UAP56 is a conserved crucial component of a divergent mRNA export pathway in Toxoplasma gondii.

PubMed

Serpeloni, Mariana; Jiménez-Ruiz, Elena; Vidal, Newton Medeiros; Kroeber, Constanze; Andenmatten, Nicole; Lemgruber, Leandro; Mörking, Patricia; Pall, Gurman S; Meissner, Markus; Ávila, Andréa R

2016-11-01

Nucleo-cytoplasmic RNA export is an essential post-transcriptional step to control gene expression in eukaryotic cells and is poorly understood in apicomplexan parasites. With the exception of UAP56, a component of TREX (Transcription Export) complex, other components of mRNA export machinery are not well conserved in divergent supergroups. Here, we use Toxoplasma gondii as a model system to functionally characterize TgUAP56 and its potential interaction factors. We demonstrate that TgUAP56 is crucial for mRNA export and that functional interference leads to significant accumulation of mRNA in the nucleus. It was necessary to employ bioinformatics and phylogenetic analysis to identify orthologs related to mRNA export, which show a remarkable low level of conservation in T. gondii. We adapted a conditional Cas9/CRISPR system to carry out a genetic screen to verify if these factors were involved in mRNA export in T. gondii. Only the disruption of TgRRM_1330 caused accumulation of mRNA in the nucleus as found with TgUAP56. This protein is potentially a divergent partner of TgUAP56, and provides insight into a divergent mRNA export pathway in apicomplexans. © 2016 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

UAP56 is a conserved crucial component of a divergent mRNA export pathway in Toxoplasma gondii

PubMed Central

Serpeloni, Mariana; Jiménez‐Ruiz, Elena; Vidal, Newton Medeiros; Kroeber, Constanze; Andenmatten, Nicole; Lemgruber, Leandro; Mörking, Patricia; Pall, Gurman S.

2016-01-01

Summary Nucleo‐cytoplasmic RNA export is an essential post‐transcriptional step to control gene expression in eukaryotic cells and is poorly understood in apicomplexan parasites. With the exception of UAP56, a component of TREX (Transcription Export) complex, other components of mRNA export machinery are not well conserved in divergent supergroups. Here, we use Toxoplasma gondii as a model system to functionally characterize TgUAP56 and its potential interaction factors. We demonstrate that TgUAP56 is crucial for mRNA export and that functional interference leads to significant accumulation of mRNA in the nucleus. It was necessary to employ bioinformatics and phylogenetic analysis to identify orthologs related to mRNA export, which show a remarkable low level of conservation in T. gondii. We adapted a conditional Cas9/CRISPR system to carry out a genetic screen to verify if these factors were involved in mRNA export in T. gondii. Only the disruption of TgRRM_1330 caused accumulation of mRNA in the nucleus as found with TgUAP56. This protein is potentially a divergent partner of TgUAP56, and provides insight into a divergent mRNA export pathway in apicomplexans. PMID:27542978

Severe neurocognitive and growth disorders due to variation in THOC2, an essential component of nuclear mRNA export machinery.

PubMed

Kumar, Raman; Gardner, Alison; Homan, Claire C; Douglas, Evelyn; Mefford, Heather; Wieczorek, Dagmar; Lüdecke, Hermann-Josef; Stark, Zornitza; Sadedin, Simon; Nowak, Catherine Bearce; Douglas, Jessica; Parsons, Gretchen; Mark, Paul; Loidi, Lourdes; Herman, Gail E; Mihalic Mosher, Theresa; Gillespie, Meredith K; Brady, Lauren; Tarnopolsky, Mark; Madrigal, Irene; Eiris, Jesús; Domènech Salgado, Laura; Rabionet, Raquel; Strom, Tim M; Ishihara, Naoko; Inagaki, Hidehito; Kurahashi, Hiroki; Dudding-Byth, Tracy; Palmer, Elizabeth E; Field, Michael; Gecz, Jozef

2018-05-31

Highly conserved TREX-mediated mRNA export is emerging as a key pathway in neuronal development and differentiation. TREX subunit variants cause neurodevelopmental disorders (NDDs) by interfering with mRNA export from the cell nucleus to the cytoplasm. Previously we implicated four missense variants in the X-linked THOC2 gene in intellectual disability (ID). We now report an additional six affected individuals from five unrelated families with two de novo and three maternally-inherited pathogenic or likely pathogenic variants in THOC2 extending the genotypic and phenotypic spectrum. These comprise three rare missense THOC2 variants that affect evolutionarily conserved amino acid residues and reduce protein stability and two with canonical splice-site THOC2 variants that result in C-terminally truncated THOC2 proteins. We present detailed clinical assessment and functional studies on a de novo variant in a female with an epileptic encephalopathy and discuss an additional four families with rare variants in THOC2 with supportive evidence for pathogenicity. Severe neurocognitive features, including movement and seizure disorders were observed in this cohort. Taken together our data show that even subtle alterations to the canonical molecular pathways such as mRNA export, otherwise essential for cellular life, can be compatible with life, but lead to NDDs in humans. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Chronic innate immune activation of TBK1 suppresses mTORC1 activity and dysregulates cellular metabolism.

PubMed

Hasan, Maroof; Gonugunta, Vijay K; Dobbs, Nicole; Ali, Aktar; Palchik, Guillermo; Calvaruso, Maria A; DeBerardinis, Ralph J; Yan, Nan

2017-01-24

Three-prime repair exonuclease 1 knockout (Trex1 -/- ) mice suffer from systemic inflammation caused largely by chronic activation of the cyclic GMP-AMP synthase-stimulator of interferon genes-TANK-binding kinase-interferon regulatory factor 3 (cGAS-STING-TBK1-IRF3) signaling pathway. We showed previously that Trex1-deficient cells have reduced mammalian target of rapamycin complex 1 (mTORC1) activity, although the underlying mechanism is unclear. Here, we performed detailed metabolic analysis in Trex1 -/- mice and cells that revealed both cellular and systemic metabolic defects, including reduced mitochondrial respiration and increased glycolysis, energy expenditure, and fat metabolism. We also genetically separated the inflammatory and metabolic phenotypes by showing that Sting deficiency rescued both inflammatory and metabolic phenotypes, whereas Irf3 deficiency only rescued inflammation on the Trex1 -/- background, and many metabolic defects persist in Trex1 -/- Irf3 -/- cells and mice. We also showed that Leptin deficiency (ob/ob) increased lipogenesis and prolonged survival of Trex1 -/- mice without dampening inflammation. Mechanistically, we identified TBK1 as a key regulator of mTORC1 activity in Trex1 -/- cells. Together, our data demonstrate that chronic innate immune activation of TBK1 suppresses mTORC1 activity, leading to dysregulated cellular metabolism.

Promoter- and RNA polymerase II–dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans

PubMed Central

Rohner, Sabine; Kalck, Veronique; Wang, Xuefei; Ikegami, Kohta; Lieb, Jason D.; Meister, Peter

2013-01-01

Some inducible yeast genes relocate to nuclear pores upon activation, but the general relevance of this phenomenon has remained largely unexplored. Here we show that the bidirectional hsp-16.2/41 promoter interacts with the nuclear pore complex upon activation by heat shock in the nematode Caenorhabditis elegans. Direct pore association was confirmed by both super-resolution microscopy and chromatin immunoprecipitation. The hsp-16.2 promoter was sufficient to mediate perinuclear positioning under basal level conditions of expression, both in integrated transgenes carrying from 1 to 74 copies of the promoter and in a single-copy genomic insertion. Perinuclear localization of the uninduced gene depended on promoter elements essential for induction and required the heat-shock transcription factor HSF-1, RNA polymerase II, and ENY-2, a factor that binds both SAGA and the THO/TREX mRNA export complex. After induction, colocalization with nuclear pores increased significantly at the promoter and along the coding sequence, dependent on the same promoter-associated factors, including active RNA polymerase II, and correlated with nascent transcripts. PMID:23460676

Clinical and Molecular Phenotype of Aicardi-Goutières Syndrome

PubMed Central

Rice, Gillian ; Patrick, Teresa ; Parmar, Rekha ; Taylor, Claire F. ; Aeby, Alec ; Aicardi, Jean ; Artuch, Rafael ; Montalto, Simon Attard ; Bacino, Carlos A. ; Barroso, Bruno ; Baxter, Peter ; Benko, Willam S. ; Bergmann, Carsten ; Bertini, Enrico ; Biancheri, Roberta ; Blair, Edward M. ; Blau, Nenad ; Bonthron, David T. ; Briggs, Tracy ; Brueton, Louise A. ; Brunner, Han G. ; Burke, Christopher J. ; Carr, Ian M. ; Carvalho, Daniel R. ; Chandler, Kate E. ; Christen, Hans-Jürgen ; Corry, Peter C. ; Cowan, Frances M. ; Cox, Helen ; D’Arrigo, Stefano ; Dean, John ; De Laet, Corinne ; De Praeter, Claudine ; Déry, Catherine ; Ferrie, Colin D. ; Flintoff, Kim ; Frints, Suzanna G. M. ; Garcia-Cazorla, Angels ; Gener, Blanca ; Goizet, Cyril ; Goutières, Françoise ; Green, Andrew J. ; Guët, Agnès ; Hamel, Ben C. J. ; Hayward, Bruce E. ; Heiberg, Arvid ; Hennekam, Raoul C. ; Husson, Marie ; Jackson, Andrew P. ; Jayatunga, Rasieka ; Jiang, Yong-Hui ; Kant, Sarina G. ; Kao, Amy ; King, Mary D. ; Kingston, Helen M. ; Klepper, Joerg ; van der Knaap, Marjo S. ; Kornberg, Andrew J. ; Kotzot, Dieter ; Kratzer, Wilfried ; Lacombe, Didier ; Lagae, Lieven ; Landrieu, Pierre Georges ; Lanzi, Giovanni ; Leitch, Andrea ; Lim, Ming J. ; Livingston, John H. ; Lourenco, Charles M. ; Lyall, E. G. Hermione ; Lynch, Sally A. ; Lyons, Michael J. ; Marom, Daphna ; McClure, John P. ; McWilliam, Robert ; Melancon, Serge B. ; Mewasingh, Leena D. ; Moutard, Marie-Laure ; Nischal, Ken K. ; Østergaard, John R. ; Prendiville, Julie ; Rasmussen, Magnhild ; Rogers, R. Curtis ; Roland, Dominique ; Rosser, Elisabeth M. ; Rostasy, Kevin ; Roubertie, Agathe ; Sanchis, Amparo ; Schiffmann, Raphael ; Scholl-Bürgi, Sabine ; Seal, Sunita ; Shalev, Stavit A. ; Corcoles, C. Sierra ; Sinha, Gyan P. ; Soler, Doriette ; Spiegel, Ronen ; Stephenson, John B. P. ; Tacke, Uta ; Tan, Tiong Yang ; Till, Marianne ; Tolmie, John L. ; Tomlin, Pam ; Vagnarelli, Federica ; Valente, Enza Maria ; Van Coster, Rudy N. A. ; Van der Aa, Nathalie ; Vanderver, Adeline ; Vles, Johannes S. H. ; Voit, Thomas ; Wassmer, Evangeline ; Weschke, Bernhard ; Whiteford, Margo L. ; Willemsen, Michel A. A. ; Zankl, Andreas ; Zuberi, Sameer M. ; Orcesi, Simona ; Fazzi, Elisa ; Lebon, Pierre ; Crow, Yanick J. 

2007-01-01

Aicardi-Goutières syndrome (AGS) is a genetic encephalopathy whose clinical features mimic those of acquired in utero viral infection. AGS exhibits locus heterogeneity, with mutations identified in genes encoding the 3′→5′ exonuclease TREX1 and the three subunits of the RNASEH2 endonuclease complex. To define the molecular spectrum of AGS, we performed mutation screening in patients, from 127 pedigrees, with a clinical diagnosis of the disease. Biallelic mutations in TREX1, RNASEH2A, RNASEH2B, and RNASEH2C were observed in 31, 3, 47, and 18 families, respectively. In five families, we identified an RNASEH2A or RNASEH2B mutation on one allele only. In one child, the disease occurred because of a de novo heterozygous TREX1 mutation. In 22 families, no mutations were found. Null mutations were common in TREX1, although a specific missense mutation was observed frequently in patients from northern Europe. Almost all mutations in RNASEH2A, RNASEH2B, and RNASEH2C were missense. We identified an RNASEH2C founder mutation in 13 Pakistani families. We also collected clinical data from 123 mutation-positive patients. Two clinical presentations could be delineated: an early-onset neonatal form, highly reminiscent of congenital infection seen particularly with TREX1 mutations, and a later-onset presentation, sometimes occurring after several months of normal development and occasionally associated with remarkably preserved neurological function, most frequently due to RNASEH2B mutations. Mortality was correlated with genotype; 34.3% of patients with TREX1, RNASEH2A, and RNASEH2C mutations versus 8.0% RNASEH2B mutation–positive patients were known to have died (P=.001). Our analysis defines the phenotypic spectrum of AGS and suggests a coherent mutation-screening strategy in this heterogeneous disorder. Additionally, our data indicate that at least one further AGS-causing gene remains to be identified. PMID:17846997

Clinical and molecular phenotype of Aicardi-Goutieres syndrome.

PubMed

Rice, Gillian; Patrick, Teresa; Parmar, Rekha; Taylor, Claire F; Aeby, Alec; Aicardi, Jean; Artuch, Rafael; Montalto, Simon Attard; Bacino, Carlos A; Barroso, Bruno; Baxter, Peter; Benko, Willam S; Bergmann, Carsten; Bertini, Enrico; Biancheri, Roberta; Blair, Edward M; Blau, Nenad; Bonthron, David T; Briggs, Tracy; Brueton, Louise A; Brunner, Han G; Burke, Christopher J; Carr, Ian M; Carvalho, Daniel R; Chandler, Kate E; Christen, Hans-Jurgen; Corry, Peter C; Cowan, Frances M; Cox, Helen; D'Arrigo, Stefano; Dean, John; De Laet, Corinne; De Praeter, Claudine; Dery, Catherine; Ferrie, Colin D; Flintoff, Kim; Frints, Suzanna G M; Garcia-Cazorla, Angels; Gener, Blanca; Goizet, Cyril; Goutieres, Francoise; Green, Andrew J; Guet, Agnes; Hamel, Ben C J; Hayward, Bruce E; Heiberg, Arvid; Hennekam, Raoul C; Husson, Marie; Jackson, Andrew P; Jayatunga, Rasieka; Jiang, Yong-Hui; Kant, Sarina G; Kao, Amy; King, Mary D; Kingston, Helen M; Klepper, Joerg; van der Knaap, Marjo S; Kornberg, Andrew J; Kotzot, Dieter; Kratzer, Wilfried; Lacombe, Didier; Lagae, Lieven; Landrieu, Pierre Georges; Lanzi, Giovanni; Leitch, Andrea; Lim, Ming J; Livingston, John H; Lourenco, Charles M; Lyall, E G Hermione; Lynch, Sally A; Lyons, Michael J; Marom, Daphna; McClure, John P; McWilliam, Robert; Melancon, Serge B; Mewasingh, Leena D; Moutard, Marie-Laure; Nischal, Ken K; Ostergaard, John R; Prendiville, Julie; Rasmussen, Magnhild; Rogers, R Curtis; Roland, Dominique; Rosser, Elisabeth M; Rostasy, Kevin; Roubertie, Agathe; Sanchis, Amparo; Schiffmann, Raphael; Scholl-Burgi, Sabine; Seal, Sunita; Shalev, Stavit A; Corcoles, C Sierra; Sinha, Gyan P; Soler, Doriette; Spiegel, Ronen; Stephenson, John B P; Tacke, Uta; Tan, Tiong Yang; Till, Marianne; Tolmie, John L; Tomlin, Pam; Vagnarelli, Federica; Valente, Enza Maria; Van Coster, Rudy N A; Van der Aa, Nathalie; Vanderver, Adeline; Vles, Johannes S H; Voit, Thomas; Wassmer, Evangeline; Weschke, Bernhard; Whiteford, Margo L; Willemsen, Michel A A; Zankl, Andreas; Zuberi, Sameer M; Orcesi, Simona; Fazzi, Elisa; Lebon, Pierre; Crow, Yanick J

2007-10-01

Aicardi-Goutieres syndrome (AGS) is a genetic encephalopathy whose clinical features mimic those of acquired in utero viral infection. AGS exhibits locus heterogeneity, with mutations identified in genes encoding the 3'-->5' exonuclease TREX1 and the three subunits of the RNASEH2 endonuclease complex. To define the molecular spectrum of AGS, we performed mutation screening in patients, from 127 pedigrees, with a clinical diagnosis of the disease. Biallelic mutations in TREX1, RNASEH2A, RNASEH2B, and RNASEH2C were observed in 31, 3, 47, and 18 families, respectively. In five families, we identified an RNASEH2A or RNASEH2B mutation on one allele only. In one child, the disease occurred because of a de novo heterozygous TREX1 mutation. In 22 families, no mutations were found. Null mutations were common in TREX1, although a specific missense mutation was observed frequently in patients from northern Europe. Almost all mutations in RNASEH2A, RNASEH2B, and RNASEH2C were missense. We identified an RNASEH2C founder mutation in 13 Pakistani families. We also collected clinical data from 123 mutation-positive patients. Two clinical presentations could be delineated: an early-onset neonatal form, highly reminiscent of congenital infection seen particularly with TREX1 mutations, and a later-onset presentation, sometimes occurring after several months of normal development and occasionally associated with remarkably preserved neurological function, most frequently due to RNASEH2B mutations. Mortality was correlated with genotype; 34.3% of patients with TREX1, RNASEH2A, and RNASEH2C mutations versus 8.0% RNASEH2B mutation-positive patients were known to have died (P=.001). Our analysis defines the phenotypic spectrum of AGS and suggests a coherent mutation-screening strategy in this heterogeneous disorder. Additionally, our data indicate that at least one further AGS-causing gene remains to be identified.

HIV-1 activation of innate immunity depends strongly on the intracellular level of TREX1 and sensing of incomplete reverse transcription products.

PubMed

Kumar, Swati; Morrison, James H; Dingli, David; Poeschla, Eric

2018-05-16

TREX1 has been reported to degrade cytosolic immune-stimulatory DNA, including viral DNA generated during HIV-1 infection, but the dynamic range of its capacity to suppress innate immune stimulation is unknown and its full role in the viral life cycle remains unclear. A main purpose of our study was to determine how the intracellular level of TREX1 affects HIV-1 activation and avoidance of innate immunity. Using stable over-expression and CRISPR-mediated gene disruption, we engineered a range of TREX1 levels in human THP-1 monocytes. Increasing the level of TREX1 dramatically suppressed HIV-1 induction of interferon-stimulated genes (ISGs). Productive infection and integrated proviruses were equal to increased. Knocking out TREX1 impaired viral infectivity, increased early viral cDNA and caused ten-fold or greater increases in HIV-1 ISG induction. Knockout of cyclic GMP-AMP synthase (cGAS) abrogated all ISG induction. Moreover, cGAS knockout produced no increase in single cycle infection, establishing that HIV-1 DNA-triggered signaling is not rapid enough to impair the initial ISG-triggering infection cycle. Disruption of the HIV-1 capsid by PF74 also induced ISGs and this was TREX1 level-dependent, required reverse transcriptase catalysis, and was eliminated by cGAS gene knockout. Thus, the intracellular level of TREX1 pivotally modulates innate immune induction by HIV-1. Partial HIV-1 genomes are the TREX1 target and are sensed by cGAS. The nearly complete lack of innate immune induction despite equal to increased viral integration observed when the TREX1 protein level is experimentally elevated indicates that integration-competent genomes are shielded from cytosolic sensor-effectors during uncoating and transit to the nucleus. IMPORTANCE Much remains unknown about how TREX1 influences HIV-1 replication, whether it targets full-length viral DNA versus partial intermediates, how intracellular TREX1 protein levels correlate with ISG induction, and whether TREX1 digestion of cytoplasmic DNA and subsequent cGAS pathway activation affects both initial and subsequent cycles of infection. To answer these questions, we experimentally varied the intracellular level of TREX1 and show that this strongly determines the innate immunogenicity of HIV-1. In addition, several lines of evidence including time of addition experiments with drugs that impair reverse transcription or capsid integrity showed that the pathogen-associated molecular patterns sensed after viral entry contain DNA, are TREX1 and cGAS substrates, and are derived from incomplete RT products. In contrast, the experiments demonstrate that full-length integration competent viral DNA is immune to TREX1. Treatment approaches that reduce TREX1 levels or facilitate release of DNA intermediates may advantageously combine enhanced innate immunity with antiviral effects. Copyright © 2018 American Society for Microbiology.

Rare variants of the 3’-5’ DNA exonuclease TREX1 in early onset small vessel stroke

PubMed Central

McGlasson, Sarah; Rannikmäe, Kristiina; Bevan, Steven; Logan, Clare; Bicknell, Louise S.; Jury, Alexa; Jackson, Andrew P.

2017-01-01

Background: Monoallelic and biallelic mutations in the exonuclease TREX1 cause monogenic small vessel diseases (SVD). Given recent evidence for genetic and pathophysiological overlap between monogenic and polygenic forms of SVD, evaluation of TREX1 in small vessel stroke is warranted. Methods: We sequenced the TREX1 gene in an exploratory cohort of patients with lacunar stroke (Edinburgh Stroke Study, n=290 lacunar stroke cases). We subsequently performed a fully blinded case-control study of early onset MRI-confirmed small vessel stroke within the UK Young Lacunar Stroke Resource (990 cases, 939 controls). Results: No patients with canonical disease-causing mutations of TREX1 were identified in cases or controls. Analysis of an exploratory cohort identified a potential association between rare variants of TREX1 and patients with lacunar stroke. However, subsequent controlled and blinded evaluation of TREX1 in a larger and MRI-confirmed patient cohort, the UK Young Lacunar Stroke Resource, identified heterozygous rare variants in 2.1% of cases and 2.3% of controls. No association was observed with stroke risk (odds ratio = 0.90; 95% confidence interval, 0.49-1.65 p=0.74). Similarly no association was seen with rare TREX1 variants with predicted deleterious effects on enzyme function (odds ratio = 1.05; 95% confidence interval, 0.43-2.61 p=0.91). Conclusions: No patients with early-onset lacunar stroke had genetic evidence of a TREX1-associated monogenic microangiopathy. These results show no evidence of association between rare variants of TREX1 and early onset lacunar stroke. This includes rare variants that significantly affect protein and enzyme function. Routine sequencing of the TREX1 gene in patients with early onset lacunar stroke is therefore unlikely to be of diagnostic utility, in the absence of syndromic features or family history. PMID:29387804

Modeling of TREX1-Dependent Autoimmune Disease using Human Stem Cells Highlights L1 Accumulation as a Source of Neuroinflammation.

PubMed

Thomas, Charles A; Tejwani, Leon; Trujillo, Cleber A; Negraes, Priscilla D; Herai, Roberto H; Mesci, Pinar; Macia, Angela; Crow, Yanick J; Muotri, Alysson R

2017-09-07

Three-prime repair exonuclease 1 (TREX1) is an anti-viral enzyme that cleaves nucleic acids in the cytosol, preventing accumulation and a subsequent type I interferon-associated inflammatory response. Autoimmune diseases, including Aicardi-Goutières syndrome (AGS) and systemic lupus erythematosus, can arise when TREX1 function is compromised. AGS is a neuroinflammatory disorder with severe and persistent intellectual and physical problems. Here we generated a human AGS model that recapitulates disease-relevant phenotypes using pluripotent stem cells lacking TREX1. We observed abundant extrachromosomal DNA in TREX1-deficient neural cells, of which endogenous Long Interspersed Element-1 retrotransposons were a major source. TREX1-deficient neurons also exhibited increased apoptosis and formed three-dimensional cortical organoids of reduced size. TREX1-deficient astrocytes further contributed to the observed neurotoxicity through increased type I interferon secretion. In this model, reverse-transcriptase inhibitors rescued the neurotoxicity of AGS neurons and organoids, highlighting their potential utility in therapeutic regimens for AGS and related disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

Toolbox for Research and Exploration (TREX): Investigations of Fine-Grained Materials on Small Bodies

NASA Technical Reports Server (NTRS)

Domingue, D. L.; Allain, J.-P.; Banks, M.; Christoffersen, R.; Cintala, M.; Clark, R.; Cloutis, E.; Graps, A.; Hendrix, A. R.; Hsieh, H.;

Mutations involved in Aicardi-Goutières syndrome implicate SAMHD1 as regulator of the innate immune response.

PubMed

Rice, Gillian I; Bond, Jacquelyn; Asipu, Aruna; Brunette, Rebecca L; Manfield, Iain W; Carr, Ian M; Fuller, Jonathan C; Jackson, Richard M; Lamb, Teresa; Briggs, Tracy A; Ali, Manir; Gornall, Hannah; Couthard, Lydia R; Aeby, Alec; Attard-Montalto, Simon P; Bertini, Enrico; Bodemer, Christine; Brockmann, Knut; Brueton, Louise A; Corry, Peter C; Desguerre, Isabelle; Fazzi, Elisa; Cazorla, Angels Garcia; Gener, Blanca; Hamel, Ben C J; Heiberg, Arvid; Hunter, Matthew; van der Knaap, Marjo S; Kumar, Ram; Lagae, Lieven; Landrieu, Pierre G; Lourenco, Charles M; Marom, Daphna; McDermott, Michael F; van der Merwe, William; Orcesi, Simona; Prendiville, Julie S; Rasmussen, Magnhild; Shalev, Stavit A; Soler, Doriette M; Shinawi, Marwan; Spiegel, Ronen; Tan, Tiong Y; Vanderver, Adeline; Wakeling, Emma L; Wassmer, Evangeline; Whittaker, Elizabeth; Lebon, Pierre; Stetson, Daniel B; Bonthron, David T; Crow, Yanick J

2009-07-01

Aicardi-Goutières syndrome is a mendelian mimic of congenital infection and also shows overlap with systemic lupus erythematosus at both a clinical and biochemical level. The recent identification of mutations in TREX1 and genes encoding the RNASEH2 complex and studies of the function of TREX1 in DNA metabolism have defined a previously unknown mechanism for the initiation of autoimmunity by interferon-stimulatory nucleic acid. Here we describe mutations in SAMHD1 as the cause of AGS at the AGS5 locus and present data to show that SAMHD1 may act as a negative regulator of the cell-intrinsic antiviral response.

Mutations involved in Aicardi-Goutières syndrome implicate SAMHD1 as regulator of the innate immune response

PubMed Central

Rice, Gillian I; Bond, Jacquelyn; Asipu, Aruna; Brunette, Rebecca L; Manfield, Iain W; Carr, Ian M; Fuller, Jonathan C; Jackson, Richard M; Lamb, Teresa; Briggs, Tracy A; Ali, Manir; Gornall, Hannah; Couthard, Lydia R; Aeby, Alec; Attard-Montalto, Simon P; Bertini, Enrico; Bodemer, Christine; Brockmann, Knut; Brueton, Louise A; Corry, Peter C; Desguerre, Isabelle; Fazzi, Elisa; Cazorla, Angels Garcia; Gener, Blanca; Hamel, Ben C J; Heiberg, Arvid; Hunter, Matthew; van der Knaap, Marjo S; Kumar, Ram; Lagae, Lieven; Landrieu, Pierre G; Lourenco, Charles M; Marom, Daphna; McDermott, Michael F; van der Merwe, William; Orcesi, Simona; Prendiville, Julie S; Rasmussen, Magnhild; Shalev, Stavit A; Soler, Doriette M; Shinawi, Marwan; Spiegel, Ronen; Tan, Tiong Y; Vanderver, Adeline; Wakeling, Emma L; Wassmer, Evangeline; Whittaker, Elizabeth; Lebon, Pierre; Stetson, Daniel B; Bonthron, David T; Crow, Yanick J

2014-01-01

Aicardi-Goutières syndrome is a mendelian mimic of congenital infection and also shows overlap with systemic lupus erythematosus at both a clinical and biochemical level. The recent identification of mutations in TREX1 and genes encoding the RNASEH2 complex and studies of the function of TREX1 in DNA metabolism have defined a previously unknown mechanism for the initiation of autoimmunity by interferon-stimulatory nucleic acid. Here we describe mutations in SAMHD1 as the cause of AGS at the AGS5 locus and present data to show that SAMHD1 may act as a negative regulator of the cell-intrinsic antiviral response. PMID:19525956

Photogrammetric Analysis of Rotor Clouds Observed during T-REX

NASA Astrophysics Data System (ADS)

Romatschke, U.; Grubišić, V.

2017-12-01

Stereo photogrammetric analysis is a rarely utilized but highly valuable tool for studying smaller, highly ephemeral clouds. In this study, we make use of data that was collected during the Terrain-induced Rotor Experiment (T-REX), which took place in Owens Valley, eastern California, in the spring of 2006. The data set consists of matched digital stereo photographs obtained at high temporal (on the order of seconds) and spatial resolution (limited by the pixel size of the cameras). Using computer vision techniques we have been able to develop algorithms for camera calibration, automatic feature matching, and ultimately reconstruction of 3D cloud scenes. Applying these techniques to images from different T-REX IOPs we capture the motion of clouds in several distinct mountain wave scenarios ranging from short lived lee wave clouds on an otherwise clear sky day to rotor clouds formed in an extreme turbulence environment with strong winds and high cloud coverage. Tracking the clouds in 3D space and time allows us to quantify phenomena such as vertical and horizontal movement of clouds, turbulent motion at the upstream edge of rotor clouds, the structure of the lifting condensation level, extreme wind shear, and the life cycle of clouds in lee waves. When placed into context with the existing literature that originated from the T-REX field campaign, our results complement and expand our understanding of the complex dynamics observed in a variety of different lee wave settings.

Verification of TREX1 as a promising indicator of judging the prognosis of osteosarcoma.

PubMed

Feng, Jinyi; Lan, Ruilong; Cai, Guanxiong; Lin, Jinluan; Wang, Xinwen; Lin, Jianhua; Han, Deping

2016-11-24

The study aimed to explore the correlation between the expression of TREX1 and the metastasis and the survival time of patients with osteosarcoma as well as biological characteristics of osteosarcoma cells for the prognosis judgment of osteosarcoma. The correlation between the expression of TREX1 protein and the occurrence of pulmonary metastasis in 45 cases of osteosarcoma was analyzed. The CD133 + and CD133 - cell subsets of osteosarcoma stem cells were sorted by the flow cytometry. The tumorsphere culture, clone formation, growth curve, osteogenic and adipogenic differentiation, tumor-formation ability in nude mice, sensitivity of chemotherapeutic drugs, and other cytobiology behaviors were compared between the cell subsets in two groups; the expressions of stem cell-related genes Nanog and Oct4 were compared; The expressions of TREX1 protein and mRNA were compared between the cell subsets in two groups. The data was statistically analyzed. The measurement data between the two groups were compared using t test. The count data between the two groups were compared using χ 2 test and Kaplan-Meier survival analysis. A P value <0.05 indicated that the difference was statistically significant. The expression of TREX1 protein in patients with osteosarcoma in the metastasis group was significantly lower than that in the non-metastasis group. The difference was statistically significant (P < 0.05). Up to the last follow-up visit, the former average survival time was significantly lower than that of the latter, and the difference was statistically significant (P < 0.05). The expression of TREX1 in human osteosarcoma CD133 + cell subsets was significantly lower than that in CD133 - cell subsets. Stemness-related genes Nanog and Oct4 were highly expressed in human osteosarcoma CD133 + cell subsets with lower expression of TREX1; the biological characteristics identification experiment showed that human CD133 + cell subsets with low TREX1 expression could form tumorspheres, the number of colony forming was more, the cell proliferation ability was strong, the osteogenic and adipogenic differentiation potential was big, the tumor-forming ability in nude mice was strong, and the sensibility of chemotherapeutics drugs on cisplatin was low. The expression of TREX1 may be related to metastasis in patients with osteosarcoma. The expression of TREX1 was closely related to the cytobiology characteristics of osteosarcoma stem cell. TREX1 can play an important role in the occurrence and development processes. And, TREX1 is expected to become an effective new index for the evaluation of the prognosis.

Evaluation of the TREX1 gene in a large multi-ancestral lupus cohort

PubMed Central

Namjou, Bahram; Kothari, Parul H.; Kelly, Jennifer A.; Glenn, Stuart B.; Ojwang, Joshua O.; Adler, Adam; Alarcón-Riquelme, Marta E.; Gallant, Caroline J.; Boackle, Susan A.; Criswell, Lindsey A.; Kimberly, Robert P.; Brown, Elizabeth; Edberg, Jeffrey; Stevens, Anne M.; Jacob, Chaim O.; Tsao, Betty P.; Gilkeson, Gary S.; Kamen, Diane L.; Merrill, Joan T.; Petri, Michelle; Goldman, Rosalind Ramsey; Vila, Luis M.; Anaya, Juan-Manuel; Niewold, Timothy B.; Martin, Javier; Pons-Estel, Bernardo A.; Sabio, Jose M.; Callejas, Jose L.; Vyse, Timothy J.; Bae, Sang-Cheol; Perrino, Fred W.; Freedman, Barry I.; Scofield, R. Hal; Moser, Kathy L.; Gaffney, Patrick M.; James, Judith A.; Langefeld, Carl D.; Kaufman, Kenneth M.; Harley, John B.; Atkinson, John P.

2011-01-01

Systemic Lupus Erythematosus (SLE) is a prototypic autoimmune disorder with a complex pathogenesis in which genetic, hormonal and environmental factors play a role. Rare mutations in the TREX1 gene, the major mammalian 3′-5′ exonuclease, have been reported in sporadic SLE cases. Some of these mutations have also been identified in a rare pediatric neurologic condition featuring an inflammatory encephalopathy known as Aicardi-Goutières syndrome (AGS). We sought to investigate the frequency of these mutations in a large multi-ancestral cohort of SLE cases and controls. Methods Forty single-nucleotide polymorphisms (SNPs), including both common and rare variants, across the TREX1 gene were evaluated in ∼8370 patients with SLE and ∼7490 control subjects. Stringent quality control procedures were applied and principal components and admixture proportions were calculated to identify outliers for removal from analysis. Population-based case-control association analyses were performed. P values, false discovery rate q values, and odds ratios with 95% confidence intervals were calculated. Results The estimated frequency of TREX1 mutations in our lupus cohort was 0.5%. Five heterozygous mutations were detected at the Y305C polymorphism in European lupus cases but none were observed in European controls. Five African cases incurred heterozygous mutations at the E266G polymorphism and, again, none were observed in the African controls. A rare homozygous R114H mutation was identified in one Asian SLE patient whereas all genotypes at this mutation in previous reports for SLE were heterozygous. Analysis of common TREX1 SNPs (MAF >10%) revealed a relatively common risk haplotype in European SLE patients with neurologic manifestations, especially seizures, with a frequency of 58% in lupus cases compared to 45% in normal controls (p=0.0008, OR=1.73, 95% CI=1.25-2.39). Finally, the presence or absence of specific autoantibodies in certain populations produced significant genetic associations. For example, a strong association with anti-nRNP was observed in the European cohort at a coding synonymous variant rs56203834 (p=2.99E-13, OR=5.2, 95% CI=3.18-8.56). Conclusion Our data confirm and expand previous reports and provide additional support for the involvement of TREX1 in lupus pathogenesis. PMID:21270825

[Retinal vasculopathy with cerebral leukoencephalopathy carrying TREX1 mutation diagnosed by the intracranial calcification: a case report].

PubMed

Komaki, Ryouhei; Ueda, Takehiro; Tsuji, Yukio; Miyawaki, Toko; Kusuhara, Sentaro; Hara, Shigeo; Toda, Tatsushi

2018-02-28

A 40-year-old woman with renal dysfunction for 2 years was admitted to our hospital suffering from a headache. Family history revealed that her mother had a headache, renal dysfunction, and brain infarction in younger age. She had a retinal hemorrhage, a retinal atrophy, pitting edema in her lower extremities. Her neurological findings were unremarkable. Brain imaging showed multiple white matter lesions accompanied with calcifications and slightly enhancement. Kidney biopsy showed the thrombotic microangiopathy, Gene analysis demonstrated a causative mutation in three-prime repair exonuclease-1 (TREX1) gene, c.703_704insG (p.Val235GlyfsX6), thereby we diagnosed her as retinal vasculopathy with cerebral leukoencephalopathy (RVCL). RVCL is an autosomal dominant condition caused by C-terminal frame-shift mutation in TREX1. TREX1 protein is a major 3' to 5' DNA exonuclease, which are important in DNA repair. While TREX1 mutations identified in Aicardi-Goutieres syndrome patients lead to a reduction of enzyme activity, it is suggested that mutations in RVCL alter an intracellular location of TREX1 protein. There are no treatments based evidences in RVCL. We administered cilostazol to protect endothelial function, and her brain lesions and renal function have not become worse for 10 months after. It is necessary to consider RVCL associated with TREX1 mutation if a patient has retinal lesions, white matter lesions accompanied with calcifications, and multiple organ dysfunction.

TREX13 Data Analysis/Modeling

DTIC Science & Technology

2015-09-30

TREX13 data analysis /modeling Dajun (DJ) Tang Applied Physics Laboratory, University of Washington 1013 NE 40th Street, Seattle, WA 98105...accuracy in those predictions. With extensive TREX13 data in hand, the objective now shifts to realizing the long-term goals using data analysis and...be quantitatively addressed. The approach to analysis can be summarized into the following steps: 1. Based on measurements, assess to what degree

Gene-targeted mice lacking the Trex1 (DNase III) 3'-->5' DNA exonuclease develop inflammatory myocarditis.

PubMed

Morita, Masashi; Stamp, Gordon; Robins, Peter; Dulic, Anna; Rosewell, Ian; Hrivnak, Geza; Daly, Graham; Lindahl, Tomas; Barnes, Deborah E

2004-08-01

TREX1, originally designated DNase III, was isolated as a major nuclear DNA-specific 3'-->5' exonuclease that is widely distributed in both proliferating and nonproliferating mammalian tissues. The cognate cDNA shows homology to the editing subunit of the Escherichia coli replicative DNA polymerase III holoenzyme and encodes an exonuclease which was able to serve a DNA-editing function in vitro, promoting rejoining of a 3' mismatched residue in a reconstituted DNA base excision repair system. Here we report the generation of gene-targeted Trex1(-/-) mice. The null mice are viable and do not show the increase in spontaneous mutation frequency or cancer incidence that would be predicted if Trex1 served an obligatory role of editing mismatched 3' termini generated during DNA repair or DNA replication in vivo. Unexpectedly, Trex1(-/-) mice exhibit a dramatically reduced survival and develop inflammatory myocarditis leading to progressive, often dilated, cardiomyopathy and circulatory failure.

Exercise Effects on Tumorigenesis in a p53-deficient Mouse Model of Breast Cancer

PubMed Central

Colbert, Lisa H.; Westerlind, Kim C.; Perkins, Susan N.; Haines, Diana C.; Berrigan, David; Donehower, Lawrence A.; Fuchs-Young, Robin; Hursting, Stephen D.

2011-01-01

Purpose Physically active women have a reduced risk of breast cancer, but the dose of activity necessary and the role of energy balance and other potential mechanisms have not been fully explored in animal models. We examined treadmill and wheel running effects on mammary tumorigenesis and biomarkers in p53-deficient (p53+/−): MMTV-Wnt-1 transgenic mice. Methods Female mice (9 wks old) were randomly assigned to the following groups in Experiment 1: treadmill exercise 5 d/wk, 45 min/d, 5% grade at 20 m/min, ~0.90 km/d (TREX1, n=20); at 24 m/min, ~1.08 km/d (TREX2, n=21); or a non-exercise control (CON-TREX, n=22). In Experiment 2, mice were randomly assigned to voluntary wheel-running (WHL, n=21, 2.46 ± 1.11 km/d (mean ± SD)) or a non-exercise control (CON-WHL, n=22). Body composition was measured at ~9 weeks and serum insulin-like growth factor-1 (IGF-1) at 2–3 monthly time points beginning at ~9 weeks on study. Mice were sacrificed when tumors reached 1.5 cm, mice became moribund, or there was only one mouse per treatment group remaining. Results TREX1 (24 wks) and TREX2 (21 wks) had shorter survival median survival times than CON-TREX (34 wks; p<0.01); WHL and CON-WHL survival was similar (23 vs. 24 wks; p=0.32). TREX2 had increased multiplicity of mammary gland carcinomas compared to CON-TREX; WHL had a higher tumor incidence than CON-WHL. All exercising animals were lighter than their respective controls, and WHL had lower body fat than CON-WHL (p<0.01). There was no difference in IGF-1 between groups (p>0.05). Conclusion Despite beneficial or no effects on body weight, body fat, or IGF-1, exercise had detrimental effects on tumorigenesis in this p53-deficient mouse model of spontaneous mammary cancer. PMID:19568200

The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally.

PubMed

García-Molinero, Varinia; García-Martínez, José; Reja, Rohit; Furió-Tarí, Pedro; Antúnez, Oreto; Vinayachandran, Vinesh; Conesa, Ana; Pugh, B Franklin; Pérez-Ortín, José E; Rodríguez-Navarro, Susana

2018-03-29

Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. Here we find that the SAGA/TREX-2 subunit Sus1 associates with upstream regulatory regions of many yeast genes and that heat shock drastically changes Sus1 binding. While Sus1 binding to TFIID-dominated genes is not affected by temperature, its recruitment to SAGA-dominated genes and RP genes is significantly disturbed under heat shock, with Sus1 relocated to environmental stress-responsive genes in these conditions. Moreover, in contrast to recent results showing that SAGA deubiquitinating enzyme Ubp8 is dispensable for RNA synthesis, genomic run-on experiments demonstrate that Sus1 contributes to synthesis and stability of a wide range of transcripts. Our study provides support for a model in which SAGA/TREX-2 factor Sus1 acts as a global transcriptional regulator in yeast but has differential activity at yeast genes as a function of their transcription rate or during stress conditions.

Neural Network Substorm Identification: Enabling TREx Sensor Web Modes

NASA Astrophysics Data System (ADS)

Chaddock, D.; Spanswick, E.; Arnason, K. M.; Donovan, E.; Liang, J.; Ahmad, S.; Jackel, B. J.

2017-12-01

Transition Region Explorer (TREx) is a ground-based sensor web of optical and radio instruments that is presently being deployed across central Canada. The project consists of an array of co-located blue-line, full-colour, and near-infrared all-sky imagers, imaging riometers, proton aurora spectrographs, and GNSS systems. A key goal of the TREx project is to create the world's first (artificial) intelligent sensor web for remote sensing space weather. The sensor web will autonomously control and coordinate instrument operations in real-time. To accomplish this, we will use real-time in-line analytics of TREx and other data to dynamically switch between operational modes. An operating mode could be, for example, to have a blue-line imager gather data at a one or two orders of magnitude higher cadence than it operates for its `baseline' mode. The software decision to increase the imaging cadence would be in response to an anticipated increase in auroral activity or other programmatic requirements. Our first test for TREx's sensor web technologies is to develop the capacity to autonomously alter the TREx operating mode prior to a substorm expansion phase onset. In this paper, we present our neural network analysis of historical optical and riometer data and our ability to predict an optical onset. We explore the preliminary insights into using a neural network to pick out trends and features which it deems are similar among substorms.

Conceptual Design of Tail-Research EXperiment (T-REX) on Space Plasma Environment Research Facility

NASA Astrophysics Data System (ADS)

Xiao, Qingmei; Wang, Xiaogang; E, Peng; Shen, Chao; Wang, Zhibin; Mao, Aohua; Xiao, Chijie; Ding, Weixing; Ji, Hantao; Ren, Yang

2016-10-01

Space Environment Simulation Research Infrastructure (SESRI), a scientific project for a major national facility of fundamental researches, has recently been launched at Harbin Institute of Technology (HIT). The Space Plasma Environment Research Facility (SPERF) for simulation of space plasma environment is one of the components of SESRI. It is designed to investigate fundamental issues in space plasma environment, such as energetic particles transportation and the interaction with waves in magnetosphere, magnetic reconnection at magnetopause and magnetotail, etc. Tail-Research Experiment (T-REX) is part of the SPERF for laboratory studies of space physics relevant to tail reconnection and dipolarization process. T-REX is designed to carry out two kinds of experiments: the tail plasmamoid for magnetic reconnection and magnetohydrodynamic waves excited by high speed plasma jet. In this presentation, the scientific goals and experimental plans for T-REX together with the means applied to generate the plasma with desired parameters are reviewed. Two typical scenarios of T-REX with operations of plasma sources and various magnetic configurations to study specific physical processes in space plasmas will also be presented.

T-REX: education and formation

NASA Astrophysics Data System (ADS)

Marconi, A.; Marano, B.

An important goal of the T-REX project is the creation and the formation of new experts and professional profiles with extremely high specialisation to prepare tomorrow astronomers and instrument scientists that will take full advantage of E-ELT and that will make the Italian participation a success. The existing tight interaction and integration between INAF institutes and universities as allowed the T-REX Project to fund and support a total of 4 PhD grants. Here we briefly summarise their present and future activities.

Dissecting Diffuse X-ray Emission in 30 Doradus with T-ReX

NASA Astrophysics Data System (ADS)

Townsley, Leisa K.; Broos, Patrick

2017-08-01

30 Doradus (the Tarantula Nebula) offers us a microscope on starburst astrophysics, having endured 25 Myrs of the birth and death of the most massive stars known. Across 30 Dor's 250-pc extent, stellar winds and supernovae have carved its ISM into an amazing display of arcs, pillars, and bubbles. For over 40 years, we have also known that 30 Dor is a bright X-ray emitter, so its familiar stars and cold ISM structures suffer irradiation by multi-million-degree plasmas. The 2-Ms Chandra X-ray Visionary Project ``The Tarantula -- Revealed by X-rays'' (T-ReX) exploits Chandra's fine spatial resolution and the ACIS-I field of view to study ISM interfaces on 1--10 pc scales across the entire 30 Dor complex. Here we give preliminary results from ongoing analyses of these data, focusing on the diffuse X-ray emission. Massive star winds and cavity supernovae over the millenia have contributed to a broad mix of X-ray-emitting plasmas and absorbing columns, showing that 30 Dor's hot ISM is just as complex and confusing as that seen at colder temperatures.

Monogenic Lupus.

PubMed

Lo, Mindy S

2016-12-01

Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease known for its clinical heterogeneity. Over time, new insights into the complex genetic origin of SLE have started to explain some of this clinical variability. These findings, reviewed here, have also yielded important understanding in the immune mechanisms behind SLE pathogenesis. Several new monogenic disorders with lupus-like phenotype have been described. These can be organized into physiologic pathways that parallel mechanisms of disease in SLE. Examples include genes important for DNA damage repair (e.g., TREX1), nucleic acid sensing and type I interferon overproduction (e.g., STING, TREX1), apoptosis (FASLG), tolerance (PRKCD), and clearance of self-antigen (DNASE1L3). Further study of monogenic lupus may lead to better genotype/phenotype correlations in SLE. Eventually, the ability to understand individual patients according to their genetic profile may allow the development of more targeted and personalized approaches to therapy.

T-ReX Spies the Stars of 30 Doradus

NASA Astrophysics Data System (ADS)

Broos, Patrick; Townsley, Leisa K.; Pollock, Andrew; Crowther, Paul

2017-08-01

30 Doradus (the Tarantula Nebula) is the Local Group's most massive young star-forming complex. At its heart is R136, the most massive resolved stellar cluster; R136 contains, in turn, the most massive stars known. The Chandra X-ray Observatory has recently observed 30 Dor for the 2-megasecond X-ray Visionary Project ``The Tarantula -- Revealed by X-rays'' (T-ReX). This deep observation exploits Chandra's fine spatial resolution to study the full complement of massive stars and the brightest pre-main sequence stars that trace 25 Myrs of star formation in this incomparable nearby starburst. Here we give preliminary results from the ongoing analyses of the data, focusing on the massive stars. While many remain undetected even in this deep ACIS-I observation, a few show dramatic X-ray lightcurves and/or high luminosities befitting this amazing starburst cluster.

Using pixel intensity as a self-regulating threshold for deterministic image sampling in Milano Retinex: the T-Rex algorithm

NASA Astrophysics Data System (ADS)

Lecca, Michela; Modena, Carla Maria; Rizzi, Alessandro

2018-01-01

Milano Retinexes are spatial color algorithms, part of the Retinex family, usually employed for image enhancement. They modify the color of each pixel taking into account the surrounding colors and their position, catching in this way the local spatial color distribution relevant to image enhancement. We present T-Rex (from the words threshold and Retinex), an implementation of Milano Retinex, whose main novelty is the use of the pixel intensity as a self-regulating threshold to deterministically sample local color information. The experiments, carried out on real-world pictures, show that T-Rex image enhancement performance are in line with those of the Milano Retinex family: T-Rex increases the brightness, the contrast, and the flatness of the channel distributions of the input image, making more intelligible the content of pictures acquired under difficult light conditions.

Expanding the spectrum: 20 years of advances in MMW imagery

NASA Astrophysics Data System (ADS)

Martin, Christopher A.; Lovberg, John A.; Kolinko, Valdimir G.

2017-05-01

Millimeter-wave imaging has expanded from the single-pixel swept imagers developed in the 1960s to large field-ofview real-time systems in use today. Trex Enterprises has been developing millimeter-wave imagers since 1991 for aviation and security applications, as well as millimeter-wave communications devices. As MMIC device development was stretching into the MMW band in the 1990s, Trex developed novel imaging architectures to create 2-D staring systems with large pixel counts and no moving parts while using a minimal number of devices. Trex also contributed to the device development in amplifiers, switches, and detectors to enable the next generation of passive MMW imaging systems. The architectures and devices developed continue to be employed in security imagers, radar, and radios produced by Trex. This paper reviews the development of the initial real-time MMW imagers and associated devices by Trex Enterprises from the 1990s through the 2000s. The devices include W-band MMIC amplifiers, switches, and detector didoes, and MMW circuit boards and optical processors. The imaging systems discussed include two different real-time passive MMW imagers flown on helicopters and a MMW radar system, as well as implementation of the devices and architectures in simpler stand-off and gateway security imagers.

Rapid generation of recombinant Pseudomonas putida secondary metabolite producers using yTREX.

PubMed

Domröse, Andreas; Weihmann, Robin; Thies, Stephan; Jaeger, Karl-Erich; Drepper, Thomas; Loeschcke, Anita

2017-12-01

Microbial secondary metabolites represent a rich source of valuable compounds with a variety of applications in medicine or agriculture. Effective exploitation of this wealth of chemicals requires the functional expression of the respective biosynthetic genes in amenable heterologous hosts. We have previously established the TREX system which facilitates the transfer, integration and expression of biosynthetic gene clusters in various bacterial hosts. Here, we describe the yTREX system, a new tool adapted for one-step yeast recombinational cloning of gene clusters. We show that with yTREX, Pseudomonas putida secondary metabolite production strains can rapidly be constructed by random targeting of chromosomal promoters by Tn5 transposition. Feasibility of this approach was corroborated by prodigiosin production after yTREX cloning, transfer and expression of the respective biosynthesis genes from Serratia marcescens . Furthermore, the applicability of the system for effective pathway rerouting by gene cluster adaptation was demonstrated using the violacein biosynthesis gene cluster from Chromobacterium violaceum , producing pathway metabolites violacein, deoxyviolacein, prodeoxyviolacein, and deoxychromoviridans. Clones producing both prodigiosin and violaceins could be readily identified among clones obtained after random chromosomal integration by their strong color-phenotype. Finally, the addition of a promoter-less reporter gene enabled facile detection also of phenazine-producing clones after transfer of the respective phenazine-1-carboxylic acid biosynthesis genes from Pseudomonas aeruginosa . All compounds accumulated to substantial titers in the mg range. We thus corroborate here the suitability of P. putida for the biosynthesis of diverse natural products, and demonstrate that the yTREX system effectively enables the rapid generation of secondary metabolite producing bacteria by activation of heterologous gene clusters, applicable for natural compound discovery and combinatorial biosynthesis.

Sub-ion scale plasmoids during collisionless reconnection on TREX

NASA Astrophysics Data System (ADS)

Olson, Joseph; Egedal, Jan; Myers, Rachel; Greess, Sam; Clark, Mike; Wallace, John; Forest, Cary; Wisconsin Plasma Astrophysics Laboratory Collaboration

2016-10-01

The Terrestrial Reconnection Experiment (TREX), operating at the Wisconsin Plasma Astrophysics Laboratory, is able to explore a collisionless regime inaccessible to previous reconnection experiments. To date, TREX has already achieved Lundquist numbers up to 104 where kinetic effects, such as electron pressure anisotropy, become important to the reconnection dynamics. During a recent run campaign in this collisionless regime, the spontaneous formation of magnetic islands (plasmoids) inside the ion diffusion region was observed. It is known that long current layers are susceptible to tearing, leading to the formation of plasmoids, and that these plasmoids have strong effects on the reconnection rate and particle energization. However, contrary to theoretical and numerical predictions, the TREX experiments show that the plasmoid instability is active even when the current layer is less than one di long. Analysis of these events shows that smaller plasmoids occur at a higher rate than larger ones, suggesting that magnetic islands could be seeded in plasmas more effectively than previously thought.

T.Rex Visual Analytics for Transactional Exploration

ScienceCinema

None

2018-01-16

T.Rex is PNNL's visual analytics tool that specializes in tabular structured data, like you might open with Excel. It's a client-server application, allowing the server to do a lot of the heavy lifting and the client to open spreadsheets with millions of rows. With datasets of that size, especially if you're unfamiliar with the contents, it's very hard to get a good grasp of what's in it using traditional tools. With T.Rex, the multiple views allow you to see categorical, temporal, numerical, relational, and summary data. The interactivity lets you look across your data and see how things relate to each other.

T.Rex Visual Analytics for Transactional Exploration

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

None

2014-07-01

T.Rex is PNNL's visual analytics tool that specializes in tabular structured data, like you might open with Excel. It's a client-server application, allowing the server to do a lot of the heavy lifting and the client to open spreadsheets with millions of rows. With datasets of that size, especially if you're unfamiliar with the contents, it's very hard to get a good grasp of what's in it using traditional tools. With T.Rex, the multiple views allow you to see categorical, temporal, numerical, relational, and summary data. The interactivity lets you look across your data and see how things relate tomore » each other.« less

T-REX Version 1.5 User's Guide for Calculating Pesticide Residues on Avian and Mammalian Food Items - Appendix B - Initial Pesticide Residues on Arthropods

EPA Pesticide Factsheets

Obtain empirical data from the scientific literature and registrant-submitted studies to refine the initial residue assumptions of pesticides on arthropods that are simulated with TIM, T-REX, and T-HERPS

TREX13 Data Analysis/Modeling

DTIC Science & Technology

2018-03-29

www.apl.washington.edu 29 Mar 2018 To: Dr. Robert H. Headrick Office of Naval Research (Code 322) 875 North Randolph Street Arlington, VA 22203-1995...Benjamin Blake Naval Research Laboratory Defense Technical Information Center DISTRIBUTION STATEMENT A. Approved for public release; distribution is... quantitatively impact sound behavior. To gain quantitative knowledge, TREX13 was designed to contemporaneously measure acoustics quantities and environmental

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

DOE PAGES

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-03

Here, we compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchangemore » (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium.« less

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom.

PubMed

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-07

We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics

PubMed Central

Li, Tang; Chamberlin, Stephen G; Caraco, M Daniel; Liberles, David A; Gaucher, Eric A; Benner, Steven A

2006-01-01

Background The exchange of nucleotides at synonymous sites in a gene encoding a protein is believed to have little impact on the fitness of a host organism. This should be especially true for synonymous transitions, where a pyrimidine nucleotide is replaced by another pyrimidine, or a purine is replaced by another purine. This suggests that transition redundant exchange (TREx) processes at the third position of conserved two-fold codon systems might offer the best approximation for a neutral molecular clock, serving to examine, within coding regions, theories that require neutrality, determine whether transition rate constants differ within genes in a single lineage, and correlate dates of events recorded in genomes with dates in the geological and paleontological records. To date, TREx analysis of the yeast genome has recognized correlated duplications that established a new metabolic strategies in fungi, and supported analyses of functional change in aromatases in pigs. TREx dating has limitations, however. Multiple transitions at synonymous sites may cause equilibration and loss of information. Further, to be useful to correlate events in the genomic record, different genes within a genome must suffer transitions at similar rates. Results A formalism to analyze divergence at two fold redundant codon systems is presented. This formalism exploits two-state approach-to-equilibrium kinetics from chemistry. This formalism captures, in a single equation, the possibility of multiple substitutions at individual sites, avoiding any need to "correct" for these. The formalism also connects specific rate constants for transitions to specific approximations in an underlying evolutionary model, including assumptions that transition rate constants are invariant at different sites, in different genes, in different lineages, and at different times. Therefore, the formalism supports analyses that evaluate these approximations. Transitions at synonymous sites within two-fold redundant coding systems were examined in the mouse, rat, and human genomes. The key metric (f2), the fraction of those sites that holds the same nucleotide, was measured for putative ortholog pairs. A transition redundant exchange (TREx) distance was calculated from f2 for these pairs. Pyrimidine-pyrimidine transitions at these sites occur approximately 14% faster than purine-purine transitions in various lineages. Transition rate constants were similar in different genes within the same lineages; within a set of orthologs, the f2 distribution is only modest overdispersed. No correlation between disparity and overdispersion is observed. In rodents, evidence was found for greater conservation of TREx sites in genes on the X chromosome, accounting for a small part of the overdispersion, however. Conclusion The TREx metric is useful to analyze the history of transition rate constants within these mammals over the past 100 million years. The TREx metric estimates the extent to which silent nucleotide substitutions accumulate in different genes, on different chromosomes, with different compositions, in different lineages, and at different times. PMID:16545144

Environmental Fluctuations in Forward Scatter and Reverberation

DTIC Science & Technology

2014-09-30

Experiment 2013 (TREX13) was carried out in ~20 m deep water off Panama City, FL [1]. The Marine Physical Laboratory ( MPL ) participated at-sea aboard the...Sharp). In addition, 16 self-recording temperature loggers were attached to two of the VLAs. Source tows and stations were carried out by MPL on 22...Reverberation Experiment 2013 (TREX13): MPL Trip Report,” Marine Physical Laboratory, Scripps Institution of Oceanography, 13 July 2013 (2013). [3

Picosecond Pulse Recirculation for High Average Brightness Thomson Scattering-based Gamma-ray Sources

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

Semenov, V. A.

2009-06-12

Pulse recirculation has been successfully demonstrated with the interaction laser system of LLNL's Thomson-Radiated Extreme X-ray (T-REX) source. The recirculation increased twenty-eight times the intensity of the light coming out of the laser system, demonstrating the capability of increasing the gamma-ray flux emitted by T-REX. The technical approach demonstrated could conceivably increase the average gamma-ray flux output by up to a hundred times.

Electron Pressure Anisotropy in the Terrestrial Reconnection Experiment and the Magnetospheric Multiscale Mission

NASA Astrophysics Data System (ADS)

Myers, Rachel; Egedal, Jan; Olson, Joseph; Greess, Samuel; Millet-Ayala, Alexander; Clark, Michael; Nonn, Paul; Wallace, John; Forest, Cary

2017-10-01

The NASA Magnetospheric Multiscale (MMS) Mission seeks to measure heating and motion of charged particles from reconnection events in the magnetotail and dayside magnetopause. MMS is paralleled by the Terrestrial Reconnection Experiment (TREX) at the Wisconsin Plasma Astrophysics Laboratory (WiPAL) in its study of collisionless magnetic reconnection. In the regimes seen by TREX and MMS, electron pressure anisotropy should develop, driving large-scale current layer formation. MMS has witnessed anisotropy, but the spatial coverage of the data is too limited to determine how the pressure anisotropy affects jet and current layer creation. Measurements of pressure anisotropy on TREX will be presented, and implications for reconnecting current layer structure in the magnetosphere, as measured by MMS, will be discussed. This research was conducted with support from a UW-Madison University Fellowship as well as the NSF/DOE award DE-SC0013032.

Chromothripsis and kataegis induced by telomere crisis

PubMed Central

Maciejowski, John; Li, Yilong; Bosco, Nazario; Campbell, Peter J.; de Lange, Titia

2015-01-01

Telomere crisis occurs during tumorigenesis when depletion of the telomere reserve leads to frequent telomere fusions. The resulting dicentric chromosomes have been proposed to drive genome instability. Here we examine the fate of dicentric human chromosomes in telomere crisis. We observed that dicentric chromosomes invariably persisted through mitosis and developed into 50-200 μm chromatin bridges connecting the daughter cells. Before their resolution at 3-20 h after anaphase, the chromatin bridges induced nuclear envelope rupture in interphase, accumulated the cytoplasmic 3' nuclease TREX1, and developed RPA-coated single stranded (ss) DNA. CRISPR knockouts showed that TREX1 contributed to the generation of the ssDNA and the resolution of the chromatin bridges. Post-crisis clones showed chromothripsis and kataegis, presumably resulting from DNA repair and APOBEC editing of the fragmented chromatin bridge DNA. We propose that chromothripsis in human cancer may arise through TREX1-mediated fragmentation of dicentric chromosomes formed in telomere crisis. PMID:26687355

Lockheed Martin T-Rex: Preliminary report

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

NONE

1997-07-31

T-Rex is a robot which may be used in toxic or flammable environments. The assessment of the T-Rex conducted at the Lockheed Martin facility was limited in its scope. The scope of the assessment was directed by the type of equipment being used and the amount of accessibility to the equipment. Due to severe time constraints--the assessment was conducted in one day--human factors interface activities were limited. This should be considered a preliminary assessment. This report covers aspects of the technology that were available to the assessment team. Recommendations for future evaluation of this technology are also included. The contentsmore » are as follows: Electrical Considerations; General Electrical Consideration; Trailing Cables; Grounding; Surface High Voltage Distribution; Low and Medium Voltage Alternating Current Circuits; Potential for Harmful Human Factor Incidents and Enterprise Disablement; Exclusion Zone Emergency Maintenance; and Recommendations.« less

Environmental Fluctuations in Forward Scatter and Reverberation

DTIC Science & Technology

2015-09-30

TREX13) was carried out in ~20 m deep water off Panama City, FL [1]. The Marine Physical Laboratory ( MPL ) participated at-sea aboard the R/V Walton...addition, 16 self-recording temperature loggers were attached to two of the VLAs. Source tows and stations were carried out by MPL on 22-24 April 2013...TREX13): MPL Trip Report,” Marine Physical Laboratory, Scripps Institution of Oceanography, 13 July 2013 (2013). [3] W.S. Hodgkiss, D.E. Ensberg, and

Cavitands Endow All-Dielectric Beads With Selectivity for Plasmon-Free Enhanced Raman Detection of Nε-Methylated Lysine.

PubMed

Alessandri, Ivano; Biavardi, Elisa; Gianoncelli, Alessandra; Bergese, Paolo; Dalcanale, Enrico

2016-06-22

SiO2/TiO2 microbeads (T-rex) are promising materials for plasmon-free surface-enhanced Raman scattering (SERS), offering several key advantages in biodiagnostics. In this paper we report the combination of T-rex beads with tetraphosphonate cavitands (Tiiii), which imparts selectivity toward Nε-methylated lysine. SERS experiments demonstrated the efficiency and selectivity of the T-rex-Tiiii assays in detecting methylated lysine hydrochloride (Nε-Me-Lys-Fmoc) from aqueous solutions, even in the presence of the parent Lys-Fmoc hydrochloride as interferent. The negative results obtained in control experiments using TSiiii ruled out any other form of surface recognition or preferential physisorption. MALDI-TOF analyses on the beads exposed to Nε-Me-Lys-Fmoc revealed the presence of the Tiiii•Nε-Me-Lys-Fmoc complex. Raman analyses based on the intensity ratio of Nε-Me-Lys-Fmoc and cavitand-specific modes resulted in a dose-response plot, which allowed for estimating the concentration of Nε-methylated lysine from initial solutions in the 1 × 10(-3) to 1 × 10(-5) M range. These results can set the basis for the development of new Raman assays for epigenetic diagnostics.

The T-REX valley wind intercomparison project

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

Schmidli, J; Billings, B J; Burton, R

2008-08-07

An accurate simulation of the evolution of the atmospheric boundary layer is very important, as the evolution of the boundary layer sets the stage for many weather phenomena, such as deep convection. Over mountain areas the evolution of the boundary layer is particularly complex, due to the nonlinear interaction between boundary layer turbulence and thermally-induced mesoscale wind systems, such as the slope and valley winds. As the horizontal resolution of operational forecasts progresses to finer and finer resolution, more and more of the thermally-induced mesoscale wind systems can be explicitly resolved, and it is very timely to document the currentmore » state-of-the-art of mesoscale models at simulating the coupled evolution of the mountain boundary layer and the valley wind system. In this paper we present an intercomparison of valley wind simulations for an idealized valley-plain configuration using eight state-of-the-art mesoscale models with a grid spacing of 1 km. Different sets of three-dimensional simulations are used to explore the effects of varying model dynamical cores and physical parameterizations. This intercomparison project was conducted as part of the Terrain-induced Rotor Experiment (T-REX; Grubisic et al., 2008).« less

Enzymatic synthesis of dimaltosyl-{beta}-cyclodextrin via a transglycosylation reaction using TreX, a Sulfolobus solfataricus P2 debranching enzyme

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

Kang, Hee-Kwon; Cha, Hyunju; Yang, Tae-Joo

2008-02-01

Di-O-{alpha}-maltosyl-{beta}-cyclodextrin ((G2){sub 2}-{beta}-CD) was synthesized from 6-O-{alpha}-maltosyl-{beta}-cyclodextrin (G2-{beta}-CD) via a transglycosylation reaction catalyzed by TreX, a debranching enzyme from Sulfolobus solfataricus P2. TreX showed no activity toward glucosyl-{beta}-CD, but a transfer product (1) was detected when the enzyme was incubated with maltosyl-{beta}-CD, indicating specificity for a branched glucosyl chain bigger than DP2. Analysis of the structure of the transfer product (1) using MALDI-TOF/MS and isoamylase or glucoamylase treatment revealed it to be dimaltosyl-{beta}-CD, suggesting that TreX transferred the maltosyl residue of a G2-{beta}-CD to another molecule of G2-{beta}-CD by forming an {alpha}-1,6-glucosidic linkage. When [{sup 14}C]-maltose and maltosyl-{beta}-CD were reactedmore » with the enzyme, the radiogram showed no labeled dimaltosyl-{beta}-CD; no condensation product between the two substrates was detected, indicating that the synthesis of dimaltosyl-{beta}-CD occurred exclusively via transglycosylation of an {alpha}-1,6-glucosidic linkage. Based on the HPLC elution profile, the transfer product (1) was identified to be isomers of 6{sup 1},6{sup 3}- and 6{sup 1},6{sup 4}-dimaltosyl-{beta}-CD. Inhibition studies with {beta}-CD on the transglycosylation activity revealed that {beta}-CD was a mixed-type inhibitor, with a K{sub i} value of 55.6 {mu}mol/mL. Thus, dimaltosyl-{beta}-CD can be more efficiently synthesized by a transglycosylation reaction with TreX in the absence of {beta}-CD. Our findings suggest that the high yield of (G2){sub 2}-{beta}-CD from G2-{beta}-CD was based on both the transglycosylation action mode and elimination of the inhibitory effect of {beta}-CD.« less

Accessing the Asymmetric Collisionless Reconnection Regime in the Terrestrial Reconnection Experiment (TREX)

NASA Astrophysics Data System (ADS)

Greess, S.; Egedal, J.; Olson, J.; Millet-Ayala, A.; Myers, R.; Wallace, J.; Clark, M.; Forest, C.

2017-12-01

Kinetic effects are expected to dominate the collisionless reconnection regime, where the mean free path is large enough that the anisotropic electron pressure can develop without being damped away by collisional pitch angle scattering. In simulations, the anisotropic pressure drives the formation of outflow jets [1]. These jets are expected to play a role in the reconnection layer at the Earth's magnetopause, which is currently being explored by Magnetospheric Multiscale Mission (MMS) [2]. Until recently, this regime of anisotropic pressure was inaccessible by laboratory experiments, but new data from the Terrestrial Reconnection Experiment (TREX) shows that fully collisionless reconnection can now be achieved in the laboratory. Future runs at TREX will delve deeper into this collisionless regime in both the antiparallel and guide-field cases. [1] Le, A. et al. JPP, 81(1). doi: 10.1017/S0022377814000907. [2] Burch, J. L. et al. Space Sci. Rev. 199,5. doi: 10.1007/s11214-015-0164-9 Supported in part by NSF/DOE award DE-SC0013032.

Acoustic Response of Underwater Munitions near a Sediment Interface: Measurement Model Comparisons and Classification Schemes

DTIC Science & Technology

2015-04-23

12 Figure 4. Pulse- compressed baseband signals for sequence 40 from TREX13 …… 13 Figure 5. SAS image for sequence 40 from TREX13...12 meshes with data …………… 28 Figure 14. FE simulations for aluminum and steel replicas of an 100-mm UXO …… 28 Figure 15. FE meshes for two targets...PCB Pulse- compressed and baseband PC SWAT Personal Computer Shallow Water Acoustic Toolset PondEx09 Pond Experiment 2009 PondEx10 Pond Experiment

Fuel of the Bacterial Flagellar Type III Protein Export Apparatus.

PubMed

Minamino, Tohru; Kinoshita, Miki; Namba, Keiichi

2017-01-01

The flagellar type III export apparatus utilizes ATP and proton motive force (PMF) across the cytoplasmic membrane as the energy sources and transports flagellar component proteins from the cytoplasm to the distal growing end of the growing structure to construct the bacterial flagellum beyond the cellular membranes. The flagellar type III export apparatus coordinates flagellar protein export with assembly by ordered export of substrates to parallel with their order of the assembly. The export apparatus is composed of a PMF-driven transmembrane export gate complex and a cytoplasmic ATPase complex. Since the ATPase complex is dispensable for flagellar protein export, PMF is the primary fuel for protein unfolding and translocation. Interestingly, the export gate complex can also use sodium motive force across the cytoplasmic membrane in addition to PMF when the ATPase complex does not work properly. Here, we describe experimental protocols, which have allowed us to identify the export substrate class and the primary fuel of the flagellar type III protein export apparatus in Salmonella enterica serovar Typhimurium.

A non-canonical mechanism for Crm1-export cargo complex assembly.

PubMed

Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Faza, Marius Boulos; Panse, Vikram Govind

2015-04-21

The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export.

A Visual Analytics Approach to Structured Data Analysis to Enhance Nonproliferation and Arms Control Verification Activities

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

Gillen, David S.

Analysis activities for Nonproliferation and Arms Control verification require the use of many types of data. Tabular structured data, such as Excel spreadsheets and relational databases, have traditionally been used for data mining activities, where specific queries are issued against data to look for matching results. The application of visual analytics tools to structured data enables further exploration of datasets to promote discovery of previously unknown results. This paper discusses the application of a specific visual analytics tool to datasets related to the field of Arms Control and Nonproliferation to promote the use of visual analytics more broadly in thismore » domain. Visual analytics focuses on analytical reasoning facilitated by interactive visual interfaces (Wong and Thomas 2004). It promotes exploratory analysis of data, and complements data mining technologies where known patterns can be mined for. Also with a human in the loop, they can bring in domain knowledge and subject matter expertise. Visual analytics has not widely been applied to this domain. In this paper, we will focus on one type of data: structured data, and show the results of applying a specific visual analytics tool to answer questions in the Arms Control and Nonproliferation domain. We chose to use the T.Rex tool, a visual analytics tool developed at PNNL, which uses a variety of visual exploration patterns to discover relationships in structured datasets, including a facet view, graph view, matrix view, and timeline view. The facet view enables discovery of relationships between categorical information, such as countries and locations. The graph tool visualizes node-link relationship patterns, such as the flow of materials being shipped between parties. The matrix visualization shows highly correlated categories of information. The timeline view shows temporal patterns in data. In this paper, we will use T.Rex with two different datasets to demonstrate how interactive exploration of the data can aid an analyst with arms control and nonproliferation verification activities. Using a dataset from PIERS (PIERS 2014), we will show how container shipment imports and exports can aid an analyst in understanding the shipping patterns between two countries. We will also use T.Rex to examine a collection of research publications from the IAEA International Nuclear Information System (IAEA 2014) to discover collaborations of concern. We hope this paper will encourage the use of visual analytics structured data analytics in the field of nonproliferation and arms control verification. Our paper outlines some of the challenges that exist before broad adoption of these kinds of tools can occur and offers next steps to overcome these challenges.« less

RPA and Rad51 constitute a cell intrinsic mechanism to protect the cytosol from self DNA.

PubMed

Wolf, Christine; Rapp, Alexander; Berndt, Nicole; Staroske, Wolfgang; Schuster, Max; Dobrick-Mattheuer, Manuela; Kretschmer, Stefanie; König, Nadja; Kurth, Thomas; Wieczorek, Dagmar; Kast, Karin; Cardoso, M Cristina; Günther, Claudia; Lee-Kirsch, Min Ae

2016-05-27

Immune recognition of cytosolic DNA represents a central antiviral defence mechanism. Within the host, short single-stranded DNA (ssDNA) continuously arises during the repair of DNA damage induced by endogenous and environmental genotoxic stress. Here we show that short ssDNA traverses the nuclear membrane, but is drawn into the nucleus by binding to the DNA replication and repair factors RPA and Rad51. Knockdown of RPA and Rad51 enhances cytosolic leakage of ssDNA resulting in cGAS-dependent type I IFN activation. Mutations in the exonuclease TREX1 cause type I IFN-dependent autoinflammation and autoimmunity. We demonstrate that TREX1 is anchored within the outer nuclear membrane to ensure immediate degradation of ssDNA leaking into the cytosol. In TREX1-deficient fibroblasts, accumulating ssDNA causes exhaustion of RPA and Rad51 resulting in replication stress and activation of p53 and type I IFN. Thus, the ssDNA-binding capacity of RPA and Rad51 constitutes a cell intrinsic mechanism to protect the cytosol from self DNA.

The Bacterial Flagellar Type III Export Gate Complex Is a Dual Fuel Engine That Can Use Both H+ and Na+ for Flagellar Protein Export

PubMed Central

Minamino, Tohru; Morimoto, Yusuke V.; Hara, Noritaka; Aldridge, Phillip D.; Namba, Keiichi

2016-01-01

The bacterial flagellar type III export apparatus utilizes ATP and proton motive force (PMF) to transport flagellar proteins to the distal end of the growing flagellar structure for self-assembly. The transmembrane export gate complex is a H+–protein antiporter, of which activity is greatly augmented by an associated cytoplasmic ATPase complex. Here, we report that the export gate complex can use sodium motive force (SMF) in addition to PMF across the cytoplasmic membrane to drive protein export. Protein export was considerably reduced in the absence of the ATPase complex and a pH gradient across the membrane, but Na+ increased it dramatically. Phenamil, a blocker of Na+ translocation, inhibited protein export. Overexpression of FlhA increased the intracellular Na+ concentration in the presence of 100 mM NaCl but not in its absence, suggesting that FlhA acts as a Na+ channel. In wild-type cells, however, neither Na+ nor phenamil affected protein export, indicating that the Na+ channel activity of FlhA is suppressed by the ATPase complex. We propose that the export gate by itself is a dual fuel engine that uses both PMF and SMF for protein export and that the ATPase complex switches this dual fuel engine into a PMF-driven export machinery to become much more robust against environmental changes in external pH and Na+ concentration. PMID:26943926

The Bacterial Flagellar Type III Export Gate Complex Is a Dual Fuel Engine That Can Use Both H+ and Na+ for Flagellar Protein Export.

PubMed

Minamino, Tohru; Morimoto, Yusuke V; Hara, Noritaka; Aldridge, Phillip D; Namba, Keiichi

2016-03-01

The bacterial flagellar type III export apparatus utilizes ATP and proton motive force (PMF) to transport flagellar proteins to the distal end of the growing flagellar structure for self-assembly. The transmembrane export gate complex is a H+-protein antiporter, of which activity is greatly augmented by an associated cytoplasmic ATPase complex. Here, we report that the export gate complex can use sodium motive force (SMF) in addition to PMF across the cytoplasmic membrane to drive protein export. Protein export was considerably reduced in the absence of the ATPase complex and a pH gradient across the membrane, but Na+ increased it dramatically. Phenamil, a blocker of Na+ translocation, inhibited protein export. Overexpression of FlhA increased the intracellular Na+ concentration in the presence of 100 mM NaCl but not in its absence, suggesting that FlhA acts as a Na+ channel. In wild-type cells, however, neither Na+ nor phenamil affected protein export, indicating that the Na+ channel activity of FlhA is suppressed by the ATPase complex. We propose that the export gate by itself is a dual fuel engine that uses both PMF and SMF for protein export and that the ATPase complex switches this dual fuel engine into a PMF-driven export machinery to become much more robust against environmental changes in external pH and Na+ concentration.

A non-canonical mechanism for Crm1-export cargo complex assembly

PubMed Central

Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Boulos Faza, Marius; Panse, Vikram Govind

2015-01-01

The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export. DOI: http://dx.doi.org/10.7554/eLife.05745.001 PMID:25895666

Macular Atrophy in Neovascular Age-Related Macular Degeneration with Monthly versus Treat-and-Extend Ranibizumab: Findings from the TREX-AMD Trial.

PubMed

Abdelfattah, Nizar S; Al-Sheikh, Mayss; Pitetta, Sean; Mousa, Ahmed; Sadda, SriniVas R; Wykoff, Charles C

2017-02-01

To compare the enlargement rate of macular atrophy (ERMA) in eyes treated with ranibizumab monthly or using a treat-and-extend (TREX) regimen for neovascular age-related macular degeneration (AMD) or fellow control eyes, as well as analyze risk factors for macular atrophy (MA) development and progression. Eighteen-month, multicenter, randomized, controlled clinical trial. Sixty patients with treatment-naïve neovascular AMD in 1 eye randomized 1:2 to monthly or TREX ranibizumab. Patients' study and fellow eyes were followed for 18 months using spectral-domain optical coherence tomography (SD OCT) and fundus autofluorescence (FAF) imaging. The MA was quantified on FAF images using Heidelberg Region Finder software (Heidelberg Engineering, Heidelberg, Germany), with suspected areas of atrophy confirmed by SD OCT and infrared reflectance imaging. For eyes without baseline MA yet developed MA by 18 months, intervening visits were assessed to determine the first visit at which MA appeared to define progression rates. Foveal choroidal thickness (FCT), subretinal hyperreflective material (SHRM), and pigment epithelial detachment (PED), were assessed at baseline to determine whether they influenced MA progression. Mean ERMA at 18 months. Relationship between visual acuity and MA, and the baseline risk factors for ERMA were also assessed. The final analysis cohort included 88 eyes in 3 groups: monthly (n = 19), TREX (n = 30), and control fellow eyes (n = 39). Mean ERMA over 18 months was 0.39±0.67 (monthly), 1.1±1.9 (TREX), and 0.49±1 mm 2 (control, P = 0.12). Mean ERMA per group among the 40.9% (n = 36) of baseline patients with MA was 0.9±1, 1.9±2.2, and 1±1.3 mm 2 , respectively (P = 0.31). The incidence rate of MA in the 3 groups was 40%, 0%, and 8.3%, respectively. Mann-Whitney U test revealed a statistically significant association between baseline FCT (127±46 vs. 155±55 μm, P = 0.01) and SHRM thickness (106±131 vs. 50±85 μm, P = 0.02) on MA. In eyes with no baseline MA, presence of SHRM, SHRM, and PED thickness, and presence of baseline hemorrhage were all significant predictors of new MA development (P = 0.04, 0.01, 0.04, 0.004, 0.01, respectively). Ranibizumab did not show a statistically significant influence on new MA development in eyes with neovascular AMD, whether dosed monthly or per TREX regimen. The FCT, SHRM thickness, and hemorrhage at baseline were all significant predictors of new MA. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Obituary: James H. "Trex" Trexler, 1918-2005

NASA Astrophysics Data System (ADS)

Barker, Ed

2007-12-01

James H. "Trex" Trexler, Naval Center for Space Technology, a retired scientist and astronomer, with a 50-year career at NRL died of cancer on October 22, 2005, at the age of 87. Born in Missoula, Montana (May 18, 1918), he grew up in Dallas, Texas, and attended Southern Methodist University (SMU) Engineering School. He combined his interests in astronomy and radio communication and operated the observatory on the SMU campus. Mr. Trexler had a most interesting and rewarding career at NRL, which resulted in notable contributions in scientific and technical developments. While at SMU, he worked on a government-sponsored project on radio detection and tracking of meteors. This work resulted in a call from NRL in 1942 to join the Navy radio detection effort being mounted against the German submarine Wolf Packs that were harassing our North Atlantic convoys on the supply routes to our European Allies. The program proved highly successful causing the breakup of the German Pack operation, and resulted in the sinking and capturing of many U-boats. After World War II, Trex and H. O. Lorenzen brought the German Navy's very advanced Wullenweber Direction Finder back to NRL, and rebuilt it at the Washington Coast Guard Station, south of Alexandria. It served as the prototype for the Direction Finder at the heart of the Navy and Air Force intercept networks and later as the first tracker of the Soviet Sputnik. He received the Navy Meritorious Civilian Service Award for his efforts. In the late l940s, Trex built the radar intercept equipment for the Navy's P4M Airborne Cold War Ferret Program. This capability provided instantaneous frequency and direction of arrival against Soviet radars from high-altitude flights along the Soviet borders. His Radio Physics Branch developed a surface mobile intercept system deployed to the Near East for which the Navy made the first group cash incentive award. With the beginning of the space age, his branch examined the moon as a possible passive radio relay satellite. Intercept of foreign radars was achieved in 1948, and this led to the large Stump Neck, Maryland Moon Propagation Facility, where voice transmission over the moon circuit was achieved in 1951. Trex received the Navy's Distinguished Civilian Service Award for his intercept work at Stump Neck and the Chesapeake Bay Annex. An immediate outgrowth was the Navy's communication Moon Relay (CMR) system that provided our Navy with satellite communication a decade before the artificial satellites were operational. A demonstration of Doppler navigation using the moon as a navigation satellite was also carried out at this time. The intercept aspects of the moon technology were pursued at the NRL Sugar Grove, West Virginia, facility from 1958 through 1986. Sugar Grove is now operated by the Navy as a first-class space radio facility. After his retirement, May 1, 1990, Trex continued his space interests. In 1997, he and his wife Fran took a special trip to the Fred Whipple Smithsonian Observatory area, Arizona, to capture some exciting photographs of the Hale-Bopp comet. Trex served as president of the National Capital Astronomers Club in Washington, DC. Also, he was a member of the Tucson Amateur Astronomical Association, and the Sonora Astronomical Society of Green Valley. He served as a volunteer tour guide for the Smithsonian Whipple Observatory, the University of Arizona Mirror Lab and on the board of the Green Valley Community Church Foundation, an organization that awards college scholarships for general education to young people in southern Arizona.

Visually Exploring Transportation Schedules.

PubMed

Palomo, Cesar; Guo, Zhan; Silva, Cláudio T; Freire, Juliana

2016-01-01

Public transportation schedules are designed by agencies to optimize service quality under multiple constraints. However, real service usually deviates from the plan. Therefore, transportation analysts need to identify, compare and explain both eventual and systemic performance issues that must be addressed so that better timetables can be created. The purely statistical tools commonly used by analysts pose many difficulties due to the large number of attributes at trip- and station-level for planned and real service. Also challenging is the need for models at multiple scales to search for patterns at different times and stations, since analysts do not know exactly where or when relevant patterns might emerge and need to compute statistical summaries for multiple attributes at different granularities. To aid in this analysis, we worked in close collaboration with a transportation expert to design TR-EX, a visual exploration tool developed to identify, inspect and compare spatio-temporal patterns for planned and real transportation service. TR-EX combines two new visual encodings inspired by Marey's Train Schedule: Trips Explorer for trip-level analysis of frequency, deviation and speed; and Stops Explorer for station-level study of delay, wait time, reliability and performance deficiencies such as bunching. To tackle overplotting and to provide a robust representation for a large numbers of trips and stops at multiple scales, the system supports variable kernel bandwidths to achieve the level of detail required by users for different tasks. We justify our design decisions based on specific analysis needs of transportation analysts. We provide anecdotal evidence of the efficacy of TR-EX through a series of case studies that explore NYC subway service, which illustrate how TR-EX can be used to confirm hypotheses and derive new insights through visual exploration.

Risk assessment of watershed erosion at Naesung Stream, South Korea.

PubMed

Ji, Un; Velleux, Mark; Julien, Pierre Y; Hwang, Manha

2014-04-01

A three-tiered approach was used to assess erosion risks within the Nakdong River Basin in South Korea and included: (1) a screening based on topography and land use; (2) a lumped parameter analysis using RUSLE; and (3) a detailed analysis using TREX, a fully distributed watershed model. These tiers span a range of spatial and temporal scales, with each tier providing increasing detail and resolution. The first two tiers were applied to the entire Nakdong River Basin and the Naesung Stream watershed was identified as having the highest soil erosion risk and potential for sedimentation problems. For the third tier, the TREX watershed model simulated runoff, channel flow, soil erosion, and stream sediment transport in the Naesung Stream watershed at very high resolution. TREX was calibrated for surface flows and sediment transport, and was used to simulate conditions for a large design storm. Highly erosive areas were identified along ridgelines in several headwater areas, with the northeast area of Songriwon having a particularly high erosion potential. Design storm simulations also indicated that sediment deposition of up to 55 cm could occur. Copyright © 2014 Elsevier Ltd. All rights reserved.

Using High Energy Precipitation for Magnetic Mapping in the Nightside Transition Region During Dynamic Events

NASA Astrophysics Data System (ADS)

Spanswick, E.

2017-12-01

Identifying the magnetic footprint of a satellite can be done using the in situ observations together with some ionospheric or low-altitude satellite observation to argue that the two measurements were made on the same field line. Nishimura et al. [2011], e.g., correlated a time series of chorus wave power near the magnetic equator with the time series of intensities of every pixel of a is roughly magnetically conjugate ASI. Often, the pattern of correlation shows a well-defined peak at the location of the satellite's magnetic footprint. Their results cannot be replicated during dynamic events (e.g., substorms), because the required auroral forms do not occur at such times. It would be important if we could make mappings with such confidence during active times. The Transition Region Explorer (TREx), which is presently being implemented, is a new ground-based facility that will remote sense electron precipitation across 3 hours of MLT and 12 degrees of magnetic latitude spanning the auroral zone in western Canada. TREx includes the world's first imaging riometers array with a contiguous field of view large enough to seamlessly track the spatio-temporal evolution of high energy electron precipitation at mesoscales. Two studies motivated the TREx riometers array. First, Baker et al. [1981] demonstrated riometer absorption is an excellent proxy for the electron energy flux integrated from 30 keV to 200keV keV at the magnetic equator on the flux tube corresponding to the location of that riometers. Second, Spanswick et al. [2007] showed the correlation between the riometers absorption and the integrated electron energy flux near the magnetic equator peaked when the satellite was nearest to conjugate to the riometers. Here we present observations using CANOPUS single beam riometers and CRRES MEB to illustrate how the relative closeness of the footpoint of an equatorial spacecraft can be assessed using high energy precipitation. As well, we present the capabilities of the new TREx riometers facility for spatio-temporal observation of the high energy electron precipitation over the TREx field of view, and our plan to use that high energy electron precipitation to provide accurate tracking of satellite footpoints during dynamic geospace events including substorm expansion phase.

Murine precision-cut liver slices (PCLS): a new tool for studying tumor microenvironments and cell signaling ex vivo.

PubMed

Koch, Alexandra; Saran, Shashank; Tran, Doan Duy Hai; Klebba-Färber, Sabine; Thiesler, Hauke; Sewald, Katherina; Schindler, Susann; Braun, Armin; Klopfleisch, Robert; Tamura, Teruko

2014-11-07

One of the most insidious characteristics of cancer is its spread to and ability to compromise distant organs via the complex process of metastasis. Communication between cancer cells and organ-resident cells via cytokines/chemokines and direct cell-cell contacts are key steps for survival, proliferation and invasion of metastasized cancer cells in organs. Precision-cut liver slices (PCLS) are considered to closely reflect the in vivo situation and are potentially useful for studying the interaction of cancer cells with liver-resident cells as well as being a potentially useful tool for screening anti-cancer reagents. Application of the PCLS technique in the field of cancer research however, has not yet been well developed. We established the mouse PCLS system using perfluorodecalin (PFD) as an artificial oxygen carrier. Using this system we show that the adherence of green fluorescent protein (GFP) labeled MDA-MB-231 (highly invasive) cells to liver tissue in the PCLS was 5-fold greater than that of SK-BR-3 (less invasive) cells. In addition, we generated PCLS from THOC5, a member of transcription/export complex (TREX), knockout (KO) mice. The PCLS still expressed Gapdh or Albumin mRNAs at normal levels, while several chemokine/growth factor or metalloprotease genes, such as Cxcl12, Pdgfa, Tgfb, Wnt11, and Mmp1a genes were downregulated more than 2-fold. Interestingly, adhesion of cancer cells to THOC5 KO liver slices was far less (greater than 80% reduction) than to wild-type liver slices. Mouse PCLS cultures in the presence of PFD may serve as a useful tool for screening local adherence and invasiveness of individual cancer cells, since single cells can be observed. This method may also prove useful for identification of genes in liver-resident cells that support cancer invasion by using PCLS from transgenic liver.

Possibilities for Nuclear Photo-Science with Intense Lasers

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

Barty, C J; Hartemann, F V; McNabb, D P

2006-06-26

The interaction of intense laser light with relativistic electrons can produce unique sources of high-energy x rays and gamma rays via Thomson scattering. ''Thomson-Radiated Extreme X-ray'' (T-REX) sources with peak photon brightness (photons per unit time per unit bandwidth per unit solid angle per unit area) that exceed that available from world's largest synchrotrons by more than 15 orders of magnitude are possible from optimally designed systems. Such sources offer the potential for development of ''nuclear photo-science'' applications in which the primary photon-atom interaction is with the nucleons and not the valence electrons. Applications include isotope-specific detection and imaging ofmore » materials, inverse density radiography, transmutation of nuclear waste and fundamental studies of nuclear structure. Because Thomson scattering cross sections are small, < 1 barn, the output from a T-REX source is optimized when the laser spot size and the electron spot size are minimized and when the electron and laser pulse durations are similar and short compared to the transit time through the focal region. The principle limitation to increased x-ray or gamma-ray brightness is ability to focus the electron beam. The effects of space charge on electron beam focus decrease approximately linearly with electron beam energy. For this reason, T-REX brightness increases rapidly as a function of the electron beam energy. As illustrated in Figure 1, above 100 keV these sources are unique in their ability to produce bright, narrow-beam, tunable, narrow-band gamma rays. New, intense, short-pulse, laser technologies for advanced T-REX sources are currently being developed at LLNL. The construction of a {approx}1 MeV-class machine with this technology is underway and will be used to excite nuclear resonance fluorescence in variety of materials. Nuclear resonance fluorescent spectra are unique signatures of each isotope and provide an ideal mechanism for identification of nuclear materials. With TREX it is possible to use NRF to provide high spatial resolution (micron scale) images of the isotopic distribution of all materials in a given object. Because of the high energy of the photons, imaging through dense and/or thick objects is possible. This technology will have applicability in many arenas including the survey of cargo for the presence of clandestine nuclear materials. It is also possible to address the more general radiographic challenge of imaging low-density objects that are shielded or placed behind high density objects. In this case, it is the NRF cross section and not the electron density of the material that provides contrast. Extensions of T-REX technology will be dependent upon the evolution of short pulse laser technology to high average powers. Concepts for sources that would produce 10's of kWs of gamma-rays by utilizing MW-class average-power, diode-pumped, short pulse lasers and energy recovery LINAC technology have been developed.« less

T-REX: Thomson-Radiated Extreme X-rays Moving X-Ray Science into the ''Nuclear'' Applications Space with Thompson Scattered Photons

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

Barty, C P; Hartemann, F V

2004-09-21

The scattering of laser photons from relativistic electrons (Thomson scattering) has been demonstrated to be a viable method for the production of ultrashort-duration pulses of tunable radiation in the 10-keV to 100-keV range. Photons in this range are capable of exciting or ionizing even the most tightly bound of atomic electrons. A wide variety of atomistic scale applications are possible. For example, Thomson x-ray sources have been constructed at LLNL (PLEIADES) and LBL as picosecond, stroboscopic probes of atomic-scale dynamics and at Vanderbilt University as element-specific tools for medical radiography and radiology. While these sources have demonstrated an attractive abilitymore » to simultaneously probe on an atomic spatial and temporal scale, they do not necessarily exploit the full potential of the Thomson scattering process to produce high-brightness, high-energy photons. In this white paper, we suggest that the peak brightness of Thomson sources can scale as fast as the 4th power of electron beam energy and that production via Thomson scattering of quasi-monochromatic, tunable radiation in the ''nuclear-range'' between 100-keV and several MeV is potentially a much more attractive application space for this process. Traditional sources in this regime are inherently ultra-broadband and decline rapidly in brightness as a function of photon energy. The output from dedicated, national-laboratory-scale, synchrotron facilities, e.g. APS, SPring8, ESRF etc., declines by more than 10 orders from 100 keV to 1 MeV. At 1 MeV, we conservatively estimate that Thomson-source, peak brightness can exceed that of APS (the best machine in the DOE complex) by more than 15 orders of magnitude. In much the same way that tunable lasers revolutionized atomic spectroscopy, this ''Peta-step'' advance in tunable, narrow-bandwidth, capability should enable entirely new fields of study and new, programmatically-interesting, applications such as: micrometer-spatial-resolution, MeV, flash radiography of dense, energetic systems (NIF, JASPER), precision, photo-nuclear absorption spectroscopy (DNT, PAT), non-destructive, resonant nuclear fluorescent imaging of special nuclear materials (NAI, DHS), dynamic, micro-crack failure analysis (aerospace industry, SSP) etc. Concepts are presented for new Thomson-Radiated Extreme X-ray (T-REX) sources at LLNL. These leverage LLNL's world-leading expertise in high-intensity lasers, high average power lasers, diffractive optics, Thomson-based x-ray source development, and advanced photoguns to produce tunable, quasi-monochromatic radiation from 50-keV to several MeV. Above {approx}100 keV, T-REX would be unique in the world with respect to BOTH peak x-ray brilliance AND average x-ray brilliance. This capability would naturally compliment the x-ray capability of large-scale, synchrotron facilities currently within the DoE complex by significantly extending the x-ray energy range over which, tunable, high-brightness applications could be pursued. It would do so at a small fraction of the cost of the purely, accelerator-based facilities. It is anticipated that T-REX could provide new opportunities for interaction of LLNL with the DoE Office of Science, DARPA, DHS etc. and would place LLNL clearly at the forefront of laser-based, x-ray generation world-wide.« less

A chirality change in XPC- and Sfi1-derived peptides affects their affinity for centrin.

PubMed

Grecu, Dora; Irudayaraj, Victor Paul Raj; Martinez-Sanz, Juan; Mallet, Jean-Maurice; Assairi, Liliane

2016-04-01

The Ca(2+)-binding protein centrin binds to a hydrophobic motif (W(1)xxL(4)xxxL(8)) included in the sequence of several cellular targets: XPC (xeroderma pigmentosum group C protein), Sfi1 (suppressor of fermentation-induced loss of stress resistance protein1), and Sac3 [the central component of the transcription and mRNA export (TREX-2) complex]. However, centrin binding occurs in a reversed orientation (L(8)xxxL(4)xxW(1)) for Sfi1 and Sac3 compared with XPC. Because D-peptides have been investigated for future therapeutic use, we analyzed their centrin-binding properties. Their affinity for centrin was measured using isothermal titration calorimetry. The chirality change in the target-derived peptides affected their ability to bind centrin in a specific manner depending on the sequence orientation of the centrin-binding motif. In contrast to L-XPC-P10, D-XPC-P10 bound C-HsCen1 in a Ca(2+)-dependent manner and to a lesser extent. D-XPC-P10 exhibited a reduced affinity for C-HsCen1 (Ka=0.064 × 10(6) M(-1)) by a factor of 2000 compared with L-XPC-P10 (Ka=132 × 10(6) M(-1)). D-peptides have a lower affinity than L-peptides for centrin, and the strength of this affinity depends on the sequence orientation of the target-derived peptides. The residual affinity observed for D-XPC suggests that the use of d-peptides represents a promising strategy for inhibiting centrin binding to its targets. Copyright © 2016 Elsevier Inc. All rights reserved.

Ran-dependent nuclear export mediators: a structural perspective

PubMed Central

Güttler, Thomas; Görlich, Dirk

2011-01-01

Nuclear export is an essential eukaryotic activity. It proceeds through nuclear pore complexes (NPCs) and is mediated by soluble receptors that shuttle between nucleus and cytoplasm. RanGTPase-dependent export mediators (exportins) constitute the largest class of these carriers and are functionally highly versatile. All of these exportins load their substrates in response to RanGTP binding in the nucleus and traverse NPCs as ternary RanGTP–exportin–cargo complexes to the cytoplasm, where GTP hydrolysis leads to export complex disassembly. The different exportins vary greatly in their substrate range. Recent structural studies of both protein- and RNA-specific exporters have illuminated how exportins bind their cargoes, how Ran triggers cargo loading and how export complexes are disassembled in the cytoplasm. Here, we review the current state of knowledge and highlight emerging principles as well as prevailing questions. PMID:21878989

Mechanistic Insights from Structural Analyses of Ran-GTPase-Driven Nuclear Export of Proteins and RNAs.

PubMed

Matsuura, Yoshiyuki

2016-05-22

Understanding how macromolecules are rapidly exchanged between the nucleus and the cytoplasm through nuclear pore complexes is a fundamental problem in biology. Exportins are Ran-GTPase-dependent nuclear transport factors that belong to the karyopherin-β family and mediate nuclear export of a plethora of proteins and RNAs, except for bulk mRNA nuclear export. Exportins bind cargo macromolecules in a Ran-GTP-dependent manner in the nucleus, forming exportin-cargo-Ran-GTP complexes (nuclear export complexes). Transient weak interactions between exportins and nucleoporins containing characteristic FG (phenylalanine-glycine) repeat motifs facilitate nuclear pore complex passage of nuclear export complexes. In the cytoplasm, nuclear export complexes are disassembled, thereby releasing the cargo. GTP hydrolysis by Ran promoted in the cytoplasm makes the disassembly reaction virtually irreversible and provides thermodynamic driving force for the overall export reaction. In the past decade, X-ray crystallography of some of the exportins in various functional states coupled with functional analyses, single-particle electron microscopy, molecular dynamics simulations, and small-angle solution X-ray scattering has provided rich insights into the mechanism of cargo binding and release and also begins to elucidate how exportins interact with the FG repeat motifs. The knowledge gained from structural analyses of nuclear export is being translated into development of clinically useful inhibitors of nuclear export to treat human diseases such as cancer and influenza. Copyright © 2015 Elsevier Ltd. All rights reserved.

Protein export through the bacterial flagellar type III export pathway.

PubMed

Minamino, Tohru

2014-08-01

For construction of the bacterial flagellum, which is responsible for bacterial motility, the flagellar type III export apparatus utilizes both ATP and proton motive force across the cytoplasmic membrane and exports flagellar proteins from the cytoplasm to the distal end of the nascent structure. The export apparatus consists of a membrane-embedded export gate made of FlhA, FlhB, FliO, FliP, FliQ, and FliR and a water-soluble ATPase ring complex consisting of FliH, FliI, and FliJ. FlgN, FliS, and FliT act as substrate-specific chaperones that do not only protect their cognate substrates from degradation and aggregation in the cytoplasm but also efficiently transfer the substrates to the export apparatus. The ATPase ring complex facilitates the initial entry of the substrates into the narrow pore of the export gate. The export gate by itself is a proton-protein antiporter that uses the two components of proton motive force, the electric potential difference and the proton concentration difference, for different steps of the export process. A specific interaction of FlhA with FliJ located in the center of the ATPase ring complex allows the export gate to efficiently use proton motive force to drive protein export. The ATPase ring complex couples ATP binding and hydrolysis to its assembly-disassembly cycle for rapid and efficient protein export cycle. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey. © 2013 Elsevier B.V. All rights reserved.

Non-FG mediated transport of the large pre-ribosomal subunit through the nuclear pore complex by the mRNA export factor Gle2

PubMed Central

Occhipinti, Laura; Chang, Yiming; Altvater, Martin; Menet, Anna M.; Kemmler, Stefan; Panse, Vikram G.

2013-01-01

Multiple export receptors passage bound pre-ribosomes through nuclear pore complexes (NPCs) by transiently interacting with the Phe-Gly (FG) meshwork of their transport channels. Here, we reveal how the non-FG interacting yeast mRNA export factor Gly-Leu-FG lethal 2 (Gle2) functions in the export of the large pre-ribosomal subunit (pre-60S). Structure-guided studies uncovered conserved platforms used by Gle2 to export pre-60S: an uncharacterized basic patch required to bind pre-60S, and a second surface that makes non-FG contacts with the nucleoporin Nup116. A basic patch mutant of Gle2 is able to function in mRNA export, but not pre-60S export. Thus, Gle2 provides a distinct interaction platform to transport pre-60S to the cytoplasm. Notably, Gle2’s interaction platforms become crucial for pre-60S export when FG-interacting receptors are either not recruited to pre-60S or are impaired. We propose that large complex cargos rely on non-FG as well as FG-interactions for their efficient translocation through the nuclear pore complex channel. PMID:23907389

Cex1p facilitates Rna1p-mediated dissociation of the Los1p-tRNA-Gsp1p-GTP export complex.

PubMed

McGuire, Andrew T; Mangroo, Dev

2012-02-01

Nuclear tRNA export plays an essential role in key cellular processes such as regulation of protein synthesis, cell cycle progression, response to nutrient availability and DNA damage and development. Like other nuclear export processes, assembly of the nuclear tRNA export complex in the nucleus is dependent on Ran-GTP/Gsp1p-GTP, and dissociation of the export receptor-tRNA-Ran-GTP/Gsp1p-GTP complex in the cytoplasm requires RanBP1/Yrb1p and RanGAP/Rna1p to activate the GTPase activity of Ran-GTP/Gsp1p-GTP. The Saccharomyces cerevisiae Cex1p and Human Scyl1 have also been proposed to participate in unloading of the tRNA export receptors at the cytoplasmic face of the nuclear pore complex (NPC). Here, we provide evidence suggesting that Cex1p is required for activation of the GTPase activity of Gsp1p and dissociation of the receptor-tRNA-Gsp1p export complex in S. cerevisiae. The data suggest that Cex1p recruits Rna1p from the cytoplasm to the NPC and facilitates Rna1p activation of the GTPase activity of Gsp1p by enabling Rna1p to gain access to Gsp1p-GTP bound to the export receptor tRNA complex. It is possible that this tRNA unloading mechanism is conserved in evolutionarily diverse organisms and that other Gsp1p-GTP-dependent export processes use a pathway-specific component to recruit Rna1p to the NPC. © 2011 John Wiley & Sons A/S.

The effects of gray scale image processing on digital mammography interpretation performance.

PubMed

Cole, Elodia B; Pisano, Etta D; Zeng, Donglin; Muller, Keith; Aylward, Stephen R; Park, Sungwook; Kuzmiak, Cherie; Koomen, Marcia; Pavic, Dag; Walsh, Ruth; Baker, Jay; Gimenez, Edgardo I; Freimanis, Rita

2005-05-01

To determine the effects of three image-processing algorithms on diagnostic accuracy of digital mammography in comparison with conventional screen-film mammography. A total of 201 cases consisting of nonprocessed soft copy versions of the digital mammograms acquired from GE, Fischer, and Trex digital mammography systems (1997-1999) and conventional screen-film mammograms of the same patients were interpreted by nine radiologists. The raw digital data were processed with each of three different image-processing algorithms creating three presentations-manufacturer's default (applied and laser printed to film by each of the manufacturers), MUSICA, and PLAHE-were presented in soft copy display. There were three radiologists per presentation. Area under the receiver operating characteristic curve for GE digital mass cases was worse than screen-film for all digital presentations. The area under the receiver operating characteristic for Trex digital mass cases was better, but only with images processed with the manufacturer's default algorithm. Sensitivity for GE digital mass cases was worse than screen film for all digital presentations. Specificity for Fischer digital calcifications cases was worse than screen film for images processed in default and PLAHE algorithms. Specificity for Trex digital calcifications cases was worse than screen film for images processed with MUSICA. Specific image-processing algorithms may be necessary for optimal presentation for interpretation based on machine and lesion type.

On the use of the T-REx tetracycline-inducible gene expression system in vivo.

PubMed

Dobrovolsky, Vasily N; Heflich, Robert H

2007-10-15

Components of the commercially available T-REx system were used to create two types of transgenic mice. The first contained the tetracycline-repressor transgene under the control of the CMV promoter/enhancer; the second type contained a green fluorescent protein (GFP) reporter transgene under the control of the CMV promoter/enhancer with a tetracycline repressor operator sequence. Transgene expression was unpredictable in animals containing the individual transgenes. Animals with the reporter transgene expressed GFP in only some tissues (e.g., pancreas, kidney), and one line of reporter transgenic animals developed kidney disease, presumably due to expression of the transgene. The two types of transgenic animals were crossbred to produce double-transgenic animals with the object of regulating the expression of the reporter in vivo. When a similar double-transgenic system was constructed in cultured cells, the repressor protein suppressed the transcription of the reporter transgene. The presence of the repressor in double-transgenic animals had no effect on the expression of the reporter; double transgenic animals developed the same kidney disease that was seen in singly transgenic mice with the reporter. Our results indicate that transgenes under the control of the CMV promoter in the T-REx system express somewhat unpredictably and in only a limited number of tissues, making the use of this system for the development of in vivo models problematical. Copyright 2007 Wiley Periodicals, Inc.

A prosurvival DNA damage-induced cytoplasmic interferon response is mediated by end resection factors and is limited by Trex1

PubMed Central

Erdal, Erkin; Haider, Syed; Rehwinkel, Jan; Harris, Adrian L.

2017-01-01

Radiotherapy and chemotherapy are effective treatment methods for many types of cancer, but resistance is common. Recent findings indicate that antiviral type I interferon (IFN) signaling is induced by these treatments. However, the underlying mechanisms still need to be elucidated. Expression of a set of IFN-stimulated genes comprises an IFN-related DNA damage resistance signature (IRDS), which correlates strongly with resistance to radiotherapy and chemotherapy across different tumors. Classically, during viral infection, the presence of foreign DNA in the cytoplasm of host cells can initiate type I IFN signaling. Here, we demonstrate that DNA-damaging modalities used during cancer therapy lead to the release of ssDNA fragments from the cell nucleus into the cytosol, engaging this innate immune response. We found that the factors that control DNA end resection during double-strand break repair, including the Bloom syndrome (BLM) helicase and exonuclease 1 (EXO1), play a major role in generating these DNA fragments and that the cytoplasmic 3′–5′ exonuclease Trex1 is required for their degradation. Analysis of mRNA expression profiles in breast tumors demonstrates that those with lower Trex1 and higher BLM and EXO1 expression levels are associated with poor prognosis. Targeting BLM and EXO1 could therefore represent a novel approach for circumventing the IRDS produced in response to cancer therapeutics. PMID:28279982

Probing lysine mono-methylation in histone H3 tail peptides with an abiotic receptor coupled to a non-plasmonic resonator.

PubMed

Bontempi, N; Biavardi, E; Bordiga, D; Candiani, G; Alessandri, I; Bergese, P; Dalcanale, E

2017-06-29

Binder and effector molecules that allow studying and manipulating epigenetic processes are of biological relevance and pose severe technical challenges. We report the first example of a synthetic receptor able to recognize mono-methylated lysines in a histone H3 tail peptide, which has relevant functions in epigenetic regulation. Recognition is robust and specific regardless of the position and the number of mono-methylated lysines along the polypeptide chain. The peptide is first captured in solution by a tetraphosphonate cavitand (Tiiii) that selectively binds its Lys-NMe + moieties. Separation from solution and detection of the peptide-Tiiii complexes is then enabled in one single step by an all dielectric SiO 2 -TiO 2 core-shell resonator (T-rex), which captures the complex and operates fully reproducible signal transduction by non-plasmonic surface enhanced Raman scattering (SERS) without degrading the complex. The realized abiotic probe is able to distinguish multiple mono-methylated peptides from the single mono-methylated ones.

[Structure and function of the bacterial flagellar type III protein export system in Salmonella
].

PubMed

Minamino, Tohru

2015-01-01

The bacterial flagellum is a filamentous organelle that propels the bacterial cell body in liquid media. For construction of the bacterial flagellum beyond the cytoplasmic membrane, flagellar component proteins are transported by its specific protein export apparatus from the cytoplasm to the distal end of the growing flagellar structure. The flagellar export apparatus consists of a transmembrane export gate complex and a cytoplasmic ATPase ring complex. Flagellar substrate-specific chaperones bind to their cognate substrates in the cytoplasm and escort the substrates to the docking platform of the export gate. The export apparatus utilizes ATP and proton motive force across the cytoplasmic membrane as the energy sources to drive protein export and coordinates protein export with assembly by ordered export of substrates to parallel with their order of assembly. In this review, we summarize our current understanding of the structure and function of the flagellar protein export system in Salmonella enterica serovar Typhimurium.

Secondary Generation of Mountain Waves in the Stratosphere

NASA Astrophysics Data System (ADS)

Woods, Bryan K.

Secondary generation of mountain waves was documented using in situ aircraft data from the Terrain-Induced Rotor Experiment (T-REX). Mountain waves propagating from the Sierra Nevada generated secondary waves due to stratospheric wave breaking. The seminal Eliassen and Palm (1961) relation of mountain wave energy and momentum fluxes is observationally verified for the first time. One case of reversed wave fluxes in the stratosphere is shown to be the result of multiscale secondary waves propagating down from the stratosphere. The Tropopause Inversion Layer (TIL) is shown to be capable of serving as a wave duct trapping such secondary waves. Simple idealized 2D simulations are shown to reproduce secondary wave patterns that bare striking resemblance to those observed in T-REX. However, 3D simulations are shown to fail to reproduce realistic secondary waves.

The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.

PubMed

Booth, David S; Cheng, Yifan; Frankel, Alan D

2014-12-08

The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is delivered to assembling virions. The RRE assembles a Rev oligomer that displays nuclear export sequences (NESs) for recognition by the Crm1-Ran(GTP) nuclear receptor complex. Here we provide the first view of an assembled HIV-host nuclear export complex using single-particle electron microscopy. Unexpectedly, Crm1 forms a dimer with an extensive interface that enhances association with Rev-RRE and poises NES binding sites to interact with a Rev oligomer. The interface between Crm1 monomers explains differences between Crm1 orthologs that alter nuclear export and determine cellular tropism for viral replication. The arrangement of the export complex identifies a novel binding surface to possibly target an HIV inhibitor and may point to a broader role for Crm1 dimerization in regulating host gene expression.

Coplanar Doppler Lidar Retrieval of Rotors from T-REX

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

Hill, Michael; Calhoun, Ron; Fernando, H. J. S.

2010-03-01

Two coherent Doppler lidars were deployed during the Terrain-induced Rotor EXperiment (T-REX). Coplanar Range Height Indicator (RHI) scans by the lidars (along the same azimuthal angle) allowed retrieval of two-dimensional velocity vectors on a vertical/cross-barrier plane using the least squares method. Vortices are shown to evolve and advect in the flow field, allowing analysis of their behavior in the mountain-wave-boundary layer system. The locations, magnitudes, and evolution of the vortices can be studied through calculated fields of velocity, vorticity, streamlines, and swirl. Two classes of vortical motions are identified: rotors and sub-rotors, which differ in scale and behavior. The levelmore » of coordination of the two lidars and the nature of the output (i.e., in range-gates) creates inherent restrictions on the spatial and temporal resolution of retrieved fields.« less

Recent achievements using chemical vapor composite silicon carbide (CVC SiC)

NASA Astrophysics Data System (ADS)

Goodman, William A.; Tanaka, Clifford

2009-08-01

This annual review documents our progress towards inexpensive mass production of silicon carbide mirrors and optical structures. Results are provided for a NASA Small Business Technology Transfer (STTR) X-Ray Mirror project. Trex partnered with the University of Alabama-Huntsville Center for Advanced Optics (UAH-CAO) to develop fabrication methods for polished cylindrical and conical chemical vapor composite (CVCTM) SiC mandrels. These mandrels are envisioned as pre-forms for the replication of fused silica x-ray optics to be eventually used in the International X-Ray Observatory (IXO). CVC SiCTM offers superior high temperature stability, thermal and mechanical performance and polishability required for this precision replication process. In this program, Trex fabricated prototype mandrels with design diameters of 10.5cm, 20cm and 45cm. UAH-CAO was Trex's university partner in this effort and worked on polishing and metrology of the unusual x-ray mandrel geometries. UAH-CAO successfully developed an innovative interferometric method for measuring the CVC SiCTM x-ray mandrels based on a precision cylindrical lens system. UAH-CAO also developed finishing and polishing methods for CVC SiCTM that utilized a Zeeko IRP200 computer controlled polishing tool. The three technologies key technologies demonstrated in this program (near net shape forming of CVC SiCTM mandrels, the x-ray mandrel metrology and free-form polishing capability on CVC SiCTM) could enable cost-effective manufacture of the x-ray mandrels required for the International X-Ray Observatory (IXO).

T-REX on-demand redox targeting in live cells.

PubMed

Parvez, Saba; Long, Marcus J C; Lin, Hong-Yu; Zhao, Yi; Haegele, Joseph A; Pham, Vanha N; Lee, Dustin K; Aye, Yimon

2016-12-01

This protocol describes targetable reactive electrophiles and oxidants (T-REX)-a live-cell-based tool designed to (i) interrogate the consequences of specific and time-resolved redox events, and (ii) screen for bona fide redox-sensor targets. A small-molecule toolset comprising photocaged precursors to specific reactive redox signals is constructed such that these inert precursors specifically and irreversibly tag any HaloTag-fused protein of interest (POI) in mammalian and Escherichia coli cells. Syntheses of the alkyne-functionalized endogenous reactive signal 4-hydroxynonenal (HNE(alkyne)) and the HaloTag-targetable photocaged precursor to HNE(alkyne) (also known as Ht-PreHNE or HtPHA) are described. Low-energy light prompts photo-uncaging (t 1/2 <1-2 min) and target-specific modification. The targeted modification of the POI enables precisely timed and spatially controlled redox events with no off-target modification. Two independent pathways are described, along with a simple setup to functionally validate known targets or discover novel sensors. T-REX sidesteps mixed responses caused by uncontrolled whole-cell swamping with reactive signals. Modification and downstream response can be analyzed by in-gel fluorescence, proteomics, qRT-PCR, immunofluorescence, fluorescence resonance energy transfer (FRET)-based and dual-luciferase reporters, or flow cytometry assays. T-REX targeting takes 4 h from initial probe treatment. Analysis of targeted redox responses takes an additional 4-24 h, depending on the nature of the pathway and the type of readouts used.

T-REX on-demand redox targeting in live cells

PubMed Central

Parvez, Saba; Long, Marcus J C; Lin, Hong-Yu; Zhao, Yi; Haegele, Joseph A; Pham, Vanha N; Lee, Dustin K; Aye, Yimon

2017-01-01

This protocol describes targetable reactive electrophiles and oxidants (T-REX)—a live-cell-based tool designed to (i) interrogate the consequences of specific and time-resolved redox events, and (ii) screen for bona fide redox-sensor targets. A small-molecule toolset comprising photocaged precursors to specific reactive redox signals is constructed such that these inert precursors specifically and irreversibly tag any HaloTag-fused protein of interest (POI) in mammalian and Escherichia coli cells. Syntheses of the alkyne-functionalized endogenous reactive signal 4-hydroxynonenal (HNE (alkyne)) and the HaloTag-targetable photocaged precursor to HNE (alkyne) (also known as Ht-PreHNE or HtPHA) are described. Low-energy light prompts photo-uncaging (t1/2 <1–2 min) and target-specific modification. The targeted modification of the POI enables precisely timed and spatially controlled redox events with no off-target modification. Two independent pathways are described, along with a simple setup to functionally validate known targets or discover novel sensors. T-REX sidesteps mixed responses caused by uncontrolled whole-cell swamping with reactive signals. Modification and downstream response can be analyzed by in-gel fluorescence, proteomics, qRT-PCR, immunofluorescence, fluorescence resonance energy transfer (FRET)-based and dual-luciferase reporters, or flow cytometry assays. T-REX targeting takes 4 h from initial probe treatment. Analysis of targeted redox responses takes an additional 4–24 h, depending on the nature of the pathway and the type of readouts used. PMID:27809314

Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p.

PubMed

Koyama, Masako; Hirano, Hidemi; Shirai, Natsuki; Matsuura, Yoshiyuki

2017-10-01

Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine-glycine (so-called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif. The crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex identified three binding sites for the SxFG/PxFG repeats on HEAT repeats 14-20 of Xpo1p. Mutational analyses of Nup42p showed that the conserved serines and prolines in the SxFG/PxFG repeats contribute to Xpo1p-Nup42p binding. Our structural and biochemical data suggest that SxFG/PxFG-Nups such as Nup42p and Nup159p at the cytoplasmic face of NPCs provide high-affinity docking sites for the Xpo1p nuclear export complex in the terminal stage of NPC passage and that subsequent disassembly of the nuclear export complex facilitates recycling of free Xpo1p back to the nucleus. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Inner nuclear envelope protein SUN1 plays a prominent role in mammalian mRNA export.

PubMed

Li, Ping; Noegel, Angelika A

2015-11-16

Nuclear export of messenger ribonucleoproteins (mRNPs) through the nuclear pore complex (NPC) can be roughly classified into two forms: bulk and specific export, involving an nuclear RNA export factor 1 (NXF1)-dependent pathway and chromosome region maintenance 1 (CRM1)-dependent pathway, respectively. SUN proteins constitute the inner nuclear envelope component of the l I: nker of N: ucleoskeleton and C: ytoskeleton (LINC) complex. Here, we show that mammalian cells require SUN1 for efficient nuclear mRNP export. The results indicate that both SUN1 and SUN2 interact with heterogeneous nuclear ribonucleoprotein (hnRNP) F/H and hnRNP K/J. SUN1 depletion inhibits the mRNP export, with accumulations of both hnRNPs and poly(A)+RNA in the nucleus. Leptomycin B treatment indicates that SUN1 functions in mammalian mRNA export involving the NXF1-dependent pathway. SUN1 mediates mRNA export through its association with mRNP complexes via a direct interaction with NXF1. Additionally, SUN1 associates with the NPC through a direct interaction with Nup153, a nuclear pore component involved in mRNA export. Taken together, our results reveal that the inner nuclear envelope protein SUN1 has additional functions aside from being a central component of the LINC complex and that it is an integral component of the mammalian mRNA export pathway suggesting a model whereby SUN1 recruits NXF1-containing mRNP onto the nuclear envelope and hands it over to Nup153. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

FliH and FliI ensure efficient energy coupling of flagellar type III protein export in Salmonella.

PubMed

Minamino, Tohru; Kinoshita, Miki; Inoue, Yumi; Morimoto, Yusuke V; Ihara, Kunio; Koya, Satomi; Hara, Noritaka; Nishioka, Noriko; Kojima, Seiji; Homma, Michio; Namba, Keiichi

2016-06-01

For construction of the bacterial flagellum, flagellar proteins are exported via its specific export apparatus from the cytoplasm to the distal end of the growing flagellar structure. The flagellar export apparatus consists of a transmembrane (TM) export gate complex and a cytoplasmic ATPase complex consisting of FliH, FliI, and FliJ. FlhA is a TM export gate protein and plays important roles in energy coupling of protein translocation. However, the energy coupling mechanism remains unknown. Here, we performed a cross-complementation assay to measure robustness of the energy transduction system of the export apparatus against genetic perturbations. Vibrio FlhA restored motility of a Salmonella ΔflhA mutant but not that of a ΔfliH-fliI flhB(P28T) ΔflhA mutant. The flgM mutations significantly increased flagellar gene expression levels, allowing Vibrio FlhA to exert its export activity in the ΔfliH-fliI flhB(P28T) ΔflhA mutant. Pull-down assays revealed that the binding affinities of Vibrio FlhA for FliJ and the FlgN-FlgK chaperone-substrate complex were much lower than those of Salmonella FlhA. These suggest that Vibrio FlhA requires the support of FliH and FliI to efficiently and properly interact with FliJ and the FlgN-FlgK complex. We propose that FliH and FliI ensure robust and efficient energy coupling of protein export during flagellar assembly. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex.

PubMed

Fukumura, Takuma; Makino, Fumiaki; Dietsche, Tobias; Kinoshita, Miki; Kato, Takayuki; Wagner, Samuel; Namba, Keiichi; Imada, Katsumi; Minamino, Tohru

2017-08-01

The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export. FliO formed a 5-nm ring structure with 3 clamp-like structures that bind to the FliP6 ring. The crystal structure of FliPP derived from Thermotoga maritia, and structure-based photo-crosslinking experiments revealed that Phe-150 and Ser-156 of FliPP are involved in the FliP-FliP interactions and that Phe-150, Arg-152, Ser-156, and Pro-158 are responsible for the FliP-FliO interactions. Overexpression of FliP restored motility of a ∆fliO mutant to the wild-type level, suggesting that the FliP6 ring is a functional unit in the export gate complex and that FliO is not part of the final gate structure. Copurification assays revealed that FlhA, FlhB, FliQ, and FliR are associated with the FliO/FliP complex. We propose that the assembly of the export gate complex begins with FliP6 ring formation with the help of the FliO scaffold, followed by FliQ, FliR, and FlhB and finally FlhA during MS ring formation.

Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex

PubMed Central

Fukumura, Takuma; Makino, Fumiaki; Dietsche, Tobias; Kinoshita, Miki; Kato, Takayuki; Wagner, Samuel; Namba, Keiichi; Imada, Katsumi

2017-01-01

The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export. FliO formed a 5-nm ring structure with 3 clamp-like structures that bind to the FliP6 ring. The crystal structure of FliPP derived from Thermotoga maritia, and structure-based photo-crosslinking experiments revealed that Phe-150 and Ser-156 of FliPP are involved in the FliP–FliP interactions and that Phe-150, Arg-152, Ser-156, and Pro-158 are responsible for the FliP–FliO interactions. Overexpression of FliP restored motility of a ∆fliO mutant to the wild-type level, suggesting that the FliP6 ring is a functional unit in the export gate complex and that FliO is not part of the final gate structure. Copurification assays revealed that FlhA, FlhB, FliQ, and FliR are associated with the FliO/FliP complex. We propose that the assembly of the export gate complex begins with FliP6 ring formation with the help of the FliO scaffold, followed by FliQ, FliR, and FlhB and finally FlhA during MS ring formation. PMID:28771466

Pressure Anisotropy Probe for the Terrestrial Reconnection Experiment (TREX)

NASA Astrophysics Data System (ADS)

Myers, Rachel; Egedal, Jan; Olson, Joseph; Greess, Samuel; Clark, Michael; Nonn, Paul; Wallace, John; Forest, Cary

2016-10-01

The Terrestrial Reconnection Experiment (TREX) at the Wisconsin Plasma Astrophysics Laboratory (WiPAL) studies magnetic reconnection primarily in the collisionless regime. In this regime, electron pressure anisotropy is expected to develop, deviating from traditional Hall reconnection dynamics and driving formation of large-scale current layers. In order to measure the anisotropy, a multi-tip electromagnetic probe similar to the M-probe described by Shadman, consisting of 32 Langmuir probe tips and two magnetic coils, has been constructed. Each tip is biased to a different potential, simultaneously measuring discrete parts of the full I-V characteristic. Pulsing the coil then locally increases the magnetic field, creating a magnetic mirror force to reflect electrons with large values of v⊥ / v . The change in electron velocity modifies the I-V characteristics and can be used to infer p∥ /p⊥ . Analysis with the new probe will be presented. DOE Grant DE-SC0010463, University of Wisconsin-Madison University Fellowship.

Development of a field-deployable method for simultaneous, real-time measurements of the four most abundant N2O isotopocules.

PubMed

Ibraim, Erkan; Harris, Eliza; Eyer, Simon; Tuzson, Béla; Emmenegger, Lukas; Six, Johan; Mohn, Joachim

2018-03-01

Understanding and quantifying the biogeochemical cycle of N 2 O is essential to develop effective N 2 O emission mitigation strategies. This study presents a novel, fully automated measurement technique that allows simultaneous, high-precision quantification of the four main N 2 O isotopocules ( 14 N 14 N 16 O, 14 N 15 N 16 O, 15 N 14 N 16 O and 14 N 14 N 18 O) in ambient air. The instrumentation consists of a trace gas extractor (TREX) coupled to a quantum cascade laser absorption spectrometer, designed for autonomous operation at remote measurement sites. The main advantages this system has over its predecessors are a compact spectrometer design with improved temperature control and a more compact and powerful TREX device. The adopted TREX device enhances the flexibility of the preconcentration technique for higher adsorption volumes to target rare isotope species and lower adsorption temperatures for highly volatile substances. All system components have been integrated into a standardized instrument rack to improve portability and accessibility for maintenance. With an average sampling frequency of approximately 1 h -1 , this instrumentation achieves a repeatability of 0.09, 0.13, 0.17 and 0.12 ‰ for δ 15 N α , δ 15 N β , δ 18 O and site preference of N 2 O, respectively, for pressurized ambient air. The repeatability for N 2 O mole fraction measurements is better than 1 ppb (parts per billion, 10 -9 moles per mole of dry air).

KLF4 Nuclear Export Requires ERK Activation and Initiates Exit from Naive Pluripotency.

PubMed

Dhaliwal, Navroop K; Miri, Kamelia; Davidson, Scott; Tamim El Jarkass, Hala; Mitchell, Jennifer A

2018-04-10

Cooperative action of a transcription factor complex containing OCT4, SOX2, NANOG, and KLF4 maintains the naive pluripotent state; however, less is known about the mechanisms that disrupt this complex, initiating exit from pluripotency. We show that, as embryonic stem cells (ESCs) exit pluripotency, KLF4 protein is exported from the nucleus causing rapid decline in Nanog and Klf4 transcription; as a result, KLF4 is the first pluripotency transcription factor removed from transcription-associated complexes during differentiation. KLF4 nuclear export requires ERK activation, and phosphorylation of KLF4 by ERK initiates interaction of KLF4 with nuclear export factor XPO1, leading to KLF4 export. Mutation of the ERK phosphorylation site in KLF4 (S132) blocks KLF4 nuclear export, the decline in Nanog, Klf4, and Sox2 mRNA, and differentiation. These findings demonstrate that relocalization of KLF4 to the cytoplasm is a critical first step in exit from the naive pluripotent state and initiation of ESC differentiation. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs

PubMed Central

Gromadzka, Agnieszka M.; Steckelberg, Anna-Lena; Singh, Kusum K.; Hofmann, Kay; Gehring, Niels H.

2016-01-01

The export of messenger RNAs (mRNAs) is the final of several nuclear posttranscriptional steps of gene expression. The formation of export-competent mRNPs involves the recruitment of export factors that are assumed to facilitate transport of the mature mRNAs. Using in vitro splicing assays, we show that a core set of export factors, including ALYREF, UAP56 and DDX39, readily associate with the spliced RNAs in an EJC (exon junction complex)- and cap-dependent manner. In order to elucidate how ALYREF and other export adaptors mediate mRNA export, we conducted a computational analysis and discovered four short, conserved, linear motifs present in RNA-binding proteins. We show that mutation in one of the new motifs (WxHD) in an unstructured region of ALYREF reduced RNA binding and abolished the interaction with eIF4A3 and CBP80. Additionally, the mutation impaired proper localization to nuclear speckles and export of a spliced reporter mRNA. Our results reveal important details of the orchestrated recruitment of export factors during the formation of export competent mRNPs. PMID:26773052

The function of the inner nuclear envelope protein SUN1 in mRNA export is regulated by phosphorylation.

PubMed

Li, Ping; Stumpf, Maria; Müller, Rolf; Eichinger, Ludwig; Glöckner, Gernot; Noegel, Angelika A

2017-08-22

SUN1, a component of the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex, functions in mammalian mRNA export through the NXF1-dependent pathway. It associates with mRNP complexes by direct interaction with NXF1. It also binds to the NPC through association with the nuclear pore component Nup153, which is involved in mRNA export. The SUN1-NXF1 association is at least partly regulated by a protein kinase C (PKC) which phosphorylates serine 113 (S113) in the N-terminal domain leading to reduced interaction. The phosphorylation appears to be important for the SUN1 function in nuclear mRNA export since GFP-SUN1 carrying a S113A mutation was less efficient in restoring mRNA export after SUN1 knockdown as compared to the wild type protein. By contrast, GFP-SUN1-S113D resembling the phosphorylated state allowed very efficient export of poly(A)+RNA. Furthermore, probing a possible role of the LINC complex component Nesprin-2 in this process we observed impaired mRNA export in Nesprin-2 knockdown cells. This effect might be independent of SUN1 as expression of a GFP tagged SUN-domain deficient SUN1, which no longer can interact with Nesprin-2, did not affect mRNA export.

Structural and Functional Analysis of the Interaction Between the Nucleoporin Nup98 and the mRNA Export Facto Rae1

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

Y Ren; H Seo; G Blobel

The export of mRNAs is a multistep process, involving the packaging of mRNAs into messenger ribonucleoprotein particles (mRNPs), their transport through nuclear pore complexes, and mRNP remodeling events prior to translation. Ribonucleic acid export 1 (Rae1) and Nup98 are evolutionarily conserved mRNA export factors that are targeted by the vesicular stomatitis virus matrix protein to inhibit host cell nuclear export. Here, we present the crystal structure of human Rae1 in complex with the Gle2-binding sequence (GLEBS) of Nup98 at 1.65 {angstrom} resolution. Rae1 forms a seven-bladed {beta}-propeller with several extensive surface loops. The Nup98 GLEBS motif forms an {approx}50-{angstrom}-long hairpinmore » that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the entire top face of the Rae1 {beta}-propeller. The C-terminal arm of the GLEBS hairpin is necessary and sufficient for Rae1 binding, and we identify a tandem glutamate element in this arm as critical for complex formation. The Rae1 {center_dot} Nup98{sup GLEBS} surface features an additional conserved patch with a positive electrostatic potential, and we demonstrate that the complex possesses single-stranded RNA-binding capability. Together, these data suggest that the Rae1 {center_dot} Nup98 complex directly binds to the mRNP at several stages of the mRNA export pathway.« less

Nuclear export of ubiquitinated proteins via the UBIN-POST system

PubMed Central

Sugihara, Munechika; Morito, Daisuke; Iemura, Shun-ichiro; Natsume, Tohru; Nagata, Kazuhiro

2018-01-01

Although mechanisms for protein homeostasis in the cytosol have been studied extensively, those in the nucleus remain largely unknown. Here, we identified that a protein complex mediates export of polyubiquitinated proteins from the nucleus to the cytosol. UBIN, a ubiquitin-associated (UBA) domain-containing protein, shuttled between the nucleus and the cytosol in a CRM1-dependent manner, despite the lack of intrinsic nuclear export signal (NES). Instead, the UBIN binding protein polyubiquitinated substrate transporter (POST) harboring an NES shuttled UBIN through nuclear pores. UBIN bound to polyubiquitin chain through its UBA domain, and the UBIN-POST complex exported them from the nucleus to the cytosol. Ubiquitinated proteins accumulated in the cytosol in response to proteasome inhibition, whereas cotreatment with CRM1 inhibitor led to their accumulation in the nucleus. Our results suggest that ubiquitinated proteins are exported from the nucleus to the cytosol in the UBIN-POST complex-dependent manner for the maintenance of nuclear protein homeostasis. PMID:29666234

Yeast Ran-Binding Protein 1 (Yrb1) Shuttles between the Nucleus and Cytoplasm and Is Exported from the Nucleus via a CRM1 (XPO1)-Dependent Pathway

PubMed Central

Künzler, Markus; Gerstberger, Thomas; Stutz, Françoise; Bischoff, F. Ralf; Hurt, Ed

2000-01-01

The RanGTP-binding protein RanBP1, which is located in the cytoplasm, has been implicated in release of nuclear export complexes from the cytoplasmic side of the nuclear pore complex. Here we show that Yrb1 (the yeast homolog of RanBP1) shuttles between the nucleus and the cytoplasm. Nuclear import of Yrb1 is a facilitated process that requires a short basic sequence within the Ran-binding domain (RBD). By contrast, nuclear export of Yrb1 requires an intact RBD, which forms a ternary complex with the Xpo1 (Crm1) NES receptor in the presence of RanGTP. Nuclear export of Yrb1, however, is insensitive towards leptomycin B, suggesting a novel type of substrate recognition between Yrb1 and Xpo1. Taken together, these data suggest that ongoing nuclear import and export is an important feature of Yrb1 function in vivo. PMID:10825193

Nuclear export of ubiquitinated proteins via the UBIN-POST system.

PubMed

Hirayama, Shoshiro; Sugihara, Munechika; Morito, Daisuke; Iemura, Shun-Ichiro; Natsume, Tohru; Murata, Shigeo; Nagata, Kazuhiro

2018-05-01

Although mechanisms for protein homeostasis in the cytosol have been studied extensively, those in the nucleus remain largely unknown. Here, we identified that a protein complex mediates export of polyubiquitinated proteins from the nucleus to the cytosol. UBIN, a ubiquitin-associated (UBA) domain-containing protein, shuttled between the nucleus and the cytosol in a CRM1-dependent manner, despite the lack of intrinsic nuclear export signal (NES). Instead, the UBIN binding protein polyubiquitinated substrate transporter (POST) harboring an NES shuttled UBIN through nuclear pores. UBIN bound to polyubiquitin chain through its UBA domain, and the UBIN-POST complex exported them from the nucleus to the cytosol. Ubiquitinated proteins accumulated in the cytosol in response to proteasome inhibition, whereas cotreatment with CRM1 inhibitor led to their accumulation in the nucleus. Our results suggest that ubiquitinated proteins are exported from the nucleus to the cytosol in the UBIN-POST complex-dependent manner for the maintenance of nuclear protein homeostasis. Copyright © 2018 the Author(s). Published by PNAS.

Soluble components of the flagellar export apparatus, FliI, FliJ, and FliH, do not deliver flagellin, the major filament protein, from the cytosol to the export gate.

PubMed

Sajó, Ráchel; Liliom, Károly; Muskotál, Adél; Klein, Agnes; Závodszky, Péter; Vonderviszt, Ferenc; Dobó, József

2014-11-01

Flagella, the locomotion organelles of bacteria, extend from the cytoplasm to the cell exterior. External flagellar proteins are synthesized in the cytoplasm and exported by the flagellar type III secretion system. Soluble components of the flagellar export apparatus, FliI, FliH, and FliJ, have been implicated to carry late export substrates in complex with their cognate chaperones from the cytoplasm to the export gate. The importance of the soluble components in the delivery of the three minor late substrates FlgK, FlgL (hook-filament junction) and FliD (filament-cap) has been convincingly demonstrated, but their role in the transport of the major filament component flagellin (FliC) is still unclear. We have used continuous ATPase activity measurements and quartz crystal microbalance (QCM) studies to characterize interactions between the soluble export components and flagellin or the FliC:FliS substrate-chaperone complex. As controls, interactions between soluble export component pairs were characterized providing Kd values. FliC or FliC:FliS did not influence the ATPase activity of FliI alone or in complex with FliH and/or FliJ suggesting lack of interaction in solution. Immobilized FliI, FliH, or FliJ did not interact with FliC or FliC:FliS detected by QCM. The lack of interaction in the fluid phase between FliC or FliC:FliS and the soluble export components, in particular with the ATPase FliI, suggests that cells use different mechanisms for the export of late minor substrates, and the major substrate, FliC. It seems that the abundantly produced flagellin does not require the assistance of the soluble export components to efficiently reach the export gate. Copyright © 2014 Elsevier B.V. All rights reserved.

A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs.

PubMed

Gromadzka, Agnieszka M; Steckelberg, Anna-Lena; Singh, Kusum K; Hofmann, Kay; Gehring, Niels H

2016-03-18

The export of messenger RNAs (mRNAs) is the final of several nuclear posttranscriptional steps of gene expression. The formation of export-competent mRNPs involves the recruitment of export factors that are assumed to facilitate transport of the mature mRNAs. Using in vitro splicing assays, we show that a core set of export factors, including ALYREF, UAP56 and DDX39, readily associate with the spliced RNAs in an EJC (exon junction complex)- and cap-dependent manner. In order to elucidate how ALYREF and other export adaptors mediate mRNA export, we conducted a computational analysis and discovered four short, conserved, linear motifs present in RNA-binding proteins. We show that mutation in one of the new motifs (WxHD) in an unstructured region of ALYREF reduced RNA binding and abolished the interaction with eIF4A3 and CBP80. Additionally, the mutation impaired proper localization to nuclear speckles and export of a spliced reporter mRNA. Our results reveal important details of the orchestrated recruitment of export factors during the formation of export competent mRNPs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A generalizable platform for interrogating target- and signal-specific consequences of electrophilic modifications in redox-dependent cell signaling.

PubMed

Lin, Hong-Yu; Haegele, Joseph A; Disare, Michael T; Lin, Qishan; Aye, Yimon

2015-05-20

Despite the known propensity of small-molecule electrophiles to react with numerous cysteine-active proteins, biological actions of individual signal inducers have emerged to be chemotype-specific. To pinpoint and quantify the impacts of modifying one target out of the whole proteome, we develop a target-protein-personalized "electrophile toolbox" with which specific intracellular targets can be selectively modified at a precise time by specific reactive signals. This general methodology, T-REX (targetable reactive electrophiles and oxidants), is established by (1) constructing a platform that can deliver a range of electronic and sterically different bioactive lipid-derived signaling electrophiles to specific proteins in cells; (2) probing the kinetics of targeted delivery concept, which revealed that targeting efficiency in cells is largely driven by initial on-rate of alkylation; and (3) evaluating the consequences of protein-target- and small-molecule-signal-specific modifications on the strength of downstream signaling. These data show that T-REX allows quantitative interrogations into the extent to which the Nrf2 transcription factor-dependent antioxidant response element (ARE) signaling is activated by selective electrophilic modifications on Keap1 protein, one of several redox-sensitive regulators of the Nrf2-ARE axis. The results document Keap1 as a promiscuous electrophile-responsive sensor able to respond with similar efficiencies to discrete electrophilic signals, promoting comparable strength of Nrf2-ARE induction. T-REX is also able to elicit cell activation in cases in which whole-cell electrophile flooding fails to stimulate ARE induction prior to causing cytotoxicity. The platform presents a previously unavailable opportunity to elucidate the functional consequences of small-molecule-signal- and protein-target-specific electrophilic modifications in an otherwise unaffected cellular background.

Measuring economic complexity of countries and products: which metric to use?

NASA Astrophysics Data System (ADS)

Mariani, Manuel Sebastian; Vidmer, Alexandre; Medo, Matsúš; Zhang, Yi-Cheng

2015-11-01

Evaluating the economies of countries and their relations with products in the global market is a central problem in economics, with far-reaching implications to our theoretical understanding of the international trade as well as to practical applications, such as policy making and financial investment planning. The recent Economic Complexity approach aims to quantify the competitiveness of countries and the quality of the exported products based on the empirical observation that the most competitive countries have diversified exports, whereas developing countries only export few low quality products - typically those exported by many other countries. Two different metrics, Fitness-Complexity and the Method of Reflections, have been proposed to measure country and product score in the Economic Complexity framework. We use international trade data and a recent ranking evaluation measure to quantitatively compare the ability of the two metrics to rank countries and products according to their importance in the network. The results show that the Fitness-Complexity metric outperforms the Method of Reflections in both the ranking of products and the ranking of countries. We also investigate a generalization of the Fitness-Complexity metric and show that it can produce improved rankings provided that the input data are reliable.

Cex1p is a novel cytoplasmic component of the Saccharomyces cerevisiae nuclear tRNA export machinery.

PubMed

McGuire, Andrew T; Mangroo, Dev

2007-01-24

The Saccharomyces cerevisiae Yor112wp, which we named Cex1p, was identified using a yeast tRNA three-hybrid interaction approach and an in vivo nuclear tRNA export assay as a cytoplasmic component of the nuclear tRNA export machinery. Cex1p binds tRNA saturably, and associates with the nuclear pore complex by interacting directly with Nup116p. Cex1p co-purifies with the nuclear tRNA export receptors Los1p and Msn5p, the eukaryotic elongation factor eEF-1A, which delivers aminoacylated tRNAs to the ribosome, and the RanGTPase Gsp1p, but not with Cca1p, a tRNA maturation enzyme that facilitates translocation of non-aminoacylated tRNAs across the nuclear pore complex. Depletion of Cex1p and eEF-1A or Los1p significantly reduced the efficiency of nuclear tRNA export. Cex1p interacts with Los1p but not with eEF-1A in vitro. These findings suggest that Cex1p is a component of the nuclear aminoacylation-dependent tRNA export pathway in S. cerevisiae. They also suggest that Cex1p collects aminoacyl-tRNAs from the nuclear export receptors at the cytoplasmic side of the nuclear pore complex, and transfers them to eEF-1A using a channelling mechanism.

Measuring the intangibles: a metrics for the economic complexity of countries and products.

PubMed

Cristelli, Matthieu; Gabrielli, Andrea; Tacchella, Andrea; Caldarelli, Guido; Pietronero, Luciano

2013-01-01

We investigate a recent methodology we have proposed to extract valuable information on the competitiveness of countries and complexity of products from trade data. Standard economic theories predict a high level of specialization of countries in specific industrial sectors. However, a direct analysis of the official databases of exported products by all countries shows that the actual situation is very different. Countries commonly considered as developed ones are extremely diversified, exporting a large variety of products from very simple to very complex. At the same time countries generally considered as less developed export only the products also exported by the majority of countries. This situation calls for the introduction of a non-monetary and non-income-based measure for country economy complexity which uncovers the hidden potential for development and growth. The statistical approach we present here consists of coupled non-linear maps relating the competitiveness/fitness of countries to the complexity of their products. The fixed point of this transformation defines a metrics for the fitness of countries and the complexity of products. We argue that the key point to properly extract the economic information is the non-linearity of the map which is necessary to bound the complexity of products by the fitness of the less competitive countries exporting them. We present a detailed comparison of the results of this approach directly with those of the Method of Reflections by Hidalgo and Hausmann, showing the better performance of our method and a more solid economic, scientific and consistent foundation.

Measuring the Intangibles: A Metrics for the Economic Complexity of Countries and Products

PubMed Central

Cristelli, Matthieu; Gabrielli, Andrea; Tacchella, Andrea; Caldarelli, Guido; Pietronero, Luciano

2013-01-01

We investigate a recent methodology we have proposed to extract valuable information on the competitiveness of countries and complexity of products from trade data. Standard economic theories predict a high level of specialization of countries in specific industrial sectors. However, a direct analysis of the official databases of exported products by all countries shows that the actual situation is very different. Countries commonly considered as developed ones are extremely diversified, exporting a large variety of products from very simple to very complex. At the same time countries generally considered as less developed export only the products also exported by the majority of countries. This situation calls for the introduction of a non-monetary and non-income-based measure for country economy complexity which uncovers the hidden potential for development and growth. The statistical approach we present here consists of coupled non-linear maps relating the competitiveness/fitness of countries to the complexity of their products. The fixed point of this transformation defines a metrics for the fitness of countries and the complexity of products. We argue that the key point to properly extract the economic information is the non-linearity of the map which is necessary to bound the complexity of products by the fitness of the less competitive countries exporting them. We present a detailed comparison of the results of this approach directly with those of the Method of Reflections by Hidalgo and Hausmann, showing the better performance of our method and a more solid economic, scientific and consistent foundation. PMID:23940633

In vivo biochemical analyses reveal distinct roles of β-importins and eEF1A in tRNA subcellular traffic

PubMed Central

Huang, Hsiao-Yun

2015-01-01

Bidirectional tRNA movement between the nucleus and the cytoplasm serves multiple biological functions. To gain a biochemical understanding of the mechanisms for tRNA subcellular dynamics, we developed in vivo β-importin complex coimmunoprecipitation (co-IP) assays using budding yeast. Our studies provide the first in vivo biochemical evidence that two β-importin family members, Los1 (exportin-t) and Msn5 (exportin-5), serve overlapping but distinct roles in tRNA nuclear export. Los1 assembles complexes with RanGTP and tRNA. Both intron-containing pre-tRNAs and spliced tRNAs, regardless of whether they are aminoacylated, assemble into Los1–RanGTP complexes, documenting that Los1 participates in both primary nuclear export and re-export of tRNAs to the cytoplasm. In contrast, β-importin Msn5 preferentially assembles with RanGTP and spliced, aminoacylated tRNAs, documenting its role in tRNA nuclear re-export. Tef1/2 (the yeast form of translation elongation factor 1α [eEF1A]) aids the specificity of Msn5 for aminoacylated tRNAs to form a quaternary complex consisting of Msn5, RanGTP, aminoacylated tRNA, and Tef1/2. Assembly and/or stability of this quaternary complex requires Tef1/2, thereby facilitating efficient re-export of aminoacylated tRNAs to the cytoplasm. PMID:25838545

Integration of mRNP formation and export.

PubMed

Björk, Petra; Wieslander, Lars

2017-08-01

Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA-protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.

Cex1p is a novel cytoplasmic component of the Saccharomyces cerevisiae nuclear tRNA export machinery

PubMed Central

McGuire, Andrew T; Mangroo, Dev

2007-01-01

The Saccharomyces cerevisiae Yor112wp, which we named Cex1p, was identified using a yeast tRNA three-hybrid interaction approach and an in vivo nuclear tRNA export assay as a cytoplasmic component of the nuclear tRNA export machinery. Cex1p binds tRNA saturably, and associates with the nuclear pore complex by interacting directly with Nup116p. Cex1p co-purifies with the nuclear tRNA export receptors Los1p and Msn5p, the eukaryotic elongation factor eEF-1A, which delivers aminoacylated tRNAs to the ribosome, and the RanGTPase Gsp1p, but not with Cca1p, a tRNA maturation enzyme that facilitates translocation of non-aminoacylated tRNAs across the nuclear pore complex. Depletion of Cex1p and eEF-1A or Los1p significantly reduced the efficiency of nuclear tRNA export. Cex1p interacts with Los1p but not with eEF-1A in vitro. These findings suggest that Cex1p is a component of the nuclear aminoacylation-dependent tRNA export pathway in S. cerevisiae. They also suggest that Cex1p collects aminoacyl-tRNAs from the nuclear export receptors at the cytoplasmic side of the nuclear pore complex, and transfers them to eEF-1A using a channelling mechanism. PMID:17203074

In vivo biochemical analyses reveal distinct roles of β-importins and eEF1A in tRNA subcellular traffic.

PubMed

Huang, Hsiao-Yun; Hopper, Anita K

2015-04-01

Bidirectional tRNA movement between the nucleus and the cytoplasm serves multiple biological functions. To gain a biochemical understanding of the mechanisms for tRNA subcellular dynamics, we developed in vivo β-importin complex coimmunoprecipitation (co-IP) assays using budding yeast. Our studies provide the first in vivo biochemical evidence that two β-importin family members, Los1 (exportin-t) and Msn5 (exportin-5), serve overlapping but distinct roles in tRNA nuclear export. Los1 assembles complexes with RanGTP and tRNA. Both intron-containing pre-tRNAs and spliced tRNAs, regardless of whether they are aminoacylated, assemble into Los1-RanGTP complexes, documenting that Los1 participates in both primary nuclear export and re-export of tRNAs to the cytoplasm. In contrast, β-importin Msn5 preferentially assembles with RanGTP and spliced, aminoacylated tRNAs, documenting its role in tRNA nuclear re-export. Tef1/2 (the yeast form of translation elongation factor 1α [eEF1A]) aids the specificity of Msn5 for aminoacylated tRNAs to form a quaternary complex consisting of Msn5, RanGTP, aminoacylated tRNA, and Tef1/2. Assembly and/or stability of this quaternary complex requires Tef1/2, thereby facilitating efficient re-export of aminoacylated tRNAs to the cytoplasm. © 2015 Huang and Hopper; Published by Cold Spring Harbor Laboratory Press.

Pyruvate dehydrogenase complex (PDC) export from the mitochondrial matrix.

PubMed

Ng, Fanny; Tang, Bor Luen

2014-01-01

Studies on mitochondria protein import had revealed in detail molecular mechanisms of how peptides and proteins could be selectively targeted and translocated across membrane bound organelles. The opposite process of mitochondrial export, while known to occur in various aspects of cellular physiology and pathology, is less well understood. Two very recent reports have indicated that a large mitochondrial matrix protein complex, the pyruvate dehydrogenase complex (PDC) (or its component subunits), could be exported to the lysosomes and the nucleus, respectively. In the case of the latter, evidence was presented to suggest that the entire complex of 8-10 MDa could translocate in its entirety from the mitochondrial matrix to the nucleus upon mitogenic or stress stimuli. We discuss these findings in perspective to what is currently known about the processes of transport in and out of the mitochondrion.

JPRS Report, East Europe

DTIC Science & Technology

1987-10-29

nonferrous ores in quarries and underground; Installations for desulfurization , cleaning, and dry- ing of gas , turbocompressors for methane gas ; Mining...Products Exportation Bucharest Minis- "Indus- try of trial- Foreign Drilling installations and equipment for oil and gas ; export- Trade...equipment; try of Refineries, complex installations, parts, and equip- the ment for the oil- and gas -refining industry; Heavy Factories, complex

Regulation of mRNA Trafficking by Nuclear Pore Complexes

PubMed Central

Bonnet, Amandine; Palancade, Benoit

2014-01-01

Over the last two decades, multiple studies have explored the mechanisms governing mRNA export out of the nucleus, a crucial step in eukaryotic gene expression. During transcription and processing, mRNAs are assembled into messenger ribonucleoparticles (mRNPs). mRNPs are then exported through nuclear pore complexes (NPCs), which are large multiprotein assemblies made of several copies of a limited number of nucleoporins. A considerable effort has been put into the dissection of mRNA export through NPCs at both cellular and molecular levels, revealing the conserved contributions of a subset of nucleoporins in this process, from yeast to vertebrates. Several reports have also demonstrated the ability of NPCs to sort out properly-processed mRNPs for entry into the nuclear export pathway. Importantly, changes in mRNA export have been associated with post-translational modifications of nucleoporins or changes in NPC composition, depending on cell cycle progression, development or exposure to stress. How NPC modifications also impact on cellular mRNA export in disease situations, notably upon viral infection, is discussed. PMID:25184662

The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns.

PubMed

Zee, Barry M; Dibona, Amy B; Alekseyenko, Artyom A; French, Christopher A; Kuroda, Mitzi I

2016-01-01

Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics. We observed significant enrichment of acetylation particularly on H3 K18 and of combinatorial patterns such as H3 K27 acetylation paired with K36 methylation. We postulate that B4N complexes override the preexisting histone code with new PTM patterns that reflect aberrant transcription and that epigenetically modulate the nucleosome environment toward the NMC state.

The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns

PubMed Central

Zee, Barry M.; Dibona, Amy B.; Alekseyenko, Artyom A.; French, Christopher A.; Kuroda, Mitzi I.

2016-01-01

Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics. We observed significant enrichment of acetylation particularly on H3 K18 and of combinatorial patterns such as H3 K27 acetylation paired with K36 methylation. We postulate that B4N complexes override the preexisting histone code with new PTM patterns that reflect aberrant transcription and that epigenetically modulate the nucleosome environment toward the NMC state. PMID:27698495

Structural basis of RND-type multidrug exporters

PubMed Central

Yamaguchi, Akihito; Nakashima, Ryosuke; Sakurai, Keisuke

2015-01-01

Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway. PMID:25941524

Structural basis of RND-type multidrug exporters.

PubMed

Yamaguchi, Akihito; Nakashima, Ryosuke; Sakurai, Keisuke

2015-01-01

Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.

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.

Localization of Nucleoporin Tpr to the Nuclear Pore Complex Is Essential for Tpr Mediated Regulation of the Export of Unspliced RNA

PubMed Central

Rajanala, Kalpana; Nandicoori, Vinay Kumar

2012-01-01

Nucleoporin Tpr is a component of the nuclear pore complex (NPC) that localizes exclusively to intranuclear filaments. Tpr functions as a scaffolding element in the nuclear phase of the NPC and plays a role in mitotic spindle checkpoint signalling. Export of intron-containing mRNA in Mason Pfizer Monkey Virus is regulated by direct interaction of cellular proteins with the cis-acting Constitutive Transport Element (CTE). In mammalian cells, the transport of Gag/Pol-CTE reporter construct is not very efficient, suggesting a regulatory mechanism to retain this unspliced RNA. Here we report that the knockdown of Tpr in mammalian cells leads to a drastic enhancement in the levels of Gag proteins (p24) in the cytoplasm, which is rescued by siRNA resistant Tpr. Tpr's role in the retention of unspliced RNA is independent of the functions of Sam68 and Tap/Nxf1 proteins, which are reported to promote CTE dependent export. Further, we investigated the possible role for nucleoporins that are known to function in nucleocytoplasmic transport in modulating unspliced RNA export. Results show that depletion of Nup153, a nucleoporin required for NPC anchoring of Tpr, plays a role in regulating the export, while depletion of other FG repeat-containing nucleoporins did not alter the unspliced RNA export. Results suggest that Tpr and Nup153 both regulate the export of unspliced RNA and they are most likely functioning through the same pathway. Importantly, we find that localization of Tpr to the NPC is necessary for Tpr mediated regulation of unspliced RNA export. Collectively, the data indicates that perinuclear localization of Tpr at the nucleopore complex is crucial for regulating intron containing mRNA export by directly or indirectly participating in the processing and degradation of aberrant mRNA transcripts. PMID:22253824

Analysis and Modeling of Target Echo and Reverberation: FY15 Annual Report for ONR

DTIC Science & Technology

2015-09-30

particular interest is the target echo, which has not yet received a lot of attention , and for which good data were obtained during the TREX...essentially cut off all paths steeper than the critical angle. The coloured lines lines correspond to the differences between the group velocity formulation

75 FR 81708 - Notice of Decision To Issue Buy American Waivers for Foreign Object Debris (FOD) Detection Equipment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-28

... Circular 150/5220-24, Airport Foreign Object Debris (FOD) detection equipment, detailing system... produce sufficient and reasonable amounts of stationary FOD detection systems; the FAA issued a notice in... manufacturing stationary FOD detection systems in the United States: Trex Aviation Systems and QinetiQ. Although...

Technologies for the fabrication of the E-ELT mirrors within the T-REX project

NASA Astrophysics Data System (ADS)

Pareschi, G.; Aliverti, M.; Bianco, A.; Basso, S.; Citterio, O.; Civitani, M.; Ghigo, M.; Pariani, G.; Sironi, G.; Riva, M.; Vecchi, G.; Zerbi, F.

With its primary mirror with 39 m of diameter, the E-ELT will be the largest optical/near-infrared telescope in the world and will gather 13 times more light than the largest optical telescopes existing today. The different optical sub-systems of E-ELT, including the primary mirror based on hundreds of reflecting tiles assembled together, represent key components for the implementation of the telescopes. A huge amount of aspherical reflecting elements have to be produced with "state of the art" figuring and polishing technologies and measured with proper metrological equipments. In the past couple of years, in the context of the T-REX project, a specific development program was carried out at the Brera Astronomical Observatory-INAF in order to address a numbers of technology aspects related to the fabrication of the E-ELT mirrors. In this paper we give a short overview of the activities that have been carried out. Other papers in this volume report on specific activities that have pursed within such a development program. skip=8pt

Uncoupling of the hnRNP Npl3p from mRNAs during the stress-induced block in mRNA export.

PubMed

Krebber, H; Taura, T; Lee, M S; Silver, P A

1999-08-01

Npl3p, the major mRNA-binding protein of the yeast Saccharomyces cerevisiae shuttles between the nucleus and the cytoplasm. A single amino acid change in the carboxyl terminus of Npl3p (E409 --> K) renders the mutant protein largely cytoplasmic because of a delay in its import into the nucleus. This import defect can be reversed by increasing the intracellular concentration of Mtr10p, the nuclear import receptor for Npl3p. Conversely, using this mutant, we show that Npl3p and mRNA export out of the nucleus is significantly slowed in cells bearing mutations in XPO1/CRM1, which encodes the export receptor for NES-containing proteins and in RAT7, which encodes an essential nucleoporin. Interestingly, following induction of stress by heat shock, high salt, or ethanol, conditions under which most mRNA export is blocked, Npl3p is still exported from the nucleus. The stress-induced export of Npl3p is independent of both the activity of Xpo1p and the continued selective export of heat-shock mRNAs that occurs following stress. UV-cross-linking experiments show that Npl3p is bound to mRNA under normal conditions, but is no longer RNA associated in stressed cells. Taken together, we suggest that the uncoupling of Npl3p and possibly other mRNA-binding proteins from mRNAs in the nucleus provides a general switch that regulates mRNA export. By this model, under normal conditions Npl3p is a major component of an export-competent RNP complex. However, under conditions of stress, Npl3p no longer associates with the export complex, rendering it export incompetent and thus nuclear.

Long-term dynamics of organic matter and elements exported as coarse particulates from two Caribbean montane watersheds

Treesearch

T. Heartsill Scalley; F.N. Scatena; S. Moya; A.E. Lugo

2012-01-01

In heterotrophic streams the retention and export of coarse particulate organic matter and associated elements are fundamental biogeochemical processes that influence water quality, food webs and the structural complexity of forested headwater streams. Nevertheless, few studies have documented the quantity and quality of exported organic matter over multiple years and...

Hydrology and landscape structure control subalpine catchment carbon export

Treesearch

Vincent Jerald Pacific

2009-01-01

Carbon export from high elevation ecosystems is a critical component of the global carbon cycle. Ecosystems in northern latitudes have become the focus of much research due to their potential as large sinks of carbon in the atmosphere. However, there exists limited understanding of the controls of carbon export from complex mountain catchments due to strong spatial and...

Real-time analysis of δ13C- and δD-CH4 in ambient air with laser spectroscopy: method development and first intercomparison results

NASA Astrophysics Data System (ADS)

Eyer, S.; Tuzson, B.; Popa, M. E.; van der Veen, C.; Röckmann, T.; Rothe, M.; Brand, W. A.; Fisher, R.; Lowry, D.; Nisbet, E. G.; Brennwald, M. S.; Harris, E.; Zellweger, C.; Emmenegger, L.; Fischer, H.; Mohn, J.

2015-08-01

In situ and simultaneous measurement of the three most abundant isotopologues of methane using mid-infrared laser absorption spectroscopy is demonstrated. A field-deployable, autonomous platform is realized by coupling a compact quantum cascade laser absorption spectrometer (QCLAS) to a preconcentration unit, called TRace gas EXtractor (TREX). This unit enhances CH4 mole fractions by a factor of up to 500 above ambient levels and quantitatively separates interfering trace gases such as N2O and CO2. The analytical precision of the QCLAS isotope measurement on the preconcentrated (750 ppm, parts-per-million, μmole/mole) methane is 0.1 and 0.5 ‰ for δ13C- and δD-CH4 at 10 min averaging time. Based on replicate measurements of compressed air during a two-week intercomparison campaign, the repeatability of the TREX-QCLAS was determined to be 0.19 and 1.9 ‰ for δ13C and δD-CH4, respectively. In this intercomparison campaign the new in situ technique is compared to isotope-ratio mass-spectrometry (IRMS) based on glass flask and bag sampling and real time CH4 isotope analysis by two commercially available laser spectrometers. Both laser-based analyzers were limited to methane mole fraction and δ13C-CH4 analysis, and only one of them, a cavity ring down spectrometer, was capable to deliver meaningful data for the isotopic composition. After correcting for scale offsets, the average difference between TREX-QCLAS data and bag/flask sampling-IRMS values are within the extended WMO compatibility goals of 0.2 and 5 ‰ for δ13C- and δD-CH4, respectively. Thus, the intercomparison also reveals the need for reference air samples with accurately determined isotopic composition of CH4 to further improve the interlaboratory compatibility.

Fluorescent Recovery after Photobleaching (FRAP) Analysis of Nuclear Export Rates Identifies Intrinsic Features of Nucleocytoplasmic Transport*

PubMed Central

Cardarelli, Francesco; Tosti, Luca; Serresi, Michela; Beltram, Fabio; Bizzarri, Ranieri

2012-01-01

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. PMID:22190681

Nuclear export of RNA: Different sizes, shapes and functions.

PubMed

Williams, Tobias; Ngo, Linh H; Wickramasinghe, Vihandha O

2018-03-01

Export of protein-coding and non-coding RNA molecules from the nucleus to the cytoplasm is critical for gene expression. This necessitates the continuous transport of RNA species of different size, shape and function through nuclear pore complexes via export receptors and adaptor proteins. Here, we provide an overview of the major RNA export pathways in humans, highlighting the similarities and differences between each. Its importance is underscored by the growing appreciation that deregulation of RNA export pathways is associated with human diseases like cancer. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Deep Downhole Seismic Testing at the Waste Treatment Plant Site, Hanford, WA. Volume IV S-Wave Measurements in Borehole C4993 Seismic Records, Wave-Arrival Identifications and Interpreted S-Wave Velocity Profile.

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

Stokoe, Kenneth H.; Li, Song Cheng; Cox, Brady R.

2007-06-06

In this volume (IV), all S-wave measurements are presented that were performed in Borehole C4993 at the Waste Treatment Plant (WTP) with T-Rex as the seismic source and the Lawrence Berkeley National Laboratory (LBNL) 3-D wireline geophone as the at-depth borehole receiver. S-wave measurements were performed over the depth range of 370 to 1300 ft, typically in 10-ft intervals. However, in some interbeds, 5-ft depth intervals were used, while below about 1200 ft, depth intervals of 20 ft were used. Shear (S) waves were generated by moving the base plate of T-Rex for a given number of cycles at amore » fixed frequency as discussed in Section 2. This process was repeated so that signal averaging in the time domain was performed using 3 to about 15 averages, with 5 averages typically used. In addition, a second average shear wave record was recorded by reversing the polarity of the motion of the T-Rex base plate. In this sense, all the signals recorded in the field were averaged signals. In all cases, the base plate was moving perpendicular to a radial line between the base plate and the borehole which is in and out of the plane of the figure shown in Figure 1.1. The definition of “in-line”, “cross-line”, “forward”, and “reversed” directions in items 2 and 3 of Section 2 was based on the moving direction of the base plate. In addition to the LBNL 3-D geophone, called the lower receiver herein, a 3-D geophone from Redpath Geophysics was fixed at a depth of 22 ft in Borehole C4993, and a 3-D geophone from the University of Texas (UT) was embedded near the borehole at about 1.5 ft below the ground surface. The Redpath geophone and the UT geophone were properly aligned so that one of the horizontal components in each geophone was aligned with the direction of horizontal shaking of the T-Rex base plate. This volume is organized into 12 sections as follows. Section 1: Introduction, Section 2: Explanation of Terminology, Section 3: Vs Profile at Borehole C4993, Sections 4 to 6: Unfiltered S-wave records of lower horizontal receiver, reaction mass, and reference receiver, respectively, Sections 7 to 9: Filtered S-wave signals of lower horizontal receiver, reaction mass and reference receiver, respectively, Section 10: Expanded and filtered S-wave signals of lower horizontal receiver, and Sections 11 and 12: Waterfall plots of unfiltered and filtered lower horizontal receiver signals, respectively.« less

Nucleocytoplasmic Transport of RNAs and RNA-Protein Complexes.

PubMed

Sloan, Katherine E; Gleizes, Pierre-Emmanuel; Bohnsack, Markus T

2016-05-22

RNAs and ribonucleoprotein complexes (RNPs) play key roles in mediating and regulating gene expression. In eukaryotes, most RNAs are transcribed, processed and assembled with proteins in the nucleus and then either function in the cytoplasm or also undergo a cytoplasmic phase in their biogenesis. This compartmentalization ensures that sequential steps in gene expression and RNP production are performed in the correct order and it allows important quality control mechanisms that prevent the involvement of aberrant RNAs/RNPs in these cellular pathways. The selective exchange of RNAs/RNPs between the nucleus and cytoplasm is enabled by nuclear pore complexes, which function as gateways between these compartments. RNA/RNP transport is facilitated by a range of nuclear transport receptors and adaptors, which are specifically recruited to their cargos and mediate interactions with nucleoporins to allow directional translocation through nuclear pore complexes. While some transport factors are only responsible for the export/import of a certain class of RNA/RNP, others are multifunctional and, in the case of large RNPs, several export factors appear to work together to bring about export. Recent structural studies have revealed aspects of the mechanisms employed by transport receptors to enable specific cargo recognition, and genome-wide approaches have provided the first insights into the diverse composition of pre-mRNPs during export. Furthermore, the regulation of RNA/RNP export is emerging as an important means to modulate gene expression under stress conditions and in disease. Copyright © 2015. Published by Elsevier Ltd.

RNA Export through the NPC in Eukaryotes.

PubMed

Okamura, Masumi; Inose, Haruko; Masuda, Seiji

2015-03-20

In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC.

RNA Export through the NPC in Eukaryotes

PubMed Central

Okamura, Masumi; Inose, Haruko; Masuda, Seiji

2015-01-01

In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC. PMID:25802992

Maximum Entropy for the International Division of Labor.

PubMed

Lei, Hongmei; Chen, Ying; Li, Ruiqi; He, Deli; Zhang, Jiang

2015-01-01

As a result of the international division of labor, the trade value distribution on different products substantiated by international trade flows can be regarded as one country's strategy for competition. According to the empirical data of trade flows, countries may spend a large fraction of export values on ubiquitous and competitive products. Meanwhile, countries may also diversify their exports share on different types of products to reduce the risk. In this paper, we report that the export share distribution curves can be derived by maximizing the entropy of shares on different products under the product's complexity constraint once the international market structure (the country-product bipartite network) is given. Therefore, a maximum entropy model provides a good fit to empirical data. The empirical data is consistent with maximum entropy subject to a constraint on the expected value of the product complexity for each country. One country's strategy is mainly determined by the types of products this country can export. In addition, our model is able to fit the empirical export share distribution curves of nearly every country very well by tuning only one parameter.

Maximum Entropy for the International Division of Labor

PubMed Central

Lei, Hongmei; Chen, Ying; Li, Ruiqi; He, Deli; Zhang, Jiang

2015-01-01

As a result of the international division of labor, the trade value distribution on different products substantiated by international trade flows can be regarded as one country’s strategy for competition. According to the empirical data of trade flows, countries may spend a large fraction of export values on ubiquitous and competitive products. Meanwhile, countries may also diversify their exports share on different types of products to reduce the risk. In this paper, we report that the export share distribution curves can be derived by maximizing the entropy of shares on different products under the product’s complexity constraint once the international market structure (the country-product bipartite network) is given. Therefore, a maximum entropy model provides a good fit to empirical data. The empirical data is consistent with maximum entropy subject to a constraint on the expected value of the product complexity for each country. One country’s strategy is mainly determined by the types of products this country can export. In addition, our model is able to fit the empirical export share distribution curves of nearly every country very well by tuning only one parameter. PMID:26172052

A SIMPLE HYDROLOGICAL MODEL FOR WATERSHED CHARACTERIZATION

EPA Science Inventory

Catchment behavior is characterized with a variety of metrics - discharge, chemical export, biological activity, to name a few. Catchments have complex temporal behavior, e.g., summer and winter storm recessions and nutrient export may look nothing alike. Further, catchment res...

Reengineering ribosome export.

PubMed

Lo, Kai-Yin; Johnson, Arlen W

2009-03-01

Large cargoes require multiple receptors for efficient transport through the nuclear pore complex. The 60S ribosomal subunit is one of the bulkiest transport cargoes, and in yeast three different receptors, Crm1, Mex67/Mtr2, and Arx1, collaborate in its export. However, only Crm1, recruited by the adapter Nmd3, appears to be conserved for 60S export in higher eukaryotes. We asked if export of the large subunit requires specific receptors. We made protein fusions between mutant Nmd3 and various export receptors. Surprisingly, fusions of Mex67, the tRNA exportin Los1, Mtr2, Cse1, or Msn5 to Nmd3, lacking its Crm1-dependent nuclear export signal (NES), all functioned in export. Furthermore, these chimeric proteins supported 60S export even in the presence of the Crm1 inhibitor leptomycin B, indicating that export was now independent of Crm1. These results suggest that there is not a requirement for a specific export receptor for the large subunit, as recruitment of any receptor will suffice. Finally we show that the addition of an NES directly to the 60S ribosomal subunit protein Rpl3 promotes export. These results imply remarkable flexibility in the export pathway for the 60S subunit and help explain how different export receptors could have evolved in different eukaryotic lineages.

Reengineering Ribosome Export

PubMed Central

Lo, Kai-Yin

2009-01-01

Large cargoes require multiple receptors for efficient transport through the nuclear pore complex. The 60S ribosomal subunit is one of the bulkiest transport cargoes, and in yeast three different receptors, Crm1, Mex67/Mtr2, and Arx1, collaborate in its export. However, only Crm1, recruited by the adapter Nmd3, appears to be conserved for 60S export in higher eukaryotes. We asked if export of the large subunit requires specific receptors. We made protein fusions between mutant Nmd3 and various export receptors. Surprisingly, fusions of Mex67, the tRNA exportin Los1, Mtr2, Cse1, or Msn5 to Nmd3, lacking its Crm1-dependent nuclear export signal (NES), all functioned in export. Furthermore, these chimeric proteins supported 60S export even in the presence of the Crm1 inhibitor leptomycin B, indicating that export was now independent of Crm1. These results suggest that there is not a requirement for a specific export receptor for the large subunit, as recruitment of any receptor will suffice. Finally we show that the addition of an NES directly to the 60S ribosomal subunit protein Rpl3 promotes export. These results imply remarkable flexibility in the export pathway for the 60S subunit and help explain how different export receptors could have evolved in different eukaryotic lineages. PMID:19144820

Validating One-on-One GPS Instruction Methodology for Natural Resource Area Assessments Using Forestry Undergraduate Students

ERIC Educational Resources Information Center

Unger, Daniel R.

2014-01-01

Undergraduate students pursuing a Bachelor of Science in Forestry (BSF) at Stephen F. Austin State University (SFA) attend an intensive 6-week residential hands-on instruction in applied field methods. The intensive 6-week instruction includes learning how to use the Global Positioning System (GPS) with a Garmin eTrex HCx GPS unit to accurately…

78 FR 45072 - Radiolocation Operations in the 78-81 GHz Bands; Request by the Trex Enterprises Corporation for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-26

... Analysis 6. This document does not contain new or modified information collection requirements. B. Report... Flexibility Analysis 8. As required by the Regulatory Flexibility Act of 1980, as amended (RFA), an Initial Regulatory Flexibility Analysis (IRFA) was incorporated in the NPRM in WT Docket No. 11-202, 77 FR 1661...

“RaMassays”: Synergistic Enhancement of Plasmon-Free Raman Scattering and Mass Spectrometry for Multimodal Analysis of Small Molecules

NASA Astrophysics Data System (ADS)

Alessandri, Ivano; Vassalini, Irene; Bertuzzi, Michela; Bontempi, Nicolò; Memo, Maurizio; Gianoncelli, Alessandra

2016-10-01

SiO2/TiO2 core/shell (T-rex) beads were exploited as “all-in-one” building-block materials to create analytical assays that combine plasmon-free surface enhanced Raman scattering (SERS) and surface assisted laser desorption/ionization (SALDI) mass spectrometry (RaMassays). Such a multi-modal approach relies on the unique optical properties of T-rex beads, which are able to harvest and manage light in both UV and Vis range, making ionization and Raman scattering more efficient. RaMassays were successfully applied to the detection of small (molecular weight, M.W. <400 Da) molecules with a key relevance in biochemistry and pharmaceutical analysis. Caffeine and cocaine were utilized as molecular probes to test the combined SERS/SALDI response of RaMassays, showing excellent sensitivity and reproducibility. The differentiation between amphetamine/ephedrine and theophylline/theobromine couples demonstrated the synergistic reciprocal reinforcement of SERS and SALDI. Finally, the conversion of L-tyrosine in L-DOPA was utilized to probe RaMassays as analytical tools for characterizing reaction intermediates without introducing any spurious effects. RaMassays exhibit important advantages over plasmonic nanoparticles in terms of reproducibility, absence of interference and potential integration in multiplexed devices.

LINE1 contributes to autoimmunity through both RIG-I- and MDA5-mediated RNA sensing pathways.

PubMed

Zhao, Ke; Du, Juan; Peng, Yanfeng; Li, Peng; Wang, Shaohua; Wang, Yu; Hou, Jingwei; Kang, Jian; Zheng, Wenwen; Hua, Shucheng; Yu, Xiao-Fang

2018-06-01

Improper host immune activation leads to the development of the autoimmune disease Aicardi-Goutières syndrome (AGS), which is attributed to defined genetic mutations in such proteins as TREX1 and ADAR1. The mechanism of immune activation in AGS patients has not been thoroughly elucidated to date. In this study, we report that endogenous LINE1 components trigger IFNβ production in multiple human cell types, including those defective for cGAS/STING-mediated DNA sensing. In these cells, LINE1 DNA synthesis and retrotransposition were not required for LINE1-triggered immune activation, but RNA sensing pathways were essential. LINE1-triggered immune activation could be suppressed by diverse LINE1 inhibitors, including AGS-associated proteins targeting LINE1 RNA or proteins. However, AGS-associated ADAR1 or TREX1 mutants were defective in suppressing LINE1 retrotransposition or LINE1-triggered immune activation. Therefore, we have revealed a new function for LINE1 as an endogenous trigger of innate immune activation, which is important for understanding the molecular basis of IFN-based autoimmune diseases and may offer new intervention strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

A method for rapid 3D scanning and replication of large paleontological specimens

PubMed Central

Das, Anshuman J.; Murmann, Denise C.; Cohrn, Kenneth; Raskar, Ramesh

2017-01-01

We demonstrate a fast and cost-effective technique to perform three dimensional (3D) scanning and replication of large paleontological specimens, in this case the entire skull of a Tyrannosaurus rex (T.rex) with a volume in the range of 2 m3. The technique involves time-of-flight (TOF) depth sensing using the Kinect scanning module commonly used in gesture recognition in gaming. Raw data from the Kinect sensor was captured using open source software and the reconstruction was done rapidly making this a viable method that can be adopted by museums and researchers in paleontology. The current method has the advantage of being low-cost as compared to industrial scanners and photogrammetric methods but also of accurately scanning a substantial volume range which is well suited for large specimens. The depth resolution from the Kinect sensor was measured to be around 0.6 mm which is ideal for scanning large specimens with reasonable structural detail. We demonstrate the efficacy of this method on the skull of FMNH PR 2081, also known as SUE, a near complete T.rex at the Field Museum of Natural History. PMID:28678817

A method for rapid 3D scanning and replication of large paleontological specimens.

PubMed

Das, Anshuman J; Murmann, Denise C; Cohrn, Kenneth; Raskar, Ramesh

2017-01-01

We demonstrate a fast and cost-effective technique to perform three dimensional (3D) scanning and replication of large paleontological specimens, in this case the entire skull of a Tyrannosaurus rex (T.rex) with a volume in the range of 2 m3. The technique involves time-of-flight (TOF) depth sensing using the Kinect scanning module commonly used in gesture recognition in gaming. Raw data from the Kinect sensor was captured using open source software and the reconstruction was done rapidly making this a viable method that can be adopted by museums and researchers in paleontology. The current method has the advantage of being low-cost as compared to industrial scanners and photogrammetric methods but also of accurately scanning a substantial volume range which is well suited for large specimens. The depth resolution from the Kinect sensor was measured to be around 0.6 mm which is ideal for scanning large specimens with reasonable structural detail. We demonstrate the efficacy of this method on the skull of FMNH PR 2081, also known as SUE, a near complete T.rex at the Field Museum of Natural History.

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

Utp22p acts in concert with Utp8p to channel aminoacyl-tRNA from the nucleolus to the nuclear tRNA export receptor Los1p but not Msn5p.

PubMed

Eswara, Manoja B K; Clayton, Ashley; Mangroo, Dev

2012-12-01

Utp8p is an essential nucleolar protein that channels aminoacyl-tRNAs from aminoacyl-tRNA synthetases in the nucleolus to the nuclear tRNA export receptors located in the nucleoplasm and nuclear pore complex in Saccharomyces cerevisiae. Utp8p is also part of the U3 snoRNA-associated protein complex involved in 18S rRNA biogenesis in the nucleolus. We report that Utp22p, which is another member of the U3 snoRNA-associated protein complex, is also an intranuclear component of the nuclear tRNA export machinery. Depletion of Utp22p results in nuclear retention of mature tRNAs derived from intron-containing and intronless precursors. Moreover, Utp22p copurifies with the nuclear tRNA export receptor Los1p, the aminoacyl-tRNA synthetase Tys1p and Utp8p, but not with the RanGTPase Gsp1p and the nuclear tRNA export receptor Msn5p. Utp22p interacts directly with Utp8p and Los1p in a tRNA-independent manner in vitro. Utp22p also interacts directly with Tys1p, but this binding is stimulated when Tys1p is bound to tRNA. However, Utp22p, unlike Utp8p, does not bind tRNA saturably. These data suggest that Utp22p recruits Utp8p to aminoacyl-tRNA synthetases in the nucleolus to collect aminoacyl-tRNA and then accompanies the Utp8p-tRNA complex to deliver the aminoacyl-tRNAs to Los1p but not Msn5p. It is possible that Nrap/Nol6, the mammalian orthologue of Utp22p, plays a role in channelling aminoacyl-tRNA to the nuclear tRNA export receptor exportin-t.

Leukemia-Associated Nup214 Fusion Proteins Disturb the XPO1-Mediated Nuclear-Cytoplasmic Transport Pathway and Thereby the NF-κB Signaling Pathway.

PubMed

Saito, Shoko; Cigdem, Sadik; Okuwaki, Mitsuru; Nagata, Kyosuke

2016-07-01

Nuclear-cytoplasmic transport through nuclear pore complexes is mediated by nuclear transport receptors. Previous reports have suggested that aberrant nuclear-cytoplasmic transport due to mutations or overexpression of nuclear pore complexes and nuclear transport receptors is closely linked to diseases. Nup214, a component of nuclear pore complexes, has been found as chimeric fusion proteins in leukemia. Among various Nup214 fusion proteins, SET-Nup214 and DEK-Nup214 have been shown to be engaged in tumorigenesis, but their oncogenic mechanisms remain unclear. In this study, we examined the functions of the Nup214 fusion proteins by focusing on their effects on nuclear-cytoplasmic transport. We found that SET-Nup214 and DEK-Nup214 interact with exportin-1 (XPO1)/CRM1 and nuclear RNA export factor 1 (NXF1)/TAP, which mediate leucine-rich nuclear export signal (NES)-dependent protein export and mRNA export, respectively. SET-Nup214 and DEK-Nup214 decreased the XPO1-mediated nuclear export of NES proteins such as cyclin B and proteins involved in the NF-κB signaling pathway by tethering XPO1 onto nuclear dots where Nup214 fusion proteins are localized. We also demonstrated that SET-Nup214 and DEK-Nup214 expression inhibited NF-κB-mediated transcription by abnormal tethering of the complex containing p65 and its inhibitor, IκB, in the nucleus. These results suggest that SET-Nup214 and DEK-Nup214 perturb the regulation of gene expression through alteration of the nuclear-cytoplasmic transport system. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Unraveling the sequence of cytosolic reactions in the export of GspB adhesin from Streptococcus gordonii

PubMed Central

Chen, Yu; Bensing, Barbara A.; Seepersaud, Ravin; Mi, Wei; Liao, Maofu; Jeffrey, Philip D.; Shajahan, Asif; Sonon, Roberto N.; Azadi, Parastoo; Sullam, Paul M.; Rapoport, Tom A.

2018-01-01

Many pathogenic bacteria, including Streptococcus gordonii, possess a pathway for the cellular export of a single serine-rich-repeat protein that mediates the adhesion of bacteria to host cells and the extracellular matrix. This adhesin protein is O-glycosylated by several cytosolic glycosyltransferases and requires three accessory Sec proteins (Asp1–3) for export, but how the adhesin protein is processed for export is not well understood. Here, we report that the S. gordonii adhesin GspB is sequentially O-glycosylated by three enzymes (GtfA/B, Nss, and Gly) that attach N-acetylglucosamine and glucose to Ser/Thr residues. We also found that modified GspB is transferred from the last glycosyltransferase to the Asp1/2/3 complex. Crystal structures revealed that both Asp1 and Asp3 are related to carbohydrate-binding proteins, suggesting that they interact with carbohydrates and bind glycosylated adhesin, a notion that was supported by further analyses. We further observed that Asp1 also has an affinity for phospholipids, which is attenuated by Asp2. In summary, our findings support a model in which the GspB adhesin is sequentially glycosylated by GtfA/B, Nss, and Gly and then transferred to the Asp1/2/3 complex in which Asp1 mediates the interaction of the Asp1/2/3 complex with the lipid bilayer for targeting of matured GspB to the export machinery. PMID:29462788

Unraveling the sequence of cytosolic reactions in the export of GspB adhesin from Streptococcus gordonii.

PubMed

Chen, Yu; Bensing, Barbara A; Seepersaud, Ravin; Mi, Wei; Liao, Maofu; Jeffrey, Philip D; Shajahan, Asif; Sonon, Roberto N; Azadi, Parastoo; Sullam, Paul M; Rapoport, Tom A

2018-04-06

Many pathogenic bacteria, including Streptococcus gordonii , possess a pathway for the cellular export of a single serine-rich-repeat protein that mediates the adhesion of bacteria to host cells and the extracellular matrix. This adhesin protein is O -glycosylated by several cytosolic glycosyltransferases and requires three accessory Sec proteins (Asp1-3) for export, but how the adhesin protein is processed for export is not well understood. Here, we report that the S. gordonii adhesin GspB is sequentially O -glycosylated by three enzymes (GtfA/B, Nss, and Gly) that attach N -acetylglucosamine and glucose to Ser/Thr residues. We also found that modified GspB is transferred from the last glycosyltransferase to the Asp1/2/3 complex. Crystal structures revealed that both Asp1 and Asp3 are related to carbohydrate-binding proteins, suggesting that they interact with carbohydrates and bind glycosylated adhesin, a notion that was supported by further analyses. We further observed that Asp1 also has an affinity for phospholipids, which is attenuated by Asp2. In summary, our findings support a model in which the GspB adhesin is sequentially glycosylated by GtfA/B, Nss, and Gly and then transferred to the Asp1/2/3 complex in which Asp1 mediates the interaction of the Asp1/2/3 complex with the lipid bilayer for targeting of matured GspB to the export machinery.

The RanBP2/RanGAP1*SUMO1/Ubc9 SUMO E3 ligase is a disassembly machine for Crm1-dependent nuclear export complexes

PubMed Central

Ritterhoff, Tobias; Das, Hrishikesh; Hofhaus, Götz; Schröder, Rasmus R.; Flotho, Annette; Melchior, Frauke

2016-01-01

Continuous cycles of nucleocytoplasmic transport require disassembly of transport receptor/Ran-GTP complexes in the cytoplasm. A basic disassembly mechanism in all eukaryotes depends on soluble RanGAP and RanBP1. In vertebrates, a significant fraction of RanGAP1 stably interacts with the nucleoporin RanBP2 at a binding site that is flanked by FG-repeats and Ran-binding domains, and overlaps with RanBP2's SUMO E3 ligase region. Here, we show that the RanBP2/RanGAP1*SUMO1/Ubc9 complex functions as an autonomous disassembly machine with a preference for the export receptor Crm1. We describe three in vitro reconstituted disassembly intermediates, which show binding of a Crm1 export complex via two FG-repeat patches, cargo-release by RanBP2's Ran-binding domains and retention of free Crm1 at RanBP2 after Ran-GTP hydrolysis. Intriguingly, all intermediates are compatible with SUMO E3 ligase activity, suggesting that the RanBP2/RanGAP1*SUMO1/Ubc9 complex may link Crm1- and SUMO-dependent functions. PMID:27160050

Why the Lack of Academic Literature on Export Controls?

NASA Technical Reports Server (NTRS)

Kremic, Tibor

2001-01-01

Export controls is currently a relevant and dynamic topic. Given the growth of global operations and the high-tech nature of many products, an increase in awareness and understanding of the impacts of export controls are necessary. A structured approach to export controls has been in existence since 1949. Despite over 50 years of history, surprisingly little academic research and literature exists on the topic. This paper explores the current export control environment and explores possible reasons for the limited academic interest. Five possible reasons are discussed: (1) dynamic nature of the topic; (2) difficulty in ensuring accurate data; (3) Complexity of the problem; (4) relatively small economic impact; and (5) sensitive information. A research approach is recommended that considers these potential obstacles.

PARTICULATE MATTER CONCENTRATIONS MEASURED IN A RESIDENTIAL NEIGHBORHOOD IN BROOKLYN, NEW YORK CITY DURING THE TRAFFIC-RELATED EXPOSURE STUDY (T-REX)

EPA Science Inventory

PM₁₀, PM_10-2.5, and PM_2.5 concentrations has been measured daily in the Sunset Park neighborhood of Brooklyn, NY from April 21 to May 17, 2005. Results showed the average concentrations of PM fractions were higher when measured closet to the majo...

The Transition Region Explorer: Observing the Multi-Scale Dynamics of Geospace

NASA Astrophysics Data System (ADS)

Donovan, E.

2015-12-01

Meso- and global-scale IT remote sensing is accomplished via satellite imagers and ground-based instruments. On the ground, the approach is arrays providing extensive as possible coverage (the "net") and powerful observatories that drill deep to provide detailed information about small-scale processes (the "drill"). Always, there is a trade between cost, spatial resolution, coverage (extent), number of parameters, and more, such that in general the larger the network the sparser the coverage. Where are we now? There are important gaps. With THEMIS-ASI, we see processes that quickly evolve beyond the field of view of one observatory, but involve space/time scales not captured by existing meso- and large-scale arrays. Many forefront questions require observations at heretofore unexplored space and time scales, and comprehensive inter-hemispheric conjugate observations than are presently available. To address this, a new ground-based observing initiative is being developed in Canada. Called TREx, for Transition Region Explorer, this new facility will incorporate dedicated blueline, redline, and Near-Infrared All-Sky Imagers, together with an unprecedented network of ten imaging riometers, with a combined field of view spanning more than three hours of magnetic local time and from equatorward to poleward of typical auroral latitudes (spanning the ionospheric footprint of the "nightside transition region" that separates the highly stretched tail and the inner magnetosphere). The TREx field-of-view is covered by HF radars, and contains a dense network of magnetometers and VLF receivers, as well as other geospace and upper atmospheric remote sensors. Taken together, TREx and these co-located instruments represent a quantum leap forward in terms of imaging, in multiple parameters (precipitation, ionization, convection, and currents), ionospheric dynamics in the above-mentioned scale gap. This represents an exciting new opportunity for studying geospace at the system level, especially for using the aurora to remote sense magnetospheric plasma physics and dynamics, and comes with a set of Big Data challenges that are going to be exciting. One such challenge is the development of a fundamentally new type of data product, namely time series of multi-parameter, geospatially referenced 'data cubes'.

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore.

PubMed

Bao, Xun X; Spanos, Christos; Kojidani, Tomoko; Lynch, Eric M; Rappsilber, Juri; Hiraoka, Yasushi; Haraguchi, Tokuko; Sawin, Kenneth E

2018-05-29

Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe , the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the g-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs. © 2018, Bao et al.

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore

PubMed Central

Bao, Xun X; Spanos, Christos; Kojidani, Tomoko; Lynch, Eric M; Rappsilber, Juri; Hiraoka, Yasushi; Haraguchi, Tokuko

2018-01-01

Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe, the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the γ-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs. PMID:29809148

Role of Mex67-Mtr2 in the Nuclear Export of 40S Pre-Ribosomes

PubMed Central

Occhipinti, Laura; Kemmler, Stefan; Panse, Vikram G.

2012-01-01

Nuclear export of mRNAs and pre-ribosomal subunits (pre40S and pre60S) is fundamental to all eukaryotes. While genetic approaches in budding yeast have identified bona fide export factors for mRNAs and pre60S subunits, little is known regarding nuclear export of pre40S subunits. The yeast heterodimeric transport receptor Mex67-Mtr2 (TAP-p15 in humans) binds mRNAs and pre60S subunits in the nucleus and facilitates their passage through the nuclear pore complex (NPC) into the cytoplasm by interacting with Phe-Gly (FG)-rich nucleoporins that line its transport channel. By exploiting a combination of genetic, cell-biological, and biochemical approaches, we uncovered an unanticipated role of Mex67-Mtr2 in the nuclear export of 40S pre-ribosomes. We show that recruitment of Mex67-Mtr2 to pre40S subunits requires loops emanating from its NTF2-like domains and that the C-terminal FG-rich nucleoporin interacting UBA-like domain within Mex67 contributes to the transport of pre40S subunits to the cytoplasm. Remarkably, the same loops also recruit Mex67-Mtr2 to pre60S subunits and to the Nup84 complex, the respective interactions crucial for nuclear export of pre60S subunits and mRNAs. Thus Mex67-Mtr2 is a unique transport receptor that employs a common interaction surface to participate in the nuclear export of both pre-ribosomal subunits and mRNAs. Mex67-Mtr2 could engage a regulatory crosstalk among the three major export pathways for optimal cellular growth and proliferation. PMID:22956913

Mechanisms of Nuclear Export in Cancer and Resistance to Chemotherapy.

PubMed

El-Tanani, Mohamed; Dakir, El-Habib; Raynor, Bethany; Morgan, Richard

2016-03-14

Tumour suppressor proteins, such as p53, BRCA1, and ABC, play key roles in preventing the development of a malignant phenotype, but those that function as transcriptional regulators need to enter the nucleus in order to function. The export of proteins between the nucleus and cytoplasm is complex. It occurs through nuclear pores and exported proteins need a nuclear export signal (NES) to bind to nuclear exportin proteins, including CRM1 (Chromosomal Region Maintenance protein 1), and the energy for this process is provided by the RanGTP/RanGDP gradient. Due to the loss of DNA repair and cell cycle checkpoints, drug resistance is a major problem in cancer treatment, and often an initially successful treatment will fail due to the development of resistance. An important mechanism underlying resistance is nuclear export, and a number of strategies that can prevent nuclear export may reverse resistance. Examples include inhibitors of CRM1, antibodies to the nuclear export signal, and alteration of nuclear pore structure. Each of these are considered in this review.

Spatial Patterns in the Efficiency of the Biological Pump: What Controls Export Ratios at the Global Scale?

NASA Astrophysics Data System (ADS)

Moore, J. K.

2016-02-01

The efficiency of the biological pump is influenced by complex interactions between chemical, biological, and physical processes. The efficiency of export out of surface waters and down through the water column to the deep ocean has been linked to a number of factors including biota community composition, production of mineral ballast components, physical aggregation and disaggregation processes, and ocean oxygen concentrations. I will examine spatial patterns in the export ratio and the efficiency of the biological pump at the global scale using the Community Earth System Model (CESM). There are strong spatial variations in the export efficiency as simulated by the CESM, which are strongly correlated with new nutrient inputs to the euphotic zone and their impacts on phytoplankton community structure. I will compare CESM simulations that include dynamic, variable export ratios driven by the phytoplankton community structure, with simulations that impose a near-constant export ratio to examine the effects of export efficiency on nutrient and surface chlorophyll distributions. The model predicted export ratios will also be compared with recent satellite-based estimates.

Resolving the Intricacies of Lateral Exports of Inorganic Carbon and Alkalinity from Coastal Salt Marshes

NASA Astrophysics Data System (ADS)

Wang, A. Z.; Chu, S. N.; Kroeger, K. D.; Gonneea, M. E.; Ganju, N. K.

2017-12-01

Dynamic lateral exports of dissolved inorganic carbon (DIC) and total alkalinity (Alk) via tidal exchange from highly productive intertidal marshes are an important piece of puzzle in the coastal carbon cycle, challenging our capability of assessing coastal carbon budgets and projecting future changes under anthropogenic pressure. The effects of these exports on seawater chemistry are profound yet complicated to study. This study presents the latest development of assessing lateral DIC and Alk fluxes from tidal marshes and examining their effects on seawater chemistry and coastal carbon budgets. The study evaluates different approaches to quantify these exports in order to obtain insights on the best and efficient way to capture the dynamics of such exports. A state-of-the-art DIC sensor, Channelized Optical System (CHANOS), was deployed to establish the true DIC fluxes. They are compared to the fluxes derived from empirical modeling and traditional bottle measurements. Salt marshes can acidify and alkalize tidal water by injecting CO2 (DIC) and Alk over a same tidal cycle. However, their generation is decoupled as a result of deferential effects of aerobic and anaerobic respirations. This creates complex scenarios of large swings of seawater chemistry and buffering capacity in tidal water over tidal and seasonal cycles. Marsh exports of DIC and Alk may have complex implications for the future, more acidified ocean. The latest estimates of marsh DIC and Alk exports suggest they are a major term in the marsh carbon budget and can be translated into one of the primary components in the coastal carbon cycle.

Broadband Scattering from Sand and Sand/Mud Sediments with Extensive Environmental Characterization

DTIC Science & Technology

2017-01-30

experiment , extensive envi- ronmental characterization was also performed to support data/model comparisons for both experimental efforts. The site...mechanisms, potentially addressing questions left unresolved from the previous sediment acoustics experiments , SAX99 and SAX04. This work was also to provide...environmental characterization to support the analysis of data collected during the Target and Reverberation Experiment in 2013 (TREX13) as well as

Radiologists' preferences for digital mammographic display. The International Digital Mammography Development Group.

PubMed

Pisano, E D; Cole, E B; Major, S; Zong, S; Hemminger, B M; Muller, K E; Johnston, R E; Walsh, R; Conant, E; Fajardo, L L; Feig, S A; Nishikawa, R M; Yaffe, M J; Williams, M B; Aylward, S R

2000-09-01

To determine the preferences of radiologists among eight different image processing algorithms applied to digital mammograms obtained for screening and diagnostic imaging tasks. Twenty-eight images representing histologically proved masses or calcifications were obtained by using three clinically available digital mammographic units. Images were processed and printed on film by using manual intensity windowing, histogram-based intensity windowing, mixture model intensity windowing, peripheral equalization, multiscale image contrast amplification (MUSICA), contrast-limited adaptive histogram equalization, Trex processing, and unsharp masking. Twelve radiologists compared the processed digital images with screen-film mammograms obtained in the same patient for breast cancer screening and breast lesion diagnosis. For the screening task, screen-film mammograms were preferred to all digital presentations, but the acceptability of images processed with Trex and MUSICA algorithms were not significantly different. All printed digital images were preferred to screen-film radiographs in the diagnosis of masses; mammograms processed with unsharp masking were significantly preferred. For the diagnosis of calcifications, no processed digital mammogram was preferred to screen-film mammograms. When digital mammograms were preferred to screen-film mammograms, radiologists selected different digital processing algorithms for each of three mammographic reading tasks and for different lesion types. Soft-copy display will eventually allow radiologists to select among these options more easily.

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding.

PubMed

Lee, Michael S; Olson, Mark A

2011-06-28

Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed "current maximization") by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.

“RaMassays”: Synergistic Enhancement of Plasmon-Free Raman Scattering and Mass Spectrometry for Multimodal Analysis of Small Molecules

PubMed Central

Alessandri, Ivano; Vassalini, Irene; Bertuzzi, Michela; Bontempi, Nicolò; Memo, Maurizio; Gianoncelli, Alessandra

2016-01-01

SiO2/TiO2 core/shell (T-rex) beads were exploited as “all-in-one” building-block materials to create analytical assays that combine plasmon-free surface enhanced Raman scattering (SERS) and surface assisted laser desorption/ionization (SALDI) mass spectrometry (RaMassays). Such a multi-modal approach relies on the unique optical properties of T-rex beads, which are able to harvest and manage light in both UV and Vis range, making ionization and Raman scattering more efficient. RaMassays were successfully applied to the detection of small (molecular weight, M.W. <400 Da) molecules with a key relevance in biochemistry and pharmaceutical analysis. Caffeine and cocaine were utilized as molecular probes to test the combined SERS/SALDI response of RaMassays, showing excellent sensitivity and reproducibility. The differentiation between amphetamine/ephedrine and theophylline/theobromine couples demonstrated the synergistic reciprocal reinforcement of SERS and SALDI. Finally, the conversion of L-tyrosine in L-DOPA was utilized to probe RaMassays as analytical tools for characterizing reaction intermediates without introducing any spurious effects. RaMassays exhibit important advantages over plasmonic nanoparticles in terms of reproducibility, absence of interference and potential integration in multiplexed devices. PMID:27698368

The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle

DOE PAGES

Mahboobi, Seyed Hanif; Javanpour, Alex A.; Mofrad, Mohammad R. K.

2015-02-27

Molecular traffic between the nucleus and the cytoplasm is regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating the nuclear envelope in eukaryotic cells. The human immunodeficiency virus (HIV) exploits the nucleocytoplasmic pathway to export its RNA transcripts across the NPC to the cytoplasm. Despite extensive study on the HIV life cycle and the many drugs developed to target this cycle, no current drugs have been successful in targeting the critical process of viral nuclear export, even though HIV’s reliance on a single host protein, CRM1, to export its unspliced and partially spliced RNAmore » transcripts makes it a tempting target. Due to recent findings implicating a DEAD-box helicase, DDX3, in HIV replication and a member of the export complex, it has become an appealing target for anti-HIV drug inhibition. In the present research, we have applied a hybrid computational protocol to analyze protein-protein interactions in the HIV mRNA export cycle. This method is based on molecular docking followed by molecular dynamics simulation and accompanied by approximate free energy calculation (MM/GBSA), computational alanine scanning, clustering, and evolutionary analysis. We highlight here some of the most likely binding modes and interfacial residues between DDX3 and CRM1 both in the absence and presence of RanGTP. This work shows that although DDX3 can bind to free CRM1, addition of RanGTP leads to more concentrated distribution of binding modes and stronger binding between CRM1 and RanGTP.« less

The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle

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

Mahboobi, Seyed Hanif; Javanpour, Alex A.; Mofrad, Mohammad R. K.

Molecular traffic between the nucleus and the cytoplasm is regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating the nuclear envelope in eukaryotic cells. The human immunodeficiency virus (HIV) exploits the nucleocytoplasmic pathway to export its RNA transcripts across the NPC to the cytoplasm. Despite extensive study on the HIV life cycle and the many drugs developed to target this cycle, no current drugs have been successful in targeting the critical process of viral nuclear export, even though HIV’s reliance on a single host protein, CRM1, to export its unspliced and partially spliced RNAmore » transcripts makes it a tempting target. Due to recent findings implicating a DEAD-box helicase, DDX3, in HIV replication and a member of the export complex, it has become an appealing target for anti-HIV drug inhibition. In the present research, we have applied a hybrid computational protocol to analyze protein-protein interactions in the HIV mRNA export cycle. This method is based on molecular docking followed by molecular dynamics simulation and accompanied by approximate free energy calculation (MM/GBSA), computational alanine scanning, clustering, and evolutionary analysis. We highlight here some of the most likely binding modes and interfacial residues between DDX3 and CRM1 both in the absence and presence of RanGTP. This work shows that although DDX3 can bind to free CRM1, addition of RanGTP leads to more concentrated distribution of binding modes and stronger binding between CRM1 and RanGTP.« less

The complex dynamics of products and its asymptotic properties

PubMed Central

Cristelli, Matthieu; Zaccaria, Andrea; Pietronero, Luciano

2017-01-01

We analyse global export data within the Economic Complexity framework. We couple the new economic dimension Complexity, which captures how sophisticated products are, with an index called logPRODY, a measure of the income of the respective exporters. Products’ aggregate motion is treated as a 2-dimensional dynamical system in the Complexity-logPRODY plane. We find that this motion can be explained by a quantitative model involving the competition on the markets, that can be mapped as a scalar field on the Complexity-logPRODY plane and acts in a way akin to a potential. This explains the movement of products towards areas of the plane in which the competition is higher. We analyse market composition in more detail, finding that for most products it tends, over time, to a characteristic configuration, which depends on the Complexity of the products. This market configuration, which we called asymptotic, is characterized by higher levels of competition. PMID:28520794

77 FR 51579 - Application for a License To Export High-Enriched Uranium

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-24

... NUCLEAR REGULATORY COMMISSION Application for a License To Export High-Enriched Uranium Pursuant.... Complex, July 30, 2012, August Uranium (93.35%). uranium-235 high-enriched 1, 2012, XSNM3726, 11006037. contained in 7.5 uranium in the kilograms uranium. form of broken metal to the Atomic Energy of Canada...

TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes

PubMed Central

Santos, António JM; Foresti, Ombretta; Zhang, Chong; Garcia-Parajo, Maria F; Campelo, Felix

2018-01-01

Collagen export from the endoplasmic reticulum (ER) requires TANGO1, COPII coats, and retrograde fusion of ERGIC membranes. How do these components come together to produce a transport carrier commensurate with the bulky cargo collagen? TANGO1 is known to form a ring that corrals COPII coats, and we show here how this ring or fence is assembled. Our data reveal that a TANGO1 ring is organized by its radial interaction with COPII, and lateral interactions with cTAGE5, TANGO1-short or itself. Of particular interest is the finding that TANGO1 recruits ERGIC membranes for collagen export via the NRZ (NBAS/RINT1/ZW10) tether complex. Therefore, TANGO1 couples retrograde membrane flow to anterograde cargo transport. Without the NRZ complex, the TANGO1 ring does not assemble, suggesting its role in nucleating or stabilising this process. Thus, coordinated capture of COPII coats, cTAGE5, TANGO1-short, and tethers by TANGO1 assembles a collagen export machine at the ER. PMID:29513218

Multiple Export Mechanisms for mRNAs

PubMed Central

Delaleau, Mildred; Borden, Katherine L. B.

2015-01-01

Nuclear mRNA export plays an important role in gene expression. We describe the mechanisms of mRNA export including the importance of mRNP assembly, docking with the nuclear basket of the nuclear pore complex (NPC), transit through the central channel of the NPC and cytoplasmic release. We describe multiple mechanisms of mRNA export including NXF1 and CRM1 mediated pathways. Selective groups of mRNAs can be preferentially transported in order to respond to cellular stimuli. RNAs can be selected based on the presence of specific cis-acting RNA elements and binding of specific adaptor proteins. The role that dysregulation of this process plays in human disease is also discussed. PMID:26343730

Cellular Nuclear Export Factors TAP and Aly Are Required for HDAg-L-mediated Assembly of Hepatitis Delta Virus.

PubMed

Huang, Hsiu-Chen; Lee, Chung-Pei; Liu, Hui-Kang; Chang, Ming-Fu; Lai, Yu-Heng; Lee, Yu-Ching; Huang, Cheng

2016-12-09

Hepatitis delta virus (HDV) is a satellite virus of hepatitis B virus (HBV). HDV genome encodes two forms of hepatitis delta antigen (HDAg), small HDAg (HDAg-S), which is required for viral replication, and large HDAg (HDAg-L), which is essential for viral assembly. HDAg-L is identical to HDAg-S except that it bears a 19-amino acid extension at the C terminus. Both HDAgs contain a nuclear localization signal (NLS), but only HDAg-L contains a CRM1-independent nuclear export signal at its C terminus. The nuclear export activity of HDAg-L is important for HDV particle formation. However, the mechanisms of HDAg-L-mediated nuclear export of HDV ribonucleoprotein are not clear. In this study, the host cellular RNA export complex TAP-Aly was found to form a complex with HDAg-L, but not with an export-defective HDAg-L mutant, in which Pro 205 was replaced by Ala. HDAg-L was found to colocalize with TAP and Aly in the nucleus. The C-terminal domain of HDAg-L was shown to directly interact with the N terminus of TAP, whereas an HDAg-L mutant lacking the NLS failed to interact with full-length TAP. In addition, small hairpin RNA-mediated down-regulation of TAP or Aly reduced nuclear export of HDAg-L and assembly of HDV virions. Furthermore, a peptide, TAT-HDAg-L(198-210), containing the 10-amino acid TAT peptide and HDAg-L(198-210), inhibited the interaction between HDAg-L and TAP and blocked HDV virion assembly and secretion. These data demonstrate that formation and release of HDV particles are mediated by TAP and Aly. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Hierarchical protein export mechanism of the bacterial flagellar type III protein export apparatus.

PubMed

Minamino, Tohru

2018-06-01

The bacterial flagellum is supramolecular motility machinery consisting of the basal body, the hook and the filament. Flagellar proteins are translocated across the cytoplasmic membrane via a type III protein export apparatus, diffuse down the central channel of the growing structure and assemble at the distal end. Flagellar assembly begins with the basal body, followed by the hook and finally the filament. The completion of hook assembly is the most important morphological checkpoint of the sequential flagellar assembly process. When the hook reaches its mature length of about 55 nm in Salmonella enterica, the type III protein export apparatus switches export specificity from proteins required for the structure and assembly of the hook to those responsible for filament assembly, thereby terminating hook assembly and initiating filament assembly. Three flagellar proteins, namely FliK, FlhB and FlhA, are responsible for this substrate specificity switching. Upon completion of the switching event, interactions among FlhA, the cytoplasmic ATPase complex and flagellar type III export chaperones establish the assembly order of the filament at the hook tip. Here, we describe our current understanding of a hierarchical protein export mechanism used in flagellar type III protein export.

Mechanisms of Nuclear Export in Cancer and Resistance to Chemotherapy

PubMed Central

El-Tanani, Mohamed; Dakir, El-Habib; Raynor, Bethany; Morgan, Richard

2016-01-01

Tumour suppressor proteins, such as p53, BRCA1, and ABC, play key roles in preventing the development of a malignant phenotype, but those that function as transcriptional regulators need to enter the nucleus in order to function. The export of proteins between the nucleus and cytoplasm is complex. It occurs through nuclear pores and exported proteins need a nuclear export signal (NES) to bind to nuclear exportin proteins, including CRM1 (Chromosomal Region Maintenance protein 1), and the energy for this process is provided by the RanGTP/RanGDP gradient. Due to the loss of DNA repair and cell cycle checkpoints, drug resistance is a major problem in cancer treatment, and often an initially successful treatment will fail due to the development of resistance. An important mechanism underlying resistance is nuclear export, and a number of strategies that can prevent nuclear export may reverse resistance. Examples include inhibitors of CRM1, antibodies to the nuclear export signal, and alteration of nuclear pore structure. Each of these are considered in this review. PMID:26985906

ABC Transporters Involved in Export of Cell Surface Glycoconjugates

PubMed Central

Cuthbertson, Leslie; Kos, Veronica; Whitfield, Chris

2010-01-01

Summary: Complex glycoconjugates play critical roles in the biology of microorganisms. Despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. One of the primary pathways involves representatives of the ATP-binding cassette (ABC) transporter superfamily. These proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both Gram-positive and Gram-negative bacteria. Recent investigations of the structure and function of ABC transporters involved in the export of lipopolysaccharide O antigens have revealed two fundamentally different strategies for coupling glycan polymerization to export. These mechanisms are distinguished by the presence (or absence) of characteristic nonreducing terminal modifications on the export substrates, which serve as chain termination and/or export signals, and by the presence (or absence) of a discrete substrate-binding domain in the nucleotide-binding domain polypeptide of the ABC transporter. A bioinformatic survey examining ABC exporters from known oligo- and polysaccharide biosynthesis loci identifies conserved nucleotide-binding domain protein families that correlate well with themes in the structures and assembly of glycans. The familial relationships among the ABC exporters generate hypotheses concerning the biosynthesis of structurally diverse oligo- and polysaccharides, which play important roles in the biology of bacteria with different lifestyles. PMID:20805402

Prediction in complex systems: The case of the international trade network

NASA Astrophysics Data System (ADS)

Vidmer, Alexandre; Zeng, An; Medo, Matúš; Zhang, Yi-Cheng

2015-10-01

Predicting the future evolution of complex systems is one of the main challenges in complexity science. Based on a current snapshot of a network, link prediction algorithms aim to predict its future evolution. We apply here link prediction algorithms to data on the international trade between countries. This data can be represented as a complex network where links connect countries with the products that they export. Link prediction techniques based on heat and mass diffusion processes are employed to obtain predictions for products exported in the future. These baseline predictions are improved using a recent metric of country fitness and product similarity. The overall best results are achieved with a newly developed metric of product similarity which takes advantage of causality in the network evolution.

Broadband Scattering from Sand and Sand/Mud Sediments with Extensive Environmental Characterization

DTIC Science & Technology

2015-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Broadband Scattering from Sand and Sand/ Mud Sediments...TERM GOALS To model the effects of volume heterogeneities, both discrete and continuous, in scattering from sand and mud sediments. A better...IMP2 has been used extensively during TREX13 and BayEx14 to measure the porosity in both sand and mud sediments. Analysis of this recent data inspired a

Measurement of Ship Air Wake Impact on a Remotely Piloted Vehicle

DTIC Science & Technology

2012-05-09

Figure 12. T-Rex 600 E Super Pro with “ spider leg” flotation system......................................... 16 Figure 13. x-IMU Inertial Measurement... spider legs” mounted underneath the helicopter. The “ spider legs” with free spinning 16 whiffle balls attached at the ends of each leg are...with “ spider leg” flotation system. 2.1.1.1 Remote Controlled Helicopter Training and Safety Program Safe operation of the RC helicopter was of

Ride-along data LOS 130, 170 & LO330 shots z3139, 3140 and 3141

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

Loisel, Guillaume Pascal

Each instrument records the x-ray emission from the Z-pinch dynamic hohlraum (ZPDH); LOS 130 TIXTLs instruments record the absorption of the pinch backlighter through an expanding NaF/Mg foil; LOS 170 MLM instruments record monochromatic images at 276 and 528 eV energies near and before ZPDH stagnation time; LOS 330 TREX 6A & B: recoded time resolved absorption spectra from a radiatively heated Ne gas.

A Down-valley Low-level Jet Event During T-REX 2006

DTIC Science & Technology

2013-09-04

various terms in the momentum and energy equations contributed to aspects of drainage flow evolution and its variation on slopes in valley environments ...outer nest were provided by the North American Model (NAM) 12 km grid spacing forecasts produced by the National Center for Environmental Pre- diction...a sub - stantially improved nocturnal LLJ speed max prediction. This seems consistent with previous research findings focused upon the Owens Valley and

Constructing the wonders of the bacterial world: biosynthesis of complex enzymes.

PubMed

Sargent, Frank

2007-03-01

The prokaryotic cytoplasmic membrane not only maintains cell integrity and forms a barrier between the cell and its outside environment, but is also the location for essential biochemical processes. Microbial model systems provide excellent bases for the study of fundamental problems in membrane biology including signal transduction, chemotaxis, solute transport and, as will be the topic of this review, energy metabolism. Bacterial respiration requires a diverse array of complex, multi-subunit, cofactor-containing redox enzymes, many of which are embedded within, or located on the extracellular side of, the membrane. The biosynthesis of these enzymes therefore requires carefully controlled expression, assembly, targeting and transport processes. Here, focusing on the molybdenum-containing respiratory enzymes central to anaerobic respiration in Escherichia coli, recent descriptions of a chaperone-mediated 'proofreading' system involved in coordinating assembly and export of complex extracellular enzymes will be discussed. The paradigm proofreading chaperones are members of a large group of proteins known as the TorD family, and recent research in this area highlights common principles that underpin biosynthesis of both exported and non-exported respiratory enzymes.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA

PubMed Central

Ajamian, Lara; Abel, Karen; Rao, Shringar; Vyboh, Kishanda; García-de-Gracia, Francisco; Soto-Rifo, Ricardo; Kulozik, Andreas E.; Gehring, Niels H.; Mouland, Andrew J.

2015-01-01

Unspliced, genomic HIV-1 RNA (vRNA) is a component of several ribonucleoprotein complexes (RNP) during the viral replication cycle. In earlier work, we demonstrated that the host upframeshift protein 1 (UPF1), a key factor in nonsense-mediated mRNA decay (NMD), colocalized and associated to the viral structural protein Gag during viral egress. In this work, we demonstrate a new function for UPF1 in the regulation of vRNA nuclear export. We establish that the nucleocytoplasmic shuttling of UPF1 is required for this function and demonstrate that UPF1 exists in two essential viral RNPs during the late phase of HIV-1 replication: the first, in a nuclear export RNP that contains Rev, CRM1, DDX3 and the nucleoporin p62, and the second, which excludes these nuclear export markers but contains Gag in the cytoplasm. Interestingly, we observed that both UPF2 and the long isoform of UPF3a, UPF3aL, but not the shorter isoforms UPF3aS and UPF3b, are excluded from the UPF1-Rev-CRM1-DDX3 complex as they are negative regulators of vRNA nuclear export. In silico protein-protein docking analyses suggest that Rev binds UPF1 in a region that overlaps the UPF2 binding site, thus explaining the exclusion of this negative regulatory factor by HIV-1 that is necessary for vRNA trafficking. This work uncovers a novel and unique regulatory circuit involving several UPF proteins that ultimately regulate vRNA nuclear export and trafficking. PMID:26492277

Real-time analysis of δ13C- and δD-CH4 in ambient air with laser spectroscopy: Method development and intercomparison

NASA Astrophysics Data System (ADS)

Harris, E. J.; Eyer, S.; Mohn, J.; Röckmann, T.; Popa, E.; Lowry, D.; Nisbet, E. G.; Fisher, R. E.; Brennwald, M. S.; Fischer, H.; Emmenegger, L.; Tuzson, B.; Zellweger, C.

2015-12-01

Methane (CH4) is the second most important anthropogenically emitted greenhouse gas after carbon dioxide (CO2). Its mole fraction has increased from around 722 ppb in pre-industrial times to 1824 ppb in 2013 and the anthropogenic fraction is estimated to be 60 % of the total emissions. A promising approach to improve the understanding of the CH4 budget is the use of isotopologues to distinguish between various CH4 source processes. In the presented study in situ and simultaneous measurement of the three most abundant isotopologues of methane using mid-infrared laser absorption spectroscopy is demonstrated. A field-deployable, autonomous platform is realized by coupling a compact quantum cascade laser absorption spectrometer (QCLAS) to a preconcentration unit, called TRace gas EXtractor (TREX). This unit enhances CH4 mole fractions by a factor of up to 500 above ambient levels and quantitatively separates interfering trace gases such as N2O and CO2. The analytical precision of the QCLAS isotope measurement on the preconcentrated (750 ppm, parts-per-million, mmole/mole) methane is 0.1‰ and 0.5 ‰ for δ13C- and δD-CH4 at 10 min averaging time. [1] Based on replicate measurements of compressed air during a two-week intercomparison campaign, the repeatability of the TREX-QCLAS was determined to be 0.19 ‰ and 1.9 ‰ for δ13C and δD-CH4, respectively. In this intercomparison campaign the new in situ technique is compared to IRMS based on glass flask and bag sampling and real time CH4 isotope analysis by two commercially available laser spectrometers (Figure). Both laser-based analyzers were limited to methane mole fraction and δ13C-CH4 analysis, and only one of them, a cavity ring down spectrometer, was capable to deliver meaningful data for the isotopic composition. After correcting for scale offsets, the average difference between TREX-QCLAS data and bag/flask sampling-IRMS values are within the extended WMO compatibility goals of 0.2 and 5 ‰ for δ13C- and δD-CH4, respectively. Thus, the intercomparison also reveals the need for reference air samples with accurately determined isotopic composition of CH4 to further improve the interlaboratory compatibility. [1] References: [1] S. Eyer et al. (2015) submitted to AMTD

Nmd3p Is a Crm1p-Dependent Adapter Protein for Nuclear Export of the Large Ribosomal Subunit

PubMed Central

Ho, Jennifer Hei-Ngam; Kallstrom, George; Johnson, Arlen W.

2000-01-01

In eukaryotic cells, nuclear export of nascent ribosomal subunits through the nuclear pore complex depends on the small GTPase Ran. However, neither the nuclear export signals (NESs) for the ribosomal subunits nor the receptor proteins, which recognize the NESs and mediate export of the subunits, have been identified. We showed previously that Nmd3p is an essential protein from yeast that is required for a late step in biogenesis of the large (60S) ribosomal subunit. Here, we show that Nmd3p shuttles and that deletion of the NES from Nmd3p leads to nuclear accumulation of the mutant protein, inhibition of the 60S subunit biogenesis, and inhibition of the nuclear export of 60S subunits. Moreover, the 60S subunits that accumulate in the nucleus can be coimmunoprecipitated with the NES-deficient Nmd3p. 60S subunit biogenesis and export of truncated Nmd3p were restored by the addition of an exogenous NES. To identify the export receptor for Nmd3p we show that Nmd3p shuttling and 60S export is blocked by the Crm1p-specific inhibitor leptomycin B. These results identify Crm1p as the receptor for Nmd3p export. Thus, export of the 60S subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway. PMID:11086007

Synonymous mutations in RNASEH2A create cryptic splice sites impairing RNase H2 enzyme function in Aicardi-Goutières syndrome

PubMed Central

Rice, Gillian I.; Reijns, Martin A.M.; Coffin, Stephanie R.; Forte, Gabriella M.A.; Anderson, Beverley H.; Szynkiewicz, Marcin; Gornall, Hannah; Gent, David; Leitch, Andrea; Botella, Maria P.; Fazzi, Elisa; Gener, Blanca; Lagae, Lieven; Olivieri, Ivana; Orcesi, Simona; Swoboda, Kathryn J.; Perrino, Fred W.; Jackson, Andrew P.; Crow, Yanick J.

2013-01-01

Aicardi-Goutières syndrome (AGS) is an inflammatory disorder resulting from mutations in TREX1, RNASEH2A/2B/2C, SAMHD1 or ADAR1. Here we provide molecular, biochemical and cellular evidence for the pathogenicity of two synonymous variants in RNASEH2A. Firstly, the c.69G>A (p.Val23Val) mutation causes the formation of a splice donor site within exon 1, resulting in an out of frame deletion at the end of exon 1, leading to reduced RNase H2 protein levels. The second mutation, c.75C>T (p.Arg25Arg), also introduces a splice donor site within exon 1, and the internal deletion of 18 amino acids. The truncated protein still forms a heterotrimeric RNase H2 complex, but lacks catalytic activity. However, as a likely result of leaky splicing, a small amount of full-length active protein is apparently produced in an individual homozygous for this mutation. Recognition of the disease causing status of these variants allows for diagnostic testing in relevant families. PMID:23592335

Quantifying the Stable Boundary Layer Structure and Evolution during T-REX 2006

DTIC Science & Technology

2014-09-30

integrating surface observations, data from in-situ measurements, and a nested numerical model with two related topics was conducted in this project. the WRF ...as well as quantify differences at a fine scale model output using the different turbulent mixing/diffusion options in the WRF -ARW model; and (2... WRF model planetary boundary layer schemes were also conducted to study a downslope windstorm and rotors in Las Vegas valley. Two events (March 20

Autophagy requires poly(adp-ribosyl)ation-dependent AMPK nuclear export

PubMed Central

Rodríguez-Vargas, José M; Rodríguez, María I; Majuelos-Melguizo, Jara; García-Diaz, Ángel; González-Flores, Ariannys; López-Rivas, Abelardo; Virág, László; Illuzzi, Giuditta; Schreiber, Valerie; Dantzer, Françoise; Oliver, F Javier

2016-01-01

AMPK is a central energy sensor linking extracellular milieu fluctuations with the autophagic machinery. In the current study we uncover that Poly(ADP-ribosyl)ation (PARylation), a post-translational modification (PTM) of proteins, accounts for the spatial and temporal regulation of autophagy by modulating AMPK subcellular localisation and activation. More particularly, we show that the minority AMPK pool needs to be exported to the cytosol in a PARylation-dependent manner for optimal induction of autophagy, including ULK1 phosphorylation and mTORC1 inactivation. PARP-1 forms a molecular complex with AMPK in the nucleus in non-starved cells. In response to nutrient deprivation, PARP-1 catalysed PARylation, induced the dissociation of the PARP-1/AMPK complex and the export of free PARylated nuclear AMPK to the cytoplasm to activate autophagy. PARP inhibition, its silencing or the expression of PARylation-deficient AMPK mutants prevented not only the AMPK nuclear-cytosolic export but also affected the activation of the cytosolic AMPK pool and autophagosome formation. These results demonstrate that PARylation of AMPK is a key early signal to efficiently convey extracellular nutrient perturbations with downstream events needed for the cell to optimize autophagic commitment before autophagosome formation. PMID:27689873

Exportin-5 mediates nuclear export of SRP RNA in vertebrates.

PubMed

Takeiwa, Toshihiko; Taniguchi, Ichiro; Ohno, Mutsuhito

2015-04-01

The signal recognition particle is a ribonucleoprotein complex that is essential for the translocation of nascent proteins into the endoplasmic reticulum. It has been shown that the RNA component (SRP RNA) is exported from the nucleus by CRM1 in the budding yeast. However, how SRP RNA is exported in higher species has been elusive. Here, we show that SRP RNA does not use the CRM1 pathway in Xenopus oocytes. Instead, SRP RNA uses the same export pathway as pre-miRNA and tRNA as showed by cross-competition experiments. Consistently, the recombinant Exportin-5 protein specifically stimulated export of SRP RNA as well as of pre-miRNA and tRNA, whereas an antibody raised against Exportin-5 specifically inhibited export of the same RNA species. Moreover, biotinylated SRP RNA can pull down Exportin-5 but not CRM1 from HeLa cell nuclear extracts in a RanGTP-dependent manner. These results, taken together, strongly suggest that the principal export receptor for SRP RNA in vertebrates is Exportin-5 unlike in the budding yeast. © 2015 The Authors. Genes to Cells published by Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

NXT1, a Novel Influenza A NP Binding Protein, Promotes the Nuclear Export of NP via a CRM1-Dependent Pathway.

PubMed

Chutiwitoonchai, Nopporn; Aida, Yoko

2016-07-28

Influenza remains a serious worldwide public health problem. After infection, viral genomic RNA is replicated in the nucleus and packed into viral ribonucleoprotein, which will then be exported to the cytoplasm via a cellular chromosome region maintenance 1 (CRM1)-dependent pathway for further assembly and budding. However, the nuclear export mechanism of influenza virus remains controversial. Here, we identify cellular nuclear transport factor 2 (NTF2)-like export protein 1 (NXT1) as a novel binding partner of nucleoprotein (NP) that stimulates NP-mediated nuclear export via the CRM1-dependent pathway. NXT1-knockdown cells exhibit decreased viral replication kinetics and nuclear accumulated viral RNA and NP. By contrast, NXT1 overexpression promotes nuclear export of NP in a CRM1-dependent manner. Pull-down assays suggest the formation of an NXT1, NP, and CRM1 complex, and demonstrate that NXT1 binds to the C-terminal region of NP. These findings reveal a distinct mechanism for nuclear export of the influenza virus and identify the NXT1/NP interaction as a potential target for antiviral drug development.

Nuclear Export of Pre-Ribosomal Subunits Requires Dbp5, but Not as an RNA-Helicase as for mRNA Export

PubMed Central

Neumann, Bettina; Wu, Haijia; Hackmann, Alexandra; Krebber, Heike

2016-01-01

The DEAD-box RNA-helicase Dbp5/Rat8 is known for its function in nuclear mRNA export, where it displaces the export receptor Mex67 from the mRNA at the cytoplasmic side of the nuclear pore complex (NPC). Here we show that Dbp5 is also required for the nuclear export of both pre-ribosomal subunits. Yeast temperature-sensitive dbp5 mutants accumulate both ribosomal particles in their nuclei. Furthermore, Dbp5 genetically and physically interacts with known ribosomal transport factors such as Nmd3. Similar to mRNA export we show that also for ribosomal transport Dbp5 is required at the cytoplasmic side of the NPC. However, unlike its role in mRNA export, Dbp5 does not seem to undergo its ATPase cycle for this function, as ATPase-deficient dbp5 mutants that selectively inhibit mRNA export do not affect ribosomal transport. Furthermore, mutants of GLE1, the ATPase stimulating factor of Dbp5, show no major ribosomal export defects. Consequently, while Dbp5 uses its ATPase cycle to displace the export receptor Mex67 from the translocated mRNAs, Mex67 remains bound to ribosomal subunits upon transit to the cytoplasm, where it is detectable on translating ribosomes. Therefore, we propose a model, in which Dbp5 supports ribosomal transport by capturing ribosomal subunits upon their cytoplasmic appearance at the NPC, possibly by binding export factors such as Mex67. Thus, our findings reveal that although different ribonucleoparticles, mRNAs and pre-ribosomal subunits, use shared export factors, they utilize different transport mechanisms. PMID:26872259

Nuclear Export of Pre-Ribosomal Subunits Requires Dbp5, but Not as an RNA-Helicase as for mRNA Export.

PubMed

Neumann, Bettina; Wu, Haijia; Hackmann, Alexandra; Krebber, Heike

2016-01-01

The DEAD-box RNA-helicase Dbp5/Rat8 is known for its function in nuclear mRNA export, where it displaces the export receptor Mex67 from the mRNA at the cytoplasmic side of the nuclear pore complex (NPC). Here we show that Dbp5 is also required for the nuclear export of both pre-ribosomal subunits. Yeast temperature-sensitive dbp5 mutants accumulate both ribosomal particles in their nuclei. Furthermore, Dbp5 genetically and physically interacts with known ribosomal transport factors such as Nmd3. Similar to mRNA export we show that also for ribosomal transport Dbp5 is required at the cytoplasmic side of the NPC. However, unlike its role in mRNA export, Dbp5 does not seem to undergo its ATPase cycle for this function, as ATPase-deficient dbp5 mutants that selectively inhibit mRNA export do not affect ribosomal transport. Furthermore, mutants of GLE1, the ATPase stimulating factor of Dbp5, show no major ribosomal export defects. Consequently, while Dbp5 uses its ATPase cycle to displace the export receptor Mex67 from the translocated mRNAs, Mex67 remains bound to ribosomal subunits upon transit to the cytoplasm, where it is detectable on translating ribosomes. Therefore, we propose a model, in which Dbp5 supports ribosomal transport by capturing ribosomal subunits upon their cytoplasmic appearance at the NPC, possibly by binding export factors such as Mex67. Thus, our findings reveal that although different ribonucleoparticles, mRNAs and pre-ribosomal subunits, use shared export factors, they utilize different transport mechanisms.

The malaria PTEX component PTEX88 interacts most closely with HSP101 at the host-parasite interface.

PubMed

Chisholm, Scott A; Kalanon, Ming; Nebl, Thomas; Sanders, Paul R; Matthews, Kathryn M; Dickerman, Benjamin K; Gilson, Paul R; de Koning-Ward, Tania F

2018-04-10

The pathogenic nature of malaria infections is due in part to the export of hundreds of effector proteins that actively remodel the host erythrocyte. The Plasmodium translocon of exported proteins (PTEX) has been shown to facilitate the trafficking of proteins into the host cell, a process that is essential for the survival of the parasite. The role of the auxiliary PTEX component PTEX88 remains unclear, as previous attempts to elucidate its function through reverse genetic approaches showed that in contrast to the core components PTEX150 and HSP101, knockdown of PTEX88 did not give rise to an export phenotype. Here, we have used biochemical approaches to understand how PTEX88 assembles within the translocation machinery. Proteomic analysis of the PTEX88 interactome showed that PTEX88 interacts closely with HSP101 but has a weaker affinity with the other core constituents of PTEX. PTEX88 was also found to associate with other PV-resident proteins, including chaperones and members of the exported protein-interacting complex that interacts with the major virulence factor PfEMP1, the latter contributing to cytoadherence and parasite virulence. Despite being expressed for the duration of the blood-stage life cycle, PTEX88 was only discretely observed at the parasitophorous vacuole membrane during ring stages and could not always be detected in the major high molecular weight complex that contains the other core components of PTEX, suggesting that its interaction with the PTEX complex may be dynamic. Together, these data have enabled the generation of an updated model of PTEX that now includes how PTEX88 assembles within the complex. © 2018 Federation of European Biochemical Societies.

In Vitro Reconstitution of Functional Type III Protein Export and Insights into Flagellar Assembly.

PubMed

Terashima, Hiroyuki; Kawamoto, Akihiro; Tatsumi, Chinatsu; Namba, Keiichi; Minamino, Tohru; Imada, Katsumi

2018-06-26

The type III secretion system (T3SS) forms the functional core of injectisomes, protein transporters that allow bacteria to deliver virulence factors into their hosts for infection, and flagella, which are critical for many pathogens to reach the site of infection. In spite of intensive genetic and biochemical studies, the T3SS protein export mechanism remains unclear due to the difficulty of accurate measurement of protein export in vivo Here, we developed an in vitro flagellar T3S protein transport assay system using an inverted cytoplasmic membrane vesicle (IMV) for accurate and controlled measurements of flagellar protein export. We show that the flagellar T3SS in the IMV fully retains export activity. The flagellar hook was constructed inside the lumen of the IMV by adding purified component proteins externally to the IMV solution. We reproduced the hook length control and export specificity switch in the IMV consistent with that seen in the native cell. Previous in vivo analyses showed that flagellar protein export is driven by proton motive force (PMF) and facilitated by ATP hydrolysis by FliI, a T3SS-specific ATPase. Our in vitro assay recapitulated these previous in vivo observations but furthermore clearly demonstrated that even ATP hydrolysis by FliI alone can drive flagellar protein export. Moreover, this assay showed that addition of the FliH 2 /FliI complex to the assay solution at a concentration similar to that in the cell dramatically enhanced protein export, confirming that the FliH 2 /FliI complex in the cytoplasm is important for effective protein transport. IMPORTANCE The type III secretion system (T3SS) is the functional core of the injectisome, a bacterial protein transporter used to deliver virulence proteins into host cells, and bacterial flagella, critical for many pathogens. The molecular mechanism of protein transport is still unclear due to difficulties in accurate measurements of protein transport under well-controlled conditions in vivo We succeeded in developing an in vitro transport assay system of the flagellar T3SS using inverted membrane vesicles (IMVs). Flagellar hook formation was reproduced in the IMV, suggesting that the export apparatus in the IMV retains a protein transport activity similar to that in the cell. Using this system, we revealed that ATP hydrolysis by the T3SS ATPase can drive protein export without PMF. Copyright © 2018 Terashima et al.

HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA.

PubMed

Ajamian, Lara; Abel, Karen; Rao, Shringar; Vyboh, Kishanda; García-de-Gracia, Francisco; Soto-Rifo, Ricardo; Kulozik, Andreas E; Gehring, Niels H; Mouland, Andrew J

2015-10-20

Unspliced, genomic HIV-1 RNA (vRNA) is a component of several ribonucleoprotein complexes (RNP) during the viral replication cycle. In earlier work, we demonstrated that the host upframeshift protein 1 (UPF1), a key factor in nonsense-mediated mRNA decay (NMD), colocalized and associated to the viral structural protein Gag during viral egress. In this work, we demonstrate a new function for UPF1 in the regulation of vRNA nuclear export. OPEN ACCESS Biomolecules 2015, 5 2809 We establish that the nucleocytoplasmic shuttling of UPF1 is required for this function and demonstrate that UPF1 exists in two essential viral RNPs during the late phase of HIV-1 replication: the first, in a nuclear export RNP that contains Rev, CRM1, DDX3 and the nucleoporin p62, and the second, which excludes these nuclear export markers but contains Gag in the cytoplasm. Interestingly, we observed that both UPF2 and the long isoform of UPF3a, UPF3aL, but not the shorter isoforms UPF3aS and UPF3b, are excluded from the UPF1-Rev-CRM1-DDX3 complex as they are negative regulators of vRNA nuclear export. In silico protein-protein docking analyses suggest that Rev binds UPF1 in a region that overlaps the UPF2 binding site, thus explaining the exclusion of this negative regulatory factor by HIV-1 that is necessary for vRNA trafficking. This work uncovers a novel and unique regulatory circuit involving several UPF proteins that ultimately regulate vRNA nuclear export and trafficking.

Nuclear Export and Expression of Human T-Cell Leukemia Virus Type 1 tax/rex mRNA Are RxRE/Rex Dependent

PubMed Central

Bai, X. T.; Sinha-Datta, U.; Ko, N. L.; Bellon, M.

2012-01-01

Human T-cell leukemia virus type 1 (HTLV-1) is a complex retrovirus associated with the lymphoproliferative disease adult T-cell leukemia/lymphoma (ATL) and the neurodegenerative disorder tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM). Replication of HTLV-1 is under the control of two major trans-acting proteins, Tax and Rex. Previous studies suggested that Tax activates transcription from the viral long terminal repeat (LTR) through recruitment of cellular CREB and transcriptional coactivators. Other studies reported that Rex acts posttranscriptionally and allows the cytoplasmic export of unspliced or incompletely spliced viral mRNAs carrying gag/pol and env only. As opposed to HIV's Rev-responsive element (RRE), the Rex-responsive element (RxRE) is present in all viral mRNAs in HTLV-1. However, based on indirect observations, it is believed that nuclear export and expression of the doubly spliced tax/rex RNA are Rex independent. In this study, we demonstrate that Rex does stimulate Tax expression, through nuclear-cytoplasmic export of the tax/rex RNA, even though a Rex-independent basal export mechanism exists. This effect was dependent upon the RxRE element and the RNA-binding activity of Rex. In addition, Rex-mediated export of tax/rex RNA was CRM1 dependent and inhibited by leptomycin B treatment. RNA immunoprecipitation (RNA-IP) experiments confirmed Rex binding to the tax/rex RNA in both transfected cells with HTLV-1 molecular clones and HTLV-1-infected T cells. Since both Rex and p30 interact with the tax/rex RNA and with one another, this may offer a temporal and dynamic regulation of HTLV-1 replication. Our results shed light on HTLV-1 replication and reveal a more complex regulatory network than previously anticipated. PMID:22318152

A New Metrics for Countries' Fitness and Products' Complexity

NASA Astrophysics Data System (ADS)

Tacchella, Andrea; Cristelli, Matthieu; Caldarelli, Guido; Gabrielli, Andrea; Pietronero, Luciano

2012-10-01

Classical economic theories prescribe specialization of countries industrial production. Inspection of the country databases of exported products shows that this is not the case: successful countries are extremely diversified, in analogy with biosystems evolving in a competitive dynamical environment. The challenge is assessing quantitatively the non-monetary competitive advantage of diversification which represents the hidden potential for development and growth. Here we develop a new statistical approach based on coupled non-linear maps, whose fixed point defines a new metrics for the country Fitness and product Complexity. We show that a non-linear iteration is necessary to bound the complexity of products by the fitness of the less competitive countries exporting them. We show that, given the paradigm of economic complexity, the correct and simplest approach to measure the competitiveness of countries is the one presented in this work. Furthermore our metrics appears to be economically well-grounded.

Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo

PubMed Central

Björk, Petra; Persson, Jan-Olov

2015-01-01

Eukaryotic gene expression requires the ordered association of numerous factors with precursor messenger RNAs (premRNAs)/messenger RNAs (mRNAs) to achieve efficiency and regulation. Here, we use the Balbiani ring (BR) genes to demonstrate the temporal and spatial association of the exon junction complex (EJC) core with gene-specific endogenous premRNAs and mRNAs. The EJC core components bind cotranscriptionally to BR premRNAs during or very rapidly after splicing. The EJC core does not recruit the nonsense-mediated decay mediaters UPF2 and UPF3 until the BR messenger RNA protein complexes (mRNPs) enter the interchromatin. Even though several known adapters for the export factor NXF1 become part of BR mRNPs already at the gene, NXF1 binds to BR mRNPs only in the interchromatin. In steady state, a subset of the BR mRNPs in the interchromatin binds NXF1, UPF2, and UPF3. This binding appears to occur stochastically, and the efficiency approximately equals synthesis and export of the BR mRNPs. Our data provide unique in vivo information on how export competent eukaryotic mRNPs are formed. PMID:26459599

Structure of the exportin Xpo4 in complex with RanGTP and the hypusine-containing translation factor eIF5A

PubMed Central

Aksu, Metin; Trakhanov, Sergei; Görlich, Dirk

2016-01-01

Xpo4 is a bidirectional nuclear transport receptor that mediates nuclear export of eIF5A and Smad3 as well as import of Sox2 and SRY. How Xpo4 recognizes such a variety of cargoes is as yet unknown. Here we present the crystal structure of the RanGTP·Xpo4·eIF5A export complex at 3.2 Å resolution. Xpo4 has a similar structure as CRM1, but the NES-binding site is occluded, and a new interaction site evolved that recognizes both globular domains of eIF5A. eIF5A contains hypusine, a unique amino acid with two positive charges, which is essential for cell viability and eIF5A function in translation. The hypusine docks into a deep, acidic pocket of Xpo4 and is thus a critical element of eIF5A's complex export signature. This further suggests that Xpo4 recognizes other cargoes differently, and illustrates how Xpo4 suppresses – in a chaperone-like manner – undesired interactions of eIF5A inside nuclei. PMID:27306458

Nuclear Export Signal Masking Regulates HIV-1 Rev Trafficking and Viral RNA Nuclear Export.

PubMed

Behrens, Ryan T; Aligeti, Mounavya; Pocock, Ginger M; Higgins, Christina A; Sherer, Nathan M

2017-02-01

HIV-1's Rev protein forms a homo-oligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study, we used a functional fluorescently tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found that Rev activity was remarkably tolerant of diverse NES sequences, including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores. Rev's ability to tolerate a SNES was both position and multimerization dependent, an observation consistent with a model wherein Rev self-association acts to transiently mask the NES peptide(s), thereby biasing Rev's trafficking into the nucleus. Combined imaging and functional assays also indicated that NES masking underpins Rev's well-known tendency to accumulate at the nucleolus, as well as Rev's capacity to activate optimal levels of late viral gene expression. We propose that Rev multimerization and NES masking regulates Rev's trafficking to and retention within the nucleus even prior to RNA binding. HIV-1 infects more than 34 million people worldwide causing >1 million deaths per year. Infectious virion production is activated by the essential viral Rev protein that mediates nuclear export of intron-bearing late-stage viral mRNAs. Rev's shuttling into and out of the nucleus is regulated by the antagonistic activities of both a peptide-encoded N-terminal nuclear localization signal and C-terminal nuclear export signal (NES). How Rev and related viral proteins balance strong import and export activities in order to achieve optimal levels of viral gene expression is incompletely understood. We provide evidence that multimerization provides a mechanism by which Rev transiently masks its NES peptide, thereby biasing its trafficking to and retention within the nucleus. Targeted pharmacological disruption of Rev-Rev interactions should perturb multiple Rev activities, both Rev-RNA binding and Rev's trafficking to the nucleus in the first place. Copyright © 2017 American Society for Microbiology.

Nuclear Export Signal Masking Regulates HIV-1 Rev Trafficking and Viral RNA Nuclear Export

PubMed Central

Behrens, Ryan T.; Aligeti, Mounavya; Pocock, Ginger M.; Higgins, Christina A.

2016-01-01

ABSTRACT HIV-1's Rev protein forms a homo-oligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study, we used a functional fluorescently tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found that Rev activity was remarkably tolerant of diverse NES sequences, including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores. Rev's ability to tolerate a SNES was both position and multimerization dependent, an observation consistent with a model wherein Rev self-association acts to transiently mask the NES peptide(s), thereby biasing Rev's trafficking into the nucleus. Combined imaging and functional assays also indicated that NES masking underpins Rev's well-known tendency to accumulate at the nucleolus, as well as Rev's capacity to activate optimal levels of late viral gene expression. We propose that Rev multimerization and NES masking regulates Rev's trafficking to and retention within the nucleus even prior to RNA binding. IMPORTANCE HIV-1 infects more than 34 million people worldwide causing >1 million deaths per year. Infectious virion production is activated by the essential viral Rev protein that mediates nuclear export of intron-bearing late-stage viral mRNAs. Rev's shuttling into and out of the nucleus is regulated by the antagonistic activities of both a peptide-encoded N-terminal nuclear localization signal and C-terminal nuclear export signal (NES). How Rev and related viral proteins balance strong import and export activities in order to achieve optimal levels of viral gene expression is incompletely understood. We provide evidence that multimerization provides a mechanism by which Rev transiently masks its NES peptide, thereby biasing its trafficking to and retention within the nucleus. Targeted pharmacological disruption of Rev-Rev interactions should perturb multiple Rev activities, both Rev-RNA binding and Rev's trafficking to the nucleus in the first place. PMID:27852860

Hepatocytes traffic and export hepatitis B virus basolaterally by polarity-dependent mechanisms.

PubMed

Bhat, Purnima; Snooks, Michelle J; Anderson, David A

2011-12-01

Viruses commonly utilize the cellular trafficking machinery of polarized cells to effect viral export. Hepatocytes are polarized in vivo, but most in vitro hepatocyte models are either nonpolarized or have morphology unsuitable for the study of viral export. Here, we investigate the mechanisms of trafficking and export for the hepadnaviruses hepatitis B virus (HBV) and duck hepatitis B virus (DHBV) in polarized hepatocyte-derived cell lines and primary duck hepatocytes. DHBV export, but not replication, was dependent on the development of hepatocyte polarity, with export significantly abrogated over time as primary hepatocytes lost polarity. Using Transwell cultures of polarized N6 cells and adenovirus-based transduction, we observed that export of both HBV and DHBV was vectorially regulated and predominantly basolateral. Monitoring of polarized N6 cells and nonpolarized C11 cells during persistent, long-term DHBV infection demonstrated that newly synthesized sphingolipid and virus displayed significant colocalization and fluorescence resonance energy transfer, implying cotransportation from the Golgi complex to the plasma membrane. Notably, 15% of virus was released apically from polarized cells, corresponding to secretion into the bile duct in vivo, also in association with sphingolipids. We conclude that DHBV and, probably, HBV are reliant upon hepatocyte polarity to be efficiently exported and this export is in association with sphingolipid structures, possibly lipid rafts. This study provides novel insights regarding the mechanisms of hepadnavirus trafficking in hepatocytes, with potential relevance to pathogenesis and immune tolerance.

The Impact of Moisture on Mountain Waves During T-REX

DTIC Science & Technology

2009-11-01

sensitivity to the upstream wind speed. After re- moving these three outliers, the linear least squares re- gression using the other 21 points yields W( U c )5...The wave amplitudes for the 24 flights normalized by the reference wave amplitude are plotted versus the upstream RH maxima in Fig. 3b. There are four...mountaintop level de- rived from the upwind sondes for 24 UWKA flights. The filled circles represent moist cases as defined in the text. The bold line

TREX13: Mid-Frequency Measurements and Modeling of Scattering by Fish

DTIC Science & Technology

2017-11-13

Another key element to the fish effort is the UW- led (Home) high frequency surveys of fish in the area. The WHOI-led ( tanton) effort focussed on...lik J from fi h with gas-filled swimbladd r . b. Presenc o[fish at experimental ile. There w •r lhr f fi h that dominated the C. numb r in the fixed...34) _., •..,, . . . ... . - ,. • ~ > (a) (b) (c) Figure 3. The dominant species of fish present at experimental site. All have swim bladders which

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

PubMed Central

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin; Adebesin, Funmilayo; Qian, Yichun; Guo, Longyun; Jaini, Rohit; Lynch, Joseph H.; McCoy, Rachel M.; Shreve, Jacob T.; Thimmapuram, Jyothi; Rhodes, David; Morgan, John A.; Dudareva, Natalia

2015-01-01

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles, as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network. PMID:26356302

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

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

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles,more » as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network.« less

Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network

DOE PAGES

Widhalm, Joshua R.; Gutensohn, Michael; Yoo, Heejin; ...

2015-09-10

In addition to proteins, L-phenylalanine is a versatile precursor for thousands of plant metabolites. Production of phenylalanine-derived compounds is a complex multi-compartmental process using phenylalanine synthesized predominantly in plastids as precursor. The transporter(s) exporting phenylalanine from plastids, however, remains unknown. Here, a gene encoding a Petunia hybrida plastidial cationic amino-acid transporter (PhpCAT) functioning in plastidial phenylalanine export is identified based on homology to an Escherichia coli phenylalanine transporter and co-expression with phenylalanine metabolic genes. Radiolabel transport assays show that PhpCAT exports all three aromatic amino acids. PhpCAT downregulation and overexpression result in decreased and increased levels, respectively, of phenylalanine-derived volatiles,more » as well as phenylalanine, tyrosine and their biosynthetic intermediates. Metabolic flux analysis reveals that flux through the plastidial phenylalanine biosynthetic pathway is reduced in PhpCAT RNAi lines, suggesting that the rate of phenylalanine export from plastids contributes to regulating flux through the aromatic amino-acid network.« less

Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export.

PubMed

Fan, Jing; Kuai, Bin; Wu, Guifen; Wu, Xudong; Chi, Binkai; Wang, Lantian; Wang, Ke; Shi, Zhubing; Zhang, Heng; Chen, She; He, Zhisong; Wang, Siyuan; Zhou, Zhaocai; Li, Guohui; Cheng, Hong

2017-10-02

The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex (CBC), and this competition is critical for determining whether an RNA is degraded or exported to the cytoplasm. Together, our results indicate that the competition between hMTR4 and ALYREF determines exosome recruitment and functions in creating balanced nuclear RNA pools for degradation and export. © 2017 The Authors.

A subset of FG-nucleoporins is necessary for efficient Msn5-mediated nuclear protein export

PubMed Central

Finn, Erin M.; DeRoo, Elise P.; Clement, George W.; Rao, Sheila; Kruse, Sarah E.; Kokanovich, Kate M.; Belanger, Kenneth D.

2013-01-01

The transport of proteins between the cytoplasm and nucleus requires interactions between soluble transport receptors (karyopherins) and phenylalanine-glycine (FG) repeat domains on nuclear pore complex proteins (nucleoporins). However, the role of specific FG repeat-containing nucleoporins in nuclear protein export has not been carefully investigated. We have developed a novel kinetic assay to investigate the relative export kinetics mediated by the karyopherin Msn5/Kap142 in yeast containing specific FG-Nup mutations. Using the Msn5 substrate Crz1 as a marker for Msn5-mediated protein export, we observe that deletions of NUP100 or NUP2 result in decreased rates of Crz1 export, while nup60Δ and nup42Δ mutants do not vary significantly from wild type. The decreased Msn5 export rate in nup100Δ was confirmed using Mig1-GFP as a transport substrate. A nup100ΔGLFG mutant shows defects in nuclear export kinetics similar to a nup100Δ deletion. Removal of FG-repeats from Nsp1 also decreases export kinetics, while a loss of Nup1 FXFGs does not. To confirm that our export data reflected functional differences in protein localization, we performed Crz1 transcription activation assays using a CDRE::LacZ reporter gene that is upregulated upon increased transcription activation by Crz1 in vivo. We observe that expression from this reporter increases in nup100ΔGLFG and nsp1ΔFGΔFXFG strains that exhibit decreased Crz1 export kinetics but resembles wild-type levels in nup1ΔFXFG strains that do not exhibit export defects. These data provide evidence that the export of Msn5 is likely mediated by a specific subset of FG-Nups and that the GLFG repeat domain of Nup100 is important for Msn5-mediated nuclear protein export. PMID:23295456

Directions of management for the development of fuel-and-energy complex as the key driver of the social-and-economic development of regions

NASA Astrophysics Data System (ADS)

Mottaeva, Asiiat

2017-10-01

The article is dedicated to the problems of the participation of the energy enterprises in the social-and-economic development of the regions and municipalities. The complex of mechanisms of the implementation of the Energy strategy in the form of strategic initiatives of the development of the energy industry representing the complex inter-industry state-private long-term projects is presented in the article. The author considers the development of the energy industry to be the key driver of the social-and-economic development of regions. The author proves, that the increase in competitiveness of Russian energy, geographical and grocery diversification of export and improvement of quality of export products might allow to solve some problems of the development of national economy.

The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module.

PubMed

Su, Zhenxia; Zhao, Lihua; Zhao, Yuanyuan; Li, Shaofang; Won, SoYoun; Cai, Hanyang; Wang, Lulu; Li, Zhenfang; Chen, Piaojuan; Qin, Yuan; Chen, Xuemei

2017-06-05

In most sexually reproducing plants, a single somatic, sub-epidermal cell in an ovule is selected to differentiate into a megaspore mother cell, which is committed to giving rise to the female germline. However, it remains unclear how intercellular signaling among somatic cells results in only one cell in the sub-epidermal layer differentiating into the megaspore mother cell. Here we uncovered a role of the THO complex in restricting the megaspore mother cell fate to a single cell. Mutations in TEX1, HPR1, and THO6, components of the THO/TREX complex, led to the formation of multiple megaspore mother cells, which were able to initiate gametogenesis. We demonstrated that TEX1 repressed the megaspore mother cell fate by promoting the biogenesis of TAS3-derived trans-acting small interfering RNA (ta-siRNA), which represses ARF3 expression. The TEX1 protein was present in epidermal cells, but not in the germline, and, through TAS3-derived ta-siRNA, restricted ARF3 expression to the medio domain of ovule primordia. Expansion of ARF3 expression into lateral epidermal cells in a TAS3 ta-siRNA-insensitive mutant led to the formation of supernumerary megaspore mother cells, suggesting that TEX1- and TAS3-mediated restriction of ARF3 expression limits excessive megaspore mother cell formation non-cell-autonomously. Our findings reveal the role of a small-RNA pathway in the regulation of female germline specification in Arabidopsis. Copyright © 2017 Elsevier Ltd. All rights reserved.

An improved export coefficient model to estimate non-point source phosphorus pollution risks under complex precipitation and terrain conditions.

PubMed

Cheng, Xian; Chen, Liding; Sun, Ranhao; Jing, Yongcai

2018-05-15

To control non-point source (NPS) pollution, it is important to estimate NPS pollution exports and identify sources of pollution. Precipitation and terrain have large impacts on the export and transport of NPS pollutants. We established an improved export coefficient model (IECM) to estimate the amount of agricultural and rural NPS total phosphorus (TP) exported from the Luanhe River Basin (LRB) in northern China. The TP concentrations of rivers from 35 selected catchments in the LRB were used to test the model's explanation capacity and accuracy. The simulation results showed that, in 2013, the average TP export was 57.20 t at the catchment scale. The mean TP export intensity in the LRB was 289.40 kg/km 2 , which was much higher than those of other basins in China. In the LRB topographic regions, the TP export intensity was the highest in the south Yanshan Mountains and was followed by the plain area, the north Yanshan Mountains, and the Bashang Plateau. Among the three pollution categories, the contribution ratios to TP export were, from high to low, the rural population (59.44%), livestock husbandry (22.24%), and land-use types (18.32%). Among all ten pollution sources, the contribution ratios from the rural population (59.44%), pigs (14.40%), and arable land (10.52%) ranked as the top three sources. This study provides information that decision makers and planners can use to develop sustainable measures for the prevention and control of NPS pollution in semi-arid regions.

Involvement of retinol dehydrogenase 10 in embryonic patterning and rescue of its loss of function by maternal retinaldehyde treatment

PubMed Central

Rhinn, Muriel; Schuhbaur, Brigitte; Niederreither, Karen; Dollé, Pascal

2011-01-01

Retinoic acid (RA), an active vitamin A metabolite, is a key signaling molecule in vertebrate embryos. Morphogenetic RA gradients are thought to be set up by tissue-specific actions of retinaldehyde dehydrogenases (RALDHs) and catabolizing enzymes. According to the species, two enzymatic pathways (β-carotene cleavage and retinol oxidation) generate retinaldehyde, the substrate of RALDHs. Placental species depend on maternal retinol transferred to the embryo. The retinol-to-retinaldehyde conversion was thought to be achieved by several redundant enzymes; however, a random mutagenesis screen identified retinol dehydrogenase 10 [Rdh10Trex allele; Sandell LL, et al. (2007) Genes Dev 21:1113–1124] as responsible for a homozygous lethal phenotype with features of RA deficiency. We report here the production and characterization of unique murine Rdh10 loss-of-function alleles generated by gene targeting. We show that although Rdh10−/− mutants die at an earlier stage than Rdh10Trex mutants, their molecular patterning defects do not reflect a complete state of RA deficiency. Furthermore, we were able to correct most developmental abnormalities by administering retinaldehyde to pregnant mothers, thereby obtaining viable Rdh10−/− mutants. This demonstrates the rescue of an embryonic lethal phenotype by simple maternal administration of the missing retinoid compound. These results underscore the importance of maternal retinoids in preventing congenital birth defects, and lead to a revised model of the importance of RDH10 and RALDHs in controlling embryonic RA distribution. PMID:21930923

Gaseous time projection chambers for rare event detection: results from the T-REX project. II. Dark matter

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

Irastorza, I.G.; Aznar, F.; Castel, J., E-mail: igor.irastorza@cern.ch, E-mail: faznar@unizar.es, E-mail: jfcastel@unizar.es

As part of the T-REX project, a number of R and D and prototyping activities have been carried out during the last years to explore the applicability of gaseous Time Projection Chambers (TPCs) with Micromesh Gas Structures (Micromegas) in rare event searches like double beta decay, axion research and low-mass WIMP searches. While in the companion paper we focus on double beta decay, in this paper we focus on the results regarding the search for dark matter candidates, both axions and WIMPs. Small (few cm wide) ultra-low background Micromegas detectors are used to image the axion-induced x-ray signal expected inmore » axion helioscopes like the CERN Axion Solar Telescope (CAST) experiment. Background levels as low as 0.8 × 10{sup −6} counts keV{sup −1} cm{sup −2} s{sup −1} have already been achieved in CAST while values down to ∼10{sup −7} counts keV{sup −1} cm{sup −2} s{sup −1} have been obtained in a test bench placed underground in the Laboratorio Subterráneo de Canfranc (LSC). Prospects to consolidate and further reduce these values down to ∼10{sup −8} counts keV{sup −1} cm{sup −2} s{sup −1} will be described. Such detectors, placed at the focal point of x-ray telescopes in the future International Axion Observatory (IAXO), would allow for 10{sup 5} better signal-to-noise ratio than CAST, and search for solar axions with g{sub a}γ down to few 10{sup 12} GeV{sup −1}, well into unexplored axion parameter space. In addition, a scaled-up version of these TPCs, properly shielded and placed underground, can be competitive in the search for low-mass WIMPs. The TREX-DM prototype, with ∼ 0.300 kg of Ar at 10 bar, or alternatively ∼ 0.160 kg of Ne at 10 bar, and energy threshold well below 1 keV, has been built to test this concept. We will describe the main technical solutions developed, as well as the results from the commissioning phase on surface. The anticipated sensitivity of this technique might reach ∼10{sup −44} cm{sup 2} for low mass (<10 GeV) WIMPs, well beyond current experimental limits in this mass range.« less

Escherichia coli tatC mutations that suppress defective twin-arginine transporter signal peptides.

PubMed

Strauch, Eva-Maria; Georgiou, George

2007-11-23

In vitro studies have suggested that the TatBC complex serves as the receptor for signal peptides targeted for export via the twin-arginine translocation (Tat) pathway. Substitution of the hallmark twin-arginine dipeptide with two lysines abrogates export of physiological substrates in all organisms. We report the isolation and characterization of suppressor mutations that allow export of an ssTor(KK)-GFP-SsrA tripartite fusion. We identified two amino acid suppressor mutations in the first cytoplasmic loop of TatC. In addition, two other amino acids in the first cytoplasmic loop exhibit epistatic suppression. Surprisingly, we also identified a suppressor mutation predicted to lie within the second periplasmic loop of TatC, a region that is not expected to interact directly with the signal peptide. The suppressor mutations allowed export of the native Esherichia coli Tat substrate trimethylamine N-oxide reductase with a twin-lysine substitution in its signal sequence. The cytoplasmic suppressor mutations conferred SDS sensitivity and partial filamentation, indicating that Tat export of authentic substrates was impaired.

SLY1 and Syntaxin 18 specify a distinct pathway for procollagen VII export from the endoplasmic reticulum

PubMed Central

Nogueira, Cristina; Erlmann, Patrik; Villeneuve, Julien; Santos, António JM; Martínez-Alonso, Emma; Martínez-Menárguez, José Ángel; Malhotra, Vivek

2014-01-01

TANGO1 binds and exports Procollagen VII from the endoplasmic reticulum (ER). In this study, we report a connection between the cytoplasmic domain of TANGO1 and SLY1, a protein that is required for membrane fusion. Knockdown of SLY1 by siRNA arrested Procollagen VII in the ER without affecting the recruitment of COPII components, general protein secretion, and retrograde transport of the KDEL-containing protein BIP, and ERGIC53. SLY1 is known to interact with the ER-specific SNARE proteins Syntaxin 17 and 18, however only Syntaxin 18 was required for Procollagen VII export. Neither SLY1 nor Syntaxin 18 was required for the export of the equally bulky Procollagen I from the ER. Altogether, these findings reveal the sorting of bulky collagen family members by TANGO1 at the ER and highlight the existence of different export pathways for secretory cargoes one of which is mediated by the specific SNARE complex containing SLY1 and Syntaxin 18. DOI: http://dx.doi.org/10.7554/eLife.02784.001 PMID:24842878

Inferring tidal wetland stability from channel sediment fluxes: observations and a conceptual model

USGS Publications Warehouse

Ganju, Neil K.; Nidzieko, Nicholas J.; Kirwan, Matthew L.

2013-01-01

Anthropogenic and climatic forces have modified the geomorphology of tidal wetlands over a range of timescales. Changes in land use, sediment supply, river flow, storminess, and sea level alter the layout of tidal channels, intertidal flats, and marsh plains; these elements define wetland complexes. Diagnostically, measurements of net sediment fluxes through tidal channels are high-temporal resolution, spatially integrated quantities that indicate (1) whether a complex is stable over seasonal timescales and (2) what mechanisms are leading to that state. We estimated sediment fluxes through tidal channels draining wetland complexes on the Blackwater and Transquaking Rivers, Maryland, USA. While the Blackwater complex has experienced decades of degradation and been largely converted to open water, the Transquaking complex has persisted as an expansive, vegetated marsh. The measured net export at the Blackwater complex (1.0 kg/s or 0.56 kg/m2/yr over the landward marsh area) was caused by northwesterly winds, which exported water and sediment on the subtidal timescale; tidally forced net fluxes were weak and precluded landward transport of suspended sediment from potential seaward sources. Though wind forcing also exported sediment at the Transquaking complex, strong tidal forcing and proximity to a turbidity maximum led to an import of sediment (0.031 kg/s or 0.70 kg/m2/yr). This resulted in a spatially averaged accretion of 3.9 mm/yr, equaling the regional relative sea level rise. Our results suggest that in areas where seaward sediment supply is dominant, seaward wetlands may be more capable of withstanding sea level rise over the short term than landward wetlands. We propose a conceptual model to determine a complex's tendency toward stability or instability based on sediment source, wetland channel location, and transport mechanisms. Wetlands with a reliable portfolio of sources and transport mechanisms appear better suited to offset natural and anthropogenic loss.

Effects of Light Quality and Intensity on Diurnal Patterns and Rates of Photo-Assimilate Translocation and Transpiration in Tomato Leaves.

PubMed

Lanoue, Jason; Leonardos, Evangelos D; Grodzinski, Bernard

2018-01-01

Translocation of assimilates is a fundamental process involving carbon and water balance affecting source/sink relationships. Diurnal patterns of CO 2 exchange, translocation (carbon export), and transpiration of an intact tomato source leaf were determined during 14 CO 2 steady-state labeling under different wavelengths at three pre-set photosynthetic rates. Daily patterns showed that photosynthesis and export were supported by all wavelengths of light tested including orange and green. Export in the light, under all wavelengths was always higher than that at night. Export in the light varied from 65-83% of the total daily carbon fixed, depending on light intensity. Photosynthesis and export were highly correlated under all wavelengths ( r = 0.90-0.96). Export as a percentage of photosynthesis (relative export) decreased as photosynthesis increased by increasing light intensity under all wavelengths. These data indicate an upper limit for export under all spectral conditions. Interestingly, only at the medium photosynthetic rate, relative export under the blue and the orange light-emitting diodes (LEDs) were higher than under white and red-white LEDs. Stomatal conductance, transpiration rates, and water-use-efficiency showed similar daily patterns under all wavelengths. Illuminating tomato leaves with different spectral quality resulted in similar carbon export rates, but stomatal conductance and transpiration rates varied due to wavelength specific control of stomatal function. Thus, we caution that the link between transpiration and C-export may be more complex than previously thought. In summary, these data indicate that orange and green LEDs, not simply the traditionally used red and blue LEDs, should be considered and tested when designing lighting systems for optimizing source leaf strength during plant production in controlled environment systems. In addition, knowledge related to the interplay between water and C-movement within a plant and how they are affected by environmental stimuli, is needed to develop a better understanding of source/sink relationships.

Effects of Light Quality and Intensity on Diurnal Patterns and Rates of Photo-Assimilate Translocation and Transpiration in Tomato Leaves

PubMed Central

Lanoue, Jason; Leonardos, Evangelos D.; Grodzinski, Bernard

2018-01-01

Translocation of assimilates is a fundamental process involving carbon and water balance affecting source/sink relationships. Diurnal patterns of CO2 exchange, translocation (carbon export), and transpiration of an intact tomato source leaf were determined during 14CO2 steady-state labeling under different wavelengths at three pre-set photosynthetic rates. Daily patterns showed that photosynthesis and export were supported by all wavelengths of light tested including orange and green. Export in the light, under all wavelengths was always higher than that at night. Export in the light varied from 65–83% of the total daily carbon fixed, depending on light intensity. Photosynthesis and export were highly correlated under all wavelengths (r = 0.90–0.96). Export as a percentage of photosynthesis (relative export) decreased as photosynthesis increased by increasing light intensity under all wavelengths. These data indicate an upper limit for export under all spectral conditions. Interestingly, only at the medium photosynthetic rate, relative export under the blue and the orange light-emitting diodes (LEDs) were higher than under white and red-white LEDs. Stomatal conductance, transpiration rates, and water-use-efficiency showed similar daily patterns under all wavelengths. Illuminating tomato leaves with different spectral quality resulted in similar carbon export rates, but stomatal conductance and transpiration rates varied due to wavelength specific control of stomatal function. Thus, we caution that the link between transpiration and C-export may be more complex than previously thought. In summary, these data indicate that orange and green LEDs, not simply the traditionally used red and blue LEDs, should be considered and tested when designing lighting systems for optimizing source leaf strength during plant production in controlled environment systems. In addition, knowledge related to the interplay between water and C-movement within a plant and how they are affected by environmental stimuli, is needed to develop a better understanding of source/sink relationships. PMID:29915612

Quantifying export production in the Southern Ocean: Implications for the Baxs proxy

NASA Astrophysics Data System (ADS)

Hernandez-Sanchez, Maria T.; Mills, Rachel A.; Planquette, HéLèNe; Pancost, Richard D.; Hepburn, Laura; Salter, Ian; Fitzgeorge-Balfour, Tania

2011-12-01

The water column and sedimentary Baxs distribution around the Crozet Plateau is used to decipher the controls and timing of barite formation and to evaluate how export production signals are recorded in sediments underlying a region of natural Fe fertilization within the Fe limited Southern Ocean. Export production estimated from preserved, vertical sedimentary Baxs accumulation rates are compared with published export fluxes assessed from an integrated study of the biological carbon pump to determine the validity of Baxs as a quantitative proxy under different Fe supply conditions typical of the Southern Ocean. Detailed assessment of the geochemical partitioning of Ba in sediments and the lithogenic end-member allows appropriate correction of the bulk Ba content and determination of the Baxs content of sediments and suspended particles. The upper water column distribution of Baxs is extremely heterogeneous spatially and temporally. Organic carbon/Baxs ratios in deep traps from the Fe fertilized region are similar to other oceanic settings allowing quantification of the inferred carbon export based on established algorithms. There appears to be some decoupling of POC and Ba export in the Fe limited region south of the Plateau. The export production across the Crozet Plateau inferred from the Baxs sedimentary proxy indicates that the Fe fertilized area to the north of the Plateau experiences enhanced export relative to equivalent Southern Ocean settings throughout the Holocene and that this influence may also have impacted the site to the south for significant periods. This interpretation is corroborated by alternative productivity proxies (opal accumulation, 231Paxs/230Thxs). Baxs can be used to quantify export production in complex settings such as naturally Fe-fertilized (volcanoclastic) areas, providing appropriate lithogenic correction is undertaken, and sediment focusing is corrected for along with evaluation of barite preservation.

Synonymous mutations in RNASEH2A create cryptic splice sites impairing RNase H2 enzyme function in Aicardi-Goutières syndrome.

PubMed

Rice, Gillian I; Reijns, Martin A M; Coffin, Stephanie R; Forte, Gabriella M A; Anderson, Beverley H; Szynkiewicz, Marcin; Gornall, Hannah; Gent, David; Leitch, Andrea; Botella, Maria P; Fazzi, Elisa; Gener, Blanca; Lagae, Lieven; Olivieri, Ivana; Orcesi, Simona; Swoboda, Kathryn J; Perrino, Fred W; Jackson, Andrew P; Crow, Yanick J

2013-08-01

Aicardi-Goutières syndrome is an inflammatory disorder resulting from mutations in TREX1, RNASEH2A/2B/2C, SAMHD1, or ADAR1. Here, we provide molecular, biochemical, and cellular evidence for the pathogenicity of two synonymous variants in RNASEH2A. Firstly, the c.69G>A (p.Val23Val) mutation causes the formation of a splice donor site within exon 1, resulting in an out of frame deletion at the end of exon 1, leading to reduced RNase H2 protein levels. The second mutation, c.75C>T (p.Arg25Arg), also introduces a splice donor site within exon 1, and the internal deletion of 18 amino acids. The truncated protein still forms a heterotrimeric RNase H2 complex, but lacks catalytic activity. However, as a likely result of leaky splicing, a small amount of full-length active protein is apparently produced in an individual homozygous for this mutation. Recognition of the disease causing status of these variants allows for diagnostic testing in relevant families. © 2013 WILEY PERIODICALS, INC.

Structural and functional analysis of mRNA export regulation by the nuclear pore complex.

PubMed

Lin, Daniel H; Correia, Ana R; Cai, Sarah W; Huber, Ferdinand M; Jette, Claudia A; Hoelz, André

2018-06-13

The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP 6 , unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1•Nup42•DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans.

CD151, a novel host factor of nuclear export signaling in influenza virus infection.

PubMed

Qiao, Yongkang; Yan, Yan; Tan, Kai Sen; Tan, Sheryl S L; Seet, Ju Ee; Arumugam, Thiruma Valavan; Chow, Vincent T K; Wang, De Yun; Tran, Thai

2018-05-01

Despite advances in our understanding of the mechanisms of influenza A virus (IAV) infection, the crucial virus-host interactions during the viral replication cycle still remain incomplete. Tetraspanin CD151 is highly expressed in the human respiratory tract, but its pathological role in IAV infection is unknown. We sought to characterize the functional role and mechanisms of action of CD151 in IAV infection of the upper and lower respiratory tracts with H1N1 and H3N2 strains. We used CD151-null mice in an in vivo model of IAV infection and clinical donor samples of in vitro-differentiated human nasal epithelial cells cultured at air-liquid interface. As compared with wild-type infected mice, CD151-null infected mice exhibited a significant reduction in virus titer and improvement in survival that is associated with pronounced host antiviral response and inflammasome activation together with accelerated lung repair. Interestingly, we show that CD151 complexes newly synthesized viral proteins with host nuclear export proteins and stabilizes microtubule complexes, which are key processes necessary for the polarized trafficking of viral progeny to the host plasma membrane for assembly. Our results provide new mechanistic insights into our understanding of IAV infection. We show that CD151 is a critical novel host factor of nuclear export signaling whereby the IAV nuclear export uses it to complement its own nuclear export proteins (a site not targeted by current therapy), making this regulation unique, and holds promise for the development of novel alternative/complementary strategies to reduce IAV severity. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

The role of TcdB and TccC subunits in secretion of the Photorhabdus Tcd toxin complex.

PubMed

Yang, Guowei; Waterfield, Nicholas R

2013-01-01

The Toxin Complex (TC) is a large multi-subunit toxin encoded by a range of bacterial pathogens. The best-characterized examples are from the insect pathogens Photorhabdus, Xenorhabdus and Yersinia. They consist of three large protein subunits, designated A, B and C that assemble in a 5∶1∶1 stoichiometry. Oral toxicity to a range of insects means that some have the potential to be developed as pest control technology. The three subunit proteins do not encode any recognisable export sequences and as such little progress has been made in understanding their secretion. We have developed heterologous TC production and secretion models in E. coli and used them to ascribe functions to different domains of the crucial B+C sub-complex. We have determined that the B and C subunits use a secretion mechanism that is either encoded by the proteins themselves or employ an as yet undefined system common to laboratory strains of E. coli. We demonstrate that both the N-terminal domains of the B and C subunits are required for secretion of the whole complex. We propose a model whereby the N-terminus of the C-subunit toxin exports the B+C sub-complex across the inner membrane while that of the B-subunit allows passage across the outer membrane. We also demonstrate that even in the absence of the B-subunit, that the C-subunit can also facilitate secretion of the larger A-subunit. The recognition of this novel export system is likely to be of importance to future protein secretion studies. Finally, the identification of homologues of B and C subunits in diverse bacterial pathogens, including Burkholderia and Pseudomonas, suggests that these toxins are likely to be important in a range of different hosts, including man.

Putative members of the Arabidopsis Nup107-160 nuclear pore sub-complex contribute to pathogen defense.

PubMed

Wiermer, Marcel; Cheng, Yu Ti; Imkampe, Julia; Li, Meilan; Wang, Dongmei; Lipka, Volker; Li, Xin

2012-06-01

In eukaryotic cells, transduction of external stimuli into the nucleus to induce transcription and export of mRNAs for translation in the cytoplasm is mediated by nuclear pore complexes (NPCs) composed of nucleoporin proteins (Nups). We previously reported that Arabidopsis MOS3, encoding the homolog of vertebrate Nup96, is required for plant immunity and constitutive resistance mediated by the de-regulated Toll interleukin 1 receptor/nucleotide-binding/leucine-rich repeat (TNL)-type R gene snc1. In vertebrates, Nup96 is a component of the conserved Nup107-160 nuclear pore sub-complex, and implicated in immunity-related mRNA export. Here, we used a reverse genetics approach to examine the requirement for additional subunits of the predicted Arabidopsis Nup107-160 complex in plant immunity. We show that, among eight putative complex members, beside MOS3, only plants with defects in Nup160 or Seh1 are impaired in basal resistance. Constitutive resistance in the snc1 mutant and immunity mediated by TNL-type R genes also depend on functional Nup160 and have a partial requirement for Seh1. Conversely, resistance conferred by coiled coil-type immune receptors operates largely independently of both genes, demonstrating specific contributions to plant defense signaling. Our functional analysis further revealed that defects in nup160 and seh1 result in nuclear accumulation of poly(A) mRNA, and, in the case of nup160, considerable depletion of EDS1, a key positive regulator of basal and TNL-triggered resistance. These findings suggest that Nup160 is required for nuclear mRNA export and full expression of EDS1-conditioned resistance pathways in Arabidopsis. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

A biochemical framework for eIF4E-dependent mRNA export and nuclear recycling of the export machinery.

PubMed

Volpon, Laurent; Culjkovic-Kraljacic, Biljana; Sohn, Hye Seon; Blanchet-Cohen, Alexis; Osborne, Michael J; Borden, Katherine L B

2017-06-01

The eukaryotic translation initiation factor eIF4E acts in the nuclear export and translation of a subset of mRNAs. Both of these functions contribute to its oncogenic potential. While the biochemical mechanisms that underlie translation are relatively well understood, the molecular basis for eIF4E's role in mRNA export remains largely unexplored. To date, over 3000 transcripts, many encoding oncoproteins, were identified as potential nuclear eIF4E export targets. These target RNAs typically contain a ∼50-nucleotide eIF4E sensitivity element (4ESE) in the 3' UTR and a 7-methylguanosine cap on the 5' end. While eIF4E associates with the cap, an unknown factor recognizes the 4ESE element. We previously identified cofactors that functionally interacted with eIF4E in mammalian cell nuclei including the leucine-rich pentatricopeptide repeat protein LRPPRC and the export receptor CRM1/XPO1. LRPPRC simultaneously interacts with both eIF4E bound to the 5' mRNA cap and the 4ESE element in the 3' UTR. In this way, LRPPRC serves as a specificity factor to recruit 4ESE-containing RNAs within the nucleus. Further, we show that CRM1 directly binds LRPPRC likely acting as the export receptor for the LRPPRC-eIF4E-4ESE RNA complex. We also found that Importin 8, the nuclear importer for cap-free eIF4E, imports RNA-free LRPPRC, potentially providing both coordinated nuclear recycling of the export machinery and an important surveillance mechanism to prevent futile export cycles. Our studies provide the first biochemical framework for the eIF4E-dependent mRNA export pathway. © 2017 Volpon et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A large homozygous deletion in the SAMHD1 gene causes atypical Aicardi–Goutiéres syndrome associated with mtDNA deletions

PubMed Central

Leshinsky-Silver, Esther; Malinger, Gustavo; Ben-Sira, Liat; Kidron, Dvora; Cohen, Sarit; Inbar, Shani; Bezaleli, Tali; Levine, Arie; Vinkler, Chana; Lev, Dorit; Lerman-Sagie, Tally

2011-01-01

Aicardi–Goutiéres syndrome (AGS) is a genetic neurodegenerative disorder with clinical symptoms mimicking a congenital viral infection. Five causative genes have been described: three prime repair exonuclease1 (TREX1), ribonucleases H2A, B and C, and most recently SAM domain and HD domain 1 (SAMHD1). We performed a detailed clinical and molecular characterization of a family with autosomal recessive neurodegenerative disorder showing white matter destruction and calcifications, presenting in utero and associated with multiple mtDNA deletions. A muscle biopsy was normal and did not show any evidence of respiratory chain dysfunction. Southern blot analysis of tissue from a living child and affected fetuses demonstrated multiple mtDNA deletions. Molecular analysis of genes involved in mtDNA synthesis and maintenance (POLGα, POLGβ, Twinkle, ANT1, TK2, SUCLA1 and DGOUK) revealed normal sequences. Sequencing of TREX1 and ribonucleases H2A, B and C failed to reveal any mutations. Whole-genome homozygosity mapping revealed a candidate region containing the SAMHD1 gene. Sequencing of the gene in the affected child and two affected fetuses revealed a large deletion (9 kb), spanning the promoter, exon1 and intron 1. The parents were found to be heterozygous for this deletion. The identification of a homozygous large deletion in the SAMHD1 gene causing atypical AGS with multiple mtDNA deletions may add information regarding the involvement of mitochondria in self-activation of innate immunity by cell intrinsic components. PMID:21102625

Assay development of inducible human renal phosphate transporter Npt2A (SLC34A1) in Flp-In-Trex-HEK293 cells.

PubMed

Wu, Hongzhong; Mao, Chonghong; Duenstl, Georg; Su, Wan; Qian, Su

2013-12-05

Hyperphosphatemia is associated with severe decline of renal function in chronic kidney disease and elevates cardiovascular mortality. Type II sodium dependent phosphate transporter 2A (Npt2A) plays a major role in renal phosphate reabsorption and could be explored as a target for anti-hyperphosphatemia therapy. Human Npt2A transporter activity was examined upon transfection into CHO, MDCK, HEK293, Flp-In-CHO and Flp-In-HEK293 cells. Only kidney-derived cells expressed functional Npt2A. HEK293 and Flp-In-HEK293 cell lines stably transfected with hNpt2A could be selected, but these cells were inactive in phosphate transport. This suggests that high-level, constitutive Npt2A expression has deleterious effects on the cell. By using the conditional promoter in the Flp-In-Trex vector, functional expression of Npt2A was achieved by doxycycline induction in HEK293 cells. The EGFP tagged and non-tagged, inducible stable hNpt2A-HEK293 cell lines afforded development of a robust phosphate uptake assay mediated by hNpt2A, which can be used to screen hNpt2A inhibitors and inducers of hNpt2A expression. Using this assay, the small molecule LC-1 was identified as a potent inhibitor of hNpt2A, suggesting that it is feasible to develop potent specific hNpt2A inhibitors to control phosphate overloading for hyperphosphatemia therapy. © 2013 Elsevier B.V. All rights reserved.

Efficient nuclear export of p65-IkappaBalpha complexes requires 14-3-3 proteins.

PubMed

Aguilera, Cristina; Fernández-Majada, Vanessa; Inglés-Esteve, Julia; Rodilla, Verónica; Bigas, Anna; Espinosa, Lluís

2006-09-01

IkappaB are responsible for maintaining p65 in the cytoplasm under non-stimulating conditions and promoting the active export of p65 from the nucleus following NFkappaB activation to terminate the signal. We now show that 14-3-3 proteins regulate the NFkappaB signaling pathway by physically interacting with p65 and IkappaBalpha proteins. We identify two functional 14-3-3 binding domains in the p65 protein involving residues 38-44 and 278-283, and map the interaction region of IkappaBalpha in residues 60-65. Mutation of these 14-3-3 binding domains in p65 or IkappaBalpha results in a predominantly nuclear distribution of both proteins. TNFalpha treatment promotes recruitment of 14-3-3 and IkappaBalpha to NFkappaB-dependent promoters and enhances the binding of 14-3-3 to p65. Disrupting 14-3-3 activity by transfection with a dominant-negative 14-3-3 leads to the accumulation of nuclear p65-IkappaBalpha complexes and the constitutive association of p65 with the chromatin. In this situation, NFkappaB-dependent genes become unresponsive to TNFalpha stimulation. Together our results indicate that 14-3-3 proteins facilitate the nuclear export of IkappaBalpha-p65 complexes and are required for the appropriate regulation of NFkappaB signaling.

Vertical export flux of metals in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Heimbürger, Lars-Eric; Migon, Christophe; Losno, Rémi; Miquel, Juan-Carlos; Thibodeau, Benoît; Stabholz, Marion; Dufour, Aurélie; Leblond, Nathalie

2014-05-01

We examined metal (Al, V, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb) and particulate organic carbon (OC) concentrations of the marine vertical export flux at the DYFAMED time-series station in the Northwestern Mediterranean Sea. We present here the first data set of natural and anthropogenic metals from sediment trap moorings deployed at 1000 m-depth between 2003 and 2007 at the DYFAMED site. A highly significant correlation was observed between most metal concentrations, whatever the nature and emission source of the metal. Cu, Zn and Cd exhibit different behaviors, presumably due to their high solubility and complexation with organic ligands. The observed difference of atmospheric and marine fluxes in terms of temporal variability and elemental concentration suggests that dense water convection and primary production and not atmospheric deposition control the marine vertical export flux. This argument is strengthened by the fact that significant Saharan dust events did not result in concomitant marine vertical export fluxes nor did they generate significant changes in metal concentrations of trapped particles.

mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway.

PubMed

Ávila, Andréa Rodrigues; Cabezas-Cruz, Alexjandro; Gissot, Mathieu

2018-01-25

Control of gene expression is crucial for parasite survival and is the result of a series of processes that are regulated to permit fine-tuning of gene expression in response to biological changes during the life-cycle of apicomplexan parasites. Control of mRNA nuclear export is a key process in eukaryotic cells but is poorly understood in apicomplexan parasites. Here, we review recent knowledge regarding this process with an emphasis on T. gondii. We describe the presence of divergent orthologs and discuss structural and functional differences in export factors between apicomplexans and other eukaryotic lineages. Undoubtedly, the use of the CRISPR/Cas9 system in high throughput screenings associated with the discovery of mRNA nuclear export complexes by proteomic analysis will contribute to identify these divergent factors. Ligand-based or structure-based strategies may be applied to investigate the potential use of these proteins as targets for new antiprotozoal agents.

Thiol-facilitated cell export and desorption of methylmercury by anaerobic bacteria

DOE PAGES

Lin, Hui; Lu, Xia; Liang, Liyuan; ...

2015-09-04

Neurotoxic methylmercury (MeHg), formed by anaerobic bacteria, is shown to be rapidly excreted from the cell, but the mechanism of this process is unclear. Using both Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132 strains, we investigated the factors affecting export and distribution of MeHg in mercury methylation and MeHg sorption-desorption assays. Thiols, such as cysteine, were found to greatly facilitate desorption and export of MeHg, particularly by PCA cells. However, in cysteine-free assays (4 h) >90% of the synthesized MeHg was associated with PCA, among which ~73% was sorbed on the cell surface and 19% remained inside the cells. Inmore » comparison, a majority of the MeHg (70%) was exported by ND132, leaving ~20% of the MeHg sorbed on the surface and 10% inside the cells. When MeHg was added directly to the cell suspensions, ND132 adsorbed much lower MeHg but took up more MeHg inside cells than PCA did. These results demonstrate that MeHg export is bacteria strain-specific, time dependent, and is influenced by thiols, implicating important roles of ligand complexation in facilitating MeHg production and mobilization in the environment.« less

Reaction mechanism of the ε subunit of E. coli DNA polymerase III: Insights into active site metal coordination and catalytically significant residues

PubMed Central

Cisneros, G. Andrés; Perera, Lalith; Schaaper, Roel M.; Pedersen, Lars C.; London, Robert E.; Pedersen, Lee G.; Darden, Thomas A.

2009-01-01

The 28kDa ε subunit of Escherichia coli DNA polymerase III is the exonucleotidic proofreader responsible for editing polymerase insertion errors. Here, we study the mechanism by which ε carries out the exonuclease activity. We performed quantum mechanics/molecular mechanics calculations on the N–terminal domain containing the exonuclease activity. Both the free–ε and a complex, ε bound to a θ homolog (HOT), were studied. For the ε–HOT complex, Mg2+ or Mn2+ were investigated as the essential divalent metal cofactors, while only Mg2+ was used for free–ε. In all calculations, a water molecule bound to the catalytic metal acts as the nucleophile for the hydrolysis of the phosphate bond. Initially, a direct proton transfer to H162 is observed. Subsequently, the nucleophilic attack takes place, followed by a second proton transfer to E14. Our results show that the reaction catalyzed with Mn2+ is faster than with Mg2+, in agreement with experiment. In addition, the ε–HOT complex shows a slightly lower energy barrier compared to free–ε. In all cases the catalytic metal is observed to be penta–coordinated. Charge and frontier orbital analyses suggest that charge transfer may stabilize the penta–coordination. Energy decomposition analysis to study the contribution of each residue to catalysis suggests that there are several important residues. Among these, H98, D103, D129 and D146 have been implicated in catalysis by mutagenesis studies. Some of these residues were found to be structurally conserved on human TREX1, the exonuclease domains from E. coli DNA–Pol I, and the DNA polymerase of bacteriophage RB69. PMID:19119875

Plasmepsin V licenses Plasmodium proteins for export into the host erythrocyte.

PubMed

Russo, Ilaria; Babbitt, Shalon; Muralidharan, Vasant; Butler, Tamira; Oksman, Anna; Goldberg, Daniel E

2010-02-04

During their intraerythrocytic development, malaria parasites export hundreds of proteins to remodel their host cell. Nutrient acquisition, cytoadherence and antigenic variation are among the key virulence functions effected by this erythrocyte takeover. Proteins destined for export are synthesized in the endoplasmic reticulum (ER) and cleaved at a conserved (PEXEL) motif, which allows translocation into the host cell via an ATP-driven translocon called the PTEX complex. We report that plasmepsin V, an ER aspartic protease with distant homology to the mammalian processing enzyme BACE, recognizes the PEXEL motif and cleaves it at the correct site. This enzyme is essential for parasite viability and ER residence is essential for its function. We propose that plasmepsin V is the PEXEL protease and is an attractive enzyme for antimalarial drug development.

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

PubMed Central

Kolodkin, Alexey N; Bruggeman, Frank J; Plant, Nick; Moné, Martijn J; Bakker, Barbara M; Campbell, Moray J; van Leeuwen, Johannes P T M; Carlberg, Carsten; Snoep, Jacky L; Westerhoff, Hans V

2010-01-01

The topology of nuclear receptor (NR) signaling is captured in a systems biological graphical notation. This enables us to identify a number of ‘design' aspects of the topology of these networks that might appear unnecessarily complex or even functionally paradoxical. In realistic kinetic models of increasing complexity, calculations show how these features correspond to potentially important design principles, e.g.: (i) cytosolic ‘nuclear' receptor may shuttle signal molecules to the nucleus, (ii) the active export of NRs may ensure that there is sufficient receptor protein to capture ligand at the cytoplasmic membrane, (iii) a three conveyor belts design dissipating GTP-free energy, greatly aids response, (iv) the active export of importins may prevent sequestration of NRs by importins in the nucleus and (v) the unspecific nature of the nuclear pore may ensure signal-flux robustness. In addition, the models developed are suitable for implementation in specific cases of NR-mediated signaling, to predict individual receptor functions and differential sensitivity toward physiological and pharmacological ligands. PMID:21179018

Iron and silicon isotope behaviour accompanying weathering in Icelandic soils, and the implications for iron export from peatlands

NASA Astrophysics Data System (ADS)

Opfergelt, S.; Williams, H. M.; Cornelis, J. T.; Guicharnaud, R. A.; Georg, R. B.; Siebert, C.; Gislason, S. R.; Halliday, A. N.; Burton, K. W.

2017-11-01

Incipient warming of peatlands at high latitudes is expected to modify soil drainage and hence the redox conditions, which has implications for Fe export from soils. This study uses Fe isotopes to assess the processes controlling Fe export in a range of Icelandic soils including peat soils derived from the same parent basalt, where Fe isotope variations principally reflect differences in weathering and drainage. In poorly weathered, well-drained soils (non-peat soils), the limited Fe isotope fractionation in soil solutions relative to the bulk soil (Δ57Fesolution-soil = -0.11 ± 0.12‰) is attributed to proton-promoted mineral dissolution. In the more weathered poorly drained soils (peat soils), the soil solutions are usually lighter than the bulk soil (Δ57Fesolution-soil = -0.41 ± 0.32‰), which indicates that Fe has been mobilised by reductive mineral dissolution and/or ligand-controlled dissolution. The results highlight the presence of Fe-organic complexes in solution in anoxic conditions. An additional constraint on soil weathering is provided by Si isotopes. The Si isotope composition of the soil solutions relative to the soil (Δ30Sisolution-soil = 0.92 ± 0.26‰) generally reflects the incorporation of light Si isotopes in secondary aluminosilicates. Under anoxic conditions in peat soils, the largest Si isotope fractionation in soil solutions relative to the bulk soil is observed (Δ30Sisolution-soil = 1.63 ± 0.40‰) and attributed to the cumulative contribution of secondary clay minerals and amorphous silica precipitation. Si supersaturation in solution with respect to amorphous silica is reached upon freezing when Al availability to form aluminosilicates is limited by the affinity of Al for metal-organic complexes. Therefore, the precipitation of amorphous silica in peat soils indirectly supports the formation of metal-organic complexes in poorly drained soils. These observations highlight that in a scenario of decreasing soil drainage with warming high latitude peatlands, Fe export from soils as Fe-organic complexes will increase, which in turn has implications for Fe transport in rivers, and ultimately the delivery of Fe to the oceans.

Transforming growth factor beta-independent shuttling of Smad4 between the cytoplasm and nucleus.

PubMed

Pierreux, C E; Nicolás, F J; Hill, C S

2000-12-01

Smad4 plays a pivotal role in all transforming growth factor beta (TGF-beta) signaling pathways. Here we describe six widely expressed alternatively spliced variants of human Smad4 with deletions of different exons in the linker, the region of Smad4 that separates the two well-conserved MH1 and MH2 domains. All these Smad4 variants form complexes with activated Smad2 and Smad3 and are incorporated into DNA-binding complexes with the transcription factor Fast-1, regardless of the amount of linker they contain. However, sequences encoded by exons 5 to 7 in the linker are essential for transcriptional activation. Most importantly, our observation that different Smad4 isoforms have different subcellular localizations has led us to the identification of a functional CRM1-dependent nuclear export signal in the Smad4 linker and a constitutively active nuclear localization signal in the N-terminal MH1 domain. In the absence of TGF-beta signaling, we conclude that Smad4 is rapidly and continuously shuttling between the nucleus and the cytoplasm, the distribution of Smad4 between the nucleus and the cytoplasm being dictated by the relative strengths of the nuclear import and export signals. We demonstrate that inhibition of CRM1-mediated nuclear export by treatment of cells with leptomycin B results in endogenous Smad4 accumulating very rapidly in the nucleus. Endogenous Smad2 and Smad3 are completely unaffected by leptomycin B treatment, indicating that the nucleocytoplasmic shuttling is specific for Smad4. We propose that, upon TGF-beta signaling, complex formation between Smad4 and activated Smad2 or -3 leads to nuclear accumulation of Smad4 through inhibition of its nuclear export. We demonstrate that after prolonged TGF-beta signaling Smad2 becomes dephosphorylated and Smad2 and Smad4 accumulate back in the cytoplasm.

Transforming Growth Factor β-Independent Shuttling of Smad4 between the Cytoplasm and Nucleus

PubMed Central

Pierreux, Christophe E.; Nicolás, Francisco J.; Hill, Caroline S.

2000-01-01

Smad4 plays a pivotal role in all transforming growth factor β (TGF-β) signaling pathways. Here we describe six widely expressed alternatively spliced variants of human Smad4 with deletions of different exons in the linker, the region of Smad4 that separates the two well-conserved MH1 and MH2 domains. All these Smad4 variants form complexes with activated Smad2 and Smad3 and are incorporated into DNA-binding complexes with the transcription factor Fast-1, regardless of the amount of linker they contain. However, sequences encoded by exons 5 to 7 in the linker are essential for transcriptional activation. Most importantly, our observation that different Smad4 isoforms have different subcellular localizations has led us to the identification of a functional CRM1-dependent nuclear export signal in the Smad4 linker and a constitutively active nuclear localization signal in the N-terminal MH1 domain. In the absence of TGF-β signaling, we conclude that Smad4 is rapidly and continuously shuttling between the nucleus and the cytoplasm, the distribution of Smad4 between the nucleus and the cytoplasm being dictated by the relative strengths of the nuclear import and export signals. We demonstrate that inhibition of CRM1-mediated nuclear export by treatment of cells with leptomycin B results in endogenous Smad4 accumulating very rapidly in the nucleus. Endogenous Smad2 and Smad3 are completely unaffected by leptomycin B treatment, indicating that the nucleocytoplasmic shuttling is specific for Smad4. We propose that, upon TGF-β signaling, complex formation between Smad4 and activated Smad2 or -3 leads to nuclear accumulation of Smad4 through inhibition of its nuclear export. We demonstrate that after prolonged TGF-β signaling Smad2 becomes dephosphorylated and Smad2 and Smad4 accumulate back in the cytoplasm. PMID:11074002

The ins and outs of nuclear re-export of retrogradely transported tRNAs in Saccharomyces cerevisiae

PubMed Central

Pierce, Jacqueline B; Eswara, Manoja BK

2010-01-01

In Saccharomyces cerevisiae intron-containing pre-tRNAs are exported from the nucleus to the cytoplasm for removal of the introns, and the spliced tRNAs are returned to the nucleus for reasons that are not understood. The re-imported spliced tRNAs are then subjected to aminoacylation in the nucleolus to ensure that they are functional prior to re-export to the cytoplasm. Previous studies have shown that re-imported spliced tRNAs and mature tRNAs made entirely in the nucleus from intronless precursors are retained in the nucleus of S. cerevisiae in response to glucose, amino acid, nitrogen or inorganic phosphate deprivation. Contrary to these studies, we recently reported that starvation of S. cerevisiae of amino acids or nitrogen results in nuclear accumulation of re-imported spliced tRNAs, but not tRNAs made from intronless precursors. This finding suggests that separate pathways are used for nuclear export of retrogradely transported spliced tRNAs and tRNAs made from intronless pre-tRNAs. In addition, the data support the conclusion that the nuclear re-export pathway for retrogradely transported spliced tRNAs, but not the pathway responsible for nuclear export of tRNAs derived from intronless precursors is regulated during amino acid or nitrogen starvation. This regulation appears to occur at a step after the re-imported spliced tRNAs have undergone aminoacylation quality assurance and, in part, involves the TORC1 signalling pathway. Moreover, it was established that Utp9p is an intranuclear component that only facilitates nuclear re-export of retrogradely transported spliced tRNAs by the β-karyopherin Msn5p. Utp9p acts in concert with Utp8p, a key player in nuclear tRNA export in S. cerevisiae, to translocate aminoacylated re-imported spliced tRNAs from the nucleolus to Msn5p and assist with formation of the Msn5p-tRNA-Gsp1p-GTP export complex. This pathway, however, is not the only one responsible for nuclear re-export of retrogradely transported spliced tRNAs. PMID:21327067

Cooperativity among Rev-Associated Nuclear Export Signals Regulates HIV-1 Gene Expression and Is a Determinant of Virus Species Tropism

PubMed Central

Aligeti, Mounavya; Behrens, Ryan T.; Pocock, Ginger M.; Schindelin, Johannes; Dietz, Christian; Eliceiri, Kevin W.; Swanson, Chad M.; Malim, Michael H.; Ahlquist, Paul

2014-01-01

ABSTRACT Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to intron-containing viral mRNAs encoding the Rev response element (RRE), thereby facilitating viral late gene expression. Here we exploited murine 3T3 fibroblasts as a gain-of-function system to study hCRM1's species-specific role in regulating Rev's effector functions. We show that Rev is rapidly exported from the nucleus by mCRM1 despite only weak contributions to HIV-1's posttranscriptional stages. Indeed, Rev preferentially accumulates in the cytoplasm of murine 3T3 cells with or without hCRM1 expression, in contrast to human HeLa cells, where Rev exhibits striking en masse transitions between the nuclear and cytoplasmic compartments. Efforts to bias Rev's trafficking either into or out of the nucleus revealed that Rev encoding a second CRM1 binding domain (Rev-2xNES) or Rev-dependent viral gag-pol mRNAs bearing tandem RREs (GP-2xRRE), rescue virus particle production in murine cells even in the absence of hCRM1. Combined, these results suggest a model wherein Rev-associated nuclear export signals cooperate to regulate the number or quality of CRM1's interactions with viral Rev/RRE ribonucleoprotein complexes in the nucleus. This mechanism regulates CRM1-dependent viral gene expression and is a determinant of HIV-1's capacity to produce virions in nonhuman cell types. IMPORTANCE Cells derived from mice and other nonhuman species exhibit profound blocks to HIV-1 replication. Here we elucidate a block to HIV-1 gene expression attributable to the murine version of the CRM1 (mCRM1) nuclear export receptor. In human cells, hCRM1 regulates the nuclear export of viral intron-containing mRNAs through the activity of the viral Rev adapter protein that forms a multimeric complex on these mRNAs prior to recruiting hCRM1. We demonstrate that Rev-dependent gene expression is poor in murine cells despite the finding that, surprisingly, the bulk of Rev interacts efficiently with mCRM1 and is rapidly exported from the nucleus. Instead, we map the mCRM1 defect to the apparent inability of this factor to engage Rev multimers in the context of large viral Rev/RNA ribonucleoprotein complexes. These findings shed new light on HIV-1 gene regulation and could inform the development of novel antiviral strategies that target viral gene expression. PMID:25275125

Protein-Phospholipid Interactions in Nonclassical Protein Secretion: Problem and Methods of Study

PubMed Central

Prudovsky, Igor; Kumar, Thallapuranam Krishnaswamy Suresh; Sterling, Sarah; Neivandt, David

2013-01-01

Extracellular proteins devoid of signal peptides use nonclassical secretion mechanisms for their export. These mechanisms are independent of the endoplasmic reticulum and Golgi. Some nonclassically released proteins, particularly fibroblast growth factors (FGF) 1 and 2, are exported as a result of their direct translocation through the cell membrane. This process requires specific interactions of released proteins with membrane phospholipids. In this review written by a cell biologist, a structural biologist and two membrane engineers, we discuss the following subjects: (i) Phenomenon of nonclassical protein release and its biological significance; (ii) Composition of the FGF1 multiprotein release complex (MRC); (iii) The relationship between FGF1 export and acidic phospholipid externalization; (iv) Interactions of FGF1 MRC components with acidic phospholipids; (v) Methods to study the transmembrane translocation of proteins; (vi) Membrane models to study nonclassical protein release. PMID:23396106

A masked NES in INI1/hSNF5 mediates hCRM1-dependent nuclear export: implications for tumorigenesis

PubMed Central

Craig, Errol; Zhang, Zhi-Kai; Davies, Kelvin P.; Kalpana, Ganjam V.

2002-01-01

INI1 (integrase interactor 1)/hSNF5 is a component of the mammalian SWI/SNF complex and a tumor suppressor mutated in malignant rhabdoid tumors (MRT). We have identified a nuclear export signal (NES) in the highly conserved repeat 2 domain of INI1 that is unmasked upon deletion of a downstream sequence. Mutation of conserved hydrophobic residues within the NES, as well as leptomycin B treatment abrogated the nuclear export. Full-length INI1 specifically associated with hCRM1/exportin1 in vivo and in vitro. A mutant INI1 [INI1(1–319) delG950] found in MRT lacking the 66 C-terminal amino acids mislocalized to the cytoplasm. Full-length INI1 but not the INI1(1–319 delG950) mutant caused flat cell formation and cell cycle arrest in cell lines derived from MRT. Disruption of the NES in the delG950 mutant caused nuclear localization of the protein and restored its ability to cause cell cycle arrest. These observations demonstrate that INI1 has a masked NES that mediates regulated hCRM1/exportin1-dependent nuclear export and we propose that mutations that cause deregulated nuclear export of the protein could lead to tumorigenesis. PMID:11782423

DNA mismatch repair gene polymorphisms affect survival in pancreatic cancer.

PubMed

Dong, Xiaoqun; Li, Yanan; Hess, Kenneth R; Abbruzzese, James L; Li, Donghui

2011-01-01

DNA mismatch repair (MMR) maintains genomic stability and mediates cellular response to DNA damage. We aim to demonstrate whether MMR genetic variants affect overall survival (OS) in pancreatic cancer. Using the Sequenom method in genomic DNA, we retrospectively genotyped 102 single-nucleotide polymorphisms (SNPs) of 13 MMR genes from 706 patients with pancreatic adenocarcinoma seen at The University of Texas MD Anderson Cancer Center. Association between genotype and OS was evaluated using multivariable Cox proportional hazard regression models. At a false discovery rate of 1% (p ≤ .0015), 15 SNPs of EXO1, MLH1, MSH2, MSH3, MSH6, PMS2, PMS2L3, TP73, and TREX1 in patients with localized disease (n = 333) and 6 SNPs of MSH3, MSH6, and TP73 in patients with locally advanced or metastatic disease (n = 373) were significantly associated with OS. In multivariable Cox proportional hazard regression models, SNPs of EXO1, MSH2, MSH3, PMS2L3, and TP73 in patients with localized disease, MSH2, MSH3, MSH6, and TP73 in patients with locally advanced or metastatic disease, and EXO1, MGMT, MSH2, MSH3, MSH6, PMS2L3, and TP73 in all patients remained significant predictors for OS (p ≤ .0015) after adjusting for all clinical predictors and all SNPs with p ≤ .0015 in single-locus analysis. Sixteen haplotypes of EXO1, MLH1, MSH2, MSH3, MSH6, PMS2, PMS2L3, RECQL, TP73, and TREX1 significantly correlated with OS in all patients (p ≤ .001). MMR gene variants may have potential value as prognostic markers for OS in pancreatic cancer patients.

Advanced Compton scattering light source R&D at LLNL

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

Albert, F; Anderson, S G; Anderson, G

2010-02-16

We report the design and current status of a monoenergetic laser-based Compton scattering 0.5-2.5 MeV {gamma}-ray source. Previous nuclear resonance fluorescence results and future linac and laser developments for the source are presented. At MeV photon energies relevant for nuclear processes, Compton scattering light sources are attractive because of their relative compactness and improved brightness above 100 keV, compared to typical 4th generation synchrotrons. Recent progress in accelerator physics and laser technology have enabled the development of a new class of tunable Mono-Energetic Gamma-Ray (MEGa-Ray) light sources based on Compton scattering between a high-brightness, relativistic electron beam and a highmore » intensity laser pulse produced via chirped-pulse amplification (CPA). A new precision, tunable gamma-ray source driven by a compact, high-gradient X-band linac is currently under development and construction at LLNL. High-brightness, relativistic electron bunches produced by an X-band linac designed in collaboration with SLAC will interact with a Joule-class, 10 ps, diode-pumped CPA laser pulse to generate tunable {gamma}-rays in the 0.5-2.5 MeV photon energy range via Compton scattering. Based on the success of the previous Thomson-Radiated Extreme X-rays (T-REX) Compton scattering source at LLNL, the source will be used to excite nuclear resonance fluorescence lines in various isotopes; applications include homeland security, stockpile science and surveillance, nuclear fuel assay, and waste imaging and assay. After a brief presentation of successful nuclear resonance fluorescence (NRF) experiments done with T-REX, the new source design, key parameters, and current status are presented.« less

A Generalizable Platform for Interrogating Target- and Signal-Specific Consequences of Electrophilic Modifications in Redox-Dependent Cell Signaling

PubMed Central

Lin, Hong-Yu; Haegele, Joseph A.; Disare, Michael T.; Lin, Qishan; Aye, Yimon

2015-01-01

Despite the known propensity of small-molecule electrophiles to react with numerous cysteine-active proteins, biological actions of individual signal inducers have emerged to be chemotype-specific. To pinpoint and quantify the impacts of modifying one target out of the whole proteome, we develop a target-protein-personalized “electrophile toolbox” with which specific intracellular targets can be selectively modified at a precise time by specific reactive signals. This general methodology—T-REX (targetable reactive electrophiles & oxidants)—is established by: (1) constructing a platform that can deliver a range of electronic and sterically different bioactive lipid-derived signaling electrophiles to specific proteins in cells; (2) probing the kinetics of targeted delivery concept which revealed that targeting efficiency in cells is largely driven by initial on-rate of alkylation; and (3) evaluating the consequences of protein-target- and small-molecule-signal-specific modifications on the strength of downstream signaling. These data show that T-REX allows quantitative interrogations into the extent to which the Nrf2 transcription factor-dependent antioxidant response element (ARE) signaling is activated by selective electrophilic modifications on Keap1 protein—one of several redox-sensitive regulators of the Nrf2–ARE axis. The results document Keap1 as a promiscuous electrophile-responsive sensor able to respond with similar efficiencies to discrete electrophilic signals, promoting comparable strength of Nrf2–ARE induction. T-REX is also able to elicit cell activation in cases in which whole-cell electrophile flooding fails to stimulate ARE induction prior to causing cytotoxicity. The platform presents a previously unavailable opportunity to elucidate the functional consequences of small-molecule-signal- and protein-target-specific electrophilic modifications in an otherwise unaffected cellular background. PMID:25909755

Subfoveal choroidal thickness predicts macular atrophy in age-related macular degeneration: results from the TREX-AMD trial.

PubMed

Fan, Wenying; Abdelfattah, Nizar Saleh; Uji, Akihito; Lei, Jianqin; Ip, Michael; Sadda, SriniVas R; Wykoff, Charles C

2018-03-01

Our purpose was to evaluate the relationship between subfoveal choroidal thickness (SCT) and development of macular atrophy (MA) in eyes with age-related macular degeneration (AMD). This was a prospective, multicenter study. Sixty participants (120 eyes) in the TREX-AMD trial (NCT01648292) with treatment-naïve neovascular AMD (NVAMD) in at least one eye were included. SCT was measured by certified reading center graders at baseline using spectral domain optical coherence tomography (SDOCT). The baseline SCT was correlated with the presence of MA at baseline and development of incident MA by month 18. Generalized estimating equations were used to account for information from both eyes. Baseline SCT in eyes with MA was statistically significantly less than in those without MA in both the dry AMD (DAMD) (P = 0.04) and NVAMD (P = 0.01) groups. Comparison of baseline SCT between MA developers and non-MA developers revealed a statistically significant difference (P = 0.03). Receiver operating characteristic curve (ROC) analysis showed the cut-off threshold of SCT for predicting the development of MA in cases without MA at baseline was 124 μm (AUC = 0.772; Sensitivity = 0.923; Specificity = 0.5). Among eyes without MA at baseline, those with baseline SCT ≤124 μm were 4.3 times more likely to develop MA (Odds ratio: 4.3, 95% confidence interval: 1.6-12, P = 0.005) than those with baseline SCT >124 μm. Eyes with AMD and MA had less SCT than those without MA. Eyes with less baseline SCT also appear to be at higher risk to develop MA within 18 months.

Decadal and seasonal trends of nutrient concentration and export from highly managed coastal catchments.

PubMed

Wan, Yongshan; Wan, Lei; Li, Yuncong; Doering, Peter

2017-05-15

Understanding anthropogenic and hydro-climatic influences on nutrient concentrations and export from highly managed catchments often necessitates trend detection using long-term monitoring data. This study analyzed the temporal trend (1979-2014) of total nitrogen (TN) and total phosphorus (TP) concentrations and export from four adjacent coastal basins in south Florida where land and water resources are highly managed through an intricate canal network. The method of integrated seasonal-trend decomposition using LOESS (LOcally weighted regrESSion) was employed for trend detection. The results indicated that long-term trends in TN and TP concentrations (increasing/decreasing) varied with basins and nutrient species, reflecting the influence of basin specific land and water management practices. These long-term trends were intervened by short-term highs driven by high rainfall and discharges and lows associated with regional droughts. Seasonal variations in TP were more apparent than for TN. Nutrient export exhibited a chemostatic behavior for TN from all the basins, largely due to the biogenic nature of organic N associated with the ubiquity of organic materials in the managed canal network. Varying degrees of chemodynamic export was present for TP, reflecting complex biogeochemical responses to the legacy of long-term fertilization, low soil P holding capacity, and intensive stormwater management. The anthropogenic and hydro-climatic influences on nutrient concentration and export behavior had great implications in nutrient loading abatement strategies for aquatic ecosystem restoration of the downstream receiving waterbody. Published by Elsevier Ltd.

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.

Cycling of the signaling protein phospholipase D through cilia requires the BBSome only for the export phase

PubMed Central

Brown, Jason M.; Sampaio, Julio L.; Craft, Julie M.; Shevchenko, Andrej; Evans, James E.; Witman, George B.

2013-01-01

The BBSome is a complex of seven proteins, including BBS4, that is cycled through cilia by intraflagellar transport (IFT). Previous work has shown that the membrane-associated signaling protein phospholipase D (PLD) accumulates abnormally in cilia of Chlamydomonas reinhardtii bbs mutants. Here we show that PLD is a component of wild-type cilia but is enriched ∼150-fold in bbs4 cilia; this accumulation occurs progressively over time and results in altered ciliary lipid composition. When wild-type BBSomes were introduced into bbs cells, PLD was rapidly removed from the mutant cilia, indicating the presence of an efficient BBSome-dependent mechanism for exporting ciliary PLD. This export requires retrograde IFT. Importantly, entry of PLD into cilia is BBSome and IFT independent. Therefore, the BBSome is required only for the export phase of a process that continuously cycles PLD through cilia. Another protein, carbonic anhydrase 6, is initially imported normally into bbs4 cilia but lost with time, suggesting that its loss is a secondary effect of BBSome deficiency. PMID:23589493

Mutational definition of functional domains within the Rev homolog encoded by human endogenous retrovirus K.

PubMed

Bogerd, H P; Wiegand, H L; Yang, J; Cullen, B R

2000-10-01

Nuclear export of the incompletely spliced mRNAs encoded by several complex retroviruses, including human immunodeficiency virus type 1 (HIV-1), is dependent on a virally encoded adapter protein, termed Rev in HIV-1, that directly binds both to a cis-acting viral RNA target site and to the cellular Crm1 export factor. Human endogenous retrovirus K, a family of ancient endogenous retroviruses that is not related to the exogenous retrovirus HIV-1, was recently shown to also encode a Crm1-dependent nuclear RNA export factor, termed K-Rev. Although HIV-1 Rev and K-Rev display little sequence identity, they share the ability not only to bind to Crm1 and to RNA but also to form homomultimers and shuttle between nucleus and cytoplasm. We have used mutational analysis to identify sequences in the 105-amino-acid K-Rev protein required for each of these distinct biological activities. While mutations in K-Rev that inactivate any one of these properties also blocked K-Rev-dependent nuclear RNA export, several K-Rev mutants were comparable to wild type when assayed for any of these individual activities yet nevertheless defective for RNA export. Although several nonfunctional K-Rev mutants acted as dominant negative inhibitors of K-Rev-, but not HIV-1 Rev-, dependent RNA export, these were not defined by their inability to bind to Crm1, as is seen with HIV-1 Rev. In total, this analysis suggests a functional architecture for K-Rev that is similar to, but distinct from, that described for HIV-1 Rev and raises the possibility that viral RNA export mediated by the approximately 25 million-year-old K-Rev protein may require an additional cellular cofactor that is not required for HIV-1 Rev function.

COPII-Dependent ER Export: A Critical Component of Insulin Biogenesis and β-Cell ER Homeostasis.

PubMed

Fang, Jingye; Liu, Ming; Zhang, Xuebao; Sakamoto, Takeshi; Taatjes, Douglas J; Jena, Bhanu P; Sun, Fei; Woods, James; Bryson, Tim; Kowluru, Anjaneyulu; Zhang, Kezhong; Chen, Xuequn

2015-08-01

Pancreatic β-cells possess a highly active protein synthetic and export machinery in the endoplasmic reticulum (ER) to accommodate the massive production of proinsulin. ER homeostasis is vital for β-cell functions and is maintained by the delicate balance between protein synthesis, folding, export, and degradation. Disruption of ER homeostasis by diabetes-causing factors leads to β-cell death. Among the 4 components to maintain ER homeostasis in β-cells, the role of ER export in insulin biogenesis is the least understood. To address this knowledge gap, the present study investigated the molecular mechanism of proinsulin ER export in MIN6 cells and primary islets. Two inhibitory mutants of the secretion-associated RAS-related protein (Sar)1 small GTPase, known to specifically block coat protein complex II (COPII)-dependent ER export, were overexpressed in β-cells using recombinant adenoviruses. Results from this approach, as well as small interfering RNA-mediated Sar1 knockdown, demonstrated that defective Sar1 function blocked proinsulin ER export and abolished its conversion to mature insulin in MIN6 cells, isolated mouse, and human islets. It is further revealed, using an in vitro vesicle formation assay, that proinsulin was packaged into COPII vesicles in a GTP- and Sar1-dependent manner. Blockage of COPII-dependent ER exit by Sar1 mutants strongly induced ER morphology change, ER stress response, and β-cell apoptosis. These responses were mediated by the PKR (double-stranded RNA-dependent kinase)-like ER kinase (PERK)/eukaryotic translation initiation factor 2α (p-eIF2α) and inositol-requiring protein 1 (IRE1)/x-box binding protein 1 (Xbp1) pathways but not via activating transcription factor 6 (ATF6). Collectively, results from the study demonstrate that COPII-dependent ER export plays a vital role in insulin biogenesis, ER homeostasis, and β-cell survival.

The RNA Export Factor, Nxt1, Is Required for Tissue Specific Transcriptional Regulation

PubMed Central

Jiang, Jianqiao; White-Cooper, Helen

2013-01-01

The highly conserved, Nxf/Nxt (TAP/p15) RNA nuclear export pathway is important for export of most mRNAs from the nucleus, by interacting with mRNAs and promoting their passage through nuclear pores. Nxt1 is essential for viability; using a partial loss of function allele, we reveal a role for this gene in tissue specific transcription. We show that many Drosophila melanogaster testis-specific mRNAs require Nxt1 for their accumulation. The transcripts that require Nxt1 also depend on a testis-specific transcription complex, tMAC. We show that loss of Nxt1 leads to reduced transcription of tMAC targets. A reporter transcript from a tMAC-dependent promoter is under-expressed in Nxt1 mutants, however the same transcript accumulates in mutants if driven by a tMAC-independent promoter. Thus, in Drosophila primary spermatocytes, the transcription factor used to activate expression of a transcript, rather than the RNA sequence itself or the core transcription machinery, determines whether this expression requires Nxt1. We additionally find that transcripts from intron-less genes are more sensitive to loss of Nxt1 function than those from intron-containing genes and propose a mechanism in which transcript processing feeds back to increase activity of a tissue specific transcription complex. PMID:23754955

Diagnosis of Processes Controlling Dissolved Organic Carbon (DOC) Export in a Subarctic Region by a Dynamic Ecosystem Model

NASA Astrophysics Data System (ADS)

Tang, J.

2015-12-01

Permafrost thawing in high latitudes allows more soil organic carbon (SOC) to become hydrologically accessible. This can increase dissolved organic carbon (DOC) exports and carbon release to the atmosphere as CO2 and CH4, with a positive feedback to regional and global climate warming. However, this portion of carbon loss through DOC export is often neglected in ecosystem models. In this paper, we incorporate a set of DOC-related processes (DOC production, mineralization, diffusion, sorption-desorption and leaching) into an Arctic-enabled version of the dynamic ecosystem model LPJ-GUESS (LPJ-GUESS WHyMe) to mechanistically model the DOC export, and to link this flux to other ecosystem processes. The extended LPJ-GUESS WHyMe with these DOC processes is applied to the Stordalen catchment in northern Sweden. The relative importance of different DOC-related processes for mineral and peatland soils for this region have been explored at both monthly and annual scales based on a detailed variance-based Sobol sensitivity analysis. For mineral soils, the annual DOC export is dominated by DOC fluxes in snowmelt seasons and the peak in spring is related to the runoff passing through top organic rich layers. Two processes, DOC sorption-desorption and production, are found to contribute most to the annual variance in DOC export. For peatland soils, the DOC export during snowmelt seasons is constrained by frozen soils and the processes of DOC production and mineralization, determining the magnitudes of DOC desorption in snowmelt seasons as well as DOC sorption in the rest of months, play the most important role in annual variances of DOC export. Generally, the seasonality of DOC fluxes is closely correlated with runoff seasonality in this region. The current implementation has demonstrated that DOC-related processes in the framework of LPJ-GUESS WHyMe are at an appropriate level of complexity to represent the main mechanism of DOC dynamics in soils. The quantified contributions from different processes on DOC export dynamics could be further linked to the climate change, vegetation composition change and permafrost thawing in this region.

The mammalian RNA-binding protein Staufen2 links nuclear and cytoplasmic RNA processing pathways in neurons.

PubMed

Monshausen, Michaela; Gehring, Niels H; Kosik, Kenneth S

2004-01-01

Members of the Staufen family of RNA-binding proteins are highly conserved cytoplasmic RNA transporters associated with RNA granules. staufen2 is specifically expressed in neurons where the delivery of RNA to dendrites is thought to have a role in plasticity. We found that Staufen2 interacts with the nuclear pore protein p62, with the RNA export protein Tap and with the exon-exon junction complex (EJC) proteins Y14-Mago. The interaction of Staufen2 with the Y14-Mago heterodimer seems to represent a highly conserved complex as the same proteins are involved in the Staufen-mediated localization of oskar mRNA in Drosophila oocytes. A pool of Staufen2 is present in neuronal nuclei and colocalizes to a large degree with p62 and partly with Tap, Y14, and Mago. We suggest a model whereby a set of conserved genes in the oskar mRNA export pathway may be recruited to direct a dendritic destination for mRNAs originating as a Staufen2 nuclear complex.

Carbon Dynamics within Cyclonic Eddies: Insights from a Biomarker Study

PubMed Central

Alonso-González, Iván J.; Arístegui, Javier; Lee, Cindy; Sanchez-Vidal, Anna; Calafat, Antoni; Fabrés, Joan; Sangrá, Pablo; Mason, Evan

2013-01-01

It is generally assumed that episodic nutrient pulses by cyclonic eddies into surface waters support a significant fraction of the primary production in subtropical low-nutrient environments in the northern hemisphere. However, contradictory results related to the influence of eddies on particulate organic carbon (POC) export have been reported. As a step toward understanding the complex mechanisms that control export of material within eddies, we present here results from a sediment trap mooring deployed within the path of cyclonic eddies generated near the Canary Islands over a 1.5-year period. We find that, during summer and autumn (when surface stratification is stronger, eddies are more intense, and a relative enrichment in CaCO3 forming organisms occurs), POC export to the deep ocean was 2–4 times higher than observed for the rest of the year. On the contrary, during winter and spring (when mixing is strongest and the seasonal phytoplankton bloom occurs), no significant enhancement of POC export associated with eddies was observed. Our biomarker results suggest that a large fraction of the material exported from surface waters during the late-winter bloom is either recycled in the mesopelagic zone or bypassed by migrant zooplankton to the deep scattering layer, where it would disaggregate to smaller particles or be excreted as dissolved organic carbon. Cyclonic eddies, however, would enhance carbon export below 1000 m depth during the summer stratification period, when eddies are more intense and frequent, highlighting the important role of eddies and their different biological communities on the regional carbon cycle. PMID:24386098

Carbon dynamics within cyclonic eddies: insights from a biomarker study.

PubMed

Alonso-González, Iván J; Arístegui, Javier; Lee, Cindy; Sanchez-Vidal, Anna; Calafat, Antoni; Fabrés, Joan; Sangrá, Pablo; Mason, Evan

2013-01-01

It is generally assumed that episodic nutrient pulses by cyclonic eddies into surface waters support a significant fraction of the primary production in subtropical low-nutrient environments in the northern hemisphere. However, contradictory results related to the influence of eddies on particulate organic carbon (POC) export have been reported. As a step toward understanding the complex mechanisms that control export of material within eddies, we present here results from a sediment trap mooring deployed within the path of cyclonic eddies generated near the Canary Islands over a 1.5-year period. We find that, during summer and autumn (when surface stratification is stronger, eddies are more intense, and a relative enrichment in CaCO3 forming organisms occurs), POC export to the deep ocean was 2-4 times higher than observed for the rest of the year. On the contrary, during winter and spring (when mixing is strongest and the seasonal phytoplankton bloom occurs), no significant enhancement of POC export associated with eddies was observed. Our biomarker results suggest that a large fraction of the material exported from surface waters during the late-winter bloom is either recycled in the mesopelagic zone or bypassed by migrant zooplankton to the deep scattering layer, where it would disaggregate to smaller particles or be excreted as dissolved organic carbon. Cyclonic eddies, however, would enhance carbon export below 1000 m depth during the summer stratification period, when eddies are more intense and frequent, highlighting the important role of eddies and their different biological communities on the regional carbon cycle.

Sources, distribution and export coefficient of phosphorus in lowland polders of Lake Taihu Basin, China.

PubMed

Huang, Jiacong; Gao, Junfeng; Jiang, Yong; Yin, Hongbin; Amiri, Bahman Jabbarian

2017-12-01

Identifying phosphorus (P) sources, distribution and export from lowland polders is important for P pollution management, however, is challenging due to the high complexity of hydrological and P transport processes in lowland areas. In this study, the spatial pattern and temporal dynamics of P export coefficient (PEC) from all the 2539 polders in Lake Taihu Basin, China were estimated using a coupled P model for describing P dynamics in a polder system. The estimated amount of P export from polders in Lake Taihu Basin during 2013 was 1916.2 t/yr, with a spatially-averaged PEC of 1.8 kg/ha/yr. PEC had peak values (more than 4.0 kg/ha/yr) in the polders near/within the large cities, and was high during the rice-cropping season. Sensitivity analysis based on the coupled P model revealed that the sensitive factors controlling the PEC varied spatially and changed through time. Precipitation and air temperature were the most sensitive factors controlling PEC. Culvert controlling and fertilization were sensitive factors controlling PEC during some periods. This study demonstrated an estimation of PEC from 2539 polders in Lake Taihu Basin, and an identification of sensitive environmental factors affecting PEC. The investigation of polder P export in a watershed scale is helpful for water managers to learn the distribution of P sources, to identify key P sources, and thus to achieve best management practice in controlling P export from lowland areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

Selective incorporation of vRNP into influenza A virions determined by its specific interaction with M1 protein

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

Chaimayo, Chutikarn

Influenza A viruses contain eight single-stranded, negative-sense RNA segments as viral genomes in the form of viral ribonucleoproteins (vRNPs). During genome replication in the nucleus, positive-sense complementary RNPs (cRNPs) are produced as replicative intermediates, which are not incorporated into progeny virions. To analyze the mechanism of selective vRNP incorporation into progeny virions, we quantified vRNPs and cRNPs in the nuclear and cytosolic fractions of infected cells, using a strand-specific qRT-PCR. Unexpectedly, we found that cRNPs were also exported to the cytoplasm. This export was chromosome region maintenance 1 (CRM1)-independent unlike that of vRNPs. Although both vRNPs and cRNPs were presentmore » in the cytosol, viral matrix (M1) protein, a key regulator for viral assembly, preferentially bound vRNPs over cRNPs. These results indicate that influenza A viruses selectively uptake cytosolic vRNPs through a specific interaction with M1 during viral assembly. - Highlights: •Influenza cRNPs are exported from the nucleus of an infected cell via a CRM1-independent pathway. •Influenza A viruses selectively incorporate cytosolic vRNPs through a specific interaction with M1 during viral assembly. •M1 dissociates from vRNP export complex after nuclear export, and is re-associated with vRNPs at the plasma membrane.« less

Linking terrestrial P inputs to riverine export across the United ...

EPA Pesticide Factsheets

Human beings have greatly accelerated phosphorus (P) flows from land to aquatic ecosystems, often resulting in eutrophication, harmful algal blooms, and hypoxia. Although a variety of statistical and mechanistic models have been used to explore the relationship between terrestrial nutrient management and losses to waterways, our understanding of how natural and anthropogenic landscape characteristics mediate losses of P from watersheds lags behind that of nitrogen. The need for higher resolution data is often identified as an important barrier that limits our capacity to predict P loading. In order to address this gap, we constructed spatially explicit datasets of terrestrial P inputs and outputs (fertilizer, confined manure, crop harvest and sewage) across the continental U.S. for 2012. We then examined how these P sources, along with climate, hydrology, and land use, influenced P exports from 72 watersheds as total P (TP) and dissolved inorganic P (DIP) concentrations and yields, and TP fractional export. TP and DIP concentrations and TP yields were best correlated with runoff, but using simple linear regression, we were not able to explain more than 56% of the variance in any of the water quality variables (TP fractional export vs P manure inputs). The lack of clear and strong relationships between contemporary, high-resolution, anthropogenic, terrestrial P and riverine P export at the national scale highlights the fact that a complex suite of factors mediat

Generation of large scale urban environments to support advanced sensor and seeker simulation

NASA Astrophysics Data System (ADS)

Giuliani, Joseph; Hershey, Daniel; McKeown, David, Jr.; Willis, Carla; Van, Tan

2009-05-01

One of the key aspects for the design of a next generation weapon system is the need to operate in cluttered and complex urban environments. Simulation systems rely on accurate representation of these environments and require automated software tools to construct the underlying 3D geometry and associated spectral and material properties that are then formatted for various objective seeker simulation systems. Under an Air Force Small Business Innovative Research (SBIR) contract, we have developed an automated process to generate 3D urban environments with user defined properties. These environments can be composed from a wide variety of source materials, including vector source data, pre-existing 3D models, and digital elevation models, and rapidly organized into a geo-specific visual simulation database. This intermediate representation can be easily inspected in the visible spectrum for content and organization and interactively queried for accuracy. Once the database contains the required contents, it can then be exported into specific synthetic scene generation runtime formats, preserving the relationship between geometry and material properties. To date an exporter for the Irma simulation system developed and maintained by AFRL/Eglin has been created and a second exporter to Real Time Composite Hardbody and Missile Plume (CHAMP) simulation system for real-time use is currently being developed. This process supports significantly more complex target environments than previous approaches to database generation. In this paper we describe the capabilities for content creation for advanced seeker processing algorithms simulation and sensor stimulation, including the overall database compilation process and sample databases produced and exported for the Irma runtime system. We also discuss the addition of object dynamics and viewer dynamics within the visual simulation into the Irma runtime environment.

Large-eddy Simulation of the Nighttime Stable Atmospheric Boundary Layer

NASA Astrophysics Data System (ADS)

Zhou, Bowen

A stable atmospheric boundary layer (ABL) develops over land at night due to radiative surface cooling. The state of turbulence in the stable boundary layer (SBL) is determined by the competing forcings of shear production and buoyancy destruction. When both forcings are comparable in strength, the SBL falls into an intermittently turbulent state, where intense turbulent bursts emerge sporadically from an overall quiescent background. This usually occurs on clear nights with weak winds when the SBL is strongly stable. Although turbulent bursts are generally short-lived (half an hour or less), their impact on the SBL is significant since they are responsible for most of the turbulent mixing. The nighttime SBL can be modeled with large-eddy simulation (LES). LES is a turbulence-resolving numerical approach which separates the large-scale energy-containing eddies from the smaller ones based on application of a spatial filter. While the large eddies are explicitly resolved, the small ones are represented by a subfilter-scale (SFS) stress model. Simulation of the SBL is more challenging than the daytime convective boundary layer (CBL) because nighttime turbulent motions are limited by buoyancy stratification, thus requiring fine grid resolution at the cost of immense computational resources. The intermittently turbulent SBL adds additional levels of complexity, requiring the model to not only sustain resolved turbulence during quiescent periods, but also to transition into a turbulent state under appropriate conditions. As a result, LES of the strongly stable SBL potentially requires even finer grid resolution, and has seldom been attempted. This dissertation takes a different approach. By improving the SFS representation of turbulence with a more sophisticated model, intermittently turbulent SBL is simulated, to our knowledge, for the first time in the LES literature. The turbulence closure is the dynamic reconstruction model (DRM), applied under an explicit filtering and reconstruction LES framework. The DRM is a mixed model that consists of subgrid scale (SGS) and resolved subfilter scale (RSFS) components. The RSFS portion is represented by a scale-similarity model that allows for backscatter of energy from the SFS to the mean flow. Compared to conventional closures, the DRM is able to sustain resolved turbulence under moderate stability at coarser resolution (thus saving computational resources). The DRM performs equally well at fine resolution. Under strong stability, the DRM simulates an intermittently turbulent SBL, whereas conventional closures predict false laminar flows. The improved simulation methodology of the SBL has many potential applications in the area of wind energy, numerical weather prediction, pollution modeling and so on. The SBL is first simulated over idealized flat terrain with prescribed forcings and periodic lateral boundaries. A wide range of stability regimes, from weakly to strongly stable conditions, is tested to evaluate model performance. Under strongly stable conditions, intermittency due to mean shear and turbulence interactions is simulated and analyzed. Furthermore, results of the strongly stable SBL are used to improve wind farm siting and nighttime operations. Moving away from the idealized setting, the SBL is simulated over relatively flat terrain at a Kansas site over the Great Plains, where the Cooperative Atmospheric-Surface Exchange Study -- 1999 (CASES-99) took place. The LES obtains realistic initial and lateral boundary conditions from a meso-scale model reanalysis through a grid nesting procedure. Shear-instability induced intermittency observed on the night of Oct 5th during CASES-99 is reproduced to good temporal and magnitude agreement. The LES locates the origin of the shear-instability waves in a shallow upwind valley, and uncovers the intermittency mechanism to be wave breaking over a standing wave (formed over a stagnant cold-air bubble) across the valley. Finally, flow over the highly complex terrain of the Owens Valley in California is modeled with a similar nesting procedure. The LES results are validated with observation data from the 2006 Terrain-Induced Rotor Experiment (T-REX). The nested LES reproduces a transient nighttime warming event observed on the valley floor on April 17 during T-REX. The intermittency mechanism is shown to be through slope-valley flow transitions. In addition, a cold-air intrusion from the eastern valley sidewall is simulated. This generates an easterly cross-valley flow, and the associated top-down mixing through breaking Kelvin-Helmholtz billows is analyzed. Finally, the nesting methodology tested and optimized in the CASES-99 and T-REX studies is transferrable to general ABL applications. For example, a nested LES is performed to model daytime methane plume dispersion over a landfill and good results are obtained.

Regulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAs

PubMed Central

Soheilypour, M.; Mofrad, M. R. K.

2016-01-01

Export of messenger ribonucleic acids (mRNAs) into the cytoplasm is a fundamental step in gene regulation processes, which is meticulously quality controlled by highly efficient mechanisms in eukaryotic cells. Yet, it remains unclear how the aberrant mRNAs are recognized and retained inside the nucleus. Using a new modelling approach for complex systems, namely the agent-based modelling (ABM) approach, we develop a minimal model of the mRNA quality control (QC) mechanism. Our results demonstrate that regulation of the affinity of RNA-binding proteins (RBPs) to export receptors along with the weak interaction between the nuclear basket protein (Mlp1 or Tpr) and RBPs are the minimum requirements to distinguish and retain aberrant mRNAs. Our results show that the affinity between Tpr and RBPs is optimized to maximize the retention of aberrant mRNAs. In addition, we demonstrate how the length of mRNA affects the QC process. Since longer mRNAs spend more time in the nuclear basket to form a compact conformation and initiate their export, nuclear basket proteins could more easily capture and retain them inside the nucleus. PMID:27805000

Regulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAs.

PubMed

Soheilypour, M; Mofrad, M R K

2016-11-02

Export of messenger ribonucleic acids (mRNAs) into the cytoplasm is a fundamental step in gene regulation processes, which is meticulously quality controlled by highly efficient mechanisms in eukaryotic cells. Yet, it remains unclear how the aberrant mRNAs are recognized and retained inside the nucleus. Using a new modelling approach for complex systems, namely the agent-based modelling (ABM) approach, we develop a minimal model of the mRNA quality control (QC) mechanism. Our results demonstrate that regulation of the affinity of RNA-binding proteins (RBPs) to export receptors along with the weak interaction between the nuclear basket protein (Mlp1 or Tpr) and RBPs are the minimum requirements to distinguish and retain aberrant mRNAs. Our results show that the affinity between Tpr and RBPs is optimized to maximize the retention of aberrant mRNAs. In addition, we demonstrate how the length of mRNA affects the QC process. Since longer mRNAs spend more time in the nuclear basket to form a compact conformation and initiate their export, nuclear basket proteins could more easily capture and retain them inside the nucleus.

Hydrological controls on riverine carbon export in a seasonally wet tropical catchment

NASA Astrophysics Data System (ADS)

Duvert, C.; Hutley, L. B.; Bossa, M.; Bird, M. I.; Munksgaard, N.; Wynn, J. G.; Setterfield, S. A.; Northwood, M.

2017-12-01

Understanding the movement of carbon (C) through the landscape is critical for accurate C accounting. Failure to account for the transport of terrestrially-derived C to aquifers and streams can result in a considerable over-estimation of the C sequestration by the biosphere. Here we report on the magnitude of C export via shallow groundwater and adjacent streams in a savanna-covered seasonally wet tropical catchment of northern Australia. Riverine fluxes of carbon dioxide (CO2), dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) were measured at a high resolution over a full year to gain insight into the drivers of C export in this system. Water and C stable isotopes were also measured in order to elucidate water sources and dominant flow pathways. Our results suggest that CO2 evasion was the major process contributing to riverine C loss in the catchment (111 kg C ha-1 yr-1). The downstream export of C was dominated by DOC (78 kg C ha-1 yr-1), while DIC accounted for 39 kg C ha-1 yr-1 of the annual export. The bulk of annual DOC export was flushed out during the very first high-flow events, with export decreasing throughout the wet season to pre-flood levels. In contrast, the DIC flux was more important during flow recession, upon activation of deeper flowpaths carrying geologically-derived C. Shallow groundwater measured in boreholes was supersaturated with CO2 (15,000 < pCO2 < 55,000 ppm), whereas in-stream concentrations were an order of magnitude lower, suggesting substantial outgassing of CO2. Our findings outline the key role of point-source groundwater discharge in riverine CO2 evasion, with C largely sourced from seasonally productive savanna vegetation. Given the complexity of this pathway and the magnitude of this flux, new methods are needed to more precisely quantify CO2 evasion.

Drivers of dissolved organic carbon export in a subarctic catchment: Importance of microbial decomposition, sorption-desorption, peatland and lateral flow.

PubMed

Tang, Jing; Yurova, Alla Y; Schurgers, Guy; Miller, Paul A; Olin, Stefan; Smith, Benjamin; Siewert, Matthias B; Olefeldt, David; Pilesjö, Petter; Poska, Anneli

2018-05-01

Tundra soils account for 50% of global stocks of soil organic carbon (SOC), and it is expected that the amplified climate warming in high latitude could cause loss of this SOC through decomposition. Decomposed SOC could become hydrologically accessible, which increase downstream dissolved organic carbon (DOC) export and subsequent carbon release to the atmosphere, constituting a positive feedback to climate warming. However, DOC export is often neglected in ecosystem models. In this paper, we incorporate processes related to DOC production, mineralization, diffusion, sorption-desorption, and leaching into a customized arctic version of the dynamic ecosystem model LPJ-GUESS in order to mechanistically model catchment DOC export, and to link this flux to other ecosystem processes. The extended LPJ-GUESS is compared to observed DOC export at Stordalen catchment in northern Sweden. Vegetation communities include flood-tolerant graminoids (Eriophorum) and Sphagnum moss, birch forest and dwarf shrub communities. The processes, sorption-desorption and microbial decomposition (DOC production and mineralization) are found to contribute most to the variance in DOC export based on a detailed variance-based Sobol sensitivity analysis (SA) at grid cell-level. Catchment-level SA shows that the highest mean DOC exports come from the Eriophorum peatland (fen). A comparison with observations shows that the model captures the seasonality of DOC fluxes. Two catchment simulations, one without water lateral routing and one without peatland processes, were compared with the catchment simulations with all processes. The comparison showed that the current implementation of catchment lateral flow and peatland processes in LPJ-GUESS are essential to capture catchment-level DOC dynamics and indicate the model is at an appropriate level of complexity to represent the main mechanism of DOC dynamics in soils. The extended model provides a new tool to investigate potential interactions among climate change, vegetation dynamics, soil hydrology and DOC dynamics at both stand-alone to catchment scales. Copyright © 2017 Elsevier B.V. All rights reserved.

“It’s my blood”: ethical complexities in the use, storage and export of biological samples: perspectives from South African research participants

PubMed Central

2014-01-01

Background The use of biological samples in research raises a number of ethical issues in relation to consent, storage, export, benefit sharing and re-use of samples. Participant perspectives have been explored in North America and Europe, with only a few studies reported in Africa. The amount of research being conducted in Africa is growing exponentially with volumes of biological samples being exported from the African continent. In order to investigate the perspectives of African research participants, we conducted a study at research sites in the Western Cape and Gauteng, South Africa. Methods Data were collected using a semi-structured questionnaire that captured both quantitative and qualitative information at 6 research sites in South Africa. Interviews were conducted in English and Afrikaans. Data were analysed both quantitatively and qualitatively. Results Our study indicates that while the majority of participants were supportive of providing samples for research, serious concerns were voiced about future use, benefit sharing and export of samples. While researchers view the provision of biosamples as a donation, participants believe that they still have ownership rights and are therefore in favour of benefit sharing. Almost half of the participants expressed a desire to be re-contacted for consent for future use of their samples. Interesting opinions were expressed with respect to export of samples. Conclusions Eliciting participant perspectives is an important part of community engagement in research involving biological sample collection, export, storage and future use. A tiered consent process appears to be more acceptable to participants in this study. Eliciting opinions of researchers and research ethics committee (REC) members would contribute multiple perspectives. Further research is required to interrogate the concept of ownership and the consent process in research involving biological samples. PMID:24447822

Export Time of Earthquake-Derived Landslides in Active Mountain Ranges

NASA Astrophysics Data System (ADS)

Croissant, T.; Lague, D.; Steer, P.; Davy, P.

2016-12-01

In active mountain ranges, large earthquakes (Mw > 5-6) trigger numerous landslides that impact river dynamics. These landslides bring local and sudden sediment deposits which are eroded and transported along the river network, causing downstream changes in river geometry, transport capacity and erosion efficiency. The progressive removal of landslide materials has implications for downstream hazards management and for landscape dynamics at the timescale of the seismic cycle. Although the export time of suspended sediments from landslides triggered by large-magnitude earthquakes has been extensively studied, the processes and time scales associated to bedload transport remains poorly studied. Here, we study the sediment export of large landslides with the 2D morphodynamic model, Eros. This model combines: (i) an hydrodynamic model, (ii) a sediment transport and deposition model and (iii) a lateral erosion model. Eros is particularly well suited for this issue as it accounts for the complex retro-actions between sediment transport and fluvial geometry for rivers submitted to external forcings such as abrupt sediment supply increase. Using a simplified synthetic topography we systematically study the influence of pulse volume (Vs) and channel transport capacity (QT) on the export time of landslides. The range of simulated river behavior includes landslide vertical incision, its subsequent removal by lateral erosion and the river morphology modifications induced by downstream sediment propagation. The morphodynamic adaptation of the river increases its transport capacity along the channel and tends to accelerate the landslide evacuation. Our results highlight two regimes: (i) the export time is linearly related to Vs/QT when the sediment pulse introduced in the river does not affect significantly the river hydrodynamic (low Vs/QT) and (ii) the export time is a non-linear function of Vs/QT when the pulse undergoes significant morphodynamic modifications during its evacuation (high Vs/QT). By combining our newly derived export time functions with the frequency-magnitude of earthquake intensity and the induced sediment production, we investigate the sediment export of several plausible earthquake scenarii in different mountain ranges (New Zealand, Taiwan, Nepal).

Computational fluid dynamics (CFD) study on the fetal aortic coarctation

NASA Astrophysics Data System (ADS)

Zhou, Yue; Zhang, Yutao; Wang, Jingying

2018-03-01

Blood flows in normal and coarctate fetal aortas are simulated by the CFD technique using T-rex grids. The three-dimensional (3-D) digital model of the fetal arota is reconstructed by the computer-aided design (CAD) software based on two-dimensional (2-D) ultrasono tomographic images. Simulation results displays the development and enhancement of the secondary flow structure in the coarctate fetal arota. As the diameter narrow ratio rises greater than 45%, the pressure and wall shear stress (WSS) of the aorta arch increase exponentially, which is consistent with the conventional clinical concept. The present study also demonstrates that CFD is a very promising assistant technique to investigate human cardiovascular diseases.

Undulator radiation from laser-plasma-accelerated electron beams

NASA Astrophysics Data System (ADS)

Shaw, B.; van Tilborg, J.; Gonsalves, A.; Nakamura, K.; Sokollik, T.; Shiraishi, S.; Mittal, R.; Esarey, E.; Schroeder, C.; Toth, C.; Leemans, W. P.

2012-12-01

Recent experiments coupled electron beams from the LOASIS TREX laser plasma accelerator (LPA) [1, 2, 3] to the Tapered Hybrid Undulator (THUNDER). Using the 1.5m, 66 period undulator, followed by an XUV spectrometer, spontaneous radiation was observed at photon energies extending to 100 eV. Previous experiments have reported visible [4] and soft-x-ray [5] radiation. The purpose of our experiments is to do highly precise, single shot diagnostics of the energy spread and emittance for each electron beam. We present recent results including measurements of electron beam transport through the undulator with and without the use of permanent magnetic quadrapoles, and measurements of XUV spectra up to 100 eV from LPA produced e-beams.

Arginine methylation of REF/ALY promotes efficient handover of mRNA to TAP/NXF1

PubMed Central

Hung, Ming-Lung; Hautbergue, Guillaume M.; Snijders, Ambrosius P. L.; Dickman, Mark J.; Wilson, Stuart A.

2010-01-01

The REF/ALY mRNA export adaptor binds TAP/NXF1 via an arginine-rich region, which overlaps with its RNA-binding domain. When TAP binds a REF:RNA complex, it triggers transfer of the RNA from REF to TAP. Here, we have examined the effects of arginine methylation on the activities of the REF protein in mRNA export. We have mapped the arginine methylation sites of REF using mass spectrometry and find that several arginines within the TAP and RNA binding domains are methylated in vivo. However, arginine methylation has no effect on the REF:TAP interaction. Instead, arginine methylation reduces the RNA-binding activity of REF in vitro and in vivo. The reduced RNA-binding activity of REF in its methylated state is essential for efficient displacement of RNA from REF by TAP in vivo. Therefore, arginine methylation fine-tunes the RNA-binding activity of REF such that the RNA–protein interaction can be readily disrupted by export factors further down the pathway. PMID:20129943

Psychoanalysis and the Challenges of Disciplinary Exportation: Notes from the African "Periphery" on the Method/Theory Distinction.

PubMed

Barratt, Barnaby B

2018-02-01

This paper briefly reports on the current expansion of opportunities for clinical education in psychoanalysis in southern Africa, various regions of Asia, and Iran. It is a preliminary reconsideration of whether the disciplinary export of psychoanalysis is another egregious exercise in neo-colonialism, as contrasted with its possibly liberatory significance. The author argues that much of the discussion around the universality of many theoretical propositions needs to be reformulated. For example, the controversies over the Oedipus complex have typically been articulated in terms of the effects of specific social arrangements, familial structures, and styles of maternal and paternal functioning, rather than in terms of the universal-but with much cultural variation in its implementation-incest taboo. It is argued that dissemination of the psychoanalytic method (and the four coordinates that follow from it) may be desirable, but in ways the export of the hermeneutic assumptions of certain theoretical models is not.

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.

How log-normal is your country? An analysis of the statistical distribution of the exported volumes of products

NASA Astrophysics Data System (ADS)

Annunziata, Mario Alberto; Petri, Alberto; Pontuale, Giorgio; Zaccaria, Andrea

2016-10-01

We have considered the statistical distributions of the volumes of 1131 products exported by 148 countries. We have found that the form of these distributions is not unique but heavily depends on the level of development of the nation, as expressed by macroeconomic indicators like GDP, GDP per capita, total export and a recently introduced measure for countries' economic complexity called fitness. We have identified three major classes: a) an incomplete log-normal shape, truncated on the left side, for the less developed countries, b) a complete log-normal, with a wider range of volumes, for nations characterized by intermediate economy, and c) a strongly asymmetric shape for countries with a high degree of development. Finally, the log-normality hypothesis has been checked for the distributions of all the 148 countries through different tests, Kolmogorov-Smirnov and Cramér-Von Mises, confirming that it cannot be rejected only for the countries of intermediate economy.

Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis.

PubMed

Moriggi, Giulia; Nieto, Blanca; Dosil, Mercedes

2014-12-01

During the biogenesis of small ribosomal subunits in eukaryotes, the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm. The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown. Here we show that yeast Rrp12 is required for the exit of pre-40S particles to the cytoplasm and for proper maturation dynamics of upstream 90S pre-ribosomes. Due to this, in vivo elimination of Rrp12 leads to an accumulation of nucleoplasmic 90S to pre-40S transitional particles, abnormal 35S pre-rRNA processing, delayed elimination of processing byproducts, and no export of intermediate pre-40S complexes. The exportin Crm1 is also required for the same pre-ribosome maturation events that involve Rrp12. Thus, in addition to their implication in nuclear export, Rrp12 and Crm1 participate in earlier biosynthetic steps that take place in the nucleolus. Our results indicate that, in the 40S subunit synthesis pathway, the completion of early pre-40S particle assembly, the initiation of byproduct degradation and the priming for nuclear export occur in an integrated manner in late 90S pre-ribosomes.

ACL reconstruction in 11 children using the Clocheville surgical technique: Objective and subjective evaluation.

PubMed

Severyns, M; Lucas, G; Jallageas, R; Briand, S; Odri, G; Fraisse, B; Marleix, S; Rochcongar, P; Violas, P

2016-06-01

The over-the-top position of the femoral metaphyseal tunnel during extraphyseal ligament reconstruction of the anterior cruciate ligament (ACL) according to Clocheville may be responsible for negative anisometry. Until now, the follow-up of children operated using this pediatric technique was limited to screening for iatrogenic epiphysiodesis and the search for postoperative clinical instability. The objective of this study was to measure residual laxity using objective tests, to quantify muscle recovery, and to evaluate the quality of life of these patients in terms of the sports activities. Eleven patients with a mean age of 13.5years were seen at a mean 2.1years of follow-up. They underwent objective clinical tests (GNRB(®) arthrometer and CON-TREX(®) dynamometer) as well as subjective questionnaires (IKDC and KOOS). No significant difference was found between the healthy knee and the operated knee for either the GNRB(®) at 134N (P=0.79) or at 200N (P=0.98). The CON-TREX(®) system allowed us to measure a median percentage of quadriceps recovery of 80.7% (range, 52.2-114.5) in terms of muscle power (60°/s) and 81.2% (range, 51.6-109.6) for muscle response (180°/s). The median subjective IKDC score was 94.73/100 (range, 73.68-98.93); 72.7% of the patients resumed competitive sports. This study's lack of statistical power did not show a significant difference in terms of residual laxity at rest of GNRB(®) transplants, while a mean differential of +0.4mm was observed. Although pediatric transphyseal ligament reconstruction techniques are increasingly used, the Clocheville technique remains, in our opinion, an attractive surgical alternative in the youngest subjects, with no major risk of iatrogenic epiphysiodesis even though it is theoretically anisometric. IV. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

The Legionella pneumophila IcmS-LvgA protein complex is important for Dot/Icm-dependent intracellular growth.

PubMed

Vincent, Carr D; Vogel, Joseph P

2006-08-01

Many bacterial pathogens require a functional type IV secretion system (T4SS) for virulence. Legionella pneumophila, the causative agent of Legionnaires' disease, employs the Dot/Icm T4SS to inject a large number of protein substrates into its host, thereby altering phagosome trafficking. The L. pneumophila T4SS substrate SdeA has been shown to require the accessory factor IcmS for its export. IcmS, defined as a type IV adaptor, exists as a heterodimer with IcmW and this complex functions in a manner similar to a type III secretion chaperone. Here we report an interaction between IcmS and the previously identified virulence factor LvgA. Similar to the icmS mutant, the lvgA mutant appears to assemble a fully functional Dot/Icm complex. Both LvgA and IcmS are small, acidic proteins localized to the cytoplasm and are not exported by the Dot/Icm system, suggesting they form a novel type IV adaptor complex. Inactivation of lvgA causes a minimal defect in growth in the human monocytic cell line U937 and the environmental host Acanthamoeba castellanii. However, the lvgA mutant was severely attenuated for intracellular growth of L. pneumophila in mouse macrophages, suggesting LvgA may be a critical factor that confers host specificity.

Nuclear traffic of influenza virus proteins and ribonucleoprotein complexes.

PubMed

Boulo, Sébastien; Akarsu, Hatice; Ruigrok, Rob W H; Baudin, Florence

2007-03-01

Influenza virus is a negative strand RNA virus and is one of the rare RNA viruses to replicate in the nucleus. The viral RNA is associated with 4 viral proteins to form ribonucleoprotein particles (RNPs). After cell entry the RNPs are dissociated from the viral matrix protein in the low pH of the endosome and are actively imported into the cell nucleus. After translation of viral mRNAs, the proteins necessary for the assembly of new RNPs (the nucleoprotein and the three subunits of the polymerase complex) are also imported into the nucleus. Apart from these four proteins, part of the newly made matrix protein is also imported and the nuclear export protein (NEP) enters the nucleus probably through diffusion. Finally, NS1 also enters the nucleus in order to regulate a number of nuclear processes. The nuclear localization signals on all these viral proteins and their interaction with the cellular transport system are discussed. In the nucleus, the matrix protein binds to the newly assembled RNPs and NEP then binds to the matrix protein. NEP contains the nuclear export signal necessary for transport of the RNPs to the cytoplasm, necessary for the budding of new virus particles. There appears to be a intricate ballet in exposing and hiding nuclear transport signals which leads to a unidirectional transport of the RNPs to the nucleus at the start of the infection process and an opposite unidirectional export of RNPs at the end of the infection.

Voice of Experience International Research Infrastructure and the Impact of Export Control Regulations

ERIC Educational Resources Information Center

Kulakowski, Elliott C.; Chronister, Lynne; Molfese, Victoria; Slocum, Michael; Studman, Cliff; Waugaman, Paul

2007-01-01

Research today has become very complex, often involving international collaborations among multidisciplinary teams. Many institutions, especially those in less economically developed countries, have a great deal of expertise to contribute to these collaborations, but often lack the instrumentation, training, and research management infrastructure…

Combating the Sigatoka disease complex on banana

USDA-ARS?s Scientific Manuscript database

Banana is the fourth most important staple food in the world behind rice, wheat and maize, with more than 100 million tons produced annually. Although the majority of bananas produced are consumed locally, banana export is a multi-billion dollar business. Bananas are grown in more than 100 countri...

Southern California Seismic Network: New Design and Implementation of Redundant and Reliable Real-time Data Acquisition Systems

NASA Astrophysics Data System (ADS)

Saleh, T.; Rico, H.; Solanki, K.; Hauksson, E.; Friberg, P.

2005-12-01

The Southern California Seismic Network (SCSN) handles more than 2500 high-data rate channels from more than 380 seismic stations distributed across southern California. These data are imported real-time from dataloggers, earthworm hubs, and partner networks. The SCSN also exports data to eight different partner networks. Both the imported and exported data are critical for emergency response and scientific research. Previous data acquisition systems were complex and difficult to operate, because they grew in an ad hoc fashion to meet the increasing needs for distributing real-time waveform data. To maximize reliability and redundancy, we apply best practices methods from computer science for implementing the software and hardware configurations for import, export, and acquisition of real-time seismic data. Our approach makes use of failover software designs, methods for dividing labor diligently amongst the network nodes, and state of the art networking redundancy technologies. To facilitate maintenance and daily operations we seek to provide some separation between major functions such as data import, export, acquisition, archiving, real-time processing, and alarming. As an example, we make waveform import and export functions independent by operating them on separate servers. Similarly, two independent servers provide waveform export, allowing data recipients to implement their own redundancy. The data import is handled differently by using one primary server and a live backup server. These data import servers, run fail-over software that allows automatic role switching in case of failure from primary to shadow. Similar to the classic earthworm design, all the acquired waveform data are broadcast onto a private network, which allows multiple machines to acquire and process the data. As we separate data import and export away from acquisition, we are also working on new approaches to separate real-time processing and rapid reliable archiving of real-time data. Further, improved network security is an integral part of the new design. Redundant firewalls will provide secure data imports, exports, and acquisition as well as DMZ zones for web servers and other publicly available servers. We will present the detailed design of this new configuration that is currently being implemented by the SCSN at Caltech. The design principals are general enough to be of use to most regional seismic networks.

Design of hydrotherapy exercise pools.

PubMed

Edlich, R F; Abidin, M R; Becker, D G; Pavlovich, L J; Dang, M T

1988-01-01

Several hydrotherapy pools have been designed specifically for a variety of aquatic exercise. Aqua-Ark positions the exerciser in the center of the pool for deep-water exercise. Aqua-Trex is a shallow underwater treadmill system for water walking or jogging. Swim-Ex generates an adjustable laminar flow that permits swimming without turning. Musculoskeletal conditioning can be accomplished in the above-ground Arjo shallow-water exercise pool. A hydrotherapy pool also can be custom designed for musculoskeletal conditioning in its shallow part and cardiovascular conditioning in a deeper portion of the pool. Regardless of the type of exercise, there is general agreement that the specific exercise conducted in water requires significantly more energy expenditure than when the same exercise is performed on land.

River Export of Dissolved and Particulate Organic Carbon from Permafrost and Peat Deposits across the Siberian Arctic

NASA Astrophysics Data System (ADS)

Wild, B.; Andersson, A.; Bröder, L.; Vonk, J.; Hugelius, G.; McClelland, J. W.; Raymond, P. A.; Gustafsson, O.

2017-12-01

Permafrost and peat deposits of northern high latitudes store more than 1300 Pg of organic carbon. This carbon has been preserved for thousands of years by cold and moist conditions, but is now increasingly mobilized as temperatures rise. While part will be degraded to CO2 and CH4 and amplify global warming, part will be exported by rivers to the Arctic Ocean where it can be degraded or re-buried by sedimentation. We here use the four large Siberian rivers Ob, Yenisey, Lena, and Kolyma as natural integrators of carbon mobilization in their catchments. We apply isotope based source apportionments and Markov Chain Monte Carlo Simulations to quantify contributions of organic carbon from permafrost and peat deposits to organic carbon exported by these rivers. More specifically, we compare the 14C signatures of dissolved and particulate organic carbon (DOC, POC) sampled close to the river mouths with those of five potential carbon sources; (1) recent aquatic and (2) terrestrial primary production, (3) the active layer of permafrost soils, (4) deep Holocene deposits (including thermokarst and peat deposits) and (5) Ice Complex Deposits. 14C signatures of these endmembers were constrained based on extensive literature review. We estimate that the four rivers together exported 2.4-4.5 Tg organic carbon from permafrost and peat deposits per year. While total organic carbon export was dominated by DOC (90%), the export of organic carbon from permafrost and peat deposits was more equally distributed between DOC (56%) and POC (44%). Recent models predict that ca. 200 Pg carbon will be lost as CO2 or CH4 by 2100 (RCP8.5) from the circumarctic permafrost area, of which roughly a quarter is drained by the Ob, Yenisey, Lena, and Kolyma rivers. Our comparatively low estimates of river carbon export thus suggest limited transfer of organic carbon from permafrost and peat deposits to high latitude rivers, or its rapid degradation within rivers. Our findings highlight the importance of both DOC and POC, and its degradation, for the fate of carbon mobilized from high latitude deposits under global warming, and indicate a low potential for its stabilization in the Arctic Ocean.

Rating Correlations Between Customs Codes and Export Control Lists: Assessing the Needs and Challenges

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

Chatelus, Renaud; Heine, Pete

Correlation tables are the linchpins between the customs codes used to classify commodities in international trade and the control lists used for strategic trade control (STC) purposes. While understanding the customs classification system can help the STC community better understand strategic trade flows, better identify which trade operations require permits, and more effectively detect illegal exports, the two systems are different in scope, philosophy, content, and objectives. Many indications point to the limitations of these correlation tables, and it is important to understand the nature of the limitations and the complex underlying reasons to conceive possible improvements. As part ofmore » its Strategic Trade and Supply Chain Analytics Initiative, Argonne National Laboratory supported a study of a subset of the European Union’s TARIC correlation table. The study included development of a methodology and an approach to rating the quality and relevance of individual correlations. The study was intended as a first step to engage the STC community in deflections and initiatives to improve the conception and use of correlations, and its conclusions illustrate the scope and complex nature of the challenges to overcome. This paper presents the two classification systems, analyzes the needs for correlation tables and the complex challenges associated with them, summarizes key findings, and proposes possible ways forward.« less

The Thoc1 Encoded Ribonucleoprotein Is Required for Myeloid Progenitor Cell Homeostasis in the Adult Mouse

PubMed Central

Chinnam, Meenalakshmi; Povinelli, Benjamin J.; Fisher, Daniel T.; Golding, Michelle; Appenheimer, Michelle M.; Nemeth, Michael J.; Evans, Sharon; Goodrich, David W.

2014-01-01

Co-transcriptionally assembled ribonucleoprotein (RNP) complexes are critical for RNA processing and nuclear export. RNPs have been hypothesized to contribute to the regulation of coordinated gene expression, and defects in RNP biogenesis contribute to genome instability and disease. Despite the large number of RNPs and the importance of the molecular processes they mediate, the requirements for individual RNP complexes in mammalian development and tissue homeostasis are not well characterized. THO is an evolutionarily conserved, nuclear RNP complex that physically links nascent transcripts with the nuclear export apparatus. THO is essential for early mouse embryonic development, limiting characterization of the requirements for THO in adult tissues. To address this shortcoming, a mouse strain has been generated allowing inducible deletion of the Thoc1 gene which encodes an essential protein subunit of THO. Bone marrow reconstitution was used to generate mice in which Thoc1 deletion could be induced specifically in the hematopoietic system. We find that granulocyte macrophage progenitors have a cell autonomous requirement for Thoc1 to maintain cell growth and viability. Lymphoid lineages are not detectably affected by Thoc1 loss under the homeostatic conditions tested. Myeloid lineages may be more sensitive to Thoc1 loss due to their relatively high rate of proliferation and turnover. PMID:24830368

The Thoc1 encoded ribonucleoprotein is required for myeloid progenitor cell homeostasis in the adult mouse.

PubMed

Pitzonka, Laura; Ullas, Sumana; Chinnam, Meenalakshmi; Povinelli, Benjamin J; Fisher, Daniel T; Golding, Michelle; Appenheimer, Michelle M; Nemeth, Michael J; Evans, Sharon; Goodrich, David W

2014-01-01

Co-transcriptionally assembled ribonucleoprotein (RNP) complexes are critical for RNA processing and nuclear export. RNPs have been hypothesized to contribute to the regulation of coordinated gene expression, and defects in RNP biogenesis contribute to genome instability and disease. Despite the large number of RNPs and the importance of the molecular processes they mediate, the requirements for individual RNP complexes in mammalian development and tissue homeostasis are not well characterized. THO is an evolutionarily conserved, nuclear RNP complex that physically links nascent transcripts with the nuclear export apparatus. THO is essential for early mouse embryonic development, limiting characterization of the requirements for THO in adult tissues. To address this shortcoming, a mouse strain has been generated allowing inducible deletion of the Thoc1 gene which encodes an essential protein subunit of THO. Bone marrow reconstitution was used to generate mice in which Thoc1 deletion could be induced specifically in the hematopoietic system. We find that granulocyte macrophage progenitors have a cell autonomous requirement for Thoc1 to maintain cell growth and viability. Lymphoid lineages are not detectably affected by Thoc1 loss under the homeostatic conditions tested. Myeloid lineages may be more sensitive to Thoc1 loss due to their relatively high rate of proliferation and turnover.

The Oncogenic Fusion Proteins SET-Nup214 and Sequestosome-1 (SQSTM1)-Nup214 Form Dynamic Nuclear Bodies and Differentially Affect Nuclear Protein and Poly(A)+ RNA Export.

PubMed

Port, Sarah A; Mendes, Adélia; Valkova, Christina; Spillner, Christiane; Fahrenkrog, Birthe; Kaether, Christoph; Kehlenbach, Ralph H

2016-10-28

Genetic rearrangements are a hallmark of several forms of leukemia and can lead to oncogenic fusion proteins. One example of an affected chromosomal region is the gene coding for Nup214, a nucleoporin that localizes to the cytoplasmic side of the nuclear pore complex (NPC). We investigated two such fusion proteins, SET-Nup214 and SQSTM1 (sequestosome)-Nup214, both containing C-terminal portions of Nup214. SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukemia cell lines LOUCY and MEGAL. Overexpression of SET-Nup214 in HeLa cells leads to the formation of similar nuclear bodies that recruit CRM1, export cargo proteins, and certain nucleoporins and concomitantly affect nuclear protein and poly(A) + RNA export. SQSTM1-Nup214, although mostly cytoplasmic, also forms nuclear bodies and inhibits nuclear protein but not poly(A) + RNA export. The interaction of the fusion proteins with CRM1 is RanGTP-dependent, as shown in co-immunoprecipitation experiments and binding assays. Further analysis revealed that the Nup214 parts mediate the inhibition of nuclear export, whereas the SET or SQSTM1 part determines the localization of the fusion protein and therefore the extent of the effect. SET-Nup214 nuclear bodies are highly mobile structures, which are in equilibrium with the nucleoplasm in interphase and disassemble during mitosis or upon treatment of cells with the CRM1-inhibitor leptomycin B. Strikingly, we found that nucleoporins can be released from nuclear bodies and reintegrated into existing NPC. Our results point to nuclear bodies as a means of preventing the formation of potentially insoluble and harmful protein aggregates that also may serve as storage compartments for nuclear transport factors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Inhibition of CRM1-mediated nuclear export of transcription factors by leukemogenic NUP98 fusion proteins.

PubMed

Takeda, Akiko; Sarma, Nayan J; Abdul-Nabi, Anmaar M; Yaseen, Nabeel R

2010-05-21

NUP98 is a nucleoporin that plays complex roles in the nucleocytoplasmic trafficking of macromolecules. Rearrangements of the NUP98 gene in human leukemia result in the expression of numerous fusion oncoproteins whose effect on nucleocytoplasmic trafficking is poorly understood. The present study was undertaken to determine the effects of leukemogenic NUP98 fusion proteins on CRM1-mediated nuclear export. NUP98-HOXA9, a prototypic NUP98 fusion, inhibited the nuclear export of two known CRM1 substrates: mutated cytoplasmic nucleophosmin and HIV-1 Rev. In vitro binding assays revealed that NUP98-HOXA9 binds CRM1 through the FG repeat motif in a Ran-GTP-dependent manner similar to but stronger than the interaction between CRM1 and its export substrates. Two NUP98 fusions, NUP98-HOXA9 and NUP98-DDX10, whose fusion partners are structurally and functionally unrelated, interacted with endogenous CRM1 in myeloid cells as shown by co-immunoprecipitation. These leukemogenic NUP98 fusion proteins interacted with CRM1, Ran, and the nucleoporin NUP214 in a manner fundamentally different from that of wild-type NUP98. NUP98-HOXA9 and NUP98-DDX10 formed characteristic aggregates within the nuclei of a myeloid cell line and primary human CD34+ cells and caused aberrant localization of CRM1 to these aggregates. These NUP98 fusions caused nuclear accumulation of two transcription factors, NFAT and NFkappaB, that are regulated by CRM1-mediated export. The nuclear entrapment of NFAT and NFkappaB correlated with enhanced transcription from promoters responsive to these transcription factors. Taken together, the results suggest a new mechanism by which NUP98 fusions dysregulate transcription and cause leukemia, namely, inhibition of CRM1-mediated nuclear export with aberrant nuclear retention of transcriptional regulators.

The Oncogenic Fusion Proteins SET-Nup214 and Sequestosome-1 (SQSTM1)-Nup214 Form Dynamic Nuclear Bodies and Differentially Affect Nuclear Protein and Poly(A)+ RNA Export*

PubMed Central

Port, Sarah A.; Mendes, Adélia; Valkova, Christina; Spillner, Christiane; Fahrenkrog, Birthe; Kaether, Christoph; Kehlenbach, Ralph H.

2016-01-01

Genetic rearrangements are a hallmark of several forms of leukemia and can lead to oncogenic fusion proteins. One example of an affected chromosomal region is the gene coding for Nup214, a nucleoporin that localizes to the cytoplasmic side of the nuclear pore complex (NPC). We investigated two such fusion proteins, SET-Nup214 and SQSTM1 (sequestosome)-Nup214, both containing C-terminal portions of Nup214. SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukemia cell lines LOUCY and MEGAL. Overexpression of SET-Nup214 in HeLa cells leads to the formation of similar nuclear bodies that recruit CRM1, export cargo proteins, and certain nucleoporins and concomitantly affect nuclear protein and poly(A)+ RNA export. SQSTM1-Nup214, although mostly cytoplasmic, also forms nuclear bodies and inhibits nuclear protein but not poly(A)+ RNA export. The interaction of the fusion proteins with CRM1 is RanGTP-dependent, as shown in co-immunoprecipitation experiments and binding assays. Further analysis revealed that the Nup214 parts mediate the inhibition of nuclear export, whereas the SET or SQSTM1 part determines the localization of the fusion protein and therefore the extent of the effect. SET-Nup214 nuclear bodies are highly mobile structures, which are in equilibrium with the nucleoplasm in interphase and disassemble during mitosis or upon treatment of cells with the CRM1-inhibitor leptomycin B. Strikingly, we found that nucleoporins can be released from nuclear bodies and reintegrated into existing NPC. Our results point to nuclear bodies as a means of preventing the formation of potentially insoluble and harmful protein aggregates that also may serve as storage compartments for nuclear transport factors. PMID:27613868

Scale and legacy controls on catchment nutrient export regimes

NASA Astrophysics Data System (ADS)

Howden, N. J. K.; Burt, T.; Worrall, F.

2017-12-01

Nutrient dynamics in river catchments are complex: water and chemical fluxes are highly variable in low-order streams, but this variability declines as fluxes move through higher-order reaches. This poses a major challenge for process understanding as much effort is focussed on long-term monitoring of the main river channel (a high-order reach), and therefore the data available to support process understanding are predominantly derived from sites where much of the transient response of nutrient export is masked by the effect of averaging over both space and time. This may be further exacerbated at all scales by the accumulation of legacy nutrient sources in soils, aquifers and pore waters, where historical activities have led to nutrient accumulation where the catchment system is transport limited. Therefore it is of particular interest to investigate how the variability of nutrient export changes both with catchment scale (from low to high-order catchment streams) and with the presence of legacy sources, such that the context of infrequent monitoring on high-order streams can be better understood. This is not only a question of characterising nutrient export regimes per se, but also developing a more thorough understanding of how the concepts of scale and legacy may modify the statistical characteristics of observed responses across scales in both space and time. In this paper, we use synthetic data series and develop a model approach to consider how space and timescales combine with impacts of legacy sources to influence observed variability in catchment export. We find that: increasing space and timescales tend to reduce the observed variance in nutrient exports, due to an increase in travel times and greater mixing, and therefore averaging, of sources; increasing the influence of legacy sources inflates the variance, with the level of inflation dictated by the residence time of the respective sources.

Scanning electrochemical microscopy of menadione-glutathione conjugate export from yeast cells

PubMed Central

Mauzeroll, Janine; Bard, Allen J.

2004-01-01

The uptake of menadione (2-methyl-1,4-naphthoquinone), which is toxic to yeast cells, and its expulsion as a glutathione complex were studied by scanning electrochemical microscopy. The progression of the in vitro reaction between menadione and glutathione was monitored electrochemically by cyclic voltammetry and correlated with the spectroscopic (UV–visible) behavior. By observing the scanning electrochemical microscope tip current of yeast cells suspended in a menadione-containing solution, the export of the conjugate from the cells with time could be measured. Similar experiments were performed on immobilized yeast cell aggregates stressed by a menadione solution. From the export of the menadione-glutathione conjugate detected at a 1-μm-diameter electrode situated 10 μm from the cells, a flux of about 30,000 thiodione molecules per second per cell was extracted. Numerical simulations based on an explicit finite difference method further revealed that the observation of a constant efflux of thiodione from the cells suggested the rate was limited by the uptake of menadione and that the efflux through the glutathione-conjugate pump was at least an order of magnitude faster. PMID:15148374

NAS Panel faults export controls

NASA Astrophysics Data System (ADS)

Katzoff, Judith A.

A study prepared by a top-level panel says that current export controls on militarily sensitive U.S. technology may be “overcorrecting” previous weaknesses in that system, resulting in “a complex and confusing control system” that makes it more difficult for U.S. businesses to compete in international markets. Moreover, this control system has “an increasingly corrosive effect” on U.S. relations with allies. The panel recommended that the United States concentrate more effort on bringing about uniformity in the export control policies of countries belonging to the Coordinating Committee on Multilateral Export Controls (CoCom), i.e., most of the member nations in NATO (the North Atlantic Treaty Organization) and Japan.The 21-member panel was appointed by the Committee on Science, Engineering, and Public Policy (COSEPUP), a joint unit of the National Academy of Sciences (NAS), the National Academy of Engineering (NAE), and the Institute of Medicine (IOM). The panel, composed of administrators, researchers, and former government officials, was chaired by AGU member Lew Allen, Jr., director of the Jet Propulsion Laboratory (Pasadena, Calif.) and former chief of staff of the U.S. Air Force. Their report was supported by NAS funds, by a number of private organizations (including AGU), by the U.S. Departments of Commerce, Defense, Energy, and State, by the National Science Foundation, and by the National Aeronautics and Space Administration.

Exploring the Diverse Motivations of Transnational Higher Education in China: Complexities and Contradictions

ERIC Educational Resources Information Center

Hou, Junxia; Montgomery, Catherine; McDowell, Liz

2014-01-01

This article analyses the current situation of transnational higher education (TNE) in China by conducting a comprehensive documentary analysis. It first situates the phenomenon in global transnational mobility in higher education and then explores the diverse motivations of importing and exporting countries taking China and the UK as linked…

Modulation of integrin-linked kinase nucleo-cytoplasmic shuttling by ILKAP and CRM1.

PubMed

Nakrieko, Kerry-Ann; Vespa, Alisa; Mason, David; Irvine, Timothy S; D'Souza, Sudhir J A; Dagnino, Lina

2008-07-15

Integrin-linked kinase (ILK) plays key roles in a variety of cell functions, including cell proliferation, adhesion and migration. Within the cell, ILK localizes to multiple sites, including the cytoplasm, focal adhesion complexes that mediate cell adhesion to extracellular substrates, as well as cell-cell junctions in epidermal keratinocytes. Central to understanding ILK function is the elucidation of the mechanisms that regulate its subcellular localization. We now demonstrate that ILK is imported into the nucleus through sequences in its N-terminus, via active transport mechanisms that involve nuclear pore complexes. In addition, nuclear ILK can be rapidly exported into the cytoplasm through a CRM1-dependent pathway, and its export is enhanced by the type 2C protein phosphatase ILKAP. Nuclear localization of ILK in epidermal keratinocytes is associated with increased DNA synthesis, which is sensitive to inhibition by ILKAP. Our studies demonstrate the importance for keratinocyte proliferation of ILK regulation through changes in its subcellular localization, and establish ILKAP and CRM1 as pivotal modulators of ILK subcellular distribution and activity in these cells.

Adaptor protein-3 is required in dendritic cells for optimal Toll-like receptor signaling from phagosomes and antigen presentation to CD4+ T cells

PubMed Central

Mantegazza, Adriana R.; Guttentag, Susan H.; El-Benna, Jamel; Sasai, Miwa; Iwasaki, Akiko; Shen, Hao; Laufer, Terri M.; Marks, Michael S.

2012-01-01

SUMMARY Effective major histocompatibility complex-II (MHC-II) antigen presentation from phagocytosed particles requires phagosome-intrinsic toll-like receptor (TLR) signaling, but the molecular mechanisms underlying TLR delivery to phagosomes and how signaling regulates antigen presentation are incompletely understood. We show a requirement in dendritic cells (DCs) for adaptor protein-3 (AP-3) in efficient TLR recruitment to phagosomes and MHC-II presentation of antigens internalized by phagocytosis but not receptor-mediated endocytosis. DCs from AP-3-deficient pearl mice elicited impaired CD4+ T cell activation and Th1 effector function to particulate antigen in vitro and to recombinant Listeria monocytogenes infection in vivo. Whereas phagolysosome maturation and peptide:MHC-II complex assembly proceeded normally in pearl DCs, peptide:MHC-II export to the cell surface was impeded. This correlated with reduced TLR4 recruitment and proinflammatory signaling from phagosomes by particulate TLR ligands. We propose that AP-3-dependent TLR delivery from endosomes to phagosomes and subsequent signaling mobilize peptide:MHC-II export from intracellular stores. PMID:22560444

Extracellular small heat shock proteins: exosomal biogenesis and function.

PubMed

Reddy, V Sudhakar; Madala, Satish K; Trinath, Jamma; Reddy, G Bhanuprakash

2018-05-01

Small heat shock proteins (sHsps) belong to the family of heat shock proteins (Hsps): some are induced in response to multiple stressful events to protect the cells while others are constitutively expressed. Until now, it was believed that Hsps, including sHsps, are present inside the cells and perform intracellular functions. Interestingly, several groups recently reported the extracellular presence of Hsps, and sHsps have also been detected in sera/cerebrospinal fluids in various pathological conditions. Secretion into the extracellular milieu during many pathological conditions suggests additional or novel functions of sHsps in addition to their intracellular properties. Extracellular sHsps are implicated in cell-cell communication, activation of immune cells, and promoting anti-inflammatory and anti-platelet responses. Interestingly, exogenous administration of sHsps showed therapeutic effects in multiple disease models implying that extracellular sHsps are beneficial in pathological conditions. sHsps do not possess signal sequence and, hence, are not exported through the classical Endoplasmic reticulum-Golgi complex (ER-Golgi) secretory pathway. Further, export of sHsps is not inhibited by ER-Golgi secretory pathway inhibitors implying the involvement of a nonclassical secretory pathway in sHsp export. In lieu, lysoendosomal and exosomal pathways have been proposed for the export of sHsps. Heat shock protein 27 (Hsp27), αB-crystallin (αBC), and Hsp20 are shown to be exported by exosomes. Exosomes packaged with sHsps have beneficial effects in in vivo disease models. However, secretion mechanisms and therapeutic use of sHsps have not been elucidated in detail. Therefore, this review aimed at highlighting the current understanding of sHsps (Hsp27, αBC, and Hsp20) in the extracellular medium.

Transient sensitivities of sea ice export through the Canadian Arctic Archipelago inferred from a coupled ocean/sea-ice adjoint model

NASA Astrophysics Data System (ADS)

Heimbach, P.; Losch, M.; Menemenlis, D.; Campin, J.; Hill, C.

2008-12-01

The sensitivity of sea-ice export through the Canadian Arctic Archipelago (CAA), measured in terms of its solid freshwater export through Lancaster Sound, to changes in various elements of the ocean and sea-ice state, and to elements of the atmospheric forcing fields through time and space is assessed by means of a coupled ocean/sea-ice adjoint model. The adjoint model furnishes full spatial sensitivity maps (also known as Lagrange multipliers) of the export metric to a variety of model variables at any chosen point in time, providing the unique capability to quantify major drivers of sea-ice export variability. The underlying model is the MIT ocean general circulation model (MITgcm), which is coupled to a Hibler-type dynamic/thermodynamic sea-ice model. The configuration is based on the Arctic face of the ECCO3 high-resolution cubed-sphere model, but coarsened to 36-km horizontal grid spacing. The adjoint of the coupled system has been derived by means of automatic differentiation using the software tool TAF. Finite perturbation simulations are performed to check the information provided by the adjoint. The sea-ice model's performance in the presence of narrow straits is assessed with different sea-ice lateral boundary conditions. The adjoint sensitivity clearly exposes the role of the model trajectory and the transient nature of the problem. The complex interplay between forcing, dynamics, and boundary condition is demonstrated in the comparison between the different calculations. The study is a step towards fully coupled adjoint-based ocean/sea-ice state estimation at basin to global scales as part of the ECCO efforts.

Required spatial resolution of hydrological models to evaluate urban flood resilience measures

NASA Astrophysics Data System (ADS)

Gires, A.; Giangola-Murzyn, A.; Tchiguirinskaia, I.; Schertzer, D.; Lovejoy, S.

2012-04-01

During a flood in urban area, several non-linear processes (rainfall, surface runoff, sewer flow, and sub-surface flow) interact. Fully distributed hydrological models are a useful tool to better understand these complex interactions between natural processes and man built environment. Developing an efficient model is a first step to improve the understanding of flood resilience in urban area. Given that the previously mentioned underlying physical phenomenon exhibit different relevant scales, determining the required spatial resolution of such model is tricky but necessary issue. For instance such model should be able to properly represent large scale effects of local scale flood resilience measures such as stop logs. The model should also be as simple as possible without being simplistic. In this paper we test two types of model. First we use an operational semi-distributed model over a 3400 ha peri-urban area located in Seine-Saint-Denis (North-East of Paris). In this model, the area is divided into sub-catchments of average size 17 ha that are considered as homogenous, and only the sewer discharge is modelled. The rainfall data, whose resolution is 1 km is space and 5 min in time, comes from the C-band radar of Trappes, located in the West of Paris, and operated by Météo-France. It was shown that the spatial resolution of both the model and the rainfall field did not enable to fully grasp the small scale rainfall variability. To achieve this, first an ensemble of realistic rainfall fields downscaled to a resolution of 100 m is generated with the help of multifractal space-time cascades whose characteristic exponents are estimated on the available radar data. Second the corresponding ensemble of sewer hydrographs is simulated by inputting each rainfall realization to the model. It appears that the probability distribution of the simulated peak flow exhibits a power-law behaviour. This indicates that there is a great uncertainty associated with small scale rainfall. Second we focus on a 50 ha catchment of this area and implement Multi-Hydro, a fully distributed urban hydrological model currently being developed at Ecole des Ponts ParisTech (El Tabach et al., 2009). The version used in this paper consists in an interactive coupling between a 2D model representing infiltration and surface runoff (TREX, Two dimensional Runoff, Erosion and eXport model, Velleux et al., 2011) and a 1D model of sewer networks (SWMM, Storm Water Management Model, Rossman, 2007). Spatial resolution ranging from 2 m to 50 m for land use, topography and rainfall are tested. A special highlight on the impact of small scales rainfall is done. To achieve this the previously mentioned methodology is implemented with rainfall fields downscaled to 10 m in space and 20 s in time. Finally, we will discuss the gains generated by the implementation of the fully distributed model.

Utp9p facilitates Msn5p-mediated nuclear reexport of retrograded tRNAs in Saccharomyces cerevisiae.

PubMed

Eswara, Manoja B K; McGuire, Andrew T; Pierce, Jacqueline B; Mangroo, Dev

2009-12-01

Utp9p is a nucleolar protein that is part of a subcomplex containing several U3 snoRNA-associated proteins including Utp8p, which is a protein that shuttles aminoacyl-tRNAs from the nucleolus to the nuclear tRNA export receptors Los1p and Msn5p in Saccharomyces cerevisiae. Here we show that Utp9p is also an intranuclear component of the Msn5p-mediated nuclear tRNA export pathway. Depletion of Utp9p caused nuclear accumulation of mature tRNAs derived from intron-containing precursors, but not tRNAs made from intronless pre-tRNAs. Utp9p binds tRNA directly and saturably, and copurifies with Utp8p, Gsp1p, and Msn5p, but not with Los1p or aminoacyl-tRNA synthetases. Utp9p interacts directly with Utp8p, Gsp1p, and Msn5p in vitro. Furthermore, Gsp1p forms a complex with Msn5p and Utp9p in a tRNA-dependent manner. However, Utp9p does not shuttle between the nucleus and the cytoplasm. Because tRNA splicing occurs in the cytoplasm and the spliced tRNAs are retrograded back to the nucleus, we propose that Utp9p facilitates nuclear reexport of retrograded tRNAs. Moreover, the data suggest that Utp9p together with Utp8p translocate aminoacyl-tRNAs from the nucleolus to Msn5p and assist with formation of the Msn5p-tRNA-Gsp1p-GTP export complex.

Postage for the messenger: Designating routes for Nuclear mRNA Export

PubMed Central

Natalizio, Barbara J.; Wente, Susan R.

2013-01-01

Transcription of messenger(m) RNA occurs in the nucleus, making the translocation of mRNA across the nuclear envelope (NE) boundary a critical determinant of proper gene expression and cell survival. A major mRNA export route occurs via the NXF1-dependent pathway through the nuclear pore complexes (NPCs) embedded in the NE. However, recent findings have discovered new evidence supporting the existence of multiple mechanisms for crossing the NE, including both NPC-mediated and NE budding-mediated pathways. An analysis of the trans-acting factors and cis components that define these pathways reveals shared elements as well as mechanistic differences. We review here the current understanding of the mechanisms that characterize each pathway and highlight the determinants that influence mRNA transport fate. PMID:23583578

7 CFR 1493.80 - Evidence of export.

Code of Federal Regulations, 2014 CFR

2014-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.80 Evidence of export. (a) Report of export. The exporter is required to provide CCC an evidence of export...

7 CFR 1493.80 - Evidence of export.

Code of Federal Regulations, 2013 CFR

2013-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.80 Evidence of export. (a) Report of export. The exporter is required to provide CCC an evidence of export...

7 CFR 1493.80 - Evidence of export.

Code of Federal Regulations, 2012 CFR

2012-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.80 Evidence of export. (a) Report of export. The exporter is required to provide CCC an evidence of export...

Navy Fact File 1984

DTIC Science & Technology

1984-10-01

Textile Fibers/Products Foods , Feeds, Beverages Industrial Supplies Value of Goods Exported ($ billions) 1958 1968 1978 $18.1 billion...character of its government, the soundness of its economy, its industrial efficiency, the development of its internal communications, the quality...decades the United States produced more raw materials than its growing industrial complex could consume. From a raw-materials-surplus-nation we

75 FR 29514 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-26

... Operation described below in the following Export Trade and Export Markets: Export Trade Export Product ALCC... being headed and gutted. Export Markets The Export Markets include all parts of the world except the... engage in Export Trade in the Export Markets, ALCC and its Members may undertake the following activities...

Nup100 regulates Saccharomyces cerevisiae replicative life span by mediating the nuclear export of specific tRNAs

PubMed Central

Lord, Christopher L.; Ospovat, Ophir; Wente, Susan R.

2017-01-01

Nuclear pore complexes (NPCs), which are composed of nucleoporins (Nups) and regulate transport between the nucleus and cytoplasm, significantly impact the replicative life span (RLS) of Saccharomyces cerevisiae. We previously reported that deletion of the nonessential gene NUP100 increases RLS, although the molecular basis for this effect was unknown. In this study, we find that nuclear tRNA accumulation contributes to increased longevity in nup100Δ cells. Fluorescence in situ hybridization (FISH) experiments demonstrate that several specific tRNAs accumulate in the nuclei of nup100Δ mutants. Protein levels of the transcription factor Gcn4 are increased when NUP100 is deleted, and GCN4 is required for the elevated life spans of nup100Δ mutants, similar to other previously described tRNA export and ribosomal mutants. Northern blots indicate that tRNA splicing and aminoacylation are not significantly affected in nup100Δ cells, suggesting that Nup100 is largely required for nuclear export of mature, processed tRNAs. Distinct tRNAs accumulate in the nuclei of nup100Δ and msn5Δ mutants, while Los1-GFP nucleocytoplasmic shuttling is unaffected by Nup100. Thus, we conclude that Nup100 regulates tRNA export in a manner distinct from Los1 or Msn5. Together, these experiments reveal a novel Nup100 role in the tRNA life cycle that impacts the S. cerevisiae life span. PMID:27932586

International trade in meat: the tip of the pork chop.

PubMed

Galloway, James N; Burke, Marshall; Bradford, G Eric; Naylor, Rosamond; Falcon, Walter; Chapagain, Ashok K; Gaskell, Joanne C; McCullough, Ellen; Mooney, Harold A; Oleson, Kirsten L L; Steinfeld, Henning; Wassenaar, Tom; Smil, Vaclav

2007-12-01

This paper provides an original account of global land, water, and nitrogen use in support of industrialized livestock production and trade, with emphasis on two of the fastest-growing sectors, pork and poultry. Our analysis focuses on trade in feed and animal products, using a new model that calculates the amount of "virtual" nitrogen, water, and land used in production but not embedded in the product. We show how key meat-importing countries, such as Japan, benefit from "virtual" trade in land, water, and nitrogen, and how key meat-exporting countries, such as Brazil, provide these resources without accounting for their true environmental cost. Results show that Japan's pig and chicken meat imports embody the virtual equivalent of 50% of Japan's total arable land, and half of Japan's virtual nitrogen total is lost in the US. Trade links with China are responsible for 15% of the virtual nitrogen left behind in Brazil due to feed and meat exports, and 20% of Brazil's area is used to grow soybean exports. The complexity of trade in meat, feed, water, and nitrogen is illustrated by the dual roles of the US and The Netherlands as both importers and exporters of meat. Mitigation of environmental damage from industrialized livestock production and trade depends on a combination of direct-pricing strategies, regulatory approaches, and use of best management practices. Our analysis indicates that increased water- and nitrogen-use efficiency and land conservation resulting from these measures could significantly reduce resource costs.

The eIF4AIII RNA helicase is a critical determinant of human cytomegalovirus replication

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

Ziehr, Ben; Lenarcic, Erik; Cecil, Chad

Human cytomegalovirus (HCMV) was recently shown to encode a large number of spliced mRNAs. While the nuclear export of unspliced viral transcripts has been extensively studied, the role of host mRNA export factors in HCMV mRNA trafficking remains poorly defined. We found that the eIF4AIII RNA helicase, a component of the exon junction complex, was necessary for efficient virus replication. Depletion of eIF4AIII limited viral DNA accumulation, export of viral mRNAs from the nucleus, and the production of progeny virus. However eIF4AIII was dispensable for the association of viral transcripts with ribosomes. We found that pateamine A, a natural compoundmore » that inhibits both eIF4AI/II and eIF4AIII, has potent antiviral activity and inhibits HCMV replication throughout the virus lytic cycle. Our results demonstrate that eIF4AIII is required for efficient HCMV replication, and suggest that eIF4A family helicases may be a new class of targets for the development of host-directed antiviral therapeutics. - Highlights: • The host eIF4AIII RNA helicase is required for efficient HCMV replication. • Depleting eIF4AIII inhibited the nuclear export of HCMV mRNAs. • HCMV mRNAs did not require eIF4AIII to associate with polyribosomes. • The eIF4A family helicases may be new targets for host-directed antiviral drugs.« less

Greenland's glacial fjords and their role in regional biogeochemical dynamics.

NASA Astrophysics Data System (ADS)

Crosby, J.; Arndt, S.

2017-12-01

Greenland's coastal fjords serve as important pathways that connect the Greenland Ice Sheet (GrIS) and the surrounding oceans. They export seasonal glacial meltwater whilst being significant sites of primary production. These fjords are home to some of the most productive ecosystems in the world and possess high socio-economic value via fisheries. A growing number of studies have proposed the GrIS as an underappreciated yet significant source of nutrients to surrounding oceans. Acting as both transfer routes and sinks for glacial nutrient export, fjords have the potential to act as significant biogeochemical processors, yet remain underexplored. Critically, an understanding of the quantitative contribution of fjords to carbon and nutrient budgets is lacking, with large uncertainties associated with limited availability of field data and the lack of robust upscaling approaches. To close this knowledge gap we developed a coupled 2D physical-biogeochemical model of the Godthåbsfjord system, a sub-Arctic sill fjord in southwest Greenland, to quantitatively assess the impact of nutrients exported from the GrIS on fjord primary productivity and biogeochemical dynamics. Glacial meltwater is found to be a key driver of fjord-scale circulation patterns, whilst tracer simulations reveal the relative nutrient contributions from meltwater-driven upwelling and meltwater export from the GrIS. Hydrodynamic circulation patterns and freshwater transit times are explored to provide a first understanding of the glacier-fjord-ocean continuum, demonstrating the complex pattern of carbon and nutrient cycling at this critical land-ocean interface.

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

Enhanced biodiversity beyond marine reserve boundaries: the cup spillith over.

PubMed

Russ, Garry R; Alcala, Angel C

2011-01-01

Overfishing can have detrimental effects on marine biodiversity and the structure of marine ecosystems. No-take marine reserves (NTMRs) are much advocated as a means of protecting biodiversity and ecosystem structure from overharvest. In contrast to terrestrial protected areas, NTMRs are not only expected to conserve or recover biodiversity and ecosystems within their boundaries, but also to enhance biodiversity beyond their boundaries by exporting species richness and more complex biological communities. Here we show that species richness of large predatory reef fish increased fourfold and 11-fold inside two Philippine no-take marine reserves over 14 and 25 years, respectively. Outside one reserve (Apo) the species richness also increased. This increase beyond the Apo reserve boundary was 78% higher closer to the boundary (200-250 m) than farther from it (250-500 m). The increase in richness beyond the boundary could not be explained by improvements over time in habitat or prey availability. Furthermore, community composition of predatory fish outside but close to (200-250 m) the Apo reserve became very similar to that inside the reserve over time, almost converging with it in multivariate space after 26 years of reserve protection. This is consistent with the suggestion that, as community composition inside Apo reserve increased in complexity, this complexity spilled over the boundary into nearby fished areas. Clearly, the spillover of species richness and community complexity is a direct consequence of the spillover of abundance of multiple species. However, this spillover of species richness and community complexity demonstrates an important benefit of biodiversity and ecosystem export from reserves, and it provides hope that reserves can help to reverse the decline of marine ecosystems and biodiversity.

Revisiting Mn and Fe removal in humic rich estuaries

NASA Astrophysics Data System (ADS)

Oldham, Véronique E.; Miller, Megan T.; Jensen, Laramie T.; Luther, George W.

2017-07-01

Metal removal by estuarine mixing has been studied for several decades, but few studies emphasize dissolved metal speciation and organic ligand complexation. Findings from the last decade indicate that metal-humic complexation can be significant for dissolved metals including Cu(II), Al(III) and Fe(III), but little consideration is given to the precipitation of these complexes with humic material at pH < 2. Given that total soluble metal analysis involves an acidification step for sample preservation, we show that Mn and other metal concentrations may have been underestimated in estuaries, especially when humic substance concentrations are high. A competitive ligand assay of selected samples from our study site, a coastal waterway bordered by wetlands (Broadkill River, DE), showed that Mn(III)-humic complexation is significant, and that some Mn(III)-L complexes precipitate during acidification. In the oxygenated surface waters of the Broadkill River, total dissolved Mn (dMnT) was up to 100% complexed to ambient ligands as Mn(III)-L, and we present evidence for humic-type Mn(III)-L complexes. The Mn(III) complexes were kinetically stabilized against Fe(II) reduction, even when [Fe(II)] was 17 times higher than [dMnT]. Unlike typical oceanic surface waters, [Fe(II)] > [Fe(III)-L] in surface waters, which may be attributed to high rates of photoreduction of Fe(III)-L complexes. Total [Mn(III)-L] ranged from 0.22 to 8.4 μM, in excess of solid MnOx (below 0.28 μM in all samples). Filtration of samples through 0.02 μm filters indicated that all Mn(III)-L complexes pass through the filters and were not colloidal species in contrast to dissolved Fe. Incubation experiments indicated that the reductive dissolution of solid MnOx by ambient ligands may be responsible for Mn(III) formation in this system. Unlike previous studies of estuarine mixing, which demonstrated metal removal during mixing, we show significant export of dMn and dissolved Fe (dFe) in the summer and fall of 2015. Thus, we propose that estuarine removal should be considered seasonal for dMn and dFe, with export in the summer and fall and removal during the winter.

Structure and functional analysis of LptC, a conserved membrane protein involved in the lipopolysaccharide export pathway in Escherichia coli.

PubMed

Tran, An X; Dong, Changjiang; Whitfield, Chris

2010-10-22

LptC is a conserved bitopic inner membrane protein from Escherichia coli involved in the export of lipopolysaccharide from its site of synthesis in the cytoplasmic membrane to the outer membrane. LptC forms a complex with the ATP-binding cassette transporter, LptBFG, which is thought to facilitate the extraction of lipopolysaccharide from the inner membrane and release it into a translocation pathway that includes the putative periplasmic chaperone LptA. Cysteine modification experiments established that the catalytic domain of LptC is oriented toward the periplasm. The structure of the periplasmic domain is described at a resolution of 2.2-Å from x-ray crystallographic data. The periplasmic domain of LptC consists of a twisted boat structure with two β-sheets in apposition to each other. The β-sheets contain seven and eight antiparallel β-strands, respectively. This structure bears a high degree of resemblance to the crystal structure of LptA. Like LptA, LptC binds lipopolysaccharide in vitro. In vitro, LptA can displace lipopolysaccharide from LptC (but not vice versa), consistent with their locations and their proposed placement in a unidirectional export pathway.

An unexpected truth: increasing nitrate loading can decrease nitrate export from watersheds

NASA Astrophysics Data System (ADS)

Askarizadeh Bardsiri, A.; Grant, S. B.; Rippy, M.

2015-12-01

The discharge of anthropogenic nitrate (e.g., from partially treated sewage, return flows from agricultural irrigation, and runoff from animal feeding operations) to streams can negatively impact both human and ecosystem health. Managing these many point and non-point sources to achieve some specific end-point—for example, reducing the annual mass of nitrate exported from a watershed—can be a challenge, particularly in rapidly growing urban areas. Adding to this complexity is the fact that streams are not inert: they too can add or remove nitrate through assimilation (e.g., by stream-associated plants and animals) and microbially-mediated biogeochemical reactions that occur in streambed sediments (e.g., respiration, ammonification, nitrification, denitrification). By coupling a previously published correlation for in-stream processing of nitrate [Mulholland et al., Nature, 2008, 452, 202-205] with a stream network model of the Jacksons Creek watershed (Victoria, Australia) I demonstrate that managing anthropogenic sources of stream nitrate without consideration of in-stream processing can result in a number of non-intuitive "surprises"; for example, wastewater effluent discharges that increase nitrate loading but decrease in-stream nitrate concentrations can reduce the mass of nitrate exported from a watershed.

Export of earthquake-triggered landslides in active mountain ranges: insights from 2D morphodynamic modelling.

NASA Astrophysics Data System (ADS)

Croissant, Thomas; Lague, Dimitri; Davy, Philippe; Steer, Philippe

2016-04-01

In active mountain ranges, large earthquakes (Mw > 5-6) trigger numerous landslides that impact river dynamics. These landslides bring local and sudden sediment piles that will be eroded and transported along the river network causing downstream changes in river geometry, transport capacity and erosion efficiency. The progressive removal of landslide materials has implications for downstream hazards management and also for understanding landscape dynamics at the timescale of the seismic cycle. The export time of landslide-derived sediments after large-magnitude earthquakes has been studied from suspended load measurements but a full understanding of the total process, including the coupling between sediment transfer and channel geometry change, still remains an issue. Note that the transport of small sediment pulses has been studied in the context of river restoration, but the magnitude of sediment pulses generated by landslides may make the problem different. Here, we study the export of large volumes (>106 m3) of sediments with the 2D hydro-morphodynamic model, Eros. This model uses a new hydrodynamic module that resolves a reduced form of the Saint-Venant equations with a particle method. It is coupled with a sediment transport and lateral and vertical erosion model. Eros accounts for the complex retroactions between sediment transport and fluvial geometry, with a stochastic description of the floods experienced by the river. Moreover, it is able to reproduce several features deemed necessary to study the evacuation of large sediment pulses, such as river regime modification (single-thread to multi-thread), river avulsion and aggradation, floods and bank erosion. Using a synthetic and simple topography we first present how granulometry, landslide volume and geometry, channel slope and flood frequency influence 1) the dominance of pulse advection vs. diffusion during its evacuation, 2) the pulse export time and 3) the remaining volume of sediment in the catchment. The model is then applied to a high resolution (5-10 m) digital elevation model of the Poerua catchment in New Zealand which has been impacted by the effect of a large landslide during the last 15 years. We investigate several plausible Alpine Faults earthquake scenarios to study the propagation of the sediment along a complex river network. We characterize and quantify the sediment pulse export time and mechanism for this river configuration and show its impact on the alluvial plain evolution. Our findings have strong implications for the understanding of aggradation rates and the temporal persistence of induced hazards in the alluvial plain as well as of sediment transfers in active mountain belts.

Characterization of Human Disease Phenotypes Associated with Mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1

PubMed Central

Crow, Yanick J.; Chase, Diana S.; Schmidt, Johanna Lowenstein; Szynkiewicz, Marcin; Forte, Gabriella M.A.; Gornall, Hannah L.; Oojageer, Anthony; Anderson, Beverley; Pizzino, Amy; Helman, Guy; Abdel-Hamid, Mohamed S.; Abdel-Salam, Ghada M.; Ackroyd, Sam; Aeby, Alec; Agosta, Guillermo; Albin, Catherine; Allon-Shalev, Stavit; Arellano, Montse; Ariaudo, Giada; Aswani, Vijay; Babul-Hirji, Riyana; Baildam, Eileen M.; Bahi-Buisson, Nadia; Bailey, Kathryn M.; Barnerias, Christine; Barth, Magalie; Battini, Roberta; Beresford, Michael W.; Bernard, Geneviève; Bianchi, Marika; de Villemeur, Thierry Billette; Blair, Edward M.; Bloom, Miriam; Burlina, Alberto B.; Carpanelli, Maria Luisa; Carvalho, Daniel R.; Castro-Gago, Manuel; Cavallini, Anna; Cereda, Cristina; Chandler, Kate E.; Chitayat, David A.; Collins, Abigail E.; Corcoles, Concepcion Sierra; Cordeiro, Nuno J.V.; Crichiutti, Giovanni; Dabydeen, Lyvia; Dale, Russell C.; D’Arrigo, Stefano; De Goede, Christian G.E.L.; De Laet, Corinne; De Waele, Liesbeth M.H.; Denzler, Ines; Desguerre, Isabelle; Devriendt, Koenraad; Di Rocco, Maja; Fahey, Michael C.; Fazzi, Elisa; Ferrie, Colin D.; Figueiredo, António; Gener, Blanca; Goizet, Cyril; Gowrinathan, Nirmala R.; Gowrishankar, Kalpana; Hanrahan, Donncha; Isidor, Bertrand; Kara, Bülent; Khan, Nasaim; King, Mary D.; Kirk, Edwin P.; Kumar, Ram; Lagae, Lieven; Landrieu, Pierre; Lauffer, Heinz; Laugel, Vincent; La Piana, Roberta; Lim, Ming J.; Lin, Jean-Pierre S.-M.; Linnankivi, Tarja; Mackay, Mark T.; Marom, Daphna R.; Lourenço, Charles Marques; McKee, Shane A.; Moroni, Isabella; Morton, Jenny E.V.; Moutard, Marie-Laure; Murray, Kevin; Nabbout, Rima; Nampoothiri, Sheela; Nunez-Enamorado, Noemi; Oades, Patrick J.; Olivieri, Ivana; Ostergaard, John R.; Pérez-Dueñas, Belén; Prendiville, Julie S.; Ramesh, Venkateswaran; Rasmussen, Magnhild; Régal, Luc; Ricci, Federica; Rio, Marlène; Rodriguez, Diana; Roubertie, Agathe; Salvatici, Elisabetta; Segers, Karin A.; Sinha, Gyanranjan P.; Soler, Doriette; Spiegel, Ronen; Stödberg, Tommy I.; Straussberg, Rachel; Swoboda, Kathryn J.; Suri, Mohnish; Tacke, Uta; Tan, Tiong Y.; Naude, Johann te Water; Teik, Keng Wee; Thomas, Maya Mary; Till, Marianne; Tonduti, Davide; Valente, Enza Maria; Van Coster, Rudy Noel; van der Knaap, Marjo S.; Vassallo, Grace; Vijzelaar, Raymon; Vogt, Julie; Wallace, Geoffrey B.; Wassmer, Evangeline; Webb, Hannah J.; Whitehouse, William P.; Whitney, Robyn N.; Zaki, Maha S.; Zuberi, Sameer M.; Livingston, John H.; Rozenberg, Flore; Lebon, Pierre; Vanderver, Adeline; Orcesi, Simona; Rice, Gillian I.

2015-01-01

Aicardi–Goutières syndrome is an inflammatory disease occurring due to mutations in any of TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR or IFIH1. We report on 374 patients from 299 families with mutations in these seven genes. Most patients conformed to one of two fairly stereotyped clinical profiles; either exhibiting an in utero disease-onset (74 patients; 22.8% of all patients where data were available), or a post-natal presentation, usually within the first year of life (223 patients; 68.6%), characterized by a sub-acute encephalopathy and a loss of previously acquired skills. Other clinically distinct phenotypes were also observed; particularly, bilateral striatal necrosis (13 patients; 3.6%) and non-syndromic spastic paraparesis (12 patients; 3.4%). We recorded 69 deaths (19.3% of patients with follow-up data). Of 285 patients for whom data were available, 210 (73.7%) were profoundly disabled, with no useful motor, speech and intellectual function. Chilblains, glaucoma, hypothyroidism, cardiomyopathy, intracerebral vasculitis, peripheral neuropathy, bowel inflammation and systemic lupus erythematosus were seen frequently enough to be confirmed as real associations with the Aicardi-Goutieres syndrome phenotype. We observed a robust relationship between mutations in all seven genes with increased type I interferon activity in cerebrospinal fluid and serum, and the increased expression of interferon-stimulated gene transcripts in peripheral blood. We recorded a positive correlation between the level of cerebrospinal fluid interferon activity assayed within one year of disease presentation and the degree of subsequent disability. Interferon-stimulated gene transcripts remained high in most patients, indicating an ongoing disease process. On the basis of substantial morbidity and mortality, our data highlight the urgent need to define coherent treatment strategies for the phenotypes associated with mutations in the Aicardi–Goutières syndrome-related genes. Our findings also make it clear that a window of therapeutic opportunity exists relevant to the majority of affected patients and indicate that the assessment of type I interferon activity might serve as a useful biomarker in future clinical trials. PMID:25604658

Characterization of human disease phenotypes associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1.

PubMed

Crow, Yanick J; Chase, Diana S; Lowenstein Schmidt, Johanna; Szynkiewicz, Marcin; Forte, Gabriella M A; Gornall, Hannah L; Oojageer, Anthony; Anderson, Beverley; Pizzino, Amy; Helman, Guy; Abdel-Hamid, Mohamed S; Abdel-Salam, Ghada M; Ackroyd, Sam; Aeby, Alec; Agosta, Guillermo; Albin, Catherine; Allon-Shalev, Stavit; Arellano, Montse; Ariaudo, Giada; Aswani, Vijay; Babul-Hirji, Riyana; Baildam, Eileen M; Bahi-Buisson, Nadia; Bailey, Kathryn M; Barnerias, Christine; Barth, Magalie; Battini, Roberta; Beresford, Michael W; Bernard, Geneviève; Bianchi, Marika; Billette de Villemeur, Thierry; Blair, Edward M; Bloom, Miriam; Burlina, Alberto B; Carpanelli, Maria Luisa; Carvalho, Daniel R; Castro-Gago, Manuel; Cavallini, Anna; Cereda, Cristina; Chandler, Kate E; Chitayat, David A; Collins, Abigail E; Sierra Corcoles, Concepcion; Cordeiro, Nuno J V; Crichiutti, Giovanni; Dabydeen, Lyvia; Dale, Russell C; D'Arrigo, Stefano; De Goede, Christian G E L; De Laet, Corinne; De Waele, Liesbeth M H; Denzler, Ines; Desguerre, Isabelle; Devriendt, Koenraad; Di Rocco, Maja; Fahey, Michael C; Fazzi, Elisa; Ferrie, Colin D; Figueiredo, António; Gener, Blanca; Goizet, Cyril; Gowrinathan, Nirmala R; Gowrishankar, Kalpana; Hanrahan, Donncha; Isidor, Bertrand; Kara, Bülent; Khan, Nasaim; King, Mary D; Kirk, Edwin P; Kumar, Ram; Lagae, Lieven; Landrieu, Pierre; Lauffer, Heinz; Laugel, Vincent; La Piana, Roberta; Lim, Ming J; Lin, Jean-Pierre S-M; Linnankivi, Tarja; Mackay, Mark T; Marom, Daphna R; Marques Lourenço, Charles; McKee, Shane A; Moroni, Isabella; Morton, Jenny E V; Moutard, Marie-Laure; Murray, Kevin; Nabbout, Rima; Nampoothiri, Sheela; Nunez-Enamorado, Noemi; Oades, Patrick J; Olivieri, Ivana; Ostergaard, John R; Pérez-Dueñas, Belén; Prendiville, Julie S; Ramesh, Venkateswaran; Rasmussen, Magnhild; Régal, Luc; Ricci, Federica; Rio, Marlène; Rodriguez, Diana; Roubertie, Agathe; Salvatici, Elisabetta; Segers, Karin A; Sinha, Gyanranjan P; Soler, Doriette; Spiegel, Ronen; Stödberg, Tommy I; Straussberg, Rachel; Swoboda, Kathryn J; Suri, Mohnish; Tacke, Uta; Tan, Tiong Y; te Water Naude, Johann; Wee Teik, Keng; Thomas, Maya Mary; Till, Marianne; Tonduti, Davide; Valente, Enza Maria; Van Coster, Rudy Noel; van der Knaap, Marjo S; Vassallo, Grace; Vijzelaar, Raymon; Vogt, Julie; Wallace, Geoffrey B; Wassmer, Evangeline; Webb, Hannah J; Whitehouse, William P; Whitney, Robyn N; Zaki, Maha S; Zuberi, Sameer M; Livingston, John H; Rozenberg, Flore; Lebon, Pierre; Vanderver, Adeline; Orcesi, Simona; Rice, Gillian I

2015-02-01

Aicardi-Goutières syndrome is an inflammatory disease occurring due to mutations in any of TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR or IFIH1. We report on 374 patients from 299 families with mutations in these seven genes. Most patients conformed to one of two fairly stereotyped clinical profiles; either exhibiting an in utero disease-onset (74 patients; 22.8% of all patients where data were available), or a post-natal presentation, usually within the first year of life (223 patients; 68.6%), characterized by a sub-acute encephalopathy and a loss of previously acquired skills. Other clinically distinct phenotypes were also observed; particularly, bilateral striatal necrosis (13 patients; 3.6%) and non-syndromic spastic paraparesis (12 patients; 3.4%). We recorded 69 deaths (19.3% of patients with follow-up data). Of 285 patients for whom data were available, 210 (73.7%) were profoundly disabled, with no useful motor, speech and intellectual function. Chilblains, glaucoma, hypothyroidism, cardiomyopathy, intracerebral vasculitis, peripheral neuropathy, bowel inflammation and systemic lupus erythematosus were seen frequently enough to be confirmed as real associations with the Aicardi-Goutieres syndrome phenotype. We observed a robust relationship between mutations in all seven genes with increased type I interferon activity in cerebrospinal fluid and serum, and the increased expression of interferon-stimulated gene transcripts in peripheral blood. We recorded a positive correlation between the level of cerebrospinal fluid interferon activity assayed within one year of disease presentation and the degree of subsequent disability. Interferon-stimulated gene transcripts remained high in most patients, indicating an ongoing disease process. On the basis of substantial morbidity and mortality, our data highlight the urgent need to define coherent treatment strategies for the phenotypes associated with mutations in the Aicardi-Goutières syndrome-related genes. Our findings also make it clear that a window of therapeutic opportunity exists relevant to the majority of affected patients and indicate that the assessment of type I interferon activity might serve as a useful biomarker in future clinical trials. © 2015 Wiley Periodicals, Inc.

Retinoic acid-independent expression of Meis2 during autopod patterning in the developing bat and mouse limb.

PubMed

Mason, Mandy K; Hockman, Dorit; Curry, Lyle; Cunningham, Thomas J; Duester, Gregg; Logan, Malcolm; Jacobs, David S; Illing, Nicola

2015-01-01

The bat has strikingly divergent forelimbs (long digits supporting wing membranes) and hindlimbs (short, typically free digits) due to the distinct requirements of both aerial and terrestrial locomotion. During embryonic development, the morphology of the bat forelimb deviates dramatically from the mouse and chick, offering an alternative paradigm for identifying genes that play an important role in limb patterning. Using transcriptome analysis of developing Natal long-fingered bat (Miniopterus natalensis) fore- and hindlimbs, we demonstrate that the transcription factor Meis2 has a significantly higher expression in bat forelimb autopods compared to hindlimbs. Validation by reverse transcriptase and quantitative polymerase chain reaction (RT-qPCR) and whole mount in situ hybridisation shows that Meis2, conventionally known as a marker of the early proximal limb bud, is upregulated in the bat forelimb autopod from CS16. Meis2 expression is localised to the expanding interdigital webbing and the membranes linking the wing to the hindlimb and tail. In mice, Meis2 is also expressed in the interdigital region prior to tissue regression. This interdigital Meis2 expression is not activated by retinoic acid (RA) signalling as it is present in the retained interdigital tissue of Rdh10 (trex/trex) mice, which lack RA. Additionally, genes encoding RA-synthesising enzymes, Rdh10 and Aldh1a2, and the RA nuclear receptor Rarβ are robustly expressed in bat fore- and hindlimb interdigital tissues indicating that the mechanism that retains interdigital tissue in bats also occurs independently of RA signalling. Mammalian interdigital Meis2 expression, and upregulation in the interdigital webbing of bat wings, suggests an important role for Meis2 in autopod development. Interdigital Meis2 expression is RA-independent, and retention of interdigital webbing in bat wings is not due to the suppression of RA-induced cell death. Rather, RA signalling may play a role in the thinning (rather than complete loss) of the interdigital tissue in the bat forelimb, while Meis2 may interact with other factors during both bat and mouse autopod development to maintain a pool of interdigital cells that contribute to digit patterning and growth.

Tec-kinase-mediated phosphorylation of fibroblast growth factor 2 is essential for unconventional secretion.

PubMed

Ebert, Antje D; Laussmann, Mareike; Wegehingel, Sabine; Kaderali, Lars; Erfle, Holger; Reichert, Jürgen; Lechner, Johannes; Beer, Hans-Dietmar; Pepperkok, Rainer; Nickel, Walter

2010-06-01

Fibroblast growth factor 2 (FGF2) is a potent mitogen that is exported from cells by an endoplasmic reticulum (ER)/Golgi-independent mechanism. Unconventional secretion of FGF2 occurs by direct translocation across plasma membranes, a process that depends on the phosphoinositide phosphatidylinositol 4,5-biphosphate (PI(4,5)P(2)) at the inner leaflet as well as heparan sulfate proteoglycans at the outer leaflet of plasma membranes; however, additional core and regulatory components of the FGF2 export machinery have remained elusive. Here, using a highly effective RNAi screening approach, we discovered Tec kinase as a novel factor involved in unconventional secretion of FGF2. Tec kinase does not affect FGF2 secretion by an indirect mechanism, but rather forms a heterodimeric complex with FGF2 resulting in phosphorylation of FGF2 at tyrosine 82, a post-translational modification shown to be essential for FGF2 membrane translocation to cell surfaces. Our findings suggest a crucial role for Tec kinase in regulating FGF2 secretion under various physiological conditions and, therefore, provide a new perspective for the development of a novel class of antiangiogenic drugs targeting the formation of the FGF2/Tec complex.

A fraction of Crm1 locates at centrosomes by its CRIME domain and regulates the centrosomal localization of pericentrin

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

Liu, Qinying; Jiang, Qing; Zhang, Chuanmao, E-mail: zhangcm@pku.edu.cn

Crm1 plays a role in exporting proteins containing nuclear export signals (NESs) from the nucleus to the cytoplasm. Some proteins that are capable of interacting with Ran/Crm1 were reported to be localized at centrosomes and to function as centrosome checkpoints. But it remains unclear how Crm1 locates at centrosomes. In this study, we found that a fraction of Crm1 is located at centrosomes through its N-terminal CRM1, importin {beta} etc. (CRIME) domain, which is responsible for interacting with RanGTP, suggesting that Crm1 might target to centrosomes through binding centrosomal RanGTP. Moreover, overexpression of the CRIME domain, which is free ofmore » NES binding domain, resulted in the dissociation of pericentrin and {gamma}-tubulin complex from centrosomes and the disruption of microtubule nucleation. Deficiency of Crm1 provoked by RNAi also decreased the spindle poles localization of pericentrin and {gamma}-tubulin complex, coupled with mitotic defects. Since pericentrin was sensitive to Crm1 specific inhibitor leptomycin B, we propose that the centrosomal Crm1 might interact with pericentrin and regulate the localization and function of pericentrin at centrosomes.« less

Greatwall is essential to prevent mitotic collapse after nuclear envelope breakdown in mammals.

PubMed

Álvarez-Fernández, Mónica; Sánchez-Martínez, Ruth; Sanz-Castillo, Belén; Gan, Pei Pei; Sanz-Flores, María; Trakala, Marianna; Ruiz-Torres, Miguel; Lorca, Thierry; Castro, Anna; Malumbres, Marcos

2013-10-22

Greatwall is a protein kinase involved in the inhibition of protein phosphatase 2 (PP2A)-B55 complexes to maintain the mitotic state. Although its biochemical activity has been deeply characterized in Xenopus, its specific relevance during the progression of mitosis is not fully understood. By using a conditional knockout of the mouse ortholog, Mastl, we show here that mammalian Greatwall is essential for mouse embryonic development and cell cycle progression. Yet, Greatwall-null cells enter into mitosis with normal kinetics. However, these cells display mitotic collapse after nuclear envelope breakdown (NEB) characterized by defective chromosome condensation and prometaphase arrest. Intriguingly, Greatwall is exported from the nucleus to the cytoplasm in a CRM1-dependent manner before NEB. This export occurs after the nuclear import of cyclin B-Cdk1 complexes, requires the kinase activity of Greatwall, and is mediated by Cdk-, but not Polo-like kinase 1-dependent phosphorylation. The mitotic collapse observed in Greatwall-deficient cells is partially rescued after concomitant depletion of B55 regulatory subunits, which are mostly cytoplasmic before NEB. These data suggest that Greatwall is an essential protein in mammals required to prevent mitotic collapse after NEB.

Direct identification of the site of binding on the chaperone SecB for the amino terminus of the translocon motor SecA.

PubMed

Randall, Linda L; Henzl, Michael T

2010-06-01

Protein export mediated by the general secretory Sec system in Escherichia coli proceeds by a dynamic transfer of a precursor polypeptide from the chaperone SecB to the SecA ATPase motor of the translocon and subsequently into and through the channel of the membrane-embedded SecYEG heterotrimer. The complex between SecA and SecB is stabilized by several separate sites of contact. Here we have demonstrated directly an interaction between the N-terminal residues 2 through 11 of SecA and the C-terminal 13 residues of SecB by isothermal titration calorimetry and analytical sedimentation velocity centrifugation. We discuss the unusual binding properties of SecA and SecB in context of a model for transfer of the precursor along the pathway of export.

7 CFR 1493.470 - Evidence of export.

Code of Federal Regulations, 2012 CFR

2012-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Supplier Credit Guarantee... provide CCC an evidence of export report for each shipment made under the payment guarantee. This report... participation in any of the following CCC or USDA export program: Export Enhancement Program, Dairy Export...

7 CFR 1493.470 - Evidence of export.

Code of Federal Regulations, 2014 CFR

2014-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Supplier Credit Guarantee... provide CCC an evidence of export report for each shipment made under the payment guarantee. This report... participation in any of the following CCC or USDA export program: Export Enhancement Program, Dairy Export...

7 CFR 1493.470 - Evidence of export.

Code of Federal Regulations, 2013 CFR

2013-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Supplier Credit Guarantee... provide CCC an evidence of export report for each shipment made under the payment guarantee. This report... participation in any of the following CCC or USDA export program: Export Enhancement Program, Dairy Export...

7 CFR 1493.470 - Evidence of export.

Code of Federal Regulations, 2011 CFR

2011-01-01

... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC... exporter is required to provide CCC an evidence of export report for each shipment made under the payment... participation in any of the following CCC or USDA export program: Export Enhancement Program, Dairy Export...

7 CFR 1493.80 - Evidence of export.

Code of Federal Regulations, 2011 CFR

2011-01-01

... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.80 Evidence of export. (a) Report of export. The exporter is required to provide CCC an...

Intertidal salt marshes as an important source of inorganic carbon to the coastal ocean

USGS Publications Warehouse

Wang, Zhaohui Aleck; Kroeger, Kevin D.; Ganju, Neil K.; Gonneea, Meagan; Chu, Sophie N.

2016-01-01

Dynamic tidal export of dissolved inorganic carbon (DIC) to the coastal ocean from highly productive intertidal marshes and its effects on seawater carbonate chemistry are thoroughly evaluated. The study uses a comprehensive approach by combining tidal water sampling of CO2parameters across seasons, continuous in situ measurements of biogeochemically-relevant parameters and water fluxes, with high-resolution modeling in an intertidal salt marsh of the U.S. northeast region. Salt marshes can acidify and alkalize tidal water by injecting CO2 (DIC) and total alkalinity (TA). DIC and TA generation may also be decoupled due to differential effects of marsh aerobic and anaerobic respiration on DIC and TA. As marsh DIC is added to tidal water, the buffering capacity first decreases to a minimum and then increases quickly. Large additions of marsh DIC can result in higher buffering capacity in ebbing tide than incoming tide. Alkalization of tidal water, which mostly occurs in the summer due to anaerobic respiration, can further modify buffering capacity. Marsh exports of DIC and alkalinity may have complex implications for the future, more acidified ocean. Marsh DIC export exhibits high variability over tidal and seasonal cycles, which is modulated by both marsh DIC generation and by water fluxes. The marsh DIC export of 414 g C m−2 yr−1, based on high-resolution measurements and modeling, is more than twice the previous estimates. It is a major term in the marsh carbon budget and translates to one of the largest carbon fluxes along the U.S. East Coast.

Nup100 regulates Saccharomyces cerevisiae replicative life span by mediating the nuclear export of specific tRNAs.

PubMed

Lord, Christopher L; Ospovat, Ophir; Wente, Susan R

2017-03-01

Nuclear pore complexes (NPCs), which are composed of nucleoporins (Nups) and regulate transport between the nucleus and cytoplasm, significantly impact the replicative life span (RLS) of Saccharomyces cerevisiae We previously reported that deletion of the nonessential gene NUP100 increases RLS, although the molecular basis for this effect was unknown. In this study, we find that nuclear tRNA accumulation contributes to increased longevity in nup100 Δ cells. Fluorescence in situ hybridization (FISH) experiments demonstrate that several specific tRNAs accumulate in the nuclei of nup100 Δ mutants. Protein levels of the transcription factor Gcn4 are increased when NUP100 is deleted, and GCN4 is required for the elevated life spans of nup100 Δ mutants, similar to other previously described tRNA export and ribosomal mutants. Northern blots indicate that tRNA splicing and aminoacylation are not significantly affected in nup100 Δ cells, suggesting that Nup100 is largely required for nuclear export of mature, processed tRNAs. Distinct tRNAs accumulate in the nuclei of nup100 Δ and msn5 Δ mutants, while Los1-GFP nucleocytoplasmic shuttling is unaffected by Nup100. Thus, we conclude that Nup100 regulates tRNA export in a manner distinct from Los1 or Msn5. Together, these experiments reveal a novel Nup100 role in the tRNA life cycle that impacts the S. cerevisiae life span. © 2017 Lord et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Expression and characterization of the Plasmodium translocon of the exported proteins component EXP2.

PubMed

Hakamada, Kazuaki; Watanabe, Hirokazu; Kawano, Ryuji; Noguchi, Keiichi; Yohda, Masafumi

2017-01-22

The malaria parasite Plasmodium falciparum requires the Plasmodium translocon of exported proteins (PTEX) to proliferate in human red blood cells. During the blood stages of malaria, several hundred parasite-encoded proteins are exported from the parasite into the cytosol of red blood cells. PTEX is the translocon for protein export and comprises 5 proteins: EXP2, PTEX150, PTEX88, Hsp101 and TRX2. Among them, EXP2 is thought to constitute the transmembrane pore, whereas the other components seem to play a role in unfolding the luggage proteins or providing a driving force. However, detailed functional and structural characterizations of PTEX proteins have not been performed. In this study, we expressed and characterized the membrane-associated component EXP2. Because expression of EXP2 is lethal to E. coli, EXP2 was expressed as a fusion protein with GST, and the recombinant EXP2 was obtained by protease digestion. The recombinant EXP2 formed pores in bilayer lipid membranes. The inner diameter of the pore was estimated to be approximately 3.5 nm based on electron microscopy images and channel currents. From this size and the molecular mass as determined by size exclusion chromatography and blue native polyacrylamide gel electrophoresis, we determined that the pore comprises approximately 10-12 EXP2 subunits. However, there is a possibility that the pore structure is different in the PTEX complex. These results provide important insights in the protein transport mechanism of PTEX, which will aid in developing new drugs targeting PTEX. Copyright © 2016 Elsevier Inc. All rights reserved.

Environmental Effects on Mesozooplankton Size Structure and Export Flux at Station ALOHA, North Pacific Subtropical Gyre

NASA Astrophysics Data System (ADS)

Valencia, Bellineth; Décima, Moira; Landry, Michael R.

2018-02-01

Using size-fractionated mesozooplankton biomass data collected over 23 years (1994-2016) of increasing primary production (PP) at station ALOHA (A Long-Term Oligotrophic Habitat Assessment), we evaluate how changing environmental conditions affect mesozooplankton size structure, trophic cycling, and export fluxes in the subtropical North Pacific. From generalized additive model analysis, size structure is significantly influenced by a nonlinear relationship with sea surface temperature that is mainly driven by the strong 1997-1998 El Niño and a positive and linear relationship with PP. Increasing PP has more strongly enhanced the biomass of smaller (0.2-0.5 mm) and larger (>5 mm) mesozooplankton, increasing evenness of the biomass spectra, while animals of 2-5 mm, the major size class for vertically migrating mesozooplankton, show no long-term trend. Measured PP is sufficient to meet feeding requirements that satisfy mesozooplankton respiration and growth rates, as determined by commonly used empirical relationships based on animal size and temperature, consistent with a tightly coupled food web with one intermediate level for protistan consumers. Estimated fecal pellet production suggests an enhanced contribution of mesozooplankton to passive particle export relative to the material collected in 150 m sediment traps. In contrast, the biomass of vertically migrants does not vary systematically with PP due to the varying responses of the different size classes. These results illustrate some complexities in understanding how varying environmental conditions can affect carbon cycling and export processes at the community level in open-ocean oligotrophic systems, which need to be confirmed and better understood by process-oriented mechanistic study.

22 CFR 123.22 - Filing, retention, and return of export licenses and filing of export information.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Filing, retention, and return of export licenses and filing of export information. 123.22 Section 123.22 Foreign Relations DEPARTMENT OF STATE....22 Filing, retention, and return of export licenses and filing of export information. (a) Any export...

U.S. hardwood product exports, hardwood exports to Korea, hardwood resource situation, and the future of U.S. exports to Korea

Treesearch

Philip A. Araman

1991-01-01

The exerpts from this seminar are intended to give an overview of U.S. hardwood exports, hardwood exports to Korea, the hardwood resource situation, and the future of U.S. hardwood exports to Korea. It includes 1) some basic information about total U.S. hardwood exports and products, 2) information on hardwood exports to Korea from the U.S., 3) U.S. hardwood resources...

Synthesis of nutrient and sediment export patterns in the Chesapeake Bay watershed: Complex and non-stationary concentration-discharge relationships.

PubMed

Zhang, Qian

2018-03-15

Derived from river monitoring data, concentration-discharge (C-Q) relationships are useful indicators of riverine export dynamics. A top-down synthesis of C-Q patterns was conducted for suspended sediment (SS), total phosphorus (TP), and total nitrogen (TN) for nine major tributaries (15 monitoring sites) to Chesapeake Bay, which represent diverse characteristics in terms of land use, physiography, and hydrological settings. Model coefficients from the recently-developed Weighted Regressions on Time, Discharge, and Season (WRTDS) method were used to make informative interpretation of C-Q relationships. Unlike many previous C-Q studies that focused on stormflow conditions, this approach allows simultaneous examination of various discharge conditions within an uncertainty framework. This synthesis on WRTDS coefficients (i.e., the sensitivity of concentration to discharge) has offered new insights on the complexity of watershed function. Results show that watershed export has been dominated by mobilization patterns for SS and TP (particulate-dominated species) and chemostasis patterns for TN (dissolved-dominated species) under many river discharge conditions. Among nine possible modalities of low-flow vs. high-flow patterns, the three most frequent modalities are mobilization vs. mobilization (17 cases), chemostasis vs. mobilization (13 cases), and chemostasis vs. chemostasis (7 cases), representing 82% of all 45 watershed-constituent pairs. The general lack of dilution patterns may suggest that none of these constituents has been supply-limited in these watersheds. For many watershed-constituent combinations, results show clear temporal non-stationarity in C-Q relationships under selected time-invariant discharges, reflecting major changes in dominant watershed sources due to anthropogenic actions. These results highlight the potential pitfalls of assuming fixed C-Q relationships in the record. Overall, this work demonstrates the utility of WRTDS model coefficients for interpretation of river water-quality data and for generation of sensible hypotheses on dominant processes in different watersheds. The approach is readily adaptable to other river systems, where long-term discretely-sampled data are available, to decipher complex interactions between hydrological and biogeochemical processes. Copyright © 2017 Elsevier B.V. All rights reserved.

15 CFR 752.15 - Export clearance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Export clearance. 752.15 Section 752... OF INDUSTRY AND SECURITY, DEPARTMENT OF COMMERCE EXPORT ADMINISTRATION REGULATIONS SPECIAL COMPREHENSIVE LICENSE § 752.15 Export clearance. (a) Shipper's Export Declaration (SED) or Automated Export...

78 FR 37518 - Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-21

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the... Texas, Lee Roy Perez (``Perez'') was convicted of violating Section 38 of the Arms Export Control Act... of knowingly and willfully exporting and causing to be exported and attempting to export and...

7 CFR 1493.130 - Recovery of losses.

Code of Federal Regulations, 2013 CFR

2013-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.130 Recovery of losses. (a) Notification. Upon payment of loss to the exporter or the exporter's assignee, CCC...

7 CFR 1493.130 - Recovery of losses.

Code of Federal Regulations, 2012 CFR

2012-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.130 Recovery of losses. (a) Notification. Upon payment of loss to the exporter or the exporter's assignee, CCC...

7 CFR 1493.130 - Recovery of losses.

Code of Federal Regulations, 2014 CFR

2014-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.130 Recovery of losses. (a) Notification. Upon payment of loss to the exporter or the exporter's assignee, CCC...

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Bogacheva, E. N.; Dadinova, L. A.; Jeffries, C. M.; Fedorova, N. V.; Golovko, A. O.; Baratova, L. A.; Batishchev, O. V.

2017-11-01

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological pH value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

Zooplankton and the Ocean Carbon Cycle.

PubMed

Steinberg, Deborah K; Landry, Michael R

2017-01-03

Marine zooplankton comprise a phylogenetically and functionally diverse assemblage of protistan and metazoan consumers that occupy multiple trophic levels in pelagic food webs. Within this complex network, carbon flows via alternative zooplankton pathways drive temporal and spatial variability in production-grazing coupling, nutrient cycling, export, and transfer efficiency to higher trophic levels. We explore current knowledge of the processing of zooplankton food ingestion by absorption, egestion, respiration, excretion, and growth (production) processes. On a global scale, carbon fluxes are reasonably constrained by the grazing impact of microzooplankton and the respiratory requirements of mesozooplankton but are sensitive to uncertainties in trophic structure. The relative importance, combined magnitude, and efficiency of export mechanisms (mucous feeding webs, fecal pellets, molts, carcasses, and vertical migrations) likewise reflect regional variability in community structure. Climate change is expected to broadly alter carbon cycling by zooplankton and to have direct impacts on key species.

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

Nishino, Tomonori G.; Department of Biotechnology, University of Tokyo, Bunkyo-ku, Tokyo 113-8657; Miyazaki, Masaya

Class IIa histone deacetylases (HDACs) form complexes with a class of transcriptional repressors in the nucleus. While screening for compounds that could block the association of HDAC4 with the BTB domain-containing transcriptional repressor Bach2, we discovered that phorbol 12-myristate 13-acetate (PMA) induced the cytoplasmic retention of HDAC4 mutants lacking a nuclear export signal (NES). Although PMA treatment and PKD overexpression has been proposed to facilitate the nuclear export of class IIa HDACs by creating 14-3-3 binding sites containing phosphoserines, our experiments using HDAC mutants demonstrated that PMA greatly reduces nuclear import. PMA treatment repressed the NLS activity in a mannermore » dependent on 14-3-3 binding. These results suggest that nuclear HDAC4 is not tethered in the nucleus, but instead shuttles between the nucleus and the cytoplasm. Phosphorylation-induced 14-3-3 binding biases the balance of nucleo-cytoplasmic shuttling toward the cytoplasm by inhibiting nuclear import.« less

76 FR 9550 - President's Export Council: Meeting of the President's Export Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-18

... DEPARTMENT OF COMMERCE International Trade Administration President's Export Council: Meeting of the President's Export Council AGENCY: International Trade Administration, U.S. Department of Commerce.... exports, jobs, and growth. DATES: March 11, 2011 at 9:30 a.m. (ET). ADDRESSES: The President's Export...

78 FR 37787 - Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-24

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the... District of Texas, Manuel Mario Pavon (``Pavon'') was convicted of violating Section 38 of the Arms Export... knowingly and willfully exporting and causing to be exported and attempting to export and attempting to...

75 FR 54540 - Effects of Foreign Policy-Based Export Controls

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-08

.... 100719301-0303-02] Effects of Foreign Policy-Based Export Controls AGENCY: Bureau of Industry and Security... foreign policy-based export controls in the Export Administration Regulations to determine whether they... comments on how existing foreign policy-based export controls have affected exporters and the general...

Replacement of the yeast TRP4 3' untranslated region by a hammerhead ribozyme results in a stable and efficiently exported mRNA that lacks a poly(A) tail.

PubMed Central

Düvel, Katrin; Valerius, Oliver; Mangus, David A; Jacobson, Allan; Braus, Gerhard H

2002-01-01

The mRNA poly(A) tail serves different purposes, including the facilitation of nuclear export, mRNA stabilization, efficient translation, and, finally, specific degradation. The posttranscriptional addition of a poly(A) tail depends on sequence motifs in the 3' untranslated region (3' UTR) of the mRNA and a complex trans-acting protein machinery. In this study, we have replaced the 3' UTR of the yeast TRP4 gene with sequences encoding a hammerhead ribozyme that efficiently cleaves itself in vivo. Expression of the TRP4-ribozyme allele resulted in the accumulation of a nonpolyadenylated mRNA. Cells expressing the TRP4-ribozyme mRNA showed a reduced growth rate due to a reduction in Trp4p enzyme activity. The reduction in enzyme activity was not caused by inefficient mRNA export from the nucleus or mRNA destabilization. Rather, analyses of mRNA association with polyribosomes indicate that translation of the ribozyme-containing mRNA is impaired. This translational defect allows sufficient synthesis of Trp4p to support growth of trp4 cells, but is, nevertheless, of such magnitude as to activate the general control network of amino acid biosynthesis. PMID:12003493

Trade-driven relocation of air pollution and health impacts in China.

PubMed

Wang, Haikun; Zhang, Yanxu; Zhao, Hongyan; Lu, Xi; Zhang, Yanxia; Zhu, Weimo; Nielsen, Chris P; Li, Xin; Zhang, Qiang; Bi, Jun; McElroy, Michael B

2017-09-29

Recent studies show that international trade affects global distributions of air pollution and public health. Domestic interprovincial trade has similar effects within countries, but has not been comprehensively investigated previously. Here we link four models to evaluate the effects of both international exports and interprovincial trade on PM 2.5 pollution and public health across China. We show that 50-60% of China's air pollutant emissions in 2007 were associated with goods and services consumed outside of the provinces where they were produced. Of an estimated 1.10 million premature deaths caused by PM 2.5 pollution throughout China, nearly 19% (208,500 deaths) are attributable to international exports. In contrast, interprovincial trade leads to improved air quality in developed coastal provinces with a net effect of 78,500 avoided deaths nationwide. However, both international export and interprovincial trade exacerbate the health burdens of air pollution in China's less developed interior provinces. Our results reveal trade to be a critical but largely overlooked consideration in effective regional air quality planning for China.International and domestic interprovincial trade of China are entangled, but their health impacts have been treated separately in earlier studies. Here Wang. quantify the complex impacts of trade on public health across China within an integrative framework.

Influenza A Virus Polymerase Recruits the RNA Helicase DDX19 to Promote the Nuclear Export of Viral mRNAs

PubMed Central

Diot, Cédric; Fournier, Guillaume; Dos Santos, Mélanie; Magnus, Julie; Komarova, Anastasia; van der Werf, Sylvie; Munier, Sandie; Naffakh, Nadia

2016-01-01

Enhancing the knowledge of host factors that are required for efficient influenza A virus (IAV) replication is essential to address questions related to pathogenicity and to identify targets for antiviral drug development. Here we focused on the interplay between IAV and DExD-box RNA helicases (DDX), which play a key role in cellular RNA metabolism by remodeling RNA-RNA or RNA-protein complexes. We performed a targeted RNAi screen on 35 human DDX proteins to identify those involved in IAV life cycle. DDX19 was a major hit. In DDX19-depleted cells the accumulation of viral RNAs and proteins was delayed, and the production of infectious IAV particles was strongly reduced. We show that DDX19 associates with intronless, unspliced and spliced IAV mRNAs and promotes their nuclear export. In addition, we demonstrate an RNA-independent association between DDX19 and the viral polymerase, that is modulated by the ATPase activity of DDX19. Our results provide a model in which DDX19 is recruited to viral mRNAs in the nucleus of infected cells to enhance their nuclear export. Information gained from this virus-host interaction improves the understanding of both the IAV replication cycle and the cellular function of DDX19. PMID:27653209

Using Coupled Models to Study the Effects of River Discharge on Biogeochemical Cycling and Hypoxia in the Northern Gulf of Mexico

NASA Technical Reports Server (NTRS)

Penta, Bradley; Ko, D.; Gould, Richard W.; Arnone, Robert A.; Greene, R.; Lehrter, J.; Hagy, James; Schaeffer, B.; Murrell, M.; Kurtz, J.;

21 CFR 1312.22 - Application for export permit.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Application for export permit. 1312.22 Section... EXPORTATION OF CONTROLLED SUBSTANCES Exportation of Controlled Substances § 1312.22 Application for export permit. (a) An application for a permit to export controlled substances shall be made on DEA Form 161...

19 CFR 191.73 - Export summary procedure.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 2 2010-04-01 2010-04-01 false Export summary procedure. 191.73 Section 191.73... TREASURY (CONTINUED) DRAWBACK Exportation and Destruction § 191.73 Export summary procedure. (a) General. The export summary procedure consists of a Chronological Summary of Exports used to support a drawback...

19 CFR 10.430 - Export requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Export requirements. 10.430 Section 10.430 Customs... Export Requirements § 10.430 Export requirements. (a) Submission of certification to CBP. An exporter or producer in the United States that signs a certification of origin for a good exported from the United...

7 CFR 1488.9a - Evidence of export for commodities delivered before export.

Code of Federal Regulations, 2013 CFR

2013-01-01

... COMMODITIES Financing of Export Sales of Agricultural Commodities From Private Stocks Under CCC Export Credit... financial period is 12 months or less, the exporter shall furnish a certification to the Treasurer, CCC... Assistant Treasurer, CCC, certifying that the commodities have been exported. The certification must include...

7 CFR 1493.110 - Notice of default and claims for loss.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493... related obligation, the exporter or the exporter's assignee must submit a notice of default to CCC as soon...

7 CFR 1493.110 - Notice of default and claims for loss.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493... related obligation, the exporter or the exporter's assignee must submit a notice of default to CCC as soon...

7 CFR 1488.9a - Evidence of export for commodities delivered before export.

Code of Federal Regulations, 2012 CFR

2012-01-01

... COMMODITIES Financing of Export Sales of Agricultural Commodities From Private Stocks Under CCC Export Credit... financial period is 12 months or less, the exporter shall furnish a certification to the Treasurer, CCC... Assistant Treasurer, CCC, certifying that the commodities have been exported. The certification must include...

7 CFR 1488.9a - Evidence of export for commodities delivered before export.

Code of Federal Regulations, 2014 CFR

2014-01-01

... COMMODITIES Financing of Export Sales of Agricultural Commodities From Private Stocks Under CCC Export Credit... financial period is 12 months or less, the exporter shall furnish a certification to the Treasurer, CCC... Assistant Treasurer, CCC, certifying that the commodities have been exported. The certification must include...

7 CFR 1493.110 - Notice of default and claims for loss.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493... related obligation, the exporter or the exporter's assignee must submit a notice of default to CCC as soon...

Estimating the contribution of strong daily export events to total pollutant export from the United States in summer

NASA Astrophysics Data System (ADS)

Fang, Yuanyuan; Fiore, Arlene M.; Horowitz, Larry W.; Gnanadesikan, Anand; Levy, Hiram; Hu, Yongtao; Russell, Armistead G.

2009-12-01

While the export of pollutants from the United States exhibits notable variability from day to day and is often considered to be "episodic," the contribution of strong daily export events to total export has not been quantified. We use carbon monoxide (CO) as a tracer of anthropogenic pollutants in the Model of OZone And Related Tracers (MOZART) to estimate this contribution. We first identify the major export pathway from the United States to be through the northeast boundary (24-48°N along 67.5°W and 80-67.5°W along 48°N), and then analyze 15 summers of daily CO export fluxes through this boundary. These daily CO export fluxes have a nearly Gaussian distribution with a mean of 1100 Gg CO day-1 and a standard deviation of 490 Gg CO day-1. To focus on the synoptic variability, we define a "synoptic background" export flux equal to the 15 day moving average export flux and classify strong export days according to their fluxes relative to this background. As expected from Gaussian statistics, 16% of summer days are "strong export days," classified as those days when the CO export flux exceeds the synoptic background by one standard deviation or more. Strong export days contributes 25% to the total export, a value determined by the relative standard deviation of the CO flux distribution. Regressing the anomalies of the CO export flux through the northeast U.S. boundary relative to the synoptic background on the daily anomalies in the surface pressure field (also relative to a 15 day running mean) suggests that strong daily export fluxes are correlated with passages of midlatitude cyclones over the Gulf of Saint Lawrence. The associated cyclonic circulation and Warm Conveyor Belts (WCBs) that lift surface pollutants over the northeastern United States have been shown previously to be associated with long-range transport events. Comparison with observations from the 2004 INTEX-NA field campaign confirms that our model captures the observed enhancements in CO outflow and resolves the processes associated with cyclone passages on strong export days. "Moderate export days," defined as days when the CO flux through the northeast boundary exceeds the 15 day running mean by less than one standard deviation, represent an additional 34% of summer days and 40% of total export. These days are also associated with migratory midlatitude cyclones. The remaining 35% of total export occurs on "weak export days" (50% of summer days) when high pressure anomalies occur over the Gulf of Saint Lawrence. Our findings for summer also apply to spring, when the U.S. pollutant export is typically strongest, with similar contributions to total export and associated meteorology on strong, moderate and weak export days. Although cyclone passages are the primary driver for strong daily export events, export during days without cyclone passages also makes a considerable contribution to the total export and thereby to the global pollutant budget.

21 CFR 1313.23 - Distribution of export declaration.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Distribution of export declaration. 1313.23... EXPORTATION OF LIST I AND LIST II CHEMICALS Exportation of Listed Chemicals § 1313.23 Distribution of export declaration. The required three copies of the listed chemical export declaration (DEA Form 486) will be...

7 CFR 1488.9 - Evidence of export.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Evidence of export. 1488.9 Section 1488.9 Agriculture... Export Sales of Agricultural Commodities From Private Stocks Under CCC Export Credit Sales Program (GSM-5) Documents Required for Financing § 1488.9 Evidence of export. (a) If the commodity is exported by rail or...

22 CFR 125.1 - Exports subject to this part.

Code of Federal Regulations, 2010 CFR

2010-04-01

... EXPORT OF TECHNICAL DATA AND CLASSIFIED DEFENSE ARTICLES § 125.1 Exports subject to this part. (a) The controls of this part apply to the export of technical data and the export of classified defense articles... to the controls of this subchapter. (b) A license for the export of technical data and the exemptions...

ExportAid: database of RNA elements regulating nuclear RNA export in mammals.

PubMed

Giulietti, Matteo; Milantoni, Sara Armida; Armeni, Tatiana; Principato, Giovanni; Piva, Francesco

2015-01-15

Regulation of nuclear mRNA export or retention is carried out by RNA elements but the mechanism is not yet well understood. To understand the mRNA export process, it is important to collect all the involved RNA elements and their trans-acting factors. By hand-curated literature screening we collected, in ExportAid database, experimentally assessed data about RNA elements regulating nuclear export or retention of endogenous, heterologous or artificial RNAs in mammalian cells. This database could help to understand the RNA export language and to study the possible export efficiency alterations owing to mutations or polymorphisms. Currently, ExportAid stores 235 and 96 RNA elements, respectively, increasing and decreasing export efficiency, and 98 neutral assessed sequences. Freely accessible without registration at http://www.introni.it/ExportAid/ExportAid.html. Database and web interface are implemented in Perl, MySQL, Apache and JavaScript with all major browsers supported. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast.

PubMed

Chen, Miao; Gartenberg, Marc R

2014-05-01

tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC-tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs.

Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast

PubMed Central

Chen, Miao; Gartenberg, Marc R.

2014-01-01

tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC–tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs. PMID:24788517

Pan Genome of the Phytoplankton Emiliania Underpins its Global Distribution

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

Read, Betsy A.; Kegel, Jessica; Klute, Mary J.

2012-06-18

Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering themvisible fromspace3.Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 production or uptake, sequestration and export to the deepmore » ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate thatE. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.« less

Pan genome of the phytoplankton Emiliania underpins its global distribution.

PubMed

Read, Betsy A; Kegel, Jessica; Klute, Mary J; Kuo, Alan; Lefebvre, Stephane C; Maumus, Florian; Mayer, Christoph; Miller, John; Monier, Adam; Salamov, Asaf; Young, Jeremy; Aguilar, Maria; Claverie, Jean-Michel; Frickenhaus, Stephan; Gonzalez, Karina; Herman, Emily K; Lin, Yao-Cheng; Napier, Johnathan; Ogata, Hiroyuki; Sarno, Analissa F; Shmutz, Jeremy; Schroeder, Declan; de Vargas, Colomban; Verret, Frederic; von Dassow, Peter; Valentin, Klaus; Van de Peer, Yves; Wheeler, Glen; Dacks, Joel B; Delwiche, Charles F; Dyhrman, Sonya T; Glöckner, Gernot; John, Uwe; Richards, Thomas; Worden, Alexandra Z; Zhang, Xiaoyu; Grigoriev, Igor V

2013-07-11

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

76 FR 66693 - President's Export Council: Meeting of the President's Export Council

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-27

.... ACTION: Notice of an open meeting. SUMMARY: The President's Export Council will hold a meeting to discuss.... exports, jobs, and growth. DATES: November 16, 2011 at 9:30 a.m. (ET) ADDRESSES: The President's Export... on December 20, 1973 to advise the President on matters relating to U.S. export trade and report to...

50 CFR 23.53 - What are the requirements for obtaining a retrospective CITES document?

Code of Federal Regulations, 2011 CFR

2011-10-01

... certain specimens for personal use as specified in paragraph (d)(7) of this section. (2) The exporter or re-exporter must notify the Management Authority in the exporting or re-exporting country of the...) In general, except when the exporter or re-exporter and importer have demonstrated they were not...

21 CFR 1313.22 - Contents of export declaration.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Contents of export declaration. 1313.22 Section... EXPORTATION OF LIST I AND LIST II CHEMICALS Exportation of Listed Chemicals § 1313.22 Contents of export... quantitative threshold criteria established in § 1310.04(f) of this chapter may be exported if that chemical is...

The export premium: why some logs are worth more abroad.

Treesearch

Donald F. Flora; Wendy J. McGinnis; Christine L. Lane

1993-01-01

For as long as logs have been exported from the Pacific Northwest, they seem to have been worth more offshore than in the domestic market. Five reasons for the export premium are the inconvenience of trade, quality, extra "haul and hassle," continuity in export arrangements, and export embargoes. A large and increasing differential remains between export and...

21 CFR 1312.23 - Issuance of export permit.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Issuance of export permit. 1312.23 Section 1312.23... CONTROLLED SUBSTANCES Exportation of Controlled Substances § 1312.23 Issuance of export permit. (a) The... regulation in § 1312.30 of this part be exported only pursuant to the issuance of an export permit. The...

76 FR 31584 - President's Export Council Subcommittee on Export Administration, Notice of Open Meeting...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-01

... DEPARTMENT OF COMMERCE Bureau of Industry and Security President's Export Council Subcommittee on Export Administration, Notice of Open Meeting; Correction: Meeting Time and Agenda The President's Export Council Subcommittee on Export Administration (PECSEA) will meet on June 9, 2011, 10 a.m., at the U.S. Department of Commerce, Herbert C. Hoove...

Nuclear localization of Schizosaccharomyces pombe Mcm2/Cdc19p requires MCM complex assembly.

PubMed

Pasion, S G; Forsburg, S L

1999-12-01

The minichromosome maintenance (MCM) proteins MCM2-MCM7 are conserved eukaryotic replication factors that assemble in a heterohexameric complex. In fission yeast, these proteins are nuclear throughout the cell cycle. In studying the mechanism that regulates assembly of the MCM complex, we analyzed the cis and trans elements required for nuclear localization of a single subunit, Mcm2p. Mutation of any single mcm gene leads to redistribution of wild-type MCM subunits to the cytoplasm, and this redistribution depends on an active nuclear export system. We identified the nuclear localization signal sequences of Mcm2p and showed that these are required for nuclear targeting of other MCM subunits. In turn, Mcm2p must associate with other MCM proteins for its proper localization; nuclear localization of MCM proteins thus requires assembly of MCM proteins in a complex. We suggest that coupling complex assembly to nuclear targeting and retention ensures that only intact heterohexameric MCM complexes remain nuclear.

Nuclear Localization of Schizosaccharomyces pombe Mcm2/Cdc19p Requires MCM Complex Assembly

PubMed Central

Pasion, Sally G.; Forsburg, Susan L.

1999-01-01

The minichromosome maintenance (MCM) proteins MCM2–MCM7 are conserved eukaryotic replication factors that assemble in a heterohexameric complex. In fission yeast, these proteins are nuclear throughout the cell cycle. In studying the mechanism that regulates assembly of the MCM complex, we analyzed the cis and trans elements required for nuclear localization of a single subunit, Mcm2p. Mutation of any single mcm gene leads to redistribution of wild-type MCM subunits to the cytoplasm, and this redistribution depends on an active nuclear export system. We identified the nuclear localization signal sequences of Mcm2p and showed that these are required for nuclear targeting of other MCM subunits. In turn, Mcm2p must associate with other MCM proteins for its proper localization; nuclear localization of MCM proteins thus requires assembly of MCM proteins in a complex. We suggest that coupling complex assembly to nuclear targeting and retention ensures that only intact heterohexameric MCM complexes remain nuclear. PMID:10588642

Insights into public export promotion programs in an emerging economy: the case of Malaysian SMEs.

PubMed

Ayob, Abu H; Freixanet, Joan

2014-10-01

This study evaluates the impact of public export promotion programs (EPPs) among small and medium-sized enterprises (SMEs) in Malaysia. Three indicators, level of awareness, frequency of use, and perception of usefulness, were examined according to a firm's export status. The global evaluation suggests that exporters are more frequent users of EPPs and perceive them to be more useful than non-exporters. Nonetheless, both groups demonstrate higher levels of awareness, are frequent users, and perceive the programs relating to export info/knowledge are more usefulness than programs relating to financial assistance. Further analysis also reveals that the frequency of use and the perception of usefulness for most programs are positively related to export experience, but not to export turnover. This study offers insights into the effectiveness of export programs for encouraging export initiation and expansion in an emerging economy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of land use changes on eutrophication indicators in five coastal lagoons of the Southwestern Atlantic Ocean

NASA Astrophysics Data System (ADS)

Rodríguez-Gallego, Lorena; Achkar, Marcel; Defeo, Omar; Vidal, Leticia; Meerhoff, Erika; Conde, Daniel

2017-03-01

Five catchment areas in Uruguay were selected to conduct a nutrient exportation analysis and to evaluate the effects of current land use on the eutrophication of coastal lagoons. Satellite images and national agriculture censuses were used for a quantitative analysis of land use changes from 1974 to 2005, and a nutrient export coefficient approximation was used to determine long-term changes in annual loads. Several eutrophication indicators (water, sediment and autotrophic communities) were assessed seasonally in the lagoon basins during 2005 and 2006. The areal annual load of nutrients exported to the lagoons increased over time. Population and extensive livestock ranching were the most important nutrient sources, while agriculture is increasing in importance. Buffer effects of riparian forests on eutrophication indicators were observed in contrast to the wetlands surrounding the lagoons, which seem to be acting as a source of nutrients. Catchment size was inversely related to most eutrophication indicators. Afforestation and agriculture were found not to directly impact eutrophication indicators, however, catchments with larger agricultural areas showed higher concentrations of suspended solids, which may indicate the export of particulate nutrients. Salinity was inversely related to most eutrophication indicators, suggesting that the manipulation of the sand bar of the lagoons is a critical management issue. Sediment-related eutrophication indicators were more sensitive to changes in land uses and covers, in contrast with the more variable water column indicators, suggesting their potential use as enduring indicators. This research provides a rapid and integral assessment for qualitatively linking catchment changes with eutrophication indicators in coastal environments, which can easily be replicated to track pollutants in locations that lack standardized monitoring programs needed for more complex catchment modeling approaches.

Scenario analysis of the impacts of socioeconomic development on phosphorous export and loading from the Dongting Lake watershed, China.

PubMed

Hou, Ying; Chen, Weiping; Liao, Yuehua; Luo, Yueping

2017-12-01

Socioeconomic development in lake watersheds is closely related with lake nutrient pollution. As the second largest freshwater lake in China, the Dongting Lake has been experiencing an increase in nutrient loading and a growing risk of eutrophication. This study aimed to reveal the likely impacts of the socioeconomic development of the Dongting Lake watershed on the phosphorous pollution in the lake. We estimated the contributions from different sources and sub-watersheds to the total phosphorous (TP) export and loading from the Dongting Lake watershed under two most likely socioeconomic development scenarios. Moreover, we predicted the likely permissible and actual TP loadings to the Dongting Lake. Under both two scenarios, three secondary sub-watersheds-the upper and lower reaches of the Xiang River watershed and the Dongting Lake Area-are expected to dominate the contribution to the TP export from the Dongting Lake watershed in 2020. Three primary sub-watersheds-the Dongting Lake Area, the Xiang River, and the Yuan River watersheds-are predicted to be the major contributors to the TP loading from the entire watershed. The two scenarios are expected to have a slight difference in TP export and lake TP loading. Livestock husbandry is expected to be the predominant anthropogenic TP source in each of the sub-watersheds under both scenarios. Compared to 2010, permissible TP loading is not expected to increase but actual TP loading is predicted to grow significantly in 2020. Our study provides methodologies to identify the key sources and regions of lake nutrient loading from watersheds with complex socioeconomic context, and to reveal the potential influences of socioeconomic development on nutrient pollution in lake watersheds.

Vectorial Entry and Release of Hepatitis A Virus in Polarized Human Hepatocytes ▿

PubMed Central

Snooks, Michelle J.; Bhat, Purnima; Mackenzie, Jason; Counihan, Natalie A.; Vaughan, Nicola; Anderson, David A.

2008-01-01

Hepatitis A virus (HAV) is an enterically transmitted virus that replicates predominantly in hepatocytes within the liver before excretion via bile through feces. Hepatocytes are polarized epithelial cells, and it has been assumed that the virus load in bile results from direct export of HAV via the apical domain of polarized hepatocytes. We have developed a subclone of hepatocyte-derived HepG2 cells (clone N6) that maintains functional characteristics of polarized hepatocytes but displays morphology typical of columnar epithelial cells, rather than the complex morphology that is typical of hepatocytes. N6 cells form microcolonies of polarized cells when grown on glass and confluent monolayers of polarized cells on semipermeable membranes. When N6 microcolonies were exposed to HAV, infection was restricted to peripheral cells of polarized colonies, whereas all cells could be infected in colonies of nonpolarized HepG2 cells (clone C11) or following disruption of tight junctions in N6 colonies with EGTA. This suggests that viral entry occurs predominantly via the basolateral plasma membrane, consistent with uptake of virus from the bloodstream after enteric exposure, as expected. Viral export was also found to be markedly vectorial in N6 but not C11 cells. However, rather than being exported from the apical domain as expected, more than 95% of HAV was exported via the basolateral domain of N6 cells, suggesting that virus is first excreted from infected hepatocytes into the bloodstream rather than to the biliary tree. Enteric excretion of HAV may therefore rely on reuptake and transcytosis of progeny HAV across hepatocytes into the bile. These studies provide the first example of the interactions between viruses and polarized hepatocytes. PMID:18579610

27 CFR 28.220a - Responsibility for return of wine withdrawn for export with benefit of drawback.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of wine withdrawn for export with benefit of drawback. 28.220a Section 28.220a Alcohol, Tobacco... EXPORTATION OF ALCOHOL Exportation of Wine With Benefit of Drawback § 28.220a Responsibility for return of wine withdrawn for export with benefit of drawback. The exporter shall be responsible for arranging the...

75 FR 52453 - Entry Requirements for Certain Softwood Lumber Products Exported From Any Country Into the United...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-26

...)(3)(iii)(B)(3), which states that ``the exporter has paid, or committed to pay, all export charges..., to his best knowledge and belief, that the exporter has paid or committed to pay ``all export charges... discrepancies between the export permit date and the entry summary data. The commenter suggests using the...

Analysis of URI nuclear interaction with RPB5 and components of the R2TP/prefoldin-like complex.

PubMed

Mita, Paolo; Savas, Jeffrey N; Ha, Susan; Djouder, Nabil; Yates, John R; Logan, Susan K

2013-01-01

Unconventional prefoldin RPB5 Interactor (URI) was identified as a transcriptional repressor that binds RNA polymerase II (pol II) through interaction with the RPB5/POLR2E subunit. Despite the fact that many other proteins involved in transcription regulation have been shown to interact with URI, its nuclear function still remains elusive. Previous mass spectrometry analyses reported that URI is part of a novel protein complex called R2TP/prefoldin-like complex responsible for the cytoplasmic assembly of RNA polymerase II. We performed a mass spectrometry (MS)-based proteomic analysis to identify nuclear proteins interacting with URI in prostate cells. We identified all the components of the R2TP/prefoldin-like complex as nuclear URI interactors and we showed that URI binds and regulates RPB5 protein stability and transcription. Moreover, we validated the interaction of URI to the P53 and DNA damage-Regulated Gene 1 (PDRG1) and show that PDRG1 protein is also stabilized by URI binding. We present data demonstrating that URI nuclear/cytoplasmic shuttling is affected by compounds that stall pol II on the DNA (α-amanitin and actinomycin-D) and by leptomycin B, an inhibitor of the CRM1 exportin that mediates the nuclear export of pol II subunits. These data suggest that URI, and probably the entire R2TP/prefoldin-like complex is exported from the nucleus through CRM1. Finally we identified putative URI sites of phosphorylation and acetylation and confirmed URI sites of post-transcriptional modification identified in previous large-scale analyses the importance of which is largely unknown. However URI post-transcriptional modification was shown to be essential for URI function and therefore characterization of novel sites of URI modification will be important to the understanding of URI function.

Analysis of URI Nuclear Interaction with RPB5 and Components of the R2TP/Prefoldin-Like Complex

PubMed Central

Mita, Paolo; Savas, Jeffrey N.; Ha, Susan; Djouder, Nabil; Yates, John R.; Logan, Susan K.

2013-01-01

Unconventional prefoldin RPB5 Interactor (URI) was identified as a transcriptional repressor that binds RNA polymerase II (pol II) through interaction with the RPB5/POLR2E subunit. Despite the fact that many other proteins involved in transcription regulation have been shown to interact with URI, its nuclear function still remains elusive. Previous mass spectrometry analyses reported that URI is part of a novel protein complex called R2TP/prefoldin-like complex responsible for the cytoplasmic assembly of RNA polymerase II. We performed a mass spectrometry (MS)-based proteomic analysis to identify nuclear proteins interacting with URI in prostate cells. We identified all the components of the R2TP/prefoldin-like complex as nuclear URI interactors and we showed that URI binds and regulates RPB5 protein stability and transcription. Moreover, we validated the interaction of URI to the P53 and DNA damage-Regulated Gene 1 (PDRG1) and show that PDRG1 protein is also stabilized by URI binding. We present data demonstrating that URI nuclear/cytoplasmic shuttling is affected by compounds that stall pol II on the DNA (α-amanitin and actinomycin-D) and by leptomycin B, an inhibitor of the CRM1 exportin that mediates the nuclear export of pol II subunits. These data suggest that URI, and probably the entire R2TP/prefoldin-like complex is exported from the nucleus through CRM1. Finally we identified putative URI sites of phosphorylation and acetylation and confirmed URI sites of post-transcriptional modification identified in previous large-scale analyses the importance of which is largely unknown. However URI post-transcriptional modification was shown to be essential for URI function and therefore characterization of novel sites of URI modification will be important to the understanding of URI function. PMID:23667685

High Current, High Density Arc Plasma as a New Source for WiPAL

NASA Astrophysics Data System (ADS)

Waleffe, Roger; Endrizzi, Doug; Myers, Rachel; Wallace, John; Clark, Mike; Forest, Cary; WiPAL Team

2016-10-01

The Wisconsin Plasma Astrophysics Lab (WiPAL) has installed a new array of nineteen plasma sources (plasma guns) on its 3 m diameter, spherical vacuum vessel. Each gun is a cylindrical, molybdenum, washer-stabilized, arc plasma source. During discharge, the guns are maintained at 1.2 kA across 100 V for 10 ms by the gun power supply establishing a high density plasma. Each plasma source is fired independently allowing for adjustable plasma parameters, with densities varying between 1018 -1019 m-3 and electron temperatures of 5-15 eV. Measurements were characterized using a 16 tip Langmuir probe. The plasma source will be used as a background plasma for the magnetized coaxial plasma gun (MCPG), the Terrestrial Reconnection Experiment (TREX), and as the plasma source for a magnetic mirror experiment. Temperature, density, and confinement results will be presented. This work is supported by the DoE and the NSF.

Pressure Anisotropy Measurements on the Terrestrial Reconnection Experiment

NASA Astrophysics Data System (ADS)

Myers, Rachel; Egedal, Jan; Olson, Joseph; Greess, Samuel; Millet-Ayala, Alexander; Clark, Michael; Nonn, Paul; Wallace, John; Forest, Cary

2017-10-01

The Terrestrial Reconnection Experiment (TREX) at the Wisconsin Plasma Astrophysics Laboratory (WiPAL) studies collisionless magnetic reconnection. In this regime, electron pressure anisotropy should develop, deviating from Hall reconnection dynamics and driving large-scale current layer formation. A multi-tip version of the M-probe of Shadman, containing 32 Langmuir probe tips and two magnetic coils, measures this anisotropy. Each tip is biased to a different potential, simultaneously measuring discrete parts of the I-V characteristic. Pulsing the coil locally increases the magnetic field near the tips, inducing a magnetic mirror force to reflect electrons with large values of v⊥ / v . The change in velocity modifies the I-V characteristic and can be used to infer p∥ /p⊥ . Results and analysis from the probe are presented. This research was conducted with support from a UW-Madison University Fellowship as well as the NSF/DOE award DE-SC0013032.

Aiding and Abetting Cancer: mRNA export and the nuclear pore

PubMed Central

Culjkovic-Kraljacic, Biljana; Borden, Katherine L.B

2013-01-01

mRNA export is a critical step in gene expression. Export of transcripts can be modulated in response to cellular signaling or stress. Consistently, mRNA export is dysregulated in primary human specimens derived from many different forms of cancer. Aberrant expression of export factors can alter export of specific transcripts encoding proteins involved in proliferation, survival and oncogenesis. These specific factors, which are not used for bulk mRNA export, are obvious therapeutic targets. Indeed, given the emerging role of mRNA export in cancer, it is not surprising that efforts to target different aspects of this pathway have reached the clinical trial stage. Thus, like transcription and translation, mRNA export may also play a critical role in cancer genesis and maintenance. PMID:23582887

77 FR 37871 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-25

... DEPARTMENT OF COMMERCE International Trade Administration [Application 12-00005] Export Trade Certificate of Review ACTION: Notice of Application for an Export Trade Certificate of Review from Colombia Rice Export Quota, Inc. SUMMARY: The Export Trading Company Affairs (``ETCA'') unit, Office of...

78 FR 85 - In the Matter of: Emenike Charles Nwankwoala Currently Incarcerated at: Inmate Number 50756-037...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-02

... willfully exporting, causing to be exported, and attempting to export from the United States to Nigeria..., causing to exported, and attempting to export from the United States to Nigeria shotguns without having...

SR proteins SRp20 and 9G8 contribute to efficient export of herpes simplex virus 1 mRNAs

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

Escudero-Paunetto, Laurimar; Li Ling; Hernandez, Felicia P.

2010-06-05

Herpes simplex virus 1 (HSV-1) mRNAs are exported to the cytoplasm through the export receptor TAP/NFX1. HSV-1 multifunctional protein ICP27 interacts with TAP/NXF1, binds viral RNAs, and is required for efficient viral RNA export. In ICP27 mutant infections, viral RNA export is reduced but not ablated, indicating that other export adaptors can aid in viral RNA export. Export adaptor protein Aly/REF is recruited to viral replication compartments, however, Aly/REF knockdown has little effect on viral RNA export. SR proteins SRp20 and 9G8 interact with TAP/NXF1 and mediate export of some cellular RNAs. We report that siRNA knockdown of SRp20 ormore » 9G8 resulted in about a 10 fold decrease in virus yields and in nuclear accumulation of poly(A+) RNA. In infected cells depleted of SRp20, newly transcribed Bromouridine-labeled RNA also accumulated in the nucleus. We conclude that SRp20 and 9G8 contribute to HSV-1 RNA export.« less

Adjusting export tax rebates to reduce the environmental impacts of trade: Lessons from China.

PubMed

Song, Peng; Mao, Xianqiang; Corsetti, Gabriel

2015-09-15

Export tax rebates are an important policy instrument for stimulating exports, which many developing countries make use of. However, excessive export tax rebates and inappropriate structural arrangements can lead to over-production in highly polluting industries and cause the environment to deteriorate. This paper, taking China as the study case, tests and verifies the statistical significance of the causal relationship between export tax rebates and pollution emissions. With a computable general equilibrium modeling, the current study further analyzes the effectiveness of export tax rebate adjustments aimed at alleviating environmental pressure for different time periods. It is found that before 2003, export tax rebates primarily promoted exports and boosted foreign exchange reserves, and highly polluting sectors enjoyed above-average export tax rebates, which led to increased pollution emissions. Between 2003 and 2010, the export tax rebate system was reformed to reduce support for the highly polluting export sectors, which led to decreases in emissions. Canceling export tax rebates for highly polluting sectors is shown to be the most favorable policy choice for improving the environmental performance of China's international trade. This study can serve as reference for other developing countries which similarly rely on export tax rebates, so that they can adjust their policies so as to combine economic growth with pollution control. Copyright © 2015 Elsevier Ltd. All rights reserved.

40 CFR 168.85 - Other export requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Other export requirements. 168.85... STATEMENTS OF ENFORCEMENT POLICIES AND INTERPRETATIONS Export Policy and Procedures for Exporting Unregistered Pesticides § 168.85 Other export requirements. This section describes other requirements found in...

7 CFR 51.2840 - Export packing requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Export packing requirements. 51.2840 Section 51.2840 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards...) Export Packing Requirements § 51.2840 Export packing requirements. Onions specified as meeting Export...

Inspection of the Department`s export licensing process for dual-use and munitions commodities

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

Not Available

1993-08-10

The purpose of our inspection was to review the Department of Energy`s (Energy) export licensing process for dual-use and military (munitions) commodities subject to nuclear nonproliferation controls. Specifically, we reviewed Energy`s authorities, procedures, and policies pertaining to the export licensing process and examined procedures for safeguarding data transmitted between Energy and other agencies involved in the export licensing process. We also reviewed Energy`s role as a member of the Subgroup on Nuclear Export Coordination. Our review of the sample of 60 export cases did not find evidence to lead us to believe that Energy`s recommendations for these cases were inappropriatemore » or incorrect. We identified, however, problems regarding management systems associated with the export license review process. We found that without documentation supporting export licensing decisions by the Export Control Operations Division (ECOD), we could not determine whether ECOD analysts considered all required criteria in their review of export cases referred to Energy. For example, we found that the ECOD did not retain records documenting the bases for its advice, recommendations, or decisions regarding its reviews of export license cases or revisions to lists of controlled commodities and, therefore, was not in compliance with certain provisions of the Export Administration Act, as amended, and Energy records management directives. Additionally, we found that the degree of compliance by Energy with the export licensing review criteria contained in the Export Administration Regulations and the Nuclear Non-Proliferation Act of 1978 could not be determined because ECOD did not retain records documenting the bases for its advice and recommendations on export cases.« less

Regulation of the Expression of Bacterial Multidrug Exporters by Two-Component Signal Transduction Systems.

PubMed

Nishino, Kunihiko

2018-01-01

Bacterial multidrug exporters confer resistance to a wide range of antibiotics, dyes, and biocides. Recent studies have shown that there are many multidrug exporters encoded in bacterial genome. For example, it was experimentally identified that E. coli has at least 20 multidrug exporters. Because many of these multidrug exporters have overlapping substrate spectra, it is intriguing that bacteria, with their economically organized genomes, harbor such large sets of multidrug exporter genes. The key to understanding how bacteria utilize these multiple exporters lies in the regulation of exporter expression. Bacteria have developed signaling systems for eliciting a variety of adaptive responses to their environments. These adaptive responses are often mediated by two-component regulatory systems. In this chapter, the method to identify response regulators that affect expression of multidrug exporters is described.

75 FR 52929 - President's Export Council: Meeting of the President's Export Council

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-30

... DEPARTMENT OF COMMERCE International Trade Administration President's Export Council: Meeting of the President's Export Council AGENCY: International Trade Administration, U.S. Department of Commerce...: The President's Export Council will convene its next meeting via live webcast on the Internet at http...

50 CFR 300.189 - Prohibitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... under § 300.182. (b) Import as an entry for consumption, purchase, receive for export, export, or re... are imported, entered for consumption, exported, or re-exported. (g) Fail to comply with the documentation requirements as specified in § 300.186, for the importation, entry for consumption, exportation...

50 CFR 300.189 - Prohibitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... under § 300.182. (b) Import as an entry for consumption, purchase, receive for export, export, or re... are imported, entered for consumption, exported, or re-exported. (g) Fail to comply with the documentation requirements as specified in § 300.186, for the importation, entry for consumption, exportation...

50 CFR 300.189 - Prohibitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... under § 300.182. (b) Import as an entry for consumption, purchase, receive for export, export, or re... are imported, entered for consumption, exported, or re-exported. (g) Fail to comply with the documentation requirements as specified in § 300.186, for the importation, entry for consumption, exportation...

78 FR 58995 - Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-25

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the...''). Specifically, Kazerani was convicted of knowingly and willfully exporting and causing the exportation of laptop..., a $10,000 criminal fine and an assessment of $100. Section 766.25 of the Export Administration...

7 CFR 1493.80 - Evidence of export.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Evidence of export. 1493.80 Section 1493.80... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103...

19 CFR 19.38 - Supervision of exportation.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Supervision of exportation. 19.38 Section 19.38... Supervision of exportation. (a) Sales ticket withdrawals. Conditionally duty-free merchandise withdrawn under the sales ticket procedure for exportation shall be exported only under Customs supervision as...

19 CFR 19.38 - Supervision of exportation.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Supervision of exportation. 19.38 Section 19.38... Supervision of exportation. (a) Sales ticket withdrawals. Conditionally duty-free merchandise withdrawn under the sales ticket procedure for exportation shall be exported only under Customs supervision as...

19 CFR 19.38 - Supervision of exportation.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 1 2011-04-01 2011-04-01 false Supervision of exportation. 19.38 Section 19.38... Supervision of exportation. (a) Sales ticket withdrawals. Conditionally duty-free merchandise withdrawn under the sales ticket procedure for exportation shall be exported only under Customs supervision as...

19 CFR 19.38 - Supervision of exportation.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Supervision of exportation. 19.38 Section 19.38... Supervision of exportation. (a) Sales ticket withdrawals. Conditionally duty-free merchandise withdrawn under the sales ticket procedure for exportation shall be exported only under Customs supervision as...

19 CFR 19.38 - Supervision of exportation.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Supervision of exportation. 19.38 Section 19.38... Supervision of exportation. (a) Sales ticket withdrawals. Conditionally duty-free merchandise withdrawn under the sales ticket procedure for exportation shall be exported only under Customs supervision as...

77 FR 73627 - 2012 LNG Export Study

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-11

... DEPARTMENT OF ENERGY 2012 LNG Export Study AGENCY: Office of Fossil Energy, Department of Energy. ACTION: Notice of availability of 2012 LNG Export Study and request for comments. Freeport LNG Expansion... liquefied natural gas (LNG) export cumulative impact study (LNG Export Study) in the above- referenced...

Differential expression of THOC1 and ALY mRNP biogenesis/export factors in human cancers.

PubMed

Domínguez-Sánchez, María S; Sáez, Carmen; Japón, Miguel A; Aguilera, Andrés; Luna, Rosa

2011-02-17

One key step in gene expression is the biogenesis of mRNA ribonucleoparticle complexes (mRNPs). Formation of the mRNP requires the participation of a number of conserved factors such as the THO complex. THO interacts physically and functionally with the Sub2/UAP56 RNA-dependent ATPase, and the Yra1/REF1/ALY RNA-binding protein linking transcription, mRNA export and genome integrity. Given the link between genome instability and cancer, we have performed a comparative analysis of the expression patterns of THOC1, a THO complex subunit, and ALY in tumor samples. The mRNA levels were measured by quantitative real-time PCR and hybridization of a tumor tissue cDNA array; and the protein levels and distribution by immunostaining of a custom tissue array containing a set of paraffin-embedded samples of different tumor and normal tissues followed by statistical analysis. We show that the expression of two mRNP factors, THOC1 and ALY are altered in several tumor tissues. THOC1 mRNA and protein levels are up-regulated in ovarian and lung tumors and down-regulated in those of testis and skin, whereas ALY is altered in a wide variety of tumors. In contrast to THOC1, ALY protein is highly detected in normal proliferative cells, but poorly in high-grade cancers. These results suggest a differential connection between tumorogenesis and the expression levels of human THO and ALY. This study opens the possibility of defining mRNP biogenesis factors as putative players in cell proliferation that could contribute to tumor development.

40 CFR 799.19 - Chemical imports and exports.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 32 2011-07-01 2011-07-01 false Chemical imports and exports. 799.19... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS General Provisions § 799.19 Chemical imports and exports. Persons who export or who intend to export...

75 FR 11118 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-10

... DEPARTMENT OF COMMERCE International Trade Administration [Application No. 99-4A005] Export Trade Certificate of Review ACTION: Notice of Application ( 99-4A005) to Amend the Export Trade Certificate of Review Issued to California Almond Export Association, LLC, Application no. 99-00005. SUMMARY: The Export...

14 CFR 21.325 - Export airworthiness approvals.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Export airworthiness approvals. 21.325... AIRCRAFT CERTIFICATION PROCEDURES FOR PRODUCTS AND PARTS Export Airworthiness Approvals § 21.325 Export airworthiness approvals. (a) Kinds of approvals. (1) Export airworthiness approval of Class I products is issued...

7 CFR 1493.470 - Evidence of export.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Evidence of export. 1493.470 Section 1493.470... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Supplier Credit Guarantee Program Operations § 1493.470 Evidence of export. (a) Report of export. The...

75 FR 51980 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-24

... DEPARTMENT OF COMMERCE International Trade Administration [Application No. 84-21A12] Export Trade Certificate of Review ACTION: Notice of Issuance of an amended Export Trade Certificate of Review to Northwest... amended Export Trade Certificate of Review to Northwest Fruit Exporters on August 18, 2010. The...

27 CFR 28.30 - Export status.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Export status. 28.30... Export status. (a) Distilled spirits and wines manufactured, produced, bottled in bottles packed in... such purposes are considered to be exported. Export status is not acquired until application on Form...

40 CFR 799.19 - Chemical imports and exports.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 31 2010-07-01 2010-07-01 true Chemical imports and exports. 799.19 Section 799.19 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES... General Provisions § 799.19 Chemical imports and exports. Persons who export or who intend to export...

40 CFR 799.19 - Chemical imports and exports.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 33 2012-07-01 2012-07-01 false Chemical imports and exports. 799.19... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS General Provisions § 799.19 Chemical imports and exports. Persons who export or who intend to export...

40 CFR 799.19 - Chemical imports and exports.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 33 2013-07-01 2013-07-01 false Chemical imports and exports. 799.19... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS General Provisions § 799.19 Chemical imports and exports. Persons who export or who intend to export...

40 CFR 799.19 - Chemical imports and exports.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 32 2014-07-01 2014-07-01 false Chemical imports and exports. 799.19... CONTROL ACT (CONTINUED) IDENTIFICATION OF SPECIFIC CHEMICAL SUBSTANCE AND MIXTURE TESTING REQUIREMENTS General Provisions § 799.19 Chemical imports and exports. Persons who export or who intend to export...

75 FR 52505 - Fiscal Year 2011 Veterinary Import/Export Services, Veterinary Diagnostic Services, and Export...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-26

...] Fiscal Year 2011 Veterinary Import/Export Services, Veterinary Diagnostic Services, and Export... certain veterinary diagnostic services; and for export certification of plants and plant products. The..., through September 30, 2011). FOR FURTHER INFORMATION CONTACT: For information on Veterinary Diagnostic...

Correlation of Laboratory Flame Propagation Testing Results with Ballistic Testing Utilizing Several Threats with Varying Explosive Energies

DTIC Science & Technology

2011-09-01

hydrocarbons, i.e.; paraffins , olefins , aromatics, and naphthenics. Because of the chemical complexity of fuels, they are classified on the basis of... Technologies Warren, Michigan Contract No. DAAE-07-99-C-L053 (WD38) UNCLASSIFIED: Distribution Statement A. Approved for public release September...Government employee(s), this document was only reviewed for export controls, and improper Army association or emblem usage considerations. All other

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2011 CFR

2011-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2012 CFR

2012-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2013 CFR

2013-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

31 CFR 592.201 - Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

Code of Federal Regulations, 2014 CFR

2014-07-01

... of any rough diamond; permitted importation or exportation of any rough diamond. 592.201 Section 592... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY ROUGH DIAMONDS CONTROL REGULATIONS Prohibitions § 592.201 Prohibited importation and exportation of any rough diamond; permitted importation or exportation...

48 CFR 552.211-88 - Vehicle export preparation.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Vehicle export preparation... Vehicle export preparation. As prescribed in 511.204(b)(8), insert the following clause: Vehicle Export Preparation (JAN 2010) Vehicles shall be prepared for export on wheels, unboxed, unless otherwise specified in...

48 CFR 552.211-88 - Vehicle export preparation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Vehicle export preparation... Vehicle export preparation. As prescribed in 511.204(b)(8), insert the following clause: Vehicle Export Preparation (JAN 2010) Vehicles shall be prepared for export on wheels, unboxed, unless otherwise specified in...

19 CFR 192.3 - Penalties.

Code of Federal Regulations, 2011 CFR

2011-04-01

...) EXPORT CONTROL Exportation of Used Self-Propelled Vehicles, Vessels, and Aircraft § 192.3 Penalties. (a... importer or exporter who knowingly imports, exports or attempts to import or export: (1) Any stolen self-propelled vehicle, vessel, aircraft or part of a self-propelled vehicle, vessel or aircraft; or (2) Any self...

19 CFR 192.3 - Penalties.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) EXPORT CONTROL Exportation of Used Self-Propelled Vehicles, Vessels, and Aircraft § 192.3 Penalties. (a... importer or exporter who knowingly imports, exports or attempts to import or export: (1) Any stolen self-propelled vehicle, vessel, aircraft or part of a self-propelled vehicle, vessel or aircraft; or (2) Any self...

50 CFR 300.183 - Permit holder reporting and recordkeeping requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... biweekly report of entries for consumption, exports and re-exports of fish and fish products regulated... products regulated under this subpart except shark fins were entered for consumption, exported, or re..., that is entered for consumption, exported, or re-exported. (3) A biweekly report is not required for...

50 CFR 300.183 - Permit holder reporting and recordkeeping requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... biweekly report of entries for consumption, exports and re-exports of fish and fish products regulated... products regulated under this subpart except shark fins were entered for consumption, exported, or re..., that is entered for consumption, exported, or re-exported. (3) A biweekly report is not required for...

50 CFR 300.183 - Permit holder reporting and recordkeeping requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... biweekly report of entries for consumption, exports and re-exports of fish and fish products regulated... products regulated under this subpart except shark fins were entered for consumption, exported, or re..., that is entered for consumption, exported, or re-exported. (3) A biweekly report is not required for...

76 FR 11756 - Action Affecting Export Privileges; Ali Amirnazmi; Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-03

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Action Affecting Export Privileges; Ali Amirnazmi; Order Denying Export Privileges In the Matter of: Ali Amirnazmi, Register 63302-066, FCI... release and forfeit $81,277.37. Section 766.25 of the Export Administration Regulations (``EAR'' or...

15 CFR 2012.3 - Export certificates.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Export certificates. 2012.3 Section... STATES TRADE REPRESENTATIVE IMPLEMENTATION OF TARIFF-RATE QUOTAS FOR BEEF § 2012.3 Export certificates... export certificate is in effect with respect to the beef. (b) To be valid, an export certificate shall...

31 CFR 592.304 - Exporting authority.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Exporting authority. 592.304 Section... § 592.304 Exporting authority. (a) The term exporting authority means one or more entities designated by a Participant from whose territory a shipment of rough diamonds is being exported as having the...

78 FR 1837 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-09

... DEPARTMENT OF COMMERCE International Trade Administration [Application No. 84-23A12] Export Trade Certificate of Review ACTION: Notice of issuance of an Export Trade Certificate of Review to Northwest Fruit Exporters, Application No. 84-23A12. SUMMARY: The U.S. Department of Commerce issued an amended Export Trade...

76 FR 55010 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-06

... DEPARTMENT OF COMMERCE International Trade Administration [Application No. 84-22A12] Export Trade Certificate of Review ACTION: Notice of issuance of an Export Trade Certificate of Review to Northwest Fruit Exporters, Application no. 84-22A12. SUMMARY: The U.S. Department of Commerce issued an amended Export Trade...

50 CFR 222.205 - Import and export requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Import and export requirements. 222.205... Certificates of Exemption for Pre-Act Endangered Species Parts § 222.205 Import and export requirements. (a... intended for importation into or exportation from the United States, shall not be imported or exported...

40 CFR 89.909 - Export exemptions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Export exemptions. 89.909 Section 89....909 Export exemptions. (a) A new nonroad engine intended solely for export, and so labeled or tagged..., 1200 Pennsylvania Ave., NW., Washington, DC 20460. New nonroad engines exported to such countries must...

78 FR 53727 - Export Trade Certificate of Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

... DEPARTMENT OF COMMERCE International Trade Administration [Application No. 84-24A12] Export Trade Certificate of Review ACTION: Notice of Issuance of an Export Trade Certificate of Review to Northwest Fruit Exporters, Application No. 84-24A12. SUMMARY: The U.S. Department of Commerce issued an amended Export Trade...

40 CFR 92.909 - Export exemptions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Export exemptions. 92.909 Section 92....909 Export exemptions. (a) A new locomotive or locomotive engine intended solely for export, and so... from EPA standards. (c) It is a condition of any exemption for the purpose of export under paragraph (a...

9 CFR 91.3 - General export requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false General export requirements. 91.3... HANDLING OF LIVESTOCK FOR EXPORTATION General Provisions § 91.3 General export requirements. (a) All... accompanied from the State of origin of the export movement to the port of embarkation by an origin health...

40 CFR 91.1009 - Export exemptions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Export exemptions. 91.1009 Section 91....1009 Export exemptions. (a) A new marine SI engine intended solely for export, and so labeled or tagged...., Washington, DC 20460. New marine SI engines exported to such countries must comply with EPA certification...

37 CFR 5.19 - Export of technical data.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Export of technical data. 5..., DEPARTMENT OF COMMERCE GENERAL SECRECY OF CERTAIN INVENTIONS AND LICENSES TO EXPORT AND FILE APPLICATIONS IN FOREIGN COUNTRIES Licenses for Foreign Exporting and Filing § 5.19 Export of technical data. (a) Under...

7 CFR 1493.280 - Evidence of export report.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 10 2010-01-01 2010-01-01 false Evidence of export report. 1493.280 Section 1493.280... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Facility Guarantee Program (FGP) Operations § 1493.280 Evidence of export report. (a) Report of export. The...

7 CFR 35.8 - Date of export.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Date of export. 35.8 Section 35.8 Agriculture... Practices), DEPARTMENT OF AGRICULTURE COMMODITY STANDARDS AND STANDARD CONTAINER REGULATIONS EXPORT GRAPES AND PLUMS Definitions § 35.8 Date of export. Date of export means the date of loading on board the...

48 CFR 552.211-88 - Vehicle export preparation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Vehicle export preparation... Vehicle export preparation. As prescribed in 511.204(b)(8), insert the following clause: Vehicle Export Preparation (JAN 2010) Vehicles shall be prepared for export on wheels, unboxed, unless otherwise specified in...

9 CFR 322.3 - Transferring products for export.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Transferring products for export. 322... INSPECTION AND CERTIFICATION EXPORTS 1 § 322.3 Transferring products for export. When inspected and passed products for export are transferred from tank cars to other containers on vessels, such transfer shall be...

78 FR 37520 - Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-21

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the... Molina, Jr. (``Molina'') was convicted of violating Section 38 of the Arms Export Control Act (22 U.S.C... attempting to export and causing to be exported from the United States to Mexico two AK47 semi-automatic...

77 FR 60377 - Order Denying Export Privileges

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-03

... DEPARTMENT OF COMMERCE Bureau of Industry and Security Order Denying Export Privileges In the... causing to be violated the United States trade restriction with Iran by exporting and attempting to export... Foreign Assets Control for such an export. Avanessian was also convicted of one count of conspiracy (18 U...

10 CFR 431.405 - Exported equipment.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 3 2010-01-01 2010-01-01 false Exported equipment. 431.405 Section 431.405 Energy... EQUIPMENT General Provisions § 431.405 Exported equipment. Under Sections 330 and 345 of the Act, this Part... for export from the United States (or such equipment was imported for export), unless such equipment...

77 FR 16768 - Export Sales Reporting Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-22

... DEPARTMENT OF AGRICULTURE Office of the Secretary 7 CFR Part 20 RIN 0551-AA70 Export Sales... for pork (fresh, chilled, and frozen box/primal cuts) and distillers dried grain (DDG) to the Export...: Contact Peter W. Burr, Branch Chief, Export Sales Reporting Branch, Import Policies and Export Reporting...

40 CFR 725.920 - Exports and imports.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Exports and imports. 725.920 Section... on Significant New Uses of Microorganisms § 725.920 Exports and imports. (a) Exports. Persons who intend to export a microorganism identified in subpart M of this part, or in any proposed rule which...

76 FR 54193 - Fiscal Year 2012 Veterinary Import/Export, Diagnostic Services, and Export Certification for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-31

...] Fiscal Year 2012 Veterinary Import/Export, Diagnostic Services, and Export Certification for Plants and.... SUMMARY: This notice pertains to user fees charged for Veterinary Services animal quarantine and other..., organisms, and vectors; for certain veterinary diagnostic services; and for export certification of plants...

7 CFR 1493.70 - Guarantee rates and fees.

Code of Federal Regulations, 2014 CFR

2014-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.70... length of the payment terms provided for in the export sale contract, the degree of risk that CCC assumes...

7 CFR 1493.90 - Certification requirements for the evidence of export.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103... certifications with respect to a GSM-102 or GSM-103 payment guarantee, CCC will have the right, notwithstanding...

7 CFR 1488.9 - Evidence of export.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Export Sales of Agricultural Commodities From Private Stocks Under CCC Export Credit Sales Program (GSM-5... truck, the exporter shall furnish to the Treasurer, CCC, one copy of the bill of lading covering the... carrier, the exporter shall furnish to the Treasurer, CCC, one non-negotiable copy or photo copy or other...

7 CFR 1493.70 - Guarantee rates and fees.

Code of Federal Regulations, 2012 CFR

2012-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.70... length of the payment terms provided for in the export sale contract, the degree of risk that CCC assumes...

7 CFR 1493.90 - Certification requirements for the evidence of export.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103... certifications with respect to a GSM-102 or GSM-103 payment guarantee, CCC will have the right, notwithstanding...

7 CFR 1493.50 - Certification requirements for obtaining payment guarantee.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program... requirements of § 1493.30, and the exporter will immediately notify CCC if there is a change of circumstances...

7 CFR 1493.50 - Certification requirements for obtaining payment guarantee.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program... requirements of § 1493.30, and the exporter will immediately notify CCC if there is a change of circumstances...

7 CFR 1493.70 - Guarantee rates and fees.

Code of Federal Regulations, 2013 CFR

2013-01-01

... OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103) Operations § 1493.70... length of the payment terms provided for in the export sale contract, the degree of risk that CCC assumes...

7 CFR 1493.50 - Certification requirements for obtaining payment guarantee.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program... requirements of § 1493.30, and the exporter will immediately notify CCC if there is a change of circumstances...

7 CFR 1493.90 - Certification requirements for the evidence of export.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE EXPORT PROGRAMS CCC EXPORT CREDIT GUARANTEE PROGRAMS CCC Export Credit Guarantee Program (GSM-102) and CCC Intermediate Export Credit Guarantee Program (GSM-103... certifications with respect to a GSM-102 or GSM-103 payment guarantee, CCC will have the right, notwithstanding...

Gaseous time projection chambers for rare event detection: results from the T-REX project. I. Double beta decay

NASA Astrophysics Data System (ADS)

Irastorza, I. G.; Aznar, F.; Castel, J.; Cebrián, S.; Dafni, T.; Galán, J.; Garcia, J. A.; Garza, J. G.; Gómez, H.; Herrera, D. C.; Iguaz, F. J.; Luzon, G.; Mirallas, H.; Ruiz, E.; Seguí, L.; Tomás, A.

2016-01-01

As part of the T-REX project, a number of R&D and prototyping activities have been carried out during the last years to explore the applicability of gaseous Time Projection Chambers (TPCs) with Micromesh Gas Structures (Micromegas) in rare event searches like double beta decay, axion research and low-mass WIMP searches. In both this and its companion paper, we compile the main results of the project and give an outlook of application prospects for this detection technique. While in the companion paper we focus on axions and WIMPs, in this paper we focus on the results regarding the measurement of the double beta decay (DBD) of 136Xe in a high pressure Xe (HPXe) TPC. Micromegas of the microbulk type have been extensively studied in high pressure Xe and Xe mixtures. Particularly relevant are the results obtained in Xe + trimethylamine (TMA) mixtures, showing very promising results in terms of gain, stability of operation, and energy resolution at high pressures up to 10 bar. The addition of TMA at levels of ~ 1% reduces electron diffusion by up to a factor of 10 with respect to pure Xe, improving the quality of the topological pattern, with a positive impact on the discrimination capability. Operation with a medium size prototype of 30 cm diameter and 38 cm of drift (holding about 1 kg of Xe at 10 bar in the fiducial volume, enough to contain high energy electron tracks in the detector volume) has allowed to test the detection concept in realistic experimental conditions. Microbulk Micromegas are able to image the DBD ionization signature with high quality while, at the same time, measuring its energy deposition with a resolution of at least a ~ 3% FWHM @ Qββ. This value was experimentally demonstrated for high-energy extended tracks at 10 bar, and is probably improvable down to the ~ 1% FWHM levels as extrapolated from low energy events. In addition, first results on the topological signature information (one straggling track ending in two blobs) show promising background discrimination capabilities out of reach of other experimental implementations. Moreover, microbulk Micromegas have very low levels of intrinsic radioactivity, and offer cost-effective scaling-up options. All these results demonstrate that Micromegas-read HPXe TPC remains a very competitive technique for the next generation DBD experiments.

The building blocks of economic complexity

PubMed Central

Hidalgo, César A.; Hausmann, Ricardo

2009-01-01

For Adam Smith, wealth was related to the division of labor. As people and firms specialize in different activities, economic efficiency increases, suggesting that development is associated with an increase in the number of individual activities and with the complexity that emerges from the interactions between them. Here we develop a view of economic growth and development that gives a central role to the complexity of a country's economy by interpreting trade data as a bipartite network in which countries are connected to the products they export, and show that it is possible to quantify the complexity of a country's economy by characterizing the structure of this network. Furthermore, we show that the measures of complexity we derive are correlated with a country's level of income, and that deviations from this relationship are predictive of future growth. This suggests that countries tend to converge to the level of income dictated by the complexity of their productive structures, indicating that development efforts should focus on generating the conditions that would allow complexity to emerge to generate sustained growth and prosperity. PMID:19549871

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

PubMed Central

Yamada, Kazunori; Kondoh, Yasumitsu; Hikono, Hirokazu; Osada, Hiroyuki; Tomii, Kentaro; Saito, Takehiko; Aida, Yoko

2015-01-01

Developing antiviral therapies for influenza A virus (IAV) infection is an ongoing process because of the rapid rate of antigenic mutation and the emergence of drug-resistant viruses. The ideal strategy is to develop drugs that target well-conserved, functionally restricted, and unique surface structures without affecting host cell function. We recently identified the antiviral compound, RK424, by screening a library of 50,000 compounds using cell-based infection assays. RK424 showed potent antiviral activity against many different subtypes of IAV in vitro and partially protected mice from a lethal dose of A/WSN/1933 (H1N1) virus in vivo. Here, we show that RK424 inhibits viral ribonucleoprotein complex (vRNP) activity, causing the viral nucleoprotein (NP) to accumulate in the cell nucleus. In silico docking analysis revealed that RK424 bound to a small pocket in the viral NP. This pocket was surrounded by three functionally important domains: the RNA binding groove, the NP dimer interface, and nuclear export signal (NES) 3, indicating that it may be involved in the RNA binding, oligomerization, and nuclear export functions of NP. The accuracy of this binding model was confirmed in a NP-RK424 binding assay incorporating photo-cross-linked RK424 affinity beads and in a plaque assay evaluating the structure-activity relationship of RK424. Surface plasmon resonance (SPR) and pull-down assays showed that RK424 inhibited both the NP-RNA and NP-NP interactions, whereas size exclusion chromatography showed that RK424 disrupted viral RNA-induced NP oligomerization. In addition, in vitro nuclear export assays confirmed that RK424 inhibited nuclear export of NP. The amino acid residues comprising the NP pocket play a crucial role in viral replication and are highly conserved in more than 7,000 NP sequences from avian, human, and swine influenza viruses. Furthermore, we found that the NP pocket has a surface structure different from that of the pocket in host molecules. Taken together, these results describe a promising new approach to developing influenza virus drugs that target a novel pocket structure within NP. PMID:26222066

Model and Analytic Processes for Export License Assessments

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

Thompson, Sandra E.; Whitney, Paul D.; Weimar, Mark R.

2011-09-29

This paper represents the Department of Energy Office of Nonproliferation Research and Development (NA-22) Simulations, Algorithms and Modeling (SAM) Program's first effort to identify and frame analytical methods and tools to aid export control professionals in effectively predicting proliferation intent; a complex, multi-step and multi-agency process. The report focuses on analytical modeling methodologies that alone, or combined, may improve the proliferation export control license approval process. It is a follow-up to an earlier paper describing information sources and environments related to international nuclear technology transfer. This report describes the decision criteria used to evaluate modeling techniques and tools to determinemore » which approaches will be investigated during the final 2 years of the project. The report also details the motivation for why new modeling techniques and tools are needed. The analytical modeling methodologies will enable analysts to evaluate the information environment for relevance to detecting proliferation intent, with specific focus on assessing risks associated with transferring dual-use technologies. Dual-use technologies can be used in both weapons and commercial enterprises. A decision-framework was developed to evaluate which of the different analytical modeling methodologies would be most appropriate conditional on the uniqueness of the approach, data availability, laboratory capabilities, relevance to NA-22 and Office of Arms Control and Nonproliferation (NA-24) research needs and the impact if successful. Modeling methodologies were divided into whether they could help micro-level assessments (e.g., help improve individual license assessments) or macro-level assessment. Macro-level assessment focuses on suppliers, technology, consumers, economies, and proliferation context. Macro-level assessment technologies scored higher in the area of uniqueness because less work has been done at the macro level. An approach to developing testable hypotheses for the macro-level assessment methodologies is provided. The outcome of this works suggests that we should develop a Bayes Net for micro-level analysis and continue to focus on Bayes Net, System Dynamics and Economic Input/Output models for assessing macro-level problems. Simultaneously, we need to develop metrics for assessing intent in export control, including the risks and consequences associated with all aspects of export control.« less

Microinjection and Fluorescence In Situ Hybridization Assay for Studying mRNA Export in Mammalian Cells.

PubMed

Wang, Ke; Shi, Min; Cheng, Hong

2017-01-01

Microinjection and Fluorescence in situ Hybridization (FISH) assay is a useful method for mRNA export studies, which can overcome the problems of traditional transfection in cells. Here, we describe the method of microinjection and FISH assay applied in investigation of mRNA export. By this method we can estimate the mRNA export kinetics, examining mRNA export in cells with low transfection efficiencies, and observing nuclear export of aberrant RNAs.

A Los1p-independent pathway for nuclear export of intronless tRNAs in Saccharomycescerevisiae.

PubMed

Feng, Wenqin; Hopper, Anita K

2002-04-16

Los1p, the Saccharomyces cerevisiae exportin-t homologue, binds tRNA and functions in pre-tRNA splicing and export of mature tRNA from the nucleus to the cytosol. Because LOS1 is unessential in yeast, other pathways for tRNA nuclear export must exist. We report that Cca1p, which adds nucleotides C, C, and A to the 3' end of tRNAs, is a multicopy suppressor of the defect in tRNA nuclear export caused by los1 null mutations. Mes1p, methionyl-tRNA synthetase, also suppresses the defect in nuclear export of tRNA(Met) in los1 cells. Thus, Cca1p and Mes1p seem to function in a Los1p-independent tRNA nuclear export pathway. Heterokaryon analysis indicates that Cca1p is a nucleus/cytosol-shuttling protein, providing the potential for Cca1p to function as an exporter or an adapter in this tRNA nuclear export pathway. In yeast, most mutations that affect tRNA nuclear export also cause defects in pre-tRNA splicing leading to tight coupling of the splicing and export processes. In contrast, we show that overexpressed Cca1p corrects the nuclear export, but not the pre-tRNA-splicing defects of los1Kan(r) cells, thereby uncoupling pre-tRNA splicing and tRNA nuclear export.

An export coefficient based inexact fuzzy bi-level multi-objective programming model for the management of agricultural nonpoint source pollution under uncertainty

NASA Astrophysics Data System (ADS)

Cai, Yanpeng; Rong, Qiangqiang; Yang, Zhifeng; Yue, Wencong; Tan, Qian

2018-02-01

In this research, an export coefficient based inexact fuzzy bi-level multi-objective programming (EC-IFBLMOP) model was developed through integrating export coefficient model (ECM), interval parameter programming (IPP) and fuzzy parameter programming (FPP) within a bi-level multi-objective programming framework. The proposed EC-IFBLMOP model can effectively deal with the multiple uncertainties expressed as discrete intervals and fuzzy membership functions. Also, the complexities in agricultural systems, such as the cooperation and gaming relationship between the decision makers at different levels, can be fully considered in the model. The developed model was then applied to identify the optimal land use patterns and BMP implementing levels for agricultural nonpoint source (NPS) pollution management in a subcatchment in the upper stream watershed of the Miyun Reservoir in north China. The results of the model showed that the desired optimal land use patterns and implementing levels of best management of practices (BMPs) would be obtained. It is the gaming result between the upper- and lower-level decision makers, when the allowable discharge amounts of NPS pollutants were limited. Moreover, results corresponding to different decision scenarios could provide a set of decision alternatives for the upper- and lower-level decision makers to identify the most appropriate management strategy. The model has a good applicability and can be effectively utilized for agricultural NPS pollution management.

NUCLEAR PORE ANCHOR, the Arabidopsis Homolog of Tpr/Mlp1/Mlp2/Megator, Is Involved in mRNA Export and SUMO Homeostasis and Affects Diverse Aspects of Plant Development[W

PubMed Central

Xu, Xianfeng Morgan; Rose, Annkatrin; Muthuswamy, Sivaramakrishnan; Jeong, Sun Yong; Venkatakrishnan, Sowmya; Zhao, Qiao; Meier, Iris

2007-01-01

Vertebrate Tpr and its yeast homologs Mlp1/Mlp2, long coiled-coil proteins of nuclear pore inner basket filaments, are involved in mRNA export, telomere organization, spindle pole assembly, and unspliced RNA retention. We identified Arabidopsis thaliana NUCLEAR PORE ANCHOR (NUA) encoding a 237-kD protein with similarity to Tpr. NUA is located at the inner surface of the nuclear envelope in interphase and in the vicinity of the spindle in prometaphase. Four T-DNA insertion lines were characterized, which comprise an allelic series of increasing severity for several correlating phenotypes, such as early flowering under short days and long days, increased abundance of SUMO conjugates, altered expression of several flowering regulators, and nuclear accumulation of poly(A)+ RNA. nua mutants phenocopy mutants of EARLY IN SHORT DAYS4 (ESD4), an Arabidopsis SUMO protease concentrated at the nuclear periphery. nua esd4 double mutants resemble nua and esd4 single mutants, suggesting that the two proteins act in the same pathway or complex, supported by yeast two-hybrid interaction. Our data indicate that NUA is a component of nuclear pore-associated steps of sumoylation and mRNA export in plants and that defects in these processes affect the signaling events of flowering time regulation and additional developmental processes. PMID:17513499

22 CFR 125.1 - Exports subject to this part.

Code of Federal Regulations, 2011 CFR

2011-04-01

... EXPORT OF TECHNICAL DATA AND CLASSIFIED DEFENSE ARTICLES § 125.1 Exports subject to this part. (a) The controls of this part apply to the export of technical data and the export of classified defense articles... defense articles if the technical data is determined by the Directorate of Defense Trade Controls to be...

26 CFR 1.970-1 - Export trade corporations.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 10 2014-04-01 2013-04-01 true Export trade corporations. 1.970-1 Section 1.970... (CONTINUED) INCOME TAXES (CONTINUED) Export Trade Corporations § 1.970-1 Export trade corporations. (a) In general. Sections 970 through 972 provide in general that if a controlled foreign corporation is an export...

26 CFR 1.970-1 - Export trade corporations.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 10 2011-04-01 2011-04-01 false Export trade corporations. 1.970-1 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Export Trade Corporations § 1.970-1 Export trade corporations. (a) In general. Sections 970 through 972 provide in general that if a controlled foreign corporation is an export...

26 CFR 1.970-1 - Export trade corporations.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 10 2012-04-01 2012-04-01 false Export trade corporations. 1.970-1 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Export Trade Corporations § 1.970-1 Export trade corporations. (a) In general. Sections 970 through 972 provide in general that if a controlled foreign corporation is an export...

26 CFR 1.970-1 - Export trade corporations.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 10 2013-04-01 2013-04-01 false Export trade corporations. 1.970-1 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Export Trade Corporations § 1.970-1 Export trade corporations. (a) In general. Sections 970 through 972 provide in general that if a controlled foreign corporation is an export...

22 CFR 123.17 - Exports of firearms, ammunition, and personal protective gear.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Exports of firearms, ammunition, and personal... REGULATIONS LICENSES FOR THE EXPORT OF DEFENSE ARTICLES § 123.17 Exports of firearms, ammunition, and personal...; (2) The firearms and accompanying ammunition to be exported is with the individual's baggage or...

26 CFR 1.970-1 - Export trade corporations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 10 2010-04-01 2010-04-01 false Export trade corporations. 1.970-1 Section 1... (CONTINUED) INCOME TAXES Export Trade Corporations § 1.970-1 Export trade corporations. (a) In general. Sections 970 through 972 provide in general that if a controlled foreign corporation is an export trade...

40 CFR 273.40 - Exports.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Exports. 273.40 Section 273.40... UNIVERSAL WASTE MANAGEMENT Standards for Large Quantity Handlers of Universal Waste § 273.40 Exports. A... exporter in 40 CFR 262.53, 262.56(a)(1) through (4), (6), and (b) and 262.57; (b) Export such universal...

77 FR 13990 - Export Sales Reporting Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-08

... DEPARTMENT OF AGRICULTURE Office of the Secretary 7 CFR Part 20 RIN 0551-AA70 Export Sales... grain (DDG) to the Export Sales Reporting Requirements. Under this proposed rule, all exporters of U.S. pork and DDG would be required to report on a weekly basis, information on the export sales of pork and...

19 CFR 10.9 - Articles exported for processing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Articles exported for processing. 10.9 Section 10... Exported and Returned § 10.9 Articles exported for processing. (a) Except as otherwise provided for in this... returned after having been exported for further processing and which are claimed to be subject to duty only...

40 CFR 94.909 - Export exemptions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Export exemptions. 94.909 Section 94... Export exemptions. (a) A new engine intended solely for export, and so labeled or tagged on the outside... of export under paragraph (a) of this section, that such exemption is void ab initio with respect to...

21 CFR 312.110 - Import and export requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Import and export requirements. 312.110 Section... export requirements. (a) Imports. An investigational new drug offered for import into the United States.... (b) Exports. An investigational new drug may be exported from the United States for use in a clinical...

40 CFR 273.20 - Exports.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Exports. 273.20 Section 273.20... UNIVERSAL WASTE MANAGEMENT Standards for Small Quantity Handlers of Universal Waste § 273.20 Exports. A... exporter in 40 CFR 262.53, 262.56(a) (1) through (4), (6), and (b) and 262.57; (b) Export such universal...

19 CFR 10.66 - Articles exported for temporary exhibition and returned; horses exported for horse racing and...

Code of Federal Regulations, 2010 CFR

2010-04-01

... exportation of such articles, an application on Customs Form 4455 (accompanied by an appropriate inventory... 19 Customs Duties 1 2010-04-01 2010-04-01 false Articles exported for temporary exhibition and... ARTICLES CONDITIONALLY FREE, SUBJECT TO A REDUCED RATE, ETC. General Provisions Articles Exported for...

40 CFR 80.1430 - Requirements for exporters of renewable fuels.

Code of Federal Regulations, 2010 CFR

2010-07-01

... calendar year i, in gallons. k = A discrete volume of exported renewable fuel. VOLk = The standardized volume of discrete volume k of exported renewable fuel that the exporter knows or has reason to know is... associated with discrete volume k. Σ = Sum involving all volumes of cellulosic biofuel exported. DCB,i-1...

19 CFR 146.67 - Transfer of merchandise for exportation.

Code of Federal Regulations, 2014 CFR

2014-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES Transfer of Merchandise From a Zone § 146.67 Transfer of merchandise for exportation. (a) Direct exportation. Any merchandise in a zone may be exported... territory for exportation at the port where the zone is located, will be made under an entry for immediate...

19 CFR 146.67 - Transfer of merchandise for exportation.

Code of Federal Regulations, 2013 CFR

2013-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES Transfer of Merchandise From a Zone § 146.67 Transfer of merchandise for exportation. (a) Direct exportation. Any merchandise in a zone may be exported... territory for exportation at the port where the zone is located, will be made under an entry for immediate...