderson L.

2011-01-01

In this extension to a classic physical chemistry experiment, students record the proton nuclear magnetic resonance spectra of the [beta]-diketones 2,4-pentanedione, 3-methyl-2,4-pentanedione, and 3-chloro-2,4-pentanedione to investigate the effect of substituents on keto-enol tautomerization equilibria. From the integrated intensities of keto and…

New calculations of gross β-decay properties for astrophysical applications: Speeding-up the classical r process

NASA Astrophysics Data System (ADS)

Möller, Peter; Pfeiffer, Bernd; Kratz, Karl-Ludwig

2003-05-01

Recent compilations of experimental gross β-decay properties, i.e., half-lives (T1/2) and neutron-emission probabilities (Pn), are compared to improved global macroscopic-microscopic model predictions. The model combines calculations within the quasiparticle (QP) random-phase approximation for the Gamow-Teller (GT) part with an empirical spreading of the QP strength and the gross theory for the first-forbidden part of β- decay. Nuclear masses are either taken from the 1995 data compilation of Audi et al., when available, otherwise from the finite-range droplet model. Especially for spherical and neutron-(sub-)magic isotopes a considerable improvement compared to our earlier predictions for pure GT decay (ADNDT, 1997) is observed. T1/2 and Pn values up to the neutron drip line have been used in r-process calculations within the classical “waiting-point” approximation. With the new nuclear-physics input, a considerable speeding-up of the r-matter flow is observed, in particular at those r-abundance peaks which are related to magic neutron-shell closures.

Mean-trajectory approximation for electronic and vibrational-electronic nonlinear spectroscopy

NASA Astrophysics Data System (ADS)

Loring, Roger F.

2017-04-01

Mean-trajectory approximations permit the calculation of nonlinear vibrational spectra from semiclassically quantized trajectories on a single electronically adiabatic potential surface. By describing electronic degrees of freedom with classical phase-space variables and subjecting these to semiclassical quantization, mean-trajectory approximations may be extended to compute both nonlinear electronic spectra and vibrational-electronic spectra. A general mean-trajectory approximation for both electronic and nuclear degrees of freedom is presented, and the results for purely electronic and for vibrational-electronic four-wave mixing experiments are quantitatively assessed for harmonic surfaces with linear electronic-nuclear coupling.

Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects.

PubMed

Pérez, Alejandro; Tuckerman, Mark E; Hjalmarson, Harold P; von Lilienfeld, O Anatole

2010-08-25

Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage.

Nuclear transition matrix elements for neutrinoless double-β decay of 76Ge and 82Se isotopes

NASA Astrophysics Data System (ADS)

Rath, P. K.

2017-10-01

Within mechanisms involving light and heavy Majorana neutrinos, the nuclear transition matrix elements (NTMEs) for the neutrinoless double-β decay of 76Ge and 82Se isotopes are calculated. Uncertainties in the average NTMEs M¯ (0 v ) and M¯ (0 N ) due to the exchange of light and heavy Majorana neutrinos, respectively, turn out to be about 10% and 37%, respectively. Limits on the effective mass of light Majorana neutrino , heavy Majorana neutrino and Majoron-neutrino coupling constant of classical Majoron model are extracted.

A comprehensive study of Interatomic Coulombic Decay in argon dimers: Extracting R-dependent absolute decay rates from the experiment

DOE PAGES

Rist, J.; Miteva, T.; Gaire, B.; ...

2016-09-15

In this paper we present a comprehensive and detailed study of Interatomic Coulombic Decay (ICD) occurring after irradiating argon dimers with XUV-synchrotron radiation. A manifold of different decay channels is observed and the corresponding initial and final states are assigned. Additionally, the effect of nuclear dynamics on the ICD electron spectrum is examined for one specific decay channel. The internuclear distance-dependent width Γ(R) of the decay is obtained from the measured kinetic energy release distribution of the ions employing a classical nuclear dynamics model.

Preface: Special Topic on Nuclear Quantum Effects

NASA Astrophysics Data System (ADS)

Tuckerman, Mark; Ceperley, David

2018-03-01

Although the observable universe strictly obeys the laws of quantum mechanics, in many instances, a classical description that either ignores quantum effects entirely or accounts for them at a very crude level is sufficient to describe a wide variety of phenomena. However, when this approximation breaks down, as is often the case for processes involving light nuclei, a full quantum treatment becomes indispensable. This Special Topic in The Journal of Chemical Physics showcases recent advances in our understanding of nuclear quantum effects in condensed phases as well as novel algorithmic developments and applications that have enhanced the capability to study these effects.

Scalable quantum computation scheme based on quantum-actuated nuclear-spin decoherence-free qubits

NASA Astrophysics Data System (ADS)

Dong, Lihong; Rong, Xing; Geng, Jianpei; Shi, Fazhan; Li, Zhaokai; Duan, Changkui; Du, Jiangfeng

2017-11-01

We propose a novel theoretical scheme of quantum computation. Nuclear spin pairs are utilized to encode decoherence-free (DF) qubits. A nitrogen-vacancy center serves as a quantum actuator to initialize, readout, and quantum control the DF qubits. The realization of CNOT gates between two DF qubits are also presented. Numerical simulations show high fidelities of all these processes. Additionally, we discuss the potential of scalability. Our scheme reduces the challenge of classical interfaces from controlling and observing complex quantum systems down to a simple quantum actuator. It also provides a novel way to handle complex quantum systems.

Preface: Special Topic on Nuclear Quantum Effects.

PubMed

Tuckerman, Mark; Ceperley, David

2018-03-14

Although the observable universe strictly obeys the laws of quantum mechanics, in many instances, a classical description that either ignores quantum effects entirely or accounts for them at a very crude level is sufficient to describe a wide variety of phenomena. However, when this approximation breaks down, as is often the case for processes involving light nuclei, a full quantum treatment becomes indispensable. This Special Topic in The Journal of Chemical Physics showcases recent advances in our understanding of nuclear quantum effects in condensed phases as well as novel algorithmic developments and applications that have enhanced the capability to study these effects.

The etiology of social aggression: a nuclear twin family study.

PubMed

Slawinski, Brooke L; Klump, Kelly L; Burt, S Alexandra

2018-04-02

Social aggression is a form of antisocial behavior in which social relationships and social status are used to damage reputations and inflict emotional harm on others. Despite extensive research examining the prevalence and consequences of social aggression, only a few studies have examined its genetic-environmental etiology, with markedly inconsistent results. We estimated the etiology of social aggression using the nuclear twin family (NTF) model. Maternal-report, paternal-report, and teacher-report data were collected for twin social aggression (N = 1030 pairs). We also examined the data using the classical twin (CT) model to evaluate whether its strict assumptions may have biased previous heritability estimates. The best-fitting NTF model for all informants was the ASFE model, indicating that additive genetic, sibling environmental, familial environmental, and non-shared environmental influences significantly contribute to the etiology of social aggression in middle childhood. However, the best-fitting CT model varied across informants, ranging from AE and ACE to CE. Specific heritability estimates for both NTF and CT models also varied across informants such that teacher reports indicated greater genetic influences and father reports indicated greater shared environmental influences. Although the specific NTF parameter estimates varied across informants, social aggression generally emerged as largely additive genetic (A = 0.15-0.77) and sibling environmental (S = 0.42-0.72) in origin. Such findings not only highlight an important role for individual genetic risk in the etiology of social aggression, but also raise important questions regarding the role of the environment.

Follicular variant of papillary thyroid carcinoma: genome-wide appraisal of a controversial entity.

PubMed

Wreesmann, Volkert B; Ghossein, Ronald A; Hezel, Michael; Banerjee, Debenranrath; Shaha, Ashok R; Tuttle, R Michael; Shah, Jatin P; Rao, Pulivarthi H; Singh, Bhuvanesh

2004-08-01

The majority of thyroid tumors are classified as papillary (papillary thyroid carcinomas; PTCs) or follicular neoplasms (follicular thyroid adenomas and carcinomas; FTA/FTC) based on nuclear features and the cellular growth pattern. However, classification of the follicular variant of papillary thyroid carcinoma (FVPTC) remains an issue of debate. These tumors contain a predominantly follicular growth pattern but display nuclear features and overall clinical behavior consistent with PTC. In this study, we used comparative genomic hybridization (CGH) to compare the global chromosomal aberrations in FVPTC to the PTC of classical variant (classical PTC) and FTA/FTC. In addition, we assessed the presence of peroxisome proliferator-activated receptor-gamma (PPARG) alteration, a genetic event specific to FTA/FTC, using Southern blot and immunohistochemistry analyses. In sharp contrast to the findings in classical PTC (4% of cases), CGH analysis demonstrated that both FVPTC (59% of cases) and FTA/FTC (36% of cases) were commonly characterized by aneuploidy (P = 0.0002). Moreover, the pattern of chromosomal aberrations (gains at chromosome arms 2q, 4q, 5q, 6q, 8q, and 13q and deletions at 1p, 9q, 16q, 17q, 19q, and 22q) in the follicular variant of PTC closely resembled that of FTA/FTC. Aberrations in PPARG were uniquely detected in FVPTC and FTA/FTC. Our findings suggest a stronger relationship between the FVPTC and FTA/FTC than previously appreciated and support further consideration of the current classification of thyroid neoplasms. Copyright 2004 Wiley-Liss, Inc.

Immunohistochemical patterns of ProEx C in vulvar squamous lesions: detection of overexpression of MCM2 and TOP2A.

PubMed

Chen, Hui; Gonzalez, Jorge L; Brennick, Jeoffry B; Liu, Miaoliang; Yan, Shaofeng

2010-09-01

Two major subtypes of vulvar squamous cell carcinomas (SCC) have been described. Basaloid and warty SCC are human papillomavirus-related and associated with classic vulvar intraepithelial neoplasia (VIN). Keratinizing SCC is associated with lichen sclerosus and differentiated VIN, but not with human papillomavirus. This study was undertaken to examine the expression patterns of ProEx C in vulvar SCC and its precursors. We analyzed 22 cases with normal vulvar epidermis, 13 cases of lichen sclerosus, 14 cases of condylomas, 23 cases of high-grade classic VIN, 6 cases of differentiated VIN, 3 cases of verrucous carcinomas, 10 cases of keratinizing SCC, and 8 cases of basaloid and warty SCC. ProEx C targets minichromosome maintenance protein and topoisomerase II alpha protein which are overexpressed in the cell nucleus during aberrant S-phase induction. Marked confluent ProEx C expression is present in high-grade classic VIN with nuclear staining extending into the middle and upper layers of the epidermis. Condylomas show parabasal nuclear immunoreactivity associated with scattered ProEx C-positive nuclei in the more differentiated suprabasilar layers. Invasive SCC shows variable staining patterns. In contrast, ProEx C staining is essentially limited to the basal and parabasal layers in normal epidermis, lichen sclerosus, differentiated VIN, and verrucous carcinoma. Overall, ProEx C is a useful proliferation marker for high-grade VIN analogous to the staining patterns reported in high-grade cervical intraepithelial neoplasia.

Myelin management by the 18.5–kDa and 21.5–kDa classic myelin basic protein isoforms

PubMed Central

Harauz, George; Boggs, Joan M.

2013-01-01

The classic myelin basic protein (MBP) splice isoforms range in nominal molecular mass from 14 to 21.5 kDa, and arise from the gene in the oligodendrocyte lineage (Golli) in maturing oligodendrocytes. The 18.5-kDa isoform that predominates in adult myelin adheres the cytosolic surfaces of oligodendrocyte membranes together, and forms a two-dimensional molecular sieve restricting protein diffusion into compact myelin. However, this protein has additional roles including cytoskeletal assembly and membrane extension, binding to SH3-domains, participation in Fyn-mediated signaling pathways, sequestration of phosphoinositides, and maintenance of calcium homeostasis. Of the diverse post-translational modifications of this isoform, phosphorylation is the most dynamic, and modulates 18.5-kDa MBP’s protein-membrane and protein-protein interactions, indicative of a rich repertoire of functions. In developing and mature myelin, phosphorylation can result in microdomain or even nuclear targeting of the protein, supporting the conclusion that 18.5-kDa MBP has significant roles beyond membrane adhesion. The full-length, early-developmental 21.5-kDa splice isoform is predominantly karyophilic due to a non-traditional P-Y nuclear localization signal, with effects such as promotion of oligodendrocyte proliferation. We discuss in vitro and recent in vivo evidence for multifunctionality of these classic basic proteins of myelin, and argue for a systematic evaluation of the temporal and spatial distributions of these protein isoforms, and their modified variants, during oligodendrocyte differentiation. PMID:23398367

Orientia tsutsugamushi uses two Ank effectors to modulate NF-κB p65 nuclear transport and inhibit NF-κB transcriptional activation.

PubMed

Evans, Sean M; Rodino, Kyle G; Adcox, Haley E; Carlyon, Jason A

2018-05-01

Orientia tsutsugamushi causes scrub typhus, a potentially fatal infection that threatens over one billion people. Nuclear translocation of the transcription factor, NF-κB, is the central initiating cellular event in the antimicrobial response. Here, we report that NF-κB p65 nuclear accumulation and NF-κB-dependent transcription are inhibited in O. tsutsugamushi infected HeLa cells and/or primary macrophages, even in the presence of TNFα. The bacterium modulates p65 subcellular localization by neither degrading it nor inhibiting IκBα degradation. Rather, it exploits host exportin 1 to mediate p65 nuclear export, as this phenomenon is leptomycin B-sensitive. O. tsutsugamushi antagonizes NF-κB-activated transcription even when exportin 1 is inhibited and NF-κB consequently remains in the nucleus. Two ankyrin repeat-containing effectors (Anks), Ank1 and Ank6, each of which possess a C-terminal F-box and exhibit 58.5% amino acid identity, are linked to the pathogen's ability to modulate NF-κB. When ectopically expressed, both translocate to the nucleus, abrogate NF-κB-activated transcription in an exportin 1-independent manner, and pronouncedly reduce TNFα-induced p65 nuclear levels by exportin 1-dependent means. Flag-tagged Ank 1 and Ank6 co-immunoprecipitate p65 and exportin 1. Both also bind importin β1, a host protein that is essential for the classical nuclear import pathway. Importazole, which blocks importin β1 activity, abrogates Ank1 and Ank6 nuclear translocation. The Ank1 and Ank6 regions that bind importin β1 also mediate their transport into the nucleus. Yet, these regions are distinct from those that bind p65/exportin 1. The Ank1 and Ank6 F-box and the region that lies between it and the ankyrin repeat domain are essential for blocking p65 nuclear accumulation. These data reveal a novel mechanism by which O. tsutsugamushi modulates the activity and nuclear transport of NF-κB p65 and identify the first microbial proteins that co-opt both importin β1 and exportin 1 to antagonize a critical arm of the antimicrobial response.

Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

PubMed Central

2011-01-01

Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression. PMID:21939538

Outer crust of nonaccreting cold neutron stars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruester, Stefan B.; Hempel, Matthias; Schaffner-Bielich, Juergen

The properties of the outer crust of nonaccreting cold neutron stars are studied by using modern nuclear data and theoretical mass tables, updating in particular the classic work of Baym, Pethick, and Sutherland. Experimental data from the atomic mass table from Audi, Wapstra, and Thibault of 2003 are used and a thorough comparison of many modern theoretical nuclear models, both relativistic and nonrelativistic, is performed for the first time. In addition, the influences of pairing and deformation are investigated. State-of-the-art theoretical nuclear mass tables are compared to check their differences concerning the neutron drip line, magic neutron numbers, the equationmore » of state, and the sequence of neutron-rich nuclei up to the drip line in the outer crust of nonaccreting cold neutron stars.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scherrer, Arne; UMR 8640 ENS-CNRS-UPMC, Département de Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris; UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris

The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similar to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that canmore » be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach.« less

Modeling flow stress constitutive behavior of SA508-3 steel for nuclear reactor pressure vessels

NASA Astrophysics Data System (ADS)

Sun, Mingyue; Hao, Luhan; Li, Shijian; Li, Dianzhong; Li, Yiyi

2011-11-01

Based on the measured stress-strain curves under different temperatures and strain rates, a series of flow stress constitutive equations for SA508-3 steel were firstly established through the classical theories on work hardening and softening. The comparison between the experimental and modeling results has confirmed that the established constitutive equations can correctly describe the mechanical responses and microstructural evolutions of the steel under various hot deformation conditions. We further represented a successful industrial application of this model to simulate a forging process for a large conical shell used in a nuclear steam generator, which evidences its practical and promising perspective of our model with an aim of widely promoting the hot plasticity processing for heavy nuclear components of fission reactors.

Extending the electron spin coherence time of atomic hydrogen by dynamical decoupling.

PubMed

Mitrikas, George; Efthimiadou, Eleni K; Kordas, George

2014-02-14

We study the electron spin decoherence of encapsulated atomic hydrogen in octasilsesquioxane cages induced by the (1)H and (29)Si nuclear spin bath. By applying the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence we significantly suppress the low-frequency noise due to nuclear spin flip-flops up to the point where a maximum T2 = 56 μs is observed. Moreover, dynamical decoupling with the CPMG sequence reveals the existence of two other sources of decoherence: first, a classical magnetic field noise imposed by the (1)H nuclear spins of the cage organic substituents, which can be described by a virtual fluctuating magnetic field with the proton Larmor frequency, and second, decoherence due to anisotropic hyperfine coupling between the electron and the inner (29)Si spins of the cage.

Radiation Safety in Nuclear Medicine Procedures.

PubMed

Cho, Sang-Geon; Kim, Jahae; Song, Ho-Chun

2017-03-01

Since the nuclear disaster at the Fukushima Daiichi Nuclear Power Plant in 2011, radiation safety has become an important issue in nuclear medicine. Many structured guidelines or recommendations of various academic societies or international campaigns demonstrate important issues of radiation safety in nuclear medicine procedures. There are ongoing efforts to fulfill the basic principles of radiation protection in daily nuclear medicine practice. This article reviews important principles of radiation protection in nuclear medicine procedures. Useful references, important issues, future perspectives of the optimization of nuclear medicine procedures, and diagnostic reference level are also discussed.

Communication: On the consistency of approximate quantum dynamics simulation methods for vibrational spectra in the condensed phase.

PubMed

Rossi, Mariana; Liu, Hanchao; Paesani, Francesco; Bowman, Joel; Ceriotti, Michele

2014-11-14

Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here, we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer model and a mixed quantum-classical model as representatives of the first family of methods, and centroid molecular dynamics and thermostatted ring polymer molecular dynamics as examples of the latter. We use as benchmarks D2O doped with HOD and pure H2O at three distinct thermodynamic state points (ice Ih at 150 K, and the liquid at 300 K and 600 K), modeled with the simple q-TIP4P/F potential energy and dipole moment surfaces. With few exceptions the different techniques yield IR absorption frequencies that are consistent with one another within a few tens of cm(-1). Comparison with classical molecular dynamics demonstrates the importance of nuclear quantum effects up to the highest temperature, and a detailed discussion of the discrepancies between the various methods let us draw some (circumstantial) conclusions about the impact of the very different approximations that underlie them. Such cross validation between radically different approaches could indicate a way forward to further improve the state of the art in simulations of condensed-phase quantum dynamics.

Organic salts formed by 2,4,6-triaminopyrimidine and selected carboxylic acids via a variety of hydrogen bonds: Synthons cooperation, and crystal structures

NASA Astrophysics Data System (ADS)

Xing, Peiqi; Li, Qingyun; Li, Yingying; Wang, Kunpeng; Zhang, Qi; Wang, Lei

2017-05-01

By using solvent evaporation method, 2,4,6-triaminopyrimidine (TAPI) is employed to crystallize with a variety of acids, including 3,5-dihydroxybenzoic acid (HDHBA), 3-nitrophthalic acid (H2NPA), 5-amino-2,4,6-triiodoisophthalic acid (H2ATIPIA), 2,5-dibromoterephthalic acid (H2DBTPA), 1,5-naphthalenedisulfonic acid (H2NDSA), sebacic acid (H2SA), 1,2,4-benzenetricarboxylic acid (H3BTA), and biphenyl-2,2‧,5,5'-tetracarboxylic acid (H4BPTA). In all eight complexes, protons are completely exchanged from O atom of acid to nitrogen of TAPI in 1, 3, 4, and, 5, partly transferred in 2, 6, 7, and 8. The crystal structure of all eight complexes exhibit that classical robust hydrogen bonds X-H⋯X (X = O/N) direct the molecular crystals to bind together in a stacking modes. Classical hydrogen bond Nsbnd H⋯O is participated in forming all eight organic salts, while hydrogen bonding Osbnd H⋯O are found in constructing the diversity structures in salts 1, 2, 3, 4, 6, and 7. The analysis shows that some classical supramolecular synthons, such as I R22(8), V R24(12), and VI S(6), are observed again in the construction of hydrogen-bonding networks. In the formation of layered and reticular structure, strong hydrogen bonds between water molecules and ligands having well-refined hydrogen atoms have been considered. Water molecules play an important role in building supramolecular structures of 1, 2, 3, 4, 7, and 8. Moreover, salts 1-8 are further characterized and analyzed by element analysis, infrared radiation, thermogravimetric analysis, proton nuclear magnetic resonance spectra, and mass spectra.

Cosmic-ray discrimination capabilities of /ΔE-/E silicon nuclear telescopes using neural networks

NASA Astrophysics Data System (ADS)

Ambriola, M.; Bellotti, R.; Cafagna, F.; Castellano, M.; Ciacio, F.; Circella, M.; Marzo, C. N. D.; Montaruli, T.

2000-02-01

An isotope classifier of cosmic-ray events collected by space detectors has been implemented using a multi-layer perceptron neural architecture. In order to handle a great number of different isotopes a modular architecture of the ``mixture of experts'' type is proposed. The performance of this classifier has been tested on simulated data and has been compared with a ``classical'' classifying procedure. The quantitative comparison with traditional techniques shows that the neural approach has classification performances comparable - within /1% - with that of the classical one, with efficiency of the order of /98%. A possible hardware implementation of such a kind of neural architecture in future space missions is considered.

Nuclear factor one B (NFIB) encodes a subtype-specific tumour suppressor in glioblastoma

PubMed Central

Stringer, Brett W.; Bunt, Jens; Day, Bryan W.; Barry, Guy; Jamieson, Paul R.; Ensbey, Kathleen S.; Bruce, Zara C.; Goasdoué, Kate; Vidal, Hélène; Charmsaz, Sara; Smith, Fiona M.; Cooper, Leanne T.; Piper, Michael

2016-01-01

Glioblastoma (GBM) is an essentially incurable and rapidly fatal cancer, with few markers predicting a favourable prognosis. Here we report that the transcription factor NFIB is associated with significantly improved survival in GBM. NFIB expression correlates inversely with astrocytoma grade and is lowest in mesenchymal GBM. Ectopic expression of NFIB in low-passage, patient-derived classical and mesenchymal subtype GBM cells inhibits tumourigenesis. Ectopic NFIB expression activated phospho-STAT3 signalling only in classical and mesenchymal GBM cells, suggesting a mechanism through which NFIB may exert its context-dependent tumour suppressor activity. Finally, NFIB expression can be induced in GBM cells by drug treatment with beneficial effects. PMID:27083054

A Genome-Wide Analysis Reveals No Nuclear Dobzhansky-Muller Pairs of Determinants of Speciation between S. cerevisiae and S. paradoxus, but Suggests More Complex Incompatibilities

PubMed Central

Kao, Katy C.; Schwartz, Katja; Sherlock, Gavin

2010-01-01

The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts, which have small genomes and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair, comprising a mitochondrially targeted product of a nuclear gene and a mitochondrially encoded locus, has been found. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. We report here the first detailed genome-wide analysis of rare meiotic products from an otherwise sterile hybrid and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions, likely involving multiple loci having weak effects, may be responsible for their post-zygotic separation. The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that the accumulation of polymorphisms leads to gamete inviability due to the activities of anti-recombination mechanisms and/or incompatibilities between the species' transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. PMID:20686707

Five classic articles in somatic cell reprogramming.

PubMed

Park, In-Hyun

2010-09-01

Research on somatic cell reprogramming has progressed significantly over the past few decades, from nuclear transfer into frogs' eggs in 1952 to the derivation of human-induced pluripotent stem (iPS) cells in the present day. In this article, I review five landmark papers that have laid the foundation for current efforts to apply somatic cell reprogramming in the clinic.

The Power of Likeness: But Analogy Can Take Us Only So Far.

ERIC Educational Resources Information Center

Filonovich, S. R.

1991-01-01

Describes the use of analogy relative to the classical theory of momentum and kinetic energy, and addresses the advantages and disadvantages of this approach with respect to modern physics. Discusses the origins of the billiard ball analogy in the work of Coriolis and its influence on later theories and investigations of nuclear fission, particle…

Quantum Computing

DTIC Science & Technology

1998-04-01

information representation and processing technology, although faster than the wheels and gears of the Charles Babbage computation machine, is still in...the same computational complexity class as the Babbage machine, with bits of information represented by entities which obey classical (non-quantum...nuclear double resonances Charles M Bowden and Jonathan P. Dowling Weapons Sciences Directorate, AMSMI-RD-WS-ST Missile Research, Development, and

BULGES OF NEARBY GALAXIES WITH SPITZER: SCALING RELATIONS IN PSEUDOBULGES AND CLASSICAL BULGES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisher, David B.; Drory, Niv, E-mail: dbfisher@astro.as.utexas.ed

2010-06-20

We investigate scaling relations of bulges using bulge-disk decompositions at 3.6 {mu}m and present bulge classifications for 173 E-Sd galaxies within 20 Mpc. Pseudobulges and classical bulges are identified using Sersic index, Hubble Space Telescope morphology, and star formation activity (traced by 8 {mu}m emission). In the near-IR pseudobulges have n{sub b} < 2 and classical bulges have n{sub b} >2, as found in the optical. Sersic index and morphology are essentially equivalent properties for bulge classification purposes. We confirm, using a much more robust sample, that the Sersic index of pseudobulges is uncorrelated with other bulge structural properties, unlikemore » for classical bulges and elliptical galaxies. Also, the half-light radius of pseudobulges is not correlated with any other bulge property. We also find a new correlation between surface brightness and pseudobulge luminosity; pseudobulges become more luminous as they become more dense. Classical bulges follow the well-known scaling relations between surface brightness, luminosity, and half-light radius that are established by elliptical galaxies. We show that those pseudobulges (as indicated by Sersic index and nuclear morphology) that have low specific star formation rates are very similar to models of galaxies in which both a pseudobulge and classical bulge exist. Therefore, pseudobulge identification that relies only on structural indicators is incomplete. Our results, especially those on scaling relations, imply that pseudobulges are very different types of objects than elliptical galaxies.« less

Nuclear quantum effects in water clusters: the role of the molecular flexibility.

PubMed

González, Briesta S; Noya, Eva G; Vega, Carlos; Sesé, Luis M

2010-02-25

With the objective of establishing the importance of water flexibility in empirical models which explicitly include nuclear quantum effects, we have carried out path integral Monte Carlo simulations in water clusters with up to seven molecules. Two recently developed models have been used for comparison: the rigid TIP4PQ/2005 and the flexible q-TIP4P/F models, both inspired by the rigid TIP4P/2005 model. To obtain a starting configuration for our simulations, we have located the global minima for the rigid TIP4P/2005 and TIP4PQ/2005 models and for the flexible q-TIP4P/F model. All the structures are similar to those predicted by the rigid TIP4P potential showing that the charge distribution mainly determines the global minimum structure. For the flexible q-TIP4P/F model, we have studied the geometrical distortion upon isotopic substitution by studying tritiated water clusters. Our results show that tritiated water clusters exhibit an r(OT) distance shorter than the r(OH) distance in water clusters, not significant changes in the Phi(HOH) angle, and a lower average dipole moment than water clusters. We have also carried out classical simulations with the rigid TIP4PQ/2005 model showing that the rotational kinetic energy is greatly affected by quantum effects, but the translational kinetic energy is only slightly modified. The potential energy is also noticeably higher than in classical simulations. Finally, as a concluding remark, we have calculated the formation energies of water clusters using both models, finding that the formation energies predicted by the rigid TIP4PQ/2005 model are lower by roughly 0.6 kcal/mol than those of the flexible q-TIP4P/F model for clusters of moderate size, the origin of this difference coming mainly from the geometrical distortion of the water molecule in the clusters that causes an increase in the intramolecular potential energy.

A Pro-Inflammatory Role for Nuclear Factor Kappa B in Childhood Obstructive Sleep Apnea Syndrome

PubMed Central

Israel, Lee P.; Benharoch, Daniel; Gopas, Jacob; Goldbart, Aviv D.

2013-01-01

Study Objectives: Childhood obstructive sleep apnea syndrome (OSAS) is associated with an elevation of inflammatory markers such as C-reactive protein (CRP) that correlates with specific morbidities and subsides following intervention. In adults, OSAS is associated with activation of the transcription factor nuclear factor kappa B (NF-kB). We explored the mechanisms underlying NF-kB activation, based on the hypothesis that specific NF-kB signaling is activated in children with OSAS. Design: Adenoid and tonsillar tissues from children with OSAS and matched controls were immunostained against NF-kB classical (p65 and p50) and alternative (RelB and p52) pathway subunits, and NF-kB-dependent cytokines: interleukin (IL)- 1α, IL-1β, tumor necrosis factor-α, and IL-8). Serum CRP levels were measured in all subjects. NF-kB induction was evaluated by a luciferase-NF-kB reporter assay in L428 cells constitutively expressing NF-kB and in Jurkat cells with inducible NF-kB expression. p65 translocation to the nucleus, reflecting NF-kB activation, was measured in cells expressing fluorescent NF-kB-p65-GFP (green fluorescent protein). Setting: Sleep research laboratory. Patients or Participants: Twenty-five children with OSAS and 24 without OSAS. Interventions: N/A. Measurements and Results: Higher expression of IL-1α and classical NF-kB subunits p65 and p50 was observed in adenoids and tonsils of children with OSAS. Patient serum induced NF-kB activity, as measured by a luciferase-NF-kB reporter assay and by induction of p65 nuclear translocation in cells permanently transfected with GFP-p65 plasmid. IL-1β showed increased epithelial expression in OSAS tissues. Conclusions: Nuclear factor kappa B is locally and systemically activated in children with obstructive sleep apnea syndrome. This observation may motivate the search for new anti-inflammatory strategies for controlling nuclear factor kappa B activation in obstructive sleep apnea syndrome. Citation: Israel LP; Benharoch D; Gopas J; Goldbart AD. A pro-inflammatory role for nuclear factor kappa B in childhood obstructive sleep apnea syndrome. SLEEP 2013;36(12):1947-1955. PMID:24293770

Application of electrical geophysics to the release of water resources, case of Ain Leuh (Morocco)

NASA Astrophysics Data System (ADS)

Zitouni, A.; Boukdir, A.; El Fjiji, H.; Baite, W.; Ekouele Mbaki, V. R.; Ben Said, H.; Echakraoui, Z.; Elissami, A.; El Maslouhi, M. R.

2018-05-01

Being seen needs in increasing waters in our contry for fine domestics, manufactures and agricultural, the prospecting of subterranean waters by geologic and hydrogeologic classic method remains inaplicable in the cases of the regions where one does not arrange drillings or polls (soundings) of gratitude (recongnition) in very sufficient (self-important) number. In that case of figure, the method of prospecting geophysics such as the method of nuclear magnetic resonance (NMR) and the method of the geophysics radar are usually used most usually because they showed, worldwide, results very desive in the projects of prospecting and evaluation of the resources in subterranean waters. In the present work, which concerns only the methodology of the electric resistivity, we treat the adopted methodological approach and the study of the case of application in the tray of Ajdir Ain Leuh.

A Review of Classical Methods of Item Analysis.

ERIC Educational Resources Information Center

French, Christine L.

Item analysis is a very important consideration in the test development process. It is a statistical procedure to analyze test items that combines methods used to evaluate the important characteristics of test items, such as difficulty, discrimination, and distractibility of the items in a test. This paper reviews some of the classical methods for…

9 CFR 94.25 - Restrictions on the importation of live swine, pork, or pork products from certain regions free...

Code of Federal Regulations, 2014 CFR

2014-01-01

... live swine, pork, or pork products from certain regions free of classical swine fever. 94.25 Section 94... DISEASE, NEWCASTLE DISEASE, HIGHLY PATHOGENIC AVIAN INFLUENZA, AFRICAN SWINE FEVER, CLASSICAL SWINE FEVER, SWINE VESICULAR DISEASE, AND BOVINE SPONGIFORM ENCEPHALOPATHY: PROHIBITED AND RESTRICTED IMPORTATIONS...

Biogeochemical behaviour and bioremediation of uranium in waters of abandoned mines.

PubMed

Mkandawire, Martin

2013-11-01

The discharges of uranium and associated radionuclides as well as heavy metals and metalloids from waste and tailing dumps in abandoned uranium mining and processing sites pose contamination risks to surface and groundwater. Although many more are being planned for nuclear energy purposes, most of the abandoned uranium mines are a legacy of uranium production that fuelled arms race during the cold war of the last century. Since the end of cold war, there have been efforts to rehabilitate the mining sites, initially, using classical remediation techniques based on high chemical and civil engineering. Recently, bioremediation technology has been sought as alternatives to the classical approach due to reasons, which include: (a) high demand of sites requiring remediation; (b) the economic implication of running and maintaining the facilities due to high energy and work force demand; and (c) the pattern and characteristics of contaminant discharges in most of the former uranium mining and processing sites prevents the use of classical methods. This review discusses risks of uranium contamination from abandoned uranium mines from the biogeochemical point of view and the potential and limitation of uranium bioremediation technique as alternative to classical approach in abandoned uranium mining and processing sites.

tRNAs promote nuclear import of HIV-1 intracellular reverse transcription complexes.

PubMed

Zaitseva, Lyubov; Myers, Richard; Fassati, Ariberto

2006-10-01

Infection of non-dividing cells is a biological property of HIV-1 crucial for virus transmission and AIDS pathogenesis. This property depends on nuclear import of the intracellular reverse transcription and pre-integration complexes (RTCs/PICs). To identify cellular factors involved in nuclear import of HIV-1 RTCs, cytosolic extracts were fractionated by chromatography and import activity examined by the nuclear import assay. A near-homogeneous fraction was obtained, which was active in inducing nuclear import of purified and labeled RTCs. The active fraction contained tRNAs, mostly with defective 3' CCA ends. Such tRNAs promoted HIV-1 RTC nuclear import when synthesized in vitro. Active tRNAs were incorporated into and recovered from virus particles. Mutational analyses indicated that the anticodon loop mediated binding to the viral complex whereas the T-arm may interact with cellular factors involved in nuclear import. These tRNA species efficiently accumulated into the nucleus on their own in a energy- and temperature-dependent way. An HIV-1 mutant containing MLV gag did not incorporate tRNA species capable of inducing HIV-1 RTC nuclear import and failed to infect cell cycle-arrested cells. Here we provide evidence that at least some tRNA species can be imported into the nucleus of human cells and promote HIV-1 nuclear import.

Nuclear and Particle Physics Simulations: The Consortium of Upper-Level Physics Software

NASA Astrophysics Data System (ADS)

Bigelow, Roberta; Moloney, Michael J.; Philpott, John; Rothberg, Joseph

1995-06-01

The Consortium for Upper Level Physics Software (CUPS) has developed a comprehensive series of Nine Book/Software packages that Wiley will publish in FY `95 and `96. CUPS is an international group of 27 physicists, all with extensive backgrounds in the research, teaching, and development of instructional software. The project is being supported by the National Science Foundation (PHY-9014548), and it has received other support from the IBM Corp., Apple Computer Corp., and George Mason University. The Simulations being developed are: Astrophysics, Classical Mechanics, Electricity & Magnetism, Modern Physics, Nuclear and Particle Physics, Quantum Mechanics, Solid State, Thermal and Statistical, and Wave and Optics.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Novel insights into mitotic chromosome condensation

PubMed Central

Piskadlo, Ewa; Oliveira, Raquel A.

2016-01-01

The fidelity of mitosis is essential for life, and successful completion of this process relies on drastic changes in chromosome organization at the onset of nuclear division. The mechanisms that govern chromosome compaction at every cell division cycle are still far from full comprehension, yet recent studies provide novel insights into this problem, challenging classical views on mitotic chromosome assembly. Here, we briefly introduce various models for chromosome assembly and known factors involved in the condensation process (e.g. condensin complexes and topoisomerase II). We will then focus on a few selected studies that have recently brought novel insights into the mysterious way chromosomes are condensed during nuclear division. PMID:27508072

Study of Electron Gas on a Neutron-Rich Nuclear Pasta

NASA Astrophysics Data System (ADS)

Ramirez-Homs, Enrique

This study used a classical molecular dynamics model to observe the role of electron gas on the formation of nuclear structures at subsaturation densities (rho < 0.015 fm-3) and low temperatures (T < 1MeV ). The simulations were performed by varying the Coulomb interaction strength on systems of isospin symmetric and asymmetric matter with periodic boundary conditions. The effect was quantified on the fragment size multiplicity, the inter-particle distance, the isospin content of the clusters, the nucleon mobility and cluster persistence, and on the nuclear structure shapes. The existence of the nuclear pasta structures was observed even with the absence of the Coulomb interaction but with a modication of the shapes formed. It was found that the presence of the electron gas tends to distribute matter more evenly, forms less compact objects, decreases the isospin content of clusters, modies the nucleon mobility, reduces the persistence and the fragment size multiplicity, but does not alter the inter-particle distance in clusters. The degree of these effects also varied on the nuclear structures and depended on their isospin content, temperature, and density.

Pasta Nucleosynthesis: Molecular dynamics simulations of nuclear statistical equilibrium

NASA Astrophysics Data System (ADS)

Caplan, Matthew; Horowitz, Charles; da Silva Schneider, Andre; Berry, Donald

2014-09-01

We simulate the decompression of cold dense nuclear matter, near the nuclear saturation density, in order to study the role of nuclear pasta in r-process nucleosynthesis in neutron star mergers. Our simulations are performed using a classical molecular dynamics model with 51 200 and 409 600 nucleons, and are run on GPUs. We expand our simulation region to decompress systems from initial densities of 0.080 fm-3 down to 0.00125 fm-3. We study proton fractions of YP = 0.05, 0.10, 0.20, 0.30, and 0.40 at T = 0.5, 0.75, and 1 MeV. We calculate the composition of the resulting systems using a cluster algorithm. This composition is in good agreement with nuclear statistical equilibrium models for temperatures of 0.75 and 1 MeV. However, for proton fractions greater than YP = 0.2 at a temperature of T = 0.5 MeV, the MD simulations produce non-equilibrium results with large rod-like nuclei. Our MD model is valid at higher densities than simple nuclear statistical equilibrium models and may help determine the initial temperatures and proton fractions of matter ejected in mergers.

Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2014-01-14

The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei (CCN), and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems.more » The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics (PIMD) method at the density functional theory (DFT) level of theory. We observe a small zero-point effect on the the equilibrium structures of certain clusters. One configuration is found to display a bimodal behaviour at 300 K in contrast to the stable ionised state suggested from a zero temperature classical geometry optimisation. The general effect of zero-point motion is to promote the extent of proton transfer with respect to classical behaviour. We thank Prof. Angelos Michaelides and his group in University College London (UCL) for practical advice and helpful discussions. This work benefited from interactions with the Thomas Young Centre through seminar and discussions involving the PIMD method. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. JLS and IJF were supported by the IMPACT scheme at UCL and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. We are grateful for use of the UCL Legion High Performance Computing Facility and the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy, Office of Science of the under Contract No. DE-AC02-05CH11231.« less

In vivo effects of a GPR30 antagonist.

PubMed

Dennis, Megan K; Burai, Ritwik; Ramesh, Chinnasamy; Petrie, Whitney K; Alcon, Sara N; Nayak, Tapan K; Bologa, Cristian G; Leitao, Andrei; Brailoiu, Eugen; Deliu, Elena; Dun, Nae J; Sklar, Larry A; Hathaway, Helen J; Arterburn, Jeffrey B; Oprea, Tudor I; Prossnitz, Eric R

2009-06-01

Estrogen is central to many physiological processes throughout the human body. We have previously shown that the G protein-coupled receptor GPR30 (also known as GPER), in addition to classical nuclear estrogen receptors (ER and ER), activates cellular signaling pathways in response to estrogen. In order to distinguish between the actions of classical estrogen receptors and GPR30, we have previously characterized G-1 (1), a selective agonist of GPR30. To complement the pharmacological properties of G-1, we sought to identify an antagonist of GPR30 that displays similar selectivity against the classical estrogen receptors. Here we describe the identification and characterization of G15 (2), a G-1 analog that binds to GPR30 with high affinity and acts as an antagonist of estrogen signaling through GPR30. In vivo administration of G15 revealed that GPR30 contributes to both uterine and neurological responses initiated by estrogen. The identification of this antagonist will accelerate the evaluation of the roles of GPR30 in human physiology.

Solving Quantum Ground-State Problems with Nuclear Magnetic Resonance

PubMed Central

Li, Zhaokai; Yung, Man-Hong; Chen, Hongwei; Lu, Dawei; Whitfield, James D.; Peng, Xinhua; Aspuru-Guzik, Alán; Du, Jiangfeng

2011-01-01

Quantum ground-state problems are computationally hard problems for general many-body Hamiltonians; there is no classical or quantum algorithm known to be able to solve them efficiently. Nevertheless, if a trial wavefunction approximating the ground state is available, as often happens for many problems in physics and chemistry, a quantum computer could employ this trial wavefunction to project the ground state by means of the phase estimation algorithm (PEA). We performed an experimental realization of this idea by implementing a variational-wavefunction approach to solve the ground-state problem of the Heisenberg spin model with an NMR quantum simulator. Our iterative phase estimation procedure yields a high accuracy for the eigenenergies (to the 10−5 decimal digit). The ground-state fidelity was distilled to be more than 80%, and the singlet-to-triplet switching near the critical field is reliably captured. This result shows that quantum simulators can better leverage classical trial wave functions than classical computers PMID:22355607

A critical review of fundamental controversies in the field of GPR30 research.

PubMed

Langer, Gernot; Bader, Benjamin; Meoli, Luca; Isensee, Jörg; Delbeck, Martina; Noppinger, Patricia Ruiz; Otto, Christiane

2010-01-01

The female sex hormone estradiol plays an important role in reproduction, mammary gland development, bone turnover, metabolism, and cardiovascular function. The effects of estradiol are mediated by two classical nuclear receptors, estrogen receptor alpha (ERalpha) and estrogen receptor beta (ERbeta). In 2005, G-protein-coupled receptor 30 (GPR30) was claimed to act as a non-classical estrogen receptor that was also activated by the ERalpha and ERbeta antagonists tamoxifen and fulvestrant (ICI 182780). Despite many conflicting results regarding the potential role of GPR30 as an estrogen receptor, the official nomenclature was changed to GPER (G-protein-coupled estrogen receptor). This review revisits the inconsistencies that still exist in the literature and focuses on selected publications that basically address the following two questions: what is the evidence for and against the hypothesis that GPR30 acts as an estrogen receptor? What is the potential in vivo role of GPR30? Thus, in the first part we focus on conflicting results from in vitro studies analysing the subcellular localization of GPR30, its ability to bind (or not to bind) estradiol and to signal (or not to signal) in response to estradiol. In the second part, we discuss the strengths and limitations of four available GPR30 mouse models. We elucidate the potential impact of different targeting strategies on phenotypic diversity. Copyright 2010 Elsevier Inc. All rights reserved.

BRAFV600E mutation is highly prevalent in thyroid carcinomas in the young population in Fukushima: a different oncogenic profile from Chernobyl

PubMed Central

Mitsutake, Norisato; Fukushima, Toshihiko; Matsuse, Michiko; Rogounovitch, Tatiana; Saenko, Vladimir; Uchino, Shinya; Ito, Masahiro; Suzuki, Keiji; Suzuki, Shinichi; Yamashita, Shunichi

2015-01-01

After the accident at the Fukushima Daiichi Nuclear Power Plant, the thyroid ultrasound screening program for children aged 0–18 at the time of the accident was started from October 2011. The prevalence of thyroid carcinomas in that population has appeared to be very high (84 cases per 296,253). To clarify the pathogenesis, we investigated the presence of driver mutations in these tumours. 61 classic papillary thyroid carcinomas (PTCs), two follicular variant PTCs, four cribriform-morular variant PTCs and one poorly-differentiated thyroid carcinoma were analysed. We detected BRAFV600E in 43 cases (63.2%), RET/PTC1 in six (8.8%), RET/PTC3 in one (1.5%) and ETV6/NTRK3 in four (5.9%). Among classic and follicular variant PTCs, BRAFV600E was significantly associated with the smaller size. The genetic pattern was completely different from post-Chernobyl PTCs, suggesting non-radiogenic etiology of these cancers. This is the first study demonstrating the oncogene profile in the thyroid cancers discovered by large mass screening, which probably reflects genetic status of all sporadic and latent tumours in the young Japanese population. It is assumed that BRAFV600E may not confer growth advantage on paediatric PTCs, and many of these cases grow slowly, suggesting that additional factors may be important for tumour progression in paediatric PTCs. PMID:26584635

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curchod, Basile F. E.; Agostini, Federica, E-mail: agostini@mpi-halle.mpg.de; Gross, E. K. U.

Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface—the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrastmore » to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities.« less

Identification of essential sequences for cellular localization in the muscle-specific ubiquitin E3 ligase MAFbx/Atrogin 1.

PubMed

Julie, Lagirand-Cantaloube; Sabrina, Batonnet-Pichon; Marie-Pierre, Leibovitch; Leibovitch, Serge A

2012-02-17

In skeletal muscle atrophy, upregulation and nuclear accumulation of the Ubiquitin E3 ligase MAFbx is essential for accelerated muscle protein loss, but the nuclear/cytoplasmic shuttling of MAFbx is undefined. Here we found that MAFbx contains two functional nuclear localization signals (NLS). Mutation or deletion of only one NLS induced cytoplasmic localization of MAFbx. We identified a non-classical NES located in the leucine charged domain (LCD) of MAFbx, which is leptomycin B insensitive. We demonstrated that mutation (L169Q) in LLXXL motif of LCD suppressed cytoplasmic retention of MAFbx. Nucleocytoplasmic shuttling of MAFbx represents a novel mechanism for targeting its substrates and its cytosolic partners in muscle atrophy. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Continuous quantum measurement and the quantum to classical transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharya, Tanmoy; Habib, Salman; Jacobs, Kurt

2003-04-01

While ultimately they are described by quantum mechanics, macroscopic mechanical systems are nevertheless observed to follow the trajectories predicted by classical mechanics. Hence, in the regime defining macroscopic physics, the trajectories of the correct classical motion must emerge from quantum mechanics, a process referred to as the quantum to classical transition. Extending previous work [Bhattacharya, Habib, and Jacobs, Phys. Rev. Lett. 85, 4852 (2000)], here we elucidate this transition in some detail, showing that once the measurement processes that affect all macroscopic systems are taken into account, quantum mechanics indeed predicts the emergence of classical motion. We derive inequalities thatmore » describe the parameter regime in which classical motion is obtained, and provide numerical examples. We also demonstrate two further important properties of the classical limit: first, that multiple observers all agree on the motion of an object, and second, that classical statistical inference may be used to correctly track the classical motion.« less

Imported pigs may have introduced the first classical swine influenza viruses into Mainland China.

PubMed

Zhu, Wenfei; Yang, Shuai; Guo, Yuanji; Yang, Lei; Bai, Tian; Yu, Zaijiang; Li, Xiaodan; Li, Ming; Guo, Junfeng; Wang, Dayan; Gao, Rongbao; Dong, Libo; Zou, Shumei; Li, Zi; Wang, Min; Shu, Yuelong

2013-07-01

The first classical swine influenza A H1N1 viruses were isolated in Mainland China in 1991. To aid surveillance of swine influenza viruses as part of pandemic preparedness, we sought to identify their origin. We sequenced and phylogenically analyzed 19 swine influenza viruses isolated in 1991 and 1992 in China and compared them with viruses isolated from other regions during the same period. All 19 swine influenza viruses analyzed in our study shared the highest similarity with the classical swine influenza virus A/Swine/Maryland/23239/1991 (H1N1). Phylogenetic trees of eight segmented genes exhibited similar topology, with all segments in the cluster of classical swine influenza viruses. In addition, antigenic analysis also indicated that the tested isolated were related to classical swine influenza isolates. Classical swine H1N1 influenza viruses were predominant in Beijing pig herds during this period. Since both antibody and virus detections did not indicate the presence of CS H1N1 before 1991 in Mainland China, we combined with the data on pigs imported to and exported from China and concluded that these viruses might spread to China via pigs imported from North America and that they could affect the genetic evolution and transmission dynamics of swine influenza viruses in Hong Kong. Copyright © 2013 Elsevier B.V. All rights reserved.

Nuclear export signal of PRRSV NSP1α is necessary for type I IFN inhibition.

PubMed

Chen, Zhi; Liu, Shaoning; Sun, Wenbo; Chen, Lei; Yoo, Dongwan; Li, Feng; Ren, Sufang; Guo, Lihui; Cong, Xiaoyan; Li, Jun; Zhou, Shun; Wu, Jiaqiang; Du, Yijun; Wang, Jinbao

2016-12-01

The nonstructural protein 1α (NSP1α) of porcine reproductive and respiratory syndrome virus (PRRSV) is a nucleo-cytoplasmic protein that suppresses the production of type I interferon (IFN). In this study, we investigated the relationship between the subcellular distribution of NSP1α and its inhibition of type I IFN. NSP1α was found to contain the classical nuclear export signal (NES) and NSP1α nuclear export was CRM-1-mediated. NSP1α was shuttling between the nucleus and cytoplasm. We also showed that the nuclear export of NSP1α was necessary for its ability for type I IFN inhibition. NSP1α was also found to interact with CBP, which implies a possible mechanism of CBP degradation by NSP1α. Taken together, our results describe a novel mechanism of PRRSV NSP1α for type I IFN inhibition and suppression of the host innate antiviral response. Copyright © 2016. Published by Elsevier Inc.

Contributions Regarding the Aircraft Nuclear Propulsion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitrica, Bogdan; Petre, Marian; Dima, Mihai Octavian

2010-01-21

The possibility to use a nuclear reactor for airplanes propulsion was investigated taking in to account 2 possible solutions: the direct cycle (where the fluid pass through the reactor's core) and the indirect cycle (where the fluid is passing through a heat exchanger). Taking in to account the radioprotection problems, the only realistic solution seems to be the indirect cycle, where the energy transfer should be performed by a heat exchanger that must work at very high speed of the fluid. The heat exchanger will replace the classical burning room. We had performed a more precise theoretical study for themore » nuclear jet engine regarding the performances of the nuclear reactor, of the heat exchanger and of the jet engine. It was taken in to account that in the moment when the burning room is replaced by a heat exchanger, a new model for gasodynamic process from the engine must be performed. Studies regarding the high flow speed heat transfer were performed.« less

Co-transcriptional nuclear actin dynamics

PubMed Central

Percipalle, Piergiorgio

2013-01-01

Actin is a key player for nuclear structure and function regulating both chromosome organization and gene activity. In the cell nucleus actin interacts with many different proteins. Among these proteins several studies have identified classical nuclear factors involved in chromatin structure and function, transcription and RNA processing as well as proteins that are normally involved in controlling the actin cytoskeleton. These discoveries have raised the possibility that nuclear actin performs its multi task activities through tight interactions with different sets of proteins. This high degree of promiscuity in the spectrum of protein-to-protein interactions correlates well with the conformational plasticity of actin and the ability to undergo regulated changes in its polymerization states. Several of the factors involved in controlling head-to-tail actin polymerization have been shown to be in the nucleus where they seem to regulate gene activity. By focusing on the multiple tasks performed by actin and actin-binding proteins, possible models of how actin dynamics controls the different phases of the RNA polymerase II transcription cycle are being identified. PMID:23138849

Plant nuclear hormone receptors: a role for small molecules in protein-protein interactions.

PubMed

Lumba, Shelley; Cutler, Sean; McCourt, Peter

2010-01-01

Plant hormones are a group of chemically diverse small molecules that direct processes ranging from growth and development to biotic and abiotic stress responses. Surprisingly, genome analyses suggest that classic animal nuclear hormone receptor homologs do not exist in plants. It now appears that plants have co-opted several protein families to perceive hormones within the nucleus. In one solution to the problem, the hormones auxin and jasmonate (JA) act as “molecular glue” that promotes protein-protein interactions between receptor F-boxes and downstream corepressor targets. In another solution, gibberellins (GAs) bind and elicit a conformational change in a novel soluble receptor family related to hormone-sensitive lipases. Abscisic acid (ABA), like GA, also acts through an allosteric mechanism involving a START-domain protein. The molecular identification of plant nuclear hormone receptors will allow comparisons with animal nuclear receptors and testing of fundamental questions about hormone function in plant development and evolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

KRASNITZ,A.; VENUGOPALAN,R.

The dynamics of low-x partons in the transverse plane of a high-energy nuclear collision is classical, and therefore admits a fully non-perturbative numerical treatment. The authors report results of a recent study estimating the initial energy density in the central region of a collision. Preliminary estimates of the number of gluons per unit rapidity, and the initial transverse momentum distribution of gluons, are also provided.

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the water exchange reactions are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium, and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium. LXD was supported by US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata.

PubMed

Pascual, Jesús; Alegre, Sara; Nagler, Matthias; Escandón, Mónica; Annacondia, María Luz; Weckwerth, Wolfram; Valledor, Luis; Cañal, María Jesús

2016-06-30

The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows. The combination of SEQUEST, de novo sequencing, and novel annotation pipelines allowed cover sensing and transduction pathways, endoplasmic reticulum-related mechanisms and the regulation of chromatin dynamism and gene expression by histones, histone-like NF-Ys, and other transcription factors previously unrelated to this stress source, as well as the role of alternative splicing and other mechanisms involved in RNA translation and protein synthesis. The determination of 33 transcription factors, including NF-YB13, Pp005698_3 (NF-YB) and Pr009668_2 (WD-40), which are correlated to stress responsive mechanisms like an increased accumulation of photoprotective pigments and reduced photosynthesis, pointing them as strong candidate biomarkers for breeding programs aimed to improve UV resistance of pine trees. The description of the nuclear proteome of Pinus radiata combining a classic approach based on the use of SEQUEST and the use of a mass accuracy precursor alignment (MAPA) allowed an unprecedented protein coverage. This workflow provided the methodological basis for characterizing the changes in the nuclear proteome triggered by UV irradiation, allowing the depiction of the nuclear events involved in stress response and adaption. The relevance of some of the discovered proteins will suppose a major advance in stress biology field, also providing a set of transcription factors that can be considered as strong biomarker candidates to select trees more tolerant to UV radiation in forest upgrade programs. Copyright © 2016 Elsevier B.V. All rights reserved.

Region of Nipah virus C protein responsible for shuttling between the cytoplasm and nucleus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horie, Ryo; Yoneda, Misako, E-mail: yone@ims.u-tok

Nipah virus (NiV) causes severe encephalitis in humans, with high mortality. NiV nonstructural C protein (NiV-C) is essential for its pathogenicity, but its functions are unclear. In this study, we focused on NiV-C trafficking in cells and found that it localizes predominantly in the cytoplasm but partly in the nucleus. An analysis of NiV-C mutants showed that amino acids 2, 21–24 and 110–139 of NiV-C are important for its localization in the cytoplasm. Inhibitor treatment indicates that the nuclear export determinant is not a classical CRM1-dependent nuclear export signal. We also determined that amino acids 60–75 and 72–75 were importantmore » for nuclear localization of NiV-C. Furthermore, NiV-C mutants that had lost their capacity for nuclear localization inhibited the interferon (IFN) response more strongly than complete NiV-C. These results indicate that the IFN-antagonist activity of NiV-C occurs in the cytoplasm. -- Highlights: •Nipah virus (NiV) infection resulted in high mortality, but effective treatment has not been established. •Several reports revealed that NiV nonstructural C protein (NiV-C) was essential for NiV pathogenicity, however, whole of NiV-C function is still unknown. •Although nonstructural C proteins of other Paramyxoviruses are expressed in similar mechanism and exert similar activity, subcellular localization and cellular targets are different. In this study, we evaluated the subcellular localization of NiV-C. •To our knowledge, this is the first report showing that NiV-C shuttles between the nucleus and cytoplasm. We also clarified that NiV-C has nuclear export signal and nuclear localization signal using NiV-C deleted, alanine substitution mutants and enhanced green fluorescent protein (EGFP) fused proteins. •And we also showed that interferon (IFN) antagonist activity of NiV-C related to its subcellular localization. Our results indicate that NiV-C exert IFN antagonist activity in the cytoplasm.« less

Measurement of the spin temperature of optically cooled nuclei and GaAs hyperfine constants in GaAs/AlGaAs quantum dots

NASA Astrophysics Data System (ADS)

Chekhovich, E. A.; Ulhaq, A.; Zallo, E.; Ding, F.; Schmidt, O. G.; Skolnick, M. S.

2017-10-01

Deep cooling of electron and nuclear spins is equivalent to achieving polarization degrees close to 100% and is a key requirement in solid-state quantum information technologies. While polarization of individual nuclear spins in diamond and SiC (ref. ) reaches 99% and beyond, it has been limited to 50-65% for the nuclei in quantum dots. Theoretical models have attributed this limit to formation of coherent `dark' nuclear spin states but experimental verification is lacking, especially due to the poor accuracy of polarization degree measurements. Here we measure the nuclear polarization in GaAs/AlGaAs quantum dots with high accuracy using a new approach enabled by manipulation of the nuclear spin states with radiofrequency pulses. Polarizations up to 80% are observed--the highest reported so far for optical cooling in quantum dots. This value is still not limited by nuclear coherence effects. Instead we find that optically cooled nuclei are well described within a classical spin temperature framework. Our findings unlock a route for further progress towards quantum dot electron spin qubits where deep cooling of the mesoscopic nuclear spin ensemble is used to achieve long qubit coherence. Moreover, GaAs hyperfine material constants are measured here experimentally for the first time.

Nuclear distribution of the Trypanosoma cruzi RNA Pol I subunit RPA31 during growth and metacyclogenesis, and characterization of its nuclear localization signal.

PubMed

Canela-Pérez, Israel; López-Villaseñor, Imelda; Cevallos, Ana María; Hernández, Roberto

2018-03-01

Trypanosoma cruzi is the aetiologic agent of Chagas disease. Our research group studies ribosomal RNA (rRNA) gene transcription and nucleolus dynamics in this species of trypanosomes. RPA31 is an essential subunit of RNA polymerase I (Pol I) whose presence is apparently restricted to trypanosomes. Using fluorescent-tagged versions of this protein (TcRPA31-EGFP), we describe its nuclear distribution during growth and metacyclogenesis. Our findings indicate that TcRPA31-EGFP alters its nuclear presence from concentrated nucleolar localization in exponentially growing epimastigotes to a dispersed granular distribution in the nucleoplasm of stationary epimastigotes and metacyclic trypomastigotes. These changes likely reflect a structural redistribution of the Pol I transcription machinery in quiescent cellular stages where downregulation of rRNA synthesis is known to occur. In addition, and related to the nuclear internalization of this protein, the presence of a classical bipartite-type nuclear localization signal was identified towards its C-terminal end. The functionality of this motif was demonstrated by its partial or total deletion in recombinant versions of the tagged fluorescent protein. Moreover, ivermectin inhibited the nuclear localization of the labelled chimaera, suggesting the involvement of the importin α/β transport system.

Parvoviral nuclear import: bypassing the host nuclear-transport machinery.

PubMed

Cohen, Sarah; Behzad, Ali R; Carroll, Jeffrey B; Panté, Nelly

2006-11-01

The parvovirus Minute virus of mice (MVM) is a small DNA virus that replicates in the nucleus of its host cells. However, very little is known about the mechanisms underlying parvovirus' nuclear import. Recently, it was found that microinjection of MVM into the cytoplasm of Xenopus oocytes causes damage to the nuclear envelope (NE), suggesting that the nuclear-import mechanism of MVM involves disruption of the NE and import through the resulting breaks. Here, fluorescence microscopy and electron microscopy were used to examine the effect of MVM on host-cell nuclear structure during infection of mouse fibroblast cells. It was found that MVM caused dramatic changes in nuclear shape and morphology, alterations of nuclear lamin immunostaining and breaks in the NE of infected cells. Thus, it seems that the unusual nuclear-import mechanism observed in Xenopus oocytes is in fact used by MVM during infection of host cells.

ASME code considerations for the compact heat exchanger

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nestell, James; Sham, Sam

2015-08-31

The mission of the U.S. Department of Energy (DOE), Office of Nuclear Energy is to advance nuclear power in order to meet the nation's energy, environmental, and energy security needs. Advanced high temperature reactor systems such as sodium fast reactors and high and very high temperature gas-cooled reactors are being considered for the next generation of nuclear reactor plant designs. The coolants for these high temperature reactor systems include liquid sodium and helium gas. Supercritical carbon dioxide (sCO₂), a fluid at a temperature and pressure above the supercritical point of CO₂, is currently being investigated by DOE as a workingmore » fluid for a nuclear or fossil-heated recompression closed Brayton cycle energy conversion system that operates at 550°C (1022°F) at 200 bar (2900 psi). Higher operating temperatures are envisioned in future developments. All of these design concepts require a highly effective heat exchanger that transfers heat from the nuclear or chemical reactor to the chemical process fluid or the to the power cycle. In the nuclear designs described above, heat is transferred from the primary to the secondary loop via an intermediate heat exchanger (IHX) and then from the intermediate loop to either a working process or a power cycle via a secondary heat exchanger (SHX). The IHX is a component in the primary coolant loop which will be classified as "safety related." The intermediate loop will likely be classified as "not safety related but important to safety." These safety classifications have a direct bearing on heat exchanger design approaches for the IHX and SHX. The very high temperatures being considered for the VHTR will require the use of very high temperature alloys for the IHX and SHX. Material cost considerations alone will dictate that the IHX and SHX be highly effective; that is, provide high heat transfer area in a small volume. This feature must be accompanied by low pressure drop and mechanical reliability and robustness. Classic shell and tube designs will be large and costly, and may only be appropriate in steam generator service in the SHX where boiling inside the tubes occurs. For other energy conversion systems, all of these features can be met in a compact heat exchanger design. This report will examine some of the ASME Code issues that will need to be addressed to allow use of a Code-qualified compact heat exchanger in IHX or SHX nuclear service. Most effort will focus on the IHX, since the safety-related (Class A) design rules are more extensive than those for important-to-safety (Class B) or commercial rules that are relevant to the SHX.« less

The effects of diseases, drugs, and chemicals on the creativity and productivity of famous sculptors, classic painters, classic music composers, and authors.

PubMed

Wolf, Paul L

2005-11-01

Many myths, theories, and speculations exist as to the exact etiology of the diseases, drugs, and chemicals that affected the creativity and productivity of famous sculptors, classic painters, classic music composers, and authors. To emphasize the importance of a modern clinical chemistry laboratory and hematology coagulation laboratory in interpreting the basis for the creativity and productivity of various artists. This investigation analyzed the lives of famous artists, including classical sculptor Benvenuto Cellini; classical sculptor and painter Michelangelo Buonarroti; classic painters Ivar Arosenius, Edvard Munch, and Vincent Van Gogh; classic music composer Louis Hector Berlioz; and English essayist Thomas De Quincey. The analysis includes their illnesses, their famous artistic works, and the modern clinical chemistry, toxicology, and hematology coagulation tests that would have been important in the diagnosis and treatment of their diseases. The associations between illness and art may be close and many because of both the actual physical limitations of the artists and their mental adaptation to disease. Although they were ill, many continued to be productive. If modern clinical chemistry, toxicology, and hematology coagulation laboratories had existed during the lifetimes of these various well-known individuals, clinical laboratories might have unraveled the mysteries of their afflictions. The illnesses these people endured probably could have been ascertained and perhaps treated. Diseases, drugs, and chemicals may have influenced their creativity and productivity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onder, Zeynep; Moroianu, Junona, E-mail: moroianu@bc.edu

We have previously discovered and characterized the nuclear import pathways for the E7 oncoproteins of mucosal alpha genus HPVs, type 16 and 11. Here we investigated the nuclear import of cutaneous beta genus HPV8 E7 protein using confocal microscopy after transfections of HeLa cells with EGFP-8E7 and mutant plasmids and nuclear import assays in digitonin-permeabilized HeLa cells. We determined that HPV8 E7 contains a nuclear localization signal (NLS) within its zinc-binding domain that mediates its nuclear import. Furthermore, we discovered that a mostly hydrophobic patch {sub 65}LRLFV{sub 69} within the zinc-binding domain is essential for the nuclear import and localizationmore » of HPV8 E7 via hydrophobic interactions with the FG nucleoporins Nup62 and Nup153. Substitution of the hydrophobic residues within the {sub 65}LRLFV{sub 69} patch to alanines, and not R66A mutation, disrupt the interactions between the 8E7 zinc-binding domain and Nup62 and Nup153 and consequently inhibit nuclear import of HPV8 E7. - Highlights: • HPV8 E7 has a cNLS within its zinc-binding domain that mediates its nuclear import. • Discovery of a hydrophobic patch that is critical for the nuclear import of HPV8 E7. • HPV8 E7 nuclear import is mediated by hydrophobic interactions with FG-Nups, Nup62 and Nup153.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Busch, Albert; Kiel, Tilman; Heupel, Wolfgang-M.

Lamins, which form the nuclear lamina, not only constitute an important determinant of nuclear architecture, but additionally play essential roles in many nuclear functions. Mutations in A-type lamins cause a wide range of human genetic disorders (laminopathies). The importance of lamin A (LaA) in the spatial arrangement of nuclear pore complexes (NPCs) prompted us to study the role of LaA mutants in nuclear protein transport. Two mutants, causing prenatal skin disease restrictive dermopathy (RD) and the premature aging disease Hutchinson Gilford progeria syndrome, were used for expression in HeLa cells to investigate their impact on the subcellular localization of NPC-associatedmore » proteins and nuclear protein import. Furthermore, dynamics of the LaA mutants within the nuclear lamina were studied. We observed affected localization of NPC-associated proteins, diminished lamina dynamics for both LaA mutants and reduced nuclear import of representative cargo molecules. Intriguingly, both LaA mutants displayed similar effects on nuclear morphology and functions, despite their differences in disease severity. Reduced nuclear protein import was also seen in RD fibroblasts and impaired lamina dynamics for the nucleoporin Nup153. Our data thus represent the first study of a direct link between LaA mutant expression and reduced nuclear protein import.« less

70-kDa Heat Shock Cognate Protein hsc70 Mediates Calmodulin-dependent Nuclear Import of the Sex-determining Factor SRY*

PubMed Central

Kaur, Gurpreet; Lieu, Kim G.; Jans, David A.

2013-01-01

We recently showed that the developmentally important family of SOX (SRY (sex determining region on the Y chromosome)-related high mobility group (HMG) box) proteins require the calcium-binding protein calmodulin (CaM) for optimal nuclear accumulation, with clinical mutations in SRY that specifically impair nuclear accumulation via this pathway resulting in XY sex reversal. However, the mechanism by which CaM facilitates nuclear accumulation is unknown. Here, we show, for the first time, that the 70-kDa heat shock cognate protein hsc70 plays a key role in CaM-dependent nuclear import of SRY. Using a reconstituted nuclear import assay, we show that antibodies to hsc70 significantly reduce nuclear accumulation of wild type SRY and mutant derivatives thereof that retain CaM-dependent nuclear import, with an increased rate of nuclear accumulation upon addition of both CaM and hsc70, in contrast to an SRY mutant derivative with impaired CaM binding. siRNA knockdown of hsc70 in intact cells showed similar results, indicating clear dependence upon hsc70 for CaM-dependent nuclear import. Analysis using the technique of fluorescence recovery after photobleaching indicated that hsc70 is required for the maximal rate of SRY nuclear import in living cells but has no impact upon SRY nuclear retention/nuclear dynamics. Finally, we demonstrate direct binding of hsc70 to the SRY·CaM complex, with immunoprecipitation experiments from cell extracts showing association of hsc70 with wild type SRY, but not with a mutant derivative with impaired CaM binding, dependent on Ca2+. Our novel findings strongly implicate hsc70 in CaM-dependent nuclear import of SRY. PMID:23235156

A real signal and its states

NASA Astrophysics Data System (ADS)

Basiladze, S. G.

2017-05-01

The paper describes the general physical theory of signals, carriers of information, which supplements Shannon's abstract classical theory and is applicable in much broader fields, including nuclear physics. It is shown that in the absence of classical noise its place should be taken by the physical threshold of signal perception for objects of both macrocosm and microcosm. The signal perception threshold allows the presence of subthreshold (virtual) signal states. For these states, Boolean algebra of logic ( A = 0/1) is transformed into the "algebraic logic" of probabilities (0 ≤ a ≤ 1). The similarity and difference of virtual states of macroand microsignals are elucidated. "Real" and "quantum" information for computers is considered briefly. The maximum information transmission rate is estimated based on physical constants.

Classical Wigner method with an effective quantum force: application to reaction rates.

PubMed

Poulsen, Jens Aage; Li, Huaqing; Nyman, Gunnar

2009-07-14

We construct an effective "quantum force" to be used in the classical molecular dynamics part of the classical Wigner method when determining correlation functions. The quantum force is obtained by estimating the most important short time separation of the Feynman paths that enter into the expression for the correlation function. The evaluation of the force is then as easy as classical potential energy evaluations. The ideas are tested on three reaction rate problems. The resulting transmission coefficients are in much better agreement with accurate results than transmission coefficients from the ordinary classical Wigner method.

A Synthetic Approach to the Transfer Matrix Method in Classical and Quantum Physics

ERIC Educational Resources Information Center

Pujol, O.; Perez, J. P.

2007-01-01

The aim of this paper is to propose a synthetic approach to the transfer matrix method in classical and quantum physics. This method is an efficient tool to deal with complicated physical systems of practical importance in geometrical light or charged particle optics, classical electronics, mechanics, electromagnetics and quantum physics. Teaching…

Multi-MGy Radiation Hardened Camera for Nuclear Facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Girard, Sylvain; Boukenter, Aziz; Ouerdane, Youcef

There is an increasing interest in developing cameras for surveillance systems to monitor nuclear facilities or nuclear waste storages. Particularly, for today's and the next generation of nuclear facilities increasing safety requirements consecutive to Fukushima Daiichi's disaster have to be considered. For some applications, radiation tolerance needs to overcome doses in the MGy(SiO{sub 2}) range whereas the most tolerant commercial or prototypes products based on solid state image sensors withstand doses up to few kGy. The objective of this work is to present the radiation hardening strategy developed by our research groups to enhance the tolerance to ionizing radiations ofmore » the various subparts of these imaging systems by working simultaneously at the component and system design levels. Developing radiation-hardened camera implies to combine several radiation-hardening strategies. In our case, we decided not to use the simplest one, the shielding approach. This approach is efficient but limits the camera miniaturization and is not compatible with its future integration in remote-handling or robotic systems. Then, the hardening-by-component strategy appears mandatory to avoid the failure of one of the camera subparts at doses lower than the MGy. Concerning the image sensor itself, the used technology is a CMOS Image Sensor (CIS) designed by ISAE team with custom pixel designs used to mitigate the total ionizing dose (TID) effects that occur well below the MGy range in classical image sensors (e.g. Charge Coupled Devices (CCD), Charge Injection Devices (CID) and classical Active Pixel Sensors (APS)), such as the complete loss of functionality, the dark current increase and the gain drop. We'll present at the conference a comparative study between these radiation-hardened pixel radiation responses with respect to conventional ones, demonstrating the efficiency of the choices made. The targeted strategy to develop the complete radiation hard camera electronics will be exposed. Another important element of the camera is the optical system that transports the image from the scene to the image sensor. This arrangement of glass-based lenses is affected by radiations through two mechanisms: the radiation induced absorption and the radiation induced refractive index changes. The first one will limit the signal to noise ratio of the image whereas the second one will directly affect the resolution of the camera. We'll present at the conference a coupled simulation/experiment study of these effects for various commercial glasses and present vulnerability study of typical optical systems to radiations at MGy doses. The last very important part of the camera is the illumination system that can be based on various technologies of emitting devices like LED, SLED or lasers. The most promising solutions for high radiation doses will be presented at the conference. In addition to this hardening-by-component approach, the global radiation tolerance of the camera can be drastically improve by working at the system level, combining innovative approaches eg. for the optical and illumination systems. We'll present at the conference the developed approach allowing to extend the camera lifetime up to the MGy dose range. (authors)« less

A Role for Caenorhabditis elegans Importin IMA-2 in Germ Line and Embryonic Mitosis

PubMed Central

Geles, Kenneth G.; Johnson, Jeffrey J.; Jong, Sena; Adam, Stephen A.

2002-01-01

The importin α family of nuclear-cytoplasmic transport factors mediates the nuclear localization of proteins containing classical nuclear localization signals. Metazoan animals express multiple importin α proteins, suggesting their possible roles in cell differentiation and development. Adult Caenorhabditis elegans hermaphrodites express three importin α proteins, IMA-1, IMA-2, and IMA-3, each with a distinct expression and localization pattern. IMA-2 was expressed exclusively in germ line cells from the early embryonic through adult stages. The protein has a dynamic pattern of localization dependent on the stage of the cell cycle. In interphase germ cells and embryonic cells, IMA-2 is cytoplasmic and nuclear envelope associated, whereas in developing oocytes, the protein is cytoplasmic and intranuclear. During mitosis in germ line cells and embryos, IMA-2 surrounded the condensed chromosomes but was not directly associated with the mitotic spindle. The timing of IMA-2 nuclear localization suggested that the protein surrounded the chromosomes after fenestration of the nuclear envelope in prometaphase. Depletion of IMA-2 by RNA-mediated gene interference (RNAi) resulted in embryonic lethality and a terminal aneuploid phenotype. ima-2(RNAi) embryos have severe defects in nuclear envelope formation, accumulating nucleoporins and lamin in the cytoplasm. We conclude that IMA-2 is required for proper chromosome dynamics in germ line and early embryonic mitosis and is involved in nuclear envelope assembly at the conclusion of mitosis. PMID:12221121

Code Development and Assessment for Reactor Outage Thermal-Hydraulic and Safety Analysis - Midloop Operation with Loss of Residual Heat Removal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Thomas K.S.; Ko, F.-K

Although only a few percent of residual power remains during plant outages, the associated risk of core uncovery and corresponding fuel overheating has been identified to be relatively high, particularly under midloop operation (MLO) in pressurized water reactors. However, to analyze the system behavior during outages, the tools currently available, such as RELAP5, RETRAN, etc., cannot easily perform the task. Therefore, a medium-sized program aiming at reactor outage simulation and evaluation, such as MLO with the loss of residual heat removal (RHR), was developed. All important thermal-hydraulic processes involved during MLO with the loss of RHR will be properly simulatedmore » by the newly developed reactor outage simulation and evaluation (ROSE) code. Important processes during MLO with loss of RHR involve a pressurizer insurge caused by the hot-leg flooding, reflux condensation, liquid holdup inside the steam generator, loop-seal clearance, core-level depression, etc. Since the accuracy of the pressure distribution from the classical nodal momentum approach will be degraded when the system is stratified and under atmospheric pressure, the two-region approach with a modified two-fluid model will be the theoretical basis of the new program to analyze the nuclear steam supply system during plant outages. To verify the analytical model in the first step, posttest calculations against the closed integral midloop experiments with loss of RHR were performed. The excellent simulation capacity of the ROSE code against the Institute of Nuclear Energy Research Integral System Test Facility (IIST) test data is demonstrated.« less

Stability of Tandem Repeats in the Drosophila Melanogaster HSR-Omega Nuclear RNA

PubMed Central

Hogan, N. C.; Slot, F.; Traverse, K. L.; Garbe, J. C.; Bendena, W. G.; Pardue, M. L.

1995-01-01

The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing >5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is ~280 bp. Sequences of 191/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than ~5 kb nor more than ~16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA. PMID:7540581

Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes

PubMed Central

Burdick, Ryan C.; Chen, Jianbo; Sastri, Jaya; Hu, Wei-Shau

2017-01-01

The dynamics and regulation of HIV-1 nuclear import and its intranuclear movements after import have not been studied. To elucidate these essential HIV-1 post-entry events, we labeled viral complexes with two fluorescently tagged virion-incorporated proteins (APOBEC3F or integrase), and analyzed the HIV-1 dynamics of nuclear envelope (NE) docking, nuclear import, and intranuclear movements in living cells. We observed that HIV-1 complexes exhibit unusually long NE residence times (1.5±1.6 hrs) compared to most cellular cargos, which are imported into the nuclei within milliseconds. Furthermore, nuclear import requires HIV-1 capsid (CA) and nuclear pore protein Nup358, and results in significant loss of CA, indicating that one of the viral core uncoating steps occurs during nuclear import. Our results showed that the CA-Cyclophilin A interaction regulates the dynamics of nuclear import by delaying the time of NE docking as well as transport through the nuclear pore, but blocking reverse transcription has no effect on the kinetics of nuclear import. We also visualized the translocation of viral complexes docked at the NE into the nucleus and analyzed their nuclear movements and determined that viral complexes exhibited a brief fast phase (<9 min), followed by a long slow phase lasting several hours. A comparison of the movement of viral complexes to those of proviral transcription sites supports the hypothesis that HIV-1 complexes quickly tether to chromatin at or near their sites of integration in both wild-type cells and cells in which LEDGF/p75 was deleted using CRISPR/cas9, indicating that the tethering interactions do not require LEDGF/p75. These studies provide novel insights into the dynamics of viral complex-NE association, regulation of nuclear import, viral core uncoating, and intranuclear movements that precede integration site selection. PMID:28827840

Protoparvovirus Knocking at the Nuclear Door.

PubMed

Mäntylä, Elina; Kann, Michael; Vihinen-Ranta, Maija

2017-10-02

Protoparvoviruses target the nucleus due to their dependence on the cellular reproduction machinery during the replication and expression of their single-stranded DNA genome. In recent years, our understanding of the multistep process of the capsid nuclear import has improved, and led to the discovery of unique viral nuclear entry strategies. Preceded by endosomal transport, endosomal escape and microtubule-mediated movement to the vicinity of the nuclear envelope, the protoparvoviruses interact with the nuclear pore complexes. The capsids are transported actively across the nuclear pore complexes using nuclear import receptors. The nuclear import is sometimes accompanied by structural changes in the nuclear envelope, and is completed by intranuclear disassembly of capsids and chromatinization of the viral genome. This review discusses the nuclear import strategies of protoparvoviruses and describes its dynamics comprising active and passive movement, and directed and diffusive motion of capsids in the molecularly crowded environment of the cell.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, Lin-Ru; Chou, Chang-Wei; Lee, I-Fang

In this study, we used a multiple copy (EGFP){sub 3} reporter system to establish a numeric nuclear index system to assess the degree of nuclear import. The system was first validated by a FRAP assay, and then was applied to evaluate the essential and multifaceted nature of basic amino acid clusters during the nuclear import of ribosomal protein L7. The results indicate that the sequence context of the basic cluster determines the degree of nuclear import, and that the number of basic residues in the cluster is irrelevant; rather the position of the pertinent basic residues is crucial. Moreover, itmore » also found that the type of carrier protein used by basic cluster has a great impact on the degree of nuclear import. In case of L7, importin β2 or importin β3 are preferentially used by clusters with a high import efficiency, notwithstanding that other importins are also used by clusters with a weaker level of nuclear import. Such a preferential usage of multiple basic clusters and importins to gain nuclear entry would seem to be a common practice among ribosomal proteins in order to ensure their full participation in high rate ribosome synthesis. - Highlights: ► We introduce a numeric index system that represents the degree of nuclear import. ► The rate of nuclear import is dictated by the sequence context of the basic cluster. ► Importin β2 and β3 were mainly responsible for the N4 mediated nuclear import.« less

Nonadiabatic Molecular Dynamics and Orthogonality Constrained Density Functional Theory

NASA Astrophysics Data System (ADS)

Shushkov, Philip Georgiev

The exact quantum dynamics of realistic, multidimensional systems remains a formidable computational challenge. In many chemical processes, however, quantum effects such as tunneling, zero-point energy quantization, and nonadiabatic transitions play an important role. Therefore, approximate approaches that improve on the classical mechanical framework are of special practical interest. We propose a novel ring polymer surface hopping method for the calculation of chemical rate constants. The method blends two approaches, namely ring polymer molecular dynamics that accounts for tunneling and zero-point energy quantization, and surface hopping that incorporates nonadiabatic transitions. We test the method against exact quantum mechanical calculations for a one-dimensional, two-state model system. The method reproduces quite accurately the tunneling contribution to the rate and the distribution of reactants between the electronic states for this model system. Semiclassical instanton theory, an approach related to ring polymer molecular dynamics, accounts for tunneling by the use of periodic classical trajectories on the inverted potential energy surface. We study a model of electron transfer in solution, a chemical process where nonadiabatic events are prominent. By representing the tunneling electron with a ring polymer, we derive Marcus theory of electron transfer from semiclassical instanton theory after a careful analysis of the tunneling mode. We demonstrate that semiclassical instanton theory can recover the limit of Fermi's Golden Rule rate in a low-temperature, deep-tunneling regime. Mixed quantum-classical dynamics treats a few important degrees of freedom quantum mechanically, while classical mechanics describes affordably the rest of the system. But the interface of quantum and classical description is a challenging theoretical problem, especially for low-energy chemical processes. We therefore focus on the semiclassical limit of the coupled nuclear-electronic dynamics. We show that the time-dependent Schrodinger equation for the electrons employed in the widely used fewest switches surface hopping method is applicable only in the limit of nearly identical classical trajectories on the different potential energy surfaces. We propose a short-time decoupling algorithm that restricts the use of the Schrodinger equation only to the interaction regions. We test the short-time approximation on three model systems against exact quantum-mechanical calculations. The approximation improves the performance of the surface hopping approach. Nonadiabatic molecular dynamics simulations require the efficient and accurate computation of ground and excited state potential energy surfaces. Unlike the ground state calculations where standard methods exist, the computation of excited state properties is a challenging task. We employ time-independent density functional theory, in which the excited state energy is represented as a functional of the total density. We suggest an adiabatic-like approximation that simplifies the excited state exchange-correlation functional. We also derive a set of minimal conditions to impose exactly the orthogonality of the excited state Kohn-Sham determinant to the ground state determinant. This leads to an efficient, variational algorithm for the self-consistent optimization of the excited state energy. Finally, we assess the quality of the excitation energies obtained by the new method on a set of 28 organic molecules. The new approach provides results of similar accuracy to time-dependent density functional theory.

Dual personality of Mad1: regulation of nuclear import by a spindle assembly checkpoint protein.

PubMed

Cairo, Lucas V; Ptak, Christopher; Wozniak, Richard W

2013-01-01

Nuclear transport is a dynamic process that can be modulated in response to changes in cellular physiology. We recently reported that the transport activity of yeast nuclear pore complexes (NPCs) is altered in response to kinetochore-microtubule (KT-MT) interaction defects. Specifically, KT detachment from MTs activates a signaling pathway that prevents the nuclear import of cargos by the nuclear transport factor Kap121p. This loss of Kap121p-mediated import is thought to influence the nuclear environment, including the phosphorylation state of nuclear proteins. A key regulator of this process is the spindle assembly checkpoint protein Mad1p. In response to unattached KTs, Mad1p dynamically cycles between NPCs and KTs. This cycling appears to induce NPC molecular rearrangements that prevent the nuclear import of Kap121p-cargo complexes. Here, we discuss the underlying mechanisms and the physiological relevance of Mad1p cycling and the inhibition of Kap121p-mediated nuclear import, focusing on outstanding questions within the pathway.

Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline

2011-10-01

This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers,more » classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.« less

Ab Initio Investigations of High-Pressure Melting of Dense Lithium

NASA Astrophysics Data System (ADS)

Clay, Raymond; Morales, Miguel; Bonev, Stanimir

Lithium at ambient conditions is the simplest alkali metal and exhibits textbook nearly-free electron behavior. As the density is increased, however, significant core/valence overlap leads to surprisingly complex chemistry. We have systematically investigated the phase diagram of lithium at pressures ranging between two and six million atmospheres. Through a combination of density functional theory based path-integral and classical molecular dynamics simulations, we have investigated the impact of both nuclear quantum effects and anharmonicity on the melting line and solid phase boundaries. We also investigate how the inclusion of nuclear quantum effects and approximations in the treatment of electronic exchange-correlation impact the robustness of previous predictions of tetrahedral clustering in dense liquid Li. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Statistical methods for thermonuclear reaction rates and nucleosynthesis simulations

NASA Astrophysics Data System (ADS)

Iliadis, Christian; Longland, Richard; Coc, Alain; Timmes, F. X.; Champagne, Art E.

2015-03-01

Rigorous statistical methods for estimating thermonuclear reaction rates and nucleosynthesis are becoming increasingly established in nuclear astrophysics. The main challenge being faced is that experimental reaction rates are highly complex quantities derived from a multitude of different measured nuclear parameters (e.g., astrophysical S-factors, resonance energies and strengths, particle and γ-ray partial widths). We discuss the application of the Monte Carlo method to two distinct, but related, questions. First, given a set of measured nuclear parameters, how can one best estimate the resulting thermonuclear reaction rates and associated uncertainties? Second, given a set of appropriate reaction rates, how can one best estimate the abundances from nucleosynthesis (i.e., reaction network) calculations? The techniques described here provide probability density functions that can be used to derive statistically meaningful reaction rates and final abundances for any desired coverage probability. Examples are given for applications to s-process neutron sources, core-collapse supernovae, classical novae, and Big Bang nucleosynthesis.

Classical Molecular Dynamics Simulation of Nuclear Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

2015-10-10

Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a varietymore » of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.« less

Revisiting Mendel and the Paradox of Gene Restoration

NASA Astrophysics Data System (ADS)

Lolle, Susan J.

2006-03-01

According to the laws of classical Mendelian genetics, genetic information contained in the nuclear genome is stably inherited and is transmitted from one generation to the next in a predictable manner. Several exceptions to the principle of stable inheritance are known but all represent specialized cases where the mechanisms have been relatively well defined. We have recently demonstrated that Arabidopsis plants can inherit specific DNA sequence information that was not present in the chromosomal genome of their parents. This process appears to occur throughout the nuclear genome. Based on our findings we propose that this process represents a completely novel and hitherto unknown mechanism for the maintenance and inheritance of DNA sequence information.

Integrated software for the detection of epileptogenic zones in refractory epilepsy.

PubMed

Mottini, Alejandro; Miceli, Franco; Albin, Germán; Nuñez, Margarita; Ferrándo, Rodolfo; Aguerrebere, Cecilia; Fernandez, Alicia

2010-01-01

In this paper we present an integrated software designed to help nuclear medicine physicians in the detection of epileptogenic zones (EZ) by means of ictal-interictal SPECT and MR images. This tool was designed to be flexible, friendly and efficient. A novel detection method was included (A-contrario) along with the classical detection method (Subtraction analysis). The software's performance was evaluated with two separate sets of validation studies: visual interpretation of 12 patient images by an experimented observer and objective analysis of virtual brain phantom experiments by proposed numerical observers. Our results support the potential use of the proposed software to help nuclear medicine physicians in the detection of EZ in clinical practice.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Espinosa-Paredes, Gilberto; Prieto-Guerrero, Alfonso; Nunez-Carrera, Alejandro

This paper introduces a wavelet-based method to analyze instability events in a boiling water reactor (BWR) during transient phenomena. The methodology to analyze BWR signals includes the following: (a) the short-time Fourier transform (STFT) analysis, (b) decomposition using the continuous wavelet transform (CWT), and (c) application of multiresolution analysis (MRA) using discrete wavelet transform (DWT). STFT analysis permits the study, in time, of the spectral content of analyzed signals. The CWT provides information about ruptures, discontinuities, and fractal behavior. To detect these important features in the signal, a mother wavelet has to be chosen and applied at several scales tomore » obtain optimum results. MRA allows fast implementation of the DWT. Features like important frequencies, discontinuities, and transients can be detected with analysis at different levels of detail coefficients. The STFT was used to provide a comparison between a classic method and the wavelet-based method. The damping ratio, which is an important stability parameter, was calculated as a function of time. The transient behavior can be detected by analyzing the maximum contained in detail coefficients at different levels in the signal decomposition. This method allows analysis of both stationary signals and highly nonstationary signals in the timescale plane. This methodology has been tested with the benchmark power instability event of Laguna Verde nuclear power plant (NPP) Unit 1, which is a BWR-5 NPP.« less

Toward an Experimental Quantum Chemistry: Exploring a New Energy Partitioning.

PubMed

Rahm, Martin; Hoffmann, Roald

2015-08-19

Following the work of L. C. Allen, this work begins by relating the central chemical concept of electronegativity with the average binding energy of electrons in a system. The average electron binding energy, χ̅, is in principle accessible from experiment, through photoelectron and X-ray spectroscopy. It can also be estimated theoretically. χ̅ has a rigorous and understandable connection to the total energy. That connection defines a new kind of energy decomposition scheme. The changing total energy in a reaction has three primary contributions to it: the average electron binding energy, the nuclear-nuclear repulsion, and multielectron interactions. This partitioning allows one to gain insight into the predominant factors behind a particular energetic preference. We can conclude whether an energy change in a transformation is favored or resisted by collective changes to the binding energy of electrons, the movement of nuclei, or multielectron interactions. For example, in the classical formation of H2 from atoms, orbital interactions dominate nearly canceling nuclear-nuclear repulsion and two-electron interactions. While in electron attachment to an H atom, the multielectron interactions drive the reaction. Looking at the balance of average electron binding energy, multielectron, and nuclear-nuclear contributions one can judge when more traditional electronegativity arguments can be justifiably invoked in the rationalization of a particular chemical event.

Nonadiabatic Dynamics May Be Probed through Electronic Coherence in Time-Resolved Photoelectron Spectroscopy.

PubMed

Bennett, Kochise; Kowalewski, Markus; Mukamel, Shaul

2016-02-09

We present a hierarchy of Fermi golden rules (FGRs) that incorporate strongly coupled electronic/nuclear dynamics in time-resolved photoelectron spectroscopy (TRPES) signals at different levels of theory. Expansion in the joint electronic and nuclear eigenbasis yields the numerically most challenging exact FGR (eFGR). The quasistatic Fermi Golden Rule (qsFGR) neglects nuclear motion during the photoionization process but takes into account electronic coherences as well as populations initially present in the pumped matter as well as those generated internally by coupling between electronic surfaces. The standard semiclassical Fermi Golden Rule (scFGR) neglects the electronic coherences and the nuclear kinetic energy during the ionizing pulse altogether, yielding the classical Condon approximation. The coherence contributions depend on the phase-profile of the ionizing field, allowing coherent control of TRPES signals. The photoelectron spectrum from model systems is simulated using these three levels of theory. The eFGR and the qsFGR show temporal oscillations originating from the electronic or vibrational coherences generated as the nuclear wave packet traverses a conical intersection. These oscillations, which are missed by the scFGR, directly reveal the time-evolving splitting between electronic states of the neutral molecule in the curve-crossing regime.

Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor

PubMed Central

Görner, Wolfram; Durchschlag, Erich; Wolf, Julia; Brown, Elizabeth L.; Ammerer, Gustav; Ruis, Helmut; Schüller, Christoph

2002-01-01

In yeast, environmental conditions control the transcription factor Msn2, the nuclear accumulation and function of which serve as a sensitive indicator of nutrient availablity and environmental stress load. We show here that the nuclear localization signal (NLS) of Msn2 is a direct target of cAMP-dependent protein kinase (cAPK). Genetic analysis suggests that Msn2-NLS function is inhibited by phosphorylation and activated by dephosphorylation. Msn2-NLS function is unaffected by many stress conditions that normally induce nuclear accumulation of full-length Msn2. The Msn2-NLS phosphorylation status is, however, highly sensitive to carbohydrate fluctuations during fermentative growth. Dephosphorylation occurs in >2 min after glucose withdrawal but the effect is reversed rapidly by refeeding with glucose. This response to glucose depletion is due to changes in cAPK activity rather than an increase in protein phosphatase activity. Surprisingly, the classical glucose-sensing systems are not connected to this rapid response system. Our results further imply that generic stress signals do not cause short-term depressions in cAPK activity. They operate on Msn2 by affecting an Msn5-dependent nuclear export and/or retention mechanism. PMID:11782433

Phenomenological study of decoherence in solid-state spin qubits due to nuclear spin diffusion

NASA Astrophysics Data System (ADS)

Biercuk, Michael J.; Bluhm, Hendrik

2011-06-01

We present a study of the prospects for coherence preservation in solid-state spin qubits using dynamical decoupling protocols. Recent experiments have provided the first demonstrations of multipulse dynamical decoupling sequences in this qubit system, but quantitative analyses of potential coherence improvements have been hampered by a lack of concrete knowledge of the relevant noise processes. We present calculations of qubit coherence under the application of arbitrary dynamical decoupling pulse sequences based on an experimentally validated semiclassical model. This phenomenological approach bundles the details of underlying noise processes into a single experimentally relevant noise power spectral density. Our results show that the dominant features of experimental measurements in a two-electron singlet-triplet spin qubit can be replicated using a 1/ω2 noise power spectrum associated with nuclear spin flips in the host material. Beginning with this validation, we address the effects of nuclear programming, high-frequency nuclear spin dynamics, and other high-frequency classical noise sources, with conjectures supported by physical arguments and microscopic calculations where relevant. Our results provide expected performance bounds and identify diagnostic metrics that can be measured experimentally in order to better elucidate the underlying nuclear spin dynamics.

Hydrodynamic Simulations of the Consequences of Accretion onto ONe White Dwarfs

NASA Astrophysics Data System (ADS)

Starrfield, Sumner; Bose, Maitrayee; Iliadis, Christian; Hix, William Raphael; Woodward, Charles E.; Wagner, Robert M.; José, Jordi; Hernanz, Margarita; Feng, Wanda

2018-06-01

Mass and luminosity variations of the white dwarf, combined with changes in the mass accretion rate and composition of the accreted material affect the evolution of the thermonuclear runaway (TNR) in classical and recurrent novae. Here we highlight continued investigations of these effects on accreting Oxygen-Neon (ONe) white dwarfs. We now use the results of the multi-dimensional studies of TNRs in white dwarfs, accreting only solar matter, which show that sufficient core material is dredged-up during the TNR to agree with the measurements of ejecta abundances in classical nova explosions. Therefore, we first accrete solar material and follow the evolution until a TNR is ongoing. We then switch the composition to a mixture with either 25% core material or 50% core material (plus accreted material) and follow the resulting evolution of the TNR through peak nuclear burning and decline. We use our 1D, Lagrangian, hydrodynamic code: NOVA. We will report on the results of these new simulations and compare the ejecta abundances to those measured in pre-solar grains that are thought to arise from classical nova explosions. We will also compare these results to our companion studies, done in a similar fashion, where we have followed the consequences of accretion onto Carbon-Oxygen white dwarfs. This work was supported in part by NASA under the Astrophysics Theory Program grant 14-ATP14-0007 and the U.S. DOE under Contract No. DE-FG02- 97ER41041. SS acknowledges partial support from NASA, NSF, and HST grants to ASU and WRH is supported by the U.S. Department of Energy, Office of Nuclear Physics.

Quantum speedup in solving the maximal-clique problem

NASA Astrophysics Data System (ADS)

Chang, Weng-Long; Yu, Qi; Li, Zhaokai; Chen, Jiahui; Peng, Xinhua; Feng, Mang

2018-03-01

The maximal-clique problem, to find the maximally sized clique in a given graph, is classically an NP-complete computational problem, which has potential applications ranging from electrical engineering, computational chemistry, and bioinformatics to social networks. Here we develop a quantum algorithm to solve the maximal-clique problem for any graph G with n vertices with quadratic speedup over its classical counterparts, where the time and spatial complexities are reduced to, respectively, O (√{2n}) and O (n2) . With respect to oracle-related quantum algorithms for the NP-complete problems, we identify our algorithm as optimal. To justify the feasibility of the proposed quantum algorithm, we successfully solve a typical clique problem for a graph G with two vertices and one edge by carrying out a nuclear magnetic resonance experiment involving four qubits.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaur, Gurpreet; Ly-Huynh, Jennifer D.; Jans, David A., E-mail: David.Jans@monash.edu

Highlights: • High intracellular calcium inhibits Impα/β1- or Impβ1-dependent nuclear protein import. • The effect of Ca{sup 2+} on nuclear import does not relate to changes in the nuclear pore. • High intracellular calcium can result in mislocalisation of Impβ1, Ran and RCC1. - Abstract: We previously showed that increased intracellular calcium can modulate Importin (Imp)β1-dependent nuclear import of SRY-related chromatin remodeling proteins. Here we extend this work to show for the first time that high intracellular calcium inhibits Impα/β1- or Impβ1-dependent nuclear protein import generally. The basis of this relates to the mislocalisation of the transport factors Impβ1 andmore » Ran, which show significantly higher nuclear localization in contrast to various other factors, and RCC1, which shows altered subnuclear localisation. The results here establish for the first time that intracellular calcium modulates conventional nuclear import through direct effects on the nuclear transport machinery.« less

Harmane and harmalan are bioactive components of classical clonidine-displacing substance.

PubMed

Parker, Christine A; Anderson, Neil J; Robinson, Emma S J; Price, Rhiannon; Tyacke, Robin J; Husbands, Stephen M; Dillon, Michael P; Eglen, Richard M; Hudson, Alan L; Nutt, David J; Crump, Matthew P; Crosby, John

2004-12-28

Elucidation of the structure of the endogenous ligand(s) for imidazoline binding sites, clonidine-displacing substance (CDS), has been a major goal for many years. Crude CDS from bovine lung was purified by reverse-phase high-pressure liquid chromatography. Electrospray mass spectrometry (ESMS) and nuclear magnetic resonance ((1)H NMR) analysis revealed the presence of L-tryptophan and 1-carboxy-1-methyltetrahydro-beta-carboline in the active CDS extract. Competition radioligand binding studies, however, failed to show displacement of specific [(3)H]clonidine binding to rat brain membranes for either compound. Further purification of the bovine lung extract allowed the isolation of the beta-carbolines harmane and harmalan as confirmed by ESMS, (1)H NMR, and comparison with synthetic standards. Both compounds exhibited a high (nanomolar) affinity for both type 1 and type 2 imidazoline binding sites, and the synthetic standards were shown to coelute with the active classical CDS extracts. We therefore propose that the beta-carbolines harmane and harmalan represent active components of classical CDS. The identification of these compounds will allow us to establish clear physiological roles for CDS.

75 FR 44072 - Export and Import of Nuclear Equipment and Material; Updates and Clarifications

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-28

... Energy Act. Retransfers of special nuclear material produced through the use of U.S.-obligated material... the Atomic Energy Act that apply to imports of special nuclear, source or byproduct material are... NUCLEAR REGULATORY COMMISSION 10 CFR Part 110 [NRC-2008-0567] RIN 3150-AI16 Export and Import of...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zohar, S.; Sterbinsky, G. E.

Here, we propose an experimental technique for extending feedback compensation of dissipative radiation used in nuclear magnetic resonance (NMR) to encompass ferromagnetic resonance (FMR). This method uses a balanced microwave power detector whose output is phase shifted π/2, amplified, and fed back to drive precession. Using classical control theory, we predict an electronically controllable narrowing of field swept FMR line-widths. This technique is predicted to compensate other sources of spin dissipation in addition to radiative loss.

National Security Strategy of Charles De Gaulle

DTIC Science & Technology

1994-01-01

nineteenth century education that was steeped in classical traditions and the collective French psychology of France as a strong, glorious and powerful...NATO in 1963 and French officers from the NATO command headquarters in 1964; and the scuttling of the United States multilateral nuclear force project ... France and about French security without her participation. The successful testing of the atomic bomb in France in 1960 ensured that France could not be

Building the H Bomb: a Personal History

NASA Astrophysics Data System (ADS)

Ford, Kenneth W.

2015-03-01

The Table of Contents for the book is as follows: * Preface * A Note on Secrecy * Prologue * The Big Idea * The Protagonists * The Choice * The Scientists, the Officials, and the President * Nuclear Energy * Some Physics * Going West * A New World * The Classical Super * Calculating and Testing * Constructing Matterhorn * Academia Cowers * New Mexico, New York, and New Jersey * The Garwin Design * Climbing Matterhorn * More Than a Boy * Epilogue * Acknowledgments * End Notes * Bibliography * Index

Nonadiabatic effects in electronic and nuclear dynamics

PubMed Central

Bircher, Martin P.; Liberatore, Elisa; Browning, Nicholas J.; Brickel, Sebastian; Hofmann, Cornelia; Patoz, Aurélien; Unke, Oliver T.; Zimmermann, Tomáš; Chergui, Majed; Hamm, Peter; Keller, Ursula; Meuwly, Markus; Woerner, Hans-Jakob; Vaníček, Jiří; Rothlisberger, Ursula

2018-01-01

Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find ways to tackle instead the full time-dependent electronic and nuclear quantum problem. In this review, we give an overview of different nonadiabatic processes that manifest themselves in electronic and nuclear dynamics ranging from the nonadiabatic phenomena taking place during tunnel ionization of atoms in strong laser fields to the radiationless relaxation through conical intersections and the nonadiabatic coupling of vibrational modes and discuss the computational approaches that have been developed to describe such phenomena. These methods range from the full solution of the combined nuclear-electronic quantum problem to a hierarchy of semiclassical approaches and even purely classical frameworks. The power of these simulation tools is illustrated by representative applications and the direct confrontation with experimental measurements performed in the National Centre of Competence for Molecular Ultrafast Science and Technology. PMID:29376108

Preservation of large-scale chromatin structure in FISH experiments

PubMed Central

Hepperger, Claudia; Otten, Simone; von Hase, Johann

2006-01-01

The nuclear organization of specific endogenous chromatin regions can be investigated only by fluorescence in situ hybridization (FISH). One of the two fixation procedures is typically applied: (1) buffered formaldehyde or (2) hypotonic shock with methanol acetic acid fixation followed by dropping of nuclei on glass slides and air drying. In this study, we compared the effects of these two procedures and some variations on nuclear morphology and on FISH signals. We analyzed mouse erythroleukemia and mouse embryonic stem cells because their clusters of subcentromeric heterochromatin provide an easy means to assess preservation of chromatin. Qualitative and quantitative analyses revealed that formaldehyde fixation provided good preservation of large-scale chromatin structures, while classical methanol acetic acid fixation after hypotonic treatment severely impaired nuclear shape and led to disruption of chromosome territories, heterochromatin structures, and large transgene arrays. Our data show that such preparations do not faithfully reflect in vivo nuclear architecture. Electronic supplementary material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00412-006-0084-2 and is accessible for authorized users. PMID:17119992

Route of steroid-activated macromolecules through nuclear pores imaged with atomic force microscopy.

PubMed

Oberleithner, H; Schäfer, C; Shahin, V; Albermann, L

2003-02-01

In eukaryotic cells, two concentric membranes, the nuclear envelope (NE), separate the nucleus from the cytoplasm. The NE is punctured by nuclear pore complexes (NPCs; molecular mass 120 MDa) that serve as regulated pathways for macromolecules entering and leaving the nuclear compartment. Transport across NPCs occurs through central channels. Such import and export of macromolecules through individual NPCs can be elicited in the Xenopus laevis oocyte by injecting the mineralocorticoid aldosterone and can be visualized with atomic force microscopy. The electrical NE resistance in intact cell nuclei can be measured in parallel. Resistance increases when macromolecules are engaged with the NPC. This article describe six observations made from these experiments and the conclusions that can be drawn from them. (i) A homogeneous population of macromolecules (approx. 100 kDa) attaches to the cytoplasmic face of the NPC 2 min after aldosterone injection. They are most likely to be aldosterone receptors. After a few minutes, they have disappeared. (ii) Large plugs (approx. molecular mass 1 MDa) appear in the central channels 20 min after hormone injection. They are most likely to be ribonucleoproteins exiting the nucleus. (iii) Electrical resistance measurements in isolated nuclei reveal transient electrical NE resistance peaks: an early (2 min) peak and a late (20 min) peak. Electrical peaks reflect macromolecule interaction with the NPC. (iv) Spironolactone blocks both the early and late peaks. This indicates that classic aldosterone receptors are involved in the pregenomic (early) and post-genomic (late) responses. (v) Actinomycin D and, independently, RNase A block the late electrical peak, confirming that plugs are genomic in nature. (vi) Intracellular calcium chelation blocks both early and late electrical peaks. Thus, the release of calcium from internal stores, which is known to be the first intracellular signal in response to aldosterone, is a prerequisite for the late genomic response.

Cleavage of bovine adenovirus type 3 non-structural 100K protein by protease is required for nuclear localization in infected cells but is not essential for virus replication.

PubMed

Makadiya, Nirajkumar; Gaba, Amit; Tikoo, Suresh K

2015-09-01

The L6 region of bovine adenovirus type 3 (BAdV-3) encodes a non-structural protein named 100K. Rabbit antiserum raised against BAdV-3 100K recognized a protein of 130 kDa at 12-24 h and proteins of 130, 100, 95 and 15 kDa at 36-48 h after BAdV-3 infection. The 100K species localized to the nucleus and the cytoplasm of BAdV-3-infected cells. In contrast, 100K localized predominantly to the cytoplasm of the transfected cells. However, BAdV-3 infection of cells transfected with 100K-enhanced yellow fluorescent protein-expressing plasmid detected fluorescent protein in the nucleus of the cells, suggesting that other viral proteins may be required for the nuclear localization of 100K. Interaction of BAdV-3 100K with BAdV-3 33K protein did not alter the cytoplasmic localization of 100K. However, co-expression of BAdV-3 100K and BAdV-3 protease localized 100K to the nucleolus of the transfected cells. Subsequent analysis suggested that BAdV-3 protease cleaves 100K at two identified potential protease cleavage sites (aa 740-745 and 781-786) in transfected or BAdV-3-infected cells. The cleaved C terminus (107 aa) was localized to the nucleolus of the transfected cells. Further analysis suggested that the cleaved C terminus contains a bipartite nuclear localization signal and utilizes import receptor importin-α3 of the classical importin-α/β transport pathway for nuclear transport. Successful isolation of recombinant BAdV-3 expressing mutant 100K (substitution of alanine for glycine in the potential protease cleavage site) suggested that cytoplasmic cleavage of BAdV-3 100K by adenoviral protease is not essential for virus replication.

Experimental contextuality in classical light

NASA Astrophysics Data System (ADS)

Li, Tao; Zeng, Qiang; Song, Xinbing; Zhang, Xiangdong

2017-03-01

The Klyachko, Can, Binicioglu, and Shumovsky (KCBS) inequality is an important contextuality inequality in three-level system, which has been demonstrated experimentally by using quantum states. Using the path and polarization degrees of freedom of classical optics fields, we have constructed the classical trit (cetrit), tested the KCBS inequality and its geometrical form (Wright’s inequality) in this work. The projection measurement has been implemented, the clear violations of the KCBS inequality and its geometrical form have been observed. This means that the contextuality inequality, which is commonly used in test of the conflict between quantum theory and noncontextual realism, may be used as a quantitative tool in classical optical coherence to describe correlation characteristics of the classical fields.

Nuclear import of HIV-1 intracellular reverse transcription complexes is mediated by importin 7

PubMed Central

Fassati, Ariberto; Görlich, Dirk; Harrison, Ian; Zaytseva, Lyubov; Mingot, José-Manuel

2003-01-01

Human immunodeficiency virus type 1 (HIV-1), like other lentiviruses, can infect non-dividing cells. This property depends on the active nuclear import of its intracellular reverse transcription complex (RTC). We have studied nuclear import of purified HIV-1 RTCs in primary macrophages and found that importin 7, an import receptor for ribosomal proteins and histone H1, is involved in the process. Nuclear import of RTCs requires, in addition, energy and the com ponents of the Ran system. Depletion of importin 7 from cultured cells by small interfering RNA inhibits HIV-1 infection. These results provide a new insight into the molecular mechanism for HIV-1 nuclear import and reveal potential targets for therapeutic intervention. PMID:12853482

Epigenetic inactivation of the p53-induced long noncoding RNA TP53 target 1 in human cancer

PubMed Central

Diaz-Lagares, Angel; Crujeiras, Ana B.; Lopez-Serra, Paula; Soler, Marta; Setien, Fernando; Goyal, Ashish; Sandoval, Juan; Hashimoto, Yutaka; Martinez-Cardús, Anna; Gomez, Antonio; Heyn, Holger; Moutinho, Catia; Espada, Jesús; Vidal, August; Paúles, Maria; Galán, Maica; Sala, Núria; Akiyama, Yoshimitsu; Martínez-Iniesta, María; Farré, Lourdes; Villanueva, Alberto; Gross, Matthias; Diederichs, Sven; Guil, Sonia; Esteller, Manel

2016-01-01

Long noncoding RNAs (lncRNAs) are important regulators of cellular homeostasis. However, their contribution to the cancer phenotype still needs to be established. Herein, we have identified a p53-induced lncRNA, TP53TG1, that undergoes cancer-specific promoter hypermethylation-associated silencing. In vitro and in vivo assays identify a tumor-suppressor activity for TP53TG1 and a role in the p53 response to DNA damage. Importantly, we show that TP53TG1 binds to the multifaceted DNA/RNA binding protein YBX1 to prevent its nuclear localization and thus the YBX1-mediated activation of oncogenes. TP53TG1 epigenetic inactivation in cancer cells releases the transcriptional repression of YBX1-targeted growth-promoting genes and creates a chemoresistant tumor. TP53TG1 hypermethylation in primary tumors is shown to be associated with poor outcome. The epigenetic loss of TP53TG1 therefore represents an altered event in an lncRNA that is linked to classical tumoral pathways, such as p53 signaling, but is also connected to regulatory networks of the cancer cell. PMID:27821766

BRAF(V600E) mutation is highly prevalent in thyroid carcinomas in the young population in Fukushima: a different oncogenic profile from Chernobyl.

PubMed

Mitsutake, Norisato; Fukushima, Toshihiko; Matsuse, Michiko; Rogounovitch, Tatiana; Saenko, Vladimir; Uchino, Shinya; Ito, Masahiro; Suzuki, Keiji; Suzuki, Shinichi; Yamashita, Shunichi

2015-11-20

After the accident at the Fukushima Daiichi Nuclear Power Plant, the thyroid ultrasound screening program for children aged 0-18 at the time of the accident was started from October 2011. The prevalence of thyroid carcinomas in that population has appeared to be very high (84 cases per 296,253). To clarify the pathogenesis, we investigated the presence of driver mutations in these tumours. 61 classic papillary thyroid carcinomas (PTCs), two follicular variant PTCs, four cribriform-morular variant PTCs and one poorly-differentiated thyroid carcinoma were analysed. We detected BRAF(V600E) in 43 cases (63.2%), RET/PTC1 in six (8.8%), RET/PTC3 in one (1.5%) and ETV6/NTRK3 in four (5.9%). Among classic and follicular variant PTCs, BRAF(V600E) was significantly associated with the smaller size. The genetic pattern was completely different from post-Chernobyl PTCs, suggesting non-radiogenic etiology of these cancers. This is the first study demonstrating the oncogene profile in the thyroid cancers discovered by large mass screening, which probably reflects genetic status of all sporadic and latent tumours in the young Japanese population. It is assumed that BRAF(V600E) may not confer growth advantage on paediatric PTCs, and many of these cases grow slowly, suggesting that additional factors may be important for tumour progression in paediatric PTCs.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

NASA Astrophysics Data System (ADS)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; Huy Pham, C.; Riera, Marc; Moberg, Daniel R.; Morales, Miguel A.; Knight, Chris; Götz, Andreas W.; Paesani, Francesco

2016-11-01

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.

A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinitskiy, Anton V.; Voth, Gregory A., E-mail: gavoth@uchicago.edu

2015-09-07

Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman’s imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionistmore » perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.« less

An Arbitrary First Order Theory Can Be Represented by a Program: A Theorem

NASA Technical Reports Server (NTRS)

Hosheleva, Olga

1997-01-01

How can we represent knowledge inside a computer? For formalized knowledge, classical logic seems to be the most adequate tool. Classical logic is behind all formalisms of classical mathematics, and behind many formalisms used in Artificial Intelligence. There is only one serious problem with classical logic: due to the famous Godel's theorem, classical logic is algorithmically undecidable; as a result, when the knowledge is represented in the form of logical statements, it is very difficult to check whether, based on this statement, a given query is true or not. To make knowledge representations more algorithmic, a special field of logic programming was invented. An important portion of logic programming is algorithmically decidable. To cover knowledge that cannot be represented in this portion, several extensions of the decidable fragments have been proposed. In the spirit of logic programming, these extensions are usually introduced in such a way that even if a general algorithm is not available, good heuristic methods exist. It is important to check whether the already proposed extensions are sufficient, or further extensions is necessary. In the present paper, we show that one particular extension, namely, logic programming with classical negation, introduced by M. Gelfond and V. Lifschitz, can represent (in some reasonable sense) an arbitrary first order logical theory.

A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals.

PubMed

Sinitskiy, Anton V; Voth, Gregory A

2015-09-07

Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman's imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionist perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.

SALO, a novel classical pathway complement inhibitor from saliva of the sand fly Lutzomyia longipalpis

PubMed Central

Ferreira, Viviana P.; Fazito Vale, Vladimir; Pangburn, Michael K.; Abdeladhim, Maha; Ferreira Mendes-Sousa, Antonio; Coutinho-Abreu, Iliano V.; Rasouli, Manoochehr; Brandt, Elizabeth A.; Meneses, Claudio; Lima, Kolyvan Ferreira; Nascimento Araújo, Ricardo; Horácio Pereira, Marcos; Kotsyfakis, Michalis; Oliveira, Fabiano; Kamhawi, Shaden; Ribeiro, Jose M. C.; Gontijo, Nelder F.; Collin, Nicolas; Valenzuela, Jesus G.

2016-01-01

Blood-feeding insects inject potent salivary components including complement inhibitors into their host’s skin to acquire a blood meal. Sand fly saliva was shown to inhibit the classical pathway of complement; however, the molecular identity of the inhibitor remains unknown. Here, we identified SALO as the classical pathway complement inhibitor. SALO, an 11 kDa protein, has no homology to proteins of any other organism apart from New World sand flies. rSALO anti-complement activity has the same chromatographic properties as the Lu. longipalpis salivary gland homogenate (SGH)counterparts and anti-rSALO antibodies blocked the classical pathway complement activity of rSALO and SGH. Both rSALO and SGH inhibited C4b deposition and cleavage of C4. rSALO, however, did not inhibit the protease activity of C1s nor the enzymatic activity of factor Xa, uPA, thrombin, kallikrein, trypsin and plasmin. Importantly, rSALO did not inhibit the alternative or the lectin pathway of complement. In conclusion our data shows that SALO is a specific classical pathway complement inhibitor present in the saliva of Lu. longipalpis. Importantly, due to its small size and specificity, SALO may offer a therapeutic alternative for complement classical pathway-mediated pathogenic effects in human diseases. PMID:26758086

Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

PubMed

Ley, A C; Hardy, O J

2013-04-01

AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species. © 2013 Blackwell Publishing Ltd.

Nuclear receptors and pathogenesis of pancreatic cancer

PubMed Central

Polvani, Simone; Tarocchi, Mirko; Tempesti, Sara; Galli, Andrea

2014-01-01

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a median overall survival time of 5 mo and the five years survival less than 5%, a rate essentially unchanged over the course of the years. A well defined progression model of accumulation of genetic alterations ranging from single point mutations to gross chromosomal abnormalities has been introduced to describe the origin of this disease. However, due to the its subtle nature and concurring events PDAC cure remains elusive. Nuclear receptors (NR) are members of a large superfamily of evolutionarily conserved ligand-regulated DNA-binding transcription factors functionally involved in important cellular functions ranging from regulation of metabolism, to growth and development. Given the nature of their ligands, NR are very tempting drug targets and their pharmacological modulation has been widely exploited for the treatment of metabolic and inflammatory diseases. There are now clear evidences that both classical ligand-activated and orphan NR are involved in the pathogenesis of PDAC from its very early stages; nonetheless many aspects of their role are not fully understood. The purpose of this review is to highlight the striking connections that link peroxisome proliferator activated receptors, retinoic acid receptors, retinoid X receptor, androgen receptor, estrogen receptors and the orphan NR Nur, chicken ovalbumin upstream promoter transcription factor II and the liver receptor homologue-1 receptor to PDAC development, connections that could lead to the identification of novel therapies for this disease. PMID:25232244

Potential clinical impact of radionuclide imaging technologies: highlights of the ITBS 2003 meeting

NASA Astrophysics Data System (ADS)

Itti, Roland

2004-07-01

Radiopharmaceuticals are major determinants of progress in Nuclear Medicine. Besides 18FDG, the most common PET tracer, several other molecules are under evaluation, such as 18F-fluoride for bone studies, numerous ligands for neurotransmission, 18F-DOPA for neuro-endocrine tumors or generator produced 68Ga-peptides for various cancers. Nuclear medicine gradually changes for "molecular imaging" and medical imaging, which was at the beginning mainly anatomic, has progressed in the direction of functional and metabolic imaging. The present challenge is to achieve some degree of "in vivo" biochemistry or even histology or genetics. The importance of anatomic/functional image fusion justifies the development of combined PET-CT instrumentation, whose objectives have to be discussed in terms of anatomical landmarks and/or additional clinical information. The question of "hard" or "soft" image co-registration remains open, involving not only CT, but also SPECT or MRI. Development of dedicated imaging devices, whether single photon or positron, is of major interest for breast imaging, allowing optimal imaging conditions, with results definitely superior to classical gamma-cameras or PET. The patient population concerned with scintimammography is still controversial, as well as the imaging modalities: FDG or sestaMIBI, planar or tomographic, scintillators or semi-conductors, and the research field remains open. This is also valid for external or per-operative probe systems for tumor or lymph nodes localization.

Finds in Belize document Late Classic Maya salt making and canoe transport

PubMed Central

McKillop, Heather

2005-01-01

How did people in preIndustrial ancient civilizations produce and distribute bulk items, such as salt, needed for everyday use by their large urban populations? This report focuses on the ancient Maya who obtained quantities of salt at cities in the interior of the Yucatan peninsula of Mexico, Belize, and Guatemala in an area where salt is scarce. I report the discovery of 41 Late Classic Maya saltworks (anno Domini 600–900) in Punta Ycacos Lagoon on the south coast of Belize, including one with the first-known ancient Maya canoe paddle. The discoveries add important empirical information for evaluating the extent of surplus salt production and river transport during the height of Late Classic civilization in the southern Maya lowlands. The discovery of the saltworks indicates that there was extensive production and distribution of goods and resources outside the cities in the interior of the Yucatan. The discovery of a wooden canoe paddle from one of the Punta Ycacos saltworks, Ka'k' Naab', ties the production of salt to its inland transport by rivers and documents the importance of canoe trade between the coast and the interior during the Late Classic. Archaeological discovery of multiple saltworks on the Belizean coast represents surplus production of salt destined largely for the inland Peten Maya during their Late Classic peak, underscoring the importance of non-state-controlled workshop production in preIndustrial societies. PMID:15809426

Reversible Oxidation of a Conserved Methionine in the Nuclear Export Sequence Determines Subcellular Distribution and Activity of the Fungal Nitrate Regulator NirA.

PubMed

Gallmetzer, Andreas; Silvestrini, Lucia; Schinko, Thorsten; Gesslbauer, Bernd; Hortschansky, Peter; Dattenböck, Christoph; Muro-Pastor, María Isabel; Kungl, Andreas; Brakhage, Axel A; Scazzocchio, Claudio; Strauss, Joseph

2015-07-01

The assimilation of nitrate, a most important soil nitrogen source, is tightly regulated in microorganisms and plants. In Aspergillus nidulans, during the transcriptional activation process of nitrate assimilatory genes, the interaction between the pathway-specific transcription factor NirA and the exportin KapK/CRM1 is disrupted, and this leads to rapid nuclear accumulation and transcriptional activity of NirA. In this work by mass spectrometry, we found that in the absence of nitrate, when NirA is inactive and predominantly cytosolic, methionine 169 in the nuclear export sequence (NES) is oxidized to methionine sulfoxide (Metox169). This oxidation depends on FmoB, a flavin-containing monooxygenase which in vitro uses methionine and cysteine, but not glutathione, as oxidation substrates. The function of FmoB cannot be replaced by alternative Fmo proteins present in A. nidulans. Exposure of A. nidulans cells to nitrate led to rapid reduction of NirA-Metox169 to Met169; this reduction being independent from thioredoxin and classical methionine sulfoxide reductases. Replacement of Met169 by isoleucine, a sterically similar but not oxidizable residue, led to partial loss of NirA activity and insensitivity to FmoB-mediated nuclear export. In contrast, replacement of Met169 by alanine transformed the protein into a permanently nuclear and active transcription factor. Co-immunoprecipitation analysis of NirA-KapK interactions and subcellular localization studies of NirA mutants lacking different parts of the protein provided evidence that Met169 oxidation leads to a change in NirA conformation. Based on these results we propose that in the presence of nitrate the activation domain is exposed, but the NES is masked by a central portion of the protein (termed nitrate responsive domain, NiRD), thus restricting active NirA molecules to the nucleus. In the absence of nitrate, Met169 in the NES is oxidized by an FmoB-dependent process leading to loss of protection by the NiRD, NES exposure, and relocation of the inactive NirA to the cytosol.

Attempts to develop a new nuclear measurement technique of β-glucuronidase levels in biological samples

NASA Astrophysics Data System (ADS)

Ünak, T.; Avcibasi, U.; Yildirim, Y.; Çetinkaya, B.

2003-01-01

β-Glucuronidase is one of the most important hydrolytic enzymes in living systems and plays an essential role in the detoxification pathway of toxic materials incorporated into the metabolism. Some organs, especially liver and some tumour tissues, have high level of β-glucuronidase activity. As a result the enzymatic activity of some kind of tumour cells, the radiolabelled glucuronide conjugates of cytotoxic, as well as radiotoxic compounds have potentially very valuable diagnostic and therapeutic applications in cancer research. For this reason, a sensitive measurement of β-glucuronidase levels in normal and tumour tissues is a very important step for these kinds of applications. According to the classical measurement method of β-glucuronidase activity, in general, the quantity of phenolphthalein liberated from its glucuronide conjugate, i.e. phenolphthalein-glucuronide, by β-glucuronidase has been measured by use of the spectrophotometric technique. The lower detection limit of phenolphthalein by the spectrophotometric technique is about 1-3 μg. This means that the β-glucuronidase levels could not be detected in biological samples having lower levels of β-glucuronidase activity and therefore the applications of the spectrophotometric technique in cancer research are very seriously limited. Starting from this consideration, we recently attempted to develop a new nuclear technique to measure much lower concentrations of β-glucuronidase in biological samples. To improve the detection limit, phenolphthalein-glucuronide and also phenyl-N-glucuronide were radioiodinated with 131I and their radioactivity was measured by use of the counting technique. Therefore, the quantity of phenolphthalein or aniline radioiodinated with 131I and liberated by the deglucuronidation reactivity of β-glucuronidase was used in an attempt to measure levels lower than the spectrophotometric measurement technique. The results obtained clearly verified that 0.01 pg level of phenolphthalein or aniline could easily be detected at least 106 times more sensitively. The preliminary results obtained on some biological samples have shown that β-glucuronidase levels could reasonably be measured by use of the nuclear technique. In addition, our results also indicate the potential application of the radiolabelling technique to measure very low β-glucuronidase levels in different biological samples in cancer research and other related fields. The objective of our study is to demonstrate the potential application of the nuclear measurement technique in different biological samples.

Human Heat shock protein 40 (Hsp40/DnaJB1) promotes influenza A virus replication by assisting nuclear import of viral ribonucleoproteins.

PubMed

Batra, Jyoti; Tripathi, Shashank; Kumar, Amrita; Katz, Jacqueline M; Cox, Nancy J; Lal, Renu B; Sambhara, Suryaprakash; Lal, Sunil K

2016-01-11

A unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins.

Human Heat shock protein 40 (Hsp40/DnaJB1) promotes influenza A virus replication by assisting nuclear import of viral ribonucleoproteins

PubMed Central

Batra, Jyoti; Tripathi, Shashank; Kumar, Amrita; Katz, Jacqueline M.; Cox, Nancy J.; Lal, Renu B.; Sambhara, Suryaprakash; Lal, Sunil K.

2016-01-01

A unique feature of influenza A virus (IAV) life cycle is replication of the viral genome in the host cell nucleus. The nuclear import of IAV genome is an indispensable step in establishing virus infection. IAV nucleoprotein (NP) is known to mediate the nuclear import of viral genome via its nuclear localization signals. Here, we demonstrate that cellular heat shock protein 40 (Hsp40/DnaJB1) facilitates the nuclear import of incoming IAV viral ribonucleoproteins (vRNPs) and is important for efficient IAV replication. Hsp40 was found to interact with NP component of IAV RNPs during early stages of infection. This interaction is mediated by the J domain of Hsp40 and N-terminal region of NP. Drug or RNAi mediated inhibition of Hsp40 resulted in reduced nuclear import of IAV RNPs, diminished viral polymerase function and attenuates overall viral replication. Hsp40 was also found to be required for efficient association between NP and importin alpha, which is crucial for IAV RNP nuclear translocation. These studies demonstrate an important role for cellular chaperone Hsp40/DnaJB1 in influenza A virus life cycle by assisting nuclear trafficking of viral ribonucleoproteins. PMID:26750153

Crosstalk between ERK2 and RXR regulates nuclear import of transcription factor NGFI-B

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobs, Chris M.; Paulsen, Ragnhild E.

2005-10-21

Transcription factor NGFI-B initiates apoptosis when allowed to translocate to mitochondria. Retinoid-X receptor (RXR), another member of the nuclear receptor family, regulates NGFI-B signaling through heterodimerization and nuclear export. Growth factor EGF activates ERK2, which phosphorylates NGFI-B and determines if NGFI-B is allowed to translocate to mitochondria. In the present study, EGF treatment resulted in an increased nuclear import of NGFI-B. Likewise, active ERK2 resulted in a preferential nuclear localization of NGFI-B. When coexpressed with RXR the nuclear import and nuclear localization induced by active ERK2 were strongly reduced. In the presence of its ligand 9-cis-retinoic acid, RXR no longermore » inhibited ERK2-induced nuclear import. Thus, RXR serves a permissive role for ERK2-mediated nuclear accumulation of NGFI-B. This finding represents a novel crosstalk between ERK2 and RXR signaling pathways, and explains how two independent inhibitors of apoptosis (EGF and 9-cis-retinoic acid) may cooperate to regulate nuclear targeting of apoptosis inducer NGFI-B.« less

Experimental implementation of heat-bath algorithmic cooling using solid-state nuclear magnetic resonance.

PubMed

Baugh, J; Moussa, O; Ryan, C A; Nayak, A; Laflamme, R

2005-11-24

The counter-intuitive properties of quantum mechanics have the potential to revolutionize information processing by enabling the development of efficient algorithms with no known classical counterparts. Harnessing this power requires the development of a set of building blocks, one of which is a method to initialize the set of quantum bits (qubits) to a known state. Additionally, fresh ancillary qubits must be available during the course of computation to achieve fault tolerance. In any physical system used to implement quantum computation, one must therefore be able to selectively and dynamically remove entropy from the part of the system that is to be mapped to qubits. One such method is an 'open-system' cooling protocol in which a subset of qubits can be brought into contact with an external system of large heat capacity. Theoretical efforts have led to an implementation-independent cooling procedure, namely heat-bath algorithmic cooling. These efforts have culminated with the proposal of an optimal algorithm, the partner-pairing algorithm, which was used to compute the physical limits of heat-bath algorithmic cooling. Here we report the experimental realization of multi-step cooling of a quantum system via heat-bath algorithmic cooling. The experiment was carried out using nuclear magnetic resonance of a solid-state ensemble three-qubit system. We demonstrate the repeated repolarization of a particular qubit to an effective spin-bath temperature, and alternating logical operations within the three-qubit subspace to ultimately cool a second qubit below this temperature. Demonstration of the control necessary for these operations represents an important step forward in the manipulation of solid-state nuclear magnetic resonance qubits.

Comparison of UV/hydrogen peroxide, potassium ferrate(VI), and ozone in oxidizing the organic fraction of oil sands process-affected water (OSPW).

PubMed

Wang, Chengjin; Klamerth, Nikolaus; Messele, Selamawit Ashagre; Singh, Arvinder; Belosevic, Miodrag; Gamal El-Din, Mohamed

2016-09-01

The efficiency of three different oxidation processes, UV/H2O2 oxidation, ferrate(VI) oxidation, and ozonation with and without hydroxyl radical (OH) scavenger tert-butyl alcohol (TBA) on the removal of organic compounds from oil sands process-affected water (OSPW) was investigated and compared. The removal of aromatics and naphthenic acids (NAs) was explored by synchronous fluorescence spectra (SFS), ion mobility spectra (IMS), proton and carbon nuclear magnetic resonance ((1)H and (13)C NMR), and ultra-performance liquid chromatography coupled with time-of-flight mass spectrometry (UPLC TOF-MS). UV/H2O2 oxidation occurred through radical reaction and photolysis, transforming one-ring, two-ring, and three-ring fluorescing aromatics simultaneously and achieving 42.4% of classical NAs removal at 2.0 mM H2O2 and 950 mJ/cm(2) UV dose provided with medium pressure mercury lamp. Ferrate(VI) oxidation exhibited high selectivity, preferentially removing two-ring and three-ring fluorescing aromatics, sulfur-containing NAs (NAs + S), and NAs with high carbon and high hydrogen deficiency. At 2.0 mM Fe(VI), 46.7% of classical NAs was removed. Ozonation achieved almost complete removal of fluorescing aromatics, NAs + S, and classical NAs (NAs with two oxygen atoms) at the dose of 2.0 mM O3. Both molecular ozone reaction and OH reaction were important pathways in transforming the organics in OSPW as supported by ozonation performance with and without TBA. (1)H NMR analyses further confirmed the removal of aromatics and NAs both qualitatively and quantitatively. All the three oxidation processes reduced the acute toxicity towards Vibrio fischeri and on goldfish primary kidney macrophages (PKMs), with ozonation being the most efficient. Copyright © 2016 Elsevier Ltd. All rights reserved.

Classical Demonstration of Polarization.

ERIC Educational Resources Information Center

Bauman, Robert P.; Moore, Dennis R.

1980-01-01

Presents a classical demonstration of polarization for high school students. The initial state of this model, which demonstrates the important concepts of the optical and quantum problems, was developed during the 1973 summer program on lecture demonstration at the U.S. Naval Academy. (HM)

Investigation of hydrogenation of toluene to methylcyclohexane in a trickle bed reactor by low-field nuclear magnetic resonance spectroscopy.

PubMed

Guthausen, Gisela; von Garnier, Agnes; Reimert, Rainer

2009-10-01

Low-field nuclear magnetic resonance (NMR) spectroscopy is applied to study the hydrogenation of toluene in a lab-scale reactor. A conventional benchtop NMR system was modified to achieve chemical shift resolution. After an off-line validity check of the approach, the reaction product is analyzed on-line during the process, applying chemometric data processing. The conversion of toluene to methylcyclohexane is compared with off-line gas chromatographic analysis. Both classic analytical and chemometric data processing was applied. As the results, which are obtained within a few tens of seconds, are equivalent within the experimental accuracy of both methods, low-field NMR spectroscopy was shown to provide an analytical tool for reaction characterization and immediate feedback.

Selection with Gene-Cytoplasm Interactions. I. Maintenance of Cytoplasm Polymorphisms

PubMed Central

Gregorius, H. R.; Ross, M. D.

1984-01-01

General conditions for the protectedness of gene-cytoplasm polymorphisms are considered for a biallelic model with two cytoplasm types and under the assumption that nuclear polymorphisms cannot be maintained in the presence of only one cytoplasm type. Analytical results involving male fertilities, female fertilities, viabilities and selfing rates are obtained, and numerical results show spiral and cyclic behavior of population trajectories. It is shown that a maternally inherited cytoplasmic polymorphism cannot be maintained in the absence of a nuclear polymorphism, and that a gene-cytoplasm polymorphism can only be maintained if the population shows sexual asymmetry, i.e. , if the ratio of male to female fertility varies among genotypes. Thus, the classical viability selection model does not allow gene-cytoplasm polymorphisms. PMID:17246213

Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach.

PubMed

Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

2017-04-04

Peptides have gained increased interest as therapeutic agents during recent years. The high specificity and relatively low toxicity of peptide drugs derive from their extremely tight binding to their targets. Indeed, understanding the molecular mechanism of protein-peptide recognition has important implications in the fields of biology, medicine, and pharmaceutical sciences. Even if crystallography and nuclear magnetic resonance are offering valuable atomic insights into the assembling of the protein-peptide complexes, the mechanism of their recognition and binding events remains largely unclear. In this work we report, for the first time, the use of a supervised molecular dynamics approach to explore the possible protein-peptide binding pathways within a timescale reduced up to three orders of magnitude compared with classical molecular dynamics. The better and faster understating of the protein-peptide recognition pathways could be very beneficial in enlarging the applicability of peptide-based drug design approaches in several biotechnological and pharmaceutical fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

GPER Signaling in Spermatogenesis and Testicular Tumors.

PubMed

Chimento, Adele; Sirianni, Rosa; Casaburi, Ivan; Pezzi, Vincenzo

2014-01-01

Estrogens play important roles in the regulation of testis development and spermatogenesis. Moreover, several evidences suggest that estrogen signaling can be involved in testicular tumorigenesis. The physiological effects of estrogen are mediated by the classical nuclear estrogen receptors ESR1 and 2, which regulate both genomic and rapid signaling events. In the recent years, a member of the seven-transmembrane G protein-coupled receptor family, GPR30 (GPER), has been identified to promote estrogen action in target cells including testicular cells. Ours and other studies reported that GPER is expressed in normal germ cells (spermatogonia, spermatocytes, spermatids), somatic cells (Sertoli and Leydig cells), and it is also involved in mediating estrogen action during spermatogenesis and testis development. In addition, GPER seems to be involved in modulating estrogen-dependent testicular cancer cell growth. However, in this context, the effects of GPER stimulation on cell survival and proliferation appear to be cell type specific. This review summarizes the current knowledge on the functions regulated by estrogens and mediated by GPER in normal and tumor testicular cells.

Issues with Strong Compression of Plasma Target by Stabilized Imploding Liner

NASA Astrophysics Data System (ADS)

Turchi, Peter; Frese, Sherry; Frese, Michael

2017-10-01

Strong compression (10:1 in radius) of an FRC by imploding liquid metal liners, stabilized against Rayleigh-Taylor modes, using different scalings for loss based on Bohm vs 100X classical diffusion rates, predict useful compressions with implosion times half the initial energy lifetime. The elongation (length-to-diameter ratio) near peak compression needed to satisfy empirical stability criterion and also retain alpha-particles is about ten. The present paper extends these considerations to issues of the initial FRC, including stability conditions (S*/E) and allowable angular speeds. Furthermore, efficient recovery of the implosion energy and alpha-particle work, in order to reduce the necessary nuclear gain for an economical power reactor, is seen as an important element of the stabilized liner implosion concept for fusion. We describe recent progress in design and construction of the high energy-density prototype of a Stabilized Liner Compressor (SLC) leading to repetitive laboratory experiments to develop the plasma target. Supported by ARPA-E ALPHA Program.

GPER Signaling in Spermatogenesis and Testicular Tumors

PubMed Central

Chimento, Adele; Sirianni, Rosa; Casaburi, Ivan; Pezzi, Vincenzo

2014-01-01

Estrogens play important roles in the regulation of testis development and spermatogenesis. Moreover, several evidences suggest that estrogen signaling can be involved in testicular tumorigenesis. The physiological effects of estrogen are mediated by the classical nuclear estrogen receptors ESR1 and 2, which regulate both genomic and rapid signaling events. In the recent years, a member of the seven-transmembrane G protein-coupled receptor family, GPR30 (GPER), has been identified to promote estrogen action in target cells including testicular cells. Ours and other studies reported that GPER is expressed in normal germ cells (spermatogonia, spermatocytes, spermatids), somatic cells (Sertoli and Leydig cells), and it is also involved in mediating estrogen action during spermatogenesis and testis development. In addition, GPER seems to be involved in modulating estrogen-dependent testicular cancer cell growth. However, in this context, the effects of GPER stimulation on cell survival and proliferation appear to be cell type specific. This review summarizes the current knowledge on the functions regulated by estrogens and mediated by GPER in normal and tumor testicular cells. PMID:24639669

Obesity, Insulin Resistance and Diabetes: Sex Differences and Role of Estrogen Receptors

PubMed Central

Meyer, Matthias R.; Clegg, Deborah J.; Prossnitz, Eric R.; Barton, Matthias

2010-01-01

Obesity increases the risk of coronary artery disease through insulin resistance, diabetes, arterial hypertension, and dyslipidemia. The prevalence of obesity has increased worldwide and is particularly high among middle-aged women and men. After menopause, women are at an increased risk to develop visceral obesity due to the loss of endogenous ovarian hormone production. Effects of estrogens are classically mediated by the two nuclear estrogen receptors (ERs) α and β. In addition, more recent research has shown that the intracellular transmembrane G protein-coupled estrogen receptor, GPER, originally designated as GPR30, also mediates some of the actions attributed to estrogens. Estrogen and its receptors are important regulators of body weight and insulin sensitivity not only in women, but also in men as demonstrated by ER mutations in rodents and humans. This article reviews the role of sex hormones and estrogen receptors in the context of obesity, insulin sensitivity and diabetes as well as the related clinical issues in females and males. PMID:21281456

Parathyroid Hormone Directs Bone Marrow Mesenchymal Cell Fate.

PubMed

Fan, Yi; Hanai, Jun-Ichi; Le, Phuong T; Bi, Ruiye; Maridas, David; DeMambro, Victoria; Figueroa, Carolina A; Kir, Serkan; Zhou, Xuedong; Mannstadt, Michael; Baron, Roland; Bronson, Roderick T; Horowitz, Mark C; Wu, Joy Y; Bilezikian, John P; Dempster, David W; Rosen, Clifford J; Lanske, Beate

2017-03-07

Intermittent PTH administration builds bone mass and prevents fractures, but its mechanism of action is unclear. We genetically deleted the PTH/PTHrP receptor (PTH1R) in mesenchymal stem cells using Prx1Cre and found low bone formation, increased bone resorption, and high bone marrow adipose tissue (BMAT). Bone marrow adipocytes traced to Prx1 and expressed classic adipogenic markers and high receptor activator of nuclear factor kappa B ligand (Rankl) expression. RANKL levels were also elevated in bone marrow supernatant and serum, but undetectable in other adipose depots. By cell sorting, Pref1 + RANKL + marrow progenitors were twice as great in mutant versus control marrow. Intermittent PTH administration to control mice reduced BMAT significantly. A similar finding was noted in male osteoporotic patients. Thus, marrow adipocytes exhibit osteogenic and adipogenic characteristics, are uniquely responsive to PTH, and secrete RANKL. These studies reveal an important mechanism for PTH's therapeutic action through its ability to direct mesenchymal cell fate. Copyright © 2017 Elsevier Inc. All rights reserved.

Importin α1 is required for nuclear import of herpes simplex virus proteins and capsid assembly in fibroblasts and neurons

PubMed Central

Anderson, Fenja; Rother, Franziska; Rudolph, Kathrin; Prank, Ute; Binz, Anne; Hügel, Stefanie; Hartmann, Enno; Bader, Michael; Bauerfeind, Rudolf; Sodeik, Beate

2018-01-01

Herpesviruses are large DNA viruses which depend on many nuclear functions, and therefore on host transport factors to ensure specific nuclear import of viral and host components. While some import cargoes bind directly to certain transport factors, most recruit importin β1 via importin α. We identified importin α1 in a small targeted siRNA screen to be important for herpes simplex virus (HSV-1) gene expression. Production of infectious virions was delayed in the absence of importin α1, but not in cells lacking importin α3 or importin α4. While nuclear targeting of the incoming capsids, of the HSV-1 transcription activator VP16, and of the viral genomes were not affected, the nuclear import of the HSV-1 proteins ICP4 and ICP0, required for efficient viral transcription, and of ICP8 and pUL42, necessary for DNA replication, were reduced. Furthermore, quantitative electron microscopy showed that fibroblasts lacking importin α1 contained overall fewer nuclear capsids, but an increased proportion of mature nuclear capsids indicating that capsid formation and capsid egress into the cytoplasm were impaired. In neurons, importin α1 was also not required for nuclear targeting of incoming capsids, but for nuclear import of ICP4 and for the formation of nuclear capsid assembly compartments. Our data suggest that importin α1 is specifically required for the nuclear localization of several important HSV1 proteins, capsid assembly, and capsid egress into the cytoplasm, and may become rate limiting in situ upon infection at low multiplicity or in terminally differentiated cells such as neurons. PMID:29304174

Heterologous mitochondrial targeting sequences can deliver functional proteins into mitochondria.

PubMed

Marcus, Dana; Lichtenstein, Michal; Cohen, Natali; Hadad, Rita; Erlich-Hadad, Tal; Greif, Hagar; Lorberboum-Galski, Haya

2016-12-01

Mitochondrial Targeting Sequences (MTSs) are responsible for trafficking nuclear-encoded proteins into mitochondria. Once entering the mitochondria, the MTS is recognized and cleaved off. Some MTSs are long and undergo two-step processing, as in the case of the human frataxin (FXN) protein (80aa), implicated in Friedreich's ataxia (FA). Therefore, we chose the FXN protein to examine whether nuclear-encoded mitochondrial proteins can efficiently be targeted via a heterologous MTS (hMTS) and deliver a functional protein into mitochondria. We examined three hMTSs; that of citrate synthase (cs), lipoamide deydrogenase (LAD) and C6ORF66 (ORF), as classically MTS sequences, known to be removed by one-step processing, to deliver FXN into mitochondria, in the form of fusion proteins. We demonstrate that using hMTSs for delivering FXN results in the production of 4-5-fold larger amounts of the fusion proteins, and at 4-5-fold higher concentrations. Moreover, hMTSs delivered a functional FXN protein into the mitochondria even more efficiently than the native MTSfxn, as evidenced by the rescue of FA patients' cells from oxidative stress; demonstrating a 18%-54% increase in cell survival; and a 13%-33% increase in ATP levels, as compared to the fusion protein carrying the native MTS. One fusion protein with MTScs increased aconitase activity within patients' cells, by 400-fold. The implications form our studies are of vast importance for both basic and translational research of mitochondrial proteins as any mitochondrial protein can be delivered efficiently by an hMTS. Moreover, effective targeting of functional proteins is important for restoration of mitochondrial function and treatment of related disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Class 1 Histone Deacetylase with Potential as an Antifungal Target.

PubMed

Bauer, Ingo; Varadarajan, Divyavaradhi; Pidroni, Angelo; Gross, Silke; Vergeiner, Stefan; Faber, Birgit; Hermann, Martin; Tribus, Martin; Brosch, Gerald; Graessle, Stefan

2016-11-01

Histone deacetylases (HDACs) remove acetyl moieties from lysine residues at histone tails and nuclear regulatory proteins and thus significantly impact chromatin remodeling and transcriptional regulation in eukaryotes. In recent years, HDACs of filamentous fungi were found to be decisive regulators of genes involved in pathogenicity and the production of important fungal metabolites such as antibiotics and toxins. Here we present proof that one of these enzymes, the class 1 type HDAC RpdA, is of vital importance for the opportunistic human pathogen Aspergillus fumigatus Recombinant expression of inactivated RpdA shows that loss of catalytic activity is responsible for the lethal phenotype of Aspergillus RpdA null mutants. Furthermore, we demonstrate that a fungus-specific C-terminal region of only a few acidic amino acids is required for both the nuclear localization and catalytic activity of the enzyme in the model organism Aspergillus nidulans Since strains with single or multiple deletions of other classical HDACs revealed no or only moderate growth deficiencies, it is highly probable that the significant delay of germination and the growth defects observed in strains growing under the HDAC inhibitor trichostatin A are caused primarily by inhibition of catalytic RpdA activity. Indeed, even at low nanomolar concentrations of the inhibitor, the catalytic activity of purified RpdA is considerably diminished. Considering these results, RpdA with its fungus-specific motif represents a promising target for novel HDAC inhibitors that, in addition to their increasing impact as anticancer drugs, might gain in importance as antifungals against life-threatening invasive infections, apart from or in combination with classical antifungal therapy regimes. This paper reports on the fungal histone deacetylase RpdA and its importance for the viability of the fungal pathogen Aspergillus fumigatus and other filamentous fungi, a finding that is without precedent in other eukaryotic pathogens. Our data clearly indicate that loss of RpdA activity, as well as depletion of the enzyme in the nucleus, results in lethality of the corresponding Aspergillus mutants. Interestingly, both catalytic activity and proper cellular localization depend on the presence of an acidic motif within the C terminus of RpdA-type enzymes of filamentous fungi that is missing from the homologous proteins of yeasts and higher eukaryotes. The pivotal role, together with the fungus-specific features, turns RpdA into a promising antifungal target of histone deacetylase inhibitors, a class of molecules that is successfully used for the treatment of certain types of cancer. Indeed, some of these inhibitors significantly delay the germination and growth of different filamentous fungi via inhibition of RpdA. Upcoming analyses of clinically approved and novel inhibitors will elucidate their therapeutic potential as new agents for the therapy of invasive fungal infections-an interesting aspect in light of the rising resistance of fungal pathogens to conventional therapies. Copyright © 2016 Bauer et al.

Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

PubMed Central

2012-01-01

Background The post-genomic era of malaria research provided unprecedented insights into the biology of Plasmodium parasites. Due to the large evolutionary distance to model eukaryotes, however, we lack a profound understanding of many processes in Plasmodium biology. One example is the cell nucleus, which controls the parasite genome in a development- and cell cycle-specific manner through mostly unknown mechanisms. To study this important organelle in detail, we conducted an integrative analysis of the P. falciparum nuclear proteome. Results We combined high accuracy mass spectrometry and bioinformatic approaches to present for the first time an experimentally determined core nuclear proteome for P. falciparum. Besides a large number of factors implicated in known nuclear processes, one-third of all detected proteins carry no functional annotation, including many phylum- or genus-specific factors. Importantly, extensive experimental validation using 30 transgenic cell lines confirmed the high specificity of this inventory, and revealed distinct nuclear localization patterns of hitherto uncharacterized proteins. Further, our detailed analysis identified novel protein domains potentially implicated in gene transcription pathways, and sheds important new light on nuclear compartments and processes including regulatory complexes, the nucleolus, nuclear pores, and nuclear import pathways. Conclusion Our study provides comprehensive new insight into the biology of the Plasmodium nucleus and will serve as an important platform for dissecting general and parasite-specific nuclear processes in malaria parasites. Moreover, as the first nuclear proteome characterized in any protist organism, it will provide an important resource for studying evolutionary aspects of nuclear biology. PMID:23181666

Cosmopolitan sociology and the classical canon: Ferdinand Tönnies and the emergence of global Gesellschaft.

PubMed

Inglis, David

2009-12-01

How relevant are figures from the classical sociological canon for present day efforts to found cosmopolitan forms of sociological thought? According to the critique of Ulrich Beck, the classical sociologists remain far too wedded to nation-state-centred ways of thinking to play an important role in the development of cosmopolitan sociology. This paper argues that such a critique fails to account for the ways in which certain classical sociologists were attuned to the emerging cosmopolitical conditions of their own time, were not wholly wedded to nation-state-based conceptualizations, and thus can function as both groundings of, and inspirations for, cosmopolitan sociological endeavours. The apparently unpromising case of Tönnies is focused on, the paper showing how he outlined an account of how and why a planet-spanning condition of Gesellschaft developed a position which diverges from and counterpoints Marx's analysis of similar phenomena in important ways. The stereotype of Tönnies as an arch-conservative is also dissolved, allowing him to be considered as one of the most important antecedents of contemporary cosmopolitan sociological practice and a canonical figure still relevant for present-day purposes.

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

PubMed Central

Zhan, Cheng; Lian, Cheng; Zhang, Yu; Thompson, Matthew W.; Xie, Yu; Wu, Jianzhong; Kent, Paul R. C.; Cummings, Peter T.; Wesolowski, David J.

2017-01-01

Supercapacitors such as electric double‐layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double‐layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte‐Carlo (MC) methods. In recent years, combining first‐principles and classical simulations to investigate the carbon‐based EDLCs has shed light on the importance of quantum capacitance in graphene‐like 2D systems. More recently, the development of joint density functional theory (JDFT) enables self‐consistent electronic‐structure calculation for an electrode being solvated by an electrolyte. In contrast with the large amount of theoretical and computational effort on EDLCs, theoretical understanding of pseudocapacitance is very limited. In this review, we first introduce popular modeling methods and then focus on several important aspects of EDLCs including nanoconfinement, quantum capacitance, dielectric screening, and novel 2D electrode design; we also briefly touch upon pseudocapactive mechanism in RuO2. We summarize and conclude with an outlook for the future of materials simulation and design for capacitive energy storage. PMID:28725531

Inhibition of CRM1-dependent nuclear export sensitizes malignant cells to cytotoxic and targeted agents

PubMed Central

Turner, Joel G.; Dawson, Jana; Cubitt, Christopher L.; Baz, Rachid; Sullivan, Daniel M.

2014-01-01

Nuclear-cytoplasmic trafficking of proteins is a significant factor in the development of cancer and drug resistance. Subcellular localization of exported proteins linked to cancer development include those involved in cell growth and proliferation, apoptosis, cell cycle regulation, transformation, angiogenesis, cell adhesion, invasion, and metastasis. Here, we examined the basic mechanisms involved in the export of proteins from the nucleus to the cytoplasm. All proteins over 40 kDa use the nuclear pore complex to gain entry or exit from the nucleus, with the primary nuclear export molecule involved in these processes being chromosome region maintenance 1 (CRM1, exportin 1 or XPO1). Proteins exported from the nucleus must possess a hydrophobic nuclear export signal (NES) peptide that binds to a hydrophobic groove containing an active-site Cys528 in the CRM1 protein. CRM1 inhibitors function largely by covalent modification of the active site Cys528 and prevent binding to the cargo protein NES. In the absence of a CRM1 inhibitor, CRM1 binds cooperatively to the NES of the cargo protein and RanGTP, forming a trimer that is actively transported out of the nucleus by facilitated diffusion. Nuclear export can be blocked by CRM1 inhibitors, NES peptide inhibitors or by preventing post-translational modification of cargo proteins. Clinical trials using the classic CRM1 inhibitor leptomycin B proved too toxic for patients; however, a new generation of less toxic small molecule inhibitors are being used in clinical trials in patients with both hematological malignancies and solid tumors. Additional trials are being initiated using small-molecule CRM1 inhibitors in combination with chemotherapeutics such as pegylated liposomal doxorubicin. In this review, we present evidence that combining the new CRM1 inhibitors with other classes of therapeutics may prove effective in the treatment of cancer. Potential combinatorial therapies discussed include the use of CRM1 inhibitors and the addition of alkylating agents (melphalan), anthracyclines (doxorubicin and daunomycin), BRAF inhibitors, platinum drugs (cisplatin and oxaliplatin), proteosome inhibitors (bortezomib and carfilzomib), or tyrosine-kinase inhibitors (imatinib). Also, the sequence of treatment may be important for combination therapy. We found that the most effective treatment regimen involved first priming the cancer cells with the CRM1 inhibitor followed by doxorubicin, bortezomib, carfilzomib, or melphalan. This order sensitized both de novo and acquired drug-resistant cancer cell lines. PMID:24631834

Testing violation of the Leggett-Garg-type inequality in neutrino oscillations of the Daya Bay experiment

NASA Astrophysics Data System (ADS)

Fu, Qiang; Chen, Xurong

2017-11-01

The Leggett-Garg inequality (LGI), derived under the assumption of realism, acts as the temporal Bell inequality. It is studied in electromagnetic and strong interaction like photonics, superconducting qubits and nuclear spin. The weak interaction two-state oscillations of neutrinos affirmed the violation of Leggett-Garg-type inequalities (LGtI). We make an empirical test for the deviation of experimental results with the classical limits by analyzing the survival probability data of reactor neutrinos at a distinct range of baseline dividing energies, as an analog to a single neutrino detected at different times. A study of the updated data of the Daya Bay experiment unambiguously depicts an obvious cluster of data over the classical bound of LGtI and shows a 6.1σ significance of the violation of them.

Noncanonical NF-κB Signaling Is Limited by Classical NF-κB Activity

PubMed Central

Gray, Carolyn M.; Remouchamps, Caroline; McCorkell, Kelly A.; Solt, Laura A.; Dejardin, Emmanuel; Orange, Jordan S.; May, Michael J.

2014-01-01

Precise regulation of nuclear factor κB (NF-κB) signaling is crucial for normal immune responses, and defective NF-κB activity underlies a range of immunodeficiencies. NF-κB is activated through two signaling cascades: the classical and noncanonical pathways. The classical pathway requires inhibitor of κB kinase β (IKKβ) and NF-κB essential modulator (NEMO), and hypomorphic mutations in the gene encoding NEMO (ikbkg) lead to inherited immunodeficiencies, collectively termed NEMO-ID. Noncanonical NF-κB activation requires NF-κB–inducing kinase (NIK) and IKKα, but not NEMO. We found that noncanonical NF-κB was basally active in peripheral blood mononuclear cells from NEMO-ID patients, and that noncanonical NF-κB signaling was similarly enhanced in cell lines lacking functional NEMO. NIK, which normally undergoes constitutive degradation, was aberrantly present in resting NEMO-deficient cells, and regulation of its abundance was rescued by reconstitution with full-length NEMO, but not a mutant NEMO protein unable to physically associate with IKKα or IKKβ. Binding of NEMO to IKKα was not required for ligand-dependent stabilization of NIK or noncanonical NF-κB signaling. Rather, an intact and functional IKK complex was essential to suppress basal NIK activity in unstimulated cells. Despite interacting with IKKα and IKKβ to form an IKK complex, NEMO mutants associated with immunodeficiency failed to rescue classical NF-κB signaling or reverse the accumulation of NIK. Together, these findings identify a crucial role for classical NF-κB activity in the suppression of basal noncanonical NF-κB signaling. PMID:24497610

Causal Diffusion and the Survival of Charge Fluctuations

NASA Astrophysics Data System (ADS)

Abdel-Aziz, Mohamed; Gavin, Sean

2004-10-01

Diffusion may obliterate fluctuation signals of the QCD phase transition in nuclear collisions at SPS and RHIC energies. We propose a hyperbolic diffusion equation to study the dissipation of net charge fluctuations [1]. This equation is needed in a relativistic context, because the classic parabolic diffusion equation violates causality. We find that causality substantially limits the extent to which diffusion can dissipate these fluctuations. [1] M. Abdel-Aziz and S. Gavin, nucl-th/0404058

Sequence and characterization of cytoplasmic nuclear protein import factor p97

PubMed Central

1995-01-01

Nuclear location sequence-mediated binding of karyophilic proteins to the nuclear pore complexes is one of the earliest steps in nuclear protein import. We previously identified two cytosolic proteins that reconstitute this step in a permeabilized cell assay: the 54/56-kD NLS receptor and p97. A monoclonal antibody to p97 localizes the protein to the cytoplasm and the nuclear envelope. p97 is extracted from nuclear envelopes under the same conditions as the O-glycosylated nucleoporins indicating a tight association with the pore complex. The antibody inhibits import in a permeabilized cell assay but does not affect binding of karyophiles to the nuclear pore complex. Immunodepletion of p97 renders the cytosol inactive for import and identifies at least three other cytosolic proteins that interact with p97. cDNA cloning of p97 shows that it is a unique protein containing 23 cysteine residues. Recombinant p97 binds zinc and a bound metal ion is required for the nuclear envelope binding activity of the protein. PMID:7615630

Old foes, new understandings: nuclear entry of small non-enveloped DNA viruses.

PubMed

Fay, Nikta; Panté, Nelly

2015-06-01

The nuclear import of viral genomes is an important step of the infectious cycle for viruses that replicate in the nucleus of their host cells. Although most viruses use the cellular nuclear import machinery or some components of this machinery, others have developed sophisticated ways to reach the nucleus. Some of these have been known for some time; however, recent studies have changed our understanding of how some non-enveloped DNA viruses access the nucleus. For example, parvoviruses enter the nucleus through small disruptions of the nuclear membranes and nuclear lamina, and adenovirus tugs at the nuclear pore complex, using kinesin-1, to disassemble their capsids and deliver viral proteins and genomes into the nucleus. Here we review recent findings of the nuclear import strategies of three small non-enveloped DNA viruses, including adenovirus, parvovirus, and the polyomavirus simian virus 40. Copyright © 2015 Elsevier B.V. All rights reserved.

Nuclear export signal of PRRSV NSP1α is necessary for type I IFN inhibition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Zhi

2016-12-15

The nonstructural protein 1α (NSP1α) of porcine reproductive and respiratory syndrome virus (PRRSV) is a nucleo-cytoplasmic protein that suppresses the production of type I interferon (IFN). In this study, we investigated the relationship between the subcellular distribution of NSP1α and its inhibition of type I IFN. NSP1α was found to contain the classical nuclear export signal (NES) and NSP1α nuclear export was CRM-1-mediated. NSP1α was shuttling between the nucleus and cytoplasm. We also showed that the nuclear export of NSP1α was necessary for its ability for type I IFN inhibition. NSP1α was also found to interact with CBP, which impliesmore » a possible mechanism of CBP degradation by NSP1α. Taken together, our results describe a novel mechanism of PRRSV NSP1α for type I IFN inhibition and suppression of the host innate antiviral response. - Highlights: •NSP1α contains the NES and NSP1α nuclear export was CRM-1-mediated. •NSP1α was shuttling between the nucleus and cytoplasm continuously. •The nuclear export of NSP1α was necessary for its ability for type I IFN inhibition. •NSP1α interacts with CBP, which implies the mechanism of CBP degradation by NSP1α.« less

Cellular stress stimulates nuclear localization signal (NLS) independent nuclear transport of MRJ

PubMed Central

Andrews, Joel F.; Sykora, Landon J.; Barik-Letostak, Tiasha; Menezes, Mitchell E.; Mitra, Aparna; Barik, Sailen; Shevde, Lalita A.; Samant, Rajeev S.

2012-01-01

HSP40 family member MRJ (DNAJB6) has been in the spot light for its relevance to Huntington’s, Parkinson’s diseases, limb-girdle muscular dystrophy, placental development, neural stem cells, cell cycle and malignancies such as breast cancer and melanoma. This gene has two spliced variants coding for 2 distinct proteins with significant homology. However, MRJ(L) (large variant) is predominantly localized to the nucleus whereas MRJ(S) (small variant) is predominantly cytoplasmic. Interestingly MRJ(S) translocates to the nucleus in response to heat shock. The classical heat shock proteins respond to crises (stress) by increasing the number of molecules, usually by transcriptional up-regulation. Our studies imply that a quick increase in the molar concentration of MRJ in the nuclear compartment is a novel method by which MRJ responds to stress. We found that MRJ(S) shows NLS (nuclear localization signal) independent nuclear localization in response to heat shock and hypoxia. The specificity of this response is realized due to lack of such response by MRJ(S) when challenged by other stressors, such as some cytokines or UV light. Deletion analysis has allowed us to narrow down on a 20 amino acid stretch at the C-terminal region of MRJ(S) as a potential stress sensing region. Functional studies indicated that constitutive nuclear localization of MRJ(S) promoted attributes of malignancy such as proliferation and invasiveness overall indicating distinct phenotypic characteristics of nuclear MRJ(S). PMID:22504047

Is it necessary to raise awareness about technologically enhanced naturally occurring radioactive materials?

PubMed

Michalik, Bogusław

2009-10-01

Since radiation risks are usually considered to be related to nuclear energy, the majority of research on radiation protection has focused on artificial radionuclides in radioactive wastes, spent nuclear fuel or global fallout caused by A-bomb tests and nuclear power plant failures. Far less attention has been paid to the radiation risk caused by exposure to ionizing radiation originating from natural radioactivity enhanced due to human activity, despite the fact that technologically enhanced naturally occurring radioactive materials are common in many branches of the non-nuclear industry. They differ significantly from "classical" nuclear materials and usually look like other industrial waste. The derived radiation risk is usually associated with risk caused by other pollutants and can not be controlled by applying rules designed for pure radioactive waste. Existing data have pointed out a strong need to take into account the non-nuclear industry where materials containing enhanced natural radioactivity occur as a special case of radiation risk and enclose them in the frame of the formal control. But up to now there are no reasonable and clear regulations in this matter. As a result, the non-nuclear industries of concern are not aware of problems connected with natural radioactivity or they would expect negative consequences in the case of implementing radiation protection measures. The modification of widely comprehended environmental legislation with requirements taken from radiation protection seems to be the first step to solve this problem and raise awareness about enhanced natural radioactivity for all stakeholders of concern.

Nuclear Science Outreach in the World Year of Physics

NASA Astrophysics Data System (ADS)

McMahan, Margaret

2006-04-01

The ability of scientists to articulate the importance and value of their research has become increasingly important in the present climate of declining budgets, and this is most critical in the field of nuclear science ,where researchers must fight an uphill battle against negative public perception. Yet nuclear science encompasses important technical and societal issues that should be of primary interest to informed citizens, and the need for scientists trained in nuclear techniques are important for many applications in nuclear medicine, national security and future energy sources. The NSAC Education Subcommittee Report [1] identified the need for a nationally coordinated effort in nuclear science outreach, naming as its first recommendation that `the highest priority for new investment in education be the creation by the DOE and NSF of a Center for Nuclear Science Outreach'. This talk will review the present status of public outreach in nuclear science and highlight some specific efforts that have taken place during the World Year of Physics. [1] Education in Nuclear Science: A Status Report and Recommendations for the Beginning of the 21^st Century, A Report of the DOE/NSF Nuclear Science Advisory Committee Subcommittee on Education, November 2004, http://www.sc.doe.gov/henp/np/nsac/docs/NSACCReducationreportfinal.pdf.

Emerging Connections: Quantum & Classical Optics Incubator Program Book

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lesky, Marcia

The Emerging Connections: Quantum & Classical Optics Incubator was a scientific meeting held in Washington, DC on 6-8 November 2016. This Incubator provided unique and focused experiences and valuable opportunities to discuss advances, challenges and opportunities regarding this important area of research. Quantum optics and classical optics have coexisted for nearly a century as two distinct, but consistent descriptions of light in their respective domains. Recently, a number of detailed examinations of the structure of classical light beams have revealed that effects widely thought to be solely quantum in origin also have a place in classical optics. These new quantum-classicalmore » connections are informing classical optics in meaningful ways specifically by expanding understanding of optical coherence. Simultaneously, relationships discovered with classical light beams now also serve as a vehicle to illuminate concepts that no longer solely belong to the quantum realm. Interference, polarization, coherence, complementarity and entanglement are a partial list of elementary notions that now appear to belong to both quantum and classical optics. The goal of this meeting was to bring emerging quantum-classical links into wider view and to indicate directions in which forthcoming and future work would promote discussion and lead to a more unified understanding of optics.« less

The nuclear import of ribosomal proteins is regulated by mTOR

PubMed Central

Kazyken, Dubek; Kaz, Yelimbek; Kiyan, Vladimir; Zhylkibayev, Assylbek A.; Chen, Chien-Hung; Agarwal, Nitin K.; Sarbassov, Dos D.

2014-01-01

Mechanistic target of rapamycin (mTOR) is a central component of the essential signaling pathway that regulates cell growth and proliferation by controlling anabolic processes in cells. mTOR exists in two distinct mTOR complexes known as mTORC1 and mTORC2 that reside mostly in cytoplasm. In our study, the biochemical characterization of mTOR led to discovery of its novel localization on nuclear envelope where it associates with a critical regulator of nuclear import Ran Binding Protein 2 (RanBP2). We show that association of mTOR with RanBP2 is dependent on the mTOR kinase activity that regulates the nuclear import of ribosomal proteins. The mTOR kinase inhibitors within thirty minutes caused a substantial decrease of ribosomal proteins in the nuclear but not cytoplasmic fraction. Detection of a nuclear accumulation of the GFP-tagged ribosomal protein rpL7a also indicated its dependence on the mTOR kinase activity. The nuclear abundance of ribosomal proteins was not affected by inhibition of mTOR Complex 1 (mTORC1) by rapamycin or deficiency of mTORC2, suggesting a distinctive role of the nuclear envelope mTOR complex in the nuclear import. Thus, we identified that mTOR in association with RanBP2 mediates the active nuclear import of ribosomal proteins. PMID:25294810

Montaigne's Uses of Classical Learning.

ERIC Educational Resources Information Center

Hall, Michael L.

1997-01-01

M. de Montaigne's essay "On the Education of Children" (1580) demonstrates the importance of examining classical authors to test understanding and develop judgment. Montaigne's method provides a way to study cultural heritage and to use the past to examine current issues. Implications for teaching today are discussed. (SLD)

Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding

PubMed Central

Vuković, Lidija D.; Jevtić, Predrag; Zhang, Zhaojie; Stohr, Bradley A.; Levy, Daniel L.

2016-01-01

ABSTRACT Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker. PMID:26823604

A multi-state trajectory method for non-adiabatic dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Guohua, E-mail: taogh@pkusz.edu.cn

2016-03-07

A multi-state trajectory approach is proposed to describe nuclear-electron coupled dynamics in nonadiabatic simulations. In this approach, each electronic state is associated with an individual trajectory, among which electronic transition occurs. The set of these individual trajectories constitutes a multi-state trajectory, and nuclear dynamics is described by one of these individual trajectories as the system is on the corresponding state. The total nuclear-electron coupled dynamics is obtained from the ensemble average of the multi-state trajectories. A variety of benchmark systems such as the spin-boson system have been tested and the results generated using the quasi-classical version of the method showmore » reasonably good agreement with the exact quantum calculations. Featured in a clear multi-state picture, high efficiency, and excellent numerical stability, the proposed method may have advantages in being implemented to realistic complex molecular systems, and it could be straightforwardly applied to general nonadiabatic dynamics involving multiple states.« less

Theory of long-lived nuclear spin states in methyl groups and quantum-rotor induced polarisation.

PubMed

Dumez, Jean-Nicolas; Håkansson, Pär; Mamone, Salvatore; Meier, Benno; Stevanato, Gabriele; Hill-Cousins, Joseph T; Roy, Soumya Singha; Brown, Richard C D; Pileio, Giuseppe; Levitt, Malcolm H

2015-01-28

Long-lived nuclear spin states have a relaxation time much longer than the longitudinal relaxation time T1. Long-lived states extend significantly the time scales that may be probed with magnetic resonance, with possible applications to transport and binding studies, and to hyperpolarised imaging. Rapidly rotating methyl groups in solution may support a long-lived state, consisting of a population imbalance between states of different spin exchange symmetries. Here, we expand the formalism for describing the behaviour of long-lived nuclear spin states in methyl groups, with special attention to the hyperpolarisation effects observed in (13)CH3 groups upon rapidly converting a material with low-barrier methyl rotation from the cryogenic solid state to a room-temperature solution [M. Icker and S. Berger, J. Magn. Reson. 219, 1 (2012)]. We analyse the relaxation properties of methyl long-lived states using semi-classical relaxation theory. Numerical simulations are supplemented with a spherical-tensor analysis, which captures the essential properties of methyl long-lived states.

NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.

PubMed

Güttler, Thomas; Madl, Tobias; Neumann, Piotr; Deichsel, Danilo; Corsini, Lorenzo; Monecke, Thomas; Ficner, Ralf; Sattler, Michael; Görlich, Dirk

2010-11-01

Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP-CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets. The different Φ spacings are compensated for by different conformations of the bound NESs: in the case of PKI, an α-helical conformation, and in the case of Rev, an extended conformation with a critical proline docking into a Φ pocket. NMR analyses of CRM1-bound and CRM1-free PKI NES suggest that CRM1 selects NES conformers that pre-exist in solution. Our data lead to a new structure-based NES consensus, and explain why NESs differ in their affinities for CRM1 and why supraphysiological NESs bind the exportin so tightly.

Quantum shielding effects on the Gamow penetration factor for nuclear fusion reaction in quantum plasmas

NASA Astrophysics Data System (ADS)

Lee, Myoung-Jae; Jung, Young-Dae

2017-01-01

The quantum shielding effects on the nuclear fusion reaction process are investigated in quantum plasmas. The closed expression of the classical turning point for the Gamow penetration factor in quantum plasmas is obtained by the Lambert W-function. The closed expressions of the Gamow penetration factor and the cross section for the nuclear fusion reaction in quantum plasmas are obtained as functions of the plasmon energy and the relative kinetic energy by using the effective interaction potential with the WKB analysis. It is shown that the influence of quantum screening suppresses the Sommerfeld reaction factor. It is also shown that the Gamow penetration factor increases with an increase of the plasmon energy. It is also shown that the quantum shielding effect enhances the deuterium formation by the proton-proton reaction in quantum plasmas. In addition, it is found that the energy dependences on the reaction cross section and the Gamow penetration factor are more significant in high plasmon-energy domains.

John Wheeler, 1933 - 1959: Particles and Weapons

NASA Astrophysics Data System (ADS)

Ford, Kenneth

2009-05-01

During the early part of his career, John Archibald Wheeler made an astonishing number of contributions to nuclear and particle physics, as well as to classical electrodynamics, often in collaboration with another physicist. He was also a major contributor to the Manhattan Project (in Chicago and Hanford rather than Los Alamos), and, following World War II, became an influential scientific cold warrior. His early achievements in physics include the calculated scattering of light by light (with Gregory Breit), the prediction of nuclear rotational states (with Edward Teller), the theory of fission (with Niels Bohr), action-at-a-distance electrodynamics (with Richard Feynman), the theory of positronium, the universal weak interaction (with Jayme Tiomno), and the proposed use of the muon as a nuclear probe particle. He gained modest fame as the person who identified xenon 135 as a reactor poison. His Project Matterhorn contributed significantly to the design of the H bomb, and his Project 137, which he had hoped would flower into a major defense lab, served as the precursor to the Jason group.

Identification of FBXO25-interacting Proteins Using an Integrated Proteomics Approach

PubMed Central

Teixeira, Felipe R.; Yokoo, Sami; Gartner, Carlos G.; Manfiolli, Adriana O.; Baqui, Munira M. A.; Assmann, Eliana M.; Maragno, Ana Leticia G. C.; Yu, Huijun; de Lanerolle, Primal; Kobarg, Jörg; Gygi, Steven P.; Gomes, Marcelo D.

2011-01-01

FBXO25 is one of 68 human F-box proteins that serve as specificity factors for a family of ubiquitin ligases composed of Skp1, Rbx1, Cullin1 and F-box protein (SCF1) that are involved in targeting proteins for destruction across the ubiquitin proteasome system. We recently reported that the FBXO25 protein accumulates in novel subnuclear structures named FBXO25-associated nuclear domains (FANDs). Combining two-step affinity purification followed by mass spectrometry with a classical two-hybrid screen, we identified 132 novel potential FBXO25 interacting partners. One of the identified proteins, β-actin, physically interacts through its N-terminus with FBXO25 and is enriched in the FBXO25 nuclear compartments. Inhibitors of actin polymerization promote a significant disruption of FANDs, indicating that they are compartments influenced by the organizational state of actin in the nucleus. Furthermore, FBXO25 antibodies interfered with RNA polymerase II transcription in vitro. Our results open new perspectives for the understanding of this novel compartment and its nuclear functions. PMID:20473970

A Distinct and Parallel Pathway for the Nuclear Import of an mRNA-binding Protein

PubMed Central

Pemberton, Lucy F.; Rosenblum, Jonathan S.; Blobel, Günter

1997-01-01

Three independent pathways of nuclear import have so far been identified in yeast, each mediated by cognate nuclear transport factors, or karyopherins. Here we have characterized a new pathway to the nucleus, mediated by Mtr10p, a protein first identified in a screen for strains defective in polyadenylated RNA export. Mtr10p is shown to be responsible for the nuclear import of the shuttling mRNA-binding protein Npl3p. A complex of Mtr10p and Npl3p was detected in cytosol, and deletion of Mtr10p was shown to lead to the mislocalization of nuclear Npl3p to the cytoplasm, correlating with a block in import. Mtr10p bound peptide repeat-containing nucleoporins and Ran, suggesting that this import pathway involves a docking step at the nuclear pore complex and is Ran dependent. This pathway of Npl3p import is distinct and does not appear to overlap with another known import pathway for an mRNA-binding protein. Thus, at least two parallel pathways function in the import of mRNA-binding proteins, suggesting the need for the coordination of these pathways. PMID:9412460

JSH-23 prevents depressive-like behaviors in mice subjected to chronic mild stress: Effects on inflammation and antioxidant defense in the hippocampus.

PubMed

Wang, Qi; Dong, Xiaomei; Li, Nannan; Wang, Yan; Guan, Xiaofeng; Lin, Yiwei; Kang, Jiguang; Zhang, Xia; Zhang, Yuchen; Li, Xiaobai; Xu, Tianchao

2018-06-01

Nuclear factor-kappa B (NF-κB), which is reported to play an important role in the pathogenesis of depression, also has a central role in the genesis and progression of inflammation. Here, we have targeted the nuclear translocation of NF-κB using 4-methyl-N1-(3-phenyl-propyl)-benzene-1,2-diamine (JSH-23) to elucidate its role in depression. We investigated the antidepressant-like effects of JSH-23 in the chronic mild stress (CMS) mouse model, which is a valid, reasonably reliable, and useful model of depression. The antidepressant-like effects of JSH-23 were evaluated using the sucrose preference test (SPT) and the forced swimming test (FST). We also assessed inflammatory markers [interleukin (IL)-6 and tumor necrosis factor-α (TNF-α)] and components of antioxidant defense [superoxide dismutase (SOD) and nuclear factor erythroid-2-related factor 2 (Nrf 2)] in the hippocampus. Fluoxetine, a classical antidepressant, was used in this study as a positive control. Administration of JSH-23 significantly prevented the decreased sucrose preference in the SPT and prevented the increased immobility time in the FST caused by CMS, but had no effect on locomotor activity. Expression of NF-κB p65 protein in the hippocampus was decreased, and elevated levels of IL-6 and TNF-α were reduced, after JSH-23 administration. In addition to its anti-inflammatory effect, JSH-23 treatment increased the expression of SOD and Nrf 2 in the hippocampus, suggesting that it strengthens antioxidant defense. The current study demonstrated that inhibiting the NF-κB signaling cascade using JSH-23 prevented depressive-like behaviors by decreasing inflammation and improving antioxidant defense in the hippocampus. We concluded that NF-κB activation plays an important role in the pathophysiology of depression and that targeting NF-κB signaling may provide a novel and effective therapy for depression. Additional preclinical studies and clinical trials are, however, needed to further elucidate the effects of this therapeutic strategy. Copyright © 2018 Elsevier Inc. All rights reserved.

A Crystal Structure of Classical Swine Fever Virus NS5B Reveals a Novel N-terminal Domain.

PubMed

Li, Weiwei; Wu, Baixing; Soca, Wibowo Adian; An, Lei

2018-05-02

Classical swine fever virus (CSFV) is the ringleader of Classical swine fever (CSF). The non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp) that is a key enzyme initiating viral RNA replication by a de novo mechanism. It is also an attractive target for the development of anti-CSFV drugs. To gain a better understanding on the mechanism of CSFV RNA synthesis, here we solved the first crystal structure of CSFV-NS5B. Our studies show that the CSFV-NS5B RdRp contains characteristic fingers, palm domain and thumb domain as well as a unique N-terminal domain (NTD) that had never been observed. Mutagenesis studies on NS5B validated the importance of NTD in the catalytic activity of this novel RNA-dependent RNA polymerase. Moreover, our results shed light on the understanding of CSFV infection. IMPORTANCE Pigs are important domestic animal. However, a highly contagious viral disease named Classical swine fever (CSF) causes devastating economic losses. Classical swine fever virus (CSFV) is the primary culprit of CSF, which is a positive-sense single-stranded RNA virus belonging to the Pestivirus genus, Flaviviridae family. Genome replication of CSFV depends on RNA-dependent RNA polymerase known as NS5B. However, the structure of CSFV-NS5B has never been reported, and the mechanism of CSFV replication is poorly understood. Here, we solved the first crystal structure of CSFV-NS5B, analyzed the function of characteristic fingers, palm, and thumb domains. Additionally, our structure also revealed the presence of a novel N-terminal domain (NTD). Biochemical studies demonstrated that the NTD of CSFV-NS5B is very important for RNA-dependent RNA polymerase (RdRp) activity. Collectively, our studies provide a structural basis for future rational design of anti-CSFV drugs which is critically important as no effective anti-CSFV drugs have been developed. Copyright © 2018 American Society for Microbiology.

Evidence for a Quantum-to-Classical Transition in a Pair of Coupled Quantum Rotors

NASA Astrophysics Data System (ADS)

Gadway, Bryce; Reeves, Jeremy; Krinner, Ludwig; Schneble, Dominik

2013-05-01

The understanding of how classical dynamics can emerge in closed quantum systems is a problem of fundamental importance. Remarkably, while classical behavior usually arises from coupling to thermal fluctuations or random spectral noise, it may also be an innate property of certain isolated, periodically driven quantum systems. Here, we experimentally realize the simplest such system, consisting of two coupled, kicked quantum rotors, by subjecting a coherent atomic matter wave to two periodically pulsed, incommensurate optical lattices. Momentum transport in this system is found to be radically different from that in a single kicked rotor, with a breakdown of dynamical localization and the emergence of classical diffusion. Our observation, which confirms a long-standing prediction for many-dimensional quantum-chaotic systems, sheds new light on the quantum-classical correspondence.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehmood, Rashid; Yasuhara, Noriko; Oe, Souichi

The transition from undifferentiated pluripotent cells to terminally differentiated neurons is coordinated by a repertoire of transcription factors. NeuroD1 is a type II basic helix loop helix (bHLH) transcription factor that plays critical roles in neuronal differentiation and maintenance in the central nervous system. Its dimerization with E47, a type I bHLH transcription factor, leads to the transcriptional regulation of target genes. Mounting evidence suggests that regulating the localization of transcription factors contributes to the regulation of their activity during development as defects in their localization underlie a variety of developmental disorders. In this study, we attempted to understand themore » nuclear import mannerisms of NeuroD1 and E47. We found that the nuclear import of NeuroD1 and E47 is energy-dependent and involves the Ran-mediated pathway. Herein, we demonstrate that NeuroD1 and E47 can dimerize inside the cytoplasm before their nuclear import. Moreover, this dimerization promotes nuclear import as the nuclear accumulation of NeuroD1 was enhanced in the presence of E47 in an in vitro nuclear import assay, and NLS-deficient NeuroD1 was successfully imported into the nucleus upon E47 overexpression. NeuroD1 also had a similar effect on the nuclear accumulation of NLS-deficient E47. These findings suggest a novel role for dimerization that may promote, at least partially, the nuclear import of transcription factors allowing them to function efficiently in the nucleus.« less

Myosin-1C uses a novel phosphoinositide-dependent pathway for nuclear localization.

PubMed

Nevzorov, Ilja; Sidorenko, Ekaterina; Wang, Weihuan; Zhao, Hongxia; Vartiainen, Maria K

2018-02-01

Accurate control of macromolecule transport between nucleus and cytoplasm underlines several essential biological processes, including gene expression. According to the canonical model, nuclear import of soluble proteins is based on nuclear localization signals and transport factors. We challenge this view by showing that nuclear localization of the actin-dependent motor protein Myosin-1C (Myo1C) resembles the diffusion-retention mechanism utilized by inner nuclear membrane proteins. We show that Myo1C constantly shuttles in and out of the nucleus and that its nuclear localization does not require soluble factors, but is dependent on phosphoinositide binding. Nuclear import of Myo1C is preceded by its interaction with the endoplasmic reticulum, and phosphoinositide binding is specifically required for nuclear import, but not nuclear retention, of Myo1C. Our results therefore demonstrate, for the first time, that membrane association and binding to nuclear partners is sufficient to drive nuclear localization of also soluble proteins, opening new perspectives to evolution of cellular protein sorting mechanisms. © 2018 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

One-electron pseudo-potential investigation of NO(X2Π)-Arn clusters (n = 1,2,3,4)

NASA Astrophysics Data System (ADS)

Hammami, H.; Ben Mohamed, F. E.; Mohamed, D.; Ben El Hadj Rhouma, M.; Al Mogren, M. M.; Hochlaf, M.

2017-10-01

In this work, we investigate the minimal energy and low-lying isomers of the ground state of NOArn clusters using a hybrid pseudo-potential model, where a single electron quantum description is combined with the classical argon-argon pair potential and an expansion in terms of the Legendre polynomials. In such model, we use two centres of polarisation for NO+, where we considered for each nuclear configuration an analytic dipole polarisation for N+ and O+. The reliability of our model is checked by comparison of the NO(X2Π)-Ar potential energy surface with that deduced using the multireference configuration interaction (MRCI+Q) approach. The results of this formalism agree quite well with the MRCI ones over a wide range of nuclear arrangements.

Molecular Dynamics Simulation of Fission Fragment Damage in Nuclear Fuel and Surrogate Material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devanathan, Ram

ABSTRACT We have performed classical molecular dynamics simulations of swift heavy ion damage, typical of fission fragments, in nuclear fuel (UO 2) for energy deposition per unit length of 3.9 keV/nm. We did not observe amorphization. The damage mainly consisted of isolated point defects. Only about 1% of the displacements occur on the uranium sublattice. Oxygen Frenkel pairs are an order of magnitude more numerous than uranium Frenkel pairs in the primary damage state. In contrast, previous results show that the ratio of Frenkel pairs on the two sublattices is close to the stoichiometric ratio in ceria. These differences inmore » the primary damage state may lead to differences in radiation response of UO 2and CeO 2.« less

The Geometry of the Arms Race. Applications of Elementary Game Theory to International Relations. Modules and Monographs in Undergraduate Mathematics and Its Applications Project. UMAP Unit 311.

ERIC Educational Resources Information Center

Brams, Steven J.; And Others

This unit views applications of elementary game theory to international relations. It is noted that of all the significant world problems, the nuclear arms race has proved one of the most intractable. The main concern of the module is to investigate a possible solution to the arms race, based on extending the classic two-person game of Prisoner's…

Augmented Ehrenfest dynamics yields a rate for surface hopping

NASA Astrophysics Data System (ADS)

Subotnik, Joseph E.

2010-04-01

We present a new algorithm for mixed quantum-classical dynamics that helps bridge the gap between mean-field (Ehrenfest) and surface-hopping dynamics by defining a natural rate of decoherence. In order to derive this decoherence result, we have expanded the number of independent variables in the usual Ehrenfest routine so that mixed quantum-classical derivatives are now propagated in time alongside the usual Ehrenfest variables. Having done so, we compute a unique rate of decoherence using two independent approaches: (i) by comparing the equations of motion for the joint nuclear-electronic probability density in phase space according to Ehrenfest dynamics versus partial Wigner transform dynamics and (ii) by introducing a frozen Gaussian interpretation of Ehrenfest dynamics which allows nuclear wave packets to separate. The first consequence of this work is a means to rigorously check the accuracy of standard Ehrenfest dynamics. Second, this paper suggests a nonadiabatic dynamics algorithm, whereby the nuclei are propagated on the mean-field (Ehrenfest) potential energy surface and undergo stochastic decoherence events. Our work resembles the surface-hopping algorithm of Schwartz and co-workers [J. Chem. Phys. 123, 234106 (2005)]—only now without any adjustable parameters. For the case of two electronic states, we present numerical results on the so-called "Tully problems" and emphasize that future numerical benchmarking is still needed. Future work will also treat the problem of three or more electronic states.

Graphical Methods for Quantifying Macromolecules through Bright Field Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Hang; DeFilippis, Rosa Anna; Tlsty, Thea D.

Bright ?eld imaging of biological samples stained with antibodies and/or special stains provides a rapid protocol for visualizing various macromolecules. However, this method of sample staining and imaging is rarely employed for direct quantitative analysis due to variations in sample fixations, ambiguities introduced by color composition, and the limited dynamic range of imaging instruments. We demonstrate that, through the decomposition of color signals, staining can be scored on a cell-by-cell basis. We have applied our method to Flbroblasts grown from histologically normal breast tissue biopsies obtained from two distinct populations. Initially, nuclear regions are segmented through conversion of color imagesmore » into gray scale, and detection of dark elliptic features. Subsequently, the strength of staining is quanti?ed by a color decomposition model that is optimized by a graph cut algorithm. In rare cases where nuclear signal is significantly altered as a result of samplepreparation, nuclear segmentation can be validated and corrected. Finally, segmented stained patterns are associated with each nuclear region following region-based tessellation. Compared to classical non-negative matrix factorization, proposed method (i) improves color decomposition, (ii) has a better noise immunity, (iii) is more invariant to initial conditions, and (iv) has a superior computing performance« less

Astromaterial Science

NASA Astrophysics Data System (ADS)

Caplan, Matthew E.

Recent work has used large scale molecular dynamics simulations to study the structures and phases of matter in the crusts of neutron stars, with an emphasis on applying techniques in material science to the study of astronomical objects. In the outer crust of an accreting neutron star, a mixture of heavy elements forms following an X-ray burst, which is buried and freezes. We will discuss the phase separation of this mixture, and the composition of the crust that forms. Additionally, calculations of the properties of the crust, such as diffusion coefficients and static structure factors, may be used to interpret observations. Deeper in the neutron star crust, at the base of the inner crust, nuclei are compressed until they touch and form structures which have come to be called 'nuclear pasta.' We study the phases of nuclear pasta with classical molecular dynamics simulations, and discuss how simulations at low density may be relevant to nucleosynthesis in neutron star mergers. Additionally, we discuss the structure factor of nuclear pasta and its impact on the properties of the crust, and use this to interpret observations of crust cooling in low mass X-ray binaries. Lastly, we discuss a correspondence between the structure of nuclear pasta and biophysics.

{Nb288O768(OH)48(CO3)12}: A Macromolecular Polyoxometalate with Niobium Atoms Close to 300.

PubMed

Wu, Yan-Lan; Li, Xin-Xiong; Qi, Yan-Jie; Yu, Hao; Jin, Lu; Zheng, Shou-Tian

2018-05-29

A protein-sized (ca. 4.2 ᵡ 4.2 ᵡ 3.6 nm3) non-biologically derived molecule {Nb288O768(OH)48(CO3)12} (Nb288) containing up to 288 niobium atoms has been obtained, which is by far the largest and the highest nuclearity polyoxoniobate (PONb). Particularly, in terms of metal nuclearity number, Nb288 is the second largest cluster so far reported in classic polyoxometalate chemistry (V, Mo, W, Nb, and Ta). Nb288 can be described as a giant windmill-like cluster aggregate of six brand-new, nanoscale high-nuclearity PONb units {Nb47O128(OH)6(CO3)2} (Nb47) joined together by six additional Nb ions. Interestingly, the in situ generated 47-nuclearity Nb47 units can be isolated and bridged by copper complexes to form an inorganic-organic hybrid three-dimensional PONb framework, which exhibits effective catalytic activity for hydrolyzing nerve agent simulant of dimethyl methylphosphonate. The unique Nb47 cluster also provides a new type of topology to very limited family of Nb-O clusters. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding.

PubMed

Vuković, Lidija D; Jevtić, Predrag; Zhang, Zhaojie; Stohr, Bradley A; Levy, Daniel L

2016-03-15

Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker. © 2016. Published by The Company of Biologists Ltd.

Genomic analysis of NF-κB signaling pathway reveals its complexity in Crassostrea gigas.

PubMed

Yu, Mingjia; Chen, Jianming; Bao, Yongbo; Li, Jun

2018-01-01

NF-κB signaling pathway is an evolutionarily conserved pathway that plays highly important roles in several developmental, cellular and immune response processes. With the recent release of the draft Pacific oyster (Crassostra gigas) genome sequence, we have sought to identify the various components of the NF-κB signaling pathway in these mollusks and investigate their gene structure. We further constructed phylogenetic trees to establish the evolutionary relationship of the oyster proteins with their homologues in vertebrates and invertebrates using BLASTX and neighbor-joining method. We report the presence of two classic NF-κB/Rel homologues in the pacific oyster namely Cgp100 and CgRel, which possess characteristic RHD domain and a consensus nuclear localization signal, similar to mammalian homologues and an additional CgRel-like protein, unique to C. gigas. Further, in addition to two classical IκB homologues, CgIκB1 and CgIκB2, we have identified three atypical IκB family members namely CgIκB3, CgIκB4 and CgBCL3 which lack the IκB degradation motif and consist of only one exon that might have arisen by retrotransposition from CgIκB1. Finally, we report the presence of three IKKs and one NEMO genes in oyster genome, named CgIKK1, CgIKK2, CgIKK3 and CgNEMO, respectively. While CgIKK1 and CgIKK3 domain structure is similar to their mammalian homologues, CgIKK2 was found to lack the HLH and NBD domains. Overall, the high conservation of the NF-κB/Rel, IκB and IKK family components in the pacific oyster and their structural similarity to the vertebrate and invertebrate homologues underline the functional importance of this pathway in regulation of critical cellular processes across species. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computational Insights into Materials and Interfaces for Capacitive Energy Storage

DOE PAGES

Zhan, Cheng; Lian, Cheng; Zhang, Yu; ...

2017-04-24

Supercapacitors such as electric double-layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double-layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte-Carlo (MC) methods. In recent years, combining first-principles and classical simulations to investigate the carbon-based EDLCs has shed light on the importance of quantum capacitance in graphene-like 2D systems. More recently, the development of joint density functional theorymore » (JDFT) enables self-consistent electronic-structure calculation for an electrode being solvated by an electrolyte. In contrast with the large amount of theoretical and computational effort on EDLCs, theoretical understanding of pseudocapacitance is very limited. In this review, we first introduce popular modeling methods and then focus on several important aspects of EDLCs including nanoconfinement, quantum capacitance, dielectric screening, and novel 2D electrode design; we also briefly touch upon pseudocapactive mechanism in RuO 2. We summarize and conclude with an outlook for the future of materials simulation and design for capacitive energy storage.« less

Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakada, Ryohei; Hirano, Hidemi; Structural Biology Research Center, Graduate School of Science, Nagoya University

Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is expressed in every EBV-positive tumor and is essential for the maintenance, replication, and transcription of the EBV genome in the nucleus of host cells. EBNA1 is a serine phosphoprotein, and it has been shown that phosphorylation of S385 in the nuclear localization signal (NLS) of EBNA1 increases the binding affinity to the nuclear import adaptor importin-α1 as well as importin-α5, and stimulates nuclear import of EBNA1. To gain insights into how phosphorylation of the EBNA1 NLS regulates nuclear import, we have determined the crystal structures of two peptide complexes of importin-α1: onemore » with S385-phosphorylated EBNA1 NLS peptide, determined at 2.0 Å resolution, and one with non-phosphorylated EBNA1 NLS peptide, determined at 2.2 Å resolution. The structures show that EBNA1 NLS binds to the major and minor NLS-binding sites of importin-α1, and indicate that the binding affinity of the EBNA1 NLS to the minor NLS-binding site could be enhanced by phosphorylation of S385 through electrostatic interaction between the phosphate group of phospho-S385 and K392 of importin-α1 (corresponding to R395 of importin-α5) on armadillo repeat 8. - Highlights: • Nuclear import of EBNA1 can be regulated by phosphorylation of NLS. • Crystal structures of importin-α1 bound to the NLS peptides of EBNA1 are solved. • Structures provide insights into how phosphorylation can regulate nuclear import.« less

Cooling molten salt reactors using "gas-lift"

NASA Astrophysics Data System (ADS)

Zitek, Pavel; Valenta, Vaclav; Klimko, Marek

2014-08-01

This study briefly describes the selection of a type of two-phase flow, suitable for intensifying the natural flow of nuclear reactors with liquid fuel - cooling mixture molten salts and the description of a "Two-phase flow demonstrator" (TFD) used for experimental study of the "gas-lift" system and its influence on the support of natural convection. The measuring device and the application of the TDF device is described. The work serves as a model system for "gas-lift" (replacing the classic pump in the primary circuit) for high temperature MSR planned for hydrogen production. An experimental facility was proposed on the basis of which is currently being built an experimental loop containing the generator, separator bubbles and necessary accessories. This loop will model the removal of gaseous fission products and tritium. The cleaning of the fuel mixture of fluoride salts eliminates problems from Xenon poisoning in classical reactors.

Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions.

PubMed

Delaunay, Rudy; Gatchell, Michael; Rousseau, Patrick; Domaracka, Alicja; Maclot, Sylvain; Wang, Yang; Stockett, Mark H; Chen, Tao; Adoui, Lamri; Alcamí, Manuel; Martín, Fernando; Zettergren, Henning; Cederquist, Henrik; Huber, Bernd A

2015-05-07

The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

THERMODYNAMICS OF FE-CU ALLOYS AS DESCRIBED BY A CLASSIC POTENTIALS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caro, A; Caro, M; Lopasso, E M

2005-04-14

The Fe-Cu system is of relevance to the nuclear industry because of the deleterious consequences of Cu precipitates in the mechanical properties of Fe. Several sets of classical potentials are used in molecular dynamics simulations studies of this system, in particular that proposed by Ludwig et al. (Modelling Simul. Mater. Sci. Eng. 6, 19 (1998)). In this work we extract thermodynamic information from this interatomic potentials. We obtain equilibrium phase diagram and find a reasonable agreement with the experimental phases in the regions of relevance to radiation damage studies. We compare the results with the predicted phase diagram based onmore » other potential, as calculated in previous work. We discuss the disagreements found between the phase diagram calculated here and experimental results, focusing on the pure components and discuss the applicability of these potentials; finally we suggest an approach to improve existing potentials for this system.« less

Effects of tunnelling and asymmetry for system-bath models of electron transfer

NASA Astrophysics Data System (ADS)

Mattiat, Johann; Richardson, Jeremy O.

2018-03-01

We apply the newly derived nonadiabatic golden-rule instanton theory to asymmetric models describing electron-transfer in solution. The models go beyond the usual spin-boson description and have anharmonic free-energy surfaces with different values for the reactant and product reorganization energies. The instanton method gives an excellent description of the behaviour of the rate constant with respect to asymmetry for the whole range studied. We derive a general formula for an asymmetric version of the Marcus theory based on the classical limit of the instanton and find that this gives significant corrections to the standard Marcus theory. A scheme is given to compute this rate based only on equilibrium simulations. We also compare the rate constants obtained by the instanton method with its classical limit to study the effect of tunnelling and other quantum nuclear effects. These quantum effects can increase the rate constant by orders of magnitude.

High-density amorphous ice: A path-integral simulation

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2012-09-01

Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.

Transferable Pseudo-Classical Electrons for Aufbau of Atomic Ions

PubMed Central

Ekesan, Solen; Kale, Seyit; Herzfeld, Judith

2014-01-01

Generalizing the LEWIS reactive force field from electron pairs to single electrons, we present LEWIS• in which explicit valence electrons interact with each other and with nuclear cores via pairwise interactions. The valence electrons are independently mobile particles, following classical equations of motion according to potentials modified from Coulombic as required to capture quantum characteristics. As proof of principle, the aufbau of atomic ions is described for diverse main group elements from the first three rows of the periodic table, using a single potential for interactions between electrons of like spin and another for electrons of unlike spin. The electrons of each spin are found to distribute themselves in a fashion akin to the major lobes of the hybrid atomic orbitals, suggesting a pointillist description of the electron density. The broader validity of the LEWIS• force field is illustrated by predicting the vibrational frequencies of diatomic and triatomic hydrogen species. PMID:24752384

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulationsmore » as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water. Published by AIP Publishing.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

DOE PAGES

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; ...

2016-11-17

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

[Discussion on six errors of formulas corresponding to syndromes in using the classic formulas].

PubMed

Bao, Yan-ju; Hua, Bao-jin

2012-12-01

The theory of formulas corresponding to syndromes is one of the characteristics of Treatise on Cold Damage and Miscellaneous Diseases (Shanghan Zabing Lun) and one of the main principles in applying classic prescriptions. It is important to take effect by following the principle of formulas corresponding to syndromes. However, some medical practitioners always feel that the actual clinical effect is far less than expected. Six errors in the use of classic prescriptions as well as the theory of formulas corresponding to syndromes are the most important causes to be considered, i.e. paying attention only to the local syndromes while neglecting the whole, paying attention only to formulas corresponding to syndromes while neglecting the pathogenesis, paying attention only to syndromes while neglecting the pulse diagnosis, paying attention only to unilateral prescription but neglecting the combined prescriptions, paying attention only to classic prescriptions while neglecting the modern formulas, and paying attention only to the formulas but neglecting the drug dosage. Therefore, not only the patients' clinical syndromes, but also the combination of main syndrome and pathogenesis simultaneously is necessary in the clinical applications of classic prescriptions and the theory of prescription corresponding to syndrome. In addition, comprehensive syndrome differentiation, modern formulas, current prescriptions, combined prescriptions, and drug dosage all contribute to avoid clinical errors and improve clinical effects.

Equations of state for real gases on the nuclear scale

NASA Astrophysics Data System (ADS)

Vovchenko, Volodymyr

2017-07-01

The formalism to augment the classical models of the equation of state for real gases with quantum statistical effects is presented. It allows an arbitrary excluded volume procedure to model repulsive interactions, and an arbitrary density-dependent mean field to model attractive interactions. Variations on the excluded volume mechanism include van der Waals (VDW) and Carnahan-Starling models, while the mean fields are based on VDW, Redlich-Kwong-Soave, Peng-Robinson, and Clausius equations of state. The VDW parameters of the nucleon-nucleon interaction are fitted in each model to the properties of the ground state of nuclear matter, and the following range of values is obtained: a =330 -430 MeV fm3 and b =2.5 -4.4 fm3 . In the context of the excluded volume approach, the fits to the nuclear ground state disfavor the values of the effective hard-core radius of a nucleon significantly smaller than 0.5 fm , at least for the nuclear matter region of the phase diagram. Modifications to the standard VDW repulsion and attraction terms allow one to improve significantly the value of the nuclear incompressibility factor K0, bringing it closer to empirical estimates. The generalization to include the baryon-baryon interactions into the hadron resonance gas model is performed. The behavior of the baryon-related lattice QCD observables at zero chemical potential is shown to be strongly correlated to the nuclear matter properties: an improved description of the nuclear incompressibility also yields an improved description of the lattice data at μ =0 .

The Pathogenesis of Obesity-Associated Adipose Tissue Inflammation.

PubMed

Engin, Atilla

2017-01-01

Obesity is characterized by a state of chronic, low-grade inflammation. However, excessive fatty acid release may worsen adipose tissue inflammation and contributes to insulin resistance. In this case, several novel and highly active molecules are released abundantly by adipocytes like leptin, resistin, adiponectin or visfatin, as well as some more classical cytokines. Most likely cytokines that are released by inflammatory cells infiltrating obese adipose tissue are such as tumor necrosis factor-alpha (TNF-alpha), interleukin 6 (IL-6), monocyte chemoattractant protein 1 (MCP-1) (CCL-2) and IL-1. All of those molecules may act on immune cells leading to local and generalized inflammation. In this process, toll-like receptor 4 (TLR4)/phosphatidylinositol-3'-kinase (PI3K)/Protein kinase B (Akt) signaling pathway, the unfolded protein response (UPR) due to endoplasmic reticulum (ER) stress through hyperactivation of c-Jun N-terminal Kinase (JNK) -Activator Protein 1 (AP1) and inhibitor of nuclear factor kappa-B kinase beta (IKKbeta)-nuclear factor kappa B (NF-kappaB) pathways play an important role, and may also affect vascular endothelial function by modulating vascular nitric oxide and superoxide release. Additionally, systemic oxidative stress, macrophage recruitment, increase in the expression of NOD-like receptor (NLR) family protein (NLRP3) inflammasone and adipocyte death are predominant determinants in the pathogenesis of obesity-associated adipose tissue inflammation. In this chapter potential involvement of these factors that contribute to the adverse effects of obesity are reviewed.

Opto-acoustic microscopy reveals adhesion mechanics of single cells

NASA Astrophysics Data System (ADS)

Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

2018-01-01

Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Zc, as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZc reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, Km, that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, Sr/St. We show that Km can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while Sr/St is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

Opto-acoustic microscopy reveals adhesion mechanics of single cells.

PubMed

Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

2018-01-01

Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Z c , as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZ c reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, K m , that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, S r /S t . We show that K m can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while S r /S t is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta).

PubMed

Bendif, El Mahdi; Probert, Ian; Carmichael, Margaux; Romac, Sarah; Hagino, Kyoko; de Vargas, Colomban

2014-02-01

Emiliania huxleyi and Gephyrocapsa oceanica are abundant coccolithophore morpho-species that play key roles in ocean carbon cycling due to their importance as both primary producers and cal-cifiers. Global change processes such as ocean acidification impact these key calcifying species. The physiology of E. huxleyi, a developing model species, has been widely studied, but its genetic delineation from G. oceanica remains unclear due to a lack of resolution in classical genetic markers. Using nuclear (18S rDNA and 28S rDNA), mitochondrial (cox1, cox2, cox3, rpl16, and dam), and plastidial (16S rDNA, rbcL, tufA, and petA) DNA markers from 99 E. huxleyi and 44 G. oceanica strains, we conducted a multigene/multistrain survey to compare the suitability of different markers for resolving phylogenetic patterns within and between these two morpho-species. The nuclear genes tested did not provide sufficient resolution to discriminate between the two morpho-species that diverged only 291Kya. Typical patterns of incomplete lineage sorting were generated in phylogenetic analyses using plastidial genes. In contrast, full morpho-species delineation was achieved with mitochondrial markers and common intra-morpho-species phylogenetic patterns were observed despite differing rates of DNA substitution. Mitochondrial genes are thus promising barcodes for distinguishing these coccolithophore morpho-species, in particular in the context of environmental monitoring. © 2013 Phycological Society of America.

A Role for Myosin Va in Human Cytomegalovirus Nuclear Egress.

PubMed

Wilkie, Adrian R; Sharma, Mayuri; Pesola, Jean M; Ericsson, Maria; Fernandez, Rosio; Coen, Donald M

2018-03-15

Herpesviruses replicate and package their genomes into capsids in replication compartments within the nuclear interior. Capsids then move to the inner nuclear membrane for envelopment and release into the cytoplasm in a process called nuclear egress. We previously found that nuclear F-actin is induced upon infection with the betaherpesvirus human cytomegalovirus (HCMV) and is important for nuclear egress and capsid localization away from replication compartment-like inclusions toward the nuclear rim. Despite these and related findings, it has not been shown that any specific motor protein is involved in herpesvirus nuclear egress. In this study, we have investigated whether the host motor protein, myosin Va, could be fulfilling this role. Using immunofluorescence microscopy and coimmunoprecipitation, we observed associations between a nuclear population of myosin Va and the viral major capsid protein, with both concentrating at the periphery of replication compartments. Immunoelectron microscopy showed that nearly 40% of assembled nuclear capsids associate with myosin Va. We also found that myosin Va and major capsid protein colocalize with nuclear F-actin. Importantly, antagonism of myosin Va with RNA interference or a dominant negative mutant revealed that myosin Va is important for the efficient production of infectious virus, capsid accumulation in the cytoplasm, and capsid localization away from replication compartment-like inclusions toward the nuclear rim. Our results lead us to suggest a working model whereby human cytomegalovirus capsids associate with myosin Va for movement from replication compartments to the nuclear periphery during nuclear egress. IMPORTANCE Little is known regarding how newly assembled and packaged herpesvirus capsids move from the nuclear interior to the periphery during nuclear egress. While it has been proposed that an actomyosin-based mechanism facilitates intranuclear movement of alphaherpesvirus capsids, a functional role for any specific myosin in nuclear egress has not been reported. Furthermore, the notion that an actomyosin-based mechanism facilitates intranuclear capsid movement is controversial. Here we show that human cytomegalovirus capsids associate with nuclear myosin Va and F-actin and that antagonism of myosin Va impairs capsid localization toward the nuclear rim and nuclear egress. Together with our previous results showing that nuclear F-actin is induced upon HCMV infection and is also important for these processes, our results lend support to the hypothesis that nascent human cytomegalovirus capsids migrate to the nuclear periphery via actomyosin-based movement. These results shed light on a poorly understood viral process and the cellular machinery involved. Copyright © 2018 American Society for Microbiology.

A Random Variable Approach to Nuclear Targeting and Survivability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Undem, Halvor A.

We demonstrate a common mathematical formalism for analyzing problems in nuclear survivability and targeting. This formalism, beginning with a random variable approach, can be used to interpret past efforts in nuclear-effects analysis, including targeting analysis. It can also be used to analyze new problems brought about by the post Cold War Era, such as the potential effects of yield degradation in a permanently untested nuclear stockpile. In particular, we illustrate the formalism through four natural case studies or illustrative problems, linking these to actual past data, modeling, and simulation, and suggesting future uses. In the first problem, we illustrate themore » case of a deterministically modeled weapon used against a deterministically responding target. Classic "Cookie Cutter" damage functions result. In the second problem, we illustrate, with actual target test data, the case of a deterministically modeled weapon used against a statistically responding target. This case matches many of the results of current nuclear targeting modeling and simulation tools, including the result of distance damage functions as complementary cumulative lognormal functions in the range variable. In the third problem, we illustrate the case of a statistically behaving weapon used against a deterministically responding target. In particular, we show the dependence of target damage on weapon yield for an untested nuclear stockpile experiencing yield degradation. Finally, and using actual unclassified weapon test data, we illustrate in the fourth problem the case of a statistically behaving weapon used against a statistically responding target.« less

Identification and Ultrastructural Characterization of a Novel Nuclear Degradation Complex in Differentiating Lens Fiber Cells

PubMed Central

Costello, M. Joseph; Brennan, Lisa A.; Gilliland, Kurt O.; Johnsen, Sönke; Kantorow, Marc

2016-01-01

An unresolved issue in structural biology is how the encapsulated lens removes membranous organelles to carry out its role as a transparent optical element. In this ultrastructural study, we establish a mechanism for nuclear elimination in the developing chick lens during the formation of the organelle-free zone. Day 12–15 chick embryo lenses were examined by high-resolution confocal light microscopy and thin section transmission electron microscopy (TEM) following fixation in 10% formalin and 4% paraformaldehyde, and then processing for confocal or TEM as described previously. Examination of developing fiber cells revealed normal nuclei with dispersed chromatin and clear nucleoli typical of cells in active ribosome production to support protein synthesis. Early signs of nuclear degradation were observed about 300 μm from the lens capsule in Day 15 lenses where the nuclei display irregular nuclear stain and prominent indentations that sometimes contained a previously undescribed macromolecular aggregate attached to the nuclear envelope. We have termed this novel structure the nuclear excisosome. This complex by confocal is closely adherent to the nuclear envelope and by TEM appears to degrade the outer leaflet of the nuclear envelope, then the inner leaflet up to 500 μm depth. The images suggest that the nuclear excisosome separates nuclear membrane proteins from lipids, which then form multilamellar assemblies that stain intensely in confocal and in TEM have 5 nm spacing consistent with pure lipid bilayers. The denuded nucleoplasm then degrades by condensation and loss of structure in the range 600 to 700 μm depth producing pyknotic nuclear remnants. None of these stages display any classic autophagic vesicles or lysosomes associated with nuclei. Uniquely, the origin of the nuclear excisosome is from filopodial-like projections of adjacent lens fiber cells that initially contact, and then appear to fuse with the outer nuclear membrane. These filopodial-like projections appear to be initiated with a clathrin-like coat and driven by an internal actin network. In summary, a specialized cellular organelle, the nuclear excisosome, generated in part by adjacent fiber cells degrades nuclei during fiber cell differentiation and maturation. PMID:27536868

Discrimination between NL1- and NL2-Mediated Nuclear Localization of the Glucocorticoid Receptor

PubMed Central

Savory, Joanne G. A.; Hsu, Brian; Laquian, Ian R.; Giffin, Ward; Reich, Terry; Haché, Robert J. G.; Lefebvre, Yvonne A.

1999-01-01

Glucocorticoid receptor (GR) cycles between a free liganded form that is localized to the nucleus and a heat shock protein (hsp)-immunophilin-complexed, unliganded form that is usually localized to the cytoplasm but that can also be nuclear. In addition, rapid nucleocytoplasmic exchange or shuttling of the receptor underlies its localization. Nuclear import of liganded GR is mediated through a well-characterized sequence, NL1, adjacent to the receptor DNA binding domain and a second, uncharacterized motif, NL2, that overlaps with the ligand binding domain. In this study we report that rapid nuclear import (half-life [t1/2] of 4 to 6 min) of agonist- and antagonist-treated GR and the localization of unliganded, hsp-associated GRs to the nucleus in G0 are mediated through NL1 and correlate with the binding of GR to pendulin/importin α. By contrast, NL2-mediated nuclear transfer of GR occurred more slowly (t1/2 = 45 min to 1 h), was agonist specific, and appeared to be independent of binding to importin α. Together, these results suggest that NL2 mediates the nuclear import of GR through an alternative nuclear import pathway. Nuclear export of GR was inhibited by leptomycin B, suggesting that the transfer of GR to the cytoplasm is mediated through the CRM1-dependent pathway. Inhibition of GR nuclear export by leptomycin B enhanced the nuclear localization of both unliganded, wild-type GR and hormone-treated NL1− GR. These results highlight that the subcellular localization of both liganded and unliganded GRs is determined, at least in part, by a flexible equilibrium between the rates of nuclear import and export. PMID:9891038

Quantum information to the home

NASA Astrophysics Data System (ADS)

Choi, Iris; Young, Robert J.; Townsend, Paul D.

2011-06-01

Information encoded on individual quanta will play an important role in our future lives, much as classically encoded digital information does today. Combining quantum information carried by single photons with classical signals encoded on strong laser pulses in modern fibre-to-the-home (FTTH) networks is a significant challenge, the solution to which will facilitate the global distribution of quantum information to the home and with it a quantum internet [1]. In real-world networks, spontaneous Raman scattering in the optical fibre would induce crosstalk between the high-power classical channels and a single-photon quantum channel, such that the latter is unable to operate. Here, we show that the integration of quantum and classical information on an FTTH network is possible by performing quantum key distribution (QKD) on a network while simultaneously transferring realistic levels of classical data. Our novel scheme involves synchronously interleaving a channel of quantum data with the Raman scattered photons from a classical channel, exploiting the periodic minima in the instantaneous crosstalk and thereby enabling secure QKD to be performed.

Importin α-importin β complex mediated nuclear translocation of insulin-like growth factor binding protein-5.

PubMed

Sun, Min; Long, Juan; Yi, Yuxin; Xia, Wei

2017-10-28

Insulin-like growth factor-binding protein (IGFBP)-5 is a secreted protein that binds to IGFs and modulates IGF actions, as well as regulates cell proliferation, migration, and apoptosis independent of IGF. Proper cellular localization is critical for the effective function of most signaling molecules. In previous studies, we have shown that the nuclear IGFBP-5 comes from ER-cytosol retro-translocation. In this study, we further investigated the pathway mediating IGFBP-5 nuclear import after it retro-translocation. Importin-α5 was identified as an IGFBP-5-interacting protein with a yeast two-hybrid system, and its interaction with IGFBP-5 was further confirmed by GST pull down and co-immunoprecipitation. Binding affinity of IGFBP-5 and importins were determined by surface plasmon resonance (IGFBP-5/importin-β: K D =2.44e-7, IGFBP-5/importin-α5: K D =3.4e-7). Blocking the importin-α5/importin-β nuclear import pathway using SiRNA or dominant negative impotin-β dramatically inhibited IGFBP-5-EGFP nuclear import, though importin-α5 overexpress does not affect IGFBP-5 nuclear import. Furthermore, nuclear IGFBP-5 was quantified using luciferase report assay. When deleted the IGFBP-5 nuclear localization sequence (NLS), IGFBP-5 ΔNLS loss the ability to translocate into the nucleus and accumulation of IGFBP-5 ΔNLS was visualized in the cytosol. Altogether, our findings provide a substantially evidence showed that the IGFBP-5 nuclear import is mediated by importin-α/importin-β complex, and NLS is critical domain in IGFBP-5 nuclear translocation.

GPER-1/GPR30 a novel estrogen receptor sited in the cell membrane: therapeutic coupling to breast cancer.

PubMed

Molina, Luis; Figueroa, Carlos D; Bhoola, Kanti D; Ehrenfeld, Pamela

2017-08-01

Breast cancer is clinically classified as 'estrogen-positive' when at least 1% of cancer cells stain for the estrogen receptor alpha (ERα). However, recent research on both basic and clinical aspects of breast cancer suggests that GPER-1 (G protein-coupled estrogen receptor-1) may have an important role in breast cancer. Areas covered: This review provides a comprehensive and systematic literature search on GPER-1. We have focused on the role of GPER-1 in breast cancer and on resistance to endocrine therapy, an unsolved clinical issue still under discussion. Expert opinion: The discovery of GPER-1 as a novel estrogen receptor is unique and the signaling pathways activated by its stimulation, when compared to the classical nuclear ERα, indicate a potential role of GPER-1 in the genesis and mechanisms of drug resistance in breast cancer. Tumors expressing ERα represent the largest group of breast cancer patients indicating that more women eventually die from ERα-positive breast tumors than from other more malignant breast cancer subtypes such as HER2-positive and the triple negative groups. It is important to develop new strategies on endocrine therapy with regard to ERα and GPER-1 receptors to achieve innovative successful therapeutic tools.

A Simple Derivation of Chemically Important Classical Observables and Superselection Rules.

ERIC Educational Resources Information Center

Muller-Herold, U.

1985-01-01

Explores the question "Why are so many stationary states allowed by traditional quantum mechanics not realized in nature?" through discussion of classical observables and superselection rules. Three examples are given that can be used in introductory courses (including the fermion/boson property and the mass of a "nonrelativistic" particle). (JN)

Understanding the side effects of classical biological control

Treesearch

Dean Pearson

2008-01-01

Classical biological control involves the use of imported natural enemies to suppress or control populations of the target pest species below an economically or ecologically relevant threshold. Biological control is a useful tool for mitigating the impacts of exotic invasive plants; however, its application is not without risk (see Carruthers and D’Antonio...

Non-classical State via Superposition of Two Opposite Coherent States

NASA Astrophysics Data System (ADS)

Ren, Gang; Du, Jian-ming; Yu, Hai-jun

2018-04-01

We study the non-classical properties of the states generated by superpositions of two opposite coherent states with the arbitrary relative phase factors. We show that the relative phase factors plays an important role in these superpositions. We demonstrate this result by discussing their squeezing properties, quantum statistical properties and fidelity in principle.

Software-aided discussion about classical picture of Mach-Zehnder interferometer

NASA Astrophysics Data System (ADS)

Cavalcanti, C. J. H.; Ostermann, F.; Lima, N. W.; Netto, J. S.

2017-11-01

The Mach-Zehnder interferometer has played an important role both in quantum and classical physics research over the years. In physics education, it has been used as a didactic tool for quantum physics teaching, allowing fundamental concepts, such as particle-wave duality, to be addressed from the very beginning. For a student to understand the novelties of the quantum scenario, it is first worth introducing the classical picture. In this paper, we introduce a new version of the software developed by our research group to deepen the discussion on the classical picture of the Mach-Zehnder interferometer. We present its equivalence with the double slit experiment and we derive the mathematical expressions relating to the interference pattern. We also explore the concept of visibility (which is very important for understanding wave-particle complementarity in quantum physics) to help students become familiar with this experiment and to enhance their knowledge of its counterintuitive aspects. We use the software articulated by the mathematical formalism and phenomenological features. We also present excerpts of the discursive interactions of students using the software in didactic situations.

Nuclear import of glucokinase in pancreatic beta-cells is mediated by a nuclear localization signal and modulated by SUMOylation.

PubMed

Johansson, Bente Berg; Fjeld, Karianne; Solheim, Marie Holm; Shirakawa, Jun; Zhang, Enming; Keindl, Magdalena; Hu, Jiang; Lindqvist, Andreas; Døskeland, Anne; Mellgren, Gunnar; Flatmark, Torgeir; Njølstad, Pål Rasmus; Kulkarni, Rohit N; Wierup, Nils; Aukrust, Ingvild; Bjørkhaug, Lise

2017-10-15

The localization of glucokinase in pancreatic beta-cell nuclei is a controversial issue. Although previous reports suggest such a localization, the mechanism for its import has so far not been identified. Using immunofluorescence, subcellular fractionation and mass spectrometry, we present evidence in support of glucokinase localization in beta-cell nuclei of human and mouse pancreatic sections, as well as in human and mouse isolated islets, and murine MIN6 cells. We have identified a conserved, seven-residue nuclear localization signal ( 30 LKKVMRR 36 ) in the human enzyme. Substituting the residues KK 31,32 and RR 35,36 with AA led to a loss of its nuclear localization in transfected cells. Furthermore, our data indicates that SUMOylation of glucokinase modulates its nuclear import, while high glucose concentrations do not significantly alter the enzyme nuclear/cytosolic ratio. Thus, for the first time, we provide data in support of a nuclear import of glucokinase mediated by a redundant mechanism, involving a nuclear localization signal, and which is modulated by its SUMOylation. These findings add new knowledge to the functional role of glucokinase in the pancreatic beta-cell. Copyright © 2017 Elsevier B.V. All rights reserved.

A proposed method for electronic feedback compensation of damping in ferromagnetic resonance

DOE PAGES

Zohar, S.; Sterbinsky, G. E.

2017-07-10

Here, we propose an experimental technique for extending feedback compensation of dissipative radiation used in nuclear magnetic resonance (NMR) to encompass ferromagnetic resonance (FMR). This method uses a balanced microwave power detector whose output is phase shifted π/2, amplified, and fed back to drive precession. Using classical control theory, we predict an electronically controllable narrowing of field swept FMR line-widths. This technique is predicted to compensate other sources of spin dissipation in addition to radiative loss.

A proposed method for electronic feedback compensation of damping in ferromagnetic resonance

NASA Astrophysics Data System (ADS)

Zohar, S.; Sterbinsky, G. E.

2017-12-01

We propose an experimental technique for extending feedback compensation of dissipative radiation used in nuclear magnetic resonance (NMR) to encompass ferromagnetic resonance (FMR). This method uses a balanced microwave power detector whose output is phase shifted π / 2 , amplified, and fed back to drive precession. Using classical control theory, we predict an electronically controllable narrowing of field swept FMR line-widths. This technique is predicted to compensate other sources of spin dissipation in addition to radiative loss.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edgue, E.

The point kinetics approach is a classical useful method for a reactor transient analysis. It is helpful to known, however, when a more elaborate transient analysis, involving the space-dependence change of the flux through a given transient, should be considered. In this paper, the authors present a rather elegant and quick method to check the need for a space-dependent flux analysis through a control rod transient in a given nuclear reactor. The method is applied to a series of rod ejection experiments in the TRIGA MARK-II reactor of Istanbul Technical University (ITU).

Solution Structure and Molecular Interactions of Lamin B Receptor Tudor Domain*

PubMed Central

Liokatis, Stamatis; Edlich, Christian; Soupsana, Katerina; Giannios, Ioannis; Panagiotidou, Parthena; Tripsianes, Konstantinos; Sattler, Michael; Georgatos, Spyros D.; Politou, Anastasia S.

2012-01-01

Lamin B receptor (LBR) is a polytopic protein of the nuclear envelope thought to connect the inner nuclear membrane with the underlying nuclear lamina and peripheral heterochromatin. To better understand the function of this protein, we have examined in detail its nucleoplasmic region, which is predicted to harbor a Tudor domain (LBR-TD). Structural analysis by multidimensional NMR spectroscopy establishes that LBR-TD indeed adopts a classical β-barrel Tudor fold in solution, which, however, features an incomplete aromatic cage. Removal of LBR-TD renders LBR more mobile at the plane of the nuclear envelope, but the isolated module does not bind to nuclear lamins, heterochromatin proteins (MeCP2), and nucleosomes, nor does it associate with methylated Arg/Lys residues through its aromatic cage. Instead, LBR-TD exhibits tight and stoichiometric binding to the “histone-fold” region of unassembled, free histone H3, suggesting an interesting role in histone assembly. Consistent with such a role, robust binding to native nucleosomes is observed when LBR-TD is extended toward its carboxyl terminus, to include an area rich in Ser-Arg residues. The Ser-Arg region, alone or in combination with LBR-TD, binds both unassembled and assembled H3/H4 histones, suggesting that the TD/RS interface may operate as a “histone chaperone-like platform.” PMID:22052904

Cytoplasmic and nuclear localization of cadherin in honey bee (Apis mellifera L.) gonads.

PubMed

Florecki, Mônica M; Hartfelder, Klaus

2011-01-01

Cadherins are crucial molecules mediating cell-cell interactions between somatic and germline cells in insect and mammalian male and female gonads. We analysed the presence and localization of cadherins in ovaries of honeybee queens and in testes of drones. Transcripts representing two classical cadherins, E-cadherin (shotgun) and N-cadherin, as well as three protocadherins (Starry night, Fat and Fat-like) were detected in gonads of both sexes. Pan-cadherin antibodies, which most probably detect a honeybee N-cadherin, were used in immunolocalization analyses. In the germarium of ovarioles, cadherin-IR (cadherin immunoreactivity) was evidenced as homogeneously distributed in the cytoplasm and as nuclear foci, in both germline and somatic cells. It was also detected in polyfusomes and ring canals. In testiolar tubules, cadherin-IR showed a cytoplasmic and nuclear distributon alike in ovaries. The unexpected nuclear localization and cytoplasmic distribution in ovaries and testes were corroborated by immunogold electron microscopy, which revealed cadherin aggregates associated with electron-dense nuclear structures. With respect to cadherin localization, the honeybee differs from Drosophila, the model for gametogenesis in insects, raising the question as to how differences among solitary and social species may be built into and generated from the general architecture of polytrophic meroistic ovaries. It also indicates the possibility of divergent roles for cadherin in the functional architecture of insect gonads, in general, especially in taxa with high reproductive output.

Few-body semiclassical approach to nucleon transfer and emission reactions

NASA Astrophysics Data System (ADS)

Sultanov, Renat A.; Guster, D.

2014-04-01

A three-body semiclassical model is proposed to describe the nucleon transfer and emission reactions in a heavy-ion collision. In this model the two heavy particles, i.e. nuclear cores A1(ZA1, MA1) and A2(ZA2, MA2), move along classical trajectories {{R}_1}( t ) and {{R}_2}( t ) respectively, while the dynamics of the lighter neutron (n) is considered from a quantum mechanical point of view. Here, Mi are the nucleon masses and Zi are the Coulomb charges of the heavy nuclei (i = 1, 2). A Faddeev-type semiclassical formulation using realistic paired nuclear-nuclear potentials is applied so that all three channels (elastic, rearrangement and break-up) are described in a unified manner. In order to solve the time-dependent equations the Faddeev components of the total three-body wave-function are expanded in terms of the input and output channel target eigenfunctions. In the special case, when the nuclear cores are identical (A1 ≡ A2) and also the two-level approximation in the expansion over the target (subsystem) functions is used, the time-dependent semiclassical Faddeev equations are resolved in an explicit way. To determine the realistic {{R}_1}( t ) and {{R}_2}( t ) trajectories of the nuclear cores, a self-consistent approach based on the Feynman path integral theory is applied.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrews, Joel F.; Sykora, Landon J.; Barik Letostak, Tiasha

HSP40 family member MRJ (DNAJB6) has been in the spot light for its relevance to Huntington's, Parkinson's diseases, limb-girdle muscular dystrophy, placental development, neural stem cells, cell cycle and malignancies such as breast cancer and melanoma. This gene has two spliced variants coding for 2 distinct proteins with significant homology. However, MRJ(L) (large variant) is predominantly localized to the nucleus whereas MRJ(S) (small variant) is predominantly cytoplasmic. Interestingly MRJ(S) translocates to the nucleus in response to heat shock. The classical heat shock proteins respond to crises (stress) by increasing the number of molecules, usually by transcriptional up-regulation. Our studies implymore » that a quick increase in the molar concentration of MRJ in the nuclear compartment is a novel method by which MRJ responds to stress. We found that MRJ(S) shows NLS (nuclear localization signal) independent nuclear localization in response to heat shock and hypoxia. The specificity of this response is realized due to lack of such response by MRJ(S) when challenged by other stressors, such as some cytokines or UV light. Deletion analysis has allowed us to narrow down on a 20 amino acid stretch at the C-terminal region of MRJ(S) as a potential stress sensing region. Functional studies indicated that constitutive nuclear localization of MRJ(S) promoted attributes of malignancy such as proliferation and invasiveness overall indicating distinct phenotypic characteristics of nuclear MRJ(S).« less

Septin 7 immunoexpression in papillary thyroid carcinoma: a preliminary study.

PubMed

Igci, Yusuf Ziya; Erkilic, Suna; Arslan, Ahmet

2014-07-01

Papillary thyroid carcinoma (PTC) is the most common type among thyroid cancers. The diagnosis of PTC may be challenging when follicular variant (FVPTC) of this disease is present due to the resemblance of nuclear properties of the classical type (CVPTC). However, making use of ancillary molecular markers in the diagnosis of PTC may help. In our study, we aimed to evaluate the SEPT7 protein expression in PTC. A total of 55 paraffin block tissue samples comprising encapsulated FVPTC (FVPTC(e), n=25), and CVPTC (n=15), and benign hyperfunctioning thyroid nodules (HypN, n=15) were used in this study. Nuclear, cytoplasmic, and overall (total) SEPT7 protein expression levels were determined by using immunohistochemistry. Nuclear, cytoplasmic, and overall SEPT7 expressions (p=0.02, p=0.001, p=0.002, respectively) were significantly lower in FVPTC(e) tissues when compared to HypN. In CVPTC group, nuclear expression was significantly lower (p=0.004) while overall and cytoplasmic expressions were not changed (p>0.05). In HypN group, highest nuclear (mean=2.73), cytoplasmic (mean=2.86), and overall (mean=2.86) expression scores were detected. Significantly lower SEPT7 expression in all expressional categories in FVPTC(e) group may be a sign of different molecular signature in this type of tissue. Copyright © 2014 Elsevier GmbH. All rights reserved.

Google in a Quantum Network

PubMed Central

Paparo, G. D.; Martin-Delgado, M. A.

2012-01-01

We introduce the characterization of a class of quantum PageRank algorithms in a scenario in which some kind of quantum network is realizable out of the current classical internet web, but no quantum computer is yet available. This class represents a quantization of the PageRank protocol currently employed to list web pages according to their importance. We have found an instance of this class of quantum protocols that outperforms its classical counterpart and may break the classical hierarchy of web pages depending on the topology of the web. PMID:22685626

Classical noise, quantum noise and secure communication

NASA Astrophysics Data System (ADS)

Tannous, C.; Langlois, J.

2016-01-01

Secure communication based on message encryption might be performed by combining the message with controlled noise (called pseudo-noise) as performed in spread-spectrum communication used presently in Wi-Fi and smartphone telecommunication systems. Quantum communication based on entanglement is another route for securing communications as demonstrated by several important experiments described in this work. The central role played by the photon in unifying the description of classical and quantum noise as major ingredients of secure communication systems is highlighted and described on the basis of the classical and quantum fluctuation dissipation theorems.

Importin α5 negatively regulates importin β1-mediated nuclear import of Newcastle disease virus matrix protein and viral replication and pathogenicity in chicken fibroblasts.

PubMed

Duan, Zhiqiang; Xu, Haixu; Ji, Xinqin; Zhao, Jiafu; Xu, Houqiang; Hu, Yan; Deng, Shanshan; Hu, Shunlin; Liu, Xiufan

2018-12-31

The matrix (M) protein of Newcastle disease virus (NDV) is demonstrated to localize in the nucleus via intrinsic nuclear localization signal (NLS), but cellular proteins involved in the nuclear import of NDV M protein and the role of M's nuclear localization in the replication and pathogenicity of NDV remain unclear. In this study, importin β1 was screened to interact with NDV M protein by yeast two-hybrid screening. This interaction was subsequently confirmed by co-immunoprecipitation and pull-down assays. In vitro binding studies indicated that the NLS region of M protein and the amino acids 336-433 of importin β1 that belonged to the RanGTP binding region were important for binding. Importantly, a recombinant virus with M/NLS mutation resulted in a pathotype change of NDV and attenuated viral replication and pathogenicity in chicken fibroblasts and SPF chickens. In agreement with the binding data, nuclear import of NDV M protein in digitonin-permeabilized HeLa cells required both importin β1 and RanGTP. Interestingly, importin α5 was verified to interact with M protein through binding importin β1. However, importin β1 or importin α5 depletion by siRNA resulted in different results, which showed the obviously cytoplasmic or nuclear accumulation of M protein and the remarkably decreased or increased replication ability and pathogenicity of NDV in chicken fibroblasts, respectively. Our findings therefore demonstrate for the first time the nuclear import mechanism of NDV M protein and the negative regulation role of importin α5 in importin β1-mediated nuclear import of M protein and the replication and pathogenicity of a paramyxovirus.

The Review of Nuclear Microscopy Techniques: An Approach for Nondestructive Trace Elemental Analysis and Mapping of Biological Materials.

PubMed

Mulware, Stephen Juma

2015-01-01

The properties of many biological materials often depend on the spatial distribution and concentration of the trace elements present in a matrix. Scientists have over the years tried various techniques including classical physical and chemical analyzing techniques each with relative level of accuracy. However, with the development of spatially sensitive submicron beams, the nuclear microprobe techniques using focused proton beams for the elemental analysis of biological materials have yielded significant success. In this paper, the basic principles of the commonly used microprobe techniques of STIM, RBS, and PIXE for trace elemental analysis are discussed. The details for sample preparation, the detection, and data collection and analysis are discussed. Finally, an application of the techniques to analysis of corn roots for elemental distribution and concentration is presented.

Physics of negative absolute temperatures.

PubMed

Abraham, Eitan; Penrose, Oliver

2017-01-01

Negative absolute temperatures were introduced into experimental physics by Purcell and Pound, who successfully applied this concept to nuclear spins; nevertheless, the concept has proved controversial: a recent article aroused considerable interest by its claim, based on a classical entropy formula (the "volume entropy") due to Gibbs, that negative temperatures violated basic principles of statistical thermodynamics. Here we give a thermodynamic analysis that confirms the negative-temperature interpretation of the Purcell-Pound experiments. We also examine the principal arguments that have been advanced against the negative temperature concept; we find that these arguments are not logically compelling, and moreover that the underlying "volume" entropy formula leads to predictions inconsistent with existing experimental results on nuclear spins. We conclude that, despite the counterarguments, negative absolute temperatures make good theoretical sense and did occur in the experiments designed to produce them.

Teaching Global Warming

NASA Astrophysics Data System (ADS)

Hobson, Art

2004-05-01

Every citizen's education should include socially relevant science courses because, as the American Association for the Advancement of Science puts it, "Without a scientifically literate population, the outlook for a better world is not promising." I have developed a conceptual liberal-arts physics course that covers the major principles of classical physics, emphasizes modern/contemporary physics, and includes societal topics such as global warming, ozone depletion, transportation, exponential growth, scientific methodology, risk assessment, nuclear weapons, nuclear power, and the energy future. The societal topics, occupying only about 15% of the class time, appear to be the main cause of the surprising popularity of this course among non-scientists. I will outline some ideas for incorporating global warming into such a course or into any other introductory physics course. For further details, see my textbook Physics: Concepts and Connections (Prentice Hall, 3rd edition 2003).

Simulations of the Neutron Gas in the Inner Crust of Neutron Stars

NASA Astrophysics Data System (ADS)

Vandegriff, Elizabeth; Horowitz, Charles; Caplan, Matthew

2017-09-01

Inside neutron stars, the structures known as `nuclear pasta' are found in the crust. This pasta forms near nuclear density as nucleons arrange in spaghetti- or lasagna-like structures to minimize their energy. We run classical molecular dynamics simulations to visualize the geometry of this pasta and study the distribution of nucleons. In the simulations, we observe that the pasta is embedded in a gas of neutrons, which we call the `sauce'. In this work, we developed two methods for determining the density of neutrons in the gas, one which is accurate at low temperatures and a second which justifies an extrapolation at high temperatures. Running simulations with no Coulomb interactions, we find that the neutron density increases linearly with temperature for every proton fraction we simulated. NSF REU Grant PHY-1460882 at Indiana University.

Structural basis for nuclear import complex dissociation by RanGTP.

PubMed

Lee, Soo Jae; Matsuura, Yoshiyuki; Liu, Sai Man; Stewart, Murray

2005-06-02

Nuclear protein import is mediated mainly by the transport factor importin-beta that binds cytoplasmic cargo, most often via the importin-alpha adaptor, and then transports it through nuclear pore complexes. This active transport is driven by disassembly of the import complex by nuclear RanGTP. The switch I and II loops of Ran change conformation with nucleotide state, and regulate its interactions with nuclear trafficking components. Importin-beta consists of 19 HEAT repeats that are based on a pair of antiparallel alpha-helices (referred to as the A- and B-helices). The HEAT repeats stack to yield two C-shaped arches, linked together to form a helicoidal molecule that has considerable conformational flexibility. Here we present the structure of full-length yeast importin-beta (Kap95p or karyopherin-beta) complexed with RanGTP, which provides a basis for understanding the crucial cargo-release step of nuclear import. We identify a key interaction site where the RanGTP switch I loop binds to the carboxy-terminal arch of Kap95p. This interaction produces a change in helicoidal pitch that locks Kap95p in a conformation that cannot bind importin-alpha or cargo. We suggest an allosteric mechanism for nuclear import complex disassembly by RanGTP.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eberhard, Jeremy; Onder, Zeynep; Moroianu, Junona, E-mail: moroianu@bc.edu

We previously discovered that nuclear import of high risk HPV16 E7 is mediated by a cNLS located within the zinc-binding domain via a pathway that is independent of karyopherins/importins (Angeline et al., 2003; Knapp et al., 2009). In this study we continued our characterization of the cNLS and nuclear import pathway of HPV16 E7. We find that an intact zinc-binding domain is essential for the cNLS function in mediating nuclear import of HPV16 E7. Mutagenesis of cysteine residues to alanine in each of the two CysXXCys motifs involved in zinc-binding changes the nuclear localization of the EGFP-16E7 and 2xEGFP-16E7 mutants.more » We further discover that a patch of hydrophobic residues, {sub 65}LRLCV{sub 69}, within the zinc-binding domain of HPV16 E7 mediates its nuclear import via hydrophobic interactions with the FG domain of the central channel nucleoporin Nup62. - Highlights: • An intact zinc-binding domain is essential for the nuclear localization of HPV16 E7. • Identification of a hydrophobic patch that is critical for the nuclear import of HPV16 E7. • HPV16 E7 interacts via its zinc-binding domain with the FG domain of Nup62.« less

Nuclear import of human MLH1, PMS2, and MutLalpha: redundancy is the key.

PubMed

Leong, Vivian; Lorenowicz, Jessica; Kozij, Natalie; Guarné, Alba

2009-08-01

DNA mismatch repair maintains genomic stability by correcting errors that have escaped polymerase proofreading. Defects on mismatch repair genes lead to an increased mutation rate, microsatellite instability and predisposition to human non-polyposis colorectal cancer (HNPCC). Human MutLalpha is a heterodimer formed by the interaction of MLH1 and PMS2 that coordinates a series of key events in mismatch repair. It has been proposed that nuclear import of MutLalpha may be the first regulatory step on the activation of the mismatch repair pathway. Using confocal microscopy and mismatch repair deficient cells, we have identified the sequence determinants that drive nuclear import of human MLH1, PMS2, and MutLalpha. Transient transfection of the individual proteins reveals that MLH1 has a bipartite and PMS2 has a single monopartite nuclear localization signal. Although dimerization is not required for nuclear localization, the MutLalpha heterodimer is imported more efficiently than the MLH1 or PMS2 monomers. Interestingly, the bipartite localization signal of MLH1 can direct import of MutLalpha even when PMS2 encompasses a mutated localization signal. Hence we conclude that the presence of redundant nuclear localization signals guarantees nuclear transport of MutLalpha and, consequently, efficient mismatch repair.

Functional Conservation of the Transportin Nuclear Import Pathway in Divergent Organisms

PubMed Central

Siomi, Mikiko C.; Fromont, Micheline; Rain, Jean-Christophe; Wan, Lili; Wang, Fan; Legrain, Pierre; Dreyfuss, Gideon

1998-01-01

Human transportin1 (hTRN1) is the nuclear import receptor for a group of pre-mRNA/mRNA-binding proteins (heterogeneous nuclear ribonucleoproteins [hnRNP]) represented by hnRNP A1, which shuttle continuously between the nucleus and the cytoplasm. hTRN1 interacts with the M9 region of hnRNP A1, a 38-amino-acid domain rich in Gly, Ser, and Asn, and mediates the nuclear import of M9-bearing proteins in vitro. Saccharomyces cerevisiae transportin (yTRN; also known as YBR017c or Kap104p) has been identified and cloned. To understanding the nuclear import mediated by yTRN, we searched with a yeast two-hybrid system for proteins that interact with it. In an exhaustive screen of the S. cerevisiae genome, the most frequently selected open reading frame was the nuclear mRNA-binding protein, Nab2p. We delineated a ca.-50-amino-acid region in Nab2p, termed NAB35, which specifically binds yTRN and is similar to the M9 motif. NAB35 also interacts with hTRN1 and functions as a nuclear localization signal in mammalian cells. Interestingly, yTRN can also mediate the import of NAB35-bearing proteins into mammalian nuclei in vitro. We also report on additional substrates for TRN as well as sequences of Drosophila melanogaster, Xenopus laevis, and Schizosaccharomyces pombe TRNs. Together, these findings demonstrate that both the M9 signal and the nuclear import machinery utilized by the transportin pathway are conserved in evolution. PMID:9632798

Quantum and classical behavior in interacting bosonic systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hertzberg, Mark P.

It is understood that in free bosonic theories, the classical field theory accurately describes the full quantum theory when the occupancy numbers of systems are very large. However, the situation is less understood in interacting theories, especially on time scales longer than the dynamical relaxation time. Recently there have been claims that the quantum theory deviates spectacularly from the classical theory on this time scale, even if the occupancy numbers are extremely large. Furthermore, it is claimed that the quantum theory quickly thermalizes while the classical theory does not. The evidence for these claims comes from noticing a spectacular differencemore » in the time evolution of expectation values of quantum operators compared to the classical micro-state evolution. If true, this would have dramatic consequences for many important phenomena, including laboratory studies of interacting BECs, dark matter axions, preheating after inflation, etc. In this work we critically examine these claims. We show that in fact the classical theory can describe the quantum behavior in the high occupancy regime, even when interactions are large. The connection is that the expectation values of quantum operators in a single quantum micro-state are approximated by a corresponding classical ensemble average over many classical micro-states. Furthermore, by the ergodic theorem, a classical ensemble average of local fields with statistical translation invariance is the spatial average of a single micro-state. So the correlation functions of the quantum and classical field theories of a single micro-state approximately agree at high occupancy, even in interacting systems. Furthermore, both quantum and classical field theories can thermalize, when appropriate coarse graining is introduced, with the classical case requiring a cutoff on low occupancy UV modes. We discuss applications of our results.« less

A Primer on Elliptic Functions with Applications in Classical Mechanics

ERIC Educational Resources Information Center

Brizard, Alain J.

2009-01-01

The Jacobi and Weierstrass elliptic functions used to be part of the standard mathematical arsenal of physics students. They appear as solutions of many important problems in classical mechanics: the motion of a planar pendulum (Jacobi), the motion of a force-free asymmetric top (Jacobi), the motion of a spherical pendulum (Weierstrass) and the…

The Process and Effects of Mass Communication. Revised Edition.

ERIC Educational Resources Information Center

Schramm, Wilbur, Ed.; Roberts, Donald F., Ed.

Composed of a mixture of old classics, new classics, reports on state of the art in important areas, and speculations about the future, this second edition of the reader in communication research provides an introduction to questions about how communication works and what it does. Papers by prominent researchers and writers in the field comprise…

Communication cost of simulating Bell correlations.

PubMed

Toner, B F; Bacon, D

2003-10-31

What classical resources are required to simulate quantum correlations? For the simplest and most important case of local projective measurements on an entangled Bell pair state, we show that exact simulation is possible using local hidden variables augmented by just one bit of classical communication. Certain quantum teleportation experiments, which teleport a single qubit, therefore admit a local hidden variables model.

75 FR 48304 - Notice of Request for Revision and Extension of Approval of an Information Collection...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-10

... Live Swine, Pork, and Pork Products from Certain Regions Free of Classical Swine Fever in Chile and... revise an information collection associated with regulations for the importation of live swine, pork, and pork products from certain regions free of classical swine fever in Chile and Mexico and to request...

Philosopher to Moderator: The Shifting Paradigm of "Ethos" in Education.

ERIC Educational Resources Information Center

Raign, Kathryn Rosser

The classical concept of "ethos" (the establishing of the speaker or writer's credibility, his or her moral character) has acquired many meanings over the centuries and has played an important role in determining the many shifting perceptions of the teacher's role, both in the classical period and the modern period. The issue can be…

Prebifurcation periodic ghost orbits in semiclassical quantization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kus, M.; Haake, F.; Delande, D.

1993-10-04

Classical periodic orbits are stationary-phase points in path integral representations of quantum propagators. We show that complex solutions of the stationary-phase equation, not corresponding to real classical periodic orbits, give additional contributions to the propagator which can be important, especially near bifurcations. We reveal the existence and relevance of such periodic ghost orbits for a kicked top.

A Simple Explanation of the Classic Hydrostatic Paradox

ERIC Educational Resources Information Center

Kontomaris, Stylianos-Vasileios; Malamou, Anna

2016-01-01

An interesting problem in fluid mechanics, with significant educational importance, is the classic hydrostatic paradox. The hydrostatic paradox states the fact that in different shaped containers, with the same base area, which are filled with a liquid of the same height, the applied force by the liquid on the base of each container is exactly the…

Nuclear localization of the dystrophin-associated protein α-dystrobrevin through importin α2/β1 is critical for interaction with the nuclear lamina/maintenance of nuclear integrity.

PubMed

Aguilar, Areli; Wagstaff, Kylie M; Suárez-Sánchez, Rocío; Zinker, Samuel; Jans, David A; Cisneros, Bulmaro

2015-05-01

Although α-dystrobrevin (DB) is assembled into the dystrophin-associated protein complex, which is central to cytoskeletal organization, it has also been found in the nucleus. Here we delineate the nuclear import pathway responsible for nuclear targeting of α-DB for the first time, together with the importance of nuclear α-DB in determining nuclear morphology. We map key residues of the nuclear localization signal of α-DB within the zinc finger domain (ZZ) using various truncated versions of the protein, and site-directed mutagenesis. Pulldown, immunoprecipitation, and AlphaScreen assays showed that the importin (IMP) α2/β1 heterodimer interacts with high affinity with the ZZ domain of α-DB. In vitro nuclear import assays using antibodies to specific importins, as well as in vivo studies using siRNA or a dominant negative importin construct, confirmed the key role of IMPα2/β1 in α-DB nuclear translocation. Knockdown of α-DB expression perturbed cell cycle progression in C2C12 myoblasts, with decreased accumulation of cells in S phase and, significantly, altered localization of lamins A/C, B1, and B2 with accompanying gross nuclear morphology defects. Because α-DB interacts specifically with lamin B1 in vivo and in vitro, nuclear α-DB would appear to play a key role in nuclear shape maintenance through association with the nuclear lamina. © FASEB.

A case of metastatic haemangiopericytoma to the thyroid gland: Case report and literature review

PubMed Central

PROIETTI, AGNESE; SARTORI, CHIARA; TORREGROSSA, LIBORIO; VITTI, PAOLO; AGHABABYAN, ALEKSANDR; FREGOLI, LORENZO; MICCOLI, PAOLO; BASOLO, FULVIO

2012-01-01

Haemangiopericytoma (HPC) is a mesenchymal neoplasm accounting for a minority of all vascular tumours. HPC mostly arises in the lower extremities and the retroperitoneum, while the head and neck area is the third most common site. The majority of HPCs are histologically benign. However, a small percentage possess atypical features, such as a high mitotic rate, high cellularity and foci of necrosis. We report a case of classical abdominal HPC that presented 7 years after the first surgical resection with thyroid metastases of malignant HPC. Microscopic examination revealed multiple hypercellular nodules with an infiltrative growth pattern. These nodules consisted of tightly packed fusiform or spindle-shaped cells with nuclear polymorphism and an increased mitotic rate. The tumour cells exhibited a marked expression of CD34. Cells were arranged around a prominent vascular network, occasionally with a ‘staghorn’ configuration. The results of this study support and confirm the theory that HPC is a rare neoplasm with unpredictable behaviour, as largely debated in the international literature. Therefore, this study emphasized the importance of applying strict diagnostic criteria in making the most appropriate diagnosis. PMID:22783428

Obesity, insulin resistance and diabetes: sex differences and role of oestrogen receptors.

PubMed

Meyer, M R; Clegg, D J; Prossnitz, E R; Barton, M

2011-09-01

Obesity increases the risk of coronary artery disease through insulin resistance, diabetes, arterial hypertension and dyslipidemia. The prevalence of obesity has increased worldwide and is particularly high among middle-aged women and men. After menopause, women are at an increased risk to develop visceral obesity due to the loss of endogenous ovarian hormone production. Effects of oestrogens are classically mediated by the two nuclear oestrogen receptors (ERs) α and β. In addition, more recent research has shown that the intracellular transmembrane G-protein-coupled oestrogen receptor (GPER) originally designated as GPR30 also mediates some of the actions attributed to oestrogens. Oestrogen and its receptors are important regulators of body weight and insulin sensitivity not only in women but also in men as demonstrated by ER mutations in rodents and humans. This article reviews the role of sex hormones and ERs in the context of obesity, insulin sensitivity and diabetes as well as the related clinical issues in women and men. © 2011 The Authors. Acta Physiologica © 2011 Scandinavian Physiological Society.

Molecular tools for cryptic Candida species identification with applications in a clinical laboratory.

PubMed

Gamarra, Soledad; Dudiuk, Catiana; Mancilla, Estefanía; Vera Garate, María Verónica; Guerrero, Sergio; Garcia-Effron, Guillermo

2013-01-01

Candida spp. includes more than 160 species but only 20 species pose clinical problems. C. albicans and C. parapsilosis account for more than 75% of all the fungemias worldwide. In 1995 and 2005, one C. albicans and two C. parapsilosis-related species were described, respectively. Using phenotypic traits, the identification of these newly described species is inconclusive or impossible. Thus, molecular-based procedures are mandatory. In the proposed educational experiment we have adapted different basic molecular biology techniques designed to identify these species including PCR, multiplex PCR, PCR-based restriction endonuclease analysis and nuclear ribosomal RNA amplification. During the classes, students acquired the ability to search and align gene sequences, design primers, and use bioinformatics software. Also, in the performed experiments, fungal molecular taxonomy concepts were introduced and the obtained results demonstrated that classic identification (phenotypic) in some cases needs to be complemented with molecular-based techniques. As a conclusion we can state that we present an inexpensive and well accepted group of classes involving important concepts that can be recreated in any laboratory. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Multinuclear nanoliter one-dimensional and two-dimensional NMR spectroscopy with a single non-resonant microcoil

NASA Astrophysics Data System (ADS)

Fratila, Raluca M.; Gomez, M. Victoria; Sýkora, Stanislav; Velders, Aldrik H.

2014-01-01

Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique, but its low sensitivity and highly sophisticated, costly, equipment severely constrain more widespread applications. Here we show that a non-resonant planar transceiver microcoil integrated in a microfluidic chip (detection volume 25 nl) can detect different nuclides in the full broad-band range of Larmor frequencies (at 9.4 T from 61 to 400 MHz). Routine one-dimensional (1D) and two-dimensional (2D), homo- and heteronuclear experiments can be carried out using the broad-band coil set-up. Noteworthy, heteronuclear 2D experiments can be performed in a straightforward manner on virtually any combination of nuclides (from classical 1H-13C to more exotic combinations like 19F-31P) both in coupled and decoupled mode. Importantly, the concept of a non-resonant system provides magnetic field-independent NMR probes; moreover, the small-volume alleviates problems related to field inhomogeneity, making the broad-band coil an attractive option for, for example, portable and table-top NMR systems.

Evidence of Natural Selection Acting on a Polymorphic Hybrid Incompatibility Locus in Mimulus

PubMed Central

Sweigart, Andrea L.; Flagel, Lex E.

2015-01-01

As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci—hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)—to small nuclear genomic regions (each <70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species. PMID:25428983

Rutherford-Bohr atom

NASA Astrophysics Data System (ADS)

Heilbron, J. L.

1981-03-01

Bohr used to introduce his attempts to explain clearly the principles of the quantum theory of the atom with an historical sketch, beginning invariably with the nuclear model proposed by Rutherford. That was sound pedagogy but bad history. The Rutherford-Bohr atom stands in the middle of a line of work initiated by J.J. Thomson and concluded by the invention of quantum mechanics. Thompson's program derived its inspiration from the peculiar emphasis on models characteristic of British physics of the 19th century. Rutherford's atom was a late product of the goals and conceptions of Victorian science. Bohr's modifications, although ultimately fatal to Thomson's program, initially gave further impetus to it. In the early 1920s the most promising approach to an adequate theory of the atom appeared to be the literal and detailed elaboration of the classical mechanics of multiply periodic orbits. The approach succeeded, demonstrating in an unexpected way the force of an argument often advanced by Thomson: because a mechanical model is richer in implications than the considerations for which it was advanced, it can suggest new directions of research that may lead to important discoveries.

Classical versus quantum dynamical chaos: Sensitivity to external perturbations, stability and reversibility

NASA Astrophysics Data System (ADS)

Sokolov, Valentin V.; Zhirov, Oleg V.; Kharkov, Yaroslav A.

The extraordinary complexity of classical trajectories of typical nonlinear systems that manifest stochastic behavior is intimately connected with exponential sensitivity to small variations of initial conditions and/or weak external perturbations. In rigorous terms, such classical systems are characterized by positive algorithmic complexity described by the Lyapunov exponent or, alternatively, by the Kolmogorov-Sinai entropy. The said implies that, in spite of the fact that, formally, any however complex trajectory of a perfectly isolated (closed) system is unique and differentiable for any certain initial conditions and the motion is perfectly reversible, it is impractical to treat that sort of classical systems as closed ones. Inevitably, arbitrary weak influence of an environment crucially impacts the dynamics. This influence, that can be considered as a noise, rapidly effaces the memory of initial conditions and turns the motion into an irreversible random process. In striking contrast, the quantum mechanics of the classically chaotic systems exhibit much weaker sensitivity and strong memory of the initial state. Qualitatively, this crucial difference could be expected in view of a much simpler structure of quantum states as compared to the extraordinary complexity of random and unpredictable classical trajectories. However the very notion of trajectories is absent in quantum mechanics so that the concept of exponential instability seems to be irrelevant in this case. The problem of a quantitative measure of complexity of a quantum state of motion, that is a very important and nontrivial issue of the theory of quantum dynamical chaos, is the one of our concern. With such a measure in hand, we quantitatively analyze the stability and reversibility of quantum dynamics in the presence of external noise. To solve this problem we point out that individual classical trajectories are of minor interest if the motion is chaotic. Properties of all of them are alike in this case and rather the behavior of their manifolds carries really valuable information. Therefore the phase-space methods and, correspondingly, the Liouville form of the classical mechanics become the most adequate. It is very important that, opposite to the classical trajectories, the classical phase space distribution and the Liouville equation have direct quantum analogs. Hence, the analogy and difference of classical and quantum dynamics can be traced by comparing the classical (W(c)(I,θ;t)) and quantum (Wigner function W(I,θ;t)) phase space distributions both expressed in identical phase-space variables but ruled by different(!) linear equations. The paramount property of the classical dynamical chaos is the exponentially fast structuring of the system's phase space on finer and finer scales. On the contrary, degree of structuring of the corresponding Wigner function is restricted by the quantization of the phase space. This makes Wigner function more coarse and relatively "simple" as compared to its classical counterpart. Fourier analysis affords quite suitable ground for analyzing complexity of a phase space distribution, that is equally valid in classical and quantum cases. We demonstrate that the typical number of Fourier harmonics is indeed a relevant measure of complexity of states of motion in both classical as well as quantum cases. This allowed us to investigate in detail and introduce a quantitative measure of sensitivity to an external noisy environment and formulate the conditions under which the quantum motion remains reversible. It turns out that while the mean number of harmonics of the classical phase-space distribution of a non-integrable system grows with time exponentially during the whole time of the motion, the time of exponential upgrowth of this number in the case of the corresponding quantum Wigner function is restricted only to the Ehrenfest interval 0 < t < tE - just the interval within which the Wigner function still satisfies the classical Liouville equation. We showed that the number of harmonics increases beyond this interval algebraically. This fact gains a crucial importance when the Ehrenfest time is so short that the exponential regime has no time to show up. Under this condition the quantum motion turns out to be quite stable and reversible.

Nuclear Fission: from more phenomenology and adjusted parameters to more fundamental theory and increased predictive power

NASA Astrophysics Data System (ADS)

Bulgac, Aurel; Jin, Shi; Magierski, Piotr; Roche, Kenneth; Schunck, Nicolas; Stetcu, Ionel

2017-11-01

Two major recent developments in theory and computational resources created the favorable conditions for achieving a microscopic description of fission dynamics in classically allowed regions of the collective potential energy surface, almost eighty years after its discovery in 1939 by Hahn and Strassmann [1]. The first major development was in theory, the extension of the Time-Dependent Density Functional Theory (TDDFT) [2-5] to superfluid fermion systems [6]. The second development was in computing, the emergence of powerful enough supercomputers capable of solving the complex systems of equations describing the time evolution in three dimensions without any restrictions of hundreds of strongly interacting nucleons. Thus the conditions have been created to renounce phenomenological models and incomplete microscopic treatments with uncontrollable approximations and/or assumptions in the description of the complex dynamics of fission. Even though the available nuclear energy density functionals (NEDFs) are phenomenological still, their accuracy is improving steadily and the prospects of being able to perform calculations of the nuclear fission dynamics and to predict many properties of the fission fragments, otherwise not possible to extract from experiments.

The human amygdaloid complex: a cytologic and histochemical atlas using Nissl, myelin, acetylcholinesterase and nicotinamide adenine dinucleotide phosphate diaphorase staining.

PubMed

Sims, K S; Williams, R S

1990-01-01

We examined the distribution of acetylcholinesterase and nicotinamide adenine dinucleotide phosphate diaphorase enzyme activity in the human amygdala using histochemical techniques. Both methods revealed compartments of higher or lower enzyme activity, in cells or neuropil, which corresponded to the nuclear subdivisions of the amygdala as defined with classical Nissl and myelin methods. The boundaries between the histochemical compartments were usually so sharp that the identification of these nuclear subdivisions was enhanced. There was also variation of staining intensity within many of the nuclear subdivisions, such as the lateral and central nuclei, anterior amygdaloid area and the intercalated groups. This histochemical difference corresponded to more subtle differences in Nissl and myelin staining patterns, and suggests further structural subdivisions of potential functional significance. We present a revised scheme of anatomical parcellation of the human amygdala based upon serial analysis with all four techniques. Our expectation is that this will allow the delineation of a clearer homology between the cytoarchitectonic subdivisions of the human amygdala and those of experimental animals.

Structural and calorimetric studies demonstrate that the hepatocyte nuclear factor 1β (HNF1β) transcription factor is imported into the nucleus via a monopartite NLS sequence.

PubMed

Wiedmann, Mareike M; Aibara, Shintaro; Spring, David R; Stewart, Murray; Brenton, James D

2016-09-01

The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in ovarian clear cell carcinoma (CCC) and is a potential therapeutic target. To explore potential approaches that block HNF1β transcription we have identified and characterised extensively the nuclear localisation signal (NLS) for HNF1β and its interactions with the nuclear protein import receptor, Importin-α. Pull-down assays demonstrated that the DNA binding domain of HNF1β interacted with a spectrum of Importin-α isoforms and deletion constructs tagged with eGFP confirmed that the HNF1β (229)KKMRRNR(235) sequence was essential for nuclear localisation. We further characterised the interaction between the NLS and Importin-α using complementary biophysical techniques and have determined the 2.4Å resolution crystal structure of the HNF1β NLS peptide bound to Importin-α. The functional, biochemical, and structural characterisation of the nuclear localisation signal present on HNF1β and its interaction with the nuclear import protein Importin-α provide the basis for the development of compounds targeting transcription factor HNF1β via its nuclear import pathway. Copyright © 2016. Published by Elsevier Inc.

78 FR 45579 - Request for a License to Import Radioactive Waste

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2013-07-29

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Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-19

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Change in the diagnosis from classical Hodgkin's lymphoma to anaplastic large cell lymphoma by (18)F flourodeoxyglucose positron emission tomography/computed tomography: Importance of recognising disease pattern on imaging and immunohistochemistry.

PubMed

Senthil, Raja; Mohapatra, Ranjan Kumar; Sampath, Mouleeswaran Koramadai; Sundaraiya, Sumati

2016-01-01

Anaplastic large cell lymphoma (ALCL) is a rare type of nonHodgkin's lymphoma (NHL), but one of the most common subtypes of T-cell lymphoma. It is an aggressive T-cell lymphoma, and some ALCL may mimic less aggressive classical HL histopathlogically. It may be misdiagnosed unless careful immunohistochemical examination is performed. As the prognosis and management of these two lymphomas vary significantly, it is important to make a correct diagnosis. We describe a case who was diagnosed as classical HL by histopathological examination of cervical lymph node, in whom (18)F-flouro deoxyglucose positron emission tomography/computed tomography appearances were unusual for HL and warranted review of histopathology that revealed anaplastic lymphoma kinase-1 negative anaplastic large T-cell lymphoma, Hodgkin-like variant, thereby changing the management.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piccioli, Zachary; McKee, Courtney H.; Leszczynski, Anna

We investigated the nuclear import of low risk HPV11 E7 protein using 1) transfection assays in HeLa cells with EGFP fusion plasmids containing 11E7 and its domains and 2) nuclear import assays in digitonin-permeabilized HeLa cells with GST fusion proteins containing 11E7 and its domains. The EGFP-11E7 and EGFP-11cE7{sub 39-98} localized mostly to the nucleus. The GST-11E7 and GST-11cE7{sub 39-98} were imported into the nuclei in the presence of either Ran-GDP or RanG19V-GTP mutant and in the absence of nuclear import receptors. This suggests that 11E7 enters the nucleus via a Ran-dependent pathway, independent of nuclear import receptors, mediated bymore » a nuclear localization signal located in its C-terminal domain (cNLS). This cNLS contains the zinc binding domain consisting of two copies of Cys-X-X-Cys motif. Mutagenesis of Cys residues in these motifs changed the localization of the EGFP-11cE7/-11E7 mutants to cytoplasmic, suggesting that the zinc binding domain is essential for nuclear localization of 11E7.« less

The modification of generalized uncertainty principle applied in the detection technique of femtosecond laser

NASA Astrophysics Data System (ADS)

Li, Ziyi

2017-12-01

Generalized uncertainty principle (GUP), also known as the generalized uncertainty relationship, is the modified form of the classical Heisenberg’s Uncertainty Principle in special cases. When we apply quantum gravity theories such as the string theory, the theoretical results suggested that there should be a “minimum length of observation”, which is about the size of the Planck-scale (10-35m). Taking into account the basic scale of existence, we need to fix a new common form of Heisenberg’s uncertainty principle in the thermodynamic system and make effective corrections to statistical physical questions concerning about the quantum density of states. Especially for the condition at high temperature and high energy levels, generalized uncertainty calculations have a disruptive impact on classical statistical physical theories but the present theory of Femtosecond laser is still established on the classical Heisenberg’s Uncertainty Principle. In order to improve the detective accuracy and temporal resolution of the Femtosecond laser, we applied the modified form of generalized uncertainty principle to the wavelength, energy and pulse time of Femtosecond laser in our work. And we designed three typical systems from micro to macro size to estimate the feasibility of our theoretical model and method, respectively in the chemical solution condition, crystal lattice condition and nuclear fission reactor condition.

Demonstration of quantum advantage in machine learning

NASA Astrophysics Data System (ADS)

Ristè, Diego; da Silva, Marcus P.; Ryan, Colm A.; Cross, Andrew W.; Córcoles, Antonio D.; Smolin, John A.; Gambetta, Jay M.; Chow, Jerry M.; Johnson, Blake R.

2017-04-01

The main promise of quantum computing is to efficiently solve certain problems that are prohibitively expensive for a classical computer. Most problems with a proven quantum advantage involve the repeated use of a black box, or oracle, whose structure encodes the solution. One measure of the algorithmic performance is the query complexity, i.e., the scaling of the number of oracle calls needed to find the solution with a given probability. Few-qubit demonstrations of quantum algorithms, such as Deutsch-Jozsa and Grover, have been implemented across diverse physical systems such as nuclear magnetic resonance, trapped ions, optical systems, and superconducting circuits. However, at the small scale, these problems can already be solved classically with a few oracle queries, limiting the obtained advantage. Here we solve an oracle-based problem, known as learning parity with noise, on a five-qubit superconducting processor. Executing classical and quantum algorithms using the same oracle, we observe a large gap in query count in favor of quantum processing. We find that this gap grows by orders of magnitude as a function of the error rates and the problem size. This result demonstrates that, while complex fault-tolerant architectures will be required for universal quantum computing, a significant quantum advantage already emerges in existing noisy systems.

HTLV-1 Tax-Induced Rapid Senescence Is Driven by the Transcriptional Activity of NF-κB and Depends on Chronically Activated IKKα and p65/RelA

PubMed Central

Ho, Yik-Khuan; Zhi, Huijun; DeBiaso, Dominic; Philip, Subha; Shih, Hsiu-Ming

2012-01-01

The HTLV-1 oncoprotein Tax is a potent activator of classical and alternative NF-κB pathways and is thought to promote cell proliferation and transformation via NF-κB activation. We showed recently that hyperactivation of NF-κB by Tax triggers a cellular senescence response (H. Zhi et al., PLoS Pathog. 7:e1002025, 2011). Inhibition of NF-κB activation by expression of I-κBα superrepressor or by small hairpin RNA (shRNA)-mediated knockdown of p65/RelA rescues cells from Tax-induced rapid senescence (Tax-IRS). Here we demonstrate that Tax-IRS is driven by the transcriptional activity of NF-κB. Knockdown of IKKγ, the primary Tax target, by shRNAs abrogated Tax-mediated activation of both classical and alternative NF-κB pathways and rendered knockdown cells resistant to Tax-IRS. Consistent with a critical role of IKKα in the transcriptional activity of NF-κB, IKKα deficiency drastically decreased NF-κB trans-activation by Tax, although it only modestly reduced Tax-mediated I-κBα degradation and NF-κB nuclear localization. In contrast, although IKKβ knockdown attenuated Tax-induced NF-κB transcriptional activation, the residual NF-κB activation in IKKβ-deficient cells was sufficient to trigger Tax-IRS. Importantly, the phenotypes of NIK and TAK1 knockdown were similar to those of IKKα and IKKβ knockdown, respectively. Finally, double knockdown of RelB and p100 had a minor effect on senescence induction by Tax. These data suggest that Tax, through its interaction with IKKγ, helps recruit NIK and TAK1 for IKKα and IKKβ activation, respectively. In the presence of Tax, the delineation between the classical and alternative NF-κB pathways becomes obscured. The senescence checkpoint triggered by Tax is driven by the transcriptional activity of NF-κB, which depends on activated IKKα and p65/RelA. PMID:22740410

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of {sup 64}Cu and {sup 67}Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nasrabadi, M. N., E-mail: mnnasrabadi@ast.ui.ac.ir; Sepiani, M.

2015-03-30

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE and LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of 64Cu and 67Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

NASA Astrophysics Data System (ADS)

Nasrabadi, M. N.; Sepiani, M.

2015-03-01

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE & LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

SUN1 Regulates HIV-1 Nuclear Import in a Manner Dependent on the Interaction between the Viral Capsid and Cellular Cyclophilin A.

PubMed

Luo, Xinlong; Yang, Wei; Gao, Guangxia

2018-07-01

Human immunodeficiency virus type 1 (HIV-1) can infect nondividing cells via passing through the nuclear pore complex. The nuclear membrane-imbedded protein SUN2 was recently reported to be involved in the nuclear import of HIV-1. Whether SUN1, which shares many functional similarities with SUN2, is involved in this process remained to be explored. Here we report that overexpression of SUN1 specifically inhibited infection by HIV-1 but not that by simian immunodeficiency virus (SIV) or murine leukemia virus (MLV). Overexpression of SUN1 did not affect reverse transcription but led to reduced accumulation of the 2-long-terminal-repeat (2-LTR) circular DNA and integrated viral DNA, suggesting a block in the process of nuclear import. HIV-1 CA was mapped as a determinant for viral sensitivity to SUN1. Treatment of SUN1-expressing cells with cyclosporine (CsA) significantly reduced the sensitivity of the virus to SUN1, and an HIV-1 mutant containing CA-G89A, which does not interact with cyclophilin A (CypA), was resistant to SUN1 overexpression. Downregulation of endogenous SUN1 inhibited the nuclear entry of the wild-type virus but not that of the G89A mutant. These results indicate that SUN1 participates in the HIV-1 nuclear entry process in a manner dependent on the interaction of CA with CypA. IMPORTANCE HIV-1 infects both dividing and nondividing cells. The viral preintegration complex (PIC) can enter the nucleus through the nuclear pore complex. It has been well known that the viral protein CA plays an important role in determining the pathways by which the PIC enters the nucleus. In addition, the interaction between CA and the cellular protein CypA has been reported to be important in the selection of nuclear entry pathways, though the underlying mechanisms are not very clear. Here we show that both SUN1 overexpression and downregulation inhibited HIV-1 nuclear entry. CA played an important role in determining the sensitivity of the virus to SUN1: the regulatory activity of SUN1 toward HIV-1 relied on the interaction between CA and CypA. These results help to explain how SUN1 is involved in the HIV-1 nuclear entry process. Copyright © 2018 American Society for Microbiology.

PREFACE: XXXIII Symposium on Nuclear Physics

NASA Astrophysics Data System (ADS)

Barrón-Palos, Libertad; Bijker, Roelof; Fossion, Ruben; Lizcano, David

2010-04-01

The attached PDF gives a full listing of contributors and organisation members. In the present volume of Journal of Physics: Conference Series we publish the proceedings of the "XXXIII Symposium on Nuclear Physics", that was held from January 5-8, 2010 at the Hacienda Cocoyoc, Morelos, Mexico. The proceedings contain the plenary talks that were presented during the conference. The abstracts of all contributions, plenary talks and posters, were published in the Conference Handbook. The Symposium on Nuclear Physics has a long and distinguished history. From the beginning it was intended to be a relatively small meeting designed to bring together some of the leading nuclear scientists in the field. Its most distinctive feature is to provide a forum for specialists in different areas of nuclear physics, both theorists and experimentalists, students, postdocs and senior scientists, in a relaxed and informal environment providing them with a unique opportunity to exchange ideas. After the first meeting in Oaxtepec in 1978, the Symposium was organized every year without interruption which makes the present one the 33rd in a row. This year's meeting was dedicated to the memory of Marcos Moshinsky, who passed away on April 1, 2009. Dr. Moshinsky was the most distinguished pioneer and promoter of nuclear physics in Mexico and Latin America and holds the record of 31 (out of 32) participations at the Symposium. In the inaugural session, Alejandro Frank (ICN-UNAM), Peter Hess (ICN-UNAM) and Jorge Flores (IF-UNAM) spoke in his honor and recalled the virtues that characterized him as a teacher, scientist, founder of schools and academic institutions, colleague and friend. His generosity, excellence and honesty were emphasized as the personal qualities that characterized both his personal and academic life. moshinksky_photo "Marcos Moshinsky (1921-2009)" The scientific program consisted of 26 invited talks and 20 posters on a wide variety of hot topics in contemporary nuclear physics, ranging from the traditional fields of nuclear structure and reactions to radioactive beams, nuclear astrophysics, hadronic physics, fundamental symmetries, ultrarelativistic heavy ions, cosmic rays and quantum chaos. The high quality of the talks, the prestige of the speakers and the broad spectrum of subjects covered in the meeting, shows that nuclear physics is a very active area at the frontier of scientific research which establishes bridges between many different disciplines. One of the exciting new areas in nuclear physics is that of radioactive beams. It provides a powerful tool not only to study exotic nuclei close to the proton and neutron drip lines to obtain important information about the nature of the nucleon-nucleon interaction in stable and unstable nuclei, but also to address questions of fundamental importance in nuclear astrophysics as well as in various applications like mass spectroscopy, the production of radioactive isotopes and medical applications (Galindo-Uribarri). There was a presentation on the FRIB project which is currently under construction in the USA and its relevance for nuclear astrophysics and the limits of stability (Sherrill and Schatz) In the session on nuclear structure, there were several talks on the nucleon-nucleon interaction in nuclei close to the proton and neutron drip lines, like neutron-proton pairing in nuclei with an equal number of protons and neutrons (Pittel), and studies of stable and unstable neutron-rich nuclei near the closed shells N = 82 and N = 50 using (d, p) transfer reactions and Coulomb excitation by means of radioactive beams (Cizewski and Padilla-Rodal). There were several talks on the importance of reaction rates for the excitation of spin-isospin resonances (Sakai), massive star evolution (Klapp) and nuclear synthesis and stellar evolution (Rolfs). In another presentation, the importance of rare isotopes for astrophysical processes was highlighted (Schatz). In addition, there were discussions about the importance of the Pauli exclusion principle and phase transitions in nuclear cluster models (Cseh and Hess) and an analysis of elastic scattering close to the Coulomb barrier in the framework of the optical model (Gómez-Camacho). Another important area is that of hadronic physics, the study of nucleons as composite systems of strongly interacting quarks and gluons. This field is situated on the borderline between nuclear and particle physics and presents a formidable challenge since the scale of the energies involved prohibits the use of the methods of perturbative QCD. In the session on hadronic physics, there were talks on chiral symmetry in non-perturbative QCD (Bietenholz), the structure of the nucleon in an unquenched quark model (Bijker), quark and meson degrees of freedom in Deeply Virtual Compton Scattering (Szczepaniak) and studies of hadronic structure by means of neutrino-induced pion production (Mariano). At ultrarelativistic energies, one can study the phase transition between hadronic matter and a new state of nuclear matter, the quark-gluon plasma. The Organizing Committee is proud to mention that the Cocoyoc 2010 meeting was one of first international conferences where the first scientific resuls from LHC were presented by the ALICE collaboration on proton-proton collisions at an energy of 900 GeV (Paic). In the session on cosmic rays, there was a talk on the origin of ultra high-energy cosmic rays (100 EeV = 1020 eV) as observed by the Pierre Auger Observatory (Medina-Tanco). Furthermore, there was a presentation of the project NuMoon which proposes to use the Moon's surface to detect cosmic rays that are out of the range of the Auger Observatory (Scholten). In addition, there was a review of the advances of the Mexican project HAWC, an observatory under construction in the Sierra Negra of Puebla (Sandoval) to study some of the most violentphenomena in the Universe through the detection of gamma rays with energies between hundreds of GeV and hundreds of TeV. At the other extreme of the energy scale is the field of the study of fundamental symmetries with novel experiments with ultra-cold neutrons. In this session, there were proposals by the NPDGamma collaboration (Gillis) and the abBA collaboration (Barr´on-Palos) to use polarized neutrons to study the weak hadronic interaction and neutron beta-decay, respectively. In another talk, there was a discussion on the measurement of the electric dipole moment of the neutron which is of fundamental importance to the standard model (Crawford). Finally, there was a session dedicated to quantum chaos where various proposals were discussed to identify chaotic behaviour in quantum systems, such as spectral fluctuations, time series and 1/f noise (Molina). Applications were presented to many-body systems in nuclear physics (Stránský) and the dripping-laser system as a quantum realization of the dripping faucet, one of the paradigms of classical chaos (Fossion). Many of the participants spent the free afternoon in the "magic village" of Tepoztlán to visit the arts and crafts market, the church, the convent or just to enjoy the good food. The most daring persons climbed the nearby cliff Tepozteco and the pyramid built on top of it to contemplate the spectacular view over the valley. As always, some of the participants of the conference prolonged their stay in Mexico to establish, to develop or to consolidate their collaborations with the local nuclear physics community. At the annual reunion of the Nuclear Physics Division which was held during the meeting, there was a long discussion on the future of the Symposium and, more generally, of the field of nuclear physics in Mexico and Latin America. Libertad Barr´on Palos, Roelof Bijker, Ruben Fossion and David Lizcano were re-elected as members of the Local Organizing Committee of the next Symposium which will be held at the Hacienda Cocoyoc from January 4-7, 2011, but now with Libertad as Chair. Libertad Barrón-Palos Roelof Bijker Ruben Fossion David Lizcano conference photo_photo

Worldwide Emerging Environmental Issues Affecting the U.S. Military. March 2011 Report

DTIC Science & Technology

2011-03-01

nuclear plant http://abcnews.go.com/Business/wireStory?id=13241596 Detection of radioactive material in the soil in Fukushima Daiichi Nuclear Power...and Nuclear Disasters in Japan The important reassessments following the Tōhoku earthquake and tsunami that hit Japan‟s northeast coast on March 11...and the nuclear waste issues are still not solved; hence, the Fukushima disaster might trigger important regime and development changes, such as

A Simple Global View of Fuel Burnup

NASA Astrophysics Data System (ADS)

Sekimoto, Hiroshi

2017-01-01

Reactor physics and fuel burnup are discussed in order to obtain a simple global view of the effects of nuclear reactor characteristics to fuel cycle system performance. It may provide some idea of free thinking and overall vision, though it is still a small part of nuclear energy system. At the beginning of this lecture, governing equations for nuclear reactors are presented. Since the set of these equations is so big and complicated, it is simplified by imposing some extreme conditions and the nuclear equilibrium equation is derived. Some features of future nuclear equilibrium state are obtained by solving this equation. The contribution of a nucleus charged into reactor core to the system performance indexes such as criticality is worth for understanding the importance of each nuclide. It is called nuclide importance and can be evaluated by using the equations adjoint to the nuclear equilibrium equation. Examples of some importances and their application to criticalily search problem are presented.

Positive nuclear BAP1 immunostaining helps differentiate non-small cell lung carcinomas from malignant mesothelioma

PubMed Central

Carbone, Michele; Shimizu, David; Napolitano, Andrea; Tanji, Mika; Pass, Harvey I.; Yang, Haining; Pastorino, Sandra

2016-01-01

The differential diagnosis between pleural malignant mesothelioma (MM) and lung cancer is often challenging. Immunohistochemical (IHC) stains used to distinguish these malignancies include markers that are most often positive in MM and less frequently positive in carcinomas, and vice versa. However, in about 10–20% of the cases, the IHC results can be confusing and inconclusive, and novel markers are sought to increase the diagnostic accuracy. We stained 45 non-small cell lung cancer samples (32 adenocarcinomas and 13 squamous cell carcinomas) with a monoclonal antibody for BRCA1-associated protein 1 (BAP1) and also with an IHC panel we routinely use to help differentiate MM from carcinomas, which include, calretinin, Wilms Tumor 1, cytokeratin 5, podoplanin D2-40, pankeratin CAM5.2, thyroid transcription factor 1, Napsin-A, and p63. Nuclear BAP1 expression was also analyzed in 35 MM biopsies. All 45 non-small cell lung cancer biopsies stained positive for nuclear BAP1, whereas 22/35 (63%) MM biopsies lacked nuclear BAP1 staining, consistent with previous data. Lack of BAP1 nuclear staining was associated with MM (two-tailed Fisher's Exact Test, P = 5.4 × 10−11). Focal BAP1 staining was observed in a subset of samples, suggesting polyclonality. Diagnostic accuracy of other classical IHC markers was in agreement with previous studies. Our study indicated that absence of nuclear BAP1 stain helps differentiate MM from lung carcinomas. We suggest that BAP1 staining should be added to the IHC panel that is currently used to distinguish these malignancies. PMID:27447750

Teaching the Interrelationship between Stress, Emotions, and Cardiovascular Risk Using a Classic Paper by Walter Cannon

ERIC Educational Resources Information Center

Gwirtz, Patricia A.

2008-01-01

Classroom discussion of the classic article by Walter B. Cannon in 1914, entitled "The emergency function of the adrenal medulla in pain and the major emotions," is an excellent tool to teach graduate students the interaction between stress, emotions, and cardiovascular function. Using this article, we are able to review important early research…

Mixed Quantum/Classical Theory for Molecule-Molecule Inelastic Scattering: Derivations of Equations and Application to N2 + H2 System.

PubMed

Semenov, Alexander; Babikov, Dmitri

2015-12-17

The mixed quantum classical theory, MQCT, for inelastic scattering of two molecules is developed, in which the internal (rotational, vibrational) motion of both collision partners is treated with quantum mechanics, and the molecule-molecule scattering (translational motion) is described by classical trajectories. The resultant MQCT formalism includes a system of coupled differential equations for quantum probability amplitudes, and the classical equations of motion in the mean-field potential. Numerical tests of this theory are carried out for several most important rotational state-to-state transitions in the N2 + H2 system, in a broad range of collision energies. Besides scattering resonances (at low collision energies) excellent agreement with full-quantum results is obtained, including the excitation thresholds, the maxima of cross sections, and even some smaller features, such as slight oscillations of energy dependencies. Most importantly, at higher energies the results of MQCT are nearly identical to the full quantum results, which makes this approach a good alternative to the full-quantum calculations that become computationally expensive at higher collision energies and for heavier collision partners. Extensions of this theory to include vibrational transitions or general asymmetric-top rotor (polyatomic) molecules are relatively straightforward.

De-quantisation

NASA Astrophysics Data System (ADS)

Gruska, Jozef

2012-06-01

One of the most basic tasks in quantum information processing, communication and security (QIPCC) research, theoretically deep and practically important, is to find bounds on how really important are inherently quantum resources for speeding up computations. This area of research is bringing a variety of results that imply, often in a very unexpected and counter-intuitive way, that: (a) surprisingly large classes of quantum circuits and algorithms can be efficiently simulated on classical computers; (b) the border line between quantum processes that can and cannot be efficiently simulated on classical computers is often surprisingly thin; (c) the addition of a seemingly very simple resource or a tool often enormously increases the power of available quantum tools. These discoveries have put also a new light on our understanding of quantum phenomena and quantum physics and on the potential of its inherently quantum and often mysteriously looking phenomena. The paper motivates and surveys research and its outcomes in the area of de-quantisation, especially presents various approaches and their outcomes concerning efficient classical simulations of various families of quantum circuits and algorithms. To motivate this area of research some outcomes in the area of de-randomization of classical randomized computations.

Nuclear Powerplant Safety: Design and Planning.

ERIC Educational Resources Information Center

Department of Energy, Washington, DC. Nuclear Energy Office.

The most important concern in the design, construction and operation of nuclear powerplants is safety. Nuclear power is one of the major contributors to the nation's supply of electricity; therefore, it is important to assure its safe use. Each different type of powerplant has special design features and systems to protect health and safety. One…

On the thermal efficiency of power cycles in finite time thermodynamics

NASA Astrophysics Data System (ADS)

Momeni, Farhang; Morad, Mohammad Reza; Mahmoudi, Ashkan

2016-09-01

The Carnot, Diesel, Otto, and Brayton power cycles are reconsidered endoreversibly in finite time thermodynamics (FTT). In particular, the thermal efficiency of these standard power cycles is compared to the well-known results in classical thermodynamics. The present analysis based on FTT modelling shows that a reduction in both the maximum and minimum temperatures of the cycle causes the thermal efficiency to increase. This is antithetical to the existing trend in the classical references. Under the assumption of endoreversibility, the relation between the efficiencies is also changed to {η }{{Carnot}}\\gt {η }{{Brayton}}\\gt {η }{{Diesel}}\\gt {η }{{Otto}}, which is again very different from the corresponding classical results. The present results benefit a better understanding of the important role of irreversibility on heat engines in classical thermodynamics.

Identification of karyopherins involved in the nuclear import of RNA exosome subunit Rrp6 in Saccharomyces cerevisiae.

PubMed

Gonzales-Zubiate, Fernando A; Okuda, Ellen K; Da Cunha, Julia P C; Oliveira, Carla Columbano

2017-07-21

The exosome is a conserved multiprotein complex essential for RNA processing and degradation. The nuclear exosome is a key factor for pre-rRNA processing through the activity of its catalytic subunits, Rrp6 and Rrp44. In Saccharomyces cerevisiae , Rrp6 is exclusively nuclear and has been shown to interact with exosome cofactors. With the aim of analyzing proteins associated with the nuclear exosome, in this work, we purified the complex with Rrp6-TAP, identified the co-purified proteins by mass spectrometry, and found karyopherins to be one of the major groups of proteins enriched in the samples. By investigating the biological importance of these protein interactions, we identified Srp1, Kap95, and Sxm1 as the most important karyopherins for Rrp6 nuclear import and the nuclear localization signals recognized by them. Based on the results shown here, we propose a model of multiple pathways for the transport of Rrp6 to the nucleus. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Nuclear Import and Export of the Thyroid Hormone Receptor.

PubMed

Zhang, Jibo; Roggero, Vincent R; Allison, Lizabeth A

2018-01-01

The thyroid hormone receptors, TRα1 and TRβ1, are members of the nuclear receptor superfamily that forms one of the most abundant classes of transcription factors in multicellular organisms. Although primarily localized to the nucleus, TRα1 and TRβ1 shuttle rapidly between the nucleus and cytoplasm. The fine balance between nuclear import and export of TRs has emerged as a critical control point for modulating thyroid hormone-responsive gene expression. Mutagenesis studies have defined two nuclear localization signal (NLS) motifs that direct nuclear import of TRα1: NLS-1 in the hinge domain and NLS-2 in the N-terminal A/B domain. Three nuclear export signal (NES) motifs reside in the ligand-binding domain. A combined approach of shRNA-mediated knockdown and coimmunoprecipitation assays revealed that nuclear entry of TRα1 is facilitated by importin 7, likely through interactions with NLS-2, and importin β1 and the adapter importin α1 interacting with both NLS-1 and NLS-2. Interestingly, TRβ1 lacks NLS-2 and nuclear import depends solely on the importin α1/β1 heterodimer. Heterokaryon and fluorescence recovery after photobleaching shuttling assays identified multiple exportins that play a role in nuclear export of TRα1, including CRM1 (exportin 1), and exportins 4, 5, and 7. Even single amino acid changes in TRs dramatically alter their intracellular distribution patterns. We conclude that mutations within NLS and NES motifs affect nuclear shuttling activity, and propose that TR mislocalization contributes to the development of some types of cancer and Resistance to Thyroid Hormone syndrome. © 2018 Elsevier Inc. All rights reserved.

Troponin T3 regulates nuclear localization of the calcium channel Ca{sub v}β{sub 1a} subunit in skeletal muscle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Tan; Taylor, Jackson; Jiang, Yang

The voltage-gated calcium channel (Ca{sub v}) β{sub 1a} subunit (Ca{sub v}β{sub 1a}) plays an important role in excitation–contraction coupling (ECC), a process in the myoplasm that leads to muscle-force generation. Recently, we discovered that the Ca{sub v}β{sub 1a} subunit travels to the nucleus of skeletal muscle cells where it helps to regulate gene transcription. To determine how it travels to the nucleus, we performed a yeast two-hybrid screening of the mouse fast skeletal muscle cDNA library and identified an interaction with troponin T3 (TnT3), which we subsequently confirmed by co-immunoprecipitation and co-localization assays in mouse skeletal muscle in vivo andmore » in cultured C2C12 muscle cells. Interacting domains were mapped to the leucine zipper domain in TnT3 COOH-terminus (160–244 aa) and Ca{sub v}β{sub 1a} NH{sub 2}-terminus (1–99 aa), respectively. The double fluorescence assay in C2C12 cells co-expressing TnT3/DsRed and Ca{sub v}β{sub 1a}/YFP shows that TnT3 facilitates Ca{sub v}β{sub 1a} nuclear recruitment, suggesting that the two proteins play a heretofore unknown role during early muscle differentiation in addition to their classical role in ECC regulation. - Highlights: • Previously, we demonstrated that Ca{sub v}β{sub 1a} is a gene transcription regulator. • Here, we show that TnT3 interacts with Ca{sub v}β{sub 1a}. • We mapped TnT3 and Ca{sub v}β{sub 1a} interaction domain. • TnT3 facilitates Ca{sub v}β{sub 1a} nuclear enrichment. • The two proteins play a heretofore unknown role during early muscle differentiation.« less

Development of Online Spectroscopic pH Monitoring for Nuclear Fuel Reprocessing Plants: Weak Acid Schemes.

PubMed

Casella, Amanda J; Ahlers, Laura R H; Campbell, Emily L; Levitskaia, Tatiana G; Peterson, James M; Smith, Frances N; Bryan, Samuel A

2015-05-19

In nuclear fuel reprocessing, separating trivalent minor actinides and lanthanide fission products is extremely challenging and often necessitates tight pH control in TALSPEAK (Trivalent Actinide-Lanthanide Separation by Phosphorus reagent Extraction from Aqueous Komplexes) separations. In TALSPEAK and similar advanced processes, aqueous pH is one of the most important factors governing the partitioning of lanthanides and actinides between an aqueous phase containing a polyaminopolycarboxylate complexing agent and a weak carboxylic acid buffer and an organic phase containing an acidic organophosphorus extractant. Real-time pH monitoring would significantly increase confidence in the separation performance. Our research is focused on developing a general method for online determination of the pH of aqueous solutions through chemometric analysis of Raman spectra. Spectroscopic process-monitoring capabilities, incorporated in a counter-current centrifugal contactor bank, provide a pathway for online, real-time measurement of solution pH. The spectroscopic techniques are process-friendly and can be easily configured for online applications, whereas classic potentiometric pH measurements require frequent calibration/maintenance and have poor long-term stability in aggressive chemical and radiation environments. Raman spectroscopy discriminates between the protonated and deprotonated forms of the carboxylic acid buffer, and the chemometric processing of the Raman spectral data with PLS (partial least-squares) regression provides a means to quantify their respective abundances and therefore determine the solution pH. Interpretive quantitative models have been developed and validated under a range of chemical composition and pH conditions using a lactic acid/lactate buffer system. The developed model was applied to new spectra obtained from online spectral measurements during a solvent extraction experiment using a counter-current centrifugal contactor bank. The model predicted the pH of this validation data set within 11% for pH > 2, thus demonstrating that this technique could provide the capability of monitoring pH online in applications such as nuclear fuel reprocessing.

Quantitative characterization of non-classic polarization of cations on clay aggregate stability.

PubMed

Hu, Feinan; Li, Hang; Liu, Xinmin; Li, Song; Ding, Wuquan; Xu, Chenyang; Li, Yue; Zhu, Longhui

2015-01-01

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10-5 to 10-1 mol L-1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation-surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability.

Quantitative Characterization of Non-Classic Polarization of Cations on Clay Aggregate Stability

PubMed Central

Hu, Feinan; Li, Hang; Liu, Xinmin; Li, Song; Ding, Wuquan; Xu, Chenyang; Li, Yue; Zhu, Longhui

2015-01-01

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10−5 to 10−1 mol L−1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation–surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability. PMID:25874864

p53 in pure epithelioid PEComa: an immunohistochemistry study and gene mutation analysis.

PubMed

Bing, Zhanyong; Yao, Yuan; Pasha, Theresa; Tomaszewski, John E; Zhang, Paul J

2012-04-01

Pure epithelioid PEComa (PEP; so-called epithelioid angiomyolipoma) is rare and is more often associated with aggressive behaviors. The pathogenesis of PEP has been poorly understood. The authors studied p53 expression and gene mutation in PEPs by immunohistochemistry, single-strand conformation polymorphism, and direct sequencing in paraffin material from 8 PEPs. A group of classic angiomyolipomas (AMLs) were also analyzed for comparison. Five PEPs were from kidneys and 1 each from the heart, the liver, and the uterus. PEPs showed much stronger p53 nuclear staining (Allred score 6.4 ± 2.5) than the classic AML (2.3 ± 2.9) (P < .01). There was no p53 single-strand conformation polymorphism identified in either the PEPs or the 8 classic AMLs. p53 mutation analyses by direct sequencing of exons 5 to 9 showed 4 mutations in 3 of 8 PEPs but none in any of the 8 classic AMLs. The mutations included 2 missense mutations in a hepatic PEComa and 2 silent mutations in 2 renal PEPs. Both the missense mutations in the hepatic PEComa involved the exon 5, one involving codon 165, with change from CAG to CAC (coding amino acid changed from glutamine to histidine), and the other involving codon 182, with change from TGC to TAC (coding amino acid changed from cysteine to tyrosine). The finding of stronger p53 expression and mutations in epithelioid angiomyolipomas might have contributed to their less predictable behavior. However, the abnormal p53 expression cannot be entirely explained by p53 mutations in the exons examined in the PEPs.

Molecular dynamics simulations of bubble nucleation in dark matter detectors.

PubMed

Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

2016-01-01

Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.

Fluorescent recovery after photobleaching (FRAP) analysis of nuclear export rates identifies intrinsic features of nucleocytoplasmic transport.

PubMed

Cardarelli, Francesco; Tosti, Luca; Serresi, Michela; Beltram, Fabio; Bizzarri, Ranieri

2012-02-17

A quantitative description of carrier-mediated nuclear export in live cells is presented. To this end, we fused a prototypical leucine-rich nuclear export signal (NES) to GFP as a cargo model and expressed the fluorescent chimera in live CHO-K1 cells. By modeling FRAP data, we calculate the NES affinity for the export machinery and the maximum rate of nuclear export achievable at saturation of endogenous carriers. The measured active-export time through the Nuclear Pore Complex (NPC) is 18 ms, remarkably similar to the previously determined active-import rate. Also, our results reveal that active export/import and active export/passive diffusion fluxes are uncoupled, thus complementing previous reports on active import/passive diffusion uncoupling. These findings suggest differential gating at the NPC level.

Notch signaling regulates the responses of lipopolysaccharide-stimulated macrophages in the presence of immune complexes.

PubMed

Wongchana, Wipawee; Kongkavitoon, Pornrat; Tangtanatakul, Pattarin; Sittplangkoon, Chutamath; Butta, Patcharavadee; Chawalitpong, Supatta; Pattarakankul, Thitiporn; Osborne, Barbara A; Palaga, Tanapat

2018-01-01

Macrophages exhibit diverse effector phenotypes depending on the stimuli and their microenvironment. Classically activated macrophages are primed with interferon (IFN)γ and stimulated with pathogen-associated molecular patterns. They produce inflammatory mediators and inflammatory cytokines, such as IL-12. In the presence of immune complexes (ICs), activated macrophages have decreased IL-12 production and increased IL-10 production and presumably act as regulatory macrophages. Notch signaling has been shown to regulate the effector functions of classically activated macrophages. In this study, we investigated whether Notch signaling is active in lipopolysaccharide (LPS)-stimulated macrophages in the presence of ICs. LPS/IC stimulation increased the level of cleaved Notch1 in murine macrophages, while IC stimulation alone did not. Delta-like 4, but not Jagged1, was responsible for generating cleaved Notch1. The activation of Notch signaling by LPS/ICs depended upon NF-κB and MEK/Erk pathway activation. Macrophages with the targeted deletion of Rbpj, which encodes a DNA-binding protein central to canonical Notch signaling, produced significantly less IL-10 upon LPS/IC stimulation. A similar impact on IL-10 production was observed when Notch signaling was inhibited with a gamma-secretase inhibitor (GSI). Defects in NF-κB p50 nuclear localization were observed in GSI-treated macrophages and in Rbpj-/- macrophages, suggesting cross-regulation between the Notch and NF-κB pathways. Transcriptomic analysis revealed that Notch signaling regulates the transcription of genes involved in the cell cycle, macrophage activation, leukocyte migration and cytokine production in LPS/IC-stimulated macrophages. Taken together, these results suggest that the Notch signaling pathway plays an important role in regulating the functions of macrophages activated by LPS and ICs.

Progesterone inhibits proliferation and modulates expression of proliferation-Related genes in classical progesterone receptor-negative human BxPC3 pancreatic adenocarcinoma cells.

PubMed

Goncharov, Alexey I; Maslakova, Aitsana A; Polikarpova, Anna V; Bulanova, Elena A; Guseva, Alexandra A; Morozov, Ivan A; Rubtsov, Petr M; Smirnova, Olga V; Shchelkunova, Tatiana A

2017-01-01

Recent studies suggest that progesterone may possess anti-tumorigenic properties. However, a growth-modulatory role of progestins in human cancer cells remains obscure. With the discovery of a new class of membrane progesterone receptors (mPRs) belonging to the progestin and adipoQ receptor gene family, it becomes important to study the effect of this hormone on proliferation of tumor cells that do not express classical nuclear progesterone receptors (nPRs). To identify a cell line expressing high levels of mPRs and lacking nPRs, we examined mRNA levels of nPRs and three forms of mPRs in sixteen human tumor cell lines of different origin. High expression of mPR mRNA has been found in pancreatic adenocarcinoma BxPC3 cells, while nPR mRNA has not been detected in these cells. Western blot analysis confirmed these findings at the protein level. We revealed specific binding of labeled progesterone in these cells with affinity constant similar to that of human mPR expressed in yeast cells. Progesterone at high concentration of 20 μM significantly reduced the mRNA levels of proliferation markers Ki67 and PCNA, as well as of cyclin D1, and increased the mRNA levels of cyclin dependent kinase inhibitors p21 and p27. Progesterone (1 μM and 20 μM) significantly inhibited proliferative activity of BxPC3 cells. These results point to anti-proliferative effects of the progesterone high concentrations on BxPC3 cells and suggest that activation of mPRs may mediate this action. Our data are a starting point for further investigations regarding the application of progesterone in pancreatic cancer. Copyright © 2016 Elsevier Ltd. All rights reserved.

Geospatial Image Mining For Nuclear Proliferation Detection: Challenges and New Opportunities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vatsavai, Raju; Bhaduri, Budhendra L; Cheriyadat, Anil M

2010-01-01

With increasing understanding and availability of nuclear technologies, and increasing persuasion of nuclear technologies by several new countries, it is increasingly becoming important to monitor the nuclear proliferation activities. There is a great need for developing technologies to automatically or semi-automatically detect nuclear proliferation activities using remote sensing. Images acquired from earth observation satellites is an important source of information in detecting proliferation activities. High-resolution remote sensing images are highly useful in verifying the correctness, as well as completeness of any nuclear program. DOE national laboratories are interested in detecting nuclear proliferation by developing advanced geospatial image mining algorithms. Inmore » this paper we describe the current understanding of geospatial image mining techniques and enumerate key gaps and identify future research needs in the context of nuclear proliferation.« less

Prolonged exposure to particulate chromate inhibits RAD51 nuclear import mediator proteins.

PubMed

Browning, Cynthia L; Wise, John Pierce

2017-09-15

Particulate hexavalent chromium (Cr(VI)) is a human lung carcinogen and a human health concern. The induction of structural chromosome instability is considered to be a driving mechanism of Cr(VI)-induced carcinogenesis. Homologous recombination repair protects against Cr(VI)-induced chromosome damage, due to its highly accurate repair of Cr(VI)-induced DNA double strand breaks. However, recent studies demonstrate Cr(VI) inhibits homologous recombination repair through the misregulation of RAD51. RAD51 is an essential protein in HR repair that facilitates the search for a homologous sequence. Recent studies show prolonged Cr(VI) exposure prevents proper RAD51 subcellular localization, causing it to accumulate in the cytoplasm. Since nuclear import of RAD51 is crucial to its function, this study investigated the effect of Cr(VI) on the RAD51 nuclear import mediators, RAD51C and BRCA2. We show acute (24h) Cr(VI) exposure induces the proper localization of RAD51C and BRCA2. In contrast, prolonged (120h) exposure increased the cytoplasmic localization of both proteins, although RAD51C localization was more severely impaired. These results correlate temporally with the previously reported Cr(VI)-induced RAD51 cytoplasmic accumulation. In addition, we found Cr(VI) does not inhibit interaction between RAD51 and its nuclear import mediators. Altogether, our results suggest prolonged Cr(VI) exposure inhibits the nuclear import of RAD51C, and to a lesser extent, BRCA2, which results in the cytoplasmic accumulation of RAD51. Cr(VI)-induced inhibition of nuclear import may play a key role in its carcinogenic mechanism since the nuclear import of many tumor suppressor proteins and DNA repair proteins is crucial to their function. Copyright © 2017 Elsevier Inc. All rights reserved.

Steady-state nuclear actin levels are determined by export competent actin pool.

PubMed

Skarp, Kari-Pekka; Huet, Guillaume; Vartiainen, Maria K

2013-10-01

A number of studies in the last decade have irrevocably promoted actin into a fully fledged member of the nuclear compartment, where it, among other crucial tasks, facilitates transcription and chromatin remodeling. Changes in nuclear actin levels have been linked to different cellular processes: decreased nuclear actin to quiescence and increased nuclear actin to differentiation. Importin 9 and exportin 6 transport factors are responsible for the continuous nucleocytoplasmic shuttling of actin, but the mechanisms, which result in modulated actin levels, have not been characterized. We find that in cells growing under normal growth conditions, the levels of nuclear actin vary considerably from cell to cell. To understand the basis for this, we have extensively quantified several cellular parameters while at the same time recording the import and export rates of green fluorescent protein (GFP)-tagged actin. Surprisingly, our dataset shows that the ratio of nuclear to cytoplasmic fluorescence intensity, but not nuclear shape, size, cytoplasm size, or their ratio, correlates negatively with both import and export rate of actin. This suggests that high-nuclear actin content is maintained by both diminished import and export. The high nuclear actin containing cells still show high mobility of actin, but it is not export competent, suggesting increased binding of actin to nuclear complexes. Creation of such export incompetent actin pool would ensure enough actin is retained in the nucleus and make it available for the various nuclear functions described for actin. Copyright © 2013 Wiley Periodicals, Inc.

Regulated transport into the nucleus of herpesviridae DNA replication core proteins.

PubMed

Gualtiero, Alvisi; Jans, David A; Camozzi, Daria; Avanzi, Simone; Loregian, Arianna; Ripalti, Alessandro; Palù, Giorgio

2013-09-16

The Herpesvirdae family comprises several major human pathogens belonging to three distinct subfamilies. Their double stranded DNA genome is replicated in the nuclei of infected cells by a number of host and viral products. Among the latter the viral replication complex, whose activity is strictly required for viral replication, is composed of six different polypeptides, including a two-subunit DNA polymerase holoenzyme, a trimeric primase/helicase complex and a single stranded DNA binding protein. The study of herpesviral DNA replication machinery is extremely important, both because it provides an excellent model to understand processes related to eukaryotic DNA replication and it has important implications for the development of highly needed antiviral agents. Even though all known herpesviruses utilize very similar mechanisms for amplification of their genomes, the nuclear import of the replication complex components appears to be a heterogeneous and highly regulated process to ensure the correct spatiotemporal localization of each protein. The nuclear transport process of these enzymes is controlled by three mechanisms, typifying the main processes through which protein nuclear import is generally regulated in eukaryotic cells. These include cargo post-translational modification-based recognition by the intracellular transporters, piggy-back events allowing coordinated nuclear import of multimeric holoenzymes, and chaperone-assisted nuclear import of specific subunits. In this review we summarize these mechanisms and discuss potential implications for the development of antiviral compounds aimed at inhibiting the Herpesvirus life cycle by targeting nuclear import of the Herpesvirus DNA replicating enzymes.

Dynamic Network-Based Epistasis Analysis: Boolean Examples

PubMed Central

Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

2011-01-01

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and single-path assumption, but also by demonstrating the importance of considering temporal dynamics, and specifically introducing the usefulness of Boolean network models and also reviewing some key properties of network approaches. PMID:22645556

A new version of JQMD for soft heavy-ion collisions

NASA Astrophysics Data System (ADS)

Mancusi, Davide; Niita, Koji; Sihver, Lembit

The JQMD model (JAERI Quantum Molecular Dynamics) has been successfully used for a long time now to describe many different aspects of nuclear reactions in a unified way. However, in soft, peripheral heavy-ion collisions, the JQMD model shows instabilities and spurious fluctuations that are responsible for an overestimation of few-nucleon-removal cross sections. The reasons of this shortcoming are, firstly, that the JQMD is not fully relativistically covariant, and secondly, that the fermionic nature of the nuclear ground state cannot be faithfully reproduced in a semi-classical framework. We present here R-JQMD, an improved and fully covariant version of JQMD that also features a new ground-state initialisation algorithm for nuclei. The new code is only marginally slower than JQMD and it produces physically sounder results. We also discuss whether R-JQMD can be adjusted to improve JQMD's agreement with measured heavy-ion fragmentation cross sections.

A didactic proposal about Rutherford backscattering spectrometry with theoretic, experimental, simulation and application activities

NASA Astrophysics Data System (ADS)

Corni, Federico; Michelini, Marisa

2018-01-01

Rutherford backscattering spectrometry is a nuclear analysis technique widely used for materials science investigation. Despite the strict technical requirements to perform the data acquisition, the interpretation of a spectrum is within the reach of general physics students. The main phenomena occurring during a collision between helium ions—with energy of a few MeV—and matter are: elastic nuclear collision, elastic scattering, and, in the case of non-surface collision, ion stopping. To interpret these phenomena, we use classical physics models: material point elastic collision, unscreened Coulomb scattering, and inelastic energy loss of ions with electrons, respectively. We present the educational proposal for Rutherford backscattering spectrometry, within the framework of the model of educational reconstruction, following a rationale that links basic physics concepts with quantities for spectra analysis. This contribution offers the opportunity to design didactic specific interventions suitable for undergraduate and secondary school students.

Dynamical and many-body correlation effects in the kinetic energy spectra of isotopes produced in nuclear multifragmentation

NASA Astrophysics Data System (ADS)

Souza, S. R.; Donangelo, R.; Lynch, W. G.; Tsang, M. B.

2018-03-01

The properties of the kinetic energy spectra of light isotopes produced in the breakup of a nuclear source and during the de-excitation of its products are examined. The initial stage, at which the hot fragments are created, is modeled by the statistical multifragmentation model, whereas the Weisskopf-Ewing evaporation treatment is adopted to describe the subsequent fragment de-excitation, as they follow their classical trajectories dictated by the Coulomb repulsion among them. The energy spectra obtained are compared to available experimental data. The influence of the fusion cross section entering into the evaporation treatment is investigated and its influence on the qualitative aspects of the energy spectra turns out to be small. Although these aspects can be fairly well described by the model, the underlying physics associated with the quantitative discrepancies remains to be understood.

DOE Office of Scientific and Technical Information (OSTI.GOV)

J-M. Laget

Exclusive reactions induced at high momentum transfer in few body systems provide us with an original way to study the production and propagation of hadrons in cold nuclear matter. In very well-defined parts of the phase space, the reaction amplitude develops a logarithmic singularity. It is on solid ground since it depends on only on-shell elementary amplitudes and on low momentum components of the nuclear wave function. This is the best window for studying the propagation of exotic configurations of hadrons such as the onset of color transparency. It may appear earlier in meson-photoproduction reactions, more particularly in the strangemore » sector, than in the more classical quasi-elastic scattering of electrons. More generally, those reactions provide us with the best tool to determine the cross section of the scattering of various hadrons (strange particles, vector mesons) from the nucleon and to obtain the production of possible exotic states.« less

Transcriptional targets shared by estrogen receptor- related receptors (ERRs) and estrogen receptor (ER) alpha, but not by ERbeta.

PubMed Central

Vanacker, J M; Pettersson, K; Gustafsson, J A; Laudet, V

1999-01-01

The physiological activities of estrogens are thought to be mediated by specific nuclear receptors, ERalpha and ERbeta. However, certain tissues, such as the bone, that are highly responsive to estrogens only express a low level of these receptors. Starting from this apparent contradiction, we have evaluated the potentials of two related receptors ERRalpha and ERRbeta to intervene in estrogen signaling. ERalpha, ERRalpha and ERRbeta bind to and activate transcription through both the classical estrogen response element (ERE) and the SF-1 response element (SFRE). In contrast, ERbeta DNA-binding and transcriptional activity is restricted to the ERE. Accordingly, the osteopontin gene promoter is stimulated through SFRE sequences, by ERRalpha as well as by ERalpha, but not by ERbeta. Analysis of the cross-talk within the ER/ERR subgroup of nuclear receptors thus revealed common targets but also functional differences between the two ERs. PMID:10428965

A Compact Nuclear Fusion Reactor for Space Flights

NASA Astrophysics Data System (ADS)

Nastoyashchiy, Anatoly F.

2006-05-01

A small-scale nuclear fusion reactor is suggested based on the concepts of plasma confinement (with a high pressure gas) which have been patented by the author. The reactor considered can be used as a power setup in space flights. Among the advantages of this reactor is the use of a D3He fuel mixture which at burning gives main reactor products — charged particles. The energy balance considerably improves, as synchrotron radiation turn out "captured" in the plasma volume, and dangerous, in the case of classical magnetic confinement, instabilities in the direct current magnetic field configuration proposed do not exist. As a result, the reactor sizes are quite suitable (of the order of several meters). A possibility of making reactive thrust due to employment of ejection of multiply charged ions formed at injection of pellets from some adequate substance into the hot plasma center is considered.

In Appreciation Julian Schwinger: From Nuclear Physics and Quantum Electrodynamics to Source Theory and Beyond

NASA Astrophysics Data System (ADS)

Milton, Kimball A.

2007-01-01

Julian Schwinger’s influence on twentieth-century science is profound and pervasive. He is most famous for his renormalization theory of quantum electrodynamics, for which he shared the Nobel Prize in Physics for 1965 with Richard Feynman and Sin-itiro Tomonaga. This triumph undoubtedly was his most heroic work, but his legacy lives on chiefly through subtle and elegant work in classical electrodynamics, quantum variational principles, proper-time methods, quantum anomalies, dynamical mass generation, partial symmetry, and much more. Starting as just a boy, he rapidly became one of the preeminent nuclear physicists in the world in the late 1930s, led the theoretical development of radar technology at the Massachusetts Institute of Technology during World War II, and soon after the war conquered quantum electrodynamics, becoming the leading quantum-field theorist for two decades, before taking a more iconoclastic route during the last quarter century of his life.

Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

PubMed

Lee, Mi Kyung; Coker, David F

2016-08-18

An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.

Effect of estetrol, a selective nuclear estrogen receptor modulator, in mouse models of arterial and venous thrombosis.

PubMed

Valéra, Marie-Cécile; Noirrit-Esclassan, Emmanuelle; Dupuis, Marion; Fontaine, Coralie; Lenfant, Françoise; Briaux, Anne; Cabou, Cendrine; Garcia, Cedric; Lairez, Olivier; Foidart, Jean-Michel; Payrastre, Bernard; Arnal, Jean-François

2018-06-19

Estetrol (E4) is a natural estrogen synthesized exclusively during pregnancy by the human fetal liver, and the physiological role of this hormone is unknown. Interestingly, E4 was recently evaluated in preclinical and phase II-III clinical studies in combination with a progestin, with the advantage to not increase the circulating level of coagulation factors, at variance to oral estradiol or ethinylestradiol. Here, we evaluated the effect of E4 on hemostasis and thrombosis in mouse. Following chronic E4 treatment, mice exhibited a prolonged tail-bleeding time and were protected from arterial and also venous thrombosis in vivo. In addition, E4 treatment decreased ex vivo thrombus growth on collagen under arterial flow conditions. We recently showed that E4 activates uterine epithelial proliferation through nuclear estrogen receptor (ER) α. To analyze the impact of nuclear ERα actions on hemostasis and thrombosis, we generated hematopoietic chimera with bone marrow cells deficient for nuclear ERα. E4-induced protection against thromboembolism was significantly reduced in the absence of hematopoietic nuclear ERα activation, while the increased tail-bleeding time was not impacted by this deletion. In addition to its "liver friendly" profile described in women, our data shows that E4 has anti-thrombotic properties in various mouse models. Altogether, the natural fetal estrogen E4 could represent an attractive alternative to classic estrogens in oral contraception and treatment of menopause. Copyright © 2018. Published by Elsevier B.V.

Blm10 facilitates nuclear import of proteasome core particles

PubMed Central

Weberruss, Marion H; Savulescu, Anca F; Jando, Julia; Bissinger, Thomas; Harel, Amnon; Glickman, Michael H; Enenkel, Cordula

2013-01-01

Short-lived proteins are degraded by proteasome complexes, which contain a proteolytic core particle (CP) but differ in the number of regulatory particles (RPs) and activators. A recently described member of conserved proteasome activators is Blm10. Blm10 contains 32 HEAT-like modules and is structurally related to the nuclear import receptor importin/karyopherin β. In proliferating yeast, RP-CP assemblies are primarily nuclear and promote cell division. During quiescence, RP-CP assemblies dissociate and CP and RP are sequestered into motile cytosolic proteasome storage granuli (PSG). Here, we show that CP sequestration into PSG depends on Blm10, whereas RP sequestration into PSG is independent of Blm10. PSG rapidly clear upon the resumption of cell proliferation and proteasomes are relocated into the nucleus. Thereby, Blm10 facilitates nuclear import of CP. Blm10-bound CP serves as an import receptor–cargo complex, as Blm10 mediates the interaction with FG-rich nucleoporins and is dissociated from the CP by Ran-GTP. Thus, Blm10 represents the first CP-dedicated nuclear import receptor in yeast. PMID:23982732

Elusive active galactic nuclei

NASA Astrophysics Data System (ADS)

Maiolino, R.; Comastri, A.; Gilli, R.; Nagar, N. M.; Bianchi, S.; Böker, T.; Colbert, E.; Krabbe, A.; Marconi, A.; Matt, G.; Salvati, M.

2003-10-01

A fraction of active galactic nuclei do not show the classical Seyfert-type signatures in their optical spectra, i.e. they are optically `elusive'. X-ray observations are an optimal tool to identify this class of objects. We combine new Chandra observations with archival X-ray data in order to obtain a first estimate of the fraction of elusive active galactic nuclei (AGN) in local galaxies and to constrain their nature. Our results suggest that elusive AGN have a local density comparable to or even higher than optically classified Seyfert nuclei. Most elusive AGN are heavily absorbed in the X-rays, with gas column densities exceeding 1024 cm-2, suggesting that their peculiar nature is associated with obscuration. It is likely that in elusive AGN the nuclear UV source is completely embedded and the ionizing photons cannot escape, which prevents the formation of a classical narrow-line region. Elusive AGN may contribute significantly to the 30-keV bump of the X-ray background.

A many-body states picture of electronic friction: The case of multiple orbitals and multiple electronic states

NASA Astrophysics Data System (ADS)

Dou, Wenjie; Subotnik, Joseph E.

2016-08-01

We present a very general form of electronic friction as present when a molecule with multiple orbitals hybridizes with a metal electrode. To develop this picture of friction, we embed the quantum-classical Liouville equation (QCLE) within a classical master equation (CME). Thus, this article extends our previous work analyzing the case of one electronic level, as we may now treat the case of multiple levels and many electronic molecular states. We show that, in the adiabatic limit, where electron transitions are much faster than nuclear motion, the QCLE-CME reduces to a Fokker-Planck equation, such that nuclei feel an average force as well as friction and a random force—as caused by their interaction with the metallic electrons. Finally, we show numerically and analytically that our frictional results agree with other published results calculated using non-equilibrium Green's functions. Numerical recipes for solving this QCLE-CME will be provided in a subsequent paper.

A many-body states picture of electronic friction: The case of multiple orbitals and multiple electronic states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dou, Wenjie; Subotnik, Joseph E.

We present a very general form of electronic friction as present when a molecule with multiple orbitals hybridizes with a metal electrode. To develop this picture of friction, we embed the quantum-classical Liouville equation (QCLE) within a classical master equation (CME). Thus, this article extends our previous work analyzing the case of one electronic level, as we may now treat the case of multiple levels and many electronic molecular states. We show that, in the adiabatic limit, where electron transitions are much faster than nuclear motion, the QCLE-CME reduces to a Fokker-Planck equation, such that nuclei feel an average forcemore » as well as friction and a random force—as caused by their interaction with the metallic electrons. Finally, we show numerically and analytically that our frictional results agree with other published results calculated using non-equilibrium Green’s functions. Numerical recipes for solving this QCLE-CME will be provided in a subsequent paper.« less

Classical swine fever virus replicated poorly in cells from MxA transgenic pigs.

PubMed

Zhao, Yicheng; Wang, Tiedong; Yao, Li; Liu, Bo; Teng, Chunbo; Ouyang, Hongsheng

2016-08-17

In addition to their value as livestock, pigs are susceptible to classical swine fever virus (CSFV) and can serve as reservoirs for CSFV, allowing it to develop into an epizootic. CSFV, a pestivirus of the Flaviviridae family, has a single-stranded RNA genome. Recent research has indicated that the human MxA protein inhibits the life cycles of certain RNA viruses, such as members of the Bunyaviridae family, the Flaviviridae family and others. To produce pigs with antiviral protection against CSFV, transgenic pigs expressing human MxA were generated by nuclear transplantation. Cells from three MxA transgenic piglets were used to investigate in vitro antiviral activity of MxA aganist CSFV, and the results of in vitro indirect immunofluorescence assays, virus titration and real-time PCR indicated that the MxA transgenic pig has an antiviral capacity against CSFV. Transgene with human MxA on pigs is feasible. High levels of MxA expression do inhibit CSFV in vitro at early time points post-infection at 60-96dpi.

Metal Ion Modeling Using Classical Mechanics

PubMed Central

2017-01-01

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems. PMID:28045509

Autonomous quantum to classical transitions and the generalized imaging theorem

NASA Astrophysics Data System (ADS)

Briggs, John S.; Feagin, James M.

2016-03-01

The mechanism of the transition of a dynamical system from quantum to classical mechanics is of continuing interest. Practically it is of importance for the interpretation of multi-particle coincidence measurements performed at macroscopic distances from a microscopic reaction zone. Here we prove the generalized imaging theorem which shows that the spatial wave function of any multi-particle quantum system, propagating over distances and times large on an atomic scale but still microscopic, and subject to deterministic external fields and particle interactions, becomes proportional to the initial momentum wave function where the position and momentum coordinates define a classical trajectory. Currently, the quantum to classical transition is considered to occur via decoherence caused by stochastic interaction with an environment. The imaging theorem arises from unitary Schrödinger propagation and so is valid without any environmental interaction. It implies that a simultaneous measurement of both position and momentum will define a unique classical trajectory, whereas a less complete measurement of say position alone can lead to quantum interference effects.

Autonomous quantum to classical transitions and the generalized imaging theorem

DOE PAGES

Briggs, John S.; Feagin, James M.

2016-03-16

The mechanism of the transition of a dynamical system from quantum to classical mechanics is of continuing interest. Practically it is of importance for the interpretation of multi-particle coincidence measurements performed at macroscopic distances from a microscopic reaction zone. We prove the generalized imaging theorem which shows that the spatial wave function of any multi-particle quantum system, propagating over distances and times large on an atomic scale but still microscopic, and subject to deterministic external fields and particle interactions, becomes proportional to the initial momentum wave function where the position and momentum coordinates define a classical trajectory. Now, the quantummore » to classical transition is considered to occur via decoherence caused by stochastic interaction with an environment. The imaging theorem arises from unitary Schrödinger propagation and so is valid without any environmental interaction. It implies that a simultaneous measurement of both position and momentum will define a unique classical trajectory, whereas a less complete measurement of say position alone can lead to quantum interference effects.« less

Landscape simplification reduces classical biological control and crop yield.

PubMed

Grab, Heather; Danforth, Bryan; Poveda, Katja; Loeb, Greg

2018-03-01

Agricultural intensification resulting in the simplification of agricultural landscapes is known to negatively impact the delivery of key ecosystem services such as the biological control of crop pests. Both conservation and classical biological control may be influenced by the landscape context in which they are deployed; yet studies examining the role of landscape structure in the establishment and success of introduced natural enemies and their interactions with native communities are lacking. In this study, we investigated the relationship between landscape simplification, classical and conservation biological control services and importantly, the outcome of these interactions for crop yield. We showed that agricultural simplification at the landscape scale is associated with an overall reduction in parasitism rates of crop pests. Additionally, only introduced parasitoids were identified, and no native parasitoids were found in crop habitat, irrespective of agricultural landscape simplification. Pest densities in the crop were lower in landscapes with greater proportions of semi-natural habitats. Furthermore, farms with less semi-natural cover in the landscape and consequently, higher pest numbers, had lower yields than farms in less agriculturally dominated landscapes. Our study demonstrates the importance of landscape scale agricultural simplification in mediating the success of biological control programs and highlights the potential risks to native natural enemies in classical biological control programs against native insects. Our results represent an important contribution to an understanding of the landscape-mediated impacts on crop yield that will be essential to implementing effective policies that simultaneously conserve biodiversity and ecosystem services. © 2018 by the Ecological Society of America.

Structure of the classical scrape-off layer of a tokamak

NASA Astrophysics Data System (ADS)

Rozhansky, V.; Kaveeva, E.; Senichenkov, I.; Vekshina, E.

2018-03-01

The structure of the scrape-off layer (SOL) of a tokamak with little or no turbulent transport is analyzed. The analytical estimates of the density and electron temperature fall-off lengths of the SOL are put forward. It is demonstrated that the SOL width could be of the order of the ion poloidal gyroradius, as suggested in Goldston (2012 Nuclear Fusion 52 013009). The analytical results are supported by the results of the 2D simulations of the edge plasma with reduced transport coefficients performed by SOLPS-ITER transport code.

New Polymorph Form of Dexamethasone Acetate.

PubMed

Silva, Ronaldo Pedro da; Ambrósio, Mateus Felipe Schuchter; Piovesan, Luciana Almeida; Freitas, Maria Clara Ramalho; Aguiar, Daniel Lima Marques de; Horta, Bruno Araújo Cautiero; Epprecht, Eugenio Kahn; San Gil, Rosane Aguiar da Silva; Visentin, Lorenzo do Canto

2018-02-01

A new monohydrated polymorph of dexamethasone acetate was crystallized and its crystal structure characterized. The different analytical techniques used for describing its structural and vibrational properties were: single crystal and polycrystal X-ray diffraction, solid state nuclear magnetic resonance, infrared spectroscopy. A Hirshfeld surface analysis was carried out through self-arrangement cemented by H-bonds observed in this new polymorph. This new polymorph form appeared because of self-arrangement via classical hydrogen bonds around the water molecule. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Polarized hydrogen/deuterium molecules

NASA Astrophysics Data System (ADS)

Shestakov, Yu V.; Nikolenko, D. M.; Rachek, I. A.; Sadykov, R. Sh; Toporkov, D. K.; Yurchenko, A. V.; Zevakov, S. A.

2017-12-01

The prototype of a polarized molecular hydrogen/deuterium source which is based on the classical Stern-Gerlach separation scheme has been tested at the Budker Institute of Nuclear Physics (BINP), Novosibirsk. It consists of the circular slit nozzle cooled down to 6.5 K and the two superconducting sextupole magnets. The flux of polarized hydrogen molecules of 3·1012 mol/s was measured for a total gas flow through the nozzle of 5·10-2 Torr·l/s. The obtained results will be used to develop a much more intense source of polarized molecules.

Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Mukamel, Shaul, E-mail: smukamel@uci.edu

2015-07-28

Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings.

Importance of Nuclear Physics to NASA's Space Missions

NASA Technical Reports Server (NTRS)

Tripathi, R. K.; Wilson, J. W.; Cucinotta, F. A.

2001-01-01

We show that nuclear physics is extremely important for accurate risk assessments for space missions. Due to paucity of experimental input radiation interaction information it is imperative to develop reliable accurate models for the interaction of radiation with matter. State-of-the-art nuclear cross sections models have been developed at the NASA Langley Research center and are discussed.

Normal Telomere Length Maintenance in Saccharomyces cerevisiae Requires Nuclear Import of the Ever Shorter Telomeres 1 (Est1) Protein via the Importin Alpha Pathway

PubMed Central

Hawkins, Charlene

2014-01-01

The Est1 (ever shorter telomeres 1) protein is an essential component of yeast telomerase, a ribonucleoprotein complex that restores the repetitive sequences at chromosome ends (telomeres) that would otherwise be lost during DNA replication. Previous work has shown that the telomerase RNA component (TLC1) transits through the cytoplasm during telomerase biogenesis, but mechanisms of protein import have not been addressed. Here we identify three nuclear localization sequences (NLSs) in Est1p. Mutation of the most N-terminal NLS in the context of full-length Est1p reduces Est1p nuclear localization and causes telomere shortening—phenotypes that are rescued by fusion with the NLS from the simian virus 40 (SV40) large-T antigen. In contrast to that of the TLC1 RNA, Est1p nuclear import is facilitated by Srp1p, the yeast homolog of importin α. The reduction in telomere length observed at the semipermissive temperature in a srp1 mutant strain is rescued by increased Est1p expression, consistent with a defect in Est1p nuclear import. These studies suggest that at least two nuclear import pathways are required to achieve normal telomere length homeostasis in yeast. PMID:24906415

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

High resolution stalagmite climate record from the Yucatán Peninsula spanning the Maya terminal classic period

NASA Astrophysics Data System (ADS)

Medina-Elizalde, Martín; Burns, Stephen J.; Lea, David W.; Asmerom, Yemane; von Gunten, Lucien; Polyak, Victor; Vuille, Mathias; Karmalkar, Ambarish

2010-09-01

The decline of the Classic Maya civilization was complex and geographically variable, and occurred over a ~ 150-year interval, known as the Terminal Classic Period (TCP, C.E. 800-950). Paleoclimate studies based on lake sediments from the Yucatán Peninsula lowlands suggested that drought prevailed during the TCP and was likely an important factor in the disintegration of the Classic Maya civilization. The lacustrine evidence for decades of severe drought in the Yucatán Peninsula, however, does not readily explain the long 150-year socio-political decline of the Classic Maya civilization. Here we present a new, absolute-dated, high-resolution stalagmite δ18O record from the northwest Yucatán Peninsula that provides a much more detailed picture of climate variability during the last 1500 years. Direct calibration between stalagmite δ18O and rainfall amount offers the first quantitative estimation of rainfall variability during the Terminal Classic Period. Our results show that eight severe droughts, lasting from 3 to 18 years, occurred during major depopulation events of Classic Maya city-states. During these droughts, rainfall was reduced by 52% to 36%. The number and short duration of the dry intervals help explain why the TCP collapse of the Mayan civilization occurred over 150 years.

Uncertainties in the production of p nuclides in thermonuclear supernovae determined by Monte Carlo variations

NASA Astrophysics Data System (ADS)

Nishimura, N.; Rauscher, T.; Hirschi, R.; Murphy, A. St J.; Cescutti, G.; Travaglio, C.

2018-03-01

Thermonuclear supernovae originating from the explosion of a white dwarf accreting mass from a companion star have been suggested as a site for the production of p nuclides. Such nuclei are produced during the explosion, in layers enriched with seed nuclei coming from prior strong s processing. These seeds are transformed into proton-richer isotopes mainly by photodisintegration reactions. Several thousand trajectories from a 2D explosion model were used in a Monte Carlo approach. Temperature-dependent uncertainties were assigned individually to thousands of rates varied simultaneously in post-processing in an extended nuclear reaction network. The uncertainties in the final nuclear abundances originating from uncertainties in the astrophysical reaction rates were determined. In addition to the 35 classical p nuclides, abundance uncertainties were also determined for the radioactive nuclides 92Nb, 97, 98Tc, 146Sm, and for the abundance ratios Y(92Mo)/Y(94Mo), Y(92Nb)/Y(92Mo), Y(97Tc)/Y(98Ru), Y(98Tc)/Y(98Ru), and Y(146Sm)/Y(144Sm), important for Galactic Chemical Evolution studies. Uncertainties found were generally lower than a factor of 2, although most nucleosynthesis flows mainly involve predicted rates with larger uncertainties. The main contribution to the total uncertainties comes from a group of trajectories with high peak density originating from the interior of the exploding white dwarf. The distinction between low-density and high-density trajectories allows more general conclusions to be drawn, also applicable to other simulations of white dwarf explosions.

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay.

PubMed

Cui, Heying; Loftus, Kyle M; Noell, Crystal R; Solmaz, Sozanne R

2018-05-03

Cyclin-dependent kinase 1 (Cdk1) is a master controller for the cell cycle in all eukaryotes and phosphorylates an estimated 8 - 13% of the proteome; however, the number of identified targets for Cdk1, particularly in human cells is still low. The identification of Cdk1-specific phosphorylation sites is important, as they provide mechanistic insights into how Cdk1 controls the cell cycle. Cell cycle regulation is critical for faithful chromosome segregation, and defects in this complicated process lead to chromosomal aberrations and cancer. Here, we describe an in vitro kinase assay that is used to identify Cdk1-specific phosphorylation sites. In this assay, a purified protein is phosphorylated in vitro by commercially available human Cdk1/cyclin B. Successful phosphorylation is confirmed by SDS-PAGE, and phosphorylation sites are subsequently identified by mass spectrometry. We also describe purification protocols that yield highly pure and homogeneous protein preparations suitable for the kinase assay, and a binding assay for the functional verification of the identified phosphorylation sites, which probes the interaction between a classical nuclear localization signal (cNLS) and its nuclear transport receptor karyopherin α. To aid with experimental design, we review approaches for the prediction of Cdk1-specific phosphorylation sites from protein sequences. Together these protocols present a very powerful approach that yields Cdk1-specific phosphorylation sites and enables mechanistic studies into how Cdk1 controls the cell cycle. Since this method relies on purified proteins, it can be applied to any model organism and yields reliable results, especially when combined with cell functional studies.