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Sample records for functional nuclear localization

  1. Identification of two functional nuclear localization signals mediating nuclear import of liver receptor homologue-1.

    PubMed

    Yang, Feng-Ming; Lin, Yu-Chi; Hu, Meng-Chun

    2011-04-01

    Liver receptor homologue-1 (LRH-1) is a member of the nuclear receptor superfamily. We characterized two functional nuclear localization signals (NLSs) in LRH-1. NLS1 (residues 117-168) overlaps the second zinc finger in the DNA binding domain. Mutagenesis showed that the zinc finger structure and two basic clusters on either side of the zinc finger loop are critical for nuclear import of NLS1. NLS2 (residues 169-204) is located in the Ftz-F1 box that contains a bipartite signal. In full-length LRH-1, mutation of either NLS1 or NLS2 had no effect on nuclear localization, but disruption of both NLS1 and NLS2 resulted in the cytoplasmic accumulation of LRH-1. Either NLS1 or NLS2 alone was sufficient to target LRH-1 to the nucleus. Both NLS1 and NLS2 mediate nuclear transport by a mechanism involving importin α/β. Finally, we showed that three crucial basic clusters in the NLSs are involved in the DNA binding and transcriptional activities of LRH-1. PMID:20853131

  2. Identification and functional characterization of a novel bipartite nuclear localization sequence in ARID1A.

    PubMed

    Bateman, Nicholas W; Shoji, Yutaka; Conrads, Kelly A; Stroop, Kevin D; Hamilton, Chad A; Darcy, Kathleen M; Maxwell, George L; Risinger, John I; Conrads, Thomas P

    2016-01-01

    AT-rich interactive domain-containing protein 1A (ARID1A) is a recently identified nuclear tumor suppressor frequently altered in solid tumor malignancies. We have identified a bipartite-like nuclear localization sequence (NLS) that contributes to nuclear import of ARID1A not previously described. We functionally confirm activity using GFP constructs fused with wild-type or mutant NLS sequences. We further show that cyto-nuclear localized, bipartite NLS mutant ARID1A exhibits greater stability than nuclear-localized, wild-type ARID1A. Identification of this undescribed functional NLS within ARID1A contributes vital insights to rationalize the impact of ARID1A missense mutations observed in patient tumors. PMID:26614907

  3. Prostaglandins regulate nuclear localization of Fascin and its function in nucleolar architecture

    PubMed Central

    Groen, Christopher M.; Jayo, Asier; Parsons, Maddy; Tootle, Tina L.

    2015-01-01

    Fascin, a highly conserved actin-bundling protein, localizes and functions at new cellular sites in both Drosophila and multiple mammalian cell types. During Drosophila follicle development, in addition to being cytoplasmic, Fascin is in the nuclei of the germline-derived nurse cells during stages 10B–12 (S10B–12) and at the nuclear periphery during stage 13 (S13). This localization is specific to Fascin, as other actin-binding proteins, Villin and Profilin, do not exhibit the same subcellular distribution. In addition, localization of fascin1 to the nucleus and nuclear periphery is observed in multiple mammalian cell types. Thus the regulation and function of Fascin at these new cellular locations is likely to be highly conserved. In Drosophila, loss of prostaglandin signaling causes a global reduction in nuclear Fascin and a failure to relocalize to the nuclear periphery. Alterations in nuclear Fascin levels result in defects in nucleolar morphology in both Drosophila follicles and cultured mammalian cells, suggesting that nuclear Fascin plays an important role in nucleolar architecture. Given the numerous roles of Fascin in development and disease, including cancer, our novel finding that Fascin has functions within the nucleus sheds new light on the potential roles of Fascin in these contexts. PMID:25808493

  4. Identification of a functional nuclear localization signal within the human USP22 protein

    SciTech Connect

    Xiong, Jianjun; Wang, Yaqin; Gong, Zhen; Liu, Jianyun; Li, Weidong

    2014-06-20

    Highlights: • USP22 was accumulated in nucleus. • We identified of a functional USP22 NLS. • The KRRK amino acid residues are indispensable in NLS. • The KRRK motif is conserved in USP22 homologues. - Abstract: Ubiquitin-specific processing enzyme 22 (USP22), a member of the deubiquitinase family, is over-expressed in most human cancers and has been implicated in tumorigenesis. Because it is an enzymatic subunit of the human SAGA transcriptional cofactor, USP22 deubiquitylates histone H2A and H2B in the nucleus, thus participating in gene regulation and cell-cycle progression. However, the mechanisms regulating its nuclear translocation have not yet been elucidated. It was here demonstrated that USP22 is imported into the nucleus through a mechanism mediated by nuclear localization signal (NLS). The bipartite NLS sequence KRELELLKHNPKRRKIT (aa152–168), was identified as the functional NLS for its nuclear localization. Furthermore, a short cluster of basic amino acid residues KRRK within this bipartite NLS plays the primary role in nuclear localization and is evolutionarily conserved in USP22 homologues. In the present study, a functional NLS and the minimal sequences required for the active targeting of USP22 to the nucleus were identified. These findings may provide a molecular basis for the mechanism underlying USP22 nuclear trafficking and function.

  5. Serine phosphorylation by SYK is critical for nuclear localization and transcription factor function of Ikaros

    PubMed Central

    Uckun, Fatih M.; Ma, Hong; Zhang, Jian; Ozer, Zahide; Dovat, Sinisa; Mao, Cheney; Ishkhanian, Rita; Goodman, Patricia; Qazi, Sanjive

    2012-01-01

    Ikaros is a zinc finger-containing DNA-binding protein that plays a pivotal role in immune homeostasis through transcriptional regulation of the earliest stages of lymphocyte ontogeny and differentiation. Functional deficiency of Ikaros has been implicated in the pathogenesis of acute lymphoblastic leukemia, the most common form of childhood cancer. Therefore, a stringent regulation of Ikaros activity is considered of paramount importance, but the operative molecular mechanisms responsible for its regulation remain largely unknown. Here we provide multifaceted genetic and biochemical evidence for a previously unknown function of spleen tyrosine kinase (SYK) as a partner and posttranslational regulator of Ikaros. We demonstrate that SYK phoshorylates Ikaros at unique C-terminal serine phosphorylation sites S358 and S361, thereby augmenting its nuclear localization and sequence-specific DNA binding activity. Mechanistically, we establish that SYK-induced Ikaros activation is essential for its nuclear localization and optimal transcription factor function. PMID:23071339

  6. Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain

    PubMed Central

    Hatayama, Minoru; Tomizawa, Tadashi; Sakai-Kato, Kumiko; Bouvagnet, Patrice; Kose, Shingo; Imamoto, Naoko; Yokoyama, Shigeyuki; Utsunomiya-Tate, Naoko; Mikoshiba, Katsuhiko; Kigawa, Takanori; Aruga, Jun

    2008-01-01

    Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left–right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense mutations in the first ZF motif (ZF1) result in defective nuclear localization, which may underlie the pathogenesis of heterotaxy. Here we revealed the structural and functional basis of the nuclear localization signal (NLS) of ZIC3 and investigated its relationship to the defect caused by ZF1 mutation. The ZIC3 NLS was located in the ZF2 and ZF3 regions, rather than ZF1. Several basic residues interspersed throughout these regions were responsible for the nuclear localization, but R320, K337 and R350 were particularly important. NMR structure analysis revealed that ZF1–4 had a similar structure to GLI ZF, and the basic side chains of the NLS clustered together in two regions on the protein surface, similar to classical bipartite NLSs. Among the residues for the ZF1 mutations, C253 and H286 were positioned for the metal chelation, whereas W255 was positioned in the hydrophobic core formed by ZF1 and ZF2. Tryptophan 255 was a highly conserved inter-finger connector and formed part of a structural motif (tandem CXW-C-H-H) that is shared with GLI, Glis and some fungal ZF proteins. Furthermore, we found that knockdown of Karyopherin α1/α6 impaired ZIC3 nuclear localization, and physical interactions between the NLS and the nuclear import adapter proteins were disturbed by mutations in the NLS but not by W255G. These results indicate that ZIC3 is imported into the cell nucleus by the Karyopherin (Importin) system and that the impaired nuclear localization by the ZF1 mutation is not due to a direct influence on the NLS. PMID:18716025

  7. A novel function for the Caenorhabditis elegans torsin OOC-5 in nucleoporin localization and nuclear import

    PubMed Central

    VanGompel, Michael J. W.; Nguyen, Ken C. Q.; Hall, David H.; Dauer, William T.; Rose, Lesilee S.

    2015-01-01

    Torsin proteins are AAA+ ATPases that localize to the endoplasmic reticular/nuclear envelope (ER/NE) lumen. A mutation that markedly impairs torsinA function causes the CNS disorder DYT1 dystonia. Abnormalities of NE membranes have been linked to torsinA loss of function and the pathogenesis of DYT1 dystonia, leading us to investigate the role of the Caenorhabditis elegans torsinA homologue OOC-5 at the NE. We report a novel role for torsin in nuclear pore biology. In ooc-5–mutant germ cell nuclei, nucleoporins (Nups) were mislocalized in large plaques beginning at meiotic entry and persisted throughout meiosis. Moreover, the KASH protein ZYG-12 was mislocalized in ooc-5 gonads. Nups were mislocalized in adult intestinal nuclei and in embryos from mutant mothers. EM analysis revealed vesicle-like structures in the perinuclear space of intestinal and germ cell nuclei, similar to defects reported in torsin-mutant flies and mice. Consistent with a functional disruption of Nups, ooc-5–mutant embryos displayed impaired nuclear import kinetics, although the nuclear pore-size exclusion barrier was maintained. Our data are the first to demonstrate a requirement for a torsin for normal Nup localization and function and suggest that these functions are likely conserved. PMID:25739455

  8. A Functional Nuclear Localization Sequence in the C. elegans TRPV Channel OCR-2

    PubMed Central

    Ezak, Meredith J.; Ferkey, Denise M.

    2011-01-01

    The ability to modulate gene expression in response to sensory experience is critical to the normal development and function of the nervous system. Calcium is a key activator of the signal transduction cascades that mediate the process of translating a cellular stimulus into transcriptional changes. With the recent discovery that the mammalian Cav1.2 calcium channel can be cleaved, enter the nucleus and act as a transcription factor to control neuronal gene expression, a more direct role for the calcium channels themselves in regulating transcription has begun to be appreciated. Here we report the identification of a nuclear localization sequence (NLS) in the C. elegans transient receptor potential vanilloid (TRPV) cation channel OCR-2. TRPV channels have previously been implicated in transcriptional regulation of neuronal genes in the nematode, although the precise mechanism remains unclear. We show that the NLS in OCR-2 is functional, being able to direct nuclear accumulation of a synthetic cargo protein as well as the carboxy-terminal cytosolic tail of OCR-2 where it is endogenously found. Furthermore, we discovered that a carboxy-terminal portion of the full-length channel can localize to the nucleus of neuronal cells. These results suggest that the OCR-2 TRPV cation channel may have a direct nuclear function in neuronal cells that was not previously appreciated. PMID:21957475

  9. Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages

    PubMed Central

    Redrejo-Rodríguez, Modesto; Muñoz-Espín, Daniel; Holguera, Isabel; Mencía, Mario; Salas, Margarita

    2012-01-01

    A number of prokaryotic proteins have been shown to contain nuclear localization signals (NLSs), although its biological role remains sometimes unclear. Terminal proteins (TPs) of bacteriophages prime DNA replication and become covalently linked to the genome ends. We predicted NLSs within the TPs of bacteriophages from diverse families and hosts and, indeed, the TPs of Φ29, Nf, PRD1, Bam35, and Cp-1, out of seven TPs tested, were found to localize to the nucleus when expressed in mammalian cells. Detailed analysis of Φ29 TP led us to identify a bona fide NLS within residues 1–37. Importantly, gene delivery into the eukaryotic nucleus is enhanced by the presence of Φ29 TP attached to the 5′ DNA ends. These findings show a common feature of TPs from diverse bacteriophages targeting the eukaryotic nucleus and suggest a possible common function by facilitating the horizontal transfer of genes between prokaryotes and eukaryotes. PMID:23091024

  10. A functional nuclear localization sequence in the VP1 capsid protein of coxsackievirus B3

    SciTech Connect

    Wang, Tianying; Yu, Bohai; Lin, Lexun; Zhai, Xia; Han, Yelu; Qin, Ying; Guo, Zhiwei; Wu, Shuo; Zhong, Xiaoyan; Wang, Yan; Tong, Lei; Zhang, Fengmin; Si, Xiaoning; Zhao, Wenran; Zhong, Zhaohua

    2012-11-25

    The capsid proteins of some RNA viruses can translocate to the nucleus and interfere with cellular phenotypes. In this study we found that the VP1 capsid protein of coxsackievirus B3 (CVB3) was dominantly localized in the nucleus of the cells transfected with VP1-expressing plasmid. The VP1 nuclear localization also occurred in the cells infected with CVB3. Truncation analysis indicated that the VP1 nuclear localization sequence located near the C-terminal. The substitution of His220 with threonine completely abolished its translocation. The VP1 proteins of other CVB types might have the nuclear localization potential because this region was highly conserved. Moreover, the VP1 nuclear localization induced cell cycle deregulation, including a prolonged S phase and shortened G2-M phase. Besides these findings, we also found a domain between Ala72 and Phe106 that caused the VP1 truncates dotted distributed in the cytoplasm. Our results suggest a new pathogenic mechanism of CVB. - Highlights: Black-Right-Pointing-Pointer The VP1 protein of coxsackievirus B3 can specifically localize in the nucleus. Black-Right-Pointing-Pointer The nuclear localization signal of coxsackievirus B3 VP1 protein locates near its C-terminal. Black-Right-Pointing-Pointer The VP1 nuclear localization of coxsackievirus B3 can deregulate cell cycle. Black-Right-Pointing-Pointer There is a domain in the VP1 that determines it dotted distributed in the cytoplasm.

  11. Functional Analysis of Nuclear Localization Signals in VP1-2 Homologues from All Herpesvirus Subfamilies

    PubMed Central

    Hennig, T.; Abaitua, F.

    2014-01-01

    ABSTRACT The herpes simplex virus (HSV) tegument protein VP1-2 contains an N-terminal nuclear localization signal (NLS) that is critical for capsid routing to the nuclear pore. Here we analyzed positionally conserved determinants in VP1-2 homologues from each of the alpha, beta, and gamma classes of human herpesviruses. The overall architectures of the VP1-2s were similar, with a conserved N-terminal ubiquitin-specific protease domain separated from an internal region by a linker that was quite poorly conserved in length and sequence. Within this linker region all herpesviruses contained a conserved, highly basic motif which nevertheless exhibited distinct class-specific features. The motif in HSV functioned as a monopartite NLS, while in varicella-zoster virus (VZV) activity required an adjacent basic section defining the motif as a bipartite NLS. Neither the beta- nor gammaherpesvirus VP1-2 motifs were identified by prediction algorithms, but they nevertheless functioned as efficient NLS motifs both in heterologous transfer assays and in HSV VP1-2. Furthermore, though with different efficiencies and with the exception of human herpesvirus 8 (HHV-8), these chimeric variants rescued the replication defect of an HSV mutant lacking its NLS motif. We demonstrate that the lysine at position 428 of HSV is critical for replication, with a single alanine substitution being sufficient to abrogate NLS function and virus growth. We conclude that the basic motifs of each of the VP1-2 proteins are likely to confer a similar function in capsid entry in the homologous setting and that while there is flexibility in the exact type of motif employed, specific individual residues are critical for function. IMPORTANCE To successfully infect cells, all herpesviruses, along with many other viruses, e.g., HIV, hepatitis B virus, and influenza virus, must navigate through the cytoplasmic environment and dock with nuclear pores for transport of their genomes into the nucleus. However, we

  12. Nuclear Localization and Functional Characteristics of Voltage-gated Potassium Channel Kv1.3*

    PubMed Central

    Jang, Soo Hwa; Byun, Jun Kyu; Jeon, Won-Il; Choi, Seon Young; Park, Jin; Lee, Bo Hyung; Yang, Ji Eun; Park, Jin Bong; O'Grady, Scott M.; Kim, Dae-Yong; Ryu, Pan Dong; Joo, Sang-Woo; Lee, So Yeong

    2015-01-01

    It is widely known that ion channels are expressed in the plasma membrane. However, a few studies have suggested that several ion channels including voltage-gated K+ (Kv) channels also exist in intracellular organelles where they are involved in the biochemical events associated with cell signaling. In the present study, Western blot analysis using fractionated protein clearly indicates that Kv1.3 channels are expressed in the nuclei of MCF7, A549, and SNU-484 cancer cells and human brain tissues. In addition, Kv1.3 is located in the plasma membrane and the nucleus of Jurkat T cells. Nuclear membrane hyperpolarization after treatment with margatoxin (MgTX), a specific blocker of Kv1.3 channels, provides evidence for functional channels at the nuclear membrane of A549 cells. MgTX-induced hyperpolarization is abolished in the nuclei of Kv1.3 silenced cells, and the effects of MgTX are dependent on the magnitude of the K+ gradient across the nuclear membrane. Selective Kv1.3 blockers induce the phosphorylation of cAMP response element-binding protein (CREB) and c-Fos activation. Moreover, Kv1.3 is shown to form a complex with the upstream binding factor 1 in the nucleus. Chromatin immunoprecipitation assay reveals that Sp1 transcription factor is directly bound to the promoter region of the Kv1.3 gene, and the Sp1 regulates Kv1.3 expression in the nucleus of A549 cells. These results demonstrate that Kv1.3 channels are primarily localized in the nucleus of several types of cancer cells and human brain tissues where they are capable of regulating nuclear membrane potential and activation of transcription factors, such as phosphorylated CREB and c-Fos. PMID:25829491

  13. Nuclear localization and functional characteristics of voltage-gated potassium channel Kv1.3.

    PubMed

    Jang, Soo Hwa; Byun, Jun Kyu; Jeon, Won-Il; Choi, Seon Young; Park, Jin; Lee, Bo Hyung; Yang, Ji Eun; Park, Jin Bong; O'Grady, Scott M; Kim, Dae-Yong; Ryu, Pan Dong; Joo, Sang-Woo; Lee, So Yeong

    2015-05-15

    It is widely known that ion channels are expressed in the plasma membrane. However, a few studies have suggested that several ion channels including voltage-gated K(+) (Kv) channels also exist in intracellular organelles where they are involved in the biochemical events associated with cell signaling. In the present study, Western blot analysis using fractionated protein clearly indicates that Kv1.3 channels are expressed in the nuclei of MCF7, A549, and SNU-484 cancer cells and human brain tissues. In addition, Kv1.3 is located in the plasma membrane and the nucleus of Jurkat T cells. Nuclear membrane hyperpolarization after treatment with margatoxin (MgTX), a specific blocker of Kv1.3 channels, provides evidence for functional channels at the nuclear membrane of A549 cells. MgTX-induced hyperpolarization is abolished in the nuclei of Kv1.3 silenced cells, and the effects of MgTX are dependent on the magnitude of the K(+) gradient across the nuclear membrane. Selective Kv1.3 blockers induce the phosphorylation of cAMP response element-binding protein (CREB) and c-Fos activation. Moreover, Kv1.3 is shown to form a complex with the upstream binding factor 1 in the nucleus. Chromatin immunoprecipitation assay reveals that Sp1 transcription factor is directly bound to the promoter region of the Kv1.3 gene, and the Sp1 regulates Kv1.3 expression in the nucleus of A549 cells. These results demonstrate that Kv1.3 channels are primarily localized in the nucleus of several types of cancer cells and human brain tissues where they are capable of regulating nuclear membrane potential and activation of transcription factors, such as phosphorylated CREB and c-Fos. PMID:25829491

  14. Function of steroidogenic factor 1 domains in nuclear localization, transactivation, and interaction with transcription factor TFIIB and c-Jun.

    PubMed

    Li, L A; Chiang, E F; Chen, J C; Hsu, N C; Chen, Y J; Chung, B C

    1999-09-01

    Normal endocrine development and function require nuclear hormone receptor SF-1 (steroidogenic factor 1). To understand the molecular mechanism of SF-1 action, we have investigated its domain function by mutagenesis and functional analyses. Our mutant studies show that the putative AF2 (activation function 2) helix located at the C-terminal end is indispensable for gene activation. SF-1 does not have an N-terminal AF1 domain. Instead, it contains a unique FP region, composed of the Ftz-F1 box and the proline cluster, after the zinc finger motif. The FP region interacts with transcription factor IIB (TFIIB) in vitro. This interaction requires residues 178-201 of TFIIB, a domain capable of binding several transcription factors. The FP region also mediates physical interaction with c-Jun, and this interaction greatly enhances SF-1 activity. The putative SF-1 ligand, 25-hydroxycholesterol, has no effects on these bindings. In addition, the Ftz-F1 box contains a bipartite nuclear localization signal (NLS). Removing the basic residues at either end of the key nuclear localization sequence NLS2.2 abolishes the nuclear transport. Expression of mutants containing only the FP region or lacking the AF2 domain blocks wild-type SF-1 activity in cells. By contrast, the mutant having a truncated nuclear localization signal lacks this dominant negative effect. These results delineate the importance of the FP and AF2 regions in nuclear localization, protein-protein interaction, and transcriptional activation. PMID:10478848

  15. SIRT6 deacetylates PKM2 to suppress its nuclear localization and oncogenic functions

    PubMed Central

    Bhardwaj, Abhishek; Das, Sanjeev

    2016-01-01

    SIRT6 (sirtuin 6) is a member of sirtuin family of deacetylases involved in diverse processes including genome stability, metabolic homeostasis, and tumorigenesis. However, the role of SIRT6 deacetylase activity in its tumor-suppressor functions is not well understood. Here we report that SIRT6 binds to and deacetylates nuclear PKM2 (pyruvate kinase M2) at the lysine 433 residue. PKM2 is a glycolytic enzyme with nonmetabolic nuclear oncogenic functions. SIRT6-mediated deacetylation results in PKM2 nuclear export. We further have identified exportin 4 as the specific transporter mediating PKM2 nuclear export. As a result of SIRT6-mediated deacetylation, PKM2 nuclear protein kinase and transcriptional coactivator functions are abolished. Thus, SIRT6 suppresses PKM2 oncogenic functions, resulting in reduced cell proliferation, migration potential, and invasiveness. Furthermore, studies in mouse tumor models demonstrate that PKM2 deacetylation is integral to SIRT6-mediated tumor suppression and inhibition of metastasis. Additionally, reduced SIRT6 levels correlate with elevated nuclear acetylated PKM2 levels in increasing grades of hepatocellular carcinoma. These findings provide key insights into the pivotal role of deacetylase activity in SIRT6 tumor-suppressor functions. PMID:26787900

  16. Nuclear import mechanism of neurofibromin for localization on the spindle and function in chromosome congression.

    PubMed

    Koliou, Xeni; Fedonidis, Constantinos; Kalpachidou, Theodora; Mangoura, Dimitra

    2016-01-01

    Neurofibromatosis type-1 (NF-1) is caused by mutations in the tumor suppressor gene NF1; its protein product neurofibromin is a RasGTPase-activating protein, a property that has yet to explain aneuploidy, most often observed in astrocytes in NF-1. Here, we provide a mechanistic model for the regulated nuclear import of neurofibromin during the cell cycle and for a role in chromosome congression. Specifically, we demonstrate that neurofibromin, phosphorylated on Ser2808, a residue adjacent to a nuclear localization signal in the C-terminal domain (CTD), by Protein Kinase C-epsilon (PKC-ε), accumulates in a Ran-dependent manner and through binding to lamin in the nucleus at G2 in glioblastoma cells. Furthermore, we identify CTD as a tubulin-binding domain and show that a phosphomimetic substitution of its Ser2808 results in a predominantly nuclear localization. Confocal analysis shows that endogenous neurofibromin localizes on the centrosomes at interphase, as well as on the mitotic spindle, through direct associations with tubulins, in glioblastoma cells and primary astrocytes. More importantly, analysis of mitotic phenotypes after siRNA-mediated depletion shows that acute loss of this tumor suppressor protein leads to aberrant chromosome congression at the metaphase plate. Therefore, neurofibromin protein abundance and nuclear import are mechanistically linked to an error-free chromosome congression. Concerned with neurofibromin's, a tumor suppressor, mechanism of action, we demonstrate in astrocytic cells that its synthesis, phosphorylation by Protein Kinase C-ε on Ser2808 (a residue adjacent to a nuclear localization sequence), and nuclear import are cell cycle-dependent, being maximal at G2. During mitosis, neurofibromin is an integral part of the spindle, while its depletion leads to aberrant chromosome congression, possibly explaining the development of chromosomal instability in Neurofibromatosis type-1. Read the Editorial Highlight for this article on page

  17. The nuclear localization signal of mitotic kinesin-like protein Mklp-1: Effect on Mklp-1 function during cytokinesis

    SciTech Connect

    Liu Xiaoqi; E-mail: liu8@purdue.edu; Erikson, Raymond L.

    2007-02-23

    The mitotic kinesin-like protein (Mklp-1) localizes in the nucleus during interphase due to the presence of nuclear localization signal(s) [NLS(s)] within its sequence. Here, we mapped two NLSs to be {sub 899}SRKRRSST{sub 906} and {sub 949}KRKKP{sub 953} in the tail domain of Mklp-1, and showed that ectopic expression of a mutant Mklp-1 without the NLSs leads to cell cycle arrest at cytokinesis, indicating that the NLSs are necessary for Mklp-1 to execute its normal function during cell division. Furthermore, mutation of two serine residues in First NLS to aspartic acid, which mimics phosphorylation, attenuated its nuclear localization function, suggesting that the function of this NLS might be regulated by phosphorylation.

  18. Phosphatidic Acid Interacts with a MYB Transcription Factor and Regulates Its Nuclear Localization and Function in Arabidopsis[C][W

    PubMed Central

    Yao, Hongyan; Wang, Geliang; Guo, Liang; Wang, Xuemin

    2013-01-01

    Phosphatidic acid (PA) has emerged as a class of cellular mediators involved in various cellular and physiological processes, but little is known about its mechanism of action. Here we show that PA interacts with WEREWOLF (WER), a R2R3 MYB transcription factor involved in root hair formation. The PA-interacting region is confined to the end of the R2 subdomain. The ablation of the PA binding motif has no effect on WER binding to DNA, but abolishes its nuclear localization and its function in regulating epidermal cell fate. Inhibition of PA production by phospholipase Dζ also suppresses WER’s nuclear localization, root hair formation, and elongation. These results suggest a role for PA in promoting protein nuclear localization. PMID:24368785

  19. Functional analysis of the C-terminal region of human adenovirus E1A reveals a misidentified nuclear localization signal

    SciTech Connect

    Cohen, Michael J.; King, Cason R.; Dikeakos, Jimmy D.; Mymryk, Joe S.

    2014-11-15

    The immortalizing function of the human adenovirus 5 E1A oncoprotein requires efficient localization to the nucleus. In 1987, a consensus monopartite nuclear localization sequence (NLS) was identified at the C-terminus of E1A. Since that time, various experiments have suggested that other regions of E1A influence nuclear import. In addition, a novel bipartite NLS was recently predicted at the C-terminal region of E1A in silico. In this study, we used immunofluorescence microscopy and co-immunoprecipitation analysis with importin-α to verify that full nuclear localization of E1A requires the well characterized NLS spanning residues 285–289, as well as a second basic patch situated between residues 258 and 263 ({sup 258}RVGGRRQAVECIEDLLNEPGQPLDLSCKRPRP{sup 289}). Thus, the originally described NLS located at the C-terminus of E1A is actually a bipartite signal, which had been misidentified in the existing literature as a monopartite signal, altering our understanding of one of the oldest documented NLSs. - Highlights: • Human adenovirus E1A is localized to the nucleus. • The C-terminus of E1A contains a bipartite nuclear localization signal (NLS). • This signal was previously misidentified to be a monopartite NLS. • Key basic amino acid residues within this sequence are highly conserved.

  20. Identification of two functional nuclear localization signals in the capsid protein of duck circovirus

    SciTech Connect

    Xiang, Qi-Wang; Zou, Jin-Feng; Wang, Xin; Sun, Ya-Ni; Gao, Ji-Ming; Xie, Zhi-Jing; Wang, Yu; Zhu, Yan-Li; Jiang, Shi-Jin

    2013-02-05

    The capsid protein (CP) of duck circovirus (DuCV) is the major immunogenic protein and has a high proportion of arginine residues concentrated at the N terminus of the protein, which inhibits efficient mRNA translation in prokaryotic expression systems. In this study, we investigated the subcellular distribution of DuCV CP expressed via recombinant baculoviruses in Sf9 cells and the DNA binding activities of the truncated recombinant DuCV CPs. The results showed that two independent bipartite nuclear localization signals (NLSs) situated at N-terminal 1-17 and 18-36 amino acid residue of the CP. Moreover, two expression level regulatory signals (ELRSs) and two DNA binding signals (DBSs) were also mapped to the N terminus of the protein and overlapped with the two NLSs. The ability of CP to bind DNA, coupled with the karyophilic nature of this protein, strongly suggests that it may be responsible for nuclear targeting of the viral genome.

  1. An unconventional nuclear localization motif is crucial for function of the Drosophila Wnt/wingless antagonist Naked cuticle.

    PubMed

    Waldrop, Sharon; Chan, Chih-Chiang; Cagatay, Tolga; Zhang, Shu; Rousset, Raphaël; Mack, Judy; Zeng, Wenlin; Fish, Matt; Zhang, Mei; Amanai, Manami; Wharton, Keith A

    2006-09-01

    Wnt/beta-catenin signals orchestrate cell fate and behavior throughout the animal kingdom. Aberrant Wnt signaling impacts nearly the entire spectrum of human disease, including birth defects, cancer, and osteoporosis. If Wnt signaling is to be effectively manipulated for therapeutic advantage, we first must understand how Wnt signals are normally controlled. Naked cuticle (Nkd) is a novel and evolutionarily conserved inducible antagonist of Wnt/beta-catenin signaling that is crucial for segmentation in the model genetic organism, the fruit fly Drosophila melanogaster. Nkd can bind and inhibit the Wnt signal transducer Dishevelled (Dsh), but the mechanism by which Nkd limits Wnt signaling in the fly embryo is not understood. Here we show that nkd mutants exhibit elevated levels of the beta-catenin homolog Armadillo but no alteration in Dsh abundance or distribution. In the fly embryo, Nkd and Dsh are predominantly cytoplasmic, although a recent report suggests that vertebrate Dsh requires nuclear localization for activity in gain-of-function assays. While Dsh-binding regions of Nkd contribute to its activity, we identify a conserved 30-amino-acid motif, separable from Dsh-binding regions, that is essential for Nkd function and nuclear localization. Replacement of the 30-aa motif with a conventional nuclear localization sequence rescued a small fraction of nkd mutant animals to adulthood. Our studies suggest that Nkd targets Dsh-dependent signal transduction steps in both cytoplasmic and nuclear compartments of cells receiving the Wnt signal. PMID:16849595

  2. Identification of two functional nuclear localization signals in the capsid protein of duck circovirus.

    PubMed

    Xiang, Qi-Wang; Zou, Jin-Feng; Wang, Xin; Sun, Ya-Ni; Gao, Ji-Ming; Xie, Zhi-Jing; Wang, Yu; Zhu, Yan-Li; Jiang, Shi-Jin

    2013-02-01

    The capsid protein (CP) of duck circovirus (DuCV) is the major immunogenic protein and has a high proportion of arginine residues concentrated at the N terminus of the protein, which inhibits efficient mRNA translation in prokaryotic expression systems. In this study, we investigated the subcellular distribution of DuCV CP expressed via recombinant baculoviruses in Sf9 cells and the DNA binding activities of the truncated recombinant DuCV CPs. The results showed that two independent bipartite nuclear localization signals (NLSs) situated at N-terminal 1-17 and 18-36 amino acid residue of the CP. Moreover, two expression level regulatory signals (ELRSs) and two DNA binding signals (DBSs) were also mapped to the N terminus of the protein and overlapped with the two NLSs. The ability of CP to bind DNA, coupled with the karyophilic nature of this protein, strongly suggests that it may be responsible for nuclear targeting of the viral genome. PMID:23174505

  3. Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping

    PubMed Central

    Kim, Christina K.; Miri, Andrew; Leung, Louis C.; Berndt, Andre; Mourrain, Philippe; Tank, David W.; Burdine, Rebecca D.

    2014-01-01

    Larval zebrafish offer the potential for large-scale optical imaging of neural activity throughout the central nervous system; however, several barriers challenge their utility. First, ~panneuronal probe expression has to date only been demonstrated at early larval stages up to 7 days post-fertilization (dpf), precluding imaging at later time points when circuits are more mature. Second, nuclear exclusion of genetically-encoded calcium indicators (GECIs) limits the resolution of functional fluorescence signals collected during imaging. Here, we report the creation of transgenic zebrafish strains exhibiting robust, nuclearly targeted expression of GCaMP3 across the brain up to at least 14 dpf utilizing a previously described optimized Gal4-UAS system. We confirmed both nuclear targeting and functionality of the modified probe in vitro and measured its kinetics in response to action potentials (APs). We then demonstrated in vivo functionality of nuclear-localized GCaMP3 in transgenic zebrafish strains by identifying eye position-sensitive fluorescence fluctuations in caudal hindbrain neurons during spontaneous eye movements. Our methodological approach will facilitate studies of larval zebrafish circuitry by both improving resolution of functional Ca2+ signals and by allowing brain-wide expression of improved GECIs, or potentially any probe, further into development. PMID:25505384

  4. Transcription-dependent nucleolar cap localization and possible nuclear function of DExH RNA helicase RHAU

    SciTech Connect

    Iwamoto, Fumiko; Stadler, Michael; Chalupnikova, Katerina; Oakeley, Edward; Nagamine, Yoshikuni

    2008-04-01

    RHAU (RNA helicase associated with AU-rich element) is a DExH protein originally identified as a factor accelerating AU-rich element-mediated mRNA degradation. The discovery that RHAU is predominantly localized in the nucleus, despite mRNA degradation occurring in the cytoplasm, prompted us to consider the nuclear functions of RHAU. In HeLa cells, RHAU was found to be localized throughout the nucleoplasm with some concentrated in nuclear speckles. Transcriptional arrest altered the localization to nucleolar caps, where RHAU is closely localized with RNA helicases p68 and p72, suggesting that RHAU is involved in transcription-related RNA metabolism in the nucleus. To see whether RHAU affects global gene expression transcriptionally or posttranscriptionally, we performed microarray analysis using total RNA from RHAU-depleted HeLa cell lines, measuring both steady-state mRNA levels and mRNA half-lives by actinomycin D chase. There was no change in the half-lives of most transcripts whose steady-state levels were affected by RHAU knockdown, suggesting that these transcripts are subjected to transcriptional regulation. We propose that RHAU has a dual function, being involved in both the synthesis and degradation of mRNA in different subcellular compartments.

  5. Nuclear and nucleolar localization signals and their targeting function in phosphatidylinositol 4-kinase PI4K230

    SciTech Connect

    Kakuk, Annamaria; Friedlaender, Elza; Vereb, Gyoergy; Lisboa, Duarte; Bagossi, Peter; Toth, Gabor; Gergely, Pal; Vereb, Gyoergy

    2008-08-01

    PI4K230, an isoform of phosphatidylinositol 4-kinase, known primarily as a cytoplasmic membrane-bound enzyme, was detected recently also in the nucleolus of several cells. Here we provide mechanistic insight on the targeting function of its putative nuclear localization signal (NLS) sequences using molecular modeling, digitonin-permeabilized HeLa cells and binding to various importins. The synthetic sequence {sup 916}NFNHIHKRIRRVADKYLSG{sup 934} comprising a putative monopartite NLS (NLS1), targeted covalently bound fluorescent BSA to the nucleoplasm via classical importin {alpha}/{beta} mechanism employing importins {alpha}1 and {alpha}3 but not {alpha}5. This transport was inhibited by wheat germ agglutinin and GTP{gamma}S. The sequence {sup 1414}SKKTNRGSQLHKYYMKRRTL{sup 1433}, a putative bipartite NLS (NLS2) proved ineffective in nuclear targeting if conjugated to fluorescently labeled BSA. Nonetheless, NLS2 or either of its basic clusters directed to the nucleolus soybean trypsin inhibitor that can pass the nuclear pore complex passively; moreover, an expressed 58 kDa fragment of PI4K230 (AA1166-1667) comprising NLS2 was also imported into the nucleus by import factors of reticulocyte lysate or by importin {alpha}1/{beta} or {alpha}3/{beta} complexes and localized to the nucleolus. We conclude that the putative bipartite NLS itself is a nucleolar targeting signal, and for nuclear import PI4K230 requires a larger sequence around it or, alternatively, the monopartite NLS.

  6. Nuclear localization of the DNA repair scaffold XRCC1: Uncovering the functional role of a bipartite NLS

    DOE PAGESBeta

    Kirby, Thomas W.; Gassman, Natalie R.; Smith, Cassandra E.; Pedersen, Lars C.; Gabel, Scott A.; Sobhany, Mack; Wilson, Samuel H.; London, Robert E.

    2015-08-25

    We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs ofmore » the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior gives a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.« less

  7. Nuclear localization of the DNA repair scaffold XRCC1: Uncovering the functional role of a bipartite NLS

    SciTech Connect

    Kirby, Thomas W.; Gassman, Natalie R.; Smith, Cassandra E.; Pedersen, Lars C.; Gabel, Scott A.; Sobhany, Mack; Wilson, Samuel H.; London, Robert E.

    2015-08-25

    We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs of the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior gives a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.

  8. Nuclear scission and quantum localization.

    PubMed

    Younes, W; Gogny, D

    2011-09-23

    We examine nuclear scission within a fully quantum-mechanical microscopic framework, focusing on the nonlocal aspects of the theory. Using (240)Pu hot fission as an example, we discuss the identification of the fragments and the calculation of their kinetic, excitation, and interaction energies, through the localization of the orbital wave functions. We show that the disentanglement of the fragment wave functions is essential to the quantum-mechanical definition of scission and the calculation of physical observables. Finally, we discuss the fragments' prescission excitation mechanisms and give a nonadiabatic description of their evolution beyond scission. PMID:22026846

  9. Functional characterization of nuclear localization and export signals in hepatitis C virus proteins and their role in the membranous web.

    PubMed

    Levin, Aviad; Neufeldt, Christopher J; Pang, Daniel; Wilson, Kristen; Loewen-Dobler, Darci; Joyce, Michael A; Wozniak, Richard W; Tyrrell, D Lorne J

    2014-01-01

    The hepatitis C virus (HCV) is a positive strand RNA virus of the Flavivirus family that replicates in the cytoplasm of infected hepatocytes. Previously, several nuclear localization signals (NLS) and nuclear export signals (NES) have been identified in HCV proteins, however, there is little evidence that these proteins travel into the nucleus during infection. We have recently shown that nuclear pore complex (NPC) proteins (termed nucleoporins or Nups) are present in the membranous web and are required during HCV infection. In this study, we identify a total of 11 NLS and NES sequences in various HCV proteins. We show direct interactions between HCV proteins and importin α5 (IPOA5/kapα1), importin β3 (IPO5/kap β3), and exportin 1 (XPO1/CRM1) both in-vitro and in cell culture. These interactions can be disrupted using peptides containing the specific NLS or NES sequences of HCV proteins. Moreover, using a synchronized infection system, we show that these peptides inhibit HCV infection during distinct phases of the HCV life cycle. The inhibitory effects of these peptides place them in two groups. The first group binds IPOA5 and inhibits infection during the replication stage of HCV life cycle. The second group binds IPO5 and is active during both early replication and early assembly. This work delineates the entire life cycle of HCV and the active involvement of NLS sequences during HCV replication and assembly. Given the abundance of NLS sequences within HCV proteins, our previous finding that Nups play a role in HCV infection, and the relocation of the NLS double-GFP reporter in HCV infected cells, this work supports our previous hypothesis that NPC-like structures and nuclear transport factors function in the membranous web to create an environment conducive to viral replication. PMID:25485706

  10. Functional Characterization of Nuclear Localization and Export Signals in Hepatitis C Virus Proteins and Their Role in the Membranous Web

    PubMed Central

    Levin, Aviad; Neufeldt, Christopher J.; Pang, Daniel; Wilson, Kristen; Loewen-Dobler, Darci; Joyce, Michael A.; Wozniak, Richard W.; Tyrrell, D. Lorne J

    2014-01-01

    The hepatitis C virus (HCV) is a positive strand RNA virus of the Flavivirus family that replicates in the cytoplasm of infected hepatocytes. Previously, several nuclear localization signals (NLS) and nuclear export signals (NES) have been identified in HCV proteins, however, there is little evidence that these proteins travel into the nucleus during infection. We have recently shown that nuclear pore complex (NPC) proteins (termed nucleoporins or Nups) are present in the membranous web and are required during HCV infection. In this study, we identify a total of 11 NLS and NES sequences in various HCV proteins. We show direct interactions between HCV proteins and importin α5 (IPOA5/kapα1), importin β3 (IPO5/kap β3), and exportin 1 (XPO1/CRM1) both in-vitro and in cell culture. These interactions can be disrupted using peptides containing the specific NLS or NES sequences of HCV proteins. Moreover, using a synchronized infection system, we show that these peptides inhibit HCV infection during distinct phases of the HCV life cycle. The inhibitory effects of these peptides place them in two groups. The first group binds IPOA5 and inhibits infection during the replication stage of HCV life cycle. The second group binds IPO5 and is active during both early replication and early assembly. This work delineates the entire life cycle of HCV and the active involvement of NLS sequences during HCV replication and assembly. Given the abundance of NLS sequences within HCV proteins, our previous finding that Nups play a role in HCV infection, and the relocation of the NLS double-GFP reporter in HCV infected cells, this work supports our previous hypothesis that NPC-like structures and nuclear transport factors function in the membranous web to create an environment conducive to viral replication. PMID:25485706

  11. Glypican and Biglycan in the Nuclei of Neurons and Glioma Cells: Presence of Functional Nuclear Localization Signals and Dynamic Changes in Glypican During the Cell Cycle

    PubMed Central

    Liang, Yu; Häring, Monika; Roughley, Peter J.; Margolis, Renée K.; Margolis, Richard U.

    1997-01-01

    We have investigated the expression patterns and subcellular localization in nervous tissue of glypican, a major glycosylphosphatidylinositol-anchored heparan sulfate proteoglycan that is predominantly synthesized by neurons, and of biglycan, a small, leucine-rich chondroitin sulfate proteoglycan. By laser scanning confocal microscopy of rat central nervous tissue and C6 glioma cells, we found that a significant portion of the glypican and biglycan immunoreactivity colocalized with nuclear staining by propidium iodide and was also seen in isolated nuclei. In certain regions, staining was selective, insofar as glypican and biglycan immunoreactivity in the nucleus was seen predominantly in a subpopulation of large spinal cord neurons. The amino acid sequences of both proteoglycans contain potential nuclear localization signals, and these were demonstrated to be functional based on their ability to target β-galactosidase fusion proteins to the nuclei of transfected 293 cells. Nuclear localization of glypican β-galactosidase or Fc fusion proteins in transfected 293 cells and C6 glioma cells was greatly reduced or abolished after mutation of the basic amino acids or deletion of the sequence containing the nuclear localization signal, and no nuclear staining was seen in the case of heparan sulfate and chondroitin sulfate proteoglycans that do not possess a nuclear localization signal, such as syndecan-3 or decorin (which is closely related in structure to biglycan). Transfection of COS-1 cells with an epitope-tagged glypican cDNA demonstrated transport of the full-length proteoglycan to the nucleus, and there are also dynamic changes in the pattern of glypican immunoreactivity in the nucleus of C6 cells both during cell division and correlated with different phases of the cell cycle. Our data therefore suggest that in certain cells and central nervous system regions, glypican and biglycan may be involved in the regulation of cell division and survival by directly

  12. The Arginine/Lysine-Rich Element within the DNA-Binding Domain Is Essential for Nuclear Localization and Function of the Intracellular Pathogen Resistance 1.

    PubMed

    Yao, Kezhen; Wu, Yongyan; Chen, Qi; Zhang, Zihan; Chen, Xin; Zhang, Yong

    2016-01-01

    The mouse intracellular pathogen resistance 1 (Ipr1) gene plays important roles in mediating host immunity and previous work showed that it enhances macrophage apoptosis upon mycobacterium infection. However, to date, little is known about the regulation pattern of Ipr1 action. Recent studies have investigated the protein-coding genes and microRNAs regulated by Ipr1 in mouse macrophages, but the structure and the functional motif of the Ipr1 protein have yet to be explored. In this study, we analyzed the domains and functional motif of the Ipr1 protein. The resulting data reveal that Ipr1 protein forms a homodimer and that the Sp100-like domain mediates the targeting of Ipr1 protein to nuclear dots (NDs). Moreover, we found that an Ipr1 mutant lacking the classic nuclear localization signal (cNLS) also translocated into the nuclei, suggesting that the cNLS is not the only factor that directs Ipr1 nuclear localization. Additionally, mechanistic studies revealed that an arginine/lysine-rich element within the DNA-binding domain (SAND domain) is critical for Ipr1 binding to the importin protein receptor NPI-1, demonstrating that this element plays an essential role in mediating the nuclear localization of Ipr1 protein. Furthermore, our results show that this arginine/lysine-rich element contributes to the transcriptional regulation and apoptotic activity of Ipr1. These findings highlight the structural foundations of Ipr1 action and provide new insights into the mechanism of Ipr1-mediated resistance to mycobacterium. PMID:27622275

  13. Nuclear Parton Distribution Functions

    SciTech Connect

    I. Schienbein, J.Y. Yu, C. Keppel, J.G. Morfin, F. Olness, J.F. Owens

    2009-06-01

    We study nuclear effects of charged current deep inelastic neutrino-iron scattering in the framework of a {chi}{sup 2} analysis of parton distribution functions (PDFs). We extract a set of iron PDFs which are used to compute x{sub Bj}-dependent and Q{sup 2}-dependent nuclear correction factors for iron structure functions which are required in global analyses of free nucleon PDFs. We compare our results with nuclear correction factors from neutrino-nucleus scattering models and correction factors for charged-lepton--iron scattering. We find that, except for very high x{sub Bj}, our correction factors differ in both shape and magnitude from the correction factors of the models and charged-lepton scattering.

  14. Nuclear Localization of the Autism Candidate Gene Neurobeachin and Functional Interaction with the NOTCH1 Intracellular Domain Indicate a Role in Regulating Transcription

    PubMed Central

    Tuand, Krizia; Stijnen, Pieter; Volders, Karolien; Declercq, Jeroen; Nuytens, Kim; Meulemans, Sandra; Creemers, John

    2016-01-01

    Background Neurobeachin (NBEA) is an autism spectrum disorders (ASD) candidate gene. NBEA deficiency affects regulated secretion, receptor trafficking, synaptic architecture and protein kinase A (PKA)-mediated phosphorylation. NBEA is a large multidomain scaffolding protein. From N- to C-terminus, NBEA has a concanavalin A-like lectin domain flanked by armadillo repeats (ACA), an A-kinase anchoring protein domain that can bind to PKA, a domain of unknown function (DUF1088) and a BEACH domain, preceded by a pleckstrin homology-like domain and followed by WD40 repeats (PBW). Although most of these domains mediate protein-protein interactions, no interaction screen has yet been performed. Methods Yeast two-hybrid screens with the ACA and PBW domain modules of NBEA gave a list of interaction partners, which were analyzed for Gene Ontology (GO) enrichment. Neuro-2a cells were used for confocal microscopy and nuclear extraction analysis. NOTCH-mediated transcription was studied with luciferase reporter assays and qRT-PCR, combined with NBEA knockdown or overexpression. Results Both domain modules showed a GO enrichment for the nucleus. PBW almost exclusively interacted with transcription regulators, while ACA interacted with a number of PKA substrates. NBEA was partially localized in the nucleus of Neuro-2a cells, albeit much less than in the cytoplasm. A nuclear localization signal was found in the DUF1088 domain, which was shown to contribute to the nuclear localization of an EGFP-DPBW fusion protein. Yeast two-hybrid identified the Notch1 intracellular domain as a physical interactor of the PBW domain and a role for NBEA as a negative regulator in Notch-mediated transcription was demonstrated. Conclusion Defining novel interaction partners of conserved NBEA domain modules identified a role for NBEA as transcriptional regulator in the nucleus. The physical interaction of NBEA with NOTCH1 is most relevant for ASD pathogenesis because NOTCH signaling is essential for

  15. Localized functionalization of single nanopores

    SciTech Connect

    Nilsson, J; Lee, J I; Ratto, T V; Letant, S E

    2005-09-12

    We demonstrate the localization of chemical functionality at the entrance of single nanopores for the first time by using the controlled growth of an oxide ring. Nanopores were fabricated by Focused Ion Beam machining on silicon platforms, locally derivatized by ion beam assisted oxide deposition, and further functionalized with DNA probes via silane chemistry. Ionic current recorded through single nanopores at various stages of the fabrication process demonstrated that the apertures can be locally functionalized with DNA probes. Future applications for this functional platform include the selective detection of biological organisms and molecules by ionic current blockade measurements.

  16. Localized RNAs and their functions.

    PubMed

    Ding, D; Lipshitz, H D

    1993-10-01

    The eukaryotic cell is partitioned by membranes into spatially and functionally discrete subcellular organelles. In addition, the cytoplasm itself is partitioned into discrete subregions that carry out specific functions. Such compartmentation can be achieved by localizing proteins and RNAs to different subcellular regions. This review will focus on localized RNAs, with a particular emphasis on RNA localization mechanisms and on the possible biological functions of localization of these RNAs. In recent years, an increasing number of localized RNAs have been identified in a variety of cell types among many animal species. Emphasis here will be on localized RNAs in the most intensively studied systems-Drosophila and Xenopus eggs and early embryos. PMID:7506023

  17. Functional Characterization of the OFD1 Protein Reveals a Nuclear Localization and Physical Interaction with Subunits of a Chromatin Remodeling Complex

    PubMed Central

    Giorgio, Giovanna; Alfieri, Mariaevelina; Prattichizzo, Clelia; Zullo, Alessandro; Cairo, Stefano

    2007-01-01

    Oral-facial-digital (OFD) type I syndrome is an X-linked dominant disease (MIM311200) characterized by malformations of oral cavity, face, and digits and by cystic kidneys. We previously identified OFD1, the gene responsible for this disorder, which encodes for a centrosomal protein with an unknown function. We now report that OFD1 localizes both to the primary cilium and to the nucleus. Moreover, we demonstrate that the OFD1 protein is able to self-associate and that this interaction is mediated by its coiled-coil rich region. Interestingly, we identify an OFD1-interacting protein RuvBl1, a protein belonging to the AAA+-family of ATPases, which has been recently associated to cystic kidney in zebrafish and to ciliary assembly and function in Chlamydomonas reinhardtii. We also provide experimental evidence that OFD1, together with RuvBl1, is able to coimmunoprecipitate with subunits of the human TIP60 histone acetyltransferase (HAT) multisubunit complex. On the basis of these results, we hypothesize that OFD1 may be part of a multi-protein complex and could play different biological functions in the centrosome-primary cilium organelles as well as in the nuclear compartment. PMID:17761535

  18. Multiple Nuclear Localization Signals Mediate Nuclear Localization of the GATA Transcription Factor AreA

    PubMed Central

    Hunter, Cameron C.; Siebert, Kendra S.; Downes, Damien J.; Wong, Koon Ho; Kreutzberger, Sara D.; Fraser, James A.; Clarke, David F.; Hynes, Michael J.; Davis, Meryl A.

    2014-01-01

    The Aspergillus nidulans GATA transcription factor AreA activates transcription of nitrogen metabolic genes in response to nitrogen limitation and is known to accumulate in the nucleus during nitrogen starvation. Sequence analysis of AreA revealed multiple nuclear localization signals (NLSs), five putative classical NLSs conserved in fungal AreA orthologs but not in the Saccharomyces cerevisiae functional orthologs Gln3p and Gat1p, and one putative noncanonical RRX33RXR bipartite NLS within the DNA-binding domain. In order to identify the functional NLSs in AreA, we constructed areA mutants with mutations in individual putative NLSs or combinations of putative NLSs and strains expressing green fluorescent protein (GFP)-AreA NLS fusion genes. Deletion of all five classical NLSs individually or collectively did not affect utilization of nitrogen sources or AreA-dependent gene expression and did not prevent AreA nuclear localization. Mutation of the bipartite NLS conferred the inability to utilize alternative nitrogen sources and abolished AreA-dependent gene expression likely due to effects on DNA binding but did not prevent AreA nuclear localization. Mutation of all six NLSs simultaneously prevented AreA nuclear accumulation. The bipartite NLS alone strongly directed GFP to the nucleus, whereas the classical NLSs collaborated to direct GFP to the nucleus. Therefore, AreA contains multiple conserved NLSs, which show redundancy and together function to mediate nuclear import. The noncanonical bipartite NLS is conserved in GATA factors from Aspergillus, yeast, and mammals, indicating an ancient origin. PMID:24562911

  19. Structure and Function of the N-terminal Nucleolin Binding Domain of Nuclear Valosin-containing Protein-like 2 (NVL2) Harboring a Nucleolar Localization Signal*

    PubMed Central

    Fujiwara, Yoshie; Fujiwara, Ken-ichiro; Goda, Natsuko; Iwaya, Naoko; Tenno, Takeshi; Shirakawa, Masahiro; Hiroaki, Hidekazu

    2011-01-01

    The N-terminal regions of AAA-ATPases (ATPase associated with various cellular activities) often contain a domain that defines the distinct functions of the enzymes, such as substrate specificity and subcellular localization. As described herein, we have determined the solution structure of an N-terminal unique domain isolated from nuclear valosin-containing protein (VCP)-like protein 2 (NVL2UD). NVL2UD contains three α helices with an organization resembling that of a winged helix motif, whereas a pair of β-strands is missing. The structure is unique and distinct from those of other known type II AAA-ATPases, such as VCP. Consequently, we identified nucleolin from a HeLa cell extract as a binding partner of this domain. Nucleolin contains a long (∼300 amino acids) intrinsically unstructured region, followed by the four tandem RNA recognition motifs and the C-terminal glycine/arginine-rich domain. Binding analyses revealed that NVL2UD potentially binds to any of the combinations of two successive RNA binding domains in the presence of RNA. Furthermore, NVL2UD has a characteristic loop, in which the key basic residues RRKR are exposed to the solvent at the edge of the molecule. The mutation study showed that these residues are necessary and sufficient for nucleolin-RNA complex binding as well as nucleolar localization. Based on the observations presented above, we propose that NVL2 serves as an unfoldase for the nucleolin-RNA complex. As inferred from its RNA dependence and its ATPase activity, NVL2 might facilitate the dissociation and recycling of nucleolin, thereby promoting efficient ribosome biogenesis. PMID:21474449

  20. Mechanotransduction and nuclear function.

    PubMed

    Graham, David M; Burridge, Keith

    2016-06-01

    Many signaling pathways converge on the nucleus to regulate crucial nuclear events such as transcription, DNA replication and cell cycle progression. Although the vast majority of research in this area has focused on signals generated in response to hormones or other soluble factors, the nucleus also responds to mechanical forces. During the past decade or so, much has been learned about how mechanical force can affect transcription, as well as the growth and differentiation of cells. Much has also been learned about how force is transmitted via the cytoskeleton to the nucleus and then across the nuclear envelope to the nuclear lamina and chromatin. In this brief review, we focus on some of the key proteins that transmit mechanical signals across the nuclear envelope. PMID:27018929

  1. Nuclear overlap functions

    SciTech Connect

    Eskola, K.J.; Vogt, R.; Wang, X.N.

    1995-07-01

    A three parameter Wood-Saxon shape is used to describe the nuclear density distribution, which R{sub A} is the nuclear radius, {approx} is the surface thickness, and {omega} allows for central irregularities. The electron scattering data is used where available for R{sub A}, z, and {omega}. When data is unavailable, the parameters {omega} = O, z = 0.54 fm and R{sub A} = 1.19 A{sup 1/3} - 1.61 A{sup -1/3} fm are used. The central density {rho}{sub 0} is found from the normalization {infinity} d{sup 3}r{rho}{sub A}(r) = A.

  2. Functional evolution of nuclear structure

    PubMed Central

    Dawson, Scott C.

    2011-01-01

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis. PMID:22006947

  3. Localization of functions defined on cantor group

    NASA Astrophysics Data System (ADS)

    Krivoshein, Aleksander V.; Lebedeva, Elena A.

    2013-10-01

    We introduce a notion of localization for dyadic functions, i. e. functions defined on Cantor group. Both non-periodic and periodic cases are discussed. Localization is characterized by functionals UCd and UCdp similar to the Heisenberg (the Breitenberger) uncertainty constants used for real-line (periodic) functions. We are looking for dyadic analogs of uncertainty principles. To justify definition we use some test functions including dyadic scaling and wavelet functions.

  4. Functional Localization of Genetic Network Programming

    NASA Astrophysics Data System (ADS)

    Eto, Shinji; Hirasawa, Kotaro; Hu, Jinglu

    According to the knowledge of brain science, it is suggested that there exists cerebral functional localization, which means that a specific part of the cerebrum is activated depending on various kinds of information human receives. The aim of this paper is to build an artificial model to realize functional localization based on Genetic Network Programming (GNP), a new evolutionary computation method recently developed. GNP has a directed graph structure suitable for realizing functional localization. We studied the basic characteristics of the proposed system by making GNP work in a functionally localized way.

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

    SciTech Connect

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

    2012-06-10

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

  6. Potential Representation - Global vs. Local Trial Functions

    NASA Astrophysics Data System (ADS)

    Michel, Volker

    2014-05-01

    Many systems of trial functions are available for representing potential fields on the sphere or parts of the sphere. We distinguish global trial functions (such as spherical harmonics) from localized trial functions (such as spline basis functions, scaling functions, wavelets, and Slepian functions). All these systems have their own pros and cons. We discuss the advantages and disadvantages of several selected systems of trial functions and propose criteria for their applicability. Moreover, we present an algorithm which is able to combine different types of trial functions. This yields a sparser solution which combines the features of the different basis systems which are used.

  7. Classic nuclear localization signals and a novel nuclear localization motif are required for nuclear transport of porcine parvovirus capsid proteins.

    PubMed

    Boisvert, Maude; Bouchard-Lévesque, Véronique; Fernandes, Sandra; Tijssen, Peter

    2014-10-01

    Nuclear targeting of capsid proteins (VPs) is important for genome delivery and precedes assembly in the replication cycle of porcine parvovirus (PPV). Clusters of basic amino acids, corresponding to potential nuclear localization signals (NLS), were found only in the unique region of VP1 (VP1up, for VP1 unique part). Of the five identified basic regions (BR), three were important for nuclear localization of VP1up: BR1 was a classic Pat7 NLS, and the combination of BR4 and BR5 was a classic bipartite NLS. These NLS were essential for viral replication. VP2, the major capsid protein, lacked these NLS and contained no region with more than two basic amino acids in proximity. However, three regions of basic clusters were identified in the folded protein, assembled into a trimeric structure. Mutagenesis experiments showed that only one of these three regions was involved in VP2 transport to the nucleus. This structural NLS, termed the nuclear localization motif (NLM), is located inside the assembled capsid and thus can be used to transport trimers to the nucleus in late steps of infection but not for virions in initial infection steps. The two NLS of VP1up are located in the N-terminal part of the protein, externalized from the capsid during endosomal transit, exposing them for nuclear targeting during early steps of infection. Globally, the determinants of nuclear transport of structural proteins of PPV were different from those of closely related parvoviruses. Importance: Most DNA viruses use the nucleus for their replication cycle. Thus, structural proteins need to be targeted to this cellular compartment at two distinct steps of the infection: in early steps to deliver viral genomes to the nucleus and in late steps to assemble new viruses. Nuclear targeting of proteins depends on the recognition of a stretch of basic amino acids by cellular transport proteins. This study reports the identification of two classic nuclear localization signals in the minor capsid

  8. Characterization of a baculovirus nuclear localization signal domain in the late expression factor 3 protein

    SciTech Connect

    Au, Victoria; Yu Mei; Carstens, Eric B.

    2009-03-01

    The baculovirus Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) single-stranded DNA binding protein LEF-3 is a multi-functional protein that is required to transport the helicase protein P143 into the nucleus of infected cells where they function to replicate viral DNA. The N-terminal 56 amino acid region of LEF-3 is required for nuclear transport. In this report, we analyzed the effect of site-specific mutagenesis of LEF-3 on its intracellular distribution. Fluorescence microscopy of expression plasmid-transfected cells demonstrated that the residues 28 to 32 formed the core nuclear localization signal, but other adjacent positively-charged residues augmented these sequences. Comparison with other group I Alphabaculoviruses suggested that this core region functionally duplicated residues including 18 and 19. This was demonstrated by the loss of nuclear localization when the equivalent residues (18 to 20) in Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) LEF-3 were mutated. The AcMNPV LEF-3 nuclear localization domain was also shown to drive nuclear transport in mammalian cells indicating that the protein nuclear import systems in insect and mammalian cells are conserved. We also demonstrated by mutagenesis that two conserved cysteine residues located at 82 and 106 were not essential for nuclear localization or for interaction with P143. However, by using a modified construct of P143 that localized on its own to the nucleus, we demonstrated that a functional nuclear localization domain on LEF-3 was required for interaction between LEF-3 and P143.

  9. Locality of correlation in density functional theory

    NASA Astrophysics Data System (ADS)

    Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano

    2016-08-01

    The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.

  10. Locality of correlation in density functional theory.

    PubMed

    Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano

    2016-08-01

    The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed. PMID:27497544

  11. Function and evolution of local repeats in the Firre locus

    PubMed Central

    Hacisuleyman, Ezgi; Shukla, Chinmay J.; Weiner, Catherine L.; Rinn, John L.

    2016-01-01

    More than half the human and mouse genomes are comprised of repetitive sequences, such as transposable elements (TEs), which have been implicated in many biological processes. In contrast, much less is known about other repeats, such as local repeats that occur in multiple instances within a given locus in the genome but not elsewhere. Here, we systematically characterize local repeats in the genomic locus of the Firre long noncoding RNA (lncRNA). We find a conserved function for the RRD repeat as a ribonucleic nuclear retention signal that is sufficient to retain an otherwise cytoplasmic mRNA in the nucleus. We also identified a repeat, termed R0, that can function as a DNA enhancer element within the intronic sequences of Firre. Collectively, our data suggest that local repeats can have diverse functionalities and molecular modalities in the Firre locus and perhaps more globally in other lncRNAs. PMID:27009974

  12. Nuclear localization signal receptor importin alpha associates with the cytoskeleton.

    PubMed Central

    Smith, H M; Raikhel, N V

    1998-01-01

    Importin alpha is the nuclear localization signal (NLS) receptor that is involved in the nuclear import of proteins containing basic NLSs. Using importin alpha as a tool, we were interested in determining whether the cytoskeleton could function in the transport of NLS-containing proteins from the cytoplasm to the nucleus. Double-labeling immunofluorescence studies showed that most of the cytoplasmic importin alpha coaligned with microtubules and microfilaments in tobacco protoplasts. Treatment of tobacco protoplasts with microtubule- or microfilament-depolymerizing agents disrupted the strands of importin alpha in the cytoplasm, whereas a microtubule-stabilizing agent had no effect. Biochemical analysis showed that importin alpha associated with microtubules and microfilaments in vitro in an NLS-dependent manner. The interaction of importin alpha with the cytoskeleton could be an essential element of protein transport from the cytoplasm to the nucleus in vivo. PMID:9811789

  13. Local dynamic nuclear polarization using quantum point contacts

    SciTech Connect

    Wald, K.R.; Kouwenhoven, L.P.; McEuen, P.L. ); van der Vaart, N.C. ); Foxon, C.T. )

    1994-08-15

    We have used quantum point contacts (QPCs) to locally create and probe dynamic nuclear polarization (DNP) in GaAs heterostructures in the quantum Hall regime. DNP is created via scattering between spin-polarized Landau level electrons and the Ga and As nuclear spins, and it leads to hysteresis in the dc transport characteristics. The nuclear origin of this hysteresis is demonstrated by nuclear magnetic resonance (NMR). Our results show that QPCs can be used to create and probe local nuclear spin populations, opening up new possibilities for mesoscopic NMR experiments.

  14. Nuclear Localization of Flavivirus RNA Synthesis in Infected Cells

    PubMed Central

    Uchil, Pradeep Devappa; Kumar, Anil V. A.; Satchidanandam, Vijaya

    2006-01-01

    Flaviviral replication is believed to be exclusively cytoplasmic, occurring within virus-induced membrane-bound replication complexes in the host cytoplasm. Here we show that a significant proportion (20%) of the total RNA-dependent RNA polymerase (RdRp) activity from cells infected with West Nile virus, Japanese encephalitis virus (JEV), and dengue virus is resident within the nucleus. Consistent with this, the major replicase proteins NS3 and NS5 of JEV also localized within the nucleus. NS5 was found distributed throughout the nucleoplasm, but NS3 was present at sites of active flaviviral RNA synthesis, colocalizing with NS5, and visible as distinct foci along the inner periphery of the nucleus by confocal and immunoelectron microscopy. Both these viral replicase proteins were also present in the nuclear matrix, colocalizing with the peripheral lamina, and revealed a well-entrenched nuclear location for the viral replication complex. In keeping with this observation, antibodies to either NS3 or NS5 coimmunoprecipitated the other protein from isolated nuclei along with newly synthesized viral RNA. Taken together these data suggest an absolute requirement for both of the replicase proteins for nucleus-localized synthesis of flavivirus RNA. Thus, we conclusively demonstrate for the first time that the host cell nucleus functions as an additional site for the presence of functionally active flaviviral replicase complex. PMID:16699025

  15. [Localization of language function in the brain].

    PubMed

    Miyashita, Hiroyuki; Sakai, Kuniyoshi L

    2011-12-01

    Since the first report of an aphasic patient by Paul Broca, the localization of brain function has been disputed for 150 years. In lesion studies, double dissociation has been a key concept to show the localization of particular cognitive functions. The advancement of non-invasive brain imaging methods enables us to investigate the brain activities under well-controlled conditions, further promoting the studies on the localization of the cognitive functions, including language function. Brain imaging studies, together with subtraction and correlation analyses, have accumulated evidence that syntax, phonology, and sentence comprehension are separately processed by modules in different cortical regions. More specifically, it has been clarified that the module for syntax localizes in the left lateral premotor cortex and the opercular/triangular parts of the left inferior frontal gyrus. This modular structure further suggests that aphasia is interpreted as deficits in either syntactic or phonological processing. Therefore, the classical model of contrasting speech production and comprehension should be updated. According to theoretical linguistics, on the other hand, the recursive computation of syntactic structures is an essential feature of human language faculty. One direction of research would be to contrast human beings and animals for the abilities of processing symbolic sequences. Another direction is to clarify that the human brain is indeed specialized in language processing, which can be revealed by well-controlled language tasks and functional imaging techniques. Here we will review recent studies that demonstrate the existence of grammar center in the left frontal cortex. The future studies in the neuroscience of language will eventually elucidate the cortical localization of language function in a more precise way, i.e., what is really computed in the human brain. PMID:22147453

  16. Localized Hartree product treatment of multiple protons in the nuclear-electronic orbital framework.

    PubMed

    Auer, Benjamin; Hammes-Schiffer, Sharon

    2010-02-28

    An approximation for treating multiple quantum nuclei within the nuclear-electronic orbital (NEO) framework for molecular systems is presented. In the approximation to NEO-Hartree-Fock, the nuclear wave function is represented by a Hartree product rather than a Slater determinant, corresponding to the neglect of the nuclear exchange interactions. In the approximation to NEO-density functional theory, the nuclear exchange-correlation functional is chosen to be the diagonal nuclear exchange interaction terms, thereby eliminating the nuclear self-interaction terms. To further enhance the simplicity and computational efficiency, the nuclear molecular orbitals or Kohn-Sham orbitals are expanded in terms of localized nuclear basis sets. These approximations are valid because of the inherent localization of the nuclear orbitals and the numerical insignificance of the nuclear exchange interactions in molecular systems. Moreover, these approximations lead to substantial computational savings due to the reduction in both the number of integrals that must be calculated and the size of the matrices that must be diagonalized. These nuclear Hartree product approximation (HPA) methods scale linearly with the number of quantum protons and are highly parallelizable. Applications to a water hexamer, glycine dimer, and 32-water cluster, where all hydrogen nuclei are treated quantum mechanically, illustrate the accuracy and computational efficiency of the nuclear HPA methods. These strategies will facilitate the implementation of explicitly correlated NEO methods for molecular systems with multiple quantum protons. PMID:20192293

  17. Nuclear localization of Merkel cell polyomavirus large T antigen in Merkel cell carcinoma

    SciTech Connect

    Nakamura, Tomoyuki; Sato, Yuko; Watanabe, Daisuke; Ito, Hideki; Shimonohara, Nozomi; Tsuji, Takahiro; Nakajima, Noriko; Suzuki, Yoshio; Matsuo, Koma; Nakagawa, Hidemi; Sata, Tetsutaro; Katano, Harutaka

    2010-03-15

    To clarify whether mutations in the large T gene encoded by Merkel cell polyomavirus affect the expression and function of large T antigen in Merkel cell carcinoma cases, we investigated the expression of large T antigen in vitro and in vivo. Immunohistochemistry using a rabbit polyclonal antibody revealed that large T antigen was expressed in the nuclei of Merkel cell carcinoma cells with Merkel cell polyomavirus infection. Deletion mutant analyses identified an Arg-Lys-Arg-Lys sequence (amino acids 277-280) as a nuclear localization signal in large T antigen. Sequence analyses revealed that there were no mutations in the nuclear localization signal in any of the eleven Merkel cell polyomavirus strains examined. Furthermore, stop codons were not observed in the upstream of the nuclear localization signal in any of the Merkel cell carcinoma cases examined. These data suggest that the nuclear localization signal is highly conserved and functional in Merkel cell carcinoma cases.

  18. [Local, central and regional functions. Obsolete concepts?].

    PubMed

    Stene-Larsen, G; Bjørnstad, E; Bergesen, O; Nordhaug, B; Abildgaard, U

    1990-11-30

    As a consequence of the regionalization of the health services in Norway hospitals were given either local, central or regional responsibility. This system was intended to improve the availability of expertise and costly equipment, and at the same time reduce the growth of expenditures on health care. In the last few years, however, many of the smaller hospitals have improved their technical and medical skills to such an extent that this classification system has become less meaningful. Aker hospital in Oslo carries out local, central and regional functions. In a prospective study at this hospital we found that 88% of 980 consecutive medical admissions could be classified as local hospital admissions. Only 5% of the patients needed service at the central level, and 5% at the regional level. In our opinion it would suffice to have two types of hospital ("treatment levels"), standard hospitals and referral hospitals. PMID:2274952

  19. Plant nuclear proteomics for unraveling physiological function.

    PubMed

    Yin, Xiaojian; Komatsu, Setsuko

    2016-09-25

    The nucleus is the subcellular organelle that functions as the regulatory hub of the cell and is responsible for regulating several critical cellular functions, including cell proliferation, gene expression, and cell survival. Nuclear proteomics is a useful approach for investigating the mechanisms underlying plant responses to abiotic stresses, including protein-protein interactions, enzyme activities, and post-translational modifications. Among abiotic stresses, flooding is a major limiting factor for plant growth and yields, particularly for soybean. In this review, plant nuclei purification methods, modifications of plant nuclear proteins, and recent contributions to the field of plant nuclear proteomics are summarized. In addition, to reveal the upstream regulating mechanisms controlling soybean responses to flooding stress, the functions of flooding-responsive nuclear proteins are reviewed based on the results of nuclear proteomic analysis of soybean in the early stages of flooding stress. PMID:27004615

  20. Local spin analyses using density functional theory

    NASA Astrophysics Data System (ADS)

    Abate, Bayileyegn; Peralta, Juan

    Local spin analysis is a valuable technique in computational investigations magnetic interactions on mono- and polynuclear transition metal complexes, which play vital roles in catalysis, molecular magnetism, artificial photosynthesis, and several other commercially important materials. The relative size and complex electronic structure of transition metal complexes often prohibits the use of multi-determinant approaches, and hence, practical calculations are often limited to single-determinant methods. Density functional theory (DFT) has become one of the most successful and widely used computational tools for the electronic structure study of complex chemical systems; transition metal complexes in particular. Within the DFT formalism, a more flexible and complete theoretical modeling of transition metal complexes can be achieved by considering noncollinear spins, in which the spin density is 'allowed to' adopt noncollinear structures in stead of being constrained to align parallel/antiparallel to a universal axis of magnetization. In this meeting, I will present local spin analyses results obtained using different DFT functionals. Local projection operators are used to decompose the expectation value of the total spin operator; first introduced by Clark and Davidson.

  1. Universal Nuclear Energy Density Functional

    SciTech Connect

    Carlson, Joseph; Furnstahl, Richard; Horoi, Mihai; Lusk, Rusty; Nazarewicz, Witold; Ng, Esmond; Thompson, Ian; Vary, James

    2012-12-01

    An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. Until recently such an undertaking was hard to imagine, and even at the present time such an ambitious endeavor would be far beyond what a single researcher or a traditional research group could carry out.

  2. Characterization of a nuclear localization signal in the foot-and-mouth disease virus polymerase

    SciTech Connect

    Sanchez-Aparicio, Maria Teresa; Rosas, Maria Flora; Sobrino, Francisco

    2013-09-15

    We have experimentally tested whether the MRKTKLAPT sequence in FMDV 3D protein (residues 16 to 24) can act as a nuclear localization signal (NLS). Mutants with substitutions in two basic residues within this sequence, K18E and K20E, were generated. A decreased nuclear localization was observed in transiently expressed 3D and its precursor 3CD, suggesting a role of K18 and K20 in nuclear targeting. Fusion of MRKTKLAPT to the green fluorescence protein (GFP) increased the nuclear localization of GFP, which was not observed when GFP was fused to the 3D mutated sequences. These results indicate that the sequence MRKTKLAPT can be functionally considered as a NLS. When introduced in a FMDV full length RNA replacements K18E and K20E led to production of revertant viruses that replaced the acidic residues introduced (E) by K, suggesting that the presence of lysins at positions 18 and 20 of 3D is essential for virus multiplication. - Highlights: • The FMDV 3D polymerase contains a nuclear localization signal. • Replacements K18E and K20E decrease nuclear localization of 3D and its precursor 3CD. • Fusion of the MRKTKLAPT 3D motif to GFP increases the nuclear localization of GFP. • Replacements K18E and K20E abolish the ability of MRKTKLAPT to relocate GFP. • RNAs harboring replacements K18E and K20E lead to recovery of revertant FMDVs.

  3. Identification and functional dissection of localization signals within ataxin-3.

    PubMed

    Antony, Paul Michel Aloyse; Mäntele, Simone; Mollenkopf, Phillip; Boy, Jana; Kehlenbach, Ralph H; Riess, Olaf; Schmidt, Thorsten

    2009-11-01

    Spinocerebellar ataxia type 3 (SCA3) or Machado-Joseph disease (MJD) belongs to a group of autosomal dominant neurodegenerative diseases, which are caused by the expansion of a polyglutamine repeat in the affected protein, in this case ataxin-3. Ataxin-3 is mainly localized in the cytoplasm; however, one hallmark of SCA3 is the formation of ataxin-3-containing protein aggregates in the nucleus of neurons. Currently, it is not known how mutant ataxin-3 translocates into the nucleus. We performed localization assays of recently proposed and novel potential signals, functionally confirmed the activity of a nuclear localization signal, identified two novel nuclear export signals (NES 77 and NES 141), and determined crucial amino acids. In addition, we demonstrate the relevance of the identified signals for the intracellular localization of the N- and C-terminus of ataxin-3. Our findings stress the importance of investigating the mechanisms, which influence the intracellular distribution of ataxin-3 during the pathogenesis of SCA3. PMID:19660550

  4. Meson's correlation functions in a nuclear medium

    NASA Astrophysics Data System (ADS)

    Park, Chanyong

    2016-09-01

    We investigate meson's spectrum, decay constant and form factor in a nuclear medium through holographic two- and three-point correlation functions. To describe a nuclear medium composed of protons and neutrons, we consider a hard wall model on the thermal charged AdS geometry and show that due to the isospin interaction with a nuclear medium, there exist splittings of the meson's spectrum, decay constant and form factor relying on the isospin charge. In addition, we show that the ρ-meson's form factor describing an interaction with pseudoscalar fluctuation decreases when the nuclear density increases, while the interaction with a longitudinal part of an axial vector meson increases.

  5. Reflection-Asymmetric Nuclear Deformations within the Density Functional Theory

    SciTech Connect

    Olsen, E; Erler, J; Nazarewicz, W.; Stoitsov, M

    2012-01-01

    Within the nuclear density functional theory (DFT) we study the effect of reflection- asymmetric shapes on ground-state binding energies and binding energy differences. To this end, we developed the new DFT solver axialhfb that uses an approximate second-order gradient to solve the Hartree-Fock-Bogoliubov equations of superconducting DFT with the quasi-local Skyrme energy density functionals. Illustrative calculations are carried out for even- even isotopes of radium and thorium.

  6. Generalized local-spin-density-functional theory

    NASA Astrophysics Data System (ADS)

    Guo, Yufei; Whitehead, M. A.

    1991-01-01

    An alternative density-functional theory, the generalized local-spin-density-functional (G-LSD) theory, is proposed based on the boundary conditions and sum rule of the Fermi-correlation factor in the Hartree-Fock (HF) limit. It avoids the physical restrictions to the boundary conditions and the sum rule used in the generalized exchange local-spin-density-functional (GX-LSD) theory completely, the homogeneous electron-density approximation in the Hartree-Fock-Slater (HFS) theory and in the Gáspár-Kohn-Sham (GKS) theory partly, and the time-consuming step to search for the optimal exchange parameter for each atom or ion in the Xα and Ξa theories. The alternative G-LSD theory generates the GX-LSD, HFS, GKS, Xα, and Ξa theories, when additional approximations or certain Fermi-hole shapes or high electron-density limit in a system are used. Theoretically, the G-LSD theory is more rigorous than the GX-LSD, HFS, GKS, and Ξa theories. Numerically, the statistical total energies for atoms in the G-LSD theory are in excellent agreement with the HF results, when the Gopinathan, Whitehead, and Bogdanovic [Phys. Rev. A 14, 1 (1976)] Fermi-hole parameters are used.

  7. Identification of a bipartite nuclear localization signal in the silkworm Masc protein.

    PubMed

    Sugano, Yudai; Kokusho, Ryuhei; Ueda, Masamichi; Fujimoto, Masaru; Tsutsumi, Nobuhiro; Shimada, Toru; Kiuchi, Takashi; Katsuma, Susumu

    2016-07-01

    The silkworm Masculinizer (Masc) gene encodes a CCCH-tandem zinc finger protein that controls both masculinization and dosage compensation. Masc protein is a nuclear protein, but the mechanism underlying the transport of this protein into the nucleus has not yet been elucidated. Here, we identified a functional bipartite nuclear localization signal (NLS) located between residues 274 and 290 of the Masc protein. Sequence comparison revealed that this bipartite NLS is evolutionarily conserved in Masc proteins from other lepidopteran insects. Furthermore, we showed that the degree of nuclear localization is not associated with the masculinizing activity of the Masc protein. PMID:27277067

  8. Beyond localization: from hodology to function

    PubMed Central

    ffytche, Dominic H; Catani, Marco

    2005-01-01

    A century on, Campbell's largely forgotten 1905 monograph on the localization of cerebral function has a distinctly contemporary feel. Although his map of cortical fields has been eclipsed by Brodmann's later contribution, Campbell's project went beyond cytoarchitectonic cartography, attempting to integrate clinical, anatomical and physiological evidence to provide a guide to function. A key component of Campbell's integrative, functional anatomical approach was hodology—the pattern of white matter connections between cortical areas—foreshadowing a recently developed functional anatomical technique: diffusion tensor tractography. Here, we revisit Campbell's model of the human visual system using tractography to illustrate prominent white matter connections within the occipital lobe and from occipital to frontal, parietal and temporal regions. Campbell used his integrative approach to support the view that vision consisted of a ‘visuo-sensory’ and a ‘visuo-psychic’ stage, combining hodological, cytoarchitectonic, physiological and clinicopathological evidence to locate the former within the calcarine cortex and the latter within the cortical field surrounding it. Speaking directly to contemporary debates surrounding the neurobiology of conscious vision and providing a framework with which to shape future developments in tractography, Campbell's integrative functional anatomical approach is as relevant today as it was 100 years ago. PMID:15937011

  9. Global network influences on local functional connectivity

    PubMed Central

    Snyder, Adam C.; Morais, Michael J.; Willis, Cory M.; Smith, Matthew A.

    2015-01-01

    A central neuroscientific pursuit is understanding neuronal interactions that support computations underlying cognition and behavior. Although neurons interact across disparate scales – from cortical columns to whole-brain networks – research has been restricted to one scale at a time. We measured local interactions through multi-neuronal recordings while accessing global networks using scalp EEG in rhesus macaques. We measured spike count correlation, an index of functional connectivity with computational relevance, and EEG oscillations, which have been linked to various cognitive functions. We found a surprising non-monotonic relationship between EEG oscillation amplitude and spike count correlation, contrary to the intuitive expectation of a direct relationship. With a widely-used network model we replicated these findings by incorporating a private signal targeting inhibitory neurons, a common mechanism proposed for gain modulation. Finally, we report that spike count correlation explains nonlinearities in the relationship between EEG oscillations and response time in a spatial selective attention task. PMID:25799040

  10. Implementing functional languages to exploit locality

    SciTech Connect

    Wolski, R.; Feo, J.; Cann, D.

    1991-01-01

    In the quest for high performance, no obstacle has been as persistent or unyielding as memory latency. It was hoped that dataflow's fine-grain asynchronous model of execution might defeat the memory latency problem. Unable to realize efficient fine-grain systems, the dataflow community is now studying medium-grain and coarse-grain implementations which, like conventional execution models, suffer the effects of memory latency. In this paper, we describe a functional language implementation that automatically exploits locality on cache-coherent multiprocessors. Our system achieves performance improvements reaching 20% for some programs. This study lends further support to the superiority of the functional paradigm for parallel processing. 11 refs., 9 figs.

  11. Chromatin binding of RCC1 during mitosis is important for its nuclear localization in interphase.

    PubMed

    Furuta, Maiko; Hori, Tetsuya; Fukagawa, Tatsuo

    2016-01-15

    RCC1, a guanine nucleotide exchange factor of the small GTPase Ran, plays various roles throughout the cell cycle. However, the functions of RCC1 in biological processes in vivo are still unclear. In particular, although RCC1 has multifunctional domains, the biological significance of each domain is unclear. To examine each domain of RCC1, we established an RCC1 conditional knockout chicken DT40 cell line and introduced various RCC1 mutants into the knockout cells. We found that nuclear reformation did not occur properly in RCC1-deficient cells and examined whether specific RCC1 mutants could rescue this phenotype. Surprisingly, we found that neither the nuclear localization signal nor the chromatin-binding domain of RCC1 is essential for its function. However, codisruption of these domains resulted in defective nuclear reformation, which was rescued by artificial nuclear localization of RCC1. Our data indicate that chromatin association of RCC1 during mitosis is crucial for its proper nuclear localization in the next interphase. Moreover, proper nuclear localization of RCC1 in interphase is essential for its function through its nucleotide exchange activity. PMID:26564799

  12. Chromatin binding of RCC1 during mitosis is important for its nuclear localization in interphase

    PubMed Central

    Furuta, Maiko; Hori, Tetsuya; Fukagawa, Tatsuo

    2016-01-01

    RCC1, a guanine nucleotide exchange factor of the small GTPase Ran, plays various roles throughout the cell cycle. However, the functions of RCC1 in biological processes in vivo are still unclear. In particular, although RCC1 has multifunctional domains, the biological significance of each domain is unclear. To examine each domain of RCC1, we established an RCC1 conditional knockout chicken DT40 cell line and introduced various RCC1 mutants into the knockout cells. We found that nuclear reformation did not occur properly in RCC1-deficient cells and examined whether specific RCC1 mutants could rescue this phenotype. Surprisingly, we found that neither the nuclear localization signal nor the chromatin-binding domain of RCC1 is essential for its function. However, codisruption of these domains resulted in defective nuclear reformation, which was rescued by artificial nuclear localization of RCC1. Our data indicate that chromatin association of RCC1 during mitosis is crucial for its proper nuclear localization in the next interphase. Moreover, proper nuclear localization of RCC1 in interphase is essential for its function through its nucleotide exchange activity. PMID:26564799

  13. LINCing complex functions at the nuclear envelope

    PubMed Central

    Rothballer, Andrea; Schwartz, Thomas U.; Kutay, Ulrike

    2013-01-01

    Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the double membrane of the nuclear envelope (NE) and physically connect nuclear structures to cytoskeletal elements. LINC complexes are envisioned as force transducers in the NE, which facilitate processes like nuclear anchorage and migration, or chromosome movements. The complexes are built from members of two evolutionary conserved families of transmembrane (TM) proteins, the SUN (Sad1/UNC-84) domain proteins in the inner nuclear membrane (INM) and the KASH (Klarsicht/ANC-1/SYNE homology) domain proteins in the outer nuclear membrane (ONM). In the lumen of the NE, the SUN and KASH domains engage in an intimate assembly to jointly form a NE bridge. Detailed insights into the molecular architecture and atomic structure of LINC complexes have recently revealed the molecular basis of nucleo-cytoskeletal coupling. They bear important implications for LINC complex function and suggest new potential and as yet unexplored roles, which the complexes may play in the cell. PMID:23324460

  14. Recent progress on nuclear parton distribution functions

    NASA Astrophysics Data System (ADS)

    Hirai, M.; Kumano, S.; Saito, K.

    2011-09-01

    We report current status of global analyses on nuclear parton distribution functions (NPDFs). The optimum NPDFs are determined by analyzing high-energy nuclear reaction data. Due to limited experimental measurements, antiquark modifications have large uncertainties at x > 0.2 and gluon modifications cannot be determined. A nuclear modification difference between u and d quark distributions could be an origin of the long-standing NuTeV sin2θw anomaly. There is also an issue of nuclear modification differences between the structure functions of charged-lepton and neutrino reactions. Next, nuclear clustering effects are discussed in structure functions F2A as a possible explanation for an anomalous result in the 9Be nucleus at the Thomas Jefferson National Accelerator Facility (JLab). Last, tensor-polarized quark and antiquark distribution functions are extracted from HERMES data on the polarized structure function b1 of the deuteron, and they could be used for testing theoretical models and for proposing future experiments, for example, the one at JLab. Such measurements could open a new field of spin physics in spin-one hadrons.

  15. Immunological and biochemical evidence for nuclear localization of annexin in peas

    NASA Technical Reports Server (NTRS)

    Clark, G. B.; Dauwalder, M.; Roux, S. J.

    1998-01-01

    Immunofluorescent localization of annexins using an anti-pea annexin polyclonal antibody (anti-p35) in pea (Pisum sativum) leaf and stem epidermal peels showed staining of the nuclei and the cell periphery. Nuclear staining was also seen in cell teases prepared from pea plumules. The amount of nuclear stain was reduced both by fixation time and by dehydration and organic solvent treatment. Observation with confocal microscopy demonstrated that the anti-p35 stain was diffusely distributed throughout the nuclear structure. Immunoblots of purified nuclei, nuclear envelope matrix, nucleolar, and chromatin fractions showed a cross-reactive protein band of 35 kDa. These data are the first to show annexins localized in plant cell nuclei where they may play a role in nuclear function.

  16. Nuclear diffractive structure functions at high energies

    SciTech Connect

    Marquet,C.; Kowalski, H.; Lappi, T.; Venugopalan, R.

    2008-08-08

    A future high-energy electron-ion collider would explore the non-linear weakly-coupled regime of QCD, and test the Color Glass Condensate (CGC) approach to high-energy scattering. Hard diffraction in deep inelastic scattering off nuclei will provide many fundamental measurements. In this work, the nuclear diffractive structure function F{sub 2,A}{sup D} is predicted in the CGC framework, and the features of nuclear enhancement and suppression are discussed.

  17. Localization and possible functions of Drosophila septins.

    PubMed Central

    Fares, H; Peifer, M; Pringle, J R

    1995-01-01

    The septins are a family of homologous proteins that were originally identified in Saccharomyces cerevisiae, where they are associated with the "neck filaments" and are involved in cytokinesis and other aspects of the organization of the cell surface. We report here the identification of Sep1, a Drosophila melanogaster septin, based on its homology to the yeast septins. The predicted Sep1 amino acid sequence is 35-42% identical to the known S. cerevisiae septins; 52% identical to Pnut, a second D. melanogaster septin; and 53-73% identical to the known mammalian septins. Sep1-specific antibodies have been used to characterize its expression and localization. The protein is concentrated at the leading edge of the cleavage furrows of dividing cells and cellularizing embryos, suggesting a role in furrow formation. Other aspects of Sep1 localization suggest roles not directly related to cytokinesis. For example, Sep1 exhibits orderly, cell-cycle-coordinated rearrangements within the cortex of syncytial blastoderm embryos and in the cells of post-gastrulation embryos; Sep1 is also concentrated at the leading edge of the epithelium during dorsal closure in the embryo, in the neurons of the embryonic nervous system, and at the baso-lateral surfaces of ovarian follicle cells. The distribution of Sep1 typically overlaps, but is distinct from, that of actin. Both immunolocalization and biochemical experiments show that Sep1 is intimately associated with Pnut, suggesting that the Drosophila septins, like those in yeast, function as part of a complex. Images PMID:8590810

  18. Functional Analysis and Intracellular Localization of Rice Cryptochromes

    PubMed Central

    Matsumoto, Nanako; Hirano, Tomoharu; Iwasaki, Toshisuke; Yamamoto, Naoki

    2003-01-01

    Blue-light-receptor cryptochrome (CRY), which mediates cotyledon expansion, increased accumulation of anthocyanin, and inhibition of hypocotyl elongation, was first identified in Arabidopsis. Two Arabidopsis cryptochromes (AtCRY1 and AtCRY2) have been reported to be localized to the nucleus. However, there is no information on the cryptochromes in monocotyledons. In this study, we isolated two cryptochrome cDNAs, OsCRY1 and OsCRY2, from rice (Oryza sativa) plants. The deduced amino acid sequences of OsCRY1 and OsCRY2 have a photolyase-like domain in their N termini and are homologous to AtCRY1. To investigate the function of OsCRY1, we overexpressed a green fluorescence protein-OsCRY1 fusion gene in Arabidopsis and assessed the phenotypes of the resulting transgenic plants. When the seedlings were germinated in the dark, no discernible effect was observed. However, light-germinated seedlings showed pronounced inhibition of hypocotyl elongation and increased accumulation of anthocyanin. These phenotypes were induced in a blue-light-dependent manner, indicating that OsCRY1 functions as a blue-light-receptor cryptochrome. We also examined the intracellular localization of green fluorescence protein-OsCRY1 in the transgenic plants. It was localized to both the nucleus and the cytoplasm. We identified two nuclear localization domains in the primary structure of OsCRY1. We discuss the relationship between the function and intracellular localization of rice cryptochromes by using additional data obtained with OsCRY2. PMID:14657402

  19. Nuclear modifications of Parton Distribution Functions

    NASA Astrophysics Data System (ADS)

    Adeluyi, Adeola Adeleke

    This dissertation addresses a central question of modern nuclear physics: how does the behavior of fundamental degrees of freedom (quarks and gluons) change in the nuclear environment? This is an important aspect of experimental studies at current facilities such as the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory and the Continuous Electron Beam Accelerator Facility (CEBAF) at the Thomas Jefferson National Laboratory (JLAB). It is also highly relevant to planned experimental efforts at the Large Hadron Collider (LHC) and the future Electron Ion Collider (EIC). All these facilities probe matter via collisions involving nuclei; thus complications arise due to the presence of the attendant nuclear medium. Theoretical efforts to understand and interpret experimental results from such collisions are therefore largely dependent on the resolution of this question. The development of nuclear physics demonstrates that theoretical description is most efficient in terms of the effective degrees of freedom relevant to the scale (energy) being probed. Thus at low energies, nuclei are described as bound states of protons and neutrons (nucleons). At higher energies, the nucleons are no longer elementary, but are revealed to possess an underlying substructure: they are made up of quarks and gluons, collectively termed partons. The mometum distributions of these partons in the nucleon are referred to as Parton Distribution Functions (PDFs). Parton distributions can be determined from experimental measurements of structure functions. The ratio of nuclear structure functions to nucleon structure functions (generically referred to as nuclear ratio) is a measure of the nuclear modifications of the free nucleon PDFs. Thus a study of the nuclear ratio suffices to gain an understanding of nuclear modifications. In this dissertation we aim to describe theoretically nuclear modifications in a restricted region where the nuclear ratio is less than unity, the so

  20. Nuclear localization signal-dependent and -independent movements of Drosophila melanogaster dUTPase isoforms during nuclear cleavage

    SciTech Connect

    Muha, Villo; Zagyva, Imre; Venkei, Zsolt; Szabad, Janos; Vertessy, Beata G.

    2009-04-03

    Two dUTPase isoforms (23 kDa and 21 kDa) are present in the fruitfly with the sole difference of an N-terminal extension. In Drosophila embryo, both isoforms are detected inside the nucleus. Here, we investigated the function of the N-terminal segment using eYFP-dUTPase constructs. In Schneider 2 cells, only the 23 kDa construct showed nuclear localization arguing that it may contain a nuclear localization signal (NLS). Sequence comparisons identified a lysine-rich nonapeptide with similarity to the human c-myc NLS. In Drosophila embryos during nuclear cleavages, the 23 kDa isoform showed the expected localization shifts. Contrariwise, although the 21 kDa isoform was excluded from the nuclei during interphase, it was shifted to the nucleus during prophase and forthcoming mitotic steps. The observed dynamic localization character showed strict timing to the nuclear cleavage phases and explained how both isoforms can be present within the nuclear microenvironment, although at different stages of cell cycle.

  1. Nuclear cyclophilins affect spliceosome assembly and function in vitro

    PubMed Central

    Adams, B.M.; Coates, Miranda N.; Jackson, S. RaElle; Jurica, Melissa S.; Davis, Tara L.

    2015-01-01

    Cyclophilins are ubiquitously expressed proteins that bind to prolines and can catalyse cis/trans isomerization of proline residues. There are 17 annotated members of the cyclophilin family in humans, ubiquitously expressed and localized variously to the cytoplasm, nucleus or mitochondria. Surprisingly, all eight of the nuclear localized cyclophilins are found associated with spliceosomal complexes. However, their particular functions within this context are unknown. We have therefore adapted three established assays for in vitro pre-mRNA splicing to probe the functional roles of nuclear cyclophilins in the context of the human spliceosome. We find that four of the eight spliceosom-associated cyclophilins exert strong effects on splicing in vitro. These effects are dose-dependent and, remarkably, uniquely characteristic of each cyclophilin. Using both qualitative and quantitative means, we show that at least half of the nuclear cyclophilins can act as regulatory factors of spliceosome function in vitro. The present work provides the first quantifiable evidence that nuclear cyclophilins are splicing factors and provides a novel approach for future work into small molecule-based modulation of pre-mRNA splicing. PMID:25967372

  2. Nuclear localization of DMP1 proteins suggests a role in intracellular signaling

    SciTech Connect

    Siyam, Arwa; Wang, Suzhen; Qin, Chunlin; Mues, Gabriele; Stevens, Roy; D'Souza, Rena N.; Lu, Yongbo

    2012-08-03

    Highlights: Black-Right-Pointing-Pointer Nuclear localization of DMP1 in various cell lines. Black-Right-Pointing-Pointer Non-synchronized cells show either nuclear or cytoplasmic localization of DMP1. Black-Right-Pointing-Pointer Nuclear DMP1 is restricted to the nucleoplasm but absent in the nucleolus. -- Abstract: Dentin matrix protein 1 (DMP1) is highly expressed in odontoblasts and osteoblasts/osteocytes and plays an essential role in tooth and bone mineralization and phosphate homeostasis. It is debatable whether DMP1, in addition to its function in the extracellular matrix, can enter the nucleus and function as a transcription factor. To better understand its function, we examined the nuclear localization of endogenous and exogenous DMP1 in C3H10T1/2 mesenchymal cells, MC3T3-E1 preosteoblast cells and 17IIA11 odontoblast-like cells. RT-PCR analyses showed the expression of endogenous Dmp1 in all three cell lines, while Western-blot analysis detected a major DMP1 protein band corresponding to the 57 kDa C-terminal fragment generated by proteolytic processing of the secreted full-length DMP1. Immunofluorescent staining demonstrated that non-synchronized cells presented two subpopulations with either nuclear or cytoplasmic localization of endogenous DMP1. In addition, cells transfected with a construct expressing HA-tagged full-length DMP1 also showed either nuclear or cytoplasmic localization of the exogenous DMP1 when examined with an antibody against the HA tag. Furthermore, nuclear DMP1 was restricted to the nucleoplasm but was absent in the nucleolus. In conclusion, these findings suggest that, apart from its role as a constituent of dentin and bone matrix, DMP1 might play a regulatory role in the nucleus.

  3. Nuclear power-plant safety functions

    SciTech Connect

    Corcoran, W.R.; Finnicum, D.J.; Hubbard, F.R. III; Musick, C.R.; Walzer, P.F.

    1981-03-01

    The concept of safety functions is discussed. Ten critical safety functions and the multiple success paths available for accomplishing them are described. Use of the safety function concept in the development of emergency procedures, operator training, and control-room displays provides a systematic approach and a hierarchy of protection that an operator can use to mitigate the consequences of an event. The safety function concept can also be applied to the design and analysis of nuclear plant systems and to the evaluation of past expierience.

  4. Progress on nuclear modifications of structure functions

    NASA Astrophysics Data System (ADS)

    Kumano, S.

    2016-03-01

    We report progress on nuclear structure functions, especially on their nuclear modifications and a new tensor structure function for the deuteron. To understand nuclear structure functions is an important step toward describing nuclei and QCD matters from low to high densities and from low to high energies in terms of fundamental quark and gluon degrees of freedom beyond conventional hadron and nuclear physics. It is also practically important for understanding new phenomena in high-energy heavy-ion collisions at RHIC and LHC. Furthermore, since systematic errors of current neutrinooscillation experiments are dominated by uncertainties of neutrino-nucleus interactions, such studies are valuable for finding new physics beyond current framework. Next, a new tensor-polarized structure function b1 is discussed for the deuteron. There was a measurement by HERMES; however, its data are inconsistent with the conventional convolution estimate based on the standard deuteron model with D-state admixture. This fact suggests that a new hadronic phenomenon should exist in the tensor-polarized deuteron at high energies, and it will be experimentally investigated at JLab from the end of 2010's.

  5. Nuclear moments in covariant density functional theory

    NASA Astrophysics Data System (ADS)

    Meng, J.; Zhao, P. W.; Zhang, S. Q.; Hu, J. N.; Li, J.

    2014-05-01

    Recent progresses on microscopic and self-consistent description of the nuclear moments in covariant density functional theory based on a point-coupling interaction are briefly reviewed. In particular, the electric quadrupole moments of Cd isotopes and the magnetic moments of Pb isotopes are discussed.

  6. Mechanical regulation of nuclear structure and function.

    PubMed

    Martins, Rui P; Finan, John D; Guilak, Farshid; Lee, David A

    2012-01-01

    Mechanical loading induces both nuclear distortion and alterations in gene expression in a variety of cell types. Mechanotransduction is the process by which extracellular mechanical forces can activate a number of well-studied cytoplasmic signaling cascades. Inevitably, such signals are transduced to the nucleus and induce transcription factor-mediated changes in gene expression. However, gene expression also can be regulated through alterations in nuclear architecture, providing direct control of genome function. One putative transduction mechanism for this phenomenon involves alterations in nuclear architecture that result from the mechanical perturbation of the cell. This perturbation is associated with direct mechanical strain or osmotic stress, which is transferred to the nucleus. This review describes the current state of knowledge relating the nuclear architecture and the transfer of mechanical forces to the nucleus mediated by the cytoskeleton, the nucleoskeleton, and the LINC (linker of the nucleoskeleton and cytoskeleton) complex. Moreover, remodeling of the nucleus induces alterations in nuclear stiffness, which may be associated with cell differentiation. These phenomena are discussed in relation to the potential influence of nuclear architecture-mediated mechanoregulation of transcription and cell fate. PMID:22655599

  7. The bovine papillomavirus type 1 E2 transactivator and repressor proteins use different nuclear localization signals.

    PubMed

    Skiadopoulos, M H; McBride, A A

    1996-02-01

    The E2 gene of bovine papillomavirus type 1 encodes at least three nuclear phosphoproteins that regulate viral transcription and DNA replication. All three proteins have a common C-terminal domain that has DNA-binding and dimerization activities. A basic region in this domain forms an alpha helix which makes direct contact with the DNA target. In this study, it is shown that in addition to its role in DNA binding, this basic region functions as a nuclear localization signal both in the E2 DNA-binding domain and in a heterologous protein. Deletion of this signal sequence resulted in increased accumulation of the E2 transactivator and repressor proteins in the cytoplasm, but nuclear localization was not eliminated. In the full-length transactivator protein, another signal, present in the N-terminal transactivation domain, is used for transport to the nucleus, and the C-terminal nuclear localization signal(s) are masked. The use of different nuclear localization signals could potentially allow differential regulation of the subcellular localization of the E2 transactivator and repressor proteins at some stage in the viral life cycle. PMID:8551571

  8. Nuclear structure functions at small x

    SciTech Connect

    Jalilian-Marian, Jamal

    2009-11-15

    I study the nuclear structure function F{sub 2}{sup A} and its logarithmic derivative in the high-energy limit (small-x region) using the color glass condensate formalism. In this limit the structure function F{sub 2} depends on the quark-antiquark dipole-target scattering cross section N{sub F}(x{sub bj},r{sub t},b{sub t}). The same dipole cross section appears in single-hadron and hadron-photon production cross sections in the forward rapidity region in deuteron (proton)-nucleus collisions at high energy, that is, at energies available at the BNL Relativistic Heavy Ion Collider (RHIC) and the CERN Large Hadron Collider (LHC). I use a parametrization of the dipole cross section, which has successfully been used to describe the deuteron-gold data at the RHIC, to compute the nuclear structure function F{sub 2}{sup A} and its log Q{sup 2} derivative (which is related to gluon distribution function in the double log limit). I provide a quantitative estimate of the nuclear shadowing of F{sub 2}{sup A} and the gluon distribution function in the kinematic region relevant to a future electron-ion collider.

  9. Regulation of Nuclear Localization of Signaling Proteins by Cytokinin

    SciTech Connect

    Kieber, J.J.

    2010-05-01

    Cytokinins are a class of mitogenic plant hormones that play an important role in most aspects of plant development, including shoot and root growth, vascular and photomorphogenic development and leaf senescence. A model for cytokinin perception and signaling has emerged that is similar to bacterial two-component phosphorelays. In this model, binding of cytokinin to the extracellular domain of the Arabidopsis histidine kinase (AHKs) receptors induces autophosphorylation within the intracellular histidine-kinase domain. The phosphoryl group is subsequently transferred to cytosolic Arabidopsis histidine phosphotransfer proteins (AHPs), which have been suggested to translocate to the nucleus in response to cytokinin treatment, where they then transfer the phosphoryl group to nuclear-localized response regulators (Type-A and Type-B ARRs). We examined the effects of cytokinin on AHP subcellular localization in Arabidopsis and, contrary to expectations, the AHPs maintained a constant nuclear/cytosolic distribution following cytokinin treatment. Furthermore, mutation of the conserved phosphoacceptor histidine residue of the AHP, as well as disruption of multiple cytokinin signaling elements, did not affect the subcellular localization of the AHP proteins. Finally, we present data indicating that AHPs maintain a nuclear/cytosolic distribution by balancing active transport into and out of the nucleus. Our findings suggest that the current models indicating relocalization of AHP protein into the nucleus in response to cytokinin are incorrect. Rather, AHPs actively maintain a consistent nuclear/cytosolic distribution regardless of the status of the cytokinin response pathway.

  10. Identification of the nuclear localization and export signals of high risk HPV16 E7 oncoprotein

    SciTech Connect

    Knapp, Alixandra A.; McManus, Patrick M.; Bockstall, Katy; Moroianu, Junona

    2009-01-05

    The E7 oncoprotein of high risk human papillomavirus type 16 (HPV16) binds and inactivates the retinoblastoma (RB) family of proteins. Our previous studies suggested that HPV16 E7 enters the nucleus via a novel Ran-dependent pathway independent of the nuclear import receptors (Angeline, M., Merle, E., and Moroianu, J. (2003). The E7 oncoprotein of high-risk human papillomavirus type 16 enters the nucleus via a nonclassical Ran-dependent pathway. Virology 317(1), 13-23.). Here, analysis of the localization of specific E7 mutants revealed that the nuclear localization of E7 is independent of its interaction with pRB or of its phosphorylation by CKII. Fluorescence microscopy analysis of enhanced green fluorescent protein (EGFP) and 2xEGFP fusions with E7 and E7 domains in HeLa cells revealed that E7 contains a novel nuclear localization signal (NLS) in the N-terminal domain (aa 1-37). Interestingly, treatment of transfected HeLa cells with two specific nuclear export inhibitors, Leptomycin B and ratjadone, changed the localization of 2xEGFP-E7{sub 38-98} from cytoplasmic to mostly nuclear. These data suggest the presence of a leucine-rich nuclear export signal (NES) and a second NLS in the C-terminal domain of E7 (aa 38-98). Mutagenesis of critical amino acids in the putative NES sequence ({sub 76}IRTLEDLLM{sub 84}) changed the localization of 2xEGFP-E7{sub 38-98} from cytoplasmic to mostly nuclear suggesting that this is a functional NES. The presence of both NLSs and an NES suggests that HPV16 E7 shuttles between the cytoplasm and nucleus which is consistent with E7 having functions in both of these cell compartments.

  11. Towards a Density Functional Theory Exchange-Correlation Functional able to describe localization/delocalization

    NASA Astrophysics Data System (ADS)

    Mattsson, Ann E.; Wills, John M.

    2013-03-01

    The inability to computationally describe the physics governing the properties of actinides and their alloys is the poster child of failure of existing Density Functional Theory exchange-correlation functionals. The intricate competition between localization and delocalization of the electrons, present in these materials, exposes the limitations of functionals only designed to properly describe one or the other situation. We will discuss the manifestation of this competition in real materials and propositions on how to construct a functional able to accurately describe properties of these materials. I addition we will discuss both the importance of using the Dirac equation to describe the relativistic effects in these materials, and the connection to the physics of transition metal oxides. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  12. Regulation of COP1 nuclear localization by the COP9 signalosome via direct interaction with CSN1.

    PubMed

    Wang, Xiping; Li, Wenjun; Piqueras, Raquel; Cao, Kaiming; Deng, Xing Wang; Wei, Ning

    2009-05-01

    COP1 and COP9 signalosome (CSN) are key regulators of plant light responses and development. Deficiency in either COP1 or CSN causes a constitutive photomorphogenic phenotype. Through coordinated actions of nuclear- and cytoplasmic-localization signals, COP1 can respond to light signals by differentially partitions between nuclear and cytoplasmic compartments. Previous genetic analysis in Arabidopsis indicated that the nuclear localization of COP1 requires CSN, an eight-subunit heteromeric complex. However the mechanism underlying the functional relationship between COP1 and CSN is unknown. We report here that COP1 weakly associates with CSN in vivo. Furthermore, we report on the direct interaction involving the coiled-coil domain of COP1 and the N-terminal domain of the CSN1 subunit. In onion epidermal cells, expression of CSN1 can stimulate nuclear localization of GUS-COP1, and the N-terminal domain of CSN1 is necessary and sufficient for this function. Moreover, CSN1-induced COP1 nuclear localization requires the nuclear-localization sequences of COP1, as well as its coiled-coil domain, which contains both the cytoplasmic localization sequences and the CSN1 interacting domain. We also provide genetic evidence that the CSN1 N-terminal domain is specifically required for COP1 nuclear localization in Arabidopsis hypocotyl cells. This study advances our understanding of COP1 localization, and the molecular interactions between COP1 and CSN. PMID:19175768

  13. Novel Nuclear Localization Signal Regulated by Ambient Tonicity in Vertebrates*

    PubMed Central

    Kwon, Min Seong; Lee, Sang Do; Kim, Jeong-Ah; Colla, Emanuela; Choi, Yu Jeong; Suh, Pann-Ghil; Kwon, H. Moo

    2008-01-01

    TonEBP is a Rel domain-containing transcription factor implicated in adaptive immunity, viral replication, and cancer. In the mammalian kidney, TonEBP is a central regulator of water homeostasis. Animals deficient in TonEBP suffer from life-threatening dehydration due to renal water loss. Ambient tonicity (effective osmolality) is the prominent signal for TonEBP in a bidirectional manner; TonEBP activity decreases in hypotonicity, whereas it increases in hypertonicity. Here we found that TonEBP displayed nuclear export in response to hypotonicity and nuclear import in response to hypertonicity. The nuclear export of TonEBP was not mediated by the nuclear export receptor CRM1 or discrete nuclear export signal. In contrast, a dominant nuclear localization signal (NLS) was found in a small region of 16 amino acid residues. When short peptides containing the NLS were fused to constitutively cytoplasmic proteins, the fusion proteins displayed tonicity-dependent nucleocytoplasmic trafficking like TonEBP. Thus, tonicity-dependent activation of the NLS is crucial in the nucleocytoplasmic trafficking of TonEBP. The novel NLS is present only in the vertebrates, indicating that it developed late in evolution. PMID:18579527

  14. Building a Universal Nuclear Energy Density Functional

    SciTech Connect

    Carlson, Joe A.; Furnstahl, Dick; Horoi, Mihai; Lust, Rusty; Nazaewicc, Witek; Ng, Esmond; Thompson, Ian; Vary, James

    2012-12-30

    During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold:  First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties;  Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data;  Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

  15. Loss of nuclear localization of TET2 in colorectal cancer.

    PubMed

    Huang, Yuji; Wang, Guanghui; Liang, Zhonglin; Yang, Yili; Cui, Long; Liu, Chen-Ying

    2016-01-01

    5-Hydroxymethylcytosine (5hmC) is lost in multiple human cancers, including colorectal cancer (CRC). Decreased ten-eleven translocation 1 (TET1) messenger RNA (mRNA), but not other two TET family members, has been observed in the colorectal cancer and is crucial for colorectal cancer initiation. Here, we show that nuclear localization of TET2 was lost in a significant portion of CRC tissues, in association with metastasis. In CRC cells, nuclear expression of TET2 were absent but not TET3. Nuclear export inhibitor can increase the 5hmC level in CRC cells, probably through regulating TET2. Our results indicate a new mechanism of TET2 dysregulation in colorectal cancer. PMID:26816554

  16. Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

    PubMed Central

    Meng, Fanchi; Na, Insung; Kurgan, Lukasz; Uversky, Vladimir N.

    2015-01-01

    The cell nucleus contains a number of membrane-less organelles or intra-nuclear compartments. These compartments are dynamic structures representing liquid-droplet phases which are only slightly denser than the bulk intra-nuclear fluid. They possess different functions, have diverse morphologies, and are typically composed of RNA (or, in some cases, DNA) and proteins. We analyzed 3005 mouse proteins localized in specific intra-nuclear organelles, such as nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinuclear compartment and compared them with ~29,863 non-nuclear proteins from mouse proteome. Our analysis revealed that intrinsic disorder is enriched in the majority of intra-nuclear compartments, except for the nuclear pore and lamina. These compartments are depleted in proteins that lack disordered domains and enriched in proteins that have multiple disordered domains. Moonlighting proteins found in multiple intra-nuclear compartments are more likely to have multiple disordered domains. Protein-protein interaction networks in the intra-nuclear compartments are denser and include more hubs compared to the non-nuclear proteins. Hubs in the intra-nuclear compartments (except for the nuclear pore) are enriched in disorder compared with non-nuclear hubs and non-nuclear proteins. Therefore, our work provides support to the idea of the functional importance of intrinsic disorder in the cell nucleus and shows that many proteins associated with sub-nuclear organelles in nuclei of mouse cells are enriched in disorder. This high level of disorder in the mouse nuclear proteins defines their ability to serve as very promiscuous binders, possessing both large quantities of potential disorder-based interaction sites and the ability of a single such site to be involved in a large number of interactions. PMID:26712748

  17. Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches.

    PubMed

    Salvetti, Anna; Couté, Yohann; Epstein, Alberto; Arata, Loredana; Kraut, Alexandra; Navratil, Vincent; Bouvet, Philippe; Greco, Anna

    2016-05-01

    Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cells' compartments. NCL plays important roles in a variety of essential functions, among which are ribosome biogenesis, gene expression, and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 proteins co-purified with NCL, among which 100 of them were specifically found to be associated with NCL after RNase digestion. The functional classification of these proteins confirmed the prominent role of NCL in ribosome biogenesis and additionally revealed the possible involvement of nuclear NCL in several pre-mRNA processing pathways through its interaction with RNA helicases and proteins participating in pre-mRNA splicing, transport, or stability. NCL knockdown experiments revealed that NCL regulates the localization of EXOSC10 and the amount of ZC3HAV1, two components of the RNA exosome, further suggesting its involvement in the control of mRNA stability. Altogether, this study describes the first nuclear interactome of human NCL and provides the basis for further understanding the mechanisms underlying the essential functions of this nucleolar protein. PMID:27049334

  18. Characterization of a beta-catenin nuclear localization defect in MCF-7 breast cancer cells.

    PubMed

    Jamieson, Cara; Mills, Kate M; Lui, Christina; Semaan, Crystal; Molloy, Mark P; Sharma, Manisha; Forwood, Jade K; Henderson, Beric R

    2016-02-15

    Beta-catenin plays a key role in transducing Wnt signals from the plasma membrane to the nucleus. Here we characterize an unusual subcellular distribution of beta-catenin in MCF-7 breast cancer cells, wherein beta-catenin localizes to the cytoplasm and membrane but atypically did not relocate to the nucleus after Wnt treatment. The inability of Wnt or the Wnt agonist LiCl to induce nuclear localization of beta-catenin was not due to defective nuclear transport, as the transport machinery was intact and ectopic GFP-beta-catenin displayed rapid nuclear entry in living cells. The mislocalization is explained by a shift in the retention of beta-catenin from nucleus to cytoplasm. The reduced nuclear retention is caused by unusually low expression of lymphoid enhancer factor/T-cell factor (LEF/TCF) transcription factors. The reconstitution of LEF-1 or TCF4 expression rescued nuclear localization of beta-catenin in Wnt treated cells. In the cytoplasm, beta-catenin accumulated in recycling endosomes, golgi and beta-COP-positive coatomer complexes. The peripheral association with endosomes diminished after Wnt treatment, potentially releasing β-catenin into the cytoplasm for nuclear entry. We propose that in MCF-7 and perhaps other breast cancer cells, beta-catenin may contribute to cytoplasmic functions such as ER-golgi transport, in addition to its transactivation role in the nucleus. PMID:26844628

  19. Remote Control of Gene Function by Local Translation

    PubMed Central

    Jung, Hosung; Gkogkas, Christos G.; Sonenberg, Nahum; Holt, Christine E.

    2014-01-01

    The subcellular position of a protein is a key determinant of its function. Mounting evidence indicates that RNA localization, where specific mRNAs are transported subcellularly and subsequently translated in response to localized signals, is an evolutionarily conserved mechanism to control protein localization. On-site synthesis confers novel signaling properties to a protein and helps to maintain local proteome homeostasis. Local translation plays particularly important roles in distal neuronal compartments, and dysregulated RNA localization and translation cause defects in neuronal wiring and survival. Here, we discuss key findings in this area and possible implications of this adaptable and swift mechanism for spatial control of gene function. PMID:24679524

  20. Nuclear localization of coactivator RAC3 is mediated by a bipartite NLS and importin {alpha}3

    SciTech Connect

    Yeung, Percy Luk; Zhang, Aihua; Chen, J. Don . E-mail: chenjd@umdnj.edu

    2006-09-15

    The nuclear receptor coactivator RAC3 (also known as SRC-3/ACTR/AIB1/p/CIP/TRAM-1) belongs to the p160 coactivator family, which are involved in several physiological processes and diseases. Here we have investigated how RAC3 is translocated into the nucleus and show that it is mediated through a bipartite NLS and importin {alpha}3. This bipartite NLS is located within the conserved bHLH domain, and its mutation abolished nuclear localization. The NLS is also sufficient to cause nuclear import of EGFP, and the activity requires basic amino acids within the NLS. RAC3 binds strongly to importin {alpha}3, which also depends on the basic amino acids. Functionally, RAC3 cytoplasmic mutant loses its ability to enhance transcription, suggesting that nuclear localization is essential for coactivator function. Together, these results reveal a previous unknown mechanism for nuclear translocation of p160 coactivators and a critical function of the conserved bHLH within the coactivator.

  1. Evaluating Functional Localizers: The Case of the FFA

    PubMed Central

    Berman, Marc G.; Park, Joonkoo; Gonzalez, Richard; Polk, Thad A.; Gehrke, Amanda; Knaffla, Scott; Jonides, John

    2010-01-01

    Functional localizers are routinely used in neuroimaging studies to test hypotheses about the function of specific brain areas. The specific tasks and stimuli used to localize particular regions vary widely from study to study even when the same cortical region is targeted. Thus, it is important to ask whether task and stimulus changes lead to differences in localization or whether localization procedures are largely immune to differences in tasks and contrasting stimuli. We present two experiments and a literature review that explore whether face localizer tasks yield differential localization in the fusiform gyrus as a function of task and contrasting stimuli. We tested standard localization tasks---passive viewing, 1-back, and 2-back memory tests---and did not find differences in localization based on task. We did, however, find differences in the extent, strength and patterns/reliabilities of the activation in the fusiform gyrus based on comparison stimuli (faces vs. houses compared to faces vs. scrambled stimuli). PMID:20025980

  2. Localized orbitals from basis sets augmented with diffuse functions

    NASA Astrophysics Data System (ADS)

    Høyvik, Ida-Marie; Jørgensen, Poul

    2013-05-01

    Orbital localization of occupied and virtual Hartree-Fock orbitals generated from basis sets augmented with diffuse functions is performed using the Pipek-Mezey, Boys, powers of the second central moment, and powers of the fourth central moment localizations. The locality of the obtained orbital sets are presented in terms of second and fourth moment orbital spreads. The results show that both local occupied and virtual orbitals may be obtained when using powers of the second central moment and powers of the fourth central moment localizations, while the Pipek-Mezey and Boys localizations fail to produce sets of local virtual orbitals. The locality of the fourth central moment virtual orbitals exhibits a locality similar to the locality of a Boys localization for non-augmented basis sets.

  3. Nuclear parton distribution functions and their uncertainties

    SciTech Connect

    Hirai, M.; Kumano, S.; Nagai, T.-H.

    2004-10-01

    We analyze experimental data of nuclear structure-function ratios F{sub 2}{sup A}/F{sub 2}{sup A{sup '}} and Drell-Yan cross section ratios for obtaining optimum parton distribution functions (PDFs) in nuclei. Then, uncertainties of the nuclear PDFs are estimated by the Hessian method. Valence-quark distributions are determined by the F{sub 2} data at large x; however, the small-x part is not obvious from the data. On the other hand, the antiquark distributions are determined well at x{approx}0.01 from the F{sub 2} data and at x{approx}0.1 by the Drell-Yan data; however, the large-x behavior is not clear. Gluon distributions cannot be fixed by the present data and they have large uncertainties in the whole x region. Parametrization results are shown in comparison with the data. We provide a useful code for calculating nuclear PDFs at given x and Q{sup 2}.

  4. Meaning of the nuclear wave function

    NASA Astrophysics Data System (ADS)

    Terry, John D.; Miller, Gerald A.

    2016-07-01

    Background: The intense current experimental interest in studying the structure of the deuteron and using it to enable accurate studies of neutron structure motivate us to examine the four-dimensional space-time nature of the nuclear wave function and the various approximations used to reduce it to an object that depends only on three spatial variables. Purpose: The aim is to determine if the ability to understand and analyze measured experimental cross sections is compromised by making the reduction from four to three dimensions. Method: Simple, exactly calculable, covariant models of a bound-state wave-state wave function (a scalar boson made of two constituent-scalar bosons) with parameters chosen to represent a deuteron are used to investigate the accuracy of using different approximations to the nuclear wave function to compute the quasielastic scattering cross section. Four different versions of the wave function are defined (light-front-spectator, light-front, light-front with scaling, and nonrelativistic) and used to compute the cross sections as a function of how far off the mass shell (how virtual) is the struck constituent. Results: We show that making an exact calculation of the quasielastic scattering cross section involves using the light-front-spectator wave function. All of the other approaches fail to reproduce the model exact calculation if the value of Bjorken x differs from unity. The model is extended to consider an essential effect of spin to show that constituent nucleons cannot be treated as being on their mass shell even when taking the matrix element of a "good" current. Conclusions: Developing realistic light-front-spectator wave functions to meet the needs of current and planned experiments is a worthwhile activity.

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

    PubMed

    Myre, Michael A; O'Day, Danton H

    2005-06-24

    Nucleomorphin is a novel nuclear calmodulin (CaM)-binding protein (CaMBP) containing an extensive DEED (glu/asp repeat) domain that regulates nuclear number. GFP-constructs of the 38 kDa NumA1 isoform localize as intranuclear patches adjacent to the inner nuclear membrane. The translocation of CaMBPs into nuclei has previously been shown by others to be mediated by both classic nuclear localization sequences (NLSs) and CaM-binding domains (CaMBDs). Here we show that NumA1 possesses a CaMBD (171EDVSRFIKGKLLQKQQKIYKDLERF195) containing both calcium-dependent-binding motifs and an IQ-like motif for calcium-independent binding. GFP-constructs containing only NumA1 residues 1-129, lacking the DEED and CaMBDs, still localized as patches at the internal periphery of nuclei thus ruling out a direct role for the CaMBD in nuclear import. These constructs contained the amino acid residues 48KKSYQDPEIIAHSRPRK64 that include both a putative bipartite and classical NLS. GFP-bipartite NLS constructs localized uniformly within nuclei but not as patches. As with previous work, removal of the DEED domain resulted in highly multinucleate cells. However as shown here, multinuclearity only occurred when the NLS was present allowing the protein to enter nuclei. Site-directed mutation analysis in which the NLS was changed to 48EF49 abolished the stability of the GFP fusion at the protein but not RNA level preventing subcellular analyses. Cells transfected with the 48EF49 construct exhibited slowed growth when compared to parental AX3 cells and other GFP-NumA1 deletion mutants. In addition to identifying an NLS that is sufficient for nuclear translocation of nucleomorphin and ruling out CaM-binding in this event, this work shows that the nuclear localization of NumA1 is crucial to its ability to regulate nuclear number in Dictyostelium. PMID:15896312

  6. Local representation of the electronic dielectric response function

    DOE PAGESBeta

    Lu, Deyu; Ge, Xiaochuan

    2015-12-11

    We present a local representation of the electronic dielectric response function, based on a spatial partition of the dielectric response into contributions from each occupied Wannier orbital using a generalized density functional perturbation theory. This procedure is fully ab initio, and therefore allows us to rigorously define local metrics, such as “bond polarizability,” on Wannier centers. We show that the locality of the bare response function is determined by the locality of three quantities: Wannier functions of the occupied manifold, the density matrix, and the Hamiltonian matrix. Furthermore, in systems with a gap, the bare dielectric response is exponentially localized,more » which supports the physical picture of the dielectric response function as a collection of interacting local responses that can be captured by a tight-binding model.« less

  7. Local representation of the electronic dielectric response function

    SciTech Connect

    Lu, Deyu; Ge, Xiaochuan

    2015-12-11

    We present a local representation of the electronic dielectric response function, based on a spatial partition of the dielectric response into contributions from each occupied Wannier orbital using a generalized density functional perturbation theory. This procedure is fully ab initio, and therefore allows us to rigorously define local metrics, such as “bond polarizability,” on Wannier centers. We show that the locality of the bare response function is determined by the locality of three quantities: Wannier functions of the occupied manifold, the density matrix, and the Hamiltonian matrix. Furthermore, in systems with a gap, the bare dielectric response is exponentially localized, which supports the physical picture of the dielectric response function as a collection of interacting local responses that can be captured by a tight-binding model.

  8. Green's function Monte Carlo in nuclear physics

    SciTech Connect

    Carlson, J.

    1990-01-01

    We review the status of Green's Function Monte Carlo (GFMC) methods as applied to problems in nuclear physics. New methods have been developed to handle the spin and isospin degrees of freedom that are a vital part of any realistic nuclear physics problem, whether at the level of quarks or nucleons. We discuss these methods and then summarize results obtained recently for light nuclei, including ground state energies, three-body forces, charge form factors and the coulomb sum. As an illustration of the applicability of GFMC to quark models, we also consider the possible existence of bound exotic multi-quark states within the framework of flux-tube quark models. 44 refs., 8 figs., 1 tab.

  9. Control of heterochromatin localization and silencing by the nuclear membrane protein Lem2

    PubMed Central

    Barrales, Ramón Ramos; Forn, Marta; Georgescu, Paula Raluca; Sarkadi, Zsuzsa; Braun, Sigurd

    2016-01-01

    Transcriptionally silent chromatin localizes to the nuclear periphery, which provides a special microenvironment for gene repression. A variety of nuclear membrane proteins interact with repressed chromatin, yet the functional role of these interactions remains poorly understood. Here, we show that, in Schizosaccharomyces pombe, the nuclear membrane protein Lem2 associates with chromatin and mediates silencing and heterochromatin localization. Unexpectedly, we found that these functions can be separated and assigned to different structural domains within Lem2, excluding a simple tethering mechanism. Chromatin association and tethering of centromeres to the periphery are mediated by the N-terminal LEM (LAP2–Emerin–MAN1) domain of Lem2, whereas telomere anchoring and heterochromatin silencing require exclusively its conserved C-terminal MSC (MAN1–Src1 C-terminal) domain. Particularly, silencing by Lem2 is epistatic with the Snf2/HDAC (histone deacetylase) repressor complex SHREC at telomeres, while its necessity can be bypassed by deleting Epe1, a JmjC protein with anti-silencing activity. Furthermore, we found that loss of Lem2 reduces heterochromatin association of SHREC, which is accompanied by increased binding of Epe1. This reveals a critical function of Lem2 in coordinating these antagonistic factors at heterochromatin. The distinct silencing and localization functions mediated by Lem2 suggest that these conserved LEM-containing proteins go beyond simple tethering to play active roles in perinuclear silencing. PMID:26744419

  10. Local hybrid functionals: An assessment for thermochemical kinetics

    SciTech Connect

    Kaupp, Martin; Bahmann, Hilke; Arbuznikov, Alexei V.

    2007-11-21

    Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b({tau}{sub W}(r)/{tau}(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.

  11. Genetic analysis of polyomavirus large T nuclear localization: nuclear localization is required for productive association with pRb family members.

    PubMed Central

    Howes, S H; Bockus, B J; Schaffhausen, B S

    1996-01-01

    Polyomavirus large T antigen (LT) is a multifunctional nuclear protein. LT has two nuclear localization signals (NLS2), one spanning residues 189 to 195 (NLS1) and another spanning residues 280 to 286 (NLS2). Site-directed mutagenesis showed that each signal contains at least two critical residues. The possibility of connections between NLSs and adjacent phosphorylations has attracted much attention. Cytoplasmic LT (CyT) mutants were underphosphorylated, particularly at sites adjacent to NLS2. However, since a nuclear LT bearing an inactivated NLS2 was phosphorylated normally at adjacent sites, the signal was not directly required for phosphorylation. Conversely, LT could be translocated to the nucleus via NLS2 even when the adjacent phosphorylation sites were deleted. CyT was examined to probe the importance of LT localization. CyT was unable to perform LT functions related to interactions with retinoblastoma susceptibility gene (pRb) family members. Hence, CyT was unable to immortalize primary cells or to transactivate an E2F-responsive promoter. Consistent with these findings, CyT, though capable of binding pRb in vitro, did not cause relocalization of pRb in cells. Assays of transactivation of the simian virus 40 late promoter and of the human c-fos promoter showed that defects of CyT were not limited to functions dependent on pRb interactions. PMID:8648692

  12. Thermalization and many-body localization in systems under dynamic nuclear polarization

    NASA Astrophysics Data System (ADS)

    De Luca, Andrea; Rodríguez-Arias, Inés; Müller, Markus; Rosso, Alberto

    2016-07-01

    We study the role of dipolar interactions in the standard protocol used to achieve dynamic nuclear polarization (DNP). We point out that a critical strength of interactions is required to obtain significant nuclear hyperpolarization. Otherwise, the electron spins do not thermalize among each other, due to the incipient many-body localization transition in the electron spin system. Only when the interactions are sufficiently strong, in the so-called spin-temperature regime, they establish an effective thermodynamic behavior in the out-of-equilibrium stationary state. The highest polarization is reached at a point where the spin temperature is just not able to establish itself anymore. We provide numerical predictions for the level of nuclear hyperpolarization and present an analytical technique to estimate the spin temperature as a function of interaction strength and quenched disorder. We show that, at sufficiently strong coupling, nuclear spins perfectly equilibrate to the spin temperature that establishes among the spins of radicals.

  13. Nuclear localization of Formyl-Peptide Receptor 2 in human cancer cells.

    PubMed

    Cattaneo, Fabio; Parisi, Melania; Fioretti, Tiziana; Sarnataro, Daniela; Esposito, Gabriella; Ammendola, Rosario

    2016-08-01

    Current models of G protein-coupled receptors (GPCRs) signaling describe binding of external agonists to cell surface receptors which, in turn, trigger several biological responses. New paradigms indicate that GPCRs localize to and signal at the nucleus, thus regulating distinct signaling cascades. The formyl-peptide receptor FPR2 belongs to the GPCR super-family and is coupled to PTX-sensitive Gi proteins. We show by western blot analysis, immunofluorescence experiments and radioligand binding assays that FPR2 is expressed at nuclear level in CaLu-6 and AGS cells. Nuclear FPR2 is a functional receptor, since it participates in intra-nuclear signaling, as assessed by decreased G protein-FPR2 association and enhanced ERK2, c-Jun and c-Myc phosphorylation upon stimulation of intact nuclei with the FPR2 agonist, WKYMVm. We analyzed FPR2 sequence for the search of a nuclear localization sequence (NLS) and we found a stretch of basic aminoacids (227-KIHKK-231) in the third cytoplasmic loop of the receptor. We performed single (K230A) and multiple (H229A/K230A/K231A) mutagenesis of NLS. The constructs were individually overexpressed in HEK293 cells and immunofluorescence and western blot analysis showed that nuclear localization or translocation of FPR2 depends on the integrity of the H(229) and K(231) residues within the NLS. PMID:27177968

  14. Nuclear localization of platelet-activating factor receptor controls retinal neovascularization

    PubMed Central

    K Bhosle, Vikrant; Rivera, José Carlos; Zhou, Tianwei (Ellen); Omri, Samy; Sanchez, Melanie; Hamel, David; Zhu, Tang; Rouget, Raphael; Rabea, Areej Al; Hou, Xin; Lahaie, Isabelle; Ribeiro-da-Silva, Alfredo; Chemtob, Sylvain

    2016-01-01

    Platelet-activating factor (PAF) is a pleiotropic phospholipid with proinflammatory, procoagulant and angiogenic actions on the vasculature. We and others have reported the presence of PAF receptor (Ptafr) at intracellular sites such as the nucleus. However, mechanisms of localization and physiologic functions of intracellular Ptafr remain poorly understood. We hereby identify the importance of C-terminal motif of the receptor and uncover novel roles of Rab11a GTPase and importin-5 in nuclear translocation of Ptafr in primary human retinal microvascular endothelial cells. Nuclear localization of Ptafr is independent of exogenous PAF stimulation as well as intracellular PAF biosynthesis. Moreover, nuclear Ptafr is responsible for the upregulation of unique set of growth factors, including vascular endothelial growth factor, in vitro and ex vivo. We further corroborate the intracrine PAF signaling, resulting in angiogenesis in vivo, using Ptafr antagonists with distinct plasma membrane permeability. Collectively, our findings show that nuclear Ptafr translocates in an agonist-independent manner, and distinctive functions of Ptafr based on its cellular localization point to another dimension needed for pharmacologic selectivity of drugs. PMID:27462464

  15. Nuclear localization sequence of FUS and induction of stress granules by ALS mutants

    PubMed Central

    Gal, Jozsef; Zhang, Jiayu; Kwinter, David M.; Zhai, Jianjun; Jia, Hongge; Jia, Jianhang; Zhu, Haining

    2010-01-01

    Mutations in FUS have been reported to cause a subset of familial amyotrophic lateral sclerosis (ALS) cases. Wild-type FUS is mostly localized in the nuclei of neurons, but the ALS mutants are partly mislocalized in the cytoplasm and can form inclusions. Little is known about the regulation of FUS subcellular localization or how the ALS mutations alter FUS function. Here we demonstrate that the C-terminal 32 amino acid residues of FUS constitute an effective nuclear localization sequence (NLS) as it targeted beta-galactosidase (LacZ, 116 kDa) to the nucleus. Deletion of or the ALS point mutations within the NLS caused cytoplasmic mislocalization of FUS. Moreover, we identified the poly-A binding protein (PABP1), a stress granule marker, as an interacting partner of FUS. PABP1 formed large cytoplasmic foci that co-localized with the mutant FUS inclusions. No such foci, which resemble stress granules, were observed in the presence of wild-type FUS. In addition, processing bodies, which are functionally related to stress granules, were adjacent to but not co-localized with the mutant FUS inclusions. Our results suggest that the ALS mutations in the C-terminal NLS of FUS can impair FUS nuclear localization and induce cytoplasmic mislocalization, inclusion formation, and potential perturbation of RNA metabolism. PMID:20674093

  16. Correlated Strength in the Nuclear Spectral Function

    SciTech Connect

    D. Rohe; C. S. Armstrong; R. Asaturyan; O. K. Baker; S. Bueltmann; C. Carasco; D. Day; R. Ent; H. C. Fenker; K. Garrow; A. Gasparian; P. Gueye; M. Hauger; A. Honegger; J. Jourdan; C. E. Keppel; G. Kubon; R. Lindgren; A. Lung; D. J. Mack; J. H. Mitchell; H. Mkrtchyan; D. Mocelj; K. Normand; T. Petitjean; O. Rondon; E. Segbefia; I. Sick; S. Stepanyan; L. Tang; F. Tiefenbacher; W. F. Vulcan; G. Warren; S. A. Wood; L. Yuan; M. Zeier; H. Zhu; B. Zihlmann

    2004-10-01

    We have carried out an (e,ep) experiment at high momentum transfer and in parallel kinematics to measure the strength of the nuclear spectral function S(k,E) at high nucleon momenta k and large removal energies E. This strength is related to the presence of short-range and tensor correlations, and was known hitherto only indirectly and with considerable uncertainty from the lack of strength in the independent-particle region. This experiment locates by direct measurement the correlated strength predicted by theory.

  17. A nuclear-localized histone-gene binding protein from rice (OsHBP1b) functions in salinity and drought stress tolerance by maintaining chlorophyll content and improving the antioxidant machinery.

    PubMed

    Lakra, Nita; Nutan, Kamlesh K; Das, Priyanka; Anwar, Khalid; Singla-Pareek, Sneh L; Pareek, Ashwani

    2015-03-15

    Plants have evolved a number of molecular strategies and regulatory mechanisms to cope with abiotic stresses. Among the various key factors/regulators, transcription factors (TFs) play critical role(s) towards regulating the gene expression patterns in response to stress conditions. Altering the expression of the key TFs can greatly influence plant stress tolerance. OsHBP1b (accession no. KM096571) is one such TF belonging to bZIP family, localized within the Saltol QTL, whose expression is induced upon salinity treatment in the rice seedlings. qRT-PCR based expression studies for OsHBP1b in seedlings of contrasting genotypes of rice showed its differential regulation in response to salinity stress. A GFP based in vivo study showed that the OsHBP1b protein is nuclear localized and possesses the trans-activation activity. As compared to the WT tobacco plants, the transgenic plants ectopically expressing OsHBP1b showed better survival and favourable osmotic parameters (such as germination and survival rate, membrane stability, K(+)/Na(+) ratio, lipid peroxidation, electrolyte leakage and proline contents) under salinity and drought stress. Under salinity conditions, the transgenic plants accumulated lower levels of reactive oxygen species as compared to the WT. It was also accompanied by higher activities of antioxidant enzymes (such as ascorbate peroxidase and superoxide dismutase), thereby demonstrating that transgenic plants are physiologically better adapted towards the oxidative damage. Taken together, our findings suggest that OsHBP1b contributes to abiotic stress tolerance through multiple physiological pathways and thus, may serve as a useful 'candidate gene' for improving multiple stress tolerance in crop plants. PMID:25543954

  18. Minimal size of prototype foamy virus integrase for nuclear localization.

    PubMed

    Hyun, U; Lee, D H; Shin, C G

    2011-01-01

    We have reported previously that the prototype foamy virus (PFV) integrase (IN) has a strong nuclear localization signal (NLS) in its C-terminal domain, in particular in a region of aa 306-334 including highly karyophilic arginines or lysines at positions 308, 313, 318, 324, and 329. In this study, we used various mutants of the C-terminal domain to further analyze its karyophilic determinants. Plasmids expressing these mutants fused to maltose binding protein (MBP) and enhanced green fluorescent protein (EGFP) were transfected to COS-1 cells and subcellular localization of these fluorescent fusion proteins was determined by fluorescent microscopy. The results revealed that a maximum karyophilicity was exhibited by a region longer than the previously described one of 29 aa (aa 306-334), in particular by a 64 aa region (aa 289-352) with Arg341 and Lys349 as critical determinants. PMID:21692567

  19. The defective nuclear lamina in Hutchinson-gilford progeria syndrome disrupts the nucleocytoplasmic Ran gradient and inhibits nuclear localization of Ubc9.

    PubMed

    Kelley, Joshua B; Datta, Sutirtha; Snow, Chelsi J; Chatterjee, Mandovi; Ni, Li; Spencer, Adam; Yang, Chun-Song; Cubeñas-Potts, Caelin; Matunis, Michael J; Paschal, Bryce M

    2011-08-01

    The mutant form of lamin A responsible for the premature aging disease Hutchinson-Gilford progeria syndrome (termed progerin) acts as a dominant negative protein that changes the structure of the nuclear lamina. How the perturbation of the nuclear lamina in progeria is transduced into cellular changes is undefined. Using patient fibroblasts and a variety of cell-based assays, we determined that progerin expression in Hutchinson-Gilford progeria syndrome inhibits the nucleocytoplasmic transport of several factors with key roles in nuclear function. We found that progerin reduces the nuclear/cytoplasmic concentration of the Ran GTPase and inhibits the nuclear localization of Ubc9, the sole E2 for SUMOylation, and of TPR, the nucleoporin that forms the basket on the nuclear side of the nuclear pore complex. Forcing the nuclear localization of Ubc9 in progerin-expressing cells rescues the Ran gradient and TPR import, indicating that these pathways are linked. Reducing nuclear SUMOylation decreases the nuclear mobility of the Ran nucleotide exchange factor RCC1 in vivo, and the addition of SUMO E1 and E2 promotes the dissociation of RCC1 and Ran from chromatin in vitro. Our data suggest that the cellular effects of progerin are transduced, at least in part, through reduced function of the Ran GTPase and SUMOylation pathways. PMID:21670151

  20. Linking Long Noncoding RNA Localization and Function.

    PubMed

    Chen, Ling-Ling

    2016-09-01

    Recent studies have revealed the regulatory potential of many long noncoding RNAs (lncRNAs). Most lncRNAs, like mRNAs, are transcribed by RNA polymerase II and are capped, polyadenylated, and spliced. However, the subcellular fates of lncRNAs are distinct and the mechanisms of action are diverse. Investigating the mechanisms that determine the subcellular fate of lncRNAs has the potential to provide new insights into their biogenesis and specialized functions. PMID:27499234

  1. Occupation-number-based energy functional for nuclear masses

    SciTech Connect

    Bertolli, Michael G.; Papenbrock, Thomas F; Wild, S. M.

    2012-01-01

    We develop an energy functional with shell-model occupations as the relevant degrees of freedom and compute nuclear masses across the nuclear chart. The functional is based on Hohenberg-Kohn theory with phenomenologically motivated terms. A global fit of the 17-parameter functional to 2049 nuclear masses yields a root-mean-square deviation of =1.31 MeV. Nuclear radii are computed within a model that employs the resulting occupation numbers.

  2. Occupation number-based energy functional for nuclear masses.

    SciTech Connect

    Bertolli, M.; Papenbrock, T.; Wild, S. M.

    2012-01-01

    We develop an energy functional with shell-model occupations as the relevant degrees of freedom and compute nuclear masses across the nuclear chart. The functional is based on Hohenberg-Kohn theory with phenomenologically motivated terms. A global fit of the 17-parameter functional to 2049 nuclear masses yields a root-mean-square deviation of {chi} = 1.31 MeV. Nuclear radii are computed within a model that employs the resulting occupation numbers.

  3. Requirements for nuclear localization of Lsm2-8p and competition between nuclear and cytoplasmic Lsm complexes

    PubMed Central

    Spiller, Michael P.; Reijns, Martin A. M.; Beggs, Jean D.

    2008-01-01

    Summary Lsm proteins are ubiquitous, multifunctional proteins that are involved in the processing and/or turnover of many RNAs. In eukaryotes, a hetero-heptameric complex of Lsm proteins (Lsm2-8p) affects the processing of small stable RNAs and pre-mRNAs in the nucleus, while a different hetero-heptameric complex of Lsm proteins (Lsm1-7p) promotes mRNA decapping and decay in the cytoplasm. These two complexes have six constituent proteins in common, yet localize to separate cellular compartments and perform apparently disparate functions. Little is known about the biogenesis of the Lsm complexes, or how they are recruited to different cellular compartments. We show that in yeast, the nuclear accumulation of Lsm proteins depends on complex formation and that the Lsm8p subunit plays a crucial role. The nuclear localization of Lsm8p is itself most strongly influenced by Lsm2p and Lsm4p, its presumed neighbors in the Lsm2-8p complex. Furthermore, over-expression and depletion experiments imply that Lsm1p and Lsm8p act competitively with respect to the localization of the two complexes, suggesting a potential mechanism for co-regulation of nuclear and cytoplasmic RNA processing. A shift of Lsm proteins from the nucleus to the cytoplasm under stress conditions indicates that this competition is biologically significant. PMID:18029398

  4. DNA Ligase IV regulates XRCC4 nuclear localization

    PubMed Central

    Francis, Dailia B.; Kozlov, Mikhail; Chavez, Jose; Chu, Jennifer; Malu, Shruti; Hanna, Mary; Cortes, Patricia

    2014-01-01

    DNA Ligase IV, along with its interacting partner XRCC4, are essential for repairing DNA double strand breaks by non-homologous end joining (NHEJ). Together, they complete the final ligation step resolving the DNA break. Ligase IV is regulated by XRCC4 and XLF. However, the mechanism(s) by which Ligase IV control the NHEJ reaction and other NHEJ factor(s) remains poorly characterized. Here, we show that a C-terminal region of Ligase IV (aa 620 to 800), which encompasses a NLS, the BRCT I, and the XRCC4 interacting region (XIR), is essential for nuclear localization of its co-factor XRCC4. In Ligase IV deficient cells, XRCC4 showed deregulated localization remaining in the cytosol even after induction of DNA double strand breaks. DNA Ligase IV was also required for efficient localization of XLF into the nucleus. Additionally, human fibroblasts that harbor hypomorphic mutations within the Ligase IV gene displayed decreased levels of XRCC4 protein, implicating that DNA Ligase IV is also regulating XRCC4 stability. Our results provide evidence for a role of DNA Ligase IV in controlling the cellular localization and protein levels of XRCC4. PMID:24984242

  5. Ras-activated RSK1 phosphorylates EBP50 to regulate its nuclear localization and promote cell proliferation

    PubMed Central

    Lim, HooiCheng; Jou, Tzuu-Shuh

    2016-01-01

    Differential subcellular localization of EBP50 leads to its controversial role in cancer biology either as a tumor suppressor when it resides at the membrane periphery, or a tumor facilitator at the nucleus. However, the mechanism behind nuclear localization of EBP50 remains unclear. A RNA interference screening identified the downstream effector of the Ras-ERK cascade, RSK1, as the molecule unique for nuclear transport of EBP50. RSK1 binds to EBP50 and phosphorylates it at a conserved threonine residue at position 156 (T156) under the regulation of growth factor. Mutagenesis experiments confirmed the significance of T156 residue in nuclear localization of EBP50, cellular proliferation, and oncogenic transformation. Our study sheds light on a possible therapeutic strategy targeting at this aberrant nuclear expression of EBP50 without affecting the normal physiological function of EBP50 at other subcellular localization. PMID:26862730

  6. [Nuclear medicine for evaluation of liver functions].

    PubMed

    Yamamoto, K

    1994-05-01

    The clinical usefulness of colloid liver scintigraphy to detect space occupying lesions in the liver has been reduced by X-ray CT and ultrasonography. However, scintigraphic examinations have potentials for characteristic diagnosis of liver tumors, such as 99mTc RBC SPECT for hepatic hemangioma, 99mTc PMT for positive imaging of hepatocellular carcinoma and its extrahepatic metastasis, and radioimmunoscintigraphy for metastatic tumors. Moreover, prediction of the prognosis and monitoring therapeutic effect to liver cancer can be made by the use of nuclear medicine techniques. Recently, 99mTc galactosyl serum albumin (GSA), a newly developed radiotracer to evaluate hepatocyte function, has become commercially available. Quantitative parameters of liver functions can be obtained by analysis of time-activity curve in blood and liver after 99mTc-GSA administration. In several cases, 99mTc-GSA study showed intrahepatic unevenness of function, which could not be depicted by other imaging examinations. Positron emission tomography (PET) with 18F-fluoro-2-deoxy glucose (FDG) is useful to detect malignant tumors in the liver. Since PET can provide absolutely quantitative data in better resolution, it is expected that regional true metabolic functions in the liver may be able to be quantitatively evaluated with PET in near future. PMID:8028225

  7. Phosphatidylinositol 3-kinase/Akt signaling enhances nuclear localization and transcriptional activity of BRCA1

    SciTech Connect

    Hinton, Cimona V.; Fitzgerald, Latricia D.; Thompson, Marilyn E. . E-mail: methompson@mmc.edu

    2007-05-15

    Signaling pathways involved in regulating nuclear-cytoplasmic distribution of BRCA1 have not been previously reported. Here, we provide evidence that heregulin {beta}1-induced activation of the Akt pathway increases the nuclear content of BRCA1. First, treatment of T47D breast cancer cells with heregulin {beta}1 results in a two-fold increase in nuclear BRCA1 as assessed by FACS analysis, immunoblotting and immunofluorescence. This heregulin-induced increase in nuclear BRCA1 is blocked by siRNA-mediated down-regulation of Akt. Second, mutation of threonine 509 in BRCA1, the site of Akt phosphorylation, to an alanine, attenuates the ability of heregulin to induce BRCA1 nuclear accumulation. These data suggest that Akt-catalyzed phosphorylation of BRCA1 is required for the heregulin-regulated nuclear concentration of BRCA1. Because most functions ascribed to BRCA1 occur within the nucleus, we postulated that phosphorylation-dependent nuclear accumulation of BRCA1 would result in enhanced nuclear activity, specifically transcriptional activity, of BRCA1. This postulate is affirmed by our observation that the ability of BRCA1 to transactivate GADD45 promoter constructs was enhanced in T47D cells treated with heregulin {beta}1. Furthermore, the heterologous expression of BRCA1 in HCC1937 human breast cancer cells, which have constitutively active Akt, also induces GADD45 promoter activity, whereas the expression of BRCA1 in which threonine 509 has been mutated to an alanine is able to only minimally induce promoter activity. These findings implicate Akt in upstream events leading to BRCA1 nuclear localization and function.

  8. Phosphatidylinositol 3-kinase/Akt signaling enhances nuclear localization and transcriptional activity of BRCA1

    PubMed Central

    Hinton, Cimona V.; Fitzgerald, Latricia D.; Thompson, Marilyn E.

    2007-01-01

    Signaling pathways involved in regulating nuclear-cytoplasmic distribution of BRCA1 have not been previously reported. Here, we provide evidence that heregulin β1-induced activation of the Akt pathway increases the nuclear content of BRCA1. First, treatment of T47D breast cancer cells with heregulin β1 results in a two-fold increase in nuclear BRCA1 as assessed by FACS analysis, immunoblotting and immunofluorescence. This heregulin-induced increase in nuclear BRCA1 is blocked by siRNA-mediated down-regulation of Akt. Second, mutation of threonine 509 in BRCA1, the site of Akt phosphorylation, to an alanine, attenuates the ability of heregulin to induce BRCA1 nuclear accumulation. These data suggest that Akt-catalyzed phosphorylation of BRCA1 is required for the heregulin-regulated nuclear concentration of BRCA1. Because most functions ascribed to BRCA1 occur within the nucleus, we postulated that phosphorylation-dependent nuclear accumulation of BRCA1 would result in enhanced nuclear activity, specifically transcriptional activity, of BRCA1. This postulate is affirmed by our observation that the ability of BRCA1 to transactivate GADD45 promoter constructs was enhanced in T47D cells treated with heregulin β1. Furthermore, the heterologous expression of BRCA1 in HCC1937 human breast cancer cells, which have constitutively active Akt, also induces GADD45 promoter activity, whereas the expression of BRCA1 in which threonine 509 has been mutated to an alanine is able to only minimally induce promoter activity. These findings implicate Akt in upstream events leading to BRCA1 nuclear localization and function. PMID:17428466

  9. A proline-tyrosine nuclear localization signal (PY-NLS) is required for the nuclear import of fission yeast PAB2, but not of human PABPN1.

    PubMed

    Mallet, Pierre-Luc; Bachand, François

    2013-03-01

    Nuclear poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that play key roles in eukaryotic gene expression. In the fission yeast Schizosaccharomyces pombe, the major nuclear PABP, Pab2, functions in the maturation of small nucleolar RNAs as well as in nuclear RNA decay. Despite knowledge about its nuclear functions, nothing is known about how Pab2 is imported into the nucleus. Here, we show that Pab2 contains a proline-tyrosine nuclear localization signal (PY-NLS) that is necessary and sufficient for its nuclear localization and function. Consistent with the role of karyopherin β2 (Kapβ2)-type receptors in the import of PY-NLS cargoes, we show that the fission yeast ortholog of human Kapβ2, Kap104, binds to recombinant Pab2 and is required for Pab2 nuclear localization. The absence of arginine methylation in a basic region N-terminal to the PY-core motif of Pab2 did not affect its nuclear localization. However, in the context of a sub-optimal PY-NLS, we found that Pab2 was more efficiently targeted to the nucleus in the absence of arginine methylation, suggesting that this modification can affect the import kinetics of a PY-NLS cargo. Although a sequence resembling a PY-NLS motif can be found in the human Pab2 ortholog, PABPN1, our results indicate that neither a functional PY-NLS nor Kapβ2 activity are required to promote entry of PABPN1 into the nucleus of human cells. Our findings describe the mechanism by which Pab2 is imported into the nucleus, providing the first example of a PY-NLS import system in fission yeast. In addition, this study suggests the existence of alternative or redundant nuclear import pathways for human PABPN1. PMID:23279110

  10. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization.

    PubMed

    Shiheido, Hirokazu; Shimizu, Jun

    2015-02-20

    BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. PMID:25600804

  11. Semiconductor band gap localization via Gaussian function

    NASA Astrophysics Data System (ADS)

    Ullrich, B.; Brown, G. J.; Xi, H.

    2012-10-01

    To determine the band gap of bulk semiconductors with transmission spectroscopy alone is considered as an extremely difficult task because in the higher energy range, approaching and exceeding the band gap energy, the material is opaque yielding no useful data to be recorded. In this paper, by investigating the transmission of industrial GaSb wafers with a thickness of 500 µm, we demonstrate how these obstacles of transmission spectroscopy can be overcome. The key is the transmission spectrums’ derivative, which coincides with the Gaussian function. This understanding can be used to transfer Beers’ law in an integral form opening the pathway of band gap determinations based on mathematical parameters only. The work also emphasizes the correlation between the thermal band gap variation and Debye temperature.

  12. Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8

    PubMed Central

    Takeda, Kojiro; Tonthat, Nam K.; Glover, Tiffany; Xu, Weijun; Koonin, Eugene V.; Yanagida, Mitsuhiro; Schumacher, Maria A.

    2011-01-01

    Degradation of nuclear proteins by the 26S proteasome is essential for cell viability. In yeast, the nuclear envelope protein Cut8 mediates nuclear proteasomal sequestration by an uncharacterized mechanism. Here we describe structures of Schizosaccharomyces pombe Cut8, which shows that it contains a unique, modular fold composed of an extended N-terminal, lysine-rich segment that when ubiquitinated binds the proteasome, a dimer domain followed by a six-helix bundle connected to a flexible C tail. The Cut8 six-helix bundle shows structural similarity to 14-3-3 phosphoprotein-binding domains, and binding assays show that this domain is necessary and sufficient for liposome and cholesterol binding. Moreover, specific mutations in the 14-3-3 regions corresponding to putative cholesterol recognition/interaction amino acid consensus motifs abrogate cholesterol binding. In vivo studies confirmed that the 14-3-3 region is necessary for Cut8 membrane localization and that dimerization is critical for its function. Thus, the data reveal the Cut8 organization at the nuclear envelope. Reconstruction of Cut8 evolution suggests that it was present in the last common ancestor of extant eukaryotes and accordingly that nuclear proteasomal sequestration is an ancestral eukaryotic feature. The importance of Cut8 for cell viability and its absence in humans suggests it as a possible target for the development of specific chemotherapeutics against invasive fungal infections. PMID:21976488

  13. Proteolytic cleavage, trafficking, and functions of nuclear receptor tyrosine kinases.

    PubMed

    Chen, Mei-Kuang; Hung, Mien-Chie

    2015-10-01

    Intracellular localization has been reported for over three-quarters of receptor tyrosine kinase (RTK) families in response to environmental stimuli. Internalized RTK may bind to non-canonical substrates and affect various cellular processes. Many of the intracellular RTKs exist as fragmented forms that are generated by γ-secretase cleavage of the full-length receptor, shedding, alternative splicing, or alternative translation initiation. Soluble RTK fragments are stabilized and intracellularly transported into subcellular compartments, such as the nucleus, by binding to chaperone or transcription factors, while membrane-bound RTKs (full-length or truncated) are transported from the plasma membrane to the ER through the well-established Rab- or clathrin adaptor protein-coated vesicle retrograde trafficking pathways. Subsequent nuclear transport of membrane-bound RTK may occur via two pathways, INFS or INTERNET, with the former characterized by release of receptors from the ER into the cytosol and the latter characterized by release of membrane-bound receptor from the ER into the nucleoplasm through the inner nuclear membrane. Although most non-canonical intracellular RTK signaling is related to transcriptional regulation, there may be other functions that have yet to be discovered. In this review, we summarize the proteolytic processing, intracellular trafficking and nuclear functions of RTKs, and discuss how they promote cancer progression, and their clinical implications. PMID:26096795

  14. Localization and function of three monothiol glutaredoxins in Schizosaccharomyces pombe

    SciTech Connect

    Chung, Woo-Hyun; Kim, Kyoung-Dong; Roe, Jung-Hye . E-mail: jhroe@plaza.snu.ac.kr

    2005-05-06

    The fission yeast Schizosaccharomyces pombe contains two dithiol glutaredoxins (Grx1 and Grx2) and genes for three putative monothiol glutaredoxins (grx3, 4, and 5). We investigated the expression, sub-cellular localization, and functions of the three monothiol glutaredoxins. Fluorescence microscopy revealed that Grx3 is targeted to nuclear rim and endoplasmic reticulum, Grx4 primarily to the nucleus, and Grx5 to mitochondria. Null mutation of grx3 did not significantly affect growth and resistance against various oxidants, whereas grx5 mutation caused slow growth and sensitivity toward oxidants such as hydrogen peroxide, paraquat, and diamide. The grx2grx5 double mutation, deficient in all mitochondrial glutaredoxins, caused further retardation in growth and severe sensitivity toward all the oxidants tested. The grx4 mutation was not viable, suggesting a critical role of Grx4 for the physiology of S. pombe. Overproduction of Grx3 and Grx5, but not the truncated form of Grx5 without mitochondrial target sequence, severely retarded growth as Grx2 did, supporting the idea that Grx2, 3, and 5 are targeted to organellar compartments. Our results propose a distinct role for each glutaredoxin to maintain thiol redox balance, and hence the growth and stress resistance, of the fission yeast.

  15. The Nuclear Energy Density Functional Formalism

    NASA Astrophysics Data System (ADS)

    Duguet, T.

    The present document focuses on the theoretical foundations of the nuclear energy density functional (EDF) method. As such, it does not aim at reviewing the status of the field, at covering all possible ramifications of the approach or at presenting recent achievements and applications. The objective is to provide a modern account of the nuclear EDF formalism that is at variance with traditional presentations that rely, at one point or another, on a Hamiltonian-based picture. The latter is not general enough to encompass what the nuclear EDF method represents as of today. Specifically, the traditional Hamiltonian-based picture does not allow one to grasp the difficulties associated with the fact that currently available parametrizations of the energy kernel E[g',g] at play in the method do not derive from a genuine Hamilton operator, would the latter be effective. The method is formulated from the outset through the most general multi-reference, i.e. beyond mean-field, implementation such that the single-reference, i.e. "mean-field", derives as a particular case. As such, a key point of the presentation provided here is to demonstrate that the multi-reference EDF method can indeed be formulated in a mathematically meaningful fashion even if E[g',g] does not derive from a genuine Hamilton operator. In particular, the restoration of symmetries can be entirely formulated without making any reference to a projected state, i.e. within a genuine EDF framework. However, and as is illustrated in the present document, a mathematically meaningful formulation does not guarantee that the formalism is sound from a physical standpoint. The price at which the latter can be enforced as well in the future is eventually alluded to.

  16. Local-hybrid functional based on the correlation length

    SciTech Connect

    Johnson, Erin R.

    2014-09-28

    Local-hybrid functionals involve position-dependent mixing of Hartree-Fock and density-functional exchange, which should allow improved performance relative to conventional hybrids by reducing the inherent delocalization error and improving the long-range behaviour. Herein, the same-spin correlation length, obtained from the Fermi-hole radius, is used as the mixing parameter. The performance of the resulting local-hybrid functional is assessed for standard thermochemical and kinetics benchmarks. The local hybrid is shown to perform significantly better than the corresponding global hybrid in almost all cases.

  17. Nuclear targeting of the maize R protein requires two nuclear localization sequences

    SciTech Connect

    Shieh, M.W.; Raikhel, N.V. ); Wessler, S.R. )

    1993-02-01

    Previous genetic and structural evidence indicates that the maize R gene encodes a nuclear transcriptional activating factor. In-frame carboxyl- and amino-terminal fusions of the R gene to the reporter gene encoding [beta]-glucuronidase (GUS) were sufficient to direct GUS to the nucleus of the transiently transformed onion (Allium cepa) epidermal cells. Further analysis of chimeric constructs containing regions of the R gene fused to the GUS cDNA revealed three specific nuclear localization sequences (NLSs) that were capable of redirecting the GUS protein to the nucleus. Amino-terminal NLS-A (amino acids 100-109, GDRRAAPARP) contained several arginine residues; a similar localization signal is found in only a few viral proteins. The medial NLS-M (amino acids 419-428, MSERKRREKL) is a simian virus 40 large T antigen-type NLS, and the carboxyl-terminal NLS-C (amino acids 598-610, MISESLRKAIGKR) is a mating type [alpha]2 type. NLSs M and C are independently sufficient to direct the GUS protein to the nucleus when it is fused at the amino terminus of GUS, whereas NLS-A fused to GUS partitioned between the nucleus and cytoplasm. Similar partitioning was observed when localization signals NLS-A and NLS-C were independently fused to the carboxy-terminal portion of GUS. A sequential deletion of the localization signals indicated that the amino-terminal and carboxyl-terminal fusions of R and GUS were redirected to the nucleus only when both NLS-A and -M, or NLS-C and -M, were present. These results indicate that multiple localization signals are necessary for nuclear targeting of this protein. The conservation of the localization signals within the alleles of R and similar proteins from other organisms is also discussed. 45 refs., 6 figs.

  18. The black hole mass function derived from local spiral galaxies

    SciTech Connect

    Davis, Benjamin L.; Berrier, Joel C.; Shields, Douglas W.; Kennefick, Daniel; Kennefick, Julia; Seigar, Marc S.; Lacy, Claud H. S.; Hartley, Matthew T.

    2014-07-10

    We present our determination of the nuclear supermassive black hole (SMBH) mass function for spiral galaxies in the local universe, established from a volume-limited sample consisting of a statistically complete collection of the brightest spiral galaxies in the southern (δ < 0°) hemisphere. Our SMBH mass function agrees well at the high-mass end with previous values given in the literature. At the low-mass end, inconsistencies exist in previous works that still need to be resolved, but our work is more in line with expectations based on modeling of black hole evolution. This low-mass end of the spectrum is critical to our understanding of the mass function and evolution of black holes since the epoch of maximum quasar activity. The sample is defined by a limiting luminosity (redshift-independent) distance, D{sub L} = 25.4 Mpc (z = 0.00572) and a limiting absolute B-band magnitude, M{sub B}=−19.12. These limits define a sample of 140 spiral galaxies, with 128 measurable pitch angles to establish the pitch angle distribution for this sample. This pitch-angle distribution function may be useful in the study of the morphology of late-type galaxies. We then use an established relationship between the logarithmic spiral arm pitch angle and the mass of the central SMBH in a host galaxy in order to estimate the mass of the 128 respective SMBHs in this volume-limited sample. This result effectively gives us the distribution of mass for SMBHs residing in spiral galaxies over a lookback time, t{sub L} ≤ 82.1 h{sub 67.77}{sup −1} Myr and contained within a comoving volume, V{sub C} = 3.37 × 10{sup 4} h{sub 67.77}{sup −3} Mpc{sup 3}. We estimate that the density of SMBHs residing in spiral galaxies in the local universe is ρ=5.54{sub −2.73}{sup +6.55} × 10{sup 4} h{sub 67.77}{sup 3} M{sub ☉} Mpc{sup –3}. Thus, our derived cosmological SMBH mass density for spiral galaxies is Ω{sub BH}=4.35{sub −2.15}{sup +5.14} × 10{sup –7} h{sub 67.77}. Assuming that

  19. Red Light-Regulated Reversible Nuclear Localization of Proteins in Mammalian Cells and Zebrafish.

    PubMed

    Beyer, Hannes M; Juillot, Samuel; Herbst, Kathrin; Samodelov, Sophia L; Müller, Konrad; Schamel, Wolfgang W; Römer, Winfried; Schäfer, Eberhard; Nagy, Ferenc; Strähle, Uwe; Weber, Wilfried; Zurbriggen, Matias D

    2015-09-18

    Protein trafficking in and out of the nucleus represents a key step in controlling cell fate and function. Here we report the development of a red light-inducible and far-red light-reversible synthetic system for controlling nuclear localization of proteins in mammalian cells and zebrafish. First, we synthetically reconstructed and validated the red light-dependent Arabidopsis phytochrome B nuclear import mediated by phytochrome-interacting factor 3 in a nonplant environment and support current hypotheses on the import mechanism in planta. On the basis of this principle we next regulated nuclear import and activity of target proteins by the spatiotemporal projection of light patterns. A synthetic transcription factor was translocated into the nucleus of mammalian cells and zebrafish to drive transgene expression. These data demonstrate the first in vivo application of a plant phytochrome-based optogenetic tool in vertebrates and expand the repertoire of available light-regulated molecular devices. PMID:25803699

  20. Automated local bright feature image analysis of nuclear proteindistribution identifies changes in tissue phenotype

    SciTech Connect

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-02-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues.

  1. Local Function Conservation in Sequence and Structure Space

    PubMed Central

    Weinhold, Nils; Sander, Oliver; Domingues, Francisco S.; Lengauer, Thomas; Sommer, Ingolf

    2008-01-01

    We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation by means of logistic curves. Based on this analysis, we propose a method for predicting molecular function of a query protein with known structure but unknown function. The prediction method is rigorously assessed and compared with a previously published function predictor. Furthermore, we apply the method to 500 functionally unannotated PDB structures and discuss selected examples. The proposed approach provides a simple yet consistent statistical model for the complex relations between protein sequence, structure, and function. The GOdot method is available online (http://godot.bioinf.mpi-inf.mpg.de). PMID:18604264

  2. Nuclear-cytoplasmic shuttling of APC regulates beta-catenin subcellular localization and turnover.

    PubMed

    Henderson, B R

    2000-09-01

    Mutational inactivation of the APC gene is a key early event in the development of familial adenomatous polyposis and colon cancer. APC suppresses tumour progression by promoting degradation of the oncogenic transcriptional activator beta-catenin. APC gene mutations can lead to abnormally high levels of beta-catenin in the nucleus, and the consequent activation of transforming genes. Here, we show that APC is a nuclear-cytoplasmic shuttling protein, and that it can function as a beta-catenin chaperone. APC contains two active nuclear export sequences (NES) at the amino terminus, and mutagenesis of these conserved motifs blocks nuclear export dependent on the CRM1 export receptor. Treatment of cells with the CRM1-specific export inhibitor leptomycin B shifts APC from cytoplasm to nucleus. beta-catenin localization is also regulated by CRM1, but in an APC-dependent manner. Transient expression of wild-type APC in SW480 (APCmut/mut) colon cancer cells enhances nuclear export and degradation of beta-catenin, and these effects can be blocked by mutagenesis of the APC NES. These findings suggest that wild-type APC controls the nuclear accumulation of beta-catenin by a combination of nuclear export and cytoplasmic degradation. PMID:10980707

  3. Local renormalization group functions from quantum renormalization group and holographic bulk locality

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu

    2015-06-01

    The bulk locality in the constructive holographic renormalization group requires miraculous cancellations among various local renormalization group functions. The cancellation is not only from the properties of the spectrum but from more detailed aspects of operator product expansions in relation to conformal anomaly. It is remarkable that one-loop computation of the universal local renormalization group functions in the weakly coupled limit of the super Yang-Mills theory fulfils the necessary condition for the cancellation in the strongly coupled limit in its SL(2, Z) duality invariant form. From the consistency between the quantum renormalization group and the holographic renormalization group, we determine some unexplored local renormalization group functions (e.g. diffusive term in the beta function for the gauge coupling constant) in the strongly coupled limit of the planar super Yang-Mills theory.

  4. How do electron localization functions describe π-electron delocalization?

    PubMed

    Steinmann, Stephan N; Mo, Yirong; Corminboeuf, Clemence

    2011-12-14

    Scalar fields provide an intuitive picture of chemical bonding. In particular, the electron localization function (ELF) has proven to be highly valuable in interpreting a broad range of bonding patterns. The discrimination between enhanced or reduced electron (de)localization within cyclic π-conjugated systems remains, however, challenging for ELF. In order to clearly distinguish between the local properties of ten highly and weakly π-(de)localized prototype systems, we compare the ELFs of both the canonical wave functions and electron-localized states (diabatic) with those of two closely related scalar fields: the electron localizability indicator (ELI-D) and the localized orbital locator (LOL). The simplest LOL function distinguishes enhanced from weak π-(de)localization in an insightful and reliable manner. LOL offers the finest contrast between annulenes with 4n/4n + 2 π electrons and their inorganic analogues as well as between hyperconjugated cyclopentadiene derivatives. LOL(π) also gives an appealing and intuitive picture of the π-bond. In contrast, the most popular ELF fails to capture subtle contrasting local electronic properties and suffers from the arbitrariness of the σ/π dissection. The orbital separation of the most recent ELI-D is clear-cut but the interpretations sometime less straightforward in the present context. PMID:21660323

  5. O-GlcNAc-glycosylation of {beta}-catenin regulates its nuclear localization and transcriptional activity

    SciTech Connect

    Sayat, Ria; Leber, Brian; Grubac, Vanja; Wiltshire, Lesley; Persad, Sujata

    2008-09-10

    {beta}-catenin plays a role in intracellular adhesion and regulating gene expression. The latter role is associated with its oncogenic properties. Phosphorylation of {beta}-catenin controls its intracellular expression but mechanism/s that regulates the nuclear localization of {beta}-catenin is unknown. We demonstrate that O-GlcNAc glycosylation (O-GlcNAcylation) of {beta}-catenin negatively regulates its levels in the nucleus. We show that normal prostate cells (PNT1A) have significantly higher amounts of O-GlcNAcylated {beta}-catenin compared to prostate cancer (CaP) cells. The total nuclear levels of {beta}-catenin are higher in the CaP cells than PNT1A but only a minimal fraction of the nuclear {beta}-catenin in the CaP cells are O-GlcNAcylated. Increasing the levels of O-GlcNAcylated {beta}-catenin in the CaP cells with PUGNAc (O- (2-acetamido-2-deoxy-D-gluco-pyranosylidene) amino-N-phenylcarbamate) treatment is associated with a progressive decrease in the levels of {beta}-catenin in the nucleus. TOPFlash reporter assay and mRNA expressions of {beta}-catenin's target genes indicate that O-GlcNAcylation of {beta}-catenin results in a decrease in its transcriptional activity. We define a novel modification of {beta}-catenin that regulates its nuclear localization and transcriptional function.

  6. Interaction with the histone chaperone Vps75 promotes nuclear localization and HAT activity of Rtt109 in vivo

    PubMed Central

    Keck, Kristin M.; Pemberton, Lucy F.

    2011-01-01

    Modification of histones is critical for the regulation of all chromatin-templated processes. Yeast Rtt109 is a histone acetyltransferase (HAT) that acetylates H3 lysines 9, 27 and 56. Rtt109 associates with and is stabilized by Nap1 family histone chaperone Vps75. Our data suggest Vps75 and Nap1 have some overlapping functions despite their different cellular localization and histone binding specificity. We determined that Vps75 contains a classical nuclear localization signal and is imported by Kap60–Kap95. Rtt109 nuclear localization depends on Vps75, and nuclear localization of the Vps75-Rtt109 complex is not critical for Rtt109-dependent functions, suggesting Rtt109 may be able to acetylate nascent histones before nuclear import. To date, the effects of VPS75 deletion on Rtt109 function had not been separated from the resulting Rtt109 degradation; thus, we used an Rtt109 mutant lacking the Vps75-interaction domain that is stable without Vps75. Our data show that in addition to promoting Rtt109 stability, Vps75 binding is necessary for Rtt109 acetylation of the H3 tail. Direct interaction of Vps75 with H3 likely allows Rtt109 access to the histone tail. Furthermore, our genetic interaction data support the idea of Rtt109-independent functions of Vps75. In summary, our data suggest that Vps75 influences chromatin structure by regulating histone modification and through its histone chaperone functions. PMID:21463458

  7. Comments on the locality in density-functional theory

    SciTech Connect

    Lindgren, Ingvar; Salomonson, Sten

    2003-05-01

    The 'locality hypothesis' in density-functional theory (DFT), implying that the functional derivative is equivalent to a multiplicative local function, forms the basis of models of Kohn-Sham type. This has been generally accepted by the community since the advent of the model, and has later been formally proved for a large class of functionals. The hypothesis has recently been questioned by Nesbet [Phys. Rev. A 58, R12 (1998) and Phys. Rev. A 65, 010502 (2001)], who claims that it fails for the kinetic-energy functional for a system with more than two noninteracting electrons with a nondegenerate ground state. This conclusion has been questioned by Gal [Phys. Rev. A 62, 044501 (2000)] and by Holas and March [Phys. Rev. A 64, 016501 (2001)]. We claim that the arguments of Nesbet are incorrect, since the orbital functional used for the kinetic energy is not a unique functional of the total density in the domain of unnormalized orbitals. We have demonstrated that with a proper definition of the kinetic energy, which is a unique density functional also in the unnormalized region, the derivative can be represented by a single local multiplicative function for all v-representable densities. Therefore, we consider the controversy connected with the issue raised by Nesbet as resolved. We believe that the proof of the differentiability given here can be extended to larger groups of DFT functionals, and works along these lines are in progress.

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

    PubMed

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

    2016-05-01

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

  9. The local characteristic function of interplanetary particle propagation

    NASA Technical Reports Server (NTRS)

    Green, G.; Schlueter, W.

    1985-01-01

    An easily measurable intensity function which characterizes the interplanetary propagation of charged solar flare particles is presented. This function is nearly time invariant during a solar event despite the large variations of intensity and anisotropy, but varies from event to event. It characterizes the systematic and stochastic forces of the interplanetary magnetic field which focus and scatter the particles in pitch angle. The model of focused transport shows that this function is essentially determined by the local shape and amplitude of the pitch angle diffusion coefficient kappa (mu) and by the local value of the focusing length. The time profile of the solar particle injection is typically of negligible influence. The local characteristic function may be used as a powerful new tool for a systematic analysis of flare particle angular distributions, Examples are given.

  10. Identification and characterization of multiple conserved nuclear localization signals within adenovirus E1A

    SciTech Connect

    Marshall, Kris S.; Cohen, Michael J.; Fonseca, Greg J.; Todorovic, Biljana; King, Cason R.; Yousef, Ahmed F.; Zhang, Zhiying; Mymryk, Joe S.

    2014-04-15

    The human adenovirus 5 (HAdV-5) E1A protein has a well defined canonical nuclear localization signal (NLS) located at its C-terminus. We used a genetic assay in the yeast Saccharomyces cerevisiae to demonstrate that the canonical NLS is present and functional in the E1A proteins of each of the six HAdV species. This assay also detects a previously described non-canonical NLS within conserved region 3 and a novel active NLS within the N-terminal/conserved region 1 portion of HAdV-5 E1A. These activities were also present in the E1A proteins of each of the other five HAdV species. These results demonstrate that, despite substantial differences in primary sequence, HAdV E1A proteins are remarkably consistent in that they contain one canonical and two non-canonical NLSs. By utilizing independent mechanisms, these multiple NLSs ensure nuclear localization of E1A in the infected cell. - Highlights: • HAdV E1A uses multiple mechanisms for nuclear import. • We identified an additional non-canonical NLS in the N-terminal/CR1 portion of E1A. • The new NLS does not contact importin-alpha directly. • All NLSs are functionally conserved in the E1A proteins of all 6 HAdV species.

  11. A COMPARATIVE ANALYSIS BETWEEN FRANCE AND JAPAN ON LOCAL GOVERNMENTS' INVOLVEMENT IN NUCLEAR SAFETY GOVERNANCE

    NASA Astrophysics Data System (ADS)

    Sugawara, Shin-Etsu; Shiroyama, Hideaki

    This paper shows a comparative analysis between France and Japan on the way of the local governments' involvement in nuclear safety governance through some interviews. In France, a law came into force that requires related local governments to establish "Commision Locale d'Information" (CLI), which means the local governments officially involve in nuclear regulatory activity. Meanwhile, in Japan, related local governments substantially involve in the operation of nuclear facilities through the "safety agreements" in spite of the lack of legal authority. As a result of comparative analysis, we can point out some institutional input from French cases as follows: to clarify the local governments' roles in the nuclear regulation system, to establish the official channels of communication among nuclear utilities, national regulatory authorities and local governments, and to stipulate explicitly the transparency as a purpose of safety regulation.

  12. Nuclear import of influenza B virus nucleoprotein: Involvement of an N-terminal nuclear localization signal and a cleavage-protection motif

    SciTech Connect

    Wanitchang, Asawin; Narkpuk, Jaraspim; Jongkaewwattana, Anan

    2013-08-15

    The nucleoprotein of influenza B virus (BNP) shares several characteristics with its influenza A virus counterpart (ANP), including localization in the host's nucleus. However, while the nuclear localization signal(s) (NLS) of ANP are well characterized, little is known about those of BNP. In this study, we showed that the fusion protein bearing the BNP N-terminus fused with GFP (N70–GFP) is exclusively nuclear, and identified a highly conserved KRXR motif spanning residues 44–47 as a putative NLS. In addition, we demonstrated that residues 3–15 of BNP, though not an NLS, are also crucial for nuclear import. Results from mutational analyses of N70–GFP and the full-length BNP suggest that this region may be required for protection of the N-terminus from proteolytic cleavage. Altogether, we propose that the N-terminal region of BNP contains the NLS and cleavage-protection motif, which together drive its nuclear localization. - Highlights: • The N-terminal region of BNP is required for nuclear accumulation. • The conserved motif at position 44–47 is a putative nuclear localization signal. • The first 15 amino acids of BNP may function as a cleavage-protection motif. • BNP may get access to the nucleus via a mechanism distinct from ANP.

  13. A Local Representation of The Dielectric Response Function

    NASA Astrophysics Data System (ADS)

    Lu, Deyu; Ge, Xiaochuan

    2015-03-01

    The screened dielectric response function (χ) is a fundamental physical quantity that captures the many-electron correlation effects, key to the accurate description of van der Waals dispersion interaction in the ground state and a range of excited state properties. Although χ is non-local by definition, a real space partition of χ onto local structural motifs can help us gain further physical insight into, e.g., effective local screening properties. Because the construction of bare response function, χ0, is associated with the product of electron - hole orbitals, standard localization procedures for electron wave functions can not be directly applied. In this work, we propose a new method to decompose χ0 into contributions from local response functions. Exemplary results of finite and bulk systems are discussed. Research carried out at the Center for Functional Nanomaterials, Brookhaven National Laboratory, which is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

  14. A Wnt-kinase network alters nuclear localization of TCF-1 in colon cancer

    PubMed Central

    Najdi, Rani; Syed, Adeela; Arce, Laura; Theisen, Heidi; Ting, Ju-Hui T.; Atcha, Fawzia; Nguyen, Anthony V.; Martinez, Micaela; Holcombe, Randall F.; Edwards, Robert A.; Marsh, J. Lawrence; Waterman, Marian L.

    2009-01-01

    Constitutive activation of the Wnt/β-catenin pathway has been implicated as the primary cause of colon cancer. However, the major transducers of Wnt signaling in the intestine, TCF-1 and TCF-4, have opposing functions. Knock-out of TCF-4 suppresses growth and maintenance of crypt stem cells, while knock-out of TCF-1 leads to adenomas. These phenotypes suggest that TCF-4 is Wnt-promoting while TCF-1 acts like a tumor suppressor. Our study of TCF expression in human colon crypts reveals a mechanistic basis for this paradox. In normal colon cells, a dominant negative isoform of TCF-1 (dnTCF-1) is expressed that is equally distributed between nuclear and cytoplasmic compartments. In colon cancer cells, TCF-1 is predominantly cytoplasmic. Localization is due to active nuclear export and is directed by an autocrine-acting Wnt ligand that requires CaMKII activity for secretion and a downstream step in the export pathway. TCF-4 remains nuclear; its unopposed activity is accompanied by downregulation of dnTCF-1 and increased expression of full-length isoforms. Thus, the dnTCF-1, TCF-4 balance is corrupted in cancer by two mechanisms, a Wnt/CaMKII kinase signal for nuclear export, and decreased dnTCF-1 expression. We propose that dnTCF-1 provides homeostatic regulation of Wnt signaling and growth in normal colon and alterations in nuclear export and promoter usage contribute to aberrant Wnt activity in colon cancer. PMID:19749792

  15. Cell cycle regulation of Greatwall kinase nuclear localization facilitates mitotic progression

    PubMed Central

    Wang, Peng; Galan, Jacob A.; Normandin, Karine; Bonneil, Éric; Hickson, Gilles R.; Roux, Philippe P.; Thibault, Pierre

    2013-01-01

    Cell division requires the coordination of critical protein kinases and phosphatases. Greatwall (Gwl) kinase activity inactivates PP2A-B55 at mitotic entry to promote the phosphorylation of cyclin B–Cdk1 substrates, but how Gwl is regulated is poorly understood. We found that the subcellular localization of Gwl changed dramatically during the cell cycle in Drosophila. Gwl translocated from the nucleus to the cytoplasm in prophase. We identified two critical nuclear localization signals in the central, poorly characterized region of Gwl, which are required for its function. The Polo kinase associated with and phosphorylated Gwl in this region, promoting its binding to 14-3-3ε and its localization to the cytoplasm in prophase. Our results suggest that cyclin B–Cdk1 phosphorylation of Gwl is also required for its nuclear exclusion by a distinct mechanism. We show that the nucleo-cytoplasmic regulation of Gwl is essential for its functions in vivo and propose that the spatial regulation of Gwl at mitotic entry contributes to the mitotic switch. PMID:23857770

  16. The Redox State of SECIS Binding Protein 2 Controls Its Localization and Selenocysteine Incorporation Function

    PubMed Central

    Papp, Laura V.; Lu, Jun; Striebel, Frank; Kennedy, Derek; Holmgren, Arne; Khanna, Kum Kum

    2006-01-01

    Selenoproteins are central controllers of cellular redox homeostasis. Incorporation of selenocysteine (Sec) into selenoproteins employs a unique mechanism to decode the UGA stop codon. The process requires the Sec insertion sequence (SECIS) element, tRNASec, and protein factors including the SECIS binding protein 2 (SBP2). Here, we report the characterization of motifs within SBP2 that regulate its subcellular localization and function. We show that SBP2 shuttles between the nucleus and the cytoplasm via intrinsic, functional nuclear localization signal and nuclear export signal motifs and that its nuclear export is dependent on the CRM1 pathway. Oxidative stress induces nuclear accumulation of SBP2 via oxidation of cysteine residues within a redox-sensitive cysteine-rich domain. These modifications are efficiently reversed in vitro by human thioredoxin and glutaredoxin, suggesting that these antioxidant systems might regulate redox status of SBP2 in vivo. Depletion of SBP2 in cell lines using small interfering RNA results in a decrease in Sec incorporation, providing direct evidence for its requirement for selenoprotein synthesis. Furthermore, Sec incorporation is reduced substantially after treatment of cells with agents that cause oxidative stress, suggesting that nuclear sequestration of SBP2 under such conditions may represent a mechanism to regulate the expression of selenoproteins. PMID:16782878

  17. Characterizing dynamic local functional connectivity in the human brain.

    PubMed

    Deng, Lifu; Sun, Junfeng; Cheng, Lin; Tong, Shanbao

    2016-01-01

    Functional connectivity (FC), obtained from functional magnetic resonance imaging (fMRI), brings insights into the functional organization of the brain. Recently, rich and complex behaviour of brain has been revealed by the dynamic fluctuation of FC, which had previously been regarded as confounding 'noise'. While the dynamics of long-distance, inter-regional FC has been extensively studied, the dynamics of local FC within a few millimetres in space remains largely unexplored. In this study, the local FC was depicted by regional homogeneity (ReHo), and the dynamics of local FC was obtained using sliding windows method. We observed a robust positive correlation between ReHo and its temporal variability, which was shown to be an intrinsic feature of the brain rather than a pure stochastic effect. Furthermore, fluctuation of ReHo was associated with global functional organization: (i) brain regions with higher centrality of inter-regional FC tended to possess higher ReHo variability; (ii) coherence of ReHo fluctuation was higher within brain's functional modules. Finally, we observed alteration of ReHo variability during a motor task compared with resting-state. Our findings associated the temporal fluctuation of ReHo with brain function, opening up the possibility of dynamic local FC study in the future. PMID:27231194

  18. Characterizing dynamic local functional connectivity in the human brain

    PubMed Central

    Deng, Lifu; Sun, Junfeng; Cheng, Lin; Tong, Shanbao

    2016-01-01

    Functional connectivity (FC), obtained from functional magnetic resonance imaging (fMRI), brings insights into the functional organization of the brain. Recently, rich and complex behaviour of brain has been revealed by the dynamic fluctuation of FC, which had previously been regarded as confounding ‘noise’. While the dynamics of long-distance, inter-regional FC has been extensively studied, the dynamics of local FC within a few millimetres in space remains largely unexplored. In this study, the local FC was depicted by regional homogeneity (ReHo), and the dynamics of local FC was obtained using sliding windows method. We observed a robust positive correlation between ReHo and its temporal variability, which was shown to be an intrinsic feature of the brain rather than a pure stochastic effect. Furthermore, fluctuation of ReHo was associated with global functional organization: (i) brain regions with higher centrality of inter-regional FC tended to possess higher ReHo variability; (ii) coherence of ReHo fluctuation was higher within brain’s functional modules. Finally, we observed alteration of ReHo variability during a motor task compared with resting-state. Our findings associated the temporal fluctuation of ReHo with brain function, opening up the possibility of dynamic local FC study in the future. PMID:27231194

  19. Density functional theory calculations of nuclear quadrupole coupling constants with calibrated 14N quadrupole moments

    NASA Astrophysics Data System (ADS)

    Sicilia, E.; de Luca, G.; Chiodo, S.; Russo, N.; Calaminici, P.; Koster, A. M.; Jug, K.

    Density functional calculations of the electric field gradient tensor at the nitrogen nucleus in 13 test molecules, containing 14 nitrogen sites, have been performed using the linear combination of Gaussian-type orbital Kohn-Sham density functional theory (LCGTO-KSDFT) approach. Local and gradient corrected functionals were used for all-electron calculations. All the molecular structures were optimized at their respective levels of theory with extended basis sets. Calibrated 14N nuclear quadrupole moments were obtained through a fitting procedure between calculated electric field gradients and experimental nuclear quadrupole coupling constants of the test set of molecules for each basis set and functional considered. With these calibrated 14N nuclear quadrupole moments, the nuclear quadrupole coupling constants of the following selected systems were determined: fluoromethylisonitrile, pyridine, pyrrole, imadazole, pyrazole, 1,8-bis(dimethyl-amino)naphthalene, cyclotetramethylenetetranitramine, cocaine and heroin.

  20. Role of SAMHD1 nuclear localization in restriction of HIV-1 and SIVmac

    PubMed Central

    2012-01-01

    Background SAMHD1 is a nuclear protein that blocks lentiviral infection before reverse transcription in macrophages and dendritic cells. The viral accessory protein Vpx overcomes the SAMHD1-mediated lentiviral block by inducing its proteasomal degradation. Results Here, we identified the nuclear localization signal (NLS) of SAMHD1, and studied its contribution to restriction of HIV-1 and SIVmac. By studying the cellular distribution of different SAMHD1 variants, we mapped the nuclear localization of SAMHD1 to residues 11KRPR14. Mutagenesis of these residues changed the cellular distribution of SAMHD1 from the nucleus to the cytoplasm. SAMHD1 mutants that lost nuclear localization restricted HIV-1 and SIV as potently as the wild type protein. Interestingly, SAMHD1 mutants that localized to the cytoplasm were not degraded by nuclear Vpx alleles. Therefore, nuclear Vpx alleles require nuclear localization of SAMHD1 in order to induce its degradation. In agreement, SIVmac viruses encoding Vpx did not overcome the restriction imposed by the cytoplasmic variants of SAMHD1. Conclusions We mapped the NLS of SAMHD1 to residues 11KRPR14 and studied the contribution of SAMHD1 nuclear localization to restriction of HIV-1 and SIV. These experiments demonstrate that cytoplasmic variants of SAMHD1 potently block lentiviral infection and are resistant to Vpx-mediated degradation. The nuclear Vpx alleles studied here are only capable of degrading a nuclearly localized SAMHD1 suggesting that Vpx-mediated degradation of SAMHD1 is initiated in the nucleus. PMID:22691373

  1. Interaction between a plasma membrane-localized ankyrin-repeat protein ITN1 and a nuclear protein RTV1

    SciTech Connect

    Sakamoto, Hikaru; Sakata, Keiko; Kusumi, Kensuke; Kojima, Mikiko; Sakakibara, Hitoshi; Iba, Koh

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer ITN1, a plasma membrane ankyrin protein, interacts with a nuclear DNA-binding protein RTV1. Black-Right-Pointing-Pointer The nuclear transport of RTV1 is partially inhibited by interaction with ITN1. Black-Right-Pointing-Pointer RTV1 can promote the nuclear localization of ITN1. Black-Right-Pointing-Pointer Both overexpression of RTV1 and the lack of ITN1 increase salicylic acids sensitivity in plants. -- Abstract: The increased tolerance to NaCl 1 (ITN1) protein is a plasma membrane (PM)-localized protein involved in responses to NaCl stress in Arabidopsis. The predicted structure of ITN1 is composed of multiple transmembrane regions and an ankyrin-repeat domain that is known to mediate protein-protein interactions. To elucidate the molecular functions of ITN1, we searched for interacting partners using a yeast two-hybrid assay, and a nuclear-localized DNA-binding protein, RTV1, was identified as a candidate. Bimolecular fluorescence complementation analysis revealed that RTV1 interacted with ITN1 at the PM and nuclei in vivo. RTV1 tagged with red fluorescent protein localized to nuclei and ITN1 tagged with green fluorescent protein localized to PM; however, both proteins localized to both nuclei and the PM when co-expressed. These findings suggest that RTV1 and ITN1 regulate the subcellular localization of each other.

  2. Two Nuclear Localization Signals in USP1 Mediate Nuclear Import of the USP1/UAF1 Complex

    PubMed Central

    Garcia-Santisteban, Iraia; Zorroza, Kerman; Rodriguez, Jose Antonio

    2012-01-01

    The human deubiquitinase USP1 plays important roles in cancer-related processes, such as the DNA damage response, and the maintenance of the undifferentiated state of osteosarcoma cells. USP1 deubiquitinase activity is critically regulated by its interaction with the WD40 repeat-containing protein UAF1. Inhibiting the function of the USP1/UAF1 complex sensitizes cancer cells to chemotherapy, suggesting that this complex is a relevant anticancer target. Intriguingly, whereas UAF1 has been reported to locate in the cytoplasm, USP1 is a nuclear protein, although the sequence motifs that mediate its nuclear import have not been functionally characterized. Here, we identify two nuclear localization signals (NLSs) in USP1 and show that these NLSs mediate the nuclear import of the USP1/UAF1 complex. Using a cellular relocation assay based on these results, we map the UAF1-binding site to a highly conserved 100 amino acid motif in USP1. Our data support a model in which USP1 and UAF1 form a complex in the cytoplasm that subsequently translocates to the nucleus through import mediated by USP1 NLSs. Importantly, our findings have practical implications for the development of USP1-directed therapies. First, the UAF1-interacting region of USP1 identified here might be targeted to disrupt the USP1/UAF1 interaction with therapeutic purposes. On the other hand, we describe a cellular relocation assay that can be easily implemented in a high throughput setting to search for drugs that may dissociate the USP1/UAF1 complex. PMID:22701671

  3. Distinct functions of the dual leucine zipper kinase depending on its subcellular localization.

    PubMed

    Wallbach, Manuel; Duque Escobar, Jorge; Babaeikelishomi, Rohollah; Stahnke, Marie-Jeannette; Blume, Roland; Schröder, Sabine; Kruegel, Jenny; Maedler, Kathrin; Kluth, Oliver; Kehlenbach, Ralph H; Miosge, Nicolai; Oetjen, Elke

    2016-04-01

    The dual leucine zipper kinase DLK induces β-cell apoptosis by inhibiting the transcriptional activity conferred by the β-cell protective transcription factor cAMP response element binding protein CREB. This action might contribute to β-cell loss and ultimately diabetes. Within its kinase domain DLK shares high homology with the mixed lineage kinase (MLK) 3, which is activated by tumor necrosis factor (TNF) α and interleukin (IL)-1β, known prediabetic signals. In the present study, the regulation of DLK in β-cells by these cytokines was investigated. Both, TNFα and IL-1β induced the nuclear translocation of DLK. Mutations within a putative nuclear localization signal (NLS) prevented basal and cytokine-induced nuclear localization of DLK and binding to the importin receptor importin α, thereby demonstrating a functional NLS within DLK. DLK NLS mutants were catalytically active as they phosphorylated their down-stream kinase c-Jun N-terminal kinase to the same extent as DLK wild-type but did neither inhibit CREB-dependent gene transcription nor transcription conferred by the promoter of the anti-apoptotic protein BCL-xL. In addition, the β-cell apoptosis-inducing effect of DLK was severely diminished by mutation of its NLS. In a murine model of prediabetes, enhanced nuclear DLK was found. These data demonstrate that DLK exerts distinct functions, depending on its subcellular localization and thus provide a novel level of regulating DLK action. Furthermore, the prevention of the nuclear localization of DLK as induced by prediabetic signals with consecutive suppression of β-cell apoptosis might constitute a novel target in the therapy of diabetes mellitus. PMID:26776303

  4. Visualizing cell structure and function with point-localization superresolution imaging

    PubMed Central

    Sengupta, Prabuddha; Van Engelenburg, Schuyler; Lippincott-Schwartz, Jennifer

    2012-01-01

    Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease. PMID:23237943

  5. Steroidogenesis in the skin: implications for local immune functions

    PubMed Central

    Slominski, Andrzej; Zbytek, Bazej; Nikolakis, Georgios; Manna, Pulak R.; Skobowiat, Cezary; Zmijewski, Michal; Li, Wei; Janjetovic, Zorica; Postlethwaite, Arnold; Zouboulis, Christos C.; Tuckey, Robert C.

    2013-01-01

    The skin has developed a hierarchy of systems that encompasses the skin immune and local steroidogenic activities in order to protect the body against the external environment and biological factors and to maintain local homeostasis. Most recently it has been established that skin cells contain the entire biochemical apparatus necessary for production of glucocorticoids, androgens and estrogens either from precursors of systemic origin or, alternatively, through the conversion of cholesterol to pregnenolone and its subsequent transformation to biologically active steroids. Examples of these products are corticosterone, cortisol, testosterone, dihydrotesterone and estradiol. Their local production can be regulated by locally produced corticotropin releasing hormone (CRH), adrenocorticotropic hormone (ACTH) or cytokines. Furthermore the production of glucocorticoids is affected by ultraviolet B radiation. The level of production and nature of the final steroid products are dependent on the cell type or cutaneous compartment, e.g., epidermis, dermis, adnexal structures or adipose tissue. Locally produced glucocorticoids, androgens and estrogens affect functions of the epidermis and adnexal structures as well as local immune activity. Malfunction of these steroidogenic activities can lead to inflammatory disorders or autoimmune diseases. The cutaneous steroidogenic system can also have systemic effects, which are emphasized by significant skin contribution to circulating androgens and/or estrogens. Furthermore, local activity of CYP11A1 can produce novel 7 -steroids and secosteroids that are biologically active. Therefore, modulation of local steroidogenic activity may serve as a new therapeutic approach for treatment of inflammatory disorders, autoimmune processes or other skin disorders. In conclusion, the skin can be defined as an independent steroidogenic organ, whose activity can affect its functions and the development of local or systemic inflammatory or

  6. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells

    PubMed Central

    Niopek, Dominik; Benzinger, Dirk; Roensch, Julia; Draebing, Thomas; Wehler, Pierre; Eils, Roland; Di Ventura, Barbara

    2014-01-01

    The function of many eukaryotic proteins is regulated by highly dynamic changes in their nucleocytoplasmic distribution. The ability to precisely and reversibly control nuclear translocation would, therefore, allow dissecting and engineering cellular networks. Here we develop a genetically encoded, light-inducible nuclear localization signal (LINuS) based on the LOV2 domain of Avena sativa phototropin 1. LINuS is a small, versatile tag, customizable for different proteins and cell types. LINuS-mediated nuclear import is fast and reversible, and can be tuned at different levels, for instance, by introducing mutations that alter AsLOV2 domain photo-caging properties or by selecting nuclear localization signals (NLSs) of various strengths. We demonstrate the utility of LINuS in mammalian cells by controlling gene expression and entry into mitosis with blue light. PMID:25019686

  7. Morbillivirus nucleoprotein possesses a novel nuclear localization signal and a CRM1-independent nuclear export signal

    SciTech Connect

    Sato, Hiroki; Masuda, Munemitsu; Miura, Ryuichi; Yoneda, Misako; Kai, Chieko . E-mail: ckai@ims.u-tokyo.ac.jp

    2006-08-15

    Morbilliviruses, which belong to the Mononegavirales, replicate its RNA genome in the cytoplasm of the host cell. However, they also form characteristic intranuclear inclusion bodies, consisting of nucleoprotein (N), in infected cells. To analyze the mechanisms of nucleocytoplasmic transport of N protein, we characterized the nuclear localization (NLS) and nuclear export (NES) signals of canine distemper virus (CDV) N protein by deletion mutation and alanine substitution of the protein. The NLS has a novel leucine/isoleucine-rich motif (TGILISIL) at positions 70-77, whereas the NES is composed of a leucine-rich motif (LLRSLTLF) at positions 4-11. The NLS and NES of the N proteins of other morbilliviruses, that is, measles virus (MV) and rinderpest virus (RPV), were also analyzed. The NLS of CDV-N protein is conserved at the same position in MV-N protein, whereas the NES of MV-N protein is located in the C-terminal region. The NES of RPV-N protein is also located at the same position as CDV-N protein, whereas the NLS motif is present not only at the same locus as CDV-N protein but also at other sites. Interestingly, the nuclear export of all these N proteins appears to proceed via a CRM1-independent pathway.

  8. Identification of a nuclear localization signal in the retinitis pigmentosa-mutated RP26 protein, ceramide kinase-like protein

    SciTech Connect

    Inagaki, Yuichi; Mitsutake, Susumu; Igarashi, Yasuyuki . E-mail: yigarash@pharm.hokudai.ac.jp

    2006-05-12

    Retinitis pigmentosa (RP) is a genetically heterogeneous disease characterized by degeneration of the retina. A mutation in a new ceramide kinase (CERK) homologous gene, named CERK-like protein (CERKL), was found to cause autosomal recessive retinitis pigmentosa (RP26). Here, we show a point mutation of one of two putative nuclear localization signal (NLS) sequences inhibited the nuclear localization of the protein. Furthermore, the tetra-GFP-tagged NLS, which cannot passively enter the nucleus, was observed not only in the nucleus but also in the nucleolus. Our results provide First evidence of the active nuclear import of CERKL and suggest that the identified NLS might be responsible for nucleolar retention of the protein. As recent studies have shown other RP-related proteins are localized in the nucleus or the nucleolus, our identification of NLS in CERKL suggests that CERKL likely plays important roles for retinal functions in the nucleus and the nucleolus.

  9. Monodisperse magnetite nanoparticles coupled with nuclear localization signal peptide for cell-nucleus targeting.

    PubMed

    Xu, Chenjie; Xie, Jin; Kohler, Nathan; Walsh, Edward G; Chin, Y Eugene; Sun, Shouheng

    2008-03-01

    Functionalization of monodisperse superparamagnetic magnetite (Fe(3)O(4)) nanoparticles for cell specific targeting is crucial for cancer diagnostics and therapeutics. Targeted magnetic nanoparticles can be used to enhance the tissue contrast in magnetic resonance imaging (MRI), to improve the efficiency in anticancer drug delivery, and to eliminate tumor cells by magnetic fluid hyperthermia. Herein we report the nucleus-targeting Fe(3)O(4) nanoparticles functionalized with protein and nuclear localization signal (NLS) peptide. These NLS-coated nanoparticles were introduced into the HeLa cell cytoplasm and nucleus, where the particles were monodispersed and non-aggregated. The success of labeling was examined and identified by fluorescence microscopy and MRI. The work demonstrates that monodisperse magnetic nanoparticles can be readily functionalized and stabilized for potential diagnostic and therapeutic applications. PMID:18080259

  10. On Extension of Measurable Functions and Local Operators

    NASA Astrophysics Data System (ADS)

    Shragin, Isaak V.; Nepomnyashchikh, Yurii V.

    2003-04-01

    In this work we generalize a number of results from1 on extension of measurable functions and local operators. In comparasion with 1 we assume neither measure to be defined on considered σ- algebras, nor the metric space on functions values is complete. As well in contrast to 1 here we do not make use Boolean algebras. This circumstance made possible essentially to simplify the presentation.

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

    SciTech Connect

    Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka

    2015-07-31

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

  12. Goal direction and effectiveness, emotional maturity, and nuclear family functioning.

    PubMed

    Klever, Phillip

    2009-07-01

    Differentiation of self, a cornerstone concept in Bowen theory, has a profound influence over time on the functioning of the individual and his or her family unit. This 5-year longitudinal study tested this hypothesis with 50 developing nuclear families. The dimensions of differentiation of self that were examined were goal direction and effectiveness and emotional maturity. A qualitative analysis of participants' goals demonstrated that couples with higher functioning developing nuclear families, when compared with couples with lower functioning families, placed more emphasis on family goals, had more balance between family and personal goals, and pursued more goals over the 5 years. The quantitative analysis supported the hypothesis that goal effectiveness and emotional maturity influenced variation in nuclear family functioning. In addition, couple goal effectiveness and emotional maturity were associated with nuclear family functioning more strongly than individual goal effectiveness and emotional maturity were associated with individual functioning. PMID:19522784

  13. Quantification of Uncertainties in Nuclear Density Functional Theory

    SciTech Connect

    Schunck, N.; McDonnell, J.D.; Higdon, D.; Sarich, J.; Wild, S.

    2015-01-15

    Reliable predictions of nuclear properties are needed as much to answer fundamental science questions as in applications such as reactor physics or data evaluation. Nuclear density functional theory is currently the only microscopic, global approach to nuclear structure that is applicable throughout the nuclear chart. In the past few years, a lot of effort has been devoted to setting up a general methodology to assess theoretical uncertainties in nuclear DFT calculations. In this paper, we summarize some of the recent progress in this direction. Most of the new material discussed here will be be published in separate articles.

  14. Quality function deployment applied to local traffic accident reduction.

    PubMed

    Sohn, S Y

    1999-11-01

    One of the major tasks of police stations is the management of local road traffic accidents. Proper prevention policy which reflects the local accident characteristics could immensely help individual police stations in decreasing various severity levels of road traffic accidents. In order to relate accident variation to local driving environmental characteristics, we use both cluster analysis and Poisson regression. The fitted result at the level of each cluster for each type of accident severity is utilized as an input to quality function deployment. Quality function deployment (QFD) has been applied to customer satisfaction in various industrial quality improvement settings, where several types of customer requirements are related to various control factors. We show how QFD enables one to set priorities on various road accident control policies to which each police station has to pay particular attention. PMID:10487350

  15. Using the electron localization function to correct for confinement physics in semi-local density functional theory

    SciTech Connect

    Hao, Feng Mattsson, Ann E.; Armiento, Rickard

    2014-05-14

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu–O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.

  16. Sperm Nuclear Architecture Is Locally Modified in Presence of a Robertsonian Translocation t(13;17)

    PubMed Central

    Acloque, Hervé; Bonnet-Garnier, Amélie; Mompart, Florence; Pinton, Alain; Yerle-Bouissou, Martine

    2013-01-01

    In mammals, the non-random organization of the sperm nucleus supports an early function during embryonic development. Altering this organization may interfere with the zygote development and reduce fertility or prolificity. Thus, rare studies on sperm cells from infertile patients described an altered nuclear organization that may be a cause or a consequence of their respective pathologies. Thereby, chromosomal rearrangements and aneuploidy can be studied not only for their adverse effects on production of normal/balanced gametes at meiosis but also for their possible impact on sperm nuclear architecture and the epigenetic consequences of altered chromosome positioning. We decided to compare the global architecture of sperm nuclei from boars, either with a normal chromosome composition or with a Robertsonian translocation involving chromosomes 13 and 17. We hypothesized that the fusion between these chromosomes may change their spatial organization and we examined to what extend it could also modify the global sperm nuclear architecture. Analysis of telomeres, centromeres and gonosomes repartition does not support a global nuclear disorganization. But specific analysis of chromosomes 13 and 17 territories highlights an influence of chromosome 17 for the positioning of the fused chromosomes within the nucleus. We also observed a specific clustering of centromeres depending of the chromosome subtypes. Altogether our results showed that chromosome fusion does not significantly alter sperm nucleus architecture but suggest that centromere remodelling after chromosome fusion locally impacts chromosome positioning. PMID:24205066

  17. The galaxy luminosity function and the Local Hole

    NASA Astrophysics Data System (ADS)

    Whitbourn, J. R.; Shanks, T.

    2016-06-01

    In a previous study Whitbourn & Shanks have reported evidence for a local void underdense by ≈15 per cent extending to 150-300 h-1 Mpc around our position in the Southern Galactic Cap (SGC). Assuming a local luminosity function they modelled K- and r-limited number counts and redshift distributions in the 6dFGS/2MASS and SDSS redshift surveys and derived normalized n(z) ratios relative to the standard homogeneous cosmological model. Here we test further these results using maximum likelihood techniques that solve for the galaxy density distributions and the galaxy luminosity function simultaneously. We confirm the results from the previous analysis in terms of the number density distributions, indicating that our detection of the `Local Hole' in the SGC is robust to the assumption of either our previous, or newly estimated, luminosity functions. However, there are discrepancies with previously published K- and r-band luminosity functions. In particular the r-band luminosity function has a steeper faint end slope than the r0.1 results of Blanton et al. but is consistent with the r0.1 results of Montero-Dorta & Prada and Loveday et al.

  18. The nuclear magnetic shielding as a function of internuclear separation

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; de Dios, Angel C.

    1993-02-01

    Ab initio calculations of nuclear magnetic shielding surfaces for 23Na in the NaH molecule, 39Ar in ArNe, 21Ne in NeHe, and 39Ar in Ar...NaH are carried out over a wide range of internuclear separations, using a local origin method (LORG) which damps out the long-range errors due to incomplete basis sets. The R dependence of the intermolecular shielding in the attractive region of the potential in these systems and in Ar...Ar and Ar...Na+ are consistent with the long-range limiting forms associated with the shielding hyperpolarizability in conjunction with a mean square electric field approximation. The Cl and F shieldings over the range of nuclear displacements spanning the classical turning points of the ground vibrational states of ClF and F2 are found to be remarkably superposable upon scaling by the factors ṡRe. This holds as well for ClH compared with FH. The shielding of 23Na and 7Li in NaH and LiH molecules are almost superposable. These and the scaling of the intermolecular shielding in rare gas pairs indicate some general similarities of shielding surfaces. The systematic variation in the signs and magnitudes of the first derivative of X nuclear shielding at the equilibrium geometry in XHn molecules of the first and second row of the Periodic Table are shown to be consistent with a general shape for the shielding function σ(R), which we have found in rare gas pairs and for 23Na in NaH.

  19. Local properties of three-body atomic wave functions

    SciTech Connect

    Krivec, R.; Mandelzweig, V. B.; Varga, K.

    2000-06-01

    The local properties and accuracy of the positronium negative-ion (Ps{sup -}) ground-state wave functions obtained by the stochastic variational method (SVM) and by direct solution of the Schroedinger equation with the help of the correlation-function hyperspherical-harmonic method (CFHHM) are studied and compared. Though the energy, calculated by both methods, agrees to up to ten digits, the amplitudes of the values of the operator D=H{psi}/E{psi}-1, characterizing local deviation of the wave function from its true value, in all of the coordinate space in the SVM are consistently larger (by up to five orders of magnitude) than in the CFHHM, despite the fact that the SVM observables except <{delta}(r{sub k})> converge to significantly more digits than the CFHHM observables for their respective selected bases. (c) 2000 The American Physical Society.

  20. Nuclear collective excitations: A relativistic density functional approach

    NASA Astrophysics Data System (ADS)

    Piekarewicz, J.

    2015-08-01

    Density functional theory provides the most promising, and likely unique, microscopic framework to describe nuclear systems ranging from finite nuclei to neutron stars. Properly optimized energy density functionals define a new paradigm in nuclear theory where predictive capability is possible and uncertainty quantification is demanded. Moreover, density functional theory offers a consistent approach to the linear response of the nuclear ground state. In this paper, we review the fundamental role played by nuclear collective modes in uncovering novel excitations and in guiding the optimization of the density functional. Indeed, without collective excitations the determination of the density functional remains incomplete. Without collective excitations, the equation of state of neutron-rich matter continues to be poorly constrained. We conclude with a discussion of some of the remaining challenges in this field and propose a path forward to address these challenges.

  1. Tissue specificity in the nuclear envelope supports its functional complexity

    PubMed Central

    de las Heras, Jose I; Meinke, Peter; Batrakou, Dzmitry G; Srsen, Vlastimil; Zuleger, Nikolaj; Kerr, Alastair RW; Schirmer, Eric C

    2013-01-01

    Nuclear envelope links to inherited disease gave the conundrum of how mutations in near-ubiquitous proteins can yield many distinct pathologies, each focused in different tissues. One conundrum-resolving hypothesis is that tissue-specific partner proteins mediate these pathologies. Such partner proteins may have now been identified with recent proteome studies determining nuclear envelope composition in different tissues. These studies revealed that the majority of the total nuclear envelope proteins are tissue restricted in their expression. Moreover, functions have been found for a number these tissue-restricted nuclear envelope proteins that fit with mechanisms proposed to explain how the nuclear envelope could mediate disease, including defects in mechanical stability, cell cycle regulation, signaling, genome organization, gene expression, nucleocytoplasmic transport, and differentiation. The wide range of functions to which these proteins contribute is consistent with not only their involvement in tissue-specific nuclear envelope disease pathologies, but also tissue evolution. PMID:24213376

  2. Automated construction of maximally localized Wannier functions: Optimized projection functions method

    NASA Astrophysics Data System (ADS)

    Mustafa, Jamal I.; Coh, Sinisa; Cohen, Marvin L.; Louie, Steven G.

    2015-10-01

    Maximally localized Wannier functions are widely used in electronic structure theory for analyses of bonding, electric polarization, orbital magnetization, and for interpolation. The state of the art method for their construction is based on the method of Marzari and Vanderbilt. One of the practical difficulties of this method is guessing functions (initial projections) that approximate the final Wannier functions. Here we present an approach based on optimized projection functions that can construct maximally localized Wannier functions without a guess. We describe and demonstrate this approach on several realistic examples.

  3. Ubc9 Mediates Nuclear Localization and Growth Suppression of BRCA1 and BRCA1a Proteins

    PubMed Central

    QIN, YUNLONG; XU, JINGYAO; AYSOLA, KARTIK; BEGUM, NURJAHAN; REDDY, VAISHALI; CHAI, YULI; GRIZZLE, WILLIAM E.; PARTRIDGE, EDWARD E.; REDDY, E. SHYAM P.; RAO, VEENA N.

    2012-01-01

    BRCA1 gene mutations are responsible for hereditary breast and ovarian cancers. In sporadic breast tumors, BRCA1 dysfunction or aberrant subcellular localization is thought to be common. BRCA1 is a nuclear–cytoplasm shuttling protein and the reason for cytoplasmic localization of BRCA1 in young breast cancer patients is not yet known. We have previously reported BRCA1 proteins unlike K109R and cancer-predisposing mutant C61G to bind Ubc9 and modulate ER-α turnover. In the present study, we have examined the consequences of altered Ubc9 binding and knockdown on the subcellular localization and growth inhibitory function of BRCA1 proteins. Our results using live imaging of YFP, GFP, RFP-tagged BRCA1, BRCA1a and BRCA1b proteins show enhanced cytoplasmic localization of K109 R and C61G mutant BRCA1 proteins in normal and cancer cells. Furthermore, down-regulation of Ubc9 in MCF-7 cells using Ubc9 siRNA resulted in enhanced cytoplasmic localization of BRCA1 protein and exclusive cytoplasmic retention of BRCA1a and BRCA1b proteins. These mutant BRCA1 proteins were transforming and impaired in their capacity to inhibit growth of MCF-7 and CAL51 breast cancer cells. Interestingly, cytoplasmic BRCA1a mutants showed more clonogenicity in soft agar and higher levels of expression of Ubc9 than parental MCF7 cells. This is the first report demonstrating the physiological link between cytoplasmic mislocalization of mutant BRCA1 proteins, loss of ER-α repression, loss of ubiquitin ligase activity and loss of growth suppression of BRCA1 proteins. Thus, binding of BRCA1 proteins to nuclear chaperone Ubc9 provides a novel mechanism for nuclear import and control of tumor growth. PMID:21344391

  4. A novel nuclear localization signal in the auxiliary domain of apobec-1 complementation factor regulates nucleocytoplasmic import and shuttling.

    PubMed

    Blanc, Valerie; Kennedy, Susan; Davidson, Nicholas O

    2003-10-17

    C to U editing of the nuclear apolipoprotein B (apoB) transcript is mediated by a core enzyme containing a catalytic deaminase, apobec-1, and an RNA binding subunit, apobec-1 complementation factor (ACF). ACF expression is predominantly nuclear, including mutant proteins with deletions of a putative nuclear localization signal. We have now identified a novel 41-residue motif (ANS) in the auxiliary domain of ACF that functions as an authentic nuclear localization signal. ANS-green fluorescence protein and ANS-beta-galactosidase chimeras were both expressed exclusively in the nucleus, whereas wild-type chimeras or an ACF deletion mutant lacking the ANS were cytoplasmic. Nuclear accumulation of ACF is transcription-dependent, temperature-sensitive, and reversible, features reminiscent of a shuttling protein. ACF relocates to the cytoplasm after actinomycin D treatment, an effect blocked by the CRM1 inhibitor leptomycin B. Heterokaryon assays confirmed directly that ACF shuttles in vivo. ACF binds to the protein carrier, transportin 2 in vivo, and colocalizes to the nucleus as determined by confocal microscopy. Co-immunoprecipitation experiments revealed that transportin 2 binds directly to the ANS motif. These data suggest that directed nuclear localization and compartmentalization of the core complex of the apoB RNA editing enzyme is regulated through a dominant targeting sequence (ANS) contained within ACF. PMID:12896982

  5. Nuclear F-actin enhances the transcriptional activity of β-catenin by increasing its nuclear localization and binding to chromatin.

    PubMed

    Yamazaki, Shota; Yamamoto, Koji; de Lanerolle, Primal; Harata, Masahiko

    2016-04-01

    Actin plays multiple roles both in the cytoplasm and in the nucleus. Cytoplasmic actin, in addition to its structural role in the cytoskeleton, also contributes to the subcellular localization of transcription factors by interacting with them or their partners. The transcriptional cofactor β-catenin, which acts as an intracellular transducer of canonical Wnt signaling, indirectly associates with the cytoplasmic filamentous actin (F-actin). Recently, it has been observed that F-actin is transiently formed within the nucleus in response to serum stimulation and integrin signaling, and also during gene reprogramming. Despite these earlier observations, information about the function of nuclear F-actin is poorly defined. Here, by facilitating the accumulation of nuclear actin artificially, we demonstrate that polymerizing nuclear actin enhanced the nuclear accumulation and transcriptional function of β-catenin. Our results also show that the nuclear F-actin colocalizes with β-catenin and enhances the binding of β-catenin to the downstream target genes of the Wnt/β-catenin signaling pathway, including the genes for the cell cycle regulators c-myc and cyclin D, and the OCT4 gene. Nuclear F-actin itself also associated with these genes. Since Wnt/β-catenin signaling has important roles in cell differentiation and pluripotency, our observations suggest that nuclear F-actin formed during these biological processes is involved in regulating Wnt/β-catenin signaling. PMID:26900020

  6. The yeast Ess1 prolyl isomerase controls Swi6 and Whi5 nuclear localization.

    PubMed

    Atencio, David; Barnes, Cassandra; Duncan, Thomas M; Willis, Ian M; Hanes, Steven D

    2014-03-01

    The Ess1 prolyl isomerase from Saccharomyces cerevisiae and its human ortholog, Pin1, play critical roles in transcription by regulating RNA polymerase II. In human cells, Pin1 also regulates a variety of signaling proteins, and Pin1 misexpression is linked to several human diseases. To gain insight into Ess1/Pin1 function, we carried out a synthetic genetic array screen to identify novel targets of Ess1 in yeast. We identified potential targets of Ess1 in transcription, stress, and cell-cycle pathways. We focused on the cell-cycle regulators Swi6 and Whi5, both of which show highly regulated nucleocytoplasmic shuttling during the cell cycle. Surprisingly, Ess1 did not control their transcription but instead was necessary for their nuclear localization. Ess1 associated with Swi6 and Whi5 in vivo and bound directly to peptides corresponding to their nuclear localization sequences in vitro. Binding by Ess1 was significant only if the Swi6 and Whi5 peptides were phosphorylated at Ser-Pro motifs, the target sites of cyclin-dependent kinases. On the basis of these results, we propose a model in which Ess1 induces a conformational switch (cis-trans isomerization) at phospho-Ser-Pro sites within the nuclear targeting sequences of Swi6 and Whi5. This switch would promote nuclear entry and/or retention during late M and G1 phases and might work by stimulating dephosphorylation at these sites by the Cdc14 phosphatase. This is the first study to identify targets of Ess1 in yeast other than RNA polymerase II. PMID:24470217

  7. Range Separation and Local Hybridization in Density Functional Theory†

    PubMed Central

    Henderson, Thomas M.; Janesko, Benjamin G.; Scuseria, Gustavo E.

    2016-01-01

    Kohn–Sham density functional theory has become a standard method for modeling energetic, spectroscopic, and chemical reactivity properties of large molecules and solids. Density functional theory provides a rigorous theoretical framework for modeling the many-body exchange-correlation effects that dominate the computational cost of traditional wave function approaches. The advent of hybrid exchange-correlation functionals which incorporate a fraction of nonlocal exact exchange has solidified the prominence of density functional theory within computational chemistry. Hybrids provide accurate treatments of properties such as thermochemistry and molecular geometry. But they also exhibit some rather spectacular failures, and often contain multiple empirical parameters. This article reviews our work on developing novel exchange-correlation functionals that build upon the successes of global hybrids. We focus on more flexible functional forms, including local and range-separated hybrid functionals, constructed to obey known exact constraints and (ideally) to incorporate a minimum of empirical parametrization. The article places our work within the context of some other new approximate density functionals and discusses prospects for future work. PMID:19006280

  8. Role of zinc finger structure in nuclear localization of transcription factor Sp1

    SciTech Connect

    Ito, Tatsuo; Azumano, Makiko; Uwatoko, Chisana; Itoh, Kohji Kuwahara, Jun

    2009-02-27

    Transcription factor Sp1 is localized in the nucleus and regulates gene expression. Our previous study demonstrated that the carboxyl terminal region of Sp1 containing 3-zinc finger region as DNA binding domain can also serve as nuclear localization signal (NLS). However, the nuclear transport mechanism of Sp1 has not been well understood. In this study, we performed a gene expression study on mutant Sp1 genes causing a set of amino acid substitutions in zinc finger domains to elucidate nuclear import activity. Nuclear localization of the GFP-fused mutant Sp1 proteins bearing concomitant substitutions in the first and third zinc fingers was highly inhibited. These mutant Sp1 proteins had also lost the binding ability as to the GC box sequence. The results suggest that the overall tertiary structure formed by the three zinc fingers is essential for nuclear localization of Sp1 as well as dispersed basic amino acids within the zinc fingers region.

  9. Specific deletion of CMF1 nuclear localization domain causes incomplete cell cycle withdrawal and impaired differentiation in avian skeletal myoblasts

    SciTech Connect

    Dees, Ellen . E-mail: ellen.dees@vanderbilt.edu; Robertson, J. Brian; Zhu, Tianli; Bader, David

    2006-10-01

    CMF1 is a protein expressed in embryonic striated muscle with onset of expression preceding that of contractile proteins. Disruption of CMF1 in myoblasts disrupts muscle-specific protein expression. Preliminary studies indicate both nuclear and cytoplasmic distribution of CMF1 protein, suggesting functional roles in both cellular compartments. Here we examine the nuclear function of CMF1, using a newly characterized antibody generated against the CMF1 nuclear localization domain and a CMF1 nuclear localization domain-deleted stable myocyte line. The antibody demonstrates nuclear distribution of the CMF1 protein both in vivo and in cell lines, with clustering of CMF1 protein around chromatin during mitosis. In more differentiated myocytes, the protein shifts to the cytoplasm. The CMF1 NLS-deleted cell lines have markedly impaired capacity to differentiate. Specifically, these cells express less contractile protein than wild-type or full-length CMF1 stably transfected cells, and do not fuse properly into multinucleate syncytia with linear nuclear alignment. In response to low serum medium, a signal to differentiate, CMF1 NLS-deleted cells enter G0, but continue to express proliferation markers and will reenter the cell cycle when stimulated by restoring growth medium. These data suggest that CMF1 is involved in regulation the transition from proliferation to differentiation in embryonic muscle.

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

    PubMed

    Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka

    2015-07-31

    Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS(SV40)) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS(SV40) in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS(SV40) formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS(SV40) likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS(SV40) can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. PMID:26032495

  11. A Role for the GSG Domain in Localizing Sam68 to Novel Nuclear Structures in Cancer Cell Lines

    PubMed Central

    Chen, Taiping; Boisvert, François-Michel; Bazett-Jones, David P.; Richard, Stéphane

    1999-01-01

    The GSG (GRP33, Sam68, GLD-1) domain is a protein module found in an expanding family of RNA-binding proteins. The numerous missense mutations identified genetically in the GSG domain support its physiological role. Although the exact function of the GSG domain is not known, it has been shown to be required for RNA binding and oligomerization. Here it is shown that the Sam68 GSG domain plays a role in protein localization. We show that Sam68 concentrates into novel nuclear structures that are predominantly found in transformed cells. These Sam68 nuclear bodies (SNBs) are distinct from coiled bodies, gems, and promyelocytic nuclear bodies. Electron microscopic studies show that SNBs are distinct structures that are enriched in phosphorus and nitrogen, indicating the presence of nucleic acids. A GFP-Sam68 fusion protein had a similar localization as endogenous Sam68 in HeLa cells, diffusely nuclear with two to five SNBs. Two other GSG proteins, the Sam68-like mammalian proteins SLM-1 and SLM-2, colocalized with endogenous Sam68 in SNBs. Different GSG domain missense mutations were investigated for Sam68 protein localization. Six separate classes of cellular patterns were obtained, including exclusive SNB localization and association with microtubules. These findings demonstrate that the GSG domain is involved in protein localization and define a new compartment for Sam68, SLM-1, and SLM-2 in cancer cell lines. PMID:10473643

  12. Comparison and characterization of α-amylase inducers in Aspergillus nidulans based on nuclear localization of AmyR.

    PubMed

    Murakoshi, Yuriko; Makita, Tomohiro; Kato, Masashi; Kobayashi, Tetsuo

    2012-06-01

    AmyR, a fungal transcriptional activator responsible for induction of amylolytic genes in Aspergillus nidulans, localizes to the nucleus in response to the physiological inducer isomaltose. Maltose, kojibiose, and D: -glucose were also found to trigger the nuclear localization of GFP-AmyR. Isomaltose- and kojibiose-triggered nuclear localization was not inhibited by the glucosidase inhibitor, castanospermine, while maltose-triggered localization was inhibited. Thus, maltose itself does not appear to be an direct inducer, but its degraded or transglycosylated product does. Non-metabolizable D: -glucose analogues were also able to trigger the nuclear localization, implying that these sugars, except maltose, directly function as the inducers of AmyR nuclear entry. The inducing activity of D: -glucose was 4 orders-of-magnitude weaker compared with isomaltose. Although D: -glucose has the ability to induce α-amylase production, this activity would generally be masked by CreA-dependent carbon catabolite repression. Significant induction of α-amylase by D: -glucose was observed in creA-defective A. nidulans. PMID:22252265

  13. Factorized molecular wave functions: Analysis of the nuclear factor

    SciTech Connect

    Lefebvre, R.

    2015-06-07

    The exact factorization of molecular wave functions leads to nuclear factors which should be nodeless functions. We reconsider the case of vibrational perturbations in a diatomic species, a situation usually treated by combining Born-Oppenheimer products. It was shown [R. Lefebvre, J. Chem. Phys. 142, 074106 (2015)] that it is possible to derive, from the solutions of coupled equations, the form of the factorized function. By increasing artificially the interstate coupling in the usual approach, the adiabatic regime can be reached, whereby the wave function can be reduced to a single product. The nuclear factor of this product is determined by the lowest of the two potentials obtained by diagonalization of the potential matrix. By comparison with the nuclear wave function of the factorized scheme, it is shown that by a simple rectification, an agreement is obtained between the modified nodeless function and that of the adiabatic scheme.

  14. Importin α1 Mediates Yorkie Nuclear Import via an N-terminal Non-canonical Nuclear Localization Signal.

    PubMed

    Wang, Shimin; Lu, Yi; Yin, Meng-Xin; Wang, Chao; Wu, Wei; Li, Jinhui; Wu, Wenqing; Ge, Ling; Hu, Lianxin; Zhao, Yun; Zhang, Lei

    2016-04-01

    The Hippo signaling pathway controls organ size by orchestrating cell proliferation and apoptosis. When the Hippo pathway was inactivated, the transcriptional co-activator Yorkie translocates into the nucleus and forms a complex with transcription factor Scalloped to promote the expression of Hippo pathway target genes. Therefore, the nuclear translocation of Yorkie is a critical step in Hippo signaling. Here, we provide evidence that the N-terminal 1-55 amino acids of Yorkie, especially Arg-15, were essential for its nuclear localization. By mass spectrometry and biochemical analyses, we found that Importin α1 can directly interact with the Yorkie N terminus and drive Yorkie into the nucleus. Further experiments show that the upstream component Hippo can inhibit Importin α1-mediated Yorkie nuclear import. Taken together, we identified a potential nuclear localization signal at the N-terminal end of Yorkie as well as a critical role for Importin α1 in Yorkie nuclear import. PMID:26887950

  15. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization

    SciTech Connect

    Shiheido, Hirokazu Shimizu, Jun

    2015-02-20

    BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND3{sub 56–58}, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. - Highlights: • BEND3 localizes to the nucleus. • The N-terminal 60 amino acids region of BEND3 contains NLS. • Amino acids located between 56 and 58 of BEND3 (KRK) are part of NLS. • KRK motif is highly conserved among BEND3 homologs.

  16. Global functions in global-local finite-element analysis of localized stresses in prismatic structures

    NASA Technical Reports Server (NTRS)

    Dong, Stanley B.

    1989-01-01

    An important consideration in the global local finite-element method (GLFEM) is the availability of global functions for the given problem. The role and mathematical requirements of these global functions in a GLFEM analysis of localized stress states in prismatic structures are discussed. A method is described for determining these global functions. Underlying this method are theorems due to Toupin and Knowles on strain energy decay rates, which are related to a quantitative expression of Saint-Venant's principle. It is mentioned that a mathematically complete set of global functions can be generated, so that any arbitrary interface condition between the finite element and global subregions can be represented. Convergence to the true behavior can be achieved with increasing global functions and finite-element degrees of freedom. Specific attention is devoted to mathematically two-dimensional and three-dimensional prismatic structures. Comments are offered on the GLFEM analysis of NASA flat panel with a discontinuous stiffener. Methods for determining global functions for other effects are also indicated, such as steady-state dynamics and bodies under initial stress.

  17. Exponentially localized Wannier functions in periodic zero flux magnetic fields

    NASA Astrophysics Data System (ADS)

    De Nittis, G.; Lein, M.

    2011-11-01

    In this work, we investigate conditions which ensure the existence of an exponentially localized Wannier basis for a given periodic hamiltonian. We extend previous results [Panati, G., Ann. Henri Poincare 8, 995-1011 (2007), 10.1007/s00023-007-0326-8] to include periodic zero flux magnetic fields which is the setting also investigated by Kuchment [J. Phys. A: Math. Theor. 42, 025203 (2009), 10.1088/1751-8113/42/2/025203]. The new notion of magnetic symmetry plays a crucial rôle; to a large class of symmetries for a non-magnetic system, one can associate "magnetic" symmetries of the related magnetic system. Observing that the existence of an exponentially localized Wannier basis is equivalent to the triviality of the so-called Bloch bundle, a rank m hermitian vector bundle over the Brillouin zone, we prove that magnetic time-reversal symmetry is sufficient to ensure the triviality of the Bloch bundle in spatial dimension d = 1, 2, 3. For d = 4, an exponentially localized Wannier basis exists provided that the trace per unit volume of a suitable function of the Fermi projection vanishes. For d > 4 and d ⩽ 2m (stable rank regime) only the exponential localization of a subset of Wannier functions is shown; this improves part of the analysis of Kuchment [J. Phys. A: Math. Theor. 42, 025203 (2009), 10.1088/1751-8113/42/2/025203]. Finally, for d > 4 and d > 2m (unstable rank regime) we show that the mere analysis of Chern classes does not suffice in order to prove triviality and thus exponential localization.

  18. Global and local curvature in density functional theory

    NASA Astrophysics Data System (ADS)

    Zhao, Qing; Ioannidis, Efthymios I.; Kulik, Heather J.

    2016-08-01

    Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a "+U" correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc-Cu) and ligand strength (CO, NH3, and H2O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide.

  19. Global and local curvature in density functional theory.

    PubMed

    Zhao, Qing; Ioannidis, Efthymios I; Kulik, Heather J

    2016-08-01

    Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a "+U" correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc-Cu) and ligand strength (CO, NH3, and H2O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide. PMID:27497541

  20. Effects of Local Compression on Peroneal Nerve Function in Humans

    NASA Technical Reports Server (NTRS)

    Hargens, Alan R.; Botte, Michael J.; Swenson, Michael R.; Gelberman, Richard H.; Rhoades, Charles E.; Akeson, Wayne H.

    1993-01-01

    A new apparatus was developed to compress the anterior compartment selectively and reproducibly in humans. Thirty-five normal volunteers were studied to determine short-term thresholds of local tissue pressure that produce significant neuromuscular dysfunction. Local tissue fluid pressure adjacent to the deep peroneal nerve was elevated by the compression apparatus and continuously monitored for 2-3 h by the slit catheter technique. Elevation of tissue fluid pressure to within 35-40 mm Hg of diastolic blood pressure (approx. 40 mm Hg of in situ pressure in our subjects) elicited a consistent progression of neuromuscular deterioration including, in order, (a) gradual loss of sensation, as assessed by Semmes-Weinstein monofilaments, (b) subjective complaints, (c) reduced nerve conduction velocity, (d) decreased action potential amplitude of the extensor digitorum brevis muscle, and (e) motor weakness of muscles within the anterior compartment. Generally, higher intracompartment at pressures caused more rapid deterioration of neuromuscular function. In two subjects, when in situ compression levels were 0 and 30 mm Hg, normal neuromuscular function was maintained for 3 h. Threshold pressures for significant dysfunction were not always the same for each functional parameter studied, and the magnitudes of each functional deficit did not always correlate with compression level. This variable tolerance to elevated pressure emphasizes the need to monitor clinical signs and symptoms carefully in the diagnosis of compartment syndromes. The nature of the present studies was short term; longer term compression of myoneural tissues may result in dysfunction at lower pressure thresholds.

  1. Novel subcellular localization for α-synuclein: possible functional consequences

    PubMed Central

    Guardia-Laguarta, Cristina; Area-Gomez, Estela; Schon, Eric A.; Przedborski, Serge

    2015-01-01

    α-synuclein (α-syn) is one of the genes that when mutated or overexpressed causes Parkinson’s Disease (PD). Initially, it was described as a synaptic terminal protein and later was found to be localized at mitochondria. Mitochondria-associated membranes (MAM) have emerged as a central endoplasmic reticulum (ER) subcellular compartments where key functions of the cell occur. These domains, enriched in cholesterol and anionic phospholipids, are where calcium homeostasis, lipid transfer, and cholesterol metabolism are regulated. Some proteins, related to mitochondrial dynamics and function, are also localized to this area. Several neurodegenerative diseases have shown alterations in MAM functions and resident proteins, including Charcot Marie-Tooth and Alzheimer’s disease (AD). We have recently reported that MAM function is downregulated in cell and mouse models of PD expressing pathogenic mutations of α-syn. This review focuses on the possible role of α-syn in these cellular domains and the early pathogenic features of PD that could be explained by α-syn-MAM disturbances. PMID:25755636

  2. Higher-order oligomerization promotes localization of SPOP to liquid nuclear speckles.

    PubMed

    Marzahn, Melissa R; Marada, Suresh; Lee, Jihun; Nourse, Amanda; Kenrick, Sophia; Zhao, Huaying; Ben-Nissan, Gili; Kolaitis, Regina-Maria; Peters, Jennifer L; Pounds, Stanley; Errington, Wesley J; Privé, Gilbert G; Taylor, J Paul; Sharon, Michal; Schuck, Peter; Ogden, Stacey K; Mittag, Tanja

    2016-06-15

    Membrane-less organelles in cells are large, dynamic protein/protein or protein/RNA assemblies that have been reported in some cases to have liquid droplet properties. However, the molecular interactions underlying the recruitment of components are not well understood. Herein, we study how the ability to form higher-order assemblies influences the recruitment of the speckle-type POZ protein (SPOP) to nuclear speckles. SPOP, a cullin-3-RING ubiquitin ligase (CRL3) substrate adaptor, self-associates into higher-order oligomers; that is, the number of monomers in an oligomer is broadly distributed and can be large. While wild-type SPOP localizes to liquid nuclear speckles, self-association-deficient SPOP mutants have a diffuse distribution in the nucleus. SPOP oligomerizes through its BTB and BACK domains. We show that BTB-mediated SPOP dimers form linear oligomers via BACK domain dimerization, and we determine the concentration-dependent populations of the resulting oligomeric species. Higher-order oligomerization of SPOP stimulates CRL3(SPOP) ubiquitination efficiency for its physiological substrate Gli3, suggesting that nuclear speckles are hotspots of ubiquitination. Dynamic, higher-order protein self-association may be a general mechanism to concentrate functional components in membrane-less cellular bodies. PMID:27220849

  3. A toolbox of endogenous and heterologous nuclear localization sequences for the methylotrophic yeast Pichia pastoris

    PubMed Central

    Weninger, Astrid; Glieder, Anton; Vogl, Thomas

    2015-01-01

    Nuclear localization sequences (NLSs) are required for the import of proteins in the nucleus of eukaryotes. However many proteins from bacteria or bacteriophages are used for basic studies in molecular biology, to generate synthetic genetic circuits or for genome editing applications. Prokaryotic recombinases, CRISPR-associated proteins such as Cas9 or bacterial and viral polymerases require efficient NLSs to function in eukaryotes. The yeast Pichia pastoris is a widely used expression platform for heterologous protein production, but molecular tools such as NLSs are limited. Here we have characterized a set of 10 NLSs for P. pastoris, including the first endogenous NLSs (derived from P. pastoris proteins) and commonly used heterologous NLSs. The NLSs were evaluated by fusing them in N- and C-terminal position to an enhanced green fluorescent protein showing pronounced differences in fluorescence levels and nuclear targeting. Thereby we provide a set of different NLSs that can be applied to optimize the nuclear import of heterologous proteins in P. pastoris, paving the way for the establishment of intricate synthetic biology applications. PMID:26347503

  4. Local and linear chemical reactivity response functions at finite temperature in density functional theory.

    PubMed

    Franco-Pérez, Marco; Ayers, Paul W; Gázquez, José L; Vela, Alberto

    2015-12-28

    We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model. PMID:26723661

  5. Local and linear chemical reactivity response functions at finite temperature in density functional theory

    SciTech Connect

    Franco-Pérez, Marco E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Ayers, Paul W. E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Gázquez, José L. E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Vela, Alberto E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx

    2015-12-28

    We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.

  6. Avoiding coral reef functional collapse requires local and global action.

    PubMed

    Kennedy, Emma V; Perry, Chris T; Halloran, Paul R; Iglesias-Prieto, Roberto; Schönberg, Christine H L; Wisshak, Max; Form, Armin U; Carricart-Ganivet, Juan P; Fine, Maoz; Eakin, C Mark; Mumby, Peter J

    2013-05-20

    Coral reefs face multiple anthropogenic threats, from pollution and overfishing to the dual effects of greenhouse gas emissions: rising sea temperature and ocean acidification. While the abundance of coral has declined in recent decades, the implications for humanity are difficult to quantify because they depend on ecosystem function rather than the corals themselves. Most reef functions and ecosystem services are founded on the ability of reefs to maintain their three-dimensional structure through net carbonate accumulation. Coral growth only constitutes part of a reef's carbonate budget; bioerosion processes are influential in determining the balance between net structural growth and disintegration. Here, we combine ecological models with carbonate budgets and drive the dynamics of Caribbean reefs with the latest generation of climate models. Budget reconstructions using documented ecological perturbations drive shallow (6-10 m) Caribbean forereefs toward an increasingly fragile carbonate balance. We then projected carbonate budgets toward 2080 and contrasted the benefits of local conservation and global action on climate change. Local management of fisheries (specifically, no-take marine reserves) and the watershed can delay reef loss by at least a decade under "business-as-usual" rises in greenhouse gas emissions. However, local action must be combined with a low-carbon economy to prevent degradation of reef structures and associated ecosystem services. PMID:23664976

  7. Spin constraints on nuclear energy density functionals

    NASA Astrophysics Data System (ADS)

    Robledo, L. M.; Bernard, R. N.; Bertsch, G. F.

    2014-02-01

    The Gallagher-Moszkowski rule in the spectroscopy of odd-odd nuclei imposes a new spin constraint on the energy functionals for self-consistent mean field theory. The commonly used parametrization of the effective three-body interaction in the Gogny and Skyrme families of energy functionals is ill suited to satisfy the spin constraint. In particular, the Gogny parametrization of the three-body interaction has the spin dependence opposite to that required by the observed spectra. The two-body part has a correct sign, but in combination the rule is violated as often as not. We conclude that a new functional form is needed for the effective three-body interaction that can take into better account the different spin-isospin channels of the interaction.

  8. New Generation Nuclear Plant -- High Level Functions and Requirements

    SciTech Connect

    J. M. Ryskamp; E. J. Gorski; E. A. Harvego; S. T. Khericha; G. A. Beitel

    2003-09-01

    This functions and requirements (F&R) document was prepared for the Next Generation Nuclear Plant (NGNP) Project. The highest-level functions and requirements for the NGNP preconceptual design are identified in this document, which establishes performance definitions for what the NGNP will achieve. NGNP designs will be developed based on these requirements by commercial vendor(s).

  9. US Nuclear Regulatory Commission organization charts and functional statements

    SciTech Connect

    1997-11-01

    This document contains organization charts for the U.S. Nuclear Regulatory Commission (NRC) and for the five offices of the NRC. Function statements are provided delineating the major responsibilities and operations of each office. Organization and function are provided to the branch level. The head of each office, division, and branch is also listed.

  10. Imaging local brain function with emission computed tomography

    SciTech Connect

    Kuhl, D.E.

    1984-03-01

    Positron emission tomography (PET) using /sup 18/F-fluorodeoxyglucose (FDG) was used to map local cerebral glucose utilization in the study of local cerebral function. This information differs fundamentally from structural assessment by means of computed tomography (CT). In normal human volunteers, the FDG scan was used to determine the cerebral metabolic response to conrolled sensory stimulation and the effects of aging. Cerebral metabolic patterns are distinctive among depressed and demented elderly patients. The FDG scan appears normal in the depressed patient, studded with multiple metabolic defects in patients with multiple infarct dementia, and in the patients with Alzheimer disease, metabolism is particularly reduced in the parietal cortex, but only slightly reduced in the caudate and thalamus. The interictal FDG scan effectively detects hypometabolic brain zones that are sites of onset for seizures in patients with partial epilepsy, even though these zones usually appear normal on CT scans. The future prospects of PET are discussed.

  11. Discrimination between NL1- and NL2-Mediated Nuclear Localization of the Glucocorticoid Receptor

    PubMed Central

    Savory, Joanne G. A.; Hsu, Brian; Laquian, Ian R.; Giffin, Ward; Reich, Terry; Haché, Robert J. G.; Lefebvre, Yvonne A.

    1999-01-01

    Glucocorticoid receptor (GR) cycles between a free liganded form that is localized to the nucleus and a heat shock protein (hsp)-immunophilin-complexed, unliganded form that is usually localized to the cytoplasm but that can also be nuclear. In addition, rapid nucleocytoplasmic exchange or shuttling of the receptor underlies its localization. Nuclear import of liganded GR is mediated through a well-characterized sequence, NL1, adjacent to the receptor DNA binding domain and a second, uncharacterized motif, NL2, that overlaps with the ligand binding domain. In this study we report that rapid nuclear import (half-life [t1/2] of 4 to 6 min) of agonist- and antagonist-treated GR and the localization of unliganded, hsp-associated GRs to the nucleus in G0 are mediated through NL1 and correlate with the binding of GR to pendulin/importin α. By contrast, NL2-mediated nuclear transfer of GR occurred more slowly (t1/2 = 45 min to 1 h), was agonist specific, and appeared to be independent of binding to importin α. Together, these results suggest that NL2 mediates the nuclear import of GR through an alternative nuclear import pathway. Nuclear export of GR was inhibited by leptomycin B, suggesting that the transfer of GR to the cytoplasm is mediated through the CRM1-dependent pathway. Inhibition of GR nuclear export by leptomycin B enhanced the nuclear localization of both unliganded, wild-type GR and hormone-treated NL1− GR. These results highlight that the subcellular localization of both liganded and unliganded GRs is determined, at least in part, by a flexible equilibrium between the rates of nuclear import and export. PMID:9891038

  12. Functional specificity of local synaptic connections in neocortical networks

    PubMed Central

    Ko, Ho; Hofer, Sonja B.; Pichler, Bruno; Buchanan, Kate; Sjöström, P. Jesper; Mrsic-Flogel, Thomas D.

    2011-01-01

    Neuronal connectivity is fundamental to information processing in the brain. Understanding the mechanisms of sensory processing, therefore, requires uncovering how connection patterns between neurons relate to their function. On a coarse scale long range projections can preferentially link cortical regions with similar responses to sensory stimuli1-4. But on the local scale, where dendrites and axons overlap substantially, the functional specificity of connections remains unknown. Here we determine synaptic connectivity between nearby layer 2/3 pyramidal neurons in vitro whose response properties were first characterized in mouse visual cortex in vivo. We found that connection probability was related to the similarity of visually driven neuronal activity. Neurons with the same preference for oriented stimuli connected at twice the rate of neurons with orthogonal orientation preferences. Neurons responding similarly to naturalistic stimuli formed connections at much higher rates than those with uncorrelated responses. Bidirectional synaptic connections were found more frequently between neuronal pairs with strongly correlated visual responses. Our results reveal the deg of functional specificity of local synaptic connections in visual cortex, and point to the existence of fine-scale subnetworks dedicated to processing related sensory information. PMID:21478872

  13. Atypical nuclear localization of VIP receptors in glioma cell lines and patients

    SciTech Connect

    Barbarin, Alice; Séité, Paule; Godet, Julie; Bensalma, Souheyla; Muller, Jean-Marc; Chadéneau, Corinne

    2014-11-28

    Highlights: • The VIP receptor VPAC1 contains a putative NLS signal. • VPAC1 is predominantly nuclear in GBM cell lines but not VPAC2. • Non-nuclear VPAC1/2 protein expression is correlated with glioma grade. • Nuclear VPAC1 is observed in 50% of stage IV glioma (GBM). - Abstract: An increasing number of G protein-coupled receptors, like receptors for vasoactive intestinal peptide (VIP), are found in cell nucleus. As VIP receptors are involved in the regulation of glioma cell proliferation and migration, we investigated the expression and the nuclear localization of the VIP receptors VPAC1 and VPAC2 in this cancer. First, by applying Western blot and immunofluorescence detection in three human glioblastoma (GBM) cell lines, we observed a strong nuclear staining for the VPAC1 receptor and a weak nuclear VPAC2 receptor staining. Second, immunohistochemical staining of VPAC1 and VPAC2 on tissue microarrays (TMA) showed that the two receptors were expressed in normal brain and glioma tissues. Expression in the non-nuclear compartment of the two receptors significantly increased with the grade of the tumors. Analysis of nuclear staining revealed a significant increase of VPAC1 staining with glioma grade, with up to 50% of GBM displaying strong VPAC1 nuclear staining, whereas nuclear VPAC2 staining remained marginal. The increase in VPAC receptor expression with glioma grades and the enhanced nuclear localization of the VPAC1 receptors in GBM might be of importance for glioma progression.

  14. The SAP motif and C-terminal RS- and RD/E-rich region influences the sub-nuclear localization of Acinus isoforms.

    PubMed

    Wang, Fang; Wendling, Karen S; Soprano, Kenneth J; Soprano, Dianne Robert

    2014-12-01

    Acinus has been reported to function in apoptosis, RNA processing and regulation of gene transcription including RA-dependent transcription. There are three different isoforms of Acinus termed Acinus-L, Acinus-S', and Acinus-S. The isoforms of Acinus differ in their N-terminus while the C-terminus is consistent in all isoforms. The sub-nuclear localization of Acinus-L and Acinus-S' was determined using fluorescence microscopy. Acinus-S' colocalizes with SC35 in nuclear speckles while Acinus-L localizes diffusely throughout the nucleoplasm. RA treatment has little effect on the sub-nuclear localization of Acinus-L and Acinus-S'. The domains/regions necessary for the distinct sub-nuclear localization of Acinus-L and Acinus-S' were identified. The speckled sub-nuclear localization of Acinus-S' is dependent on its C-terminal RS- and RD/E-rich region but is independent of the phosphorylation status of Ser-453 and Ser-604 within this region. The unique N-terminal SAP motif of Acinus-L is responsible for its diffuse localization in the nucleus. Moreover, the sub-nuclear localization of Acinus isoforms is affected by each other, which is determined by the combinatorial effect of the more potent SAP motif of Acinus-L and the C-terminal RS- and RD/E-rich region in all Acinus isoforms. The C-terminal RS- and RD/E-rich region of Acinus mediates the colocalization of Acinus isoforms as well as with its interacting protein RNPS1. In conclusion, the SAP motif is responsible for the difference in the nuclear localization between Acinus-L and Acinus-S'. This difference in the nuclear localization of Acinus-S' and Acinus-L may suggest that these two isoforms have different functional roles. PMID:25079509

  15. Identification of an unconventional nuclear localization signal in human ribosomal protein S2

    SciTech Connect

    Antoine, M.; Reimers, K.; Wirz, W.; Gressner, A.M.; Mueller, R.; Kiefer, P. . E-Mail: pkiefer@ukaachen.de

    2005-09-16

    Ribosomal proteins must be imported into the nucleus after being synthesized in the cytoplasm. Since the rpS2 amino acid sequence does not contain a typical nuclear localization signal, we used deletion mutant analysis and rpS2-{beta}-galactosidase chimeric proteins to identify the nuclear targeting domains in rpS2. Nuclear rpS2 is strictly localized in the nucleoplasm and is not targeted to the nucleoli. Subcellular localization analysis of deletion mutants of rpS2-{beta}-galactosidase chimeras identified a central domain comprising 72 amino acids which is necessary and sufficient to target the chimeric {beta}-galactosidase to the nucleus. The nuclear targeting domain shares no significant similarity to already characterized nuclear localization signals in ribosomal proteins or other nuclear proteins. Although a Nup153 fragment containing the importin{beta} binding site fused to VP22 blocks nuclear import of rpS2-{beta}-galactosidase fusion proteins, nuclear uptake of rpS2 could be mediated by several import receptors since it binds to importin{alpha}/{beta} and transportin.

  16. Nucleolar and nuclear localization properties of a herpesvirus bZIP oncoprotein, MEQ.

    PubMed Central

    Liu, J L; Lee, L F; Ye, Y; Qian, Z; Kung, H J

    1997-01-01

    Marek's disease virus (MDV) is one of the most oncogenic herpesviruses and induces T lymphomas in chickens within weeks after infection. Only a limited number of viral transcripts are detected in MDV tumor samples and cell lines. One of the major transcripts encodes MEQ, a 339-amino-acid bZIP protein which is homologous to the Jun/Fos family of transcription factors. The C-terminal half of MEQ contains proline-rich repeats and, when fused to the DNA-binding domain of a yeast transcription factor, Gal4 (residues 1 to 147), exhibits transactivation function. MEQ can dimerize with itself and with c-Jun. The MEQ-c-Jun heterodimers bind to an AP-1-like enhancer within the MEQ promoter region with greater affinity than do homodimers of either protein, and they transactivate MEQ expression. Here we show that MEQ is expressed in the nucleus but, interestingly, with a predominant fraction in the nucleoli and coiled bodies. This makes MEQ the first bZIP protein to be identified in the nucleoli. MEQ contains two stretches of basic residues, designated basic region 1 (BR1) and basic region 2 (BR2). Using a series of deletion mutants, we have mapped the primary nuclear localization signal (NLS) and the sole nucleolar localization signal (NoLS) to the BR2 region. BR1 was shown to provide an auxiliary signal in nuclear translocation. To demonstrate that BR2 is an authentic NoLS, BR2 was fused to cytoplasmic v-Raf (delta gag) kinase. The BR2-Raf fusion protein was observed to migrate into the nucleoplasm and the nucleolus. The BR2 region can be further divided into two long arginine-lysine stretches, BR2N and BR2C, which are separated by the five amino acids Asn-Arg-Asp-Ala-Ala (NRDAA). We provide evidence that the requirement for nuclear translocation is less stringent than that for nucleolar translocation, as either BR2N or BR2C alone is sufficient to translocate the cytoplasmic v-Raf (delta gag) into the nucleus, but only in combination can they translocate v-Raf (delta gag

  17. Overlapping signal sequences control nuclear localization and endoplasmic reticulum retention of GRP58

    SciTech Connect

    Adikesavan, Anbu Karani; Unni, Emmanual; Jaiswal, Anil K.

    2008-12-12

    Glucose-regulated GRP58 has shown clinical applications to endoplasmic reticulum (ER) stress and cancer. GRP58 is localized in the cytosol, endoplasmic reticulum (ER) and nucleus. Twenty-four amino acids at the N-terminal hydrophobic region are known to target GRP58 to ER for synthesis at the ER membrane and translocation into the ER lumen. In addition, GRP58 contains putative nuclear localization (494KPKKKKK500) and ER retention (502QEDL505) signals. However, the role of these signals in nuclear import and ER retention of GRP58 remains unknown. Present studies investigated the signals that control nuclear localization and ER retention of GRP58. Deletion/mutation of nuclear localization signal (NLS) abrogated nuclear import of GRP58. NLS attached to EGFP localized EGFP in the nucleus. However, deletion/mutation of putative ER retention signal alone did not alter ER retention of GRP58. Interestingly, a combined deletion/mutation of NLS and ER retention signals blocked the GRP58 retention in the ER. These results concluded that overlapping NLS and ER retention signal sequences regulate nuclear localization and ER retention of GRP58.

  18. Hairless is a nuclear receptor corepressor essential for skin function

    PubMed Central

    Thompson, Catherine C.

    2009-01-01

    The activity of nuclear receptors is modulated by numerous coregulatory factors. Corepressors can either mediate the ability of nuclear receptors to repress transcription, or can inhibit transactivation by nuclear receptors. As we learn more about the mechanisms of transcriptional repression, the importance of repression by nuclear receptors in development and disease has become clear. The protein encoded by the mammalian Hairless (Hr) gene was shown to be a corepressor by virtue of its functional similarity to the well-established corepressors N-CoR and SMRT. Mutation of the Hr gene results in congenital hair loss in both mice and men. Investigation of Hairless function both in vitro and in mouse models in vivo has revealed a critical role in maintaining skin and hair by regulating the differentiation of epithelial stem cells, as well as a putative role in regulating gene expression via chromatin remodeling. PMID:20087431

  19. Involvement of Local Lamellipodia in Endothelial Barrier Function

    PubMed Central

    Breslin, Jerome W.; Zhang, Xun E.; Worthylake, Rebecca A.; Souza-Smith, Flavia M.

    2015-01-01

    Recently we observed that endothelial cells cultured in tightly confluent monolayers display frequent local lamellipodia, and that thrombin, an agent that increases endothelial permeability, reduces lamellipodia protrusions. This led us to test the hypothesis that local lamellipodia contribute to endothelial barrier function. Movements of subcellular structures containing GFP-actin or VE-cadherin-GFP expressed in endothelial cells were recorded using time-lapse microscopy. Transendothelial electrical resistance (TER) served as an index of endothelial barrier function. Changes in both lamellipodia dynamics and TER were assessed during baseline and after cells were treated with either the barrier-disrupting agent thrombin, or the barrier-stabilizing agent sphingosine-1-phosphate (S1P). The myosin II inhibitor blebbistatin was used to selectively block lamellipodia formation, and was used to test their role in the barrier function of endothelial cell monolayers and isolated, perfused rat mesenteric venules. Myosin light chain (MLC) phosphorylation was assessed by immunofluorescence microscopy. Rac1 and RhoA activation were evaluated using G-LISA assays. The role of Rac1 was tested with the specific inhibitor NSC23766 or by expressing wild-type or dominant negative GFP-Rac1. The results show that thrombin rapidly decreased both TER and the lamellipodia protrusion frequency. S1P rapidly increased TER in association with increased protrusion frequency. Blebbistatin nearly abolished local lamellipodia protrusions while cortical actin fibers and stress fibers remained intact. Blebbistatin also significantly decreased TER of cultured endothelial cells and increased permeability of isolated rat mesenteric venules. Both thrombin and S1P increased MLC phosphorylation and activation of RhoA. However, thrombin and S1P had differential impacts on Rac1, correlating with the changes in TER and lamellipodia protrusion frequency. Overexpression of Rac1 elevated, while NSC23766 and

  20. Involvement of local lamellipodia in endothelial barrier function.

    PubMed

    Breslin, Jerome W; Zhang, Xun E; Worthylake, Rebecca A; Souza-Smith, Flavia M

    2015-01-01

    Recently we observed that endothelial cells cultured in tightly confluent monolayers display frequent local lamellipodia, and that thrombin, an agent that increases endothelial permeability, reduces lamellipodia protrusions. This led us to test the hypothesis that local lamellipodia contribute to endothelial barrier function. Movements of subcellular structures containing GFP-actin or VE-cadherin-GFP expressed in endothelial cells were recorded using time-lapse microscopy. Transendothelial electrical resistance (TER) served as an index of endothelial barrier function. Changes in both lamellipodia dynamics and TER were assessed during baseline and after cells were treated with either the barrier-disrupting agent thrombin, or the barrier-stabilizing agent sphingosine-1-phosphate (S1P). The myosin II inhibitor blebbistatin was used to selectively block lamellipodia formation, and was used to test their role in the barrier function of endothelial cell monolayers and isolated, perfused rat mesenteric venules. Myosin light chain (MLC) phosphorylation was assessed by immunofluorescence microscopy. Rac1 and RhoA activation were evaluated using G-LISA assays. The role of Rac1 was tested with the specific inhibitor NSC23766 or by expressing wild-type or dominant negative GFP-Rac1. The results show that thrombin rapidly decreased both TER and the lamellipodia protrusion frequency. S1P rapidly increased TER in association with increased protrusion frequency. Blebbistatin nearly abolished local lamellipodia protrusions while cortical actin fibers and stress fibers remained intact. Blebbistatin also significantly decreased TER of cultured endothelial cells and increased permeability of isolated rat mesenteric venules. Both thrombin and S1P increased MLC phosphorylation and activation of RhoA. However, thrombin and S1P had differential impacts on Rac1, correlating with the changes in TER and lamellipodia protrusion frequency. Overexpression of Rac1 elevated, while NSC23766 and

  1. Localization of Pom121 to the inner nuclear membrane is required for an early step of interphase nuclear pore complex assembly

    PubMed Central

    Funakoshi, Tomoko; Clever, Michaela; Watanabe, Ai; Imamoto, Naoko

    2011-01-01

    The nuclear pore complex (NPC) is a large protein assembly that mediates molecular trafficking between the cytoplasm and the nucleus. NPCs assemble twice during the cell cycle in metazoans: postmitosis and during interphase. In this study, using small interfering RNA (siRNA) in conjunction with a cell fusion–based NPC assembly assay, we demonstrated that pore membrane protein (Pom)121, a vertebrate-specific integral membrane nucleoporin, is indispensable for an early step in interphase NPC assembly. Functional domain analysis of Pom121 showed that its nuclear localization signals, which bind to importin β via importin α and likely function with RanGTP, play an essential role in targeting Pom121 to the interphase NPC. Furthermore, a region of Pom121 that interacts with the inner nuclear membrane (INM) and lamin B receptor was found to be crucial for its NPC targeting. Based on these findings and on evidence that Pom121 localizes at the INM in the absence of a complete NPC structure, we propose that the nuclear migration of Pom121 and its subsequent interaction with INM proteins are required to initiate interphase NPC assembly. Our data also suggest, for the first time, the importance of the INM as a seeding site for “prepores” during interphase NPC assembly. PMID:21289085

  2. Calculating dispersion interactions using maximally localized Wannier functions.

    PubMed

    Andrinopoulos, Lampros; Hine, Nicholas D M; Mostofi, Arash A

    2011-10-21

    We investigate a recently developed approach [P. L. Silvestrelli, Phys. Rev. Lett. 100, 053002 (2008); J. Phys. Chem. A 113, 5224 (2009)] that uses maximally localized Wannier functions to evaluate the van der Waals contribution to the total energy of a system calculated with density-functional theory. We test it on a set of atomic and molecular dimers of increasing complexity (argon, methane, ethene, benzene, phthalocyanine, and copper phthalocyanine) and demonstrate that the method, as originally proposed, has a number of shortcomings that hamper its predictive power. In order to overcome these problems, we have developed and implemented a number of improvements to the method and show that these modifications give rise to calculated binding energies and equilibrium geometries that are in closer agreement to results of quantum-chemical coupled-cluster calculations. PMID:22029295

  3. Learning Task-Optimal Registration Cost Functions for Localizing Cytoarchitecture and Function in the Cerebral Cortex

    PubMed Central

    Sabuncu, Mert R.; Vercauteren, Tom; Holt, Daphne J.; Amunts, Katrin; Zilles, Karl; Golland, Polina; Fischl, Bruce

    2013-01-01

    Image registration is typically formulated as an optimization problem with multiple tunable, manually set parameters. We present a principled framework for learning thousands of parameters of registration cost functions, such as a spatially-varying tradeoff between the image dissimilarity and regularization terms. Our approach belongs to the classic machine learning framework of model selection by optimization of cross-validation error. This second layer of optimization of cross-validation error over and above registration selects parameters in the registration cost function that result in good registration as measured by the performance of the specific application in a training data set. Much research effort has been devoted to developing generic registration algorithms, which are then specialized to particular imaging modalities, particular imaging targets and particular postregistration analyses. Our framework allows for a systematic adaptation of generic registration cost functions to specific applications by learning the “free” parameters in the cost functions. Here, we consider the application of localizing underlying cytoarchitecture and functional regions in the cerebral cortex by alignment of cortical folding. Most previous work assumes that perfectly registering the macro-anatomy also perfectly aligns the underlying cortical function even though macro-anatomy does not completely predict brain function. In contrast, we learn 1) optimal weights on different cortical folds or 2) optimal cortical folding template in the generic weighted sum of squared differences dissimilarity measure for the localization task. We demonstrate state-of-the-art localization results in both histological and functional magnetic resonance imaging data sets. PMID:20529736

  4. Nuclear correlation functions in lattice QCD

    SciTech Connect

    Detmold, William; Orginos, Konstantinos

    2013-06-01

    We consider the problem of calculating the large number of Wick contractions necessary to compute states with the quantum numbers of many baryons in lattice QCD. We consider a constructive approach and a determinant-based approach and show that these methods allow the required contractions to be performed for certain choices of interpolating operators. Examples of correlation functions computed using these techniques are shown for the quantum numbers of the light nuclei, $^4$He, $^8$Be, $^{12}$C, $^{16}$O and $^{28}$Si.

  5. Exact density functional and wave function embedding schemes based on orbital localization

    NASA Astrophysics Data System (ADS)

    Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály

    2016-08-01

    Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

  6. To the non-local theory of cold nuclear fusion.

    PubMed

    Alexeev, Boris V

    2014-10-01

    In this paper, we revisit the cold fusion (CF) phenomenon using the generalized Bolzmann kinetics theory which can represent the non-local physics of this CF phenomenon. This approach can identify the conditions when the CF can take place as the soliton creation under the influence of the intensive sound waves. The vast mathematical modelling leads to affirmation that all parts of soliton move with the same velocity and with the small internal change of the pressure. The zone of the high density is shaped on the soliton's front. It means that the regime of the 'acoustic CF' could be realized from the position of the non-local hydrodynamics. PMID:26064528

  7. Nuclear cardiology: Myocardial perfusion and function

    SciTech Connect

    Seldin, D.W. )

    1991-08-01

    Myocardial perfusion studies continue to be a major focus of research, with new investigations of the relationship of exercise-redistribution thallium imaging to diagnosis, prognosis, and case management. The redistribution phenomenon, which seemed to be fairly well understood a few years ago, is now recognized to be much more complex than originally thought, and various strategies have been proposed to clarify the meaning of persistent defects. Pharmacologic intervention with dipyridamole and adenosine has become available as an alternative to exercise, and comparisons with exercise imaging and catheterization results have been described. Thallium itself is no longer the sole single-photon perfusion radiopharmaceutical; two new technetium agents are now widely available. In addition to perfusion studies, advances in the study of ventricular function have been made, including reports of studies performed in conjunction with technetium perfusion studies, new insights into cardiac physiology, and the prognostic and case-management information that function studies provide. Finally, work has continued with monoclonal antibodies for the identification of areas of myocyte necrosis. 41 references.

  8. A-dependence of weak nuclear structure functions

    SciTech Connect

    Haider, H.; Athar, M. Sajjad; Simo, I. Ruiz

    2015-05-15

    Effect of nuclear medium on the weak structure functions F{sub 2}{sup A}(x, Q{sup 2}) and F{sub 3}{sup A}(x, Q{sup 2}) have been studied using charged current (anti)neutrino deep inelastic scattering on various nuclear targets. Relativistic nuclear spectral function which incorporate Fermi motion, binding and nucleon correlations are used for the calculations. We also consider the pion and rho meson cloud contributions calculated from a microscopic model for meson-nucleus self-energies. Using these structure functions, F{sub i}{sup A}/F{sub i}{sup proton} and F{sub i}{sup A}/F{sub i}{sup deuteron}(i=2,3, A={sup 12}C, {sup 16}O, CH and H{sub 2}O) are obtained.

  9. Local functional descriptors for surface comparison based binding prediction

    PubMed Central

    2012-01-01

    Background Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to predict interactions without regard to the underlying structural scaffold that creates the surface. Results We present a new descriptor for protein functional surfaces and algorithms for using these descriptors to compare protein surface regions to identify ligand binding interfaces. Our approach uses descriptors of local regions of the surface, and assembles collections of matches to compare larger regions. Our approach uses a variety of physical, chemical, and geometric properties, adaptively weighting these properties as appropriate for different regions of the interface. Our approach builds a classifier based on a training corpus of examples of binding sites of the target ligand. The constructed classifiers can be applied to a query protein providing a probability for each position on the protein that the position is part of a binding interface. We demonstrate the effectiveness of the approach on a number of benchmarks, demonstrating performance that is comparable to the state-of-the-art, with an approach with more generality than these prior methods. Conclusions Local functional descriptors offer a new method for protein surface comparison that is sufficiently flexible to serve in a variety of applications. PMID:23176080

  10. Interferon regulatory factor subcellular localization is determined by a bipartite nuclear localization signal in the DNA-binding domain and interaction with cytoplasmic retention factors

    PubMed Central

    Lau, Joe F.; Parisien, Jean-Patrick; Horvath, Curt M.

    2000-01-01

    The transduction of type I interferon signals to the nucleus relies on activation of a protein complex, ISGF3, involving two signal transducers and activators of transcription (STAT) proteins, STAT1 and STAT2, and the interferon (IFN) regulatory factor (IRF) protein, p48/ISGF3γ. The STAT subunits are cytoplasmically localized in unstimulated cells and rapidly translocate to the nucleus of IFN-stimulated cells, but the p48/ISGF3γ protein is found in both the nucleus and the cytoplasm, regardless of IFN stimulation. Here, we demonstrate that p48 is efficiently and constitutively targeted to the nucleus. Analysis of the subcellular distribution of green fluorescent protein-p48 fragments indicates that p48 contains a bipartite nuclear retention signal within its amino-terminal DNA-binding domain. This signal is preserved in two other IRF proteins involved in immune responses, ICSBP and IRF4. Mutations to clustered basic residues within amino acids 50–100 of p48 or IRF4 disrupt their nuclear accumulation, and DNA-binding ability is not required for nuclear targeting. This is the only example of a nuclear localization signal for any ISGF3 component and assigns a second function to the IRF DNA-binding domain. We also demonstrate that the nuclear distribution of p48 is dramatically altered by coexpression of the STAT2 protein, indicating that STAT2 forms a cytoplasmic complex with p48, overriding the intrinsic p48 nuclear targeting. Retention by STAT2 may serve to regulate the activity of free p48 and/or guarantee that cytoplasmic pools of preassociated STAT2:p48 are available for rapid activation of the IFN response. These findings suggest that analogous mechanisms may exist for regulating the distribution of other IRF proteins. PMID:10860992

  11. Maximally-localized Wannier functions for GW quasiparticles

    NASA Astrophysics Data System (ADS)

    Hamann, D. R.; Vanderbilt, David

    2009-03-01

    Recent efforts carrying the GW many-body approximation to self-consistency have given improved electronic structure results.^1 Maximally-localized Wannier functions^2 formed from the quasiparticle wave functions^3 provide an efficient and highly accurate basis for interpolating the SCGW bands from a coarse Brillouin-zone mesh to symmetry lines. Since the MLWF's correspond to chemists' bond orbitals, they potentially also provide insight into the qualitative effects of the improved treatment of correlations in SCGW compared to LDA. We report results on SrTiO3, solid Ar, and molecular CO. Band interpolation is accurate and effective for both solids. Small shifts in the degree of hybridization can be visualized for some of the SrTiO3 and CO MLWF's. In Ar, individual conduction-band Bloch functions were found to have large differences between LDA and SCGW.^1 However, a manifold of 9 d and spd-hybrid MLWF's which proved to be the minimum necessary for the lower conduction bands showed minimal differences in the two cases. A fully-functional interface to the WANNIER90 library within the SCGW-capable ABINIT code has been implemented and will be publicly available in the near future. 1. F. Bruneval et al., Phys. Rev. B 74, 045102 (2006). 2. N. Marzari and D. Vanderbilt, Phys. Rev. B 56, 12 847 (1997). 3. M. van Schilfgaarde et al., Phys. Rev. Lett. 96, 226402 (2006).

  12. Lysine 271 but not lysine 210 of XRCC4 is required for the nuclear localization of XRCC4 and DNA ligase IV.

    PubMed

    Fukuchi, Mikoto; Wanotayan, Rujira; Liu, Sicheng; Imamichi, Shoji; Sharma, Mukesh Kumar; Matsumoto, Yoshihisa

    2015-06-12

    XRCC4 and DNA Ligase IV (LIG4) cooperate to join two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). However, it is not fully understood how these proteins are localized to the nucleus. Here we created XRCC4(K271R) mutant, as Lys271 lies within the putative nuclear localization signal (NLS), and XRCC4(K210R) mutant, as Lys210 was reported to undergo SUMOylation, implicated in the nuclear localization of XRCC4. Wild-type and mutated XRCC4 with EGFP tag were introduced into HeLa cell, in which endogenous XRCC4 had been knocked down using siRNA directed to 3'-untranslated region, and tested for the nuclear localization function by fluorescence microscopy. XRCC4(K271R) was defective in the nuclear localization of itself and LIG4, whereas XRCC4(K210R) was competent for the nuclear localization with LIG4. To examine DSB repair function, wild-type and mutated XRCC4 were introduced into XRCC4-deficient M10. M10-XRCC4(K271R), but not M10-XRCC4(K210R), showed significantly reduced surviving fraction after 2 Gy γ-ray irradiation as compared to M10-XRCC4(WT). The number of γ-H2AX foci remaining 2 h after 2 Gy γ-ray irradiation was significantly greater in M10-XRCC4(K271R) than in M10-XRCC4(WT), whereas it was only marginally increased in M10-XRCC4(K210R) as compared to M10-XRCC4(WT). The present results collectively indicated that Lys271, but not Lys210, of XRCC4 is required for the nuclear localization of XRCC4 and LIG4 and that the nuclear localizing ability is essential for DSB repair function of XRCC4. PMID:25934149

  13. Characterization of the nuclear localization signals of duck circovirus replication proteins.

    PubMed

    Wang, X; Wu, Z; Xiang, Q; Li, Z; Zhang, R; Chen, J; Xia, L; Lin, S; Yu, W; Ma, Z; Xie, Z; Jiang, S

    2015-12-01

    Duck circovirus (DuCV) possess a circular, single-stranded DNA genome that requires the replication protein (Rep) for its replication. Based on the viral genotype, there are two categories of Rep proteins: Rep1 and Rep2. To characterize the nuclear localization signals (NLSs) conferring the nuclear localization of the Rep proteins, defined coding regions of the rep gene of two genotypes of DuCV were cloned and co-expressed with the red fluorescent protein DsRed2. The results showed that deleting the putative N-terminal NLS located at amino acid residues 10-37 of Rep1 and Rep2 abrogated nuclear translocation, while deleting the putative C-terminal NLS located at residues 244-274 of Rep1 did not significantly alter its subcellular localization, confirming that only the NLS located at residues 10-37 in the N-termini of the Rep proteins had nuclear targeting activity. PMID:26666192

  14. Nuclear AURKA acquires kinase-independent transactivating function to enhance breast cancer stem cell phenotype

    PubMed Central

    Zheng, Feimeng; Yue, Caifeng; Li, Guohui; He, Bin; Cheng, Wei; Wang, Xi; Yan, Min; Long, Zijie; Qiu, Wanshou; Yuan, Zhongyu; Xu, Jie; Liu, Bing; Shi, Qian; Lam, Eric W.-F.; Hung, Mien-Chie; Liu, Quentin

    2016-01-01

    Centrosome-localized mitotic Aurora kinase A (AURKA) facilitates G2/M events. Here we show that AURKA translocates to the nucleus and causes distinct oncogenic properties in malignant cells by enhancing breast cancer stem cell (BCSC) phenotype. Unexpectedly, this function is independent of its kinase activity. Instead, AURKA preferentially interacts with heterogeneous nuclear ribonucleoprotein K (hnRNP K) in the nucleus and acts as a transcription factor in a complex that induces a shift in MYC promoter usage and activates the MYC promoter. Blocking AURKA nuclear localization inhibits this newly discovered transactivating function of AURKA, sensitizing resistant BCSC to kinase inhibition. These findings identify a previously unknown oncogenic property of the spatially deregulated AURKA in tumorigenesis and provide a potential therapeutic opportunity to overcome kinase inhibitor resistance. PMID:26782714

  15. Autographa californica Multiple Nucleopolyhedrovirus DNA Polymerase C Terminus Is Required for Nuclear Localization and Viral DNA Replication

    PubMed Central

    Feng, Guozhong

    2014-01-01

    ABSTRACT The DNA polymerase (DNApol) of the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is essential for viral DNA replication. The DNApol exonuclease and polymerase domains are highly conserved and are considered functional in DNA replication. However, the role of the DNApol C terminus has not yet been characterized. To identify whether only the exonuclease and polymerase domains are sufficient for viral DNA replication, several DNApol C-terminal truncations were cloned into a dnapol-null AcMNPV bacmid with a green fluorescent protein (GFP) reporter. Surprisingly, most of the truncation constructs, despite containing both exonuclease and polymerase domains, could not rescue viral DNA replication and viral production in bacmid-transfected Sf21 cells. Moreover, GFP fusions of these same truncations failed to localize to the nucleus. Truncation of the C-terminal amino acids 950 to 984 showed nuclear localization but allowed for only limited and delayed viral spread. The C terminus contains a typical bipartite nuclear localization signal (NLS) motif at residues 804 to 827 and a monopartite NLS motif at residues 939 to 948. Each NLS, as a GFP fusion peptide, localized to the nucleus, but both NLSs were required for nuclear localization of DNApol. Alanine substitutions in a highly conserved baculovirus DNApol sequence at AcMNPV DNApol amino acids 972 to 981 demonstrated its importance for virus production and DNA replication. Collectively, the data indicated that the C terminus of AcMNPV DNApol contains two NLSs and a conserved motif, all of which are required for nuclear localization of DNApol, viral DNA synthesis, and virus production. IMPORTANCE The baculovirus DNA polymerase (DNApol) is a highly specific polymerase that allows viral DNA synthesis and hence virus replication in infected insect cells. We demonstrated that the exonuclease and polymerase domains of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) alone are

  16. The nuclear localization of SOCS6 requires the N-terminal region and negatively regulates Stat3 protein levels

    SciTech Connect

    Hwang, Mi-Na; Min, Chan-Hee; Kim, Hyung Sik; Lee, Ho; Yoon, Kyong-Ah; Park, Sung Yong; Lee, Eun Sook; Yoon, Sungpil . E-mail: yoons@ncc.re.kr

    2007-08-24

    We determined that endogenous- and overexpressed- SOCS6 was localized in both the nucleus and cytoplasm. The localization of SOCS6 depended on amino acids 1-210 in the N-terminal region of the protein, which contains an unidentified domain. GFP-tagged SOCS6 or the N-terminal region, was exclusively localized and widely distributed throughout the entire nucleus, whereas the C-terminal region displayed a nuclear omission pattern. We also demonstrated that the SOCS6 protein could decrease the levels of the Stat3 protein in the nucleus, and that its negative regulation of the Stat3 protein level was dependent on its C-terminal region. These observations suggest that SOCS6 is composed of at least two functional domains required for its biological role in localizing and degrading Stat3 in the nucleus.

  17. To the non-local theory of cold nuclear fusion

    PubMed Central

    Alexeev, Boris V.

    2014-01-01

    In this paper, we revisit the cold fusion (CF) phenomenon using the generalized Bolzmann kinetics theory which can represent the non-local physics of this CF phenomenon. This approach can identify the conditions when the CF can take place as the soliton creation under the influence of the intensive sound waves. The vast mathematical modelling leads to affirmation that all parts of soliton move with the same velocity and with the small internal change of the pressure. The zone of the high density is shaped on the soliton's front. It means that the regime of the ‘acoustic CF’ could be realized from the position of the non-local hydrodynamics. PMID:26064528

  18. Lysine 271 but not lysine 210 of XRCC4 is required for the nuclear localization of XRCC4 and DNA ligase IV

    SciTech Connect

    Fukuchi, Mikoto; Wanotayan, Rujira; Liu, Sicheng; Imamichi, Shoji; Sharma, Mukesh Kumar; Matsumoto, Yoshihisa

    2015-06-12

    XRCC4 and DNA Ligase IV (LIG4) cooperate to join two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). However, it is not fully understood how these proteins are localized to the nucleus. Here we created XRCC4{sup K271R} mutant, as Lys271 lies within the putative nuclear localization signal (NLS), and XRCC4{sup K210R} mutant, as Lys210 was reported to undergo SUMOylation, implicated in the nuclear localization of XRCC4. Wild-type and mutated XRCC4 with EGFP tag were introduced into HeLa cell, in which endogenous XRCC4 had been knocked down using siRNA directed to 3′-untranslated region, and tested for the nuclear localization function by fluorescence microscopy. XRCC4{sup K271R} was defective in the nuclear localization of itself and LIG4, whereas XRCC4{sup K210R} was competent for the nuclear localization with LIG4. To examine DSB repair function, wild-type and mutated XRCC4 were introduced into XRCC4-deficient M10. M10-XRCC4{sup K271R}, but not M10-XRCC4{sup K210R}, showed significantly reduced surviving fraction after 2 Gy γ-ray irradiation as compared to M10-XRCC4{sup WT}. The number of γ-H2AX foci remaining 2 h after 2 Gy γ-ray irradiation was significantly greater in M10-XRCC4{sup K271R} than in M10-XRCC4{sup WT}, whereas it was only marginally increased in M10-XRCC4{sup K210R} as compared to M10-XRCC4{sup WT}. The present results collectively indicated that Lys271, but not Lys210, of XRCC4 is required for the nuclear localization of XRCC4 and LIG4 and that the nuclear localizing ability is essential for DSB repair function of XRCC4. - Highlights: • XRCC4{sup K271R} is defective in the nuclear localization of itself and LIG4. • XRCC4{sup K210R} is competent for the nuclear localization of itself and LIG4. • XRCC4{sup K271R} is deficient in DSB repair function. • XRCC4{sup K210R} is mostly normal in DSB repair function.

  19. A combined nuclear and nucleolar localization motif in activation-induced cytidine deaminase (AID) controls immunoglobulin class switching.

    PubMed

    Hu, Yi; Ericsson, Ida; Torseth, Kathrin; Methot, Stephen P; Sundheim, Ottar; Liabakk, Nina B; Slupphaug, Geir; Di Noia, Javier M; Krokan, Hans E; Kavli, Bodil

    2013-01-23

    Activation-induced cytidine deaminase (AID) is a DNA mutator enzyme essential for adaptive immunity. AID initiates somatic hypermutation and class switch recombination (CSR) by deaminating cytosine to uracil in specific immunoglobulin (Ig) gene regions. However, other loci, including cancer-related genes, are also targeted. Thus, tight regulation of AID is crucial to balance immunity versus disease such as cancer. AID is regulated by several mechanisms including nucleocytoplasmic shuttling. Here we have studied nuclear import kinetics and subnuclear trafficking of AID in live cells and characterized in detail its nuclear localization signal. Importantly, we find that the nuclear localization signal motif also directs AID to nucleoli where it colocalizes with its interaction partner, catenin-β-like 1 (CTNNBL1), and physically associates with nucleolin and nucleophosmin. Moreover, we demonstrate that release of AID from nucleoli is dependent on its C-terminal motif. Finally, we find that CSR efficiency correlates strongly with the arithmetic product of AID nuclear import rate and DNA deamination activity. Our findings suggest that directional nucleolar transit is important for the physiological function of AID and demonstrate that nuclear/nucleolar import and DNA cytosine deamination together define the biological activity of AID. This is the first study on subnuclear trafficking of AID and demonstrates a new level in its complex regulation. In addition, our results resolve the problem related to dissociation of deamination activity and CSR activity of AID mutants. PMID:23183374

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

    PubMed Central

    Dang, Van-Dinh; Levin, Henry L.

    2000-01-01

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

  1. Quantum-defect functions. Interconverters of electronic and nuclear motion

    SciTech Connect

    Dill, D.; Jungen, C.

    1980-08-21

    In 1964 Mulliken systematically extended the ideas of Rydberg states and quantum defects from atoms to molecules. The key point of that extension is stated in several sentences: In molecules...all that has just been stated for atomic Rydberg states finds a parallel if one considers any one fixed nuclear configuration... However the mode of variation of the MOs and their energies as one varies the nuclear configuration is a new feature of interest. A complication...is the fact that the interaction of the molecular rotation with the l vector of the Rydberg electron changes radically as n increases in a Rydberg series. Thereby Mulliken introduced the concept of the quantum-defect function, ..mu lambda..(R), depending on nuclear configuration R and orbital-momentum projection ..lambda.. along the molecular axis. This concept has emerged as central to the understanding of the interconversion of electronic and nuclear motion in molecular systems. 13 figures.

  2. The N-terminus of porcine circovirus type 2 replication protein is required for nuclear localization and ori binding activities

    SciTech Connect

    Lin, W.-L.; Chien, M.-S.; Du, Y.-W.; Wu, P.-C.; Huang Chienjin

    2009-02-20

    Porcine circovirus type 2 possesses a circular, single-stranded DNA genome that requires the replication protein (Rep) for virus replication. To characterize the DNA binding potential and the significant region that confers the nuclear localization of the Rep protein, the defined coding regions of rep gene were cloned and expressed. All of the recombinant proteins except for the N-terminal 110 residues deletion mutant could bind to the double-stranded minimal binding site of replication origin (ori). In addition, the N-terminal deletion mutant lacking 110 residues exhibited mainly cytoplasmic staining in the transfected cells in contrast to the others, which localized dominantly in the nucleus, suggesting that this N-terminal domain is essential for nuclear localization. Furthermore, a series of green fluorescence proteins (GFP) containing potential nuclear localization signal (NLS) sequences were tested for their cellular distribution. The ability of the utmost 20 residues of the N-terminal region to target the GFP to the nucleus confirmed its role as a functional NLS.

  3. The role of local scale heterogeneities in terrestrial ecosystem functioning

    NASA Astrophysics Data System (ADS)

    Pappas, C.; Fatichi, S.; Rimkus, S.; Burlando, P.; Bugmann, H.; Huber, M.

    2013-12-01

    The coarse-grained spatial representation of many terrestrial ecosystem models hampers the importance of local scale heterogeneities. To discuss this issue, we combine a range of observations (forest inventories, eddy flux tower data, remote sensing products) and modeling approaches which allow us to investigate the role of local climate, topography and initial conditions (land cover and soil properties) when simulating vegetation dynamics. Three approaches for modeling terrestrial ecosystems, with contrasting degrees of abstraction, were selected: (i) LPJ, a well-established, area-based, Dynamic Global Vegetation Model (DGVM) that incorporates plant physiological and biogeochemical processes; (ii) LPJ-GUESS, a hybrid, individual-based approach that additionally considers more detailed processes of plant population dynamics; and (iii) D-LPJ, a spatially distributed version of LPJ, operating at a fine resolution (100m x 100m), which uses an enhanced hydrological representation accounting for lateral connectivity of surface and subsurface water fluxes. By confronting model simulations with a multivariate data-set available at the catchment scale, we argue that: (i) local environmental and topographic attributes that are often ignored or at best crudely represented within DGVM applications exert a strong control on terrestrial ecosystem functioning; (ii) the assumption of steady-state vegetation and soil carbon pools at the beginning of simulation studies (e.g., under 'current conditions'), as embedded in many DGVM applications, is in contradiction with the current state of many forests that, due to natural or anthropogenic disturbances, are often out of equilibrium; (iii) model evaluation against vegetation carbon fluxes (i.e., photosynthetic activity and respiration rates) does not imply an accurate simulation of vegetation carbon stocks (i.e., biomass). In addition, having gained insights about model performance at the catchment scale, where a wealth of information

  4. Public meetings on nuclear waste management: their function and organization

    SciTech Connect

    Duvernoy, E.G.; Marcus, A.A.; Overcast, T.; Schilling, A.H.

    1981-05-01

    This report focuses on public meetings as a vehicle for public participation in nuclear waste management. The nature of public meetings is reviewed and the functions served by meetings highlighted. The range of participants and their concerns are addressed, including a review of the participants from past nuclear waste management meetings. A sound understanding of the expected participants allows DOE to tailor elements of the meeting, such as notification, format, and agenda to accommodate the attendees. Finally, the report discusses the organization of public meetings on nuclear waste management in order to enhance the DOE's functions for such meetings. Possible structures are suggested for a variety of elements that are relevant prior to, during and after the public meeting. These suggestions are intended to supplement the DOE Public Participation Manual.

  5. Uncertainty Quantification and Propagation in Nuclear Density Functional Theory

    SciTech Connect

    Schunck, N; McDonnell, J D; Higdon, D; Sarich, J; Wild, S M

    2015-03-17

    Nuclear density functional theory (DFT) is one of the main theoretical tools used to study the properties of heavy and superheavy elements, or to describe the structure of nuclei far from stability. While on-going eff orts seek to better root nuclear DFT in the theory of nuclear forces, energy functionals remain semi-phenomenological constructions that depend on a set of parameters adjusted to experimental data in fi nite nuclei. In this paper, we review recent eff orts to quantify the related uncertainties, and propagate them to model predictions. In particular, we cover the topics of parameter estimation for inverse problems, statistical analysis of model uncertainties and Bayesian inference methods. Illustrative examples are taken from the literature.

  6. BUILDING A UNIVERSAL NUCLEAR ENERGY DENSITY FUNCTIONAL (UNEDF)

    SciTech Connect

    Nazarewicz, Witold

    2012-07-01

    The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties. Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data. Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

  7. Local structure studies of materials using pair distribution function analysis

    NASA Astrophysics Data System (ADS)

    Peterson, Joseph W.

    A collection of pair distribution function studies on various materials is presented in this dissertation. In each case, local structure information of interest pushes the current limits of what these studies can accomplish. The goal is to provide insight into the individual material behaviors as well as to investigate ways to expand the current limits of PDF analysis. Where possible, I provide a framework for how PDF analysis might be applied to a wider set of material phenomena. Throughout the dissertation, I discuss 0 the capabilities of the PDF method to provide information pertaining to a material's structure and properties, ii) current limitations in the conventional approach to PDF analysis, iii) possible solutions to overcome certain limitations in PDF analysis, and iv) suggestions for future work to expand and improve the capabilities PDF analysis.

  8. A modified Monte Carlo 'local importance function transform' method

    SciTech Connect

    Keady, K. P.; Larsen, E. W.

    2013-07-01

    The Local Importance Function Transform (LIFT) method uses an approximation of the contribution transport problem to bias a forward Monte-Carlo (MC) source-detector simulation [1-3]. Local (cell-based) biasing parameters are calculated from an inexpensive deterministic adjoint solution and used to modify the physics of the forward transport simulation. In this research, we have developed a new expression for the LIFT biasing parameter, which depends on a cell-average adjoint current to scalar flux (J{sup *}/{phi}{sup *}) ratio. This biasing parameter differs significantly from the original expression, which uses adjoint cell-edge scalar fluxes to construct a finite difference estimate of the flux derivative; the resulting biasing parameters exhibit spikes in magnitude at material discontinuities, causing the original LIFT method to lose efficiency in problems with high spatial heterogeneity. The new J{sup *}/{phi}{sup *} expression, while more expensive to obtain, generates biasing parameters that vary smoothly across the spatial domain. The result is an improvement in simulation efficiency. A representative test problem has been developed and analyzed to demonstrate the advantage of the updated biasing parameter expression with regards to solution figure of merit (FOM). For reference, the two variants of the LIFT method are compared to a similar variance reduction method developed by Depinay [4, 5], as well as MC with deterministic adjoint weight windows (WW). (authors)

  9. Localization and potential function of kindlin-1 in periodontal tissues

    PubMed Central

    Petricca, Giorgio; Leppilampi, Mari; Jiang, Guoqiao; Owen, Gethin Rhys; Wiebe, Colin; Tu, Yizeng; Koivisto, Leeni; Häkkinen, Lari; Wu, Chuanyue; Larjava, Hannu

    2009-01-01

    Kindlin-1 is an intracellular focal adhesion protein that regulates actin cytoskeleton. Patients suffering from Kindler syndrome have a homologous mutation of the kindlin-1 gene and develop skin blisters, periodontal disease and intestinal complications because of deficient adhesion of the basal epithelial cells. We investigated kindlin-1 localization in periodontal tissue and its functions in cultured keratinocytes and showed that kindlin-1 co-localizes with migfilin and paxillin in the basal epithelial cells of oral mucosa and in cultured keratinocytes. The kindlin-1 deficient oral mucosal tissue from a Kindler syndrome patient showed a complete lack of paxillin and reduced migfilin immunostaining in the basal keratinocytes. Co-immunoprecipitation showed that migfilin directly interacted with kindlin-1. RNA interference-induced kindlin-1 deficiency in keratinocytes led to an altered distribution of migfilin containing focal adhesions, reduced cell spreading, decreased cell proliferation and decelerated cell migration. Disruption of microtubules in the kindling-1-deficient cells further reduced cell spreading, suggesting that microtubules can partially compensate for kindlin-1 deficiency. Kindlin-1 supported mature cell-extracellular matrix adhesions of keratinocytes, as downregulation of kindlin-1 expression significantly reduced cell adhesion strength. In summary, kindlin-1 interacts with migfilin and plays a crucial role in actin-dependent keratinocyte cell adhesion essential for epidermal and periodontal health. PMID:19758247

  10. A conformational change in PBX1A is necessary for its nuclear localization.

    PubMed

    Saleh, M; Huang, H; Green, N C; Featherstone, M S

    2000-10-10

    The fly homeodomain (HD) protein EXTRADENTICLE (EXD) is dependent on a second HD protein, HOMOTHORAX (HTH), for nuclear localization. We show here that in insect cells the mammalian homolog of EXD, PBX1A, shows a similar dependence on the HTH homologs MEIS1, 2, and 3 and the MEIS-like protein PREP1. Paradoxically, removal of residues N-terminal to the PBX1A HD abolishes interactions with MEIS/PREP but allows nuclear accumulation of PBX1A. We use deletion mapping and fusion to green fluorescent protein to map two cooperative nuclear localization signals (NLSs) in the PBX HD. The results of DNA-binding assays and pull-down experiments are consistent with a model whereby the PBX N-terminus binds to the HD and masks the two NLSs. In support of the model, a mutation in the PBX HD that disrupts contact with the N-terminus leads to constitutive nuclear localization. The HD mutation also increases sensitivity to protease digestion, consistent with a change in conformation. We propose that MEIS family proteins induce a conformational change in PBX that unmasks the NLS, leading to nuclear localization and increased DNA-binding activity. Consistent with this, PBX1 is nuclear only where Meis1 is expressed in the mouse limb bud. PMID:11010815

  11. Nanotopographical Modulation of Cell Function through Nuclear Deformation

    PubMed Central

    Wang, Kai; Bruce, Allison; Mezan, Ryan; Kadiyala, Anand; Wang, Liying; Dawson, Jeremy; Rojanasakul, Yon; Yang, Yong

    2016-01-01

    Although nanotopography has been shown to be a potent modulator of cell behavior, it is unclear how the nanotopographical cue, through focal adhesions, affects the nucleus, eventually influencing cell phenotype and function. Thus, current methods to apply nanotopography to regulate cell behavior are basically empirical. We, herein, engineered nanotopographies of various shapes (gratings and pillars) and dimensions (feature size, spacing and height), and thoroughly investigated cell spreading, focal adhesion organization and nuclear deformation of human primary fibroblasts as the model cell grown on the nanotopographies. We examined the correlation between nuclear deformation and cell functions such as cell proliferation, transfection and extracellular matrix protein type I collagen production. It was found that the nanoscale gratings and pillars could facilitate focal adhesion elongation by providing anchoring sites, and the nanogratings could orient focal adhesions and nuclei along the nanograting direction, depending on not only the feature size but also the spacing of the nanogratings. Compared with continuous nanogratings, discrete nanopillars tended to disrupt the formation and growth of focal adhesions and thus had less profound effects on nuclear deformation. Notably, nuclear volume could be effectively modulated by the height of nanotopography. Further, we demonstrated that cell proliferation, transfection, and type I collagen production were strongly associated with the nuclear volume, indicating that the nucleus serves as a critical mechanosensor for cell regulation. Our study delineated the relationships between focal adhesions, nucleus and cell function and highlighted that the nanotopography could regulate cell phenotype and function by modulating nuclear deformation. This study provides insight into the rational design of nanotopography for new biomaterials and the cell–substrate interfaces of implants and medical devices. PMID:26844365

  12. Goal Direction and Effectiveness, Emotional Maturity, and Nuclear Family Functioning

    ERIC Educational Resources Information Center

    Klever, Phillip

    2009-01-01

    Differentiation of self, a cornerstone concept in Bowen theory, has a profound influence over time on the functioning of the individual and his or her family unit. This 5-year longitudinal study tested this hypothesis with 50 developing nuclear families. The dimensions of differentiation of self that were examined were goal direction and…

  13. Leukocyte Protease Binding to Nucleic Acids Promotes Nuclear Localization and Cleavage of Nucleic Acid Binding Proteins

    PubMed Central

    Thomas, Marshall P.; Whangbo, Jennifer; McCrossan, Geoffrey; Deutsch, Aaron; Martinod, Kimberly; Walch, Michael; Lieberman, Judy

    2014-01-01

    Killer lymphocyte granzyme (Gzm) serine proteases induce apoptosis of pathogen-infected cells and tumor cells. Many known Gzm substrates are nucleic acid binding proteins, and the Gzms accumulate in the target cell nucleus by an unknown mechanism. Here we show that human Gzms bind to DNA and RNA with nanomolar affinity. Gzms cleave their substrates most efficiently when both are bound to nucleic acids. RNase treatment of cell lysates reduces Gzm cleavage of RNA binding protein (RBP) targets, while adding RNA to recombinant RBP substrates increases in vitro cleavage. Binding to nucleic acids also influences Gzm trafficking within target cells. Pre-incubation with competitor DNA and DNase treatment both reduce Gzm nuclear localization. The Gzms are closely related to neutrophil proteases, including neutrophil elastase (NE) and cathepsin G (CATG). During neutrophil activation, NE translocates to the nucleus to initiate DNA extrusion into neutrophil extracellular traps (NETs), which bind NE and CATG. These myeloid cell proteases, but not digestive serine proteases, also bind DNA strongly and localize to nuclei and NETs in a DNA-dependent manner. Thus, high affinity nucleic acid binding is a conserved and functionally important property specific to leukocyte serine proteases. Furthermore, nucleic acid binding provides an elegant and simple mechanism to confer specificity of these proteases for cleavage of nucleic acid binding protein substrates that play essential roles in cellular gene expression and cell proliferation. PMID:24771851

  14. Dynamic localization of tripartite motif-containing 22 in nuclear and nucleolar bodies

    SciTech Connect

    Sivaramakrishnan, Gayathri; Sun, Yang; Tan, Si Kee; Lin, Valerie C.L.

    2009-05-01

    Tripartite motif-containing 22 (TRIM22) exhibits antiviral and growth inhibitory properties, but there has been no study on the localization and dynamics of the endogenous TRIM22 protein. We report here that TRIM22 is dramatically induced by progesterone in MDA-MB-231-derived ABC28 cells and T47D cells. This induction was associated with an increase in TRIM22 nuclear bodies (NB), and an even more prominent increase in nucleolar TRIM22 bodies. Distinct endogenous TRIM22 NB were also demonstrated in several other cell lines including MCF7 and HeLa cells. These TRIM22 NB resemble Cajal bodies, co-localized with these structures and co-immunoprecipitated with p80-coilin. However, IFN{gamma}-induced TRIM22 in HeLa and MCF7 cells did not form NB, implying the forms and distribution of TRIM22 are regulated by specific cellular signals. This notion is also supported by the observation that TRIM22 NB undergoes dynamic cell-cycle dependent changes in distribution such that TRIM22 NB started to form in early G0/G1 but became dispersed in the S-phase. In light of its potential antiviral and antitumor properties, the findings here provide an interesting gateway to study the relationship between the different forms and functions of TRIM22.

  15. A Mapping of the Electron Localization Function for Earth Materials

    SciTech Connect

    Gibbs, Gerald V.; Cox, David F.; Ross, Nancy; Crawford, T Daniel; Burt, Jason; Rosso, Kevin M.

    2005-06-01

    The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering it more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies

  16. Studies with GFP-Vpr fusion proteins: induction of apoptosis but ablation of cell-cycle arrest despite nuclear membrane or nuclear localization.

    PubMed

    Waldhuber, Megan G; Bateson, Michael; Tan, Judith; Greenway, Alison L; McPhee, Dale A

    2003-08-15

    The human immunodeficiency virus type 1 (HIV-1) Vpr protein is known to arrest the cell cycle in G(2)/M and induce apoptosis following arrest. The functions of Vpr relative to its location in the cell remain unresolved. We now demonstrate that the location and function of Vpr are dependent on the makeup of fusion proteins and that the functions of G(2)/M arrest and apoptosis are separable. Using green fluorescence protein mutants (EGFP or EYFP), we found that fusion at either the N- or C-terminus compromised the ability of Vpr to arrest cell cycling, relative to that of His-Vpr or wild-type protein. Additionally, utilizing the ability to specifically identify cells expressing the fusion proteins, we confirm that Vpr can induce apoptosis, but appears to be independent of cell-cycle arrest in G(2)/M. Both N- and C-terminal Vpr/EYFP fusion proteins induced apoptosis but caused minimal G(2)/M arrest. These studies with Vpr fusion proteins indicate that the functions of Vpr leading to G(2)/M arrest and apoptosis are separable and that fusion of Vpr to EGFP or EYFP affected the localization of the protein. Our findings suggest that nuclear membrane localization and nuclear import and export are strongly governed by modification of the N-terminus of Vpr. PMID:12951024

  17. Probability density function transformation using seeded localized averaging

    SciTech Connect

    Dimitrov, N. B.; Jordanov, V. T.

    2011-07-01

    Seeded Localized Averaging (SLA) is a spectrum acquisition method that averages pulse-heights in dynamic windows. SLA sharpens peaks in the acquired spectra. This work investigates the transformation of the original probability density function (PDF) in the process of applying SLA procedure. We derive an analytical expression for the resulting probability density function after an application of SLA. In addition, we prove the following properties: 1) for symmetric distributions, SLA preserves both the mean and symmetry. 2) for uni-modal symmetric distributions, SLA reduces variance, sharpening the distributions peak. Our results are the first to prove these properties, reinforcing past experimental observations. Specifically, our results imply that in the typical case of a spectral peak with Gaussian PDF the full width at half maximum (FWHM) of the transformed peak becomes narrower even with averaging of only two pulse-heights. While the Gaussian shape is no longer preserved, our results include an analytical expression for the resulting distribution. Examples of the transformation of other PDFs are presented. (authors)

  18. Ritz analysis of discontinuous beams using local trigonometric functions

    NASA Astrophysics Data System (ADS)

    Dang, Thi D.; Kapania, Rakesh K.; Patil, Mayuresh J.

    2011-03-01

    The objective of the current paper is to present a Ritz-type analytical model for predicting the behavior of discontinuous beams such as thin-walled beams with cracks and multiply-stepped beams. The beam is discretized in the cracked as well as the un-cracked domains for a cracked thin-walled beam and in uniform beams for a multiple-stepped beam. A set of local trigonometric trial functions is used to define the twist angle for the cracked domain and the un-cracked domains, as well as to define the displacement field for uniform domains. A global equation system of unknown Ritz coefficients is derived by minimizing the Lagrangian functional or the total potential energy. In the present Ritz model, the interface continuity conditions between sub-domains are investigated and enforced into the global equation system using the condensation procedure or the Lagrange multipliers. Examples are presented to illustrate the effectiveness of the current model for free vibration and torsional analysis. Results obtained from the current model are found to agree well with those obtained using a detailed finite element method or with existing results in literature. The proposed model offers an efficient approach to reduce the modeling efforts and computational time required to analyze complex beams with cracks or multiple steps.

  19. TOPICAL REVIEW: Spatial localization in nuclear magnetic resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Keevil, Stephen F.

    2006-08-01

    The ability to select a discrete region within the body for signal acquisition is a fundamental requirement of in vivo NMR spectroscopy. Ideally, it should be possible to tailor the selected volume to coincide exactly with the lesion or tissue of interest, without loss of signal from within this volume or contamination with extraneous signals. Many techniques have been developed over the past 25 years employing a combination of RF coil properties, static magnetic field gradients and pulse sequence design in an attempt to meet these goals. This review presents a comprehensive survey of these techniques, their various advantages and disadvantages, and implications for clinical applications. Particular emphasis is placed on the reliability of the techniques in terms of signal loss, contamination and the effect of nuclear relaxation and J-coupling. The survey includes techniques based on RF coil and pulse design alone, those using static magnetic field gradients, and magnetic resonance spectroscopic imaging. Although there is an emphasis on techniques currently in widespread use (PRESS, STEAM, ISIS and MRSI), the review also includes earlier techniques, in order to provide historical context, and techniques that are promising for future use in clinical and biomedical applications.

  20. Nuclear medium effects in structure functions of nucleon at moderate Q2

    NASA Astrophysics Data System (ADS)

    Haider, H.; Zaidi, F.; Sajjad Athar, M.; Singh, S. K.; Ruiz Simo, I.

    2015-11-01

    Recent experiments performed on inclusive electron scattering from nuclear targets have measured the nucleon electromagnetic structure functions F1 (x, Q2), F2 (x, Q2) and FL (x, Q2) in 12C, 27Al, 56Fe and 64Cu nuclei. The measurements have been done in the energy region of 1 GeV2 nuclear medium effects in these structure functions arising due to the Fermi motion, binding energy, nucleon correlations, mesonic contributions from pion and rho mesons and shadowing effects. The calculations are performed in a local density approximation using a relativistic nucleon spectral function which includes nucleon correlations. The numerical results are compared with the recent experimental data from JLab and also with some earlier experiments.

  1. Localization of P-glycoprotein at the nuclear envelope of rat brain cells

    SciTech Connect

    Babakhanian, Karlo; Bendayan, Moise; Bendayan, Reina . E-mail: r.bendayan@utoronto.ca

    2007-09-21

    P-Glycoprotein is a plasma membrane drug efflux protein implicated in extrusion of cytotoxic compounds out of a cell. There is now evidence that suggests expression of this transporter at several subcellular sites, including the nucleus, mitochondria, and Golgi apparatus. This study investigated the localization and expression of P-glycoprotein at the nuclear membrane of rat brain microvessel endothelial (RBE4) and microglial (MLS-9) cell lines. Immunocytochemistry at the light and electron microscope levels using P-glycoprotein monoclonals antibodies demonstrated the localization of the protein at the nuclear envelope of RBE4 and MLS-9 cells. Western blot analysis revealed a single band of 170-kDa in purified nuclear membranes prepared from isolated nuclei of RBE4 and MLS-9 cells. These findings indicate that P-glycoprotein is expressed at the nuclear envelope of rat brain cells and suggest a role in multidrug resistance at this subcellular site.

  2. Building A Universal Nuclear Energy Density Functional (UNEDF)

    SciTech Connect

    Joe Carlson; Dick Furnstahl; Mihai Horoi; Rusty Lusk; Witek Nazarewicz; Esmond Ng; Ian Thompson; James Vary

    2012-09-30

    During the period of Dec. 1 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory. The main physics areas of UNEDF, defined at the beginning of the project, were: ab initio structure; ab initio functionals; DFT applications; DFT extensions; reactions.

  3. Ciliary subcellular localization of TGR5 determines the cholangiocyte functional response to bile acid signaling

    PubMed Central

    Masyuk, Anatoliy I.; Huang, Bing Q.; Radtke, Brynn N.; Gajdos, Gabriella B.; Splinter, Patrick L.; Masyuk, Tatyana V.; Gradilone, Sergio A.

    2013-01-01

    TGR5, the G protein-coupled bile acid receptor that transmits bile acid signaling into a cell functional response via the intracellular cAMP signaling pathway, is expressed in human and rodent cholangiocytes. However, detailed information on the localization and function of cholangiocyte TGR5 is limited. We demonstrated that in human (H69 cells) and rat cholangiocytes, TGR5 is localized to multiple, diverse subcellular compartments, with its strongest expression on the apical plasma, ciliary, and nuclear membranes. To evaluate the relationship between ciliary TGR5 and the cholangiocyte functional response to bile acid signaling, we used a model of ciliated and nonciliated H69 cells and demonstrated that TGR5 agonists induce opposite changes in cAMP and ERK levels in cells with and without primary cilia. The cAMP level was increased in nonciliated cholangiocytes but decreased in ciliated cells. In contrast, ERK signaling was induced in ciliated cholangiocytes but suppressed in cells without cilia. TGR5 agonists inhibited proliferation of ciliated cholangiocytes but activated proliferation of nonciliated cells. The observed differential effects of TGR5 agonists were associated with the coupling of TGR5 to Gαi protein in ciliated cells and Gαs protein in nonciliated cholangiocytes. The functional responses of nonciliated and ciliated cholangiocytes to TGR5-mediated bile acid signaling may have important pathophysiological significance in cilia-related liver disorders (i.e., cholangiociliopathies), such as polycystic liver disease. In summary, TGR5 is expressed on diverse cholangiocyte compartments, including a primary cilium, and its ciliary localization determines the cholangiocyte functional response to bile acid signaling. PMID:23578785

  4. Ciliary subcellular localization of TGR5 determines the cholangiocyte functional response to bile acid signaling.

    PubMed

    Masyuk, Anatoliy I; Huang, Bing Q; Radtke, Brynn N; Gajdos, Gabriella B; Splinter, Patrick L; Masyuk, Tatyana V; Gradilone, Sergio A; LaRusso, Nicholas F

    2013-06-01

    TGR5, the G protein-coupled bile acid receptor that transmits bile acid signaling into a cell functional response via the intracellular cAMP signaling pathway, is expressed in human and rodent cholangiocytes. However, detailed information on the localization and function of cholangiocyte TGR5 is limited. We demonstrated that in human (H69 cells) and rat cholangiocytes, TGR5 is localized to multiple, diverse subcellular compartments, with its strongest expression on the apical plasma, ciliary, and nuclear membranes. To evaluate the relationship between ciliary TGR5 and the cholangiocyte functional response to bile acid signaling, we used a model of ciliated and nonciliated H69 cells and demonstrated that TGR5 agonists induce opposite changes in cAMP and ERK levels in cells with and without primary cilia. The cAMP level was increased in nonciliated cholangiocytes but decreased in ciliated cells. In contrast, ERK signaling was induced in ciliated cholangiocytes but suppressed in cells without cilia. TGR5 agonists inhibited proliferation of ciliated cholangiocytes but activated proliferation of nonciliated cells. The observed differential effects of TGR5 agonists were associated with the coupling of TGR5 to Gαi protein in ciliated cells and Gαs protein in nonciliated cholangiocytes. The functional responses of nonciliated and ciliated cholangiocytes to TGR5-mediated bile acid signaling may have important pathophysiological significance in cilia-related liver disorders (i.e., cholangiociliopathies), such as polycystic liver disease. In summary, TGR5 is expressed on diverse cholangiocyte compartments, including a primary cilium, and its ciliary localization determines the cholangiocyte functional response to bile acid signaling. PMID:23578785

  5. Nuclear envelope-localized EGF family protein amphiregulin activates breast cancer cell migration in an EGF-like domain independent manner

    SciTech Connect

    Tanaka, Hisae; Nishioka, Yu; Yokoyama, Yuhki; Higashiyama, Shigeki; Matsuura, Nariaki; Matsuura, Shuji; Hieda, Miki

    2012-04-20

    Highlights: Black-Right-Pointing-Pointer Nuclear envelope-localized proAREG activates cancer cell migration via its cytoplasmic domain. Black-Right-Pointing-Pointer The induction of cell migration does not require the EGF-like domain or EGR function. Black-Right-Pointing-Pointer Nuclear envelope-localized proAREG suppresses breast cancer cell growth without EGFR function. Black-Right-Pointing-Pointer This study revealed a novel function mediated by the intracellular domain of proAREG. -- Abstract: Amphiregulin (AREG), an EGF family protein, is synthesized as a type I transmembrane precursor (proAREG) and expressed on the cell surface with an extracellular EGF-like domain and an intracellular short cytoplasmic tail. The ectodomain shedding yields a soluble EGF receptor ligand (soluble AREG) which binds to EGF receptor (EGFR) and concomitantly induces migration of unshed proAREG from the plasma membrane to the nuclear envelope (NE). AREG is known to play a potential role in breast cancer and has been intensively investigated as an EGF receptor ligand, while the function of the NE-localized proAREG remains unknown. In this study we used a truncated mutant that mimics NE-localized proAREG without shedding stimuli to discriminate between the functions of NE-localized and plasma membrane-localized proAREG and demonstrate that NE-localized proAREG activates breast cancer cell migration, but suppresses cell growth. Moreover, the present study shows that induction of cell migration by NE-localized proAREG does not require the extracellular growth factor domain or EGF receptor function. Collectively these data demonstrate a novel function mediated by the intracellular domain of proAREG and suggest a significant role for NE-localized proAREG in driving human breast cancer progression.

  6. Mutations within the nuclear localization signal of the porcine reproductive and respiratory syndrome virus nucleocapsid protein attenuate virus replication

    SciTech Connect

    Lee, Changhee; Hodgins, Douglas; Calvert, Jay G.; Welch, Siao-Kun W.; Jolie, Rika; Yoo, Dongwan . E-mail: dyoo@uoguelph.ca

    2006-03-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus replicating in the cytoplasm, but the nucleocapsid (N) protein is specifically localized to the nucleus and nucleolus in virus-infected cells. A 'pat7' motif of 41-PGKK(N/S)KK has previously been identified in the N protein as the functional nuclear localization signal (NLS); however, the biological consequences of N protein nuclear localization are unknown. In the present study, the role of N protein nuclear localization during infection was investigated in pigs using an NLS-null mutant virus. When two lysines at 43 and 44 at the NLS locus were substituted to glycines, the modified NLS with 41-PGGGNKK restricted the N protein to the cytoplasm. This NLS-null mutation was introduced into a full-length infectious cDNA clone of PRRSV. Upon transfection of cells, the NLS-null full-length clone induced cytopathic effects and produced infectious progeny. The NLS-null virus grew to a titer 100-fold lower than that of wild-type virus. To examine the response to NLS-null PRRSV in the natural host, three groups of pigs, consisting of seven animals per group, were intranasally inoculated with wild-type, placebo, or NLS-null virus, and the animals were maintained for 4 weeks. The NLS-null-infected pigs had a significantly shorter mean duration of viremia than wild-type-infected pigs but developed significantly higher titers of neutralizing antibodies. Mutations occurred at the NLS locus in one pig during viremia, and four types of mutations were identified: 41-PGRGNKK, 41-PGGRNKK, and 41-PGRRNKK, and 41-PGKKSKK. Both wild-type and NLS-null viruses persisted in the tonsils for at least 4 weeks, and the NLS-null virus persisting in the tonsils was found to be mutated to either 41-PGRGNKK or 41-PGGRNKK in all pigs. No other mutation was found in the N gene. All types of reversions which occurred during viremia and persistence were able to translocate the mutated N proteins to the nucleus, indicating a

  7. Different subcellular localizations and functions of Arabidopsis myosin VIII

    PubMed Central

    Golomb, Lior; Abu-Abied, Mohamad; Belausov, Eduard; Sadot, Einat

    2008-01-01

    Background Myosins are actin-activated ATPases that use energy to generate force and move along actin filaments, dragging with their tails different cargos. Plant myosins belong to the group of unconventional myosins and Arabidopsis myosin VIII gene family contains four members: ATM1, ATM2, myosin VIIIA and myosin VIIIB. Results In transgenic plants expressing GFP fusions with ATM1 (IQ-tail truncation, lacking the head domain), fluorescence was differentially distributed: while in epidermis cells at the root cap GFP-ATM1 equally distributed all over the cell, in epidermal cells right above this region it accumulated in dots. Further up, in cells of the elongation zone, GFP-ATM1 was preferentially positioned at the sides of transversal cell walls. Interestingly, the punctate pattern was insensitive to brefeldin A (BFA) while in some cells closer to the root cap, ATM1 was found in BFA bodies. With the use of different markers and transient expression in Nicotiana benthamiana leaves, it was found that myosin VIII co-localized to the plasmodesmata and ER, colocalized with internalized FM4-64, and partially overlapped with the endosomal markers ARA6, and rarely with ARA7 and FYVE. Motility of ARA6 labeled organelles was inhibited whenever associated with truncated ATM1 but motility of FYVE labeled organelles was inhibited only when associated with large excess of ATM1. Furthermore, GFP-ATM1 and RFP-ATM2 (IQ-tail domain) co-localized to the same spots on the plasma membrane, indicating a specific composition at these sites for myosin binding. Conclusion Taken together, our data suggest that myosin VIII functions differently in different root cells and can be involved in different steps of endocytosis, BFA-sensitive and insensitive pathways, ER tethering and plasmodesmatal activity. PMID:18179725

  8. A novel fragile X syndrome mutation reveals a conserved role for the carboxy-terminus in FMRP localization and function

    PubMed Central

    Okray, Zeynep; de Esch, Celine EF; Van Esch, Hilde; Devriendt, Koen; Claeys, Annelies; Yan, Jiekun; Verbeeck, Jelle; Froyen, Guy; Willemsen, Rob; de Vrij, Femke MS; Hassan, Bassem A

    2015-01-01

    Loss of function of the FMR1 gene leads to fragile X syndrome (FXS), the most common form of intellectual disability. The loss of FMR1 function is usually caused by epigenetic silencing of the FMR1 promoter leading to expansion and subsequent methylation of a CGG repeat in the 5′ untranslated region. Very few coding sequence variations have been experimentally characterized and shown to be causal to the disease. Here, we describe a novel FMR1 mutation and reveal an unexpected nuclear export function for the C-terminus of FMRP. We screened a cohort of patients with typical FXS symptoms who tested negative for CGG repeat expansion in the FMR1 locus. In one patient, we identified a guanine insertion in FMR1 exon 15. This mutation alters the open reading frame creating a short novel C-terminal sequence, followed by a stop codon. We find that this novel peptide encodes a functional nuclear localization signal (NLS) targeting the patient FMRP to the nucleolus in human cells. We also reveal an evolutionarily conserved nuclear export function associated with the endogenous C-terminus of FMRP. In vivo analyses in Drosophila demonstrate that a patient-mimetic mutation alters the localization and function of Dfmrp in neurons, leading to neomorphic neuronal phenotypes. PMID:25693964

  9. Structural protein 4.1R is integrally involved in nuclear envelope protein localization, centrosome–nucleus association and transcriptional signaling

    PubMed Central

    Meyer, Adam J.; Almendrala, Donna K.; Go, Minjoung M.; Krauss, Sharon Wald

    2011-01-01

    The multifunctional structural protein 4.1R is required for assembly and maintenance of functional nuclei but its nuclear roles are unidentified. 4.1R localizes within nuclei, at the nuclear envelope, and in cytoplasm. Here we show that 4.1R, the nuclear envelope protein emerin and the intermediate filament protein lamin A/C co-immunoprecipitate, and that 4.1R-specific depletion in human cells by RNA interference produces nuclear dysmorphology and selective mislocalization of proteins from several nuclear subcompartments. Such 4.1R-deficiency causes emerin to partially redistribute into the cytoplasm, whereas lamin A/C is disorganized at nuclear rims and displaced from nucleoplasmic foci. The nuclear envelope protein MAN1, nuclear pore proteins Tpr and Nup62, and nucleoplasmic proteins NuMA and LAP2α also have aberrant distributions, but lamin B and LAP2β have normal localizations. 4.1R-deficient mouse embryonic fibroblasts show a similar phenotype. We determined the functional effects of 4.1R-deficiency that reflect disruption of the association of 4.1R with emerin and A-type lamin: increased nucleus–centrosome distances, increased β-catenin signaling, and relocalization of β-catenin from the plasma membrane to the nucleus. Furthermore, emerin- and lamin-A/C-null cells have decreased nuclear 4.1R. Our data provide evidence that 4.1R has important functional interactions with emerin and A-type lamin that impact upon nuclear architecture, centrosome–nuclear envelope association and the regulation of β-catenin transcriptional co-activator activity that is dependent on β-catenin nuclear export. PMID:21486941

  10. Dipole polarizability of 120Sn and nuclear energy density functionals

    NASA Astrophysics Data System (ADS)

    Hashimoto, T.; Krumbholz, A. M.; Reinhard, P.-G.; Tamii, A.; von Neumann-Cosel, P.; Adachi, T.; Aoi, N.; Bertulani, C. A.; Fujita, H.; Fujita, Y.; Ganioǧlu, E.; Hatanaka, K.; Ideguchi, E.; Iwamoto, C.; Kawabata, T.; Khai, N. T.; Krugmann, A.; Martin, D.; Matsubara, H.; Miki, K.; Neveling, R.; Okamura, H.; Ong, H. J.; Poltoratska, I.; Ponomarev, V. Yu.; Richter, A.; Sakaguchi, H.; Shimbara, Y.; Shimizu, Y.; Simonis, J.; Smit, F. D.; Süsoy, G.; Suzuki, T.; Thies, J. H.; Yosoi, M.; Zenihiro, J.

    2015-09-01

    The electric dipole strength distribution in 120Sn between 5 and 22 MeV has been determined at the Research Center for Nuclear Physics, Osaka, from polarization transfer observables measured in proton inelastic scattering at E0=295 MeV and forward angles including 0∘. Combined with photoabsorption data, a highly precise electric dipole polarizability αD(120Sn) =8.93 (36 ) fm3 is extracted. The dipole polarizability as isovector observable par excellence carries direct information on nuclear symmetry energy and its density dependence. The correlation of the new value with the well-established αD(208Pb) serves as a test of its prediction by nuclear energy density functionals. Models based on modern Skyrme interactions describe the data fairly well while most calculations based on relativistic Hamiltonians cannot.

  11. Optical pump-probe measurements of local nuclear spin coherence in semiconductor quantum wells.

    PubMed

    Sanada, H; Kondo, Y; Matsuzaka, S; Morita, K; Hu, C Y; Ohno, Y; Ohno, H

    2006-02-17

    We demonstrate local manipulation and detection of nuclear spin coherence in semiconductor quantum wells by an optical pump-probe technique combined with pulse rf NMR. The Larmor precession of photoexcited electron spins is monitored by time-resolved Kerr rotation (TRKR) as a measure of nuclear magnetic field. Under the irradiation of resonant pulsed rf magnetic fields, Rabi oscillations of nuclear spins are traced by TRKR signals. The intrinsic coherence time evaluated by a spin-echo technique reveals the dependence on the orientation of the magnetic field with respect to the crystalline axis as expected by the nearest neighbor dipole-dipole interaction. PMID:16606048

  12. Atypical nuclear localization of CD133 plasma membrane glycoprotein in rhabdomyosarcoma cell lines.

    PubMed

    Nunukova, Alena; Neradil, Jakub; Skoda, Jan; Jaros, Josef; Hampl, Ales; Sterba, Jaroslav; Veselska, Renata

    2015-07-01

    CD133 (also known as prominin-1) is a cell surface glycoprotein that is widely used for the identification of stem cells. Furthermore, its glycosylated epitope, AC133, has recently been discussed as a marker of cancer stem cells in various human malignancies. During our recent experiments on rhabdomyosarcomas (RMS), we unexpectedly identified an atypical nuclear localization of CD133 in a relatively stable subset of cells in five RMS cell lines established in our laboratory. To the best of our knowledge, this atypical localization of CD133 has not yet been proven or analyzed in detail in cancer cells. In the present study, we verified the nuclear localization of CD133 in RMS cells using three independent anti-CD133 antibodies, including both rabbit polyclonal and mouse monoclonal antibodies. Indirect immunofluorescence and confocal microscopy followed by software cross-section analysis, transmission electron microscopy and cell fractionation with immunoblotting were also employed, and all the results undeniably confirmed the presence of CD133 in the nuclei of stable minor subpopulations of all five RMS cell lines. The proportion of cells showing an exclusive nuclear localization of CD133 ranged from 3.4 to 7.5%, with only minor differences observed among the individual anti-CD133 antibodies. Although the role of CD133 in the cell nucleus remains unclear, these results clearly indicate that this atypical nuclear localization of CD133 in a minor subpopulation of cancer cells is a common phenomenon in RMS cell lines. PMID:25977066

  13. Phosphorylation of nucleoporin Tpr governs its differential localization and is required for its mitotic function

    PubMed Central

    Rajanala, Kalpana; Sarkar, Anshuk; Jhingan, Gagan Deep; Priyadarshini, Raina; Jalan, Manisha; Sengupta, Sagar; Nandicoori, Vinay Kumar

    2014-01-01

    ABSTRACT A major constituent of the nuclear basket region of the nuclear pore complex (NPC), nucleoporin Tpr, plays roles in regulating multiple important processes. We have previously established that Tpr is phosphorylated in both a MAP-kinase-dependent and MAP-kinase-independent manner, and that Tpr acts as both a substrate and as a scaffold for ERK2 (also known as MAPK1). Here, we report the identification of S2059 and S2094 as the major novel ERK-independent phosphorylation sites and T1677, S2020, S2023 and S2034 as additional ERK-independent phosphorylation sites found in the Tpr protein in vivo. Our results suggest that protein kinase A phosphorylates the S2094 residue and that the site is hyperphosphorylated during mitosis. Furthermore, we find that Tpr is phosphorylated at the S2059 residue by CDK1 and the phosphorylated form distinctly localizes with chromatin during telophase. Abrogation of S2059 phosphorylation abolishes the interaction of Tpr with Mad1, thus compromising the localization of both Mad1 and Mad2 proteins, resulting in cell cycle defects. The identification of novel phosphorylation sites on Tpr and the observations presented in this study allow better understanding of Tpr functions. PMID:24938596

  14. SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS

    SciTech Connect

    Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J

    2010-12-20

    We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.

  15. Spent Nuclear Fuel Project Canister Storage Building Functions and Requirements

    SciTech Connect

    KLEM, M.J.

    2000-10-18

    In 1998, a major change in the technical strategy for managing Multi Canister Overpacks (MCO) while stored within the Canister Storage Building (CSB) occurred. The technical strategy is documented in Baseline Change Request (BCR) No. SNF-98-006, Simplified SNF Project Baseline (MCO Sealing) (FDH 1998). This BCR deleted the hot conditioning process initially adopted for the Spent Nuclear Fuel Project (SNF Project) as documented in WHC-SD-SNF-SP-005, Integrated Process Strategy for K Basins Spent Nuclear Fuel (WHC 199.5). In summary, MCOs containing Spent Nuclear Fuel (SNF) from K Basins would be placed in interim storage following processing through the Cold Vacuum Drying (CVD) facility. With this change, the needs for the Hot Conditioning System (HCS) and inerting/pressure retaining capabilities of the CSB storage tubes and the MCO Handling Machine (MHM) were eliminated. Mechanical seals will be used on the MCOs prior to transport to the CSB. Covers will be welded on the MCOs for the final seal at the CSB. Approval of BCR No. SNF-98-006, imposed the need to review and update the CSB functions and requirements baseline documented herein including changing the document title to ''Spent Nuclear Fuel Project Canister Storage Building Functions and Requirements.'' This revision aligns the functions and requirements baseline with the CSB Simplified SNF Project Baseline (MCO Sealing). This document represents the Canister Storage Building (CSB) Subproject technical baseline. It establishes the functions and requirements baseline for the implementation of the CSB Subproject. The document is organized in eight sections. Sections 1.0 Introduction and 2.0 Overview provide brief introductions to the document and the CSB Subproject. Sections 3.0 Functions, 4.0 Requirements, 5.0 Architecture, and 6.0 Interfaces provide the data described by their titles. Section 7.0 Glossary lists the acronyms and defines the terms used in this document. Section 8.0 References lists the

  16. A-type lamins regulate retinoblastoma protein function by promoting subnuclear localization and preventing proteasomal degradation.

    PubMed

    Johnson, Brett R; Nitta, Ryan T; Frock, Richard L; Mounkes, Leslie; Barbie, David A; Stewart, Colin L; Harlow, Ed; Kennedy, Brian K

    2004-06-29

    The retinoblastoma protein (pRB) is a critical regulator of cell proliferation and differentiation and an important tumor suppressor. In the G(1) phase of the cell cycle, pRB localizes to perinucleolar sites associated with lamin A/C intranuclear foci. Here, we examine pRB function in cells lacking lamin A/C, finding that pRB levels are dramatically decreased and that the remaining pRB is mislocalized. We demonstrate that A-type lamins protect pRB from proteasomal degradation. Both pRB levels and localization are restored upon reintroduction of lamin A. Lmna(-/-) cells resemble Rb(-/-) cells, exhibiting altered cell-cycle properties and reduced capacity to undergo cell-cycle arrest in response to DNA damage. These findings establish a functional link between a core nuclear structural component and an important cell-cycle regulator. They further raise the possibility that altered pRB function may be a contributing factor in dystrophic syndromes arising from LMNA mutation. PMID:15210943

  17. Regulating Set-β's Subcellular Localization Toggles Its Function between Inhibiting and Promoting Axon Growth and Regeneration

    PubMed Central

    Wang, Yan; Morkin, Melina I.; Fernandez, Stephanie G.; Mlacker, Gregory M.; Shechter, Jesse M.; Liu, Xiongfei; Patel, Karan H.; Lapins, Allison; Yang, Steven; Dombrowski, Susan M.

    2014-01-01

    The failure of the CNS neurons to regenerate axons after injury or stroke is a major clinical problem. Transcriptional regulators like Set-β are well positioned to regulate intrinsic axon regeneration capacity, which declines developmentally in maturing CNS neurons. Set-β also functions at cellular membranes and its subcellular localization is disrupted in Alzheimer's disease, but many of its biological mechanisms have not been explored in neurons. We found that Set-β was upregulated postnatally in CNS neurons, and was primarily localized to the nucleus but was also detected in the cytoplasm and adjacent to the plasma membrane. Remarkably, nuclear Set-β suppressed, whereas Set-β localized to cytoplasmic membranes promoted neurite growth in rodent retinal ganglion cells and hippocampal neurons. Mimicking serine 9 phosphorylation, as found in Alzheimer's disease brains, delayed nuclear import and furthermore blocked the ability of nuclear Set-β to suppress neurite growth. We also present data on gene regulation and protein binding partner recruitment by Set-β in primary neurons, raising the hypothesis that nuclear Set-β may preferentially regulate gene expression whereas Set-β at cytoplasmic membranes may regulate unique cofactors, including PP2A, which we show also regulates axon growth in vitro. Finally, increasing recruitment of Set-β to cellular membranes promoted adult rat optic nerve axon regeneration after injury in vivo. Thus, Set-β differentially regulates axon growth and regeneration depending on subcellular localization and phosphorylation. PMID:24849368

  18. Description of induced nuclear fission with Skyrme energy functionals. II. Finite temperature effects

    NASA Astrophysics Data System (ADS)

    Schunck, N.; Duke, D.; Carr, H.

    2015-03-01

    Understanding the mechanisms of induced nuclear fission for a broad range of neutron energies could help resolve fundamental science issues, such as the formation of elements in the universe, but could have also a large impact on societal applications in energy production or nuclear waste management. The goal of this paper is to set up the foundations of a microscopic theory to study the static aspects of induced fission as a function of the excitation energy of the incident neutron, from thermal to fast neutrons. To account for the high excitation energy of the compound nucleus, we employ a statistical approach based on finite temperature nuclear density functional theory with Skyrme energy densities, which we benchmark on the 239Pu(n ,f ) reaction. We compute the evolution of the least-energy fission pathway across multidimensional potential energy surfaces with up to five collective variables as a function of the nuclear temperature and predict the evolution of both the inner and the outer fission barriers as a function of the excitation energy of the compound nucleus. We show that the coupling to the continuum induced by the finite temperature is negligible in the range of neutron energies relevant for many applications of neutron-induced fission. We prove that the concept of quantum localization introduced recently can be extended to T >0 , and we apply the method to study the interaction energy and total kinetic energy of fission fragments as a function of the temperature for the most probable fission. While large uncertainties in theoretical modeling remain, we conclude that a finite temperature nuclear density functional may provide a useful framework to obtain accurate predictions of fission fragment properties.

  19. Dynamic Susceptibility Contrast MRI with Localized Arterial Input Functions

    PubMed Central

    Lee, J.J.; Bretthorst, G.L.; Derdeyn, C.P.; Powers, W.J.; Videen, T.O.; Snyder, A.Z.; Markham, J.; Shimony, J.S.

    2010-01-01

    Compared to gold-standard measurements of cerebral perfusion with positron emission tomography (PET) using H2[15O] tracers, measurements with dynamic susceptibility contrast (DSC) MR are more accessible, less expensive and less invasive. However, existing methods for analyzing and interpreting data from DSC MR have characteristic disadvantages that include sensitivity to incorrectly modeled delay and dispersion in a single, global arterial input function (AIF). We describe a model of tissue microcirculation derived from tracer kinetics which estimates for each voxel a unique, localized AIF (LAIF). Parameters of the model were estimated using Bayesian probability theory and Markov-chain Monte Carlo, circumventing difficulties arising from numerical deconvolution. Applying the new method to imaging studies from a cohort of fourteen patients with chronic, atherosclerotic, occlusive disease showed strong correlations between perfusion measured by DSC MR with LAIF and perfusion measured by quantitative PET with H2[15O]. Regression to PET measurements enabled conversion of DSC MR to a physiological scale. Regression analysis for LAIF gave estimates of a scaling factor for quantitation which described perfusion accurately in patients with substantial variability in hemodynamic impairment. PMID:20432301

  20. The Tobamovirus Turnip Vein Clearing Virus 30-Kilodalton Movement Protein Localizes to Novel Nuclear Filaments To Enhance Virus Infection

    PubMed Central

    Levy, Amit; Zheng, Judy Y.

    2013-01-01

    Plant viruses overcome the barrier of the plant cell wall by encoding cell-to-cell movement proteins (MPs), which direct newly replicated viral genomes to, and across, the wall. The paradigm for how a single MP regulates and coordinates these activities is the Tobacco mosaic virus (TMV) 30-kDa protein (MPTMV). Detailed studies demonstrate that TMV multiplies exclusively in the cytoplasm and have documented associations of MPTMV with endoplasmic reticulum (ER) membrane, microtubules, and plasmodesmata throughout the course of infection. As TMV poorly infects Arabidopsis thaliana, Turnip vein clearing virus (TVCV) is the tobamovirus of choice for studies in this model plant. A key problem, which has contributed to confusion in the field, is the unproven assumption that the TVCV and TMV life cycles are identical. We engineered an infectious TVCV replicon that expressed a functional fluorescence-tagged MPTVCV and report here the unexpected discovery that MPTVCV, beyond localizing to ER membrane and plasmodesmata, targeted to the nucleus in a nuclear localization signal (NLS)-dependent manner, where it localized to novel F-actin-containing filaments that associated with chromatin. The MPTVCV NLS appeared to be conserved in the subgroup 3 tobamoviruses, and our mutational analyses showed that nuclear localization of MPTVCV was necessary for efficient TVCV cell-to-cell movement and systemic infection in Nicotiana benthamiana and Arabidopsis thaliana. Our studies identify a novel nuclear stage in TVCV infection and suggest that nuclear MP encoded by TVCV and other subgroup 3 tobamoviruses interacts with F-actin and chromatin to modulate host defenses or cellular physiology to favor virus movement and infection. PMID:23536678

  1. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    PubMed Central

    Hernández-Sánchez, Itzell E.; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P.; Jiménez-Bremont, Juan F.

    2015-01-01

    The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization. PMID:26442018

  2. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif.

    PubMed

    Hernández-Sánchez, Itzell E; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P; Jiménez-Bremont, Juan F

    2015-01-01

    The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization. PMID:26442018

  3. Nuclear Import of Bovine Papillomavirus Type 1 E1 Protein Is Mediated by Multiple Alpha Importins and Is Negatively Regulated by Phosphorylation near a Nuclear Localization Signal▿

    PubMed Central

    Bian, Xue-Lin; Rosas-Acosta, Germán; Wu, Yu-Chieh; Wilson, Van G.

    2007-01-01

    Papillomavirus DNA replication occurs in the nucleus of infected cells and requires the viral E1 protein, which enters the nuclei of host epithelial cells and carries out enzymatic functions required for the initiation of viral DNA replication. In this study, we investigated the pathway and regulation of the nuclear import of the E1 protein from bovine papillomavirus type 1 (BPV1). Using an in vitro binding assay, we determined that the E1 protein interacted with importins α3, α4, and α5 via its nuclear localization signal (NLS) sequence. In agreement with this result, purified E1 protein was effectively imported into the nucleus of digitonin-permeabilized HeLa cells after incubation with importin α3, α4, or α5 and other necessary import factors. We also observed that in vitro binding of E1 protein to all three α importins was significantly decreased by the introduction of pseudophosphorylation mutations in the NLS region. Consistent with the binding defect, pseudophosphorylated E1 protein failed to enter the nucleus of digitonin-permeabilized HeLa cells in vitro. Likewise, the pseudophosphorylation mutant showed aberrant intracellular localization in vivo and accumulated primarily on the nuclear envelope in transfected HeLa cells, while the corresponding alanine replacement mutant displayed the same cellular location pattern as wild-type E1 protein. Collectively, our data demonstrate that BPV1 E1 protein can be transported into the nucleus by more than one importin α and suggest that E1 phosphorylation by host cell kinases plays a regulatory role in modulating E1 nucleocytoplasmic localization. This phosphoregulation of nuclear E1 protein uptake may contribute to the coordination of viral replication with keratinocyte proliferation and differentiation. PMID:17192311

  4. Gain-of-Function Alleles in Caenorhabditis elegans Nuclear Hormone Receptor nhr-49 Are Functionally Distinct.

    PubMed

    Lee, Kayoung; Goh, Grace Ying Shyen; Wong, Marcus Andrew; Klassen, Tara Leah; Taubert, Stefan

    2016-01-01

    Nuclear hormone receptors (NHRs) are transcription factors that regulate numerous physiological and developmental processes and represent important drug targets. NHR-49, an ortholog of Hepatocyte Nuclear Factor 4 (HNF4), has emerged as a key regulator of lipid metabolism and life span in the nematode worm Caenorhabditis elegans. However, many aspects of NHR-49 function remain poorly understood, including whether and how it regulates individual sets of target genes and whether its activity is modulated by a ligand. A recent study identified three gain-of-function (gof) missense mutations in nhr-49 (nhr-49(et7), nhr-49(et8), and nhr-49(et13), respectively). These substitutions all affect the ligand-binding domain (LBD), which is critical for ligand binding and protein interactions. Thus, these alleles provide an opportunity to test how three specific residues contribute to NHR-49 dependent gene regulation. We used computational and molecular methods to delineate how these mutations alter NHR-49 activity. We find that despite originating from a screen favoring the activation of specific NHR-49 targets, all three gof alleles cause broad upregulation of NHR-49 regulated genes. Interestingly, nhr-49(et7) and nhr-49(et8) exclusively affect nhr-49 dependent activation, whereas the nhr-49(et13) surprisingly affects both nhr-49 mediated activation and repression, implicating the affected residue as dually important. We also observed phenotypic non-equivalence of these alleles, as they unexpectedly caused a long, short, and normal life span, respectively. Mechanistically, the gof substitutions altered neither protein interactions with the repressive partner NHR-66 and the coactivator MDT-15 nor the subcellular localization or expression of NHR-49. However, in silico structural modeling revealed that NHR-49 likely interacts with small molecule ligands and that the missense mutations might alter ligand binding, providing a possible explanation for increased NHR-49 activity. In

  5. Living with nuclear power: A Q-method study of local community perceptions.

    PubMed

    Venables, Dan; Pidgeon, Nick; Simmons, Peter; Henwood, Karen; Parkhill, Karen

    2009-08-01

    The issue of new nuclear power is once again high up on the public policy agenda in many countries, and candidate sites for new civilian stations are likely to include those that have existing nuclear facilities. A common assumption is that existing nuclear communities will be more accepting of new build because of the direct economic and other benefits nuclear power already makes to a local area. Surprisingly, there is a dearth of contemporary data on perceptions of the risks, benefits, and values associated with nuclear power within such communities. This study uses Q-methodology to investigate the perspectives on living with nuclear risk among people (n = 84) drawn from communities near to two nuclear power stations in the United Kingdom. Both stations, at Bradwell-on-Sea and Oldbury-on-Severn, had been in operation for over 40 years. The Q-analysis identified four main perspectives, or points of view, accounting for 53% of total variance. These were interpreted as: Beneficial and Safe; Threat and Distrust; Reluctant Acceptance; and There's No Point Worrying. We conclude that the "landscape of beliefs" about nuclear power in such communities is both subtle and complex, avoiding simplistic bipolar dichotomies such as "for" or "against," and that there is a need for extensive and meaningful dialogue with such communities over any new build plans. The usefulness of Q-methodology for investigating the ways in which people live with risk is highlighted, as are the implications of the results for theories of risk and trust. PMID:19619217

  6. Relativistic spectral function of nucleons in hot nuclear matter

    NASA Astrophysics Data System (ADS)

    Ghosh, Sabyasachi; Sarkar, Sourav; Mallik, S.

    2010-10-01

    We present a simple calculation of the nucleon self-energy in nuclear matter at finite temperature in a relativistic framework, using the real-time thermal field theory. The imaginary parts of one-loop graphs are identified with discontinuities across the unitary and the Landau cuts. We find that in general both the cuts contribute significantly to the spectral function in the region of (virtual) nucleon mass usually considered, even though the unitary cut is ignored in the literature. Furthermore, our relativistic spectral function differs from the one in nonrelativistic approximation, used in some earlier calculations.

  7. Surface localization of the nuclear receptor CAR in influenza A virus-infected cells

    SciTech Connect

    Takahashi, Tadanobu; Moriyama, Yusuke; Ikari, Akira; Sugatani, Junko; Suzuki, Takashi; Miwa, Masao

    2008-04-11

    Constitutive active/androstane receptor CAR is a member of the nuclear receptors which regulate transcription of xenobiotic metabolism enzymes. CAR is usually localized in the cytosol and nucleus. Here, we found that CAR was localized at the cell surface of influenza A virus (IAV)-infected cells. Additionally, we demonstrated that expression of a viral envelope glycoprotein, either hemagglutinin (HA) or neuraminidase (NA), but not viral nucleoprotein (NP), was responsible for this localization. This report is the first demonstration of CAR at the surface of tissue culture cells, and suggests that CAR may exert the IAV infection mechanism.

  8. Mechanisms of progesterone receptor export from nuclei: role of nuclear localization signal, nuclear export signal, and ran guanosine triphosphate.

    PubMed

    Tyagi, R K; Amazit, L; Lescop, P; Milgrom, E; Guiochon-Mantel, A

    1998-11-01

    Steroid hormone receptors are, in most cases, mainly nuclear proteins that undergo a continuous nucleocytoplasmic shuttling. The mechanism of the nuclear export of these proteins remains largely unknown. To approach this problem experimentally in vivo, we have prepared cell lines permanently coexpressing the wild-type nuclear progesterone receptor (PR) and a cytoplasmic receptor mutant deleted of its nuclear localization signal (NLS) [(deltaNLS)PR]. Each receptor species was deleted from the epitope recognized by a specific monoclonal antibody, thus allowing separated observation of the two receptor forms in the same cells. Administration of hormone provoked formation of heterodimers during nucleocytoplasmic shuttling and import of (deltaNLS)PR into the nucleus. Washing out of the hormone allowed us to follow the export of (deltaNLS)PR into the cytoplasm. Microinjection of BSA coupled to a NLS inhibited the export of (deltaNLS)PR. On the contrary, microinjection of BSA coupled to a nuclear export signal (NES) was without effect. Moreover, leptomycin B, which inhibits NES-mediated export, was also without effect. tsBN2 cells contain a thermosensitive RCC1 protein (Ran GTP exchange protein). At the nonpermissive temperature, the nuclear export of (deltaNLS)PR could be observed, whereas the export of NES-BSA was suppressed. Microinjection of GTPgammaS confirmed that the export of (deltaNLS)PR was not dependent on GTP hydrolysis. These experiments show that the nuclear export of PR is not NES mediated but probably involves the NLS. It does not involve Ran GTP, and it is not dependent on the hydrolysis of GTP. The nucleocytoplasmic shuttling of steroid hormone receptors thus appears to utilize mechanisms different from those previously described for some viral, regulatory, and heterogeneous ribonuclear proteins. PMID:9817595

  9. Feedback Regulation of DYT1 by Interactions with Downstream bHLH Factors Promotes DYT1 Nuclear Localization and Anther Development.

    PubMed

    Cui, Jie; You, Chenjiang; Zhu, Engao; Huang, Qiang; Ma, Hong; Chang, Fang

    2016-05-01

    Transcriptional regulation is one of the most important mechanisms controlling development and cellular functions in plants and animals. The Arabidopsis thaliana bHLH transcription factor (TF) DYSFUNCTIONL TAPETUM1 (DYT1) is required for normal male fertility and anther development and activates the expression of the bHLH010/bHLH089/bHLH091 genes. Here, we showed that DYT1 is localized to both the cytoplasm and nucleus at anther stage 5 but specifically to the nucleus at anther stage 6 and onward. The bHLH010/bHLH089/bHLH091 proteins have strong nuclear localization signals, interact with DYT1, and facilitate the nuclear localization of DYT1. We further found that the conserved C-terminal BIF domain of DYT1 is required for its dimerization, nuclear localization, transcriptional activation activity, and function in anther development. Interestingly, when the BIF domain of DYT1 was replaced with that of bHLH010, the DYT1(N)-bHLH010(BIF) chimeric protein shows nuclear-preferential localization at anther stage 5 but could not fully rescue the dyt1-3 phenotype, suggesting that the normal spatio-temporal subcellular localization of DYT1 is important for DYT1 function and/or that the BIF domains from different bHLH members might be functionally distinct. Our results support an important positive feedback regulatory mechanism whereby downstream TFs increase the function of an upstream TF by enhancing its nucleus localization through the BIF domain. PMID:27113773

  10. Nuclear localization of Rad51B is independent of BRCA2

    SciTech Connect

    Miller, K A; Hinz, J M; Yamada, A; Thompson, L H; Albala, J S

    2005-06-28

    Human Rad51 is critical for the maintenance of genome stability through its role in the repair of DNA double-strand breaks. Rad51B (Rad51L1/hRec2) is one of the five known paralogs of human Rad51 found in a multi-protein complex with three other Rad51 paralogs, Rad51C, Rad51D and Xrcc2. Examination of EGFP-Rad51B fusion protein in HeLa S3 cells and immunofluorescence in several human cell lines confirms the nuclear localization of Rad51B. This is the first report to detail putative interactions of a Rad51 paralog protein with BRCA2. Utilization of a BRCA2 mutant cell line, CAPAN-1 suggests that Rad51B localizes to the nucleus independent of BRCA2. Although both Rad51B and BRCA2 are clearly involved in the homologous recombinational repair pathway, Rad51B and BRCA2 do not appear to associate directly. Furthermore, mutations in the KKLK motif of Rad51B, amino acid residues 4-7, mislocalizes Rad51B to the cytoplasm suggesting that this is the nuclear localization signal for the Rad51B protein. Examination of wild-type EGFP-Rad51B fusion protein in mammalian cells deficient in Rad51C showed that Rad51B localizes to the nucleus independent of Rad51C; further suggesting that Rad51B, like Rad51C, contains its own nuclear localization signal.

  11. The C175R mutation alters nuclear localization and transcriptional activity of the nephronophthisis NPHP7 gene product

    PubMed Central

    Ramachandran, Haribaskar; Yakulov, Toma A; Engel, Christina; Müller, Barbara; Walz, Gerd

    2016-01-01

    Nephronophthisis (NPH) is a rare autosomal ciliopathy, but the leading cause for hereditary end-stage renal disease in children. Most NPH family members form large protein networks, which appear to participate in structural elements of the cilium and/or function to restrict access of molecules to the ciliary compartment. The zinc-finger protein GLIS2/NPHP7 represents an exception as it has been implicated in transcriptional regulation; only two families with GLIS2/NPHP7 mutations and typical NPH manifestations have been identified so far. We describe here that the recently identified GLIS2/NPHP7C175R point mutation abolished the nuclear localization of GLIS2/NPHP7. Forced nuclear import did not rescue the transcriptional defects of GLIS2/NPHP7C175R, indicating additional defects as DNA-binding protein. We further observed that wild type, but not GLIS2/NPHP7C175R, prevented the cyst formation caused by depletion of nphp7 in zebrafish embryos. Taken together, our findings indicate that the C175R mutation affects both localization and function of GLIS2/NPHP7, supporting a role of this mutation in NPH, but questioning the direct involvement of GLIS2/NPHP7 in ciliary functions. PMID:26374130

  12. The Subcellular Localization and Functional Analysis of Fibrillarin2, a Nucleolar Protein in Nicotiana benthamiana

    PubMed Central

    Zheng, Luping; Yao, Jinai; Gao, Fangluan; Chen, Lin; Zhang, Chao; Lian, Lingli; Xie, Liyan; Wu, Zujian; Xie, Lianhui

    2016-01-01

    Nucleolar proteins play important roles in plant cytology, growth, and development. Fibrillarin2 is a nucleolar protein of Nicotiana benthamiana (N. benthamiana). Its cDNA was amplified by RT-PCR and inserted into expression vector pEarley101 labeled with yellow fluorescent protein (YFP). The fusion protein was localized in the nucleolus and Cajal body of leaf epidermal cells of N. benthamiana. The N. benthamiana fibrillarin2 (NbFib2) protein has three functional domains (i.e., glycine and arginine rich domain, RNA-binding domain, and α-helical domain) and a nuclear localization signal (NLS) in C-terminal. The protein 3D structure analysis predicted that NbFib2 is an α/β protein. In addition, the virus induced gene silencing (VIGS) approach was used to determine the function of NbFib2. Our results showed that symptoms including growth retardation, organ deformation, chlorosis, and necrosis appeared in NbFib2-silenced N. benthamiana. PMID:26885505

  13. Oscillator strengths, first-order properties, and nuclear gradients for local ADC(2)

    SciTech Connect

    Schütz, Martin

    2015-06-07

    We describe theory and implementation of oscillator strengths, orbital-relaxed first-order properties, and nuclear gradients for the local algebraic diagrammatic construction scheme through second order. The formalism is derived via time-dependent linear response theory based on a second-order unitary coupled cluster model. The implementation presented here is a modification of our previously developed algorithms for Laplace transform based local time-dependent coupled cluster linear response (CC2LR); the local approximations thus are state specific and adaptive. The symmetry of the Jacobian leads to considerable simplifications relative to the local CC2LR method; as a result, a gradient evaluation is about four times less expensive. Test calculations show that in geometry optimizations, usually very similar geometries are obtained as with the local CC2LR method (provided that a second-order method is applicable). As an exemplary application, we performed geometry optimizations on the low-lying singlet states of chlorophyllide a.

  14. Acetylation regulates subcellular localization of the Wnt signaling nuclear effector POP-1

    PubMed Central

    Gay, Frédérique; Calvo, Dominica; Lo, Miao-Chia; Ceron, Julian; Maduro, Morris; Lin, Rueyling; Shi, Yang

    2003-01-01

    Lymphoid enhancer factor/T-cell factor (LEF/TCF) are transcription factors that mediate the Wnt signaling pathway, and have crucial roles during embryonic development in various organisms. Here we report that acetylation enhances nuclear retention of POP-1, the Caenorhabditis elegans LEF/TCF homolog, through increasing nuclear import and blocking nuclear export. We identify three lysines that are acetylated in vivo, and demonstrate their essential requirement for proper nuclear localization and biological activity of POP-1 during C. elegans embryogenesis. The conservation of these lysines among other LEF/TCF family members suggests that acetylation may be an important, evolutionarily conserved mechanism regulating subcellular distribution of LEF/TCF factors. PMID:12651889

  15. Yeast Vps13 promotes mitochondrial function and is localized at membrane contact sites.

    PubMed

    Park, Jae-Sook; Thorsness, Mary K; Policastro, Robert; McGoldrick, Luke L; Hollingsworth, Nancy M; Thorsness, Peter E; Neiman, Aaron M

    2016-08-01

    The Vps13 protein family is highly conserved in eukaryotic cells. Mutations in human VPS13 genes result in a variety of diseases, such as chorea acanthocytosis (ChAc), but the cellular functions of Vps13 proteins are not well defined. In yeast, there is a single VPS13 orthologue, which is required for at least two different processes: protein sorting to the vacuole and sporulation. This study demonstrates that VPS13 is also important for mitochondrial integrity. In addition to preventing transfer of DNA from the mitochondrion to the nucleus, VPS13 suppresses mitophagy and functions in parallel with the endoplasmic reticulum-mitochondrion encounter structure (ERMES). In different growth conditions, Vps13 localizes to endosome-mitochondrion contacts and to the nuclear-vacuole junctions, indicating that Vps13 may function at membrane contact sites. The ability of VPS13 to compensate for the absence of ERMES correlates with its intracellular distribution. We propose that Vps13 is present at multiple membrane contact sites and that separation-of-function mutants are due to loss of Vps13 at specific junctions. Introduction of VPS13A mutations identified in ChAc patients at cognate sites in yeast VPS13 are specifically defective in compensating for the lack of ERMES, suggesting that mitochondrial dysfunction might be the basis for ChAc. PMID:27280386

  16. EGFR Signaling Regulates Maspin/SerpinB5 Phosphorylation and Nuclear Localization in Mammary Epithelial Cells

    PubMed Central

    Reina, Jeffrey; Morais Freitas, Vanessa

    2016-01-01

    Maspin (SerpinB5) is a non-inhibitory serpin (serine protease inhibitor) with very diverse biological activities including regulation of cell adhesion, migration, death, control of gene expression and oxidative stress response. Initially described as a tumor and metastasis suppressor, clinical data brought controversies to the field, as some studies reported no correlation between SerpinB5 expression and prognosis value. These data underscore the importance of understanding SerpinB5 function in a normal physiological context and the molecular mechanism involved. Several SerpinB5 phosphoforms have been detected in different cell lines, but the signaling pathways involved and the biological significance of this post-translational modification in vivo remains to be explored. In this study we investigated SerpinB5 expression, subcellular localization and phosphorylation in different stages of the mouse mammary gland development and the signaling pathway involved. Here we show that SerpinB5 is first detected in late pregnancy, reaches its highest levels in lactation and remains at constant levels during post-lactational regression (involution). Using high resolution isoelectric focusing followed but immunoblot, we found at least 8 different phosphoforms of SerpinB5 during lactation, which decreases steadily at the onset of involution. In order to investigate the signaling pathway involved in SerpinB5 phosphorylation, we took advantage of the non-transformed MCF-10A model system, as we have previously observed SerpinB5 phosphorylation in these cells. We detected basal levels of SerpinB5 phosphorylation in serum- and growth factor-starved cells, which is due to amphiregulin autocrine activity on MCF-10A cells. EGF and TGF alpha, two other EGFR ligands, promote important SerpinB5 phosphorylation. Interestingly, EGF treatment is followed by SerpinB5 nuclear accumulation. Altogether, these data indicate that SerpinB5 expression and phosphorylation are developmentally

  17. Identification of a novel nuclear localization signal and speckle-targeting sequence of tuftelin-interacting protein 11, a splicing factor involved in spliceosome disassembly

    SciTech Connect

    Tannukit, Sissada; Crabb, Tara L.; Hertel, Klemens J.; Wen, Xin; Jans, David A.; Paine, Michael L.

    2009-12-18

    Tuftelin-interacting protein 11 (TFIP11) is a protein component of the spliceosome complex that promotes the release of the lariat-intron during late-stage splicing through a direct recruitment and interaction with DHX15/PRP43. Expression of TFIP11 is essential for cell and organismal survival. TFIP11 contains a G-patch domain, a signature motif of RNA-processing proteins that is responsible for TFIP11-DHX15 interactions. No other functional domains within TFIP11 have been described. TFIP11 is localized to distinct speckled regions within the cell nucleus, although excluded from the nucleolus. In this study sequential C-terminal deletions and mutational analyses have identified two novel protein elements in mouse TFIP11. The first domain covers amino acids 701-706 (VKDKFN) and is an atypical nuclear localization signal (NLS). The second domain is contained within amino acids 711-735 and defines TFIP11's distinct speckled nuclear localization. The identification of a novel TFIP11 nuclear speckle-targeting sequence (TFIP11-STS) suggests that this domain directly interacts with additional spliceosomal components. These data help define the mechanism of nuclear/nuclear speckle localization of the splicing factor TFIP11, with implications for it's function.

  18. Nuclear receptor corepressor complexes in cancer: mechanism, function and regulation

    PubMed Central

    Wong, Madeline M; Guo, Chun; Zhang, Jinsong

    2014-01-01

    Nuclear receptor corepressor (NCoR) and silencing mediator for retinoid and thyroid hormone receptors (SMRT) function as corepressors for diverse transcription factors including nuclear receptors such as estrogen receptors and androgen receptors. Deregulated functions of NCoR and SMRT have been observed in many types of cancers and leukemias. NCoR and SMRT directly bind to transcription factors and nucleate the formation of stable complexes that include histone deacetylase 3, transducin b-like protein 1/TBL1-related protein 1, and G-protein pathway suppressor 2. These NCoR/SMRT-interacting proteins also show deregulated functions in cancers. In this review, we summarize the literature on the mechanism, regulation, and function of the core components of NCoR/SMRT complexes in the context of their involvement in cancers and leukemias. While the current studies support the view that the corepressors are promising targets for cancer treatment, elucidation of the mechanisms of corepressors involved in individual types of cancers is likely required for effective therapy. PMID:25374920

  19. Long isoform of ErbB3 binding protein, p48, mediates protein kinase B/Akt-dependent HDM2 stabilization and nuclear localization

    SciTech Connect

    Kim, Chung Kwon; Lee, Sang Bae; Nguyen, Truong L.X.; Lee, Kyung-Hoon; Um, Sung Hee; Kim, Jihoe; Ahn, Jee-Yin

    2012-01-15

    p48 is a long isoform of the ErbB3 binding protein that has oncogenic functions including promotion of carcinogenesis and induction of malignant transformation through negative regulation of tumor suppressor p53. Here, we show that high level of p48 protein expression leads to enhance HDM2 phosphorylation by Akt and inhibits the self-ubiquitination of HDM2 by up-regulation of Akt activity, thereby promoting its protein stability. Moreover, p48 expression leads to accumulated nuclear localization of HDM2, whereas p48 depletion disturbs its nuclear localization. Hence, higher expression of p48 in cancer cells reduces p53 levels through modulation of HDM2 nuclear localization and protein stability via regulation of its Akt-mediated phosphorylation.

  20. Nuclear chiral and magnetic rotation in covariant density functional theory

    NASA Astrophysics Data System (ADS)

    Meng, Jie; Zhao, Pengwei

    2016-05-01

    Excitations of chiral rotation observed in triaxial nuclei and magnetic and/or antimagnetic rotations (AMR) seen in near-spherical nuclei have attracted a lot of attention. Unlike conventional rotation in well-deformed or superdeformed nuclei, here the rotational axis is not necessary coinciding with any principal axis of the nuclear density distribution. Thus, tilted axis cranking (TAC) is mandatory to describe these excitations self-consistently in the framework of covariant density functional theory (CDFT). We will briefly introduce the formalism of TAC–CDFT and its application for magnetic and AMR phenomena. Configuration-fixed CDFT and its predictions for nuclear chiral configurations and for favorable triaxial deformation parameters are also presented, and the discoveries of the multiple chiral doublets in 133Ce and 103Rh are discussed.

  1. The Homothorax homeoprotein activates the nuclear localization of another homeoprotein, Extradenticle, and suppresses eye development in Drosophila

    PubMed Central

    Pai, Chi-Yun; Kuo, Tung-Sheng; Jaw, Thomas J.; Kurant, Estee; Chen, Cheng-Tse; Bessarab, Dmitri A.; Salzberg, Adi; Sun, Y. Henry

    1998-01-01

    The Extradenticle (Exd) protein in Drosophila acts as a cofactor to homeotic proteins. Its nuclear localization is regulated. We report the cloning of the Drosophila homothorax (hth) gene, a homolog of the mouse Meis1 proto-oncogene that has a homeobox related to that of exd. Comparison with Meis1 finds two regions of high homology: a novel MH domain and the homeodomain. In imaginal discs, hth expression coincides with nuclear Exd. hth and exd also have virtually identical, mutant clonal phenotypes in adults. These results suggest that hth and exd function in the same pathway. We show that hth acts upstream of exd and is required and sufficient for Exd protein nuclear localization. We also show that hth and exd are both negative regulators of eye development; their mutant clones caused ectopic eye formation. Targeted expression of hth, but not of exd, in the eye disc abolished eye development completely. We suggest that hth acts with exd to delimit the eye field and prevent inappropriate eye development. PMID:9450936

  2. Characterization of the nuclear localization signal of high risk HPV16 E2 protein

    SciTech Connect

    Klucevsek, Kristin; Wertz, Mary; Lucchi, John; Leszczynski, Anna; Moroianu, Junona . E-mail: moroianu@bc.edu

    2007-03-30

    The E2 protein of high risk human papillomavirus type 16 (HPV16) contains an amino-terminal (N) domain, a hinge (H) region and a carboxyl-terminal (C) DNA-binding domain. Using enhanced green fluorescent protein (EGFP) fusions with full length E2 and E2 domains in transfection assays in HeLa cells, we found that the C domain is responsible for the nuclear localization of E2 in vivo, whereas the N and H domains do not contain additional nuclear localization signals (NLSs). Deletion analysis of EGFP-E2 and EGFP-cE2 determined that the C domain contains an {alpha} helix cNLS that overlaps with the DNA-binding region. Mutational analysis revealed that the arginine and lysine residues in this cNLS are essential for nuclear localization of HPV16 E2. Interestingly, these basic amino acid residues are well conserved among the E2 proteins of BPV-1 and some high risk HPV types but not in the low risk HPV types, suggesting that there are differences between the NLSs and corresponding nuclear import pathways between these E2 proteins.

  3. Recent results on nuclear structure functions for light nuclei

    SciTech Connect

    Kulagin, S. A.; Petti, R.

    2011-09-21

    We discuss the nuclear EMC effect with particular emphasis on recent data for light nuclei including {sup 2}H, {sup 3}He, {sup 4}He, {sup 9}Be, {sup 12}C and {sup 14}N. In order to verify the consistency of available data, we calculate the {chi}{sup 2} deviation between different data sets. We find a good agreement between the results from the NMC, SLAC E139, and HERMES experiments. However, our analysis indicates an overall normalization offset of about 2% in the data from the recent JLab E03-103 experiment with respect to previous data for nuclei heavier than {sup 3}He. We also discuss the extraction of the neutron/proton structure function ratio F{sub 2}{sup n}/F{sub 2}{sup p} from the nuclear ratios {sup 3}He/{sup 2}H and {sup 2}H/{sup 1}H. Our analysis shows that the E03-103 data on {sup 3}He/{sup 2}H require a renormalization of about 3% in order to be consistent with the F{sub 2}{sup n}/F{sub 2}{sup p} ratio obtained from the NMC experiment. After such a renormalization, the {sup 3}He data from the E03-103 data and HERMES experiments are in a good agreement. We also present a detailed comparison between data and model calculations, which include a description of the nuclear binding, Fermi motion and off-shell corrections to the structure functions of bound proton and neutron, as well as the nuclear pion and shadowing corrections.

  4. Intracellular Expression of Camelid Single-Domain Antibodies Specific for Influenza Virus Nucleoprotein Uncovers Distinct Features of Its Nuclear Localization

    PubMed Central

    Ashour, Joseph; Schmidt, Florian I.; Hanke, Leo; Cragnolini, Juanjo; Cavallari, Marco; Altenburg, Arwen; Brewer, Rebeccah; Ingram, Jessica; Shoemaker, Charles

    2014-01-01

    ABSTRACT Perturbation of protein-protein interactions relies mostly on genetic approaches or on chemical inhibition. Small RNA viruses, such as influenza A virus, do not easily lend themselves to the former approach, while chemical inhibition requires that the target protein be druggable. A lack of tools thus constrains the functional analysis of influenza virus-encoded proteins. We generated a panel of camelid-derived single-domain antibody fragments (VHHs) against influenza virus nucleoprotein (NP), a viral protein essential for nuclear trafficking and packaging of the influenza virus genome. We show that these VHHs can target NP in living cells and perturb NP's function during infection. Cytosolic expression of NP-specific VHHs (αNP-VHHs) disrupts virus replication at an early stage of the life cycle. Based on their specificity, these VHHs fall into two distinct groups. Both prevent nuclear import of the viral ribonucleoprotein (vRNP) complex without disrupting nuclear import of NP alone. Different stages of the virus life cycle thus rely on distinct nuclear localization motifs of NP. Their molecular characterization may afford new means of intervention in the virus life cycle. IMPORTANCE Many proteins encoded by RNA viruses are refractory to manipulation due to their essential role in replication. Thus, studying their function and determining how to disrupt said function through pharmaceutical intervention are difficult. We present a novel method based on single-domain-antibody technology that permits specific targeting and disruption of an essential influenza virus protein in the absence of genetic manipulation of influenza virus itself. Characterization of such interactions may help identify new targets for pharmaceutical intervention. This approach can be extended to study proteins encoded by other viral pathogens. PMID:25540369

  5. Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS).

    PubMed

    Wehler, Pierre; Niopek, Dominik; Eils, Roland; Di Ventura, Barbara

    2016-01-01

    Many biological processes are regulated by the timely import of specific proteins into the nucleus. The ability to spatiotemporally control the nuclear import of proteins of interest therefore allows study of their role in a given biological process as well as controlling this process in space and time. The light-inducible nuclear localization signal (LINuS) was developed based on a natural plant photoreceptor that reversibly triggers the import of proteins of interest into the nucleus with blue light. Each LINuS is a small, genetically encoded domain that is fused to the protein of interest at the N or C terminus. These protocols describe how to carry out initial microscopy-based screening to assess which LINuS variant works best with a protein of interest. © 2016 by John Wiley & Sons, Inc. PMID:27258691

  6. 34 CFR 489.1 - What is the Functional Literacy for State and Local Prisoners Program?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 3 2010-07-01 2010-07-01 false What is the Functional Literacy for State and Local... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION FUNCTIONAL LITERACY FOR STATE AND LOCAL PRISONERS PROGRAM General § 489.1 What is the Functional Literacy for State and...

  7. 34 CFR 489.1 - What is the Functional Literacy for State and Local Prisoners Program?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 3 2011-07-01 2011-07-01 false What is the Functional Literacy for State and Local... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION FUNCTIONAL LITERACY FOR STATE AND LOCAL PRISONERS PROGRAM General § 489.1 What is the Functional Literacy for State and...

  8. 34 CFR 489.1 - What is the Functional Literacy for State and Local Prisoners Program?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 3 2012-07-01 2012-07-01 false What is the Functional Literacy for State and Local... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION FUNCTIONAL LITERACY FOR STATE AND LOCAL PRISONERS PROGRAM General § 489.1 What is the Functional Literacy for State and...

  9. 34 CFR 489.1 - What is the Functional Literacy for State and Local Prisoners Program?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 3 2014-07-01 2014-07-01 false What is the Functional Literacy for State and Local... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION FUNCTIONAL LITERACY FOR STATE AND LOCAL PRISONERS PROGRAM General § 489.1 What is the Functional Literacy for State and...

  10. 34 CFR 489.1 - What is the Functional Literacy for State and Local Prisoners Program?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 3 2013-07-01 2013-07-01 false What is the Functional Literacy for State and Local... (Continued) OFFICE OF VOCATIONAL AND ADULT EDUCATION, DEPARTMENT OF EDUCATION FUNCTIONAL LITERACY FOR STATE AND LOCAL PRISONERS PROGRAM General § 489.1 What is the Functional Literacy for State and...

  11. Casein kinase 2 (CK2) phosphorylates the deubiquitylase OTUB1 at Ser16 to trigger its nuclear localization.

    PubMed

    Herhaus, Lina; Perez-Oliva, Ana B; Cozza, Giorgio; Gourlay, Robert; Weidlich, Simone; Campbell, David G; Pinna, Lorenzo A; Sapkota, Gopal P

    2015-01-01

    The deubiquitylating enzyme OTUB1 is present in all tissues and targets many substrates, in both the cytosol and nucleus. We found that casein kinase 2 (CK2) phosphorylated OTUB1 at Ser(16) to promote its nuclear accumulation in cells. Pharmacological inhibition or genetic ablation of CK2 blocked the phosphorylation of OTUB1 at Ser(16), causing its nuclear exclusion in various cell types. Whereas we detected unphosphorylated OTUB1 mainly in the cytosol, we detected Ser(16)-phosphorylated OTUB1 only in the nucleus. In vitro, Ser(16)-phosphorylated OTUB1 and nonphosphorylated OTUB1 exhibited similar catalytic activity, bound K63-linked ubiquitin chains, and interacted with the E2 enzyme UBE2N. CK2-mediated phosphorylation and subsequent nuclear localization of OTUB1 promoted the formation of 53BP1 (p53-binding protein 1) DNA repair foci in the nucleus of osteosarcoma cells exposed to ionizing radiation. Our findings indicate that the activity of CK2 is necessary for the nuclear translocation and subsequent function of OTUB1 in DNA damage repair. PMID:25872870

  12. Nuclear clustering in the energy density functional approach

    SciTech Connect

    Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.

    2015-10-15

    Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.

  13. Nuclear clustering in the energy density functional approach

    NASA Astrophysics Data System (ADS)

    Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.

    2015-10-01

    Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.

  14. Nuclear materials transportation workshops: USDOE outreach to local governments. Final report

    SciTech Connect

    Not Available

    1987-09-28

    To provide direct outreach to local governments, the Transportation Management Division of the United States Department of Energy asked the Urban Consortium and its Energy Task Force to assemble representatives for two workshops focusing on the transport of nuclear materials. The first session, for jurisdictions east of the Mississippi River, was held in New Orleans on May 5--6, 1988; the second was conducted on June 6--7, 1988 in Denver for jurisdictions to the west. Twenty local government professionals with management or operational responsibility for hazardous materials transportation within their jurisdictions were selected to attend each workshop. The discussions identified five major areas of concern to local government professionals; coordination; training; information resources; marking and placarding; and responder resources. Integrated federal, state, and local levels of government emerged as a priority coordination issue along with the need for expanded availability of training and training resources for first-reponders.

  15. Interaction of nucleosome assembly proteins abolishes nuclear localization of DGK{zeta} by attenuating its association with importins

    SciTech Connect

    Okada, Masashi; Hozumi, Yasukazu; Ichimura, Tohru; Tanaka, Toshiaki; Hasegawa, Hiroshi; Yamamoto, Masakazu; Takahashi, Nobuya; Iseki, Ken; Yagisawa, Hitoshi; Shinkawa, Takashi; Isobe, Toshiaki; Goto, Kaoru

    2011-12-10

    Diacylglycerol kinase (DGK) is involved in the regulation of lipid-mediated signal transduction through the metabolism of a second messenger diacylglycerol. Of the DGK family, DGK{zeta}, which contains a nuclear localization signal, localizes mainly to the nucleus but translocates to the cytoplasm under pathological conditions. However, the detailed mechanism of translocation and its functional significance remain unclear. To elucidate these issues, we used a proteomic approach to search for protein targets that interact with DGK{zeta}. Results show that nucleosome assembly protein (NAP) 1-like 1 (NAP1L1) and NAP1-like 4 (NAP1L4) are identified as novel DGK{zeta} binding partners. NAP1Ls constitutively shuttle between the nucleus and the cytoplasm in transfected HEK293 cells. The molecular interaction of DGK{zeta} and NAP1Ls prohibits nuclear import of DGK{zeta} because binding of NAP1Ls to DGK{zeta} blocks import carrier proteins, Qip1 and NPI1, to interact with DGK{zeta}, leading to cytoplasmic tethering of DGK{zeta}. In addition, overexpression of NAP1Ls exerts a protective effect against doxorubicin-induced cytotoxicity. These findings suggest that NAP1Ls are involved in a novel molecular basis for the regulation of nucleocytoplasmic shuttling of DGK{zeta} and provide a clue to examine functional significance of its translocation under pathological conditions.

  16. Identification of a Functional, CRM-1-Dependent Nuclear Export Signal in Hepatitis C Virus Core Protein

    PubMed Central

    Cerutti, Andrea; Maillard, Patrick; Minisini, Rosalba; Vidalain, Pierre-Olivier; Roohvand, Farzin; Pecheur, Eve-Isabelle; Pirisi, Mario; Budkowska, Agata

    2011-01-01

    Hepatitis C virus (HCV) infection is a major cause of chronic liver disease worldwide. HCV core protein is involved in nucleocapsid formation, but it also interacts with multiple cytoplasmic and nuclear molecules and plays a crucial role in the development of liver disease and hepatocarcinogenesis. The core protein is found mostly in the cytoplasm during HCV infection, but also in the nucleus in patients with hepatocarcinoma and in core-transgenic mice. HCV core contains nuclear localization signals (NLS), but no nuclear export signal (NES) has yet been identified. We show here that the aa(109–133) region directs the translocation of core from the nucleus to the cytoplasm by the CRM-1-mediated nuclear export pathway. Mutagenesis of the three hydrophobic residues (L119, I123 and L126) in the identified NES or in the sequence encoding the mature core aa(1–173) significantly enhanced the nuclear localisation of the corresponding proteins in transfected Huh7 cells. Both the NES and the adjacent hydrophobic sequence in domain II of core were required to maintain the core protein or its fragments in the cytoplasmic compartment. Electron microscopy studies of the JFH1 replication model demonstrated that core was translocated into the nucleus a few minutes after the virus entered the cell. The blockade of nucleocytoplasmic export by leptomycin B treatment early in infection led to the detection of core protein in the nucleus by confocal microscopy and coincided with a decrease in virus replication. Our data suggest that the functional NLS and NES direct HCV core protein shuttling between the cytoplasmic and nuclear compartments, with at least some core protein transported to the nucleus. These new properties of HCV core may be essential for virus multiplication and interaction with nuclear molecules, influence cell signaling and the pathogenesis of HCV infection. PMID:22039426

  17. Instructional Quality as a Function of Locale, Grade, and Subject

    ERIC Educational Resources Information Center

    Randhawa, Bikkar S.

    1977-01-01

    Sixty urban and 57 rural elementary school classrooms were observed to document the effects of rural versus urban locale, grade level, and subject matter taught on instructional quality. Teachers' verbal behaviors were grouped into 16 process-by-substance categories. Results showed that all three main effects were significant. (Author/MV)

  18. Instructional Quality as a Function of Locale, Grade, and Subject.

    ERIC Educational Resources Information Center

    Randhawa, Bikkar S.

    This study investigated the effect of locale, grade, and subject on instructional quality. Rural and urban teachers were observed teaching grades 4, 5, and 6 in social studies, mathematics, and language arts. It was hypothesized that teacher verbal behavior in a classroom predicated the quality and quantity of cognitive behavior of pupils. Rural…

  19. Function and subcellular localization of Gcn5, a histone acetyltransferase in Candida albicans.

    PubMed

    Chang, Peng; Fan, Xueyi; Chen, Jiangye

    2015-08-01

    Candida albicans is an opportunistic fungal pathogen commonly found in humans. It has the ability to switch reversibly between three growth forms: budding yeast, pseudohypha, and hypha. The transition between yeast and hyphal growth forms is critical for the pathogenesis of C. albicans. During the yeast-to-hypha morphologic transition, gene expression is regulated by transcriptional regulators including histone modifying complexes and chromatin remodeling complexes. We previously reported that Esa1, a catalytic subunit in the histone acetyltransferase complex NuA4, is essential for the hyphal development of C. albicans. In this study, we analyzed the functional roles of Gcn5, a catalytic subunit in the histone acetyltransferase complex SAGA, in C. albicans. Gcn5 is required for the invasive and filamentous growth of C. albicans. Deletion of GCN5 impaired hyphal elongation in sensing serum and attenuated the virulence of C. albicans in a mouse systemic infection model. The C. albicans gcn5/gcn5 mutant cells also exhibited sensitivity to cell wall stress. Functional analysis showed that the HAT domain and Bromodomain in Gcn5 play distinct roles in morphogenesis and cell wall stress response of C. albicans. Our results show that the conserved residue Glu188 is crucial for the Gcn5 HAT activity and for Gcn5 function during filamentous growth. In addition, the subcellular distribution of ectopically expressed GFP-Gcn5 correlates with the different growth states of C. albicans. In stationary phase, Gcn5 accumulated in the nucleus, while during vegetative growth it localized in the cytoplasm in a morpha-independent manner. Our results suggest that the nuclear localization of Gcn5 depends on the existence of its N-terminal NLS and HAT domains. PMID:25656079

  20. Nuclear localization of Rad52 is pre-requisite for its sumoylation

    SciTech Connect

    Ohuchi, Takashi; Seki, Masayuki Enomoto, Takemi

    2008-07-18

    In Saccharomyces cerevisiae, Rad52 plays major roles in several types of homologous recombination. Here, we found that rad52-K200R mutation greatly reduced sumoylation of Rad52. The rad52-K200R mutant exhibited defects in various types of recombination, such as intrachromosomal recombination and mating-type switching. The K200 residue of Rad52 is part of the nuclear localization signal (NLS), which is important for transport into the nucleus. Indeed, the addition of a SV40 NLS to Rad52-K200R suppressed the sumoylation defect of Rad52-K200R. These findings indicate that nuclear localization of Rad52 is pre-requisite for its sumoylation.

  1. Characterization of the nuclear localization signal of the mouse TET3 protein

    SciTech Connect

    Xiao, Peng; Zhou, Xiao-long; Zhang, Hong-xiao; Xiong, Kai; Teng, Yun; Huang, Xian-ju; Cao, Rui; Wang, Yi; Liu, Hong-lin

    2013-09-27

    Highlights: •Amino acid sequence KKRK is responsible for nuclear localization of TET3. •Amino acid sequence KKRK are capable of targeting the cytoplasmic proteins to the nucleus. •Amino acid sequence KKRK are conserved in TET3 orthologs. -- Abstract: DNA demethylation is associated with gene activation and is mediated by a family of ten-eleven translocation (TET) dioxygenase. The TET3 protein is a 1668-amino-acid DNA demethylase that is predicted to possess five nuclear localization signals (NLSs). In this paper, we used a series of green fluorescent protein-tagged and mutation constructs to identify a conserved NLS (KKRK) embedded between amino acid 1615 and 1618 of mouse TET3. The KKRK sequence facilitates the cytoplasmic protein’s translocation into the nucleus. Additionally TET3 may be imported into the nucleus by importin-α and importin-β.

  2. Impact of Nucleoporin-Mediated Chromatin Localization and Nuclear Architecture on HIV Integration Site Selection.

    PubMed

    Wong, Richard W; Mamede, João I; Hope, Thomas J

    2015-10-01

    It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal locations. A number of viral and cellular proteins are implicated in this process, but the underlying mechanism is not clear. Two recent breakthrough publications advance our understanding of HIV integration site selection by focusing on the localization of the preferred target genes of integration. These studies reveal that knockdown of certain nucleoporins and components of nucleocytoplasmic trafficking alter integration site preference, not by altering the trafficking of the viral genome but by altering the chromatin subtype localization relative to the structure of the nucleus. Here, we describe the link between the nuclear basket nucleoporins (Tpr and Nup153) and chromatin organization and how altering the host environment by manipulating nuclear structure may have important implications for the preferential integration of HIV into actively transcribed genes, facilitating efficient viral replication. PMID:26136574

  3. Characterization of two different Asf1 histone chaperones with distinct cellular localizations and functions in Trypanosoma brucei

    PubMed Central

    Pascoalino, Bruno; Dindar, Gülcin; Vieira-da-Rocha, João P.; Machado, Carlos Renato; Janzen, Christian J.; Schenkman, Sergio

    2014-01-01

    The anti-silencing function protein 1 (Asf1) is a chaperone that forms a complex with histones H3 and H4 facilitating dimer deposition and removal from chromatin. Most eukaryotes possess two different Asf1 chaperones but their specific functions are still unknown. Trypanosomes, a group of early-diverged eukaryotes, also have two, but more divergent Asf1 paralogs than Asf1 of higher eukaryotes. To unravel possible different functions, we characterized the two Asf1 proteins in Trypanosoma brucei. Asf1A is mainly localized in the cytosol but translocates to the nucleus in S phase. In contrast, Asf1B is predominantly localized in the nucleus, as described for other organisms. Cytosolic Asf1 knockdown results in accumulation of cells in early S phase of the cell cycle, whereas nuclear Asf1 knockdown arrests cells in S/G2 phase. Overexpression of cytosolic Asf1 increases the levels of histone H3 and H4 acetylation. In contrast to cytosolic Asf1, overexpression of nuclear Asf1 causes less pronounced growth defects in parasites exposed to genotoxic agents, prompting a function in chromatin remodeling in response to DNA damage. Only the cytosolic Asf1 interacts with recombinant H3/H4 dimers in vitro. These findings denote the early appearance in evolution of distinguishable functions for the two Asf1 chaperons in trypanosomes. PMID:24322299

  4. Mechanisms Directing the Nuclear Localization of the CtBP Family Proteins

    PubMed Central

    Verger, Alexis; Quinlan, Kate G. R.; Crofts, Linda A.; Spanò, Stefania; Corda, Daniela; Kable, Eleanor P. W.; Braet, Filip; Crossley, Merlin

    2006-01-01

    The C-terminal binding protein (CtBP) family includes four proteins (CtBP1 [CtBP1-L], CtBP3/BARS [CtBP1-S], CtBP2, and RIBEYE) which are implicated both in transcriptional repression and in intracellular trafficking. However, the precise mechanisms by which different CtBP proteins are targeted to different subcellular regions remains unknown. Here, we report that the nuclear import of the various CtBP proteins and splice isoforms is differentially regulated. We show that CtBP2 contains a unique nuclear localization signal (NLS) located within its N-terminal region, which contributes to its nuclear accumulation. Using heterokaryon assays, we show that CtBP2 is capable of shuttling between the nucleus and cytoplasm of the cell. Moreover, CtBP2 can heterodimerize with CtBP1-L and CtBP1-S and direct them to the nucleus. This effect strongly depends on the CtBP2 NLS. PXDLS motif-containing transcription factors, such as BKLF, that bind CtBP proteins can also direct them to the nucleus. We also report the identification of a splice isoform of CtBP2, CtBP2-S, that lacks the N-terminal NLS and localizes to the cytoplasm. Finally, we show that mutation of the CtBP NADH binding site impairs the ability of the proteins to dimerize and to associate with BKLF. This reduces the nuclear accumulation of CtBP1. Our results suggest a model in which the nuclear localization of CtBP proteins is influenced by the CtBP2 NLS, by binding to PXDLS motif partner proteins, and through the effect of NADH on CtBP dimerization. PMID:16782877

  5. Selected Interventions in Nuclear Medicine: Gastrointestinal Motor Functions

    PubMed Central

    Odunsi, Suwebatu T.; Camilleri, Michael

    2009-01-01

    Measurement of gastrointestinal functions by scintigraphy is established in clinical practice and research. The most commonly used test is the gastric emptying test. This is acknowledged as the gold standard and is conducted according to a consensus statement from the national nuclear medicine and motility societies. Other techniques are somewhat more esoteric (e.g. measurement of gastric accommodation with SPECT) or the scintigraphic approach is not the acknowledged gold standard (e.g. colonic transit, recto-anal angle and emptying, esophageal transit). The performance characteristics of many of the scintigraphic measurements have been published and the pros and cons established in the literature. Gastrointestinal scintigraphy is an integral and important component of the assessment of gastrointestinal function. PMID:19341838

  6. Next Generation Nuclear Plant Resilient Control System Functional Analysis

    SciTech Connect

    Lynne M. Stevens

    2010-07-01

    Control Systems and their associated instrumentation must meet reliability, availability, maintainability, and resiliency criteria in order for high temperature gas-cooled reactors (HTGRs) to be economically competitive. Research, perhaps requiring several years, may be needed to develop control systems to support plant availability and resiliency. This report functionally analyzes the gaps between traditional and resilient control systems as applicable to HTGRs, which includes the Next Generation Nuclear Plant; defines resilient controls; assesses the current state of both traditional and resilient control systems; and documents the functional gaps existing between these two controls approaches as applicable to HTGRs. This report supports the development of an overall strategy for applying resilient controls to HTGRs by showing that control systems with adequate levels of resilience perform at higher levels, respond more quickly to disturbances, increase operational efficiency, and increase public protection.

  7. Global NLO Analysis of Nuclear Parton Distribution Functions

    SciTech Connect

    Hirai, M.; Kumano, S.; Nagai, T.-H.

    2008-02-21

    Nuclear parton distribution functions (NPDFs) are determined by a global analysis of experimental measurements on structure-function ratios F{sub 2}{sup A}/F{sub 2}{sup A{sup '}} and Drell-Yan cross section ratios {sigma}{sub DY}{sup A}/{sigma}{sub DY}{sup A{sup '}}, and their uncertainties are estimated by the Hessian method. The NPDFs are obtained in both leading order (LO) and next-to-leading order (NLO) of {alpha}{sub s}. As a result, valence-quark distributions are relatively well determined, whereas antiquark distributions at x>0.2 and gluon distributions in the whole x region have large uncertainties. The NLO uncertainties are slightly smaller than the LO ones; however, such a NLO improvement is not as significant as the nucleonic case.

  8. Bipartite nuclear localization signal of matrin 3 is essential for vertebrate cells

    SciTech Connect

    Hisada-Ishii, Shoji; Ebihara, Mizuki; Kobayashi, Nao; Kitagawa, Yasuo . E-mail: yasuok@agr.nagoya-u.ac.jp

    2007-03-02

    Matrin 3, a nuclear matrix protein has potential (1) to withhold promiscuously edited RNAs within the nucleus in cooperation with p54{sup nrb} and PSF (2) to mediate NMDA-induced neuronal death, and (3) to modulate promoter activity of genes proximal to matrix/scaffold attachment region (MAR/SAR). We identified a bipartite nuclear localization signal (NLS) of chicken matrin 3 (cmatr3) at residues 583-602. By expressing green fluorescent protein (GFP) fused to the NLS mutant in chicken DT40 cells, we showed an essential role of the NLS for cell proliferation. Furthermore, we showed that both clusters of basic amino acids and a linker of the bipartite NLS were essential and sufficient for the nuclear import of GFP. Exogenous cmatr3 rescued the HeLa cells where human matrin 3 was suppressed by RNA interference, but cmatr3 containing deletions at either of the basic amino acid clusters or the linker could not.

  9. Characterization of the nuclear localization signal of the hepatitis delta virus antigen

    SciTech Connect

    Alves, Carolina; Freitas, Natalia; Cunha, Celso

    2008-01-05

    The delta antigen (HDAg) is the only protein encoded by the hepatitis delta virus (HDV) RNA genome. The HDAg contains an RNA binding domain, a dimerization domain, and a nuclear localization signal (NLS). The nuclear import of HDV RNPs is thought to be one of the first tasks of the HDAg during the HDV replication cycle. Using c-myc-PK fusions with several regions of the HDAg in transfection assays in Huh7 cells, we found that the HDAg NLS consists of a single stretch of 10 amino acids, EGAPPAKRAR, located in positions 66-75. Deletion and mutation analysis of this region showed that both the acidic glutamic acid residue at position 66 and the basic arginine residue at position 75 are essential for promoting nuclear import.

  10. Subcellular localization of CrmA: identification of a novel leucine-rich nuclear export signal conserved in anti-apoptotic serpins.

    PubMed Central

    Rodriguez, Jose A; Span, Simone W; Kruyt, Frank A E; Giaccone, Giuseppe

    2003-01-01

    The cowpox virus-encoded anti-apoptotic protein cytokine response modifier A (CrmA) is a member of the serpin family that specifically inhibits the cellular proteins caspase 1, caspase 8 and granzyme B. In this study, we have used Flag- and yellow fluorescent protein (YFP)-tagged versions of CrmA to investigate the mechanisms that regulate its subcellular localization. We show that CrmA can actively enter and exit the nucleus and we demonstrate the role of the nuclear export receptor CRM1 in this shuttling process. CrmA contains a novel leucine-rich nuclear export signal (NES) that is functionally conserved in the anti-apoptotic cellular serpin PI-9. Besides this leucine-rich export signal, additional sequences mapping to a 103-amino-acid region flanking the NES contribute to the CRM1-dependent nuclear export of CrmA. Although YFP-tagged CrmA is primarily located in the cytoplasm, shifting its localization to be predominantly nuclear by fusion of a heterologous nuclear localization signal did not impair its ability to prevent Fas-induced apoptosis. We propose that nucleocytoplasmic shuttling would allow CrmA to efficiently target cellular pro-apoptotic proteins not only in the cytoplasm, but also in the nucleus, and thus to carry out its anti-apoptotic function in both compartments. PMID:12667137

  11. Validation of local hybrid functionals for TDDFT calculations of electronic excitation energies

    NASA Astrophysics Data System (ADS)

    Maier, Toni M.; Bahmann, Hilke; Arbuznikov, Alexei V.; Kaupp, Martin

    2016-02-01

    The first systematic evaluation of local hybrid functionals for the calculation of electronic excitation energies within linear-response time-dependent density functional theory (TDDFT) is reported. Using our recent efficient semi-numerical TDDFT implementation [T. M. Maier et al., J. Chem. Theory Comput. 11, 4226 (2015)], four simple, thermochemically optimized one-parameter local hybrid functionals based on local spin-density exchange are evaluated against a database of singlet and triplet valence excitations of organic molecules, and against a mixed database including also Rydberg, intramolecular charge-transfer (CT) and core excitations. The four local hybrids exhibit comparable performance to standard global or range-separated hybrid functionals for common singlet valence excitations, but several local hybrids outperform all other functionals tested for the triplet excitations of the first test set, as well as for relative energies of excited states. Evaluation for the combined second test set shows that local hybrids can also provide excellent Rydberg and core excitations, in the latter case rivaling specialized functionals optimized specifically for such excitations. This good performance of local hybrids for different excitation types could be traced to relatively large exact-exchange (EXX) admixtures in a spatial region intermediate between valence and asymptotics, as well as close to the nucleus, and lower EXX admixtures in the valence region. In contrast, the tested local hybrids cannot compete with the best range-separated hybrids for intra- and intermolecular CT excitation energies. Possible directions for improvement in the latter category are discussed. As the used efficient TDDFT implementation requires essentially the same computational effort for global and local hybrids, applications of local hybrid functionals to excited-state problems appear promising in a wide range of fields. Influences of current-density dependence of local kinetic

  12. Dynamic nuclear polarization enhanced nuclear magnetic resonance and electron spin resonance studies of hydration and local water dynamics in micelle and vesicle assemblies.

    PubMed

    McCarney, Evan R; Armstrong, Brandon D; Kausik, Ravinath; Han, Songi

    2008-09-16

    We present a unique analysis tool for the selective detection of local water inside soft molecular assemblies (hydrophobic cores, vesicular bilayers, and micellar structures) suspended in bulk water. Through the use of dynamic nuclear polarization (DNP), the (1)H NMR signal of water is amplified, as it interacts with stable radicals that possess approximately 658 times higher spin polarization. We utilized stable nitroxide radicals covalently attached along the hydrophobic tail of stearic acid molecules that incorporate themselves into surfactant-based micelle or vesicle structures. Here, we present a study of local water content and fluid viscosity inside oleate micelles and vesicles and Triton X-100 micelles to serve as model systems for soft molecular assemblies. This approach is unique because the amplification of the NMR signal is performed in bulk solution and under ambient conditions with site-specific spin labels that only detect the water that is directly interacting with the localized spin labels. Continuous wave (cw) electron spin resonance (ESR) analysis provides rotational dynamics of the spin-labeled molecular chain segments and local polarity parameters that can be related to hydration properties, whereas we show that DNP-enhanced (1)H NMR analysis of fluid samples directly provides translational water dynamics and permeability of the local environment probed by the spin label. Our technique therefore has the potential to become a powerful analysis tool, complementary to cw ESR, to study hydration characteristics of surfactant assemblies, lipid bilayers, or protein aggregates, where water dynamics is a key parameter of their structure and function. In this study, we find that there is significant penetration of water inside the oleate micelles with a higher average local water viscosity (approximately 1.8 cP) than in bulk water, and Triton X-100 micelles and oleate vesicle bilayers mostly exclude water while allowing for considerable surfactant chain

  13. Local fracture properties and dissimilar weld integrity in nuclear power plants

    NASA Astrophysics Data System (ADS)

    Wang, Guozhen; Wang, Haitao; Xuan, Fuzhen; Tu, Shantung; Liu, Changjun

    2013-09-01

    In this paper, the local fracture properties in a Alloy52M dissimilar metal welded joint (DMWJ) between A508 ferritic steel and 316 L stainless steel in nuclear power plants were investigated by using the single-edge notched bend (SENB) specimens, and their use in integrity assessment of DMWJ structures was analyzed. The results show that the local fracture resistance in the DMWJ is determined by local fracture mechanism, and which is mainly related to the microstructures and local strength mismatches of materials at the crack locations. The initial cracks always grow towards the materials with lower strength, and the crack path deviation is mainly controlled by the local strength mismatch. If the local fracture properties could not be used for cracks in the heat affected zones (HAZs), interface and near interface zones, the use of the fracture properties ( J-resistance curves) of base metals or weld metals following present codes will unavoidably produce non-conservative (unsafe) or excessive conservative assessment results. In most cases, the assessment results will be potentially unsafe. Therefore, it is recommended to obtain and use local mechanical and fracture properties in the integrity assessment of DMWJs.

  14. Local negotiation on compensation siting of the spent nuclear fuel repository in Finland

    SciTech Connect

    Kojo, Matti

    2007-07-01

    The aim of the paper is to analyse the local negotiation process between the Municipality of Eurajoki and the nuclear power company Teollisuuden Voima (TVO) and the nuclear waste management company Posiva Oy. The aim of the negotiations was to find an acceptable form of compensation for siting a spent nuclear fuel repository in Olkiluoto, Finland. The paper includes background information on the siting process in Finland, the local political setting in the Municipality of Eurajoki and a description of the negotiation process. The analysis of the negotiations on compensation is important for better understanding the progress of the Finnish siting process. The paper describes the picture of the contest to host the spent nuclear fuel repository. It also provides more information on the relationship between the Municipality of Eurajoki and the power company TVO. The negotiations on compensation and the roles of various players in the negotiations have not been studied in detail because the minutes of the Vuojoki liaison group were not available before the decision of the Supreme Administrative Court in May 2006. (author)

  15. Transcription-dependent nuclear localization of DAZAP1 requires an N-terminal signal

    SciTech Connect

    Lin, Yi-Tzu; Wen, Wan-Ching; Yen, Pauline H.

    2012-11-23

    Highlights: Black-Right-Pointing-Pointer DAZAP1 shuttles between the nucleus and the cytoplasm. Black-Right-Pointing-Pointer DAZAP1 accumulates in the cytoplasm when the nuclear transcription is inhibited. Black-Right-Pointing-Pointer DAZAP1's transcription-dependent nuclear localization requires N-terminal N42. Black-Right-Pointing-Pointer SLIRP binds to N42 and may be involved in the process. -- Abstract: Deleted in Azoospermia Associated Protein 1 (DAZAP1) is a ubiquitous hnRNP protein required for normal development and spermatogenesis. It resides predominantly in the nucleus and moves between the nucleus and the cytoplasm via a ZNS shuttling signal at its C-terminus. DAZAP1 accumulates in the cytoplasm when RNA polymerase II activity is inhibited by actinomycin D. Here we report the mapping of a 42-amino acid segment (N42) at the N-terminus of DAZAP1 that is both necessary and sufficient for its transcription-dependent nuclear localization. In addition, using a yeast two-hybrid system, we have identified SLIRP as a N42-binding protein which may regulate DAZAP1 subcellular localization.

  16. In vivo functional protein-protein interaction: nuclear targeted hsp90 shifts cytoplasmic steroid receptor mutants into the nucleus.

    PubMed Central

    Kang, K I; Devin, J; Cadepond, F; Jibard, N; Guiochon-Mantel, A; Baulieu, E E; Catelli, M G

    1994-01-01

    In target tissue extracts, heat shock protein hsp90 has been found associated to all unliganded steroid receptors. Modulation of important functions of these receptors, including prevention of DNA binding and optimization of transcriptional activity, has been attributed to hsp90. However no unequivocal in vivo demonstration of interaction between receptors and hsp90 has been presented. We targeted chicken hsp90, a mainly cytoplasmic protein, with the nucleoplasmin nuclear localization signal (90NLS). After transfection into COS-7 cells, 90NLS was found in the nucleus with specific immunofluorescence and confocal microscopy techniques. A human glucocorticosteroid receptor mutant devoid of NLS sequence was also expressed in COS-7 cells and found exclusively cytoplasmic. Coexpression of 90NLS and of the cytoplasmic human glucocorticosteroid receptor mutant led to complete nuclear localization of the receptor, indicating its piggyback transport by 90NLS and thus physical and functional interaction between the two proteins in the absence of hormone. The same nuclear localization was obtained after cotransfection of 90NLS and a cytoplasmic rabbit progesterone receptor mutant. Finally, coexpression of wild-type rabbit progesterone receptor (nuclear) and wildtype hsp90 (cytoplasmic) into COS-7 cells provoked partial relocalization of hsp90 into the nucleus. These experiments lay the groundwork on which to study hsp90 as a chaperone, regulating activities of steroid receptors and possibly participating in their nuclear-cytoplasmic shuttling. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8278390

  17. Local thermodynamic mapping for effective liquid density-functional theory

    NASA Technical Reports Server (NTRS)

    Kyrlidis, Agathagelos; Brown, Robert A.

    1992-01-01

    The structural-mapping approximation introduced by Lutsko and Baus (1990) in the generalized effective-liquid approximation is extended to include a local thermodynamic mapping based on a spatially dependent effective density for approximating the solid phase in terms of the uniform liquid. This latter approximation, called the local generalized effective-liquid approximation (LGELA) yields excellent predictions for the free energy of hard-sphere solids and for the conditions of coexistence of a hard-sphere fcc solid with a liquid. Moreover, the predicted free energy remains single valued for calculations with more loosely packed crystalline structures, such as the diamond lattice. The spatial dependence of the weighted density makes the LGELA useful in the study of inhomogeneous solids.

  18. Influencing uptake and localization of aminoglycoside-functionalized peptoids.

    PubMed

    Lee, Melissa M; French, Jonathan M; Disney, Matthew D

    2011-08-01

    The development of small-molecule therapeutics that target RNA remains a promising field but one hampered with considerable challenges that include programming high affinity, specificity, cell permeability, and favorable pharmacokinetic profiles. Previously, we employed the use of peptoids to modularly display RNA-binding modules to enhance binding affinity and specificity by altering valency and the distance between ligand modules. Herein, factors that affect uptake, localization, and toxicity of peptoids that display a kanamycin derivative into a variety of mammalian cells lines are reported. A series of peptoids that display various spacing modules was synthesized to determine if the spacing module affects permeability and localization. The spacing module does affect cellular permeability into C2C12, A549, HeLa, and MCF7 cell lines but not into Jurkat cells. Moreover, the modularly assembled peptoids carrying the kanamycin cargo localize in the cytoplasm and perinuclear region of C2C12 and A549 cells and throughout HeLa cells, including the nucleus. These studies could contribute to the development of general strategies to afford cell permeable, modularly assembled small molecules that specifically target RNAs present in a variety of cell types. PMID:21611644

  19. Influencing uptake and localization of aminoglycoside-functionalized peptoids†

    PubMed Central

    Lee, Melissa M.; French, Jonathan M.; Disney, Matthew D.

    2011-01-01

    The development of small-molecule therapeutics that target RNA remains a promising field but one hampered with considerable challenges that include programming high affinity, specificity, cell permeability, and favorable pharmacokinetic profiles. Previously, we employed the use of peptoids to modularly display RNA-binding modules to enhance binding affinity and specificity by altering valency and the distance between ligand modules. Herein, factors that affect uptake, localization, and toxicity of peptoids that display a kanamycin derivative into a variety of mammalian cells lines are reported. A series of peptoids that display various spacing modules was synthesized to determine if the spacing module affects permeability and localization. The spacing module does affect cellular permeability into C2C12, A549, HeLa, and MCF7 cell lines but not into Jurkat cells. Moreover, the modularly assembled peptoids carrying the kanamycin cargo localize in the cytoplasm and perinuclear region of C2C12 and A549 cells and throughout HeLa cells, including the nucleus. These studies could contribute to the development of general strategies to afford cell permeable, modularly assembled small molecules that specifically target RNAs present in a variety of cell types. PMID:21611644

  20. Protein kinase A activation enhances β-catenin transcriptional activity through nuclear localization to PML bodies.

    PubMed

    Zhang, Mei; Mahoney, Emilia; Zuo, Tao; Manchanda, Parmeet K; Davuluri, Ramana V; Kirschner, Lawrence S

    2014-01-01

    The Protein Kinase A (PKA) and Wnt signaling cascades are fundamental pathways involved in cellular development and maintenance. In the osteoblast lineage, these pathways have been demonstrated functionally to be essential for the production of mineralized bone. Evidence for PKA-Wnt crosstalk has been reported both during tumorigenesis and during organogenesis, and the nature of the interaction is thought to rely on tissue and cell context. In this manuscript, we analyzed bone tumors arising from mice with activated PKA caused by mutation of the PKA regulatory subunit Prkar1a. In primary cells from these tumors, we observed relocalization of β-catenin to intranuclear punctuate structures, which were identified as PML bodies. Cellular redistribution of β-catenin could be recapitulated by pharmacologic activation of PKA. Using 3T3-E1 pre-osteoblasts as a model system, we found that PKA phosphorylation sites on β-catenin were required for nuclear re-localization. Further, β-catenin's transport to the nucleus was accompanied by an increase in canonical Wnt-dependent transcription, which also required the PKA sites. PKA-Wnt crosstalk in the cells was bi-directional, including enhanced interactions between β-catenin and the cAMP-responsive element binding protein (CREB) and transcriptional crosstalk between the Wnt and PKA signaling pathways. Increases in canonical Wnt/β-catenin signaling were associated with a decrease in the activity of the non-canonical Wnt/Ror2 pathway, which has been shown to antagonize canonical Wnt signaling. Taken together, this study provides a new understanding of the complex regulation of the subcellular distribution of β-catenin and its differential protein-protein interaction that can be modulated by PKA signaling. PMID:25299576

  1. Nuclear charge and neutron radii and nuclear matter: Trend analysis in Skyrme density-functional-theory approach

    NASA Astrophysics Data System (ADS)

    Reinhard, P.-G.; Nazarewicz, W.

    2016-05-01

    Background: Radii of charge and neutron distributions are fundamental nuclear properties. They depend on both nuclear interaction parameters related to the equation of state of infinite nuclear matter and on quantal shell effects, which are strongly impacted by the presence of nuclear surface. Purpose: In this work, by studying the correlation of charge and neutron radii, and neutron skin, with nuclear matter parameters, we assess different mechanisms that drive nuclear sizes. Method: We apply nuclear density functional theory using a family of Skyrme functionals obtained by means of optimization protocols, which do not include any radius information. By performing the Monte Carlo sampling of reasonable functionals around the optimal parametrization, we scan all correlations between nuclear matter properties and observables characterizing charge and neutron distributions of spherical closed-shell nuclei 48Ca,208Pb, and 298Fl. Results: By considering the influence of various nuclear matter properties on charge and neutron radii in a multidimensional parameter space of Skyrme functionals, we demonstrate the existence of two strong relationships: (i) between the nuclear charge radii and the saturation density of symmetric nuclear matter ρ0, and (ii) between the neutron skins and the slope of the symmetry energy L . The impact of other nuclear matter properties on nuclear radii is weak or nonexistent. For functionals optimized to experimental binding energies only, proton and neutron radii are found to be weakly correlated due to canceling trends from different nuclear matter characteristics. Conclusion: The existence of only two strong relations connecting nuclear radii with nuclear matter properties has important consequences. First, by requiring that the nuclear functional reproduces the empirical saturation point of symmetric nuclear matter practically fixes the charge (or proton) radii, and vice versa. This explains the recent results of ab initio calculations

  2. The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization

    SciTech Connect

    Lalime, Erin N.; Pekosz, Andrew

    2014-06-15

    The influenza A virus NS1 protein has a nuclear localization sequence (NLS) in the amino terminal region. This NLS overlaps sequences that are important for RNA binding as well as protein dimerization. To assess the significance of the NS1 NLS on influenza virus replication, the NLS amino acids were individually mutated to alanines and recombinant viruses encoding these mutations were rescued. Viruses containing NS1 proteins with mutations at R37, R38 and K41 displayed minimal changes in replication or NS1 protein nuclear localization. Recombinant viruses encoding NS1 R35A were not recovered but viruses containing second site mutations at position D39 in addition to the R35A mutation were isolated. The mutations at position 39 were shown to partially restore NS1 protein dimerization but had minimal effects on nuclear localization. These data indicate that the amino acids in the NS1 NLS region play a more important role in protein dimerization compared to nuclear localization. - Highlights: • Mutations were introduced into influenza NS1 NLS1. • NS1 R37A, R38A, K41A viruses had minimal changes in replication and NS1 localization. • Viruses from NS1 R35A rescue all contained additional mutations at D39. • NS1 R35A D39X mutations recover dimerization lost in NS1 R35A mutations. • These results reaffirm the importance of dimerization for NS1 protein function.

  3. Alimentary Tract Absorption (f1 Values) for Radionuclides in Local and Regional Fallout from Nuclear Tests

    PubMed Central

    Ibrahim, Shawki; Simon, Steven L; Bouville, André; Melo, Dunstana; Beck, Harold

    2009-01-01

    This paper presents gastrointestinal absorption fractions (f1 values) for estimating internal doses from local and regional fallout radionuclides due to nuclear tests. The choice of f1 values are based on specific circumstances of weapons test conditions and a review of reported f1 values for elements in different physical and chemical states. Special attention is given to fallout from nuclear tests conducted at the Marshall Islands. We make a distinction between the f1 values for intakes of radioactive materials immediately after deposition (acute intakes) and intakes that occur in the course of months and years after deposition, following incorporation into terrestrial and aquatic foodstuffs (chronic intakes). Multiple f1 values for different circumstances where persons are exposed to radioactive fallout (e.g. local vs. regional fallout and coral vs. continental tests) are presented when supportive information is available. In some cases, our selected f1 values are similar to those adopted by the ICRP (e.g. iodine and most actinides). However, f1 values for cesium and strontium derived from urine bioassay data of the Marshallese population are notably lower than the generic f1 values recommended by ICRP, particularly for acute intakes from local fallout (0.4 and 0.05 for Cs and Sr, respectively. The f1 values presented here form the first complete set of values relevant to realistic dose assessments for exposure to local or regional radioactive fallout. PMID:20622554

  4. Alimentary tract absorption (f1 values) for radionuclides in local and regional fallout from nuclear tests.

    PubMed

    Ibrahim, Shawki A; Simon, Steven L; Bouville, André; Melo, Dunstana; Beck, Harold L

    2010-08-01

    This paper presents gastrointestinal absorption fractions (f1 values) for estimating internal doses from local and regional fallout radionuclides due to nuclear tests. The choice of f1 values are based on specific circumstances of weapons test conditions and a review of reported f1 values for elements in different physical and chemical states. Special attention is given to fallout from nuclear tests conducted at the Marshall Islands. We make a distinction between the f1 values for intakes of radioactive materials immediately after deposition (acute intakes) and intakes that occur in the course of months and years after deposition, following incorporation into terrestrial and aquatic foodstuffs (chronic intakes). Multiple f1 values for different circumstances where persons are exposed to radioactive fallout (e.g., local vs. regional fallout and coral vs. continental tests) are presented when supportive information is available. In some cases, our selected f1 values are similar to those adopted by the International Commission on Radiological Protection (ICRP) (e.g., iodine and most actinides). However, f1 values for cesium and strontium derived from urine bioassay data of the Marshallese population are notably lower than the generic f1 values recommended by ICRP, particularly for acute intakes from local fallout (0.4 and 0.05 for Cs and Sr, respectively). The f1 values presented here form the first complete set of values relevant to realistic dose assessments for exposure to local or regional radioactive fallout. PMID:20622554

  5. Functional redundancy in the nuclear compartmentalization of the late-replicating genome

    PubMed Central

    Ragoczy, Tobias; Telling, Agnes; Scalzo, David; Kooperberg, Charles; Groudine, Mark

    2014-01-01

    The eukaryotic nucleus is structurally and functionally organized, as reflected in the distribution of its protein and DNA components. The genome itself is segregated into euchromatin and heterochromatin that replicate in a distinct spatio-temporal manner. We used a combination of fluorescence in situ hybridization (FISH) and DamID to investigate the localization of the early and late replicating components of the genome in a lymphoblastoid cell background. Our analyses revealed that the bulk of late replicating chromatin localizes to the nuclear peripheral heterochromatin (PH) in a chromosome size and gene density dependent manner. Late replicating DNA on small chromosomes exhibits a much lower tendency to localize to PH and tends to associate with alternate repressive subcompartments such as pericentromeric (PCH) and perinucleolar heterochromatin (PNH). Furthermore, multicolor FISH analysis revealed that late replicating loci, particularly on the smaller chromosomes, may associate with any of these 3 repressive subcompartments, including more than one at the same time. These results suggest a functional equivalence or redundancy among the 3 subcompartments. Consistent with this notion, disruption of nucleoli resulted in an increased association of late replicating loci with peripheral heterochromatin. Our analysis reveals that rather than considering the morphologically distinct PH, PCH and PNH as individual subcompartments, they should be considered in aggregate as a functional compartment for late replicating chromatin. PMID:25493640

  6. CRM1-dependent nuclear export and dimerization with hMSH5 contribute to the regulation of hMSH4 subcellular localization

    SciTech Connect

    Neyton, Sophie; Lespinasse, Francoise; Lahaye, Francois; Staccini, Pascal; Paquis-Flucklinger, Veronique; Santucci-Darmanin, Sabine

    2007-10-15

    MSH4 and MSH5 are members of the MutS homolog family, a conserved group of proteins involved in DNA mismatch correction and homologous recombination. Although several studies have provided compelling evidences suggesting that MSH4 and MSH5 could act together in early and late stages of meiotic recombination, their precise roles are poorly understood and recent findings suggest that the human MSH4 protein may also exert a cytoplasmic function. Here we show that MSH4 is present in the cytoplasm and the nucleus of both testicular cells and transfected somatic cells. Confocal studies on transfected cells provide the first evidence that the subcellular localization of MSH4 is regulated, at least in part, by an active nuclear export pathway dependent on the exportin CRM1. We used deletion mapping and mutagenesis to define two functional nuclear export sequences within the C-terminal part of hMSH4 that mediate nuclear export through the CRM1 pathway. Our results suggest that CRM1 is also involved in MSH5 nuclear export. In addition, we demonstrate that dimerization of MSH4 and MSH5 facilitates their nuclear localization suggesting that dimerization may regulate the intracellular trafficking of these proteins. Our findings suggest that nucleocytoplasmic traffic may constitute a regulatory mechanism for MSH4 and MSH5 functions.

  7. Localization of latency-associated nuclear antigen (LANA) on mitotic chromosomes.

    PubMed

    Rahayu, Retno; Ohsaki, Eriko; Omori, Hiroko; Ueda, Keiji

    2016-09-01

    In latent infection of Kaposi's sarcoma-associated herpesvirus (KSHV), viral gene expression is extremely limited and copy numbers of viral genomes remain constant. Latency-associated nuclear antigen (LANA) is known to have a role in maintaining viral genome copy numbers in growing cells. Several studies have shown that LANA is localized in particular regions on mitotic chromosomes, such as centromeres/pericentromeres. We independently examined the distinct localization of LANA on mitotic chromosomes during mitosis, using super-resolution laser confocal microscopy and correlative fluorescence microscopy-electron microscopy (FM-EM) analyses. We found that the majority of LANA were not localized at particular regions such as telomeres/peritelomeres, centromeres/pericentromeres, and cohesion sites, but at the bodies of condensed chromosomes. Thus, LANA may undergo various interactions with the host factors on the condensed chromosomes in order to tether the viral genome to mitotic chromosomes and realize faithful viral genome segregation during cell division. PMID:27254595

  8. Protein Function Annotation By Local Binding Site Surface Similarity

    PubMed Central

    Spitzer, Russell; Cleves, Ann E.; Varela, Rocco; Jain, Ajay N.

    2013-01-01

    Hundreds of protein crystal structures exist for proteins whose function cannot be confidently determined from sequence similarity. Surflex-PSIM, a previously reported surface-based protein similarity algorithm, provides an alternative method for hypothesizing function for such proteins. The method now supports fully automatic binding site detection and is fast enough to screen comprehensive databases of protein binding sites. The binding site detection methodology was validated on apo/holo cognate protein pairs, correctly identifying 91% of ligand binding sites in holo structures and 88% in apo structures where corresponding sites existed. For correctly detected apo binding sites, the cognate holo site was the most similar binding site 87% of the time. PSIM was used to screen a set of proteins that had poorly characterized functions at the time of crystallization, but were later biochemically annotated. Using a fully automated protocol, this set of 8 proteins was screened against approximately 60,000 ligand binding sites from the PDB. PSIM correctly identified functional matches that pre-dated query protein biochemical annotation for five out of the eight query proteins. A panel of twelve currently unannotated proteins was also screened, resulting in a large number of statistically significant binding site matches, some of which suggest likely functions for the poorly characterized proteins. PMID:24166661

  9. DSCAM Localization and Function at the Mouse Cone Synapse

    PubMed Central

    de Andrade, Gabriel Belem; Long, Samuel S.; Fleming, Harrison; Li, Wei; Fuerst, Peter G.

    2014-01-01

    The Down Syndrome Cell Adhesion Molecule (DSCAM) is required for regulation of cell number, soma spacing and cell type specific dendrite avoidance in many types of retinal ganglion and amacrine cells. In this study we assay the organization of cells making up the outer plexiform layer of the retina in the absence of Dscam. Some types of OFF bipolar cells, type 3b and type 4 bipolar cells, had defects in dendrite arborization in the Dscam mutant retina, while other cell types appeared similar to wild type. The cone synapses that these cells project their dendrites to were intact, as visualized by electron microscopy, and had a distribution and density that was not significantly different than wild type. The spacing of type 3b bipolar cell dendrites was further analyzed by Voronoi domain analysis, Density Recovery Profiling (DRP) analysis and Nearest Neighbor Analysis (NNA). Spacing was found to be significantly different when comparing wild type and mutant type 3b bipolar cell dendrites. Defects in arborization of these bipolar cells could not be attributed to the disorganization of inner plexiform layer cells that occurs in the Dscam mutant retina or an increase in cell number, as they arborized when Dscam was targeted in retinal ganglion cells only or in the bax null retina. Localization of DSCAM was assayed and the protein was localized near to cone synapses in mouse, macaque and ground squirrel retinas. DSCAM protein was detected in several types of bipolar cells, including type 3b and type 4 bipolar cells. PMID:24477985

  10. Real-time Kadanoff-Baym approach to nuclear response functions

    NASA Astrophysics Data System (ADS)

    Köhler, H. S.; Kwong, N. H.

    2016-03-01

    Linear density response functions are calculated for symmetric nuclear matter of normal density by time-evolving two-time Green's functions in real time. Of particular interest is the effect of correlations. The system is therefore initially time-evolved with a collision term calculated in a direct Born approximation until fully correlated. An external time-dependent potential is then applied. The ensuing density fluctuations are recorded to calculate the density response. This method was previously used by Kwong and Bonitz for studying plasma oscillations in a correlated electron gas. The energy-weighted sum-rule for the response function is guaranteed by using conserving self-energy insertions as the method then generates the full vertex-functions. These can alternatively be calculated by solving a Bethe -Salpeter equation as done in works by Bozek et al. The (first order) mean field is derived from a momentum-dependent (non-local) interaction while 2nd order self-energies are calculated using a particle-hole two-body effective (or residual) interaction given by a gaussian local potential. We show results of calculations of the response function S(ɷ,q0 ) for q0 = 0.2, 0.4 and 0.8fm -1. Comparison is made with the nucleons being un-correlated i.e. with only the first order mean field included. We discuss the relation of our work with the Landau quasi-particle theory as applied to nuclear systems by Babu and Brown and followers.

  11. Local hybrid functionals with orbital-free mixing functions and balanced elimination of self-interaction error

    SciTech Connect

    Silva, Piotr de E-mail: clemence.corminboeuf@epfl.ch; Corminboeuf, Clémence E-mail: clemence.corminboeuf@epfl.ch

    2015-02-21

    The recently introduced density overlap regions indicator (DORI) [P. de Silva and C. Corminboeuf, J. Chem. Theory Comput. 10(9), 3745–3756 (2014)] is a density-dependent scalar field revealing regions of high density overlap between shells, atoms, and molecules. In this work, we exploit its properties to construct local hybrid exchange-correlation functionals aiming at balanced reduction of the self-interaction error. We show that DORI can successfully replace the ratio of the von Weizsäcker and exact positive-definite kinetic energy densities, which is commonly used in mixing functions of local hybrids. Additionally, we introduce several semi-empirical parameters to control the local and global admixture of exact exchange. The most promising of our local hybrids clearly outperforms the underlying semi-local functionals as well as their global hybrids.

  12. A Tomographic Method for the Reconstruction of Local Probability Density Functions

    NASA Technical Reports Server (NTRS)

    Sivathanu, Y. R.; Gore, J. P.

    1993-01-01

    A method of obtaining the probability density function (PDF) of local properties from path integrated measurements is described. The approach uses a discrete probability function (DPF) method to infer the PDF of the local extinction coefficient from measurements of the PDFs of the path integrated transmittance. The local PDFs obtained using the method are compared with those obtained from direct intrusive measurements in propylene/air and ethylene/air diffusion flames. The results of this comparison are good.

  13. Localization of Daucus carota NMCP1 to the nuclear periphery: the role of the N-terminal region and an NLS-linked sequence motif, RYNLRR, in the tail domain

    PubMed Central

    Kimura, Yuta; Fujino, Kaien; Ogawa, Kana; Masuda, Kiyoshi

    2014-01-01

    Recent ultrastructural studies revealed that a structure similar to the vertebrate nuclear lamina exists in the nuclei of higher plants. However, plant genomes lack genes for lamins and intermediate-type filament proteins, and this suggests that plant-specific nuclear coiled-coil proteins make up the lamina-like structure in plants. NMCP1 is a protein, first identified in Daucus carota cells, that localizes exclusively to the nuclear periphery in interphase cells. It has a tripartite structure comprised of head, rod, and tail domains, and includes putative nuclear localization signal (NLS) motifs. We identified the functional NLS of DcNMCP1 (carrot NMCP1) and determined the protein regions required for localizing to the nuclear periphery using EGFP-fused constructs transiently expressed in Apium graveolens epidermal cells. Transcription was driven under a CaMV35S promoter, and the genes were introduced into the epidermal cells by a DNA-coated microprojectile delivery system. Of the NLS motifs, KRRRK and RRHK in the tail domain were highly functional for nuclear localization. Addition of the N-terminal 141 amino acids from DcNMCP1 shifted the localization of a region including these NLSs from the entire nucleus to the nuclear periphery. Using this same construct, the replacement of amino acids in RRHK or its preceding sequence, YNL, with alanine residues abolished localization to the nuclear periphery, while replacement of KRRRK did not affect localization. The sequence R/Q/HYNLRR/H, including YNL and the first part of the sequence of RRHK, is evolutionarily conserved in a subclass of NMCP1 sequences from many plant species. These results show that NMCP1 localizes to the nuclear periphery by a combined action of a sequence composed of R/Q/HYNLRR/H, NLS, and the N-terminal region including the head and a portion of the rod domain, suggesting that more than one binding site is implicated in localization of NMCP1. PMID:24616728

  14. Local Analytic Solutions of a Functional Differential Equation

    NASA Astrophysics Data System (ADS)

    Liu, Lingxia

    This paper is concerned with the existence of analytic solutions of an iterative functional differential equation. Employing the method of majorant series, we need to discuss the constant α given in Schröder transformation. we study analytic solutions of the equation in the case of α at resonance and the case of α near resonance under the Brjuno condition.

  15. Radiation doses to local populations near nuclear weapons test sites worldwide.

    PubMed

    Simon, Steven L; Bouville, André

    2002-05-01

    Nuclear weapons testing was conducted in the atmosphere at numerous sites worldwide between 1946 and 1980, which resulted in exposures to local populations as a consequence of fallout of radioactive debris. The nuclear tests were conducted by five nations (United States, Soviet Union, United Kingdom, France, and China) primarily at 16 sites. The 16 testing sites, located in nine different countries on five continents (plus Oceania) contributed nearly all of the radioactive materials released to the environment by atmospheric testing; only small amounts were released at a fewother minor testing sites. The 16 sites discussed here are Nevada Test Site, USA (North American continent), Bikini and Enewetak, Marshall Islands (Oceania); Johnston Island, USA (Oceania), Christmas and Malden Island, Kiribati (Oceania); Emu Field, Maralinga, and Monte Bello Islands, Australia (Australian continent); Mururoa and Fangataufa, French Polynesia (Oceania), Reggane, Algeria (Africa), Novaya Zemlya and Kapustin Yar, Russia (Europe), Semipalatinsk, Kazakhstan (Asia), and Lop Nor, China (Asia). There were large differences in the numbers of tests conducted at each location and in the total explosive yields. Those factors, as well as differences in population density, lifestyle, environment, and climate at each site, led to large differences in the doses received by local populations. In general, the tests conducted earliest led to the highest individual and population exposures, although the amount of information available for a few of these sites is insufficient to provide any detailed evaluation of radiation exposures. The most comprehensive information for any site is for the Nevada Test Site. The disparities in available information add difficulty to determining the radiation exposures of local populations at each site. It is the goal of this paper to summarize the available information on external and internal doses received by the public living in the regions near each of the

  16. Structural and Functional Insight into Proliferating Cell Nuclear Antigen.

    PubMed

    Park, So Young; Jeong, Mi Suk; Han, Chang Woo; Yu, Hak Sun; Jang, Se Bok

    2016-04-28

    Proliferating cell nuclear antigen (PCNA) is a critical eukaryotic replication accessory factor that supports DNA binding in DNA processing, such as DNA replication, repair, and recombination. PCNA consists of three toroidal-shaped monomers that encircle doublestranded DNA. The diverse functions of PCNA may be regulated by its interactions with partner proteins. Many of the PCNA partner proteins generally have a conserved PCNAinteracting peptide (PIP) motif, located at the N- or C- terminal region. The PIP motif forms a 310 helix that enters into the hydrophobic groove produced by an interdomain-connecting loop, a central loop, and a C-terminal tail in the PCNA. Post-translational modification of PCNA also plays a critical role in regulation of its function and binding partner proteins. Structural and biochemical studies of PCNA-protein will be useful in designing therapeutic agents, as well as estimating the outcome of anticancer drug development. This review summarizes the characterization of eukaryotic PCNA in relation to the protein structures, functions, and modifications, and interaction with proteins. PMID:26699741

  17. hnRNP M interacts with PSF and p54{sup nrb} and co-localizes within defined nuclear structures

    SciTech Connect

    Marko, Marija; Leichter, Michael; Patrinou-Georgoula, Meropi; Guialis, Apostolia

    2010-02-01

    The abundant heterogeneous nuclear ribonucleoprotein M (hnRNP M) is able to associate with early spliceosomes and to influence splicing patterns of specific pre-mRNAs. Here, by a combination of immunoprecipitation and pull-down assays, we have identified PSF (polypyrimidine tract-binding protein-associated splicing factor) and p54{sup nrb}, two highly related proteins involved in transcription and RNA processing, as new binding partners of hnRNP M. HnRNP M was found to co-localize with PSF within a subset of nuclear paraspeckles and to largely co-fractionate with PSF and p54{sup nrb} in biochemical nuclear matrix preparations. In cells transfected with an alternatively spliced preprotachykinin (PPT) minigene expression of hnRNP M promoted exon skipping while expression of PSF favours exon inclusion. The latter effect was reverted specifically by co-expressing the full length hnRNP M or a deletion mutant capable of interaction with PSF and p54{sup nrb}. Together our data provide new insights and some functional implications on the hnRNP M network of interactions.

  18. Modified Dihadron Fragmentation Functions in Hot and Nuclear Matter

    SciTech Connect

    Majumder, A.; Wang Enke; Wang Xinnian

    2007-10-12

    Medium modification of dihadron fragmentation functions due to gluon bremsstrahlung induced by multiple partonic scattering is studied in both deep-inelastic scattering (DIS) off large nuclei and high-energy heavy-ion collisions within the same framework of twist expansion. The modification for dihadrons is found to closely follow that for single hadrons, leading to a weak nuclear suppression of their ratios in DIS experiments. A mild enhancement of the near-side correlation of two high transverse momentum hadrons with increasing centrality is found in heavy-ion collisions due to trigger bias and the rise in parton energy loss with centrality. Successful comparisons between theory and experiment for multihadron observables in both confining and deconfined media offer comprehensive evidence for partonic energy loss as the mechanism of jet modification in dense matter.

  19. Membrane anchoring domain of herpes simplex virus glycoprotein gB is sufficient for nuclear envelope localization.

    PubMed Central

    Gilbert, R; Ghosh, K; Rasile, L; Ghosh, H P

    1994-01-01

    We have used the glycoprotein gB of herpes simplex virus type 1 (gB-1), which buds from the inner nuclear membrane, as a model protein to study localization of membrane proteins in the nuclear envelope. To determine whether specific domains of gB-1 glycoprotein are involved in localization in the nuclear envelope, we have used deletion mutants of gB-1 protein as well as chimeric proteins constructed by replacing the domains of the cell surface glycoprotein G of vesicular stomatitis virus with the corresponding domains of gB. Mutant and chimeric proteins expressed in COS cells were localized by immunoelectron microscopy. A chimeric protein (gB-G) containing the ectodomain of gB and the transmembrane and cytoplasmic domains of G did not localize in the nuclear envelope. When the ectodomain of G was fused to the transmembrane and cytoplasmic domains of gB, however, the resulting chimeric protein (G-gB) was localized in the nuclear envelope. Substitution of the transmembrane domain of G with the 69 hydrophobic amino acids containing the membrane anchoring domain of gB allowed the hybrid protein (G-tmgB) to be localized in the nuclear envelope, suggesting that residues 721 to 795 of gB can promote retention of proteins in the nuclear envelope. Deletion mutations in the hydrophobic region further showed that a transmembrane segment of 21 hydrophobic amino acids, residues 774 to 795 of gB, was sufficient for localization in the nuclear envelope. Since wild-type gB and the mutant and chimeric proteins that were localized in the nuclear envelope were also retained in the endoplasmic reticulum, the membrane spanning segment of gB could also influence retention in the endoplasmic reticulum. Images PMID:8139012

  20. DSCAM localization and function at the mouse cone synapse.

    PubMed

    de Andrade, Gabriel Belem; Long, Samuel S; Fleming, Harrison; Li, Wei; Fuerst, Peter G

    2014-08-01

    The Down syndrome cell adhesion molecule (DSCAM) is required for regulation of cell number, soma spacing, and cell type-specific dendrite avoidance in many types of retinal ganglion and amacrine cells. In this study we assay the organization of cells making up the outer plexiform layer of the retina in the absence of Dscam. Some types of OFF bipolar cells, type 3b and type 4 bipolar cells, had defects in dendrite arborization in the Dscam mutant retina, whereas other cell types appeared similar to wild type. The cone synapses that these cells project their dendrites to were intact, as visualized by electron microscopy, and had a distribution and density that was not significantly different from that of wild type. The spacing of type 3b bipolar cell dendrites was further analyzed by Voronoi domain analysis, density recovery profiling (DRP) analysis, and nearest neighbor analysis. Spacing was found to be significantly different when wild-type and mutant type 3b bipolar cell dendrites were compared. Defects in arborization of these bipolar cells could not be attributed to the disorganization of inner plexiform layer cells that occurs in the Dscam mutant retina or an increase in cell number, as they arborized when Dscam was targeted in retinal ganglion cells only or in the bax null retina. Localization of DSCAM was assayed and the protein was localized near to cone synapses in mouse, macaque, and ground squirrel retinas. DSCAM protein was detected in several types of bipolar cells, including type 3b and type 4 bipolar cells. PMID:24477985

  1. Divergent Evolution of Nuclear Localization Signal Sequences in Herpesvirus Terminase Subunits.

    PubMed

    Sankhala, Rajeshwer S; Lokareddy, Ravi K; Cingolani, Gino

    2016-05-20

    The tripartite terminase complex of herpesviruses assembles in the cytoplasm of infected cells and exploits the host nuclear import machinery to gain access to the nucleus, where capsid assembly and genome-packaging occur. Here we analyzed the structure and conservation of nuclear localization signal (NLS) sequences previously identified in herpes simplex virus 1 (HSV-1) large terminase and human cytomegalovirus (HCMV) small terminase. We found a monopartite NLS at the N terminus of large terminase, flanking the ATPase domain, that is conserved only in α-herpesviruses. In contrast, small terminase exposes a classical NLS at the far C terminus of its helical structure that is conserved only in two genera of the β-subfamily and absent in α- and γ-herpesviruses. In addition, we predicted a classical NLS in the third terminase subunit that is partially conserved among herpesviruses. Bioinformatic analysis revealed that both location and potency of NLSs in terminase subunits evolved more rapidly than the rest of the amino acid sequence despite the selective pressure to keep terminase gene products active and localized in the nucleus. We propose that swapping NLSs among terminase subunits is a regulatory mechanism that allows different herpesviruses to regulate the kinetics of terminase nuclear import, reflecting a mechanism of virus:host adaptation. PMID:27033706

  2. Localization of Asymmetric Brain Function in Emotion and Depression

    PubMed Central

    Herrington, John D.; Heller, Wendy; Mohanty, Aprajita; Engels, Anna S.; Banich, Marie T.; Webb, Andrew G.; Miller, Gregory A.

    2011-01-01

    Although numerous EEG studies have shown that depression is associated with abnormal functional asymmetries in frontal cortex, fMRI and PET studies have largely failed to identify specific brain areas showing this effect. The present study tested the hypothesis that emotion processes are related to asymmetric patterns of fMRI activity, particularly within dorsolateral prefrontal cortex (DLPFC). Eleven depressed and 18 control participants identified the color in which pleasant, neutral, and unpleasant words were printed. Both groups showed a leftward lateralization for pleasant words in DLPFC. In a neighboring DLPFC area, the depression group showed more right-lateralized activation than controls, replicating EEG findings. These data confirm that emotional stimulus processing and trait depression are associated with asymmetric brain functions in distinct subregions of the DLPFC that may go undetected unless appropriate analytic procedures are used. PMID:20070577

  3. The BRCA1-binding protein BRAP2 can act as a cytoplasmic retention factor for nuclear and nuclear envelope-localizing testicular proteins.

    PubMed

    Davies, Rebecca G; Wagstaff, Kylie M; McLaughlin, Eileen A; Loveland, Kate L; Jans, David A

    2013-12-01

    Regulation of nuclear protein import is central to many cellular processes such as development, with a key mechanism being factors that retain cargoes in the cytoplasm that normally localize in the nucleus. The breast cancer antigen BRCA1-binding protein BRAP2 has been reported as a novel negative regulator of nuclear import of various nuclear localization signal (NLS)-containing viral and cellular proteins, but although implicated in differentiation pathways and highly expressed in tissues including testis, the gamut of targets for BRAP2 action in a developmental context is unknown. As a first step towards defining the BRAP2 interactome, we performed a yeast-2-hybrid screen to identify binding partners of BRAP2 in human testis. Here we report characterization for the first time of three of these: the high mobility group (HMG)-box-domain-containing chromatin component HMG20A, nuclear mitotic apparatus protein NuMA1 and synaptic nuclear envelope protein SYNE2. Co-immunoprecipitation experiments indicate association of BRAP2 with HMG20A, NuMA1, and SYNE2 in testis, underlining the physiological relevance of the interactions, with immunohistochemistry showing that where BRAP2 is co-expressed with HMG20A and NuMA1, both are present in the cytoplasm, in contrast to their nuclear localization in other testicular cell types. Importantly, quantitative confocal microscopic analysis of cultured cells indicates that ectopic expression of BRAP2 inhibits nuclear localization of HMG20A and NuMA1, and prevents nuclear envelope accumulation of SYNE2, the first report of BRAP2 altering localization of a non-nuclear protein. These results imply for the first time that BRAP2 may have an important role in modulating subcellular localization during testicular development. PMID:23707952

  4. Identification of Nuclear Genes Encoding Chloroplast-Localized Proteins Required for Embryo Development in Arabidopsis1[W][OA

    PubMed Central

    Bryant, Nicole; Lloyd, Johnny; Sweeney, Colleen; Myouga, Fumiyoshi; Meinke, David

    2011-01-01

    We describe here the diversity of chloroplast proteins required for embryo development in Arabidopsis (Arabidopsis thaliana). Interfering with certain chloroplast functions has long been known to result in embryo lethality. What has not been reported before is a comprehensive screen for embryo-defective (emb) mutants altered in chloroplast proteins. From a collection of transposon and T-DNA insertion lines at the RIKEN chloroplast function database (http://rarge.psc.riken.jp/chloroplast/) that initially appeared to lack homozygotes and segregate for defective seeds, we identified 23 additional examples of EMB genes that likely encode chloroplast-localized proteins. Fourteen gene identities were confirmed with allelism tests involving duplicate mutant alleles. We then queried journal publications and the SeedGenes database (www.seedgenes.org) to establish a comprehensive dataset of 381 nuclear genes encoding chloroplast proteins of Arabidopsis associated with embryo-defective (119 genes), plant pigment (121 genes), gametophyte (three genes), and alternate (138 genes) phenotypes. Loci were ranked based on the level of certainty that the gene responsible for the phenotype had been identified and the protein product localized to chloroplasts. Embryo development is frequently arrested when amino acid, vitamin, or nucleotide biosynthesis is disrupted but proceeds when photosynthesis is compromised and when levels of chlorophyll, carotenoids, or terpenoids are reduced. Chloroplast translation is also required for embryo development, with genes encoding chloroplast ribosomal and pentatricopeptide repeat proteins well represented among EMB datasets. The chloroplast accD locus, which is necessary for fatty acid biosynthesis, is essential in Arabidopsis but not in Brassica napus or maize (Zea mays), where duplicated nuclear genes compensate for its absence or loss of function. PMID:21139083

  5. Localization and function of the renal calcium-sensing receptor.

    PubMed

    Riccardi, Daniela; Valenti, Giovanna

    2016-07-01

    The ability to monitor changes in the ionic composition of the extracellular environment is a crucial feature that has evolved in all living organisms. The cloning and characterization of the extracellular calcium-sensing receptor (CaSR) from the mammalian parathyroid gland in the early 1990s provided the first description of a cellular, ion-sensing mechanism. This finding demonstrated how cells can detect small, physiological variations in free ionized calcium (Ca(2+)) in the extracellular fluid and subsequently evoke an appropriate biological response by altering the secretion of parathyroid hormone (PTH) that acts on PTH receptors expressed in target tissues, including the kidney, intestine, and bone. Aberrant Ca(2+) sensing by the parathyroid glands, as a result of altered CaSR expression or function, is associated with impaired divalent cation homeostasis. CaSR activators that mimic the effects of Ca(2+) (calcimimetics) have been designed to treat hyperparathyroidism, and CaSR antagonists (calcilytics) are in development for the treatment of hypercalciuric disorders. The kidney expresses a CaSR that might directly contribute to the regulation of many aspects of renal function in a PTH-independent manner. This Review discusses the roles of the renal CaSR and the potential impact of pharmacological modulation of the CaSR on renal function. PMID:27157444

  6. Nuclear localization of dengue virus nonstructural protein 5 does not strictly correlate with efficient viral RNA replication and inhibition of type I interferon signaling.

    PubMed

    Kumar, Anil; Bühler, Sandra; Selisko, Barbara; Davidson, Andrew; Mulder, Klaas; Canard, Bruno; Miller, Sven; Bartenschlager, Ralf

    2013-04-01

    Dengue virus (DENV) is an important human pathogen, especially in the tropical and subtropical parts of the world, causing considerable morbidity and mortality. DENV replication occurs in the cytoplasm; however, a high proportion of nonstructural protein 5 (NS5), containing methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) activities, accumulates in the nuclei of infected cells. The present study investigates the impact of nuclear localization of NS5 on its known functions, including viral RNA replication and subversion of the type I interferon response. By using a mutation analysis approach, we identified the most critical residues within the αβ nuclear localization signal (αβNLS), which are essential for the nuclear accumulation of this protein. Although we observed an overall correlation between reduced nuclear accumulation of NS5 and impaired RNA replication, we identified one mutant with drastically reduced amounts of nuclear NS5 and virtually unaffected RNA replication, arguing that nuclear localization of NS5 does not correlate strictly with DENV replication, at least in cell culture. Because NS5 plays an important role in blocking interferon signaling via STAT-2 (signal transducer and activator of transcription 2) degradation, the abilities of the NLS mutants to block this pathway were investigated. All mutants were able to degrade STAT-2, with accordingly similar type I interferon resistance phenotypes. Since the NLS is contained within the RdRp domain, the MTase and RdRp activities of the mutants were determined by using recombinant full-length NS5. We found that the C-terminal region of the αβNLS is a critical functional element of the RdRp domain required for polymerase activity. These results indicate that efficient DENV RNA replication requires only minimal, if any, nuclear NS5, and they identify the αβNLS as a structural element required for proper RdRp activity. PMID:23408610

  7. Importin α: a key molecule in nuclear transport and non-transport functions.

    PubMed

    Miyamoto, Yoichi; Yamada, Kohji; Yoneda, Yoshihiro

    2016-08-01

    Importin α performs the indispensable role of ferrying proteins from the cytoplasm into the nucleus with a transport carrier, importin β1. Mammalian cells from mouse or human contain either six or seven importin α subtypes, respectively, each with a tightly regulated expression. Therefore, the combination of subtype expression in a cell defines distinct signaling pathways to achieve progressive changes in gene expression essential for cellular events, such as differentiation. Recent studies reveal that, in addition to nucleocytoplasmic transport, importin αs also serve non-transport functions. In this review, we first discuss the physiological significance of importin α as a nuclear transport regulator, and then focus on the functional diversities of importin αs based on their specific subcellular and cellular localizations, such as the nucleus and plasma membrane. These findings enrich our knowledge of how importin αs actively contribute to various cellular events. PMID:27289017

  8. Identification of a nuclear localization sequence in the polyomavirus capsid protein VP2

    NASA Technical Reports Server (NTRS)

    Chang, D.; Haynes, J. I. 2nd; Brady, J. N.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    A nuclear localization signal (NLS) has been identified in the C-terminal (Glu307-Glu-Asp-Gly-Pro-Gln-Lys-Lys-Lys-Arg-Arg-Leu318) amino acid sequence of the polyomavirus minor capsid protein VP2. The importance of this amino acid sequence for nuclear transport of newly synthesized VP2 was demonstrated by a genetic "subtractive" study using the constructs pSG5VP2 (expressing full-length VP2) and pSG5 delta 3VP2 (expressing truncated VP2, lacking amino acids Glu307-Leu318). These constructs were transfected into COS-7 cells, and the intracellular localization of the VP2 protein was determined by indirect immunofluorescence. These studies revealed that the full-length VP2 was localized in the nucleus, while the truncated VP2 protein was localized in the cytoplasm and not transported to the nucleus. A biochemical "additive" approach was also used to determine whether this sequence could target nonnuclear proteins to the nucleus. A synthetic peptide identical to VP2 amino acids Glu307-Leu318 was cross-linked to the nonnuclear proteins bovine serum albumin (BSA) or immunoglobulin G (IgG). The conjugates were then labeled with fluorescein isothiocyanate and microinjected into the cytoplasm of NIH 3T6 cells. Both conjugates localized in the nucleus of the microinjected cells, whereas unconjugated BSA and IgG remained in the cytoplasm. Taken together, these genetic subtractive and biochemical additive approaches have identified the C-terminal sequence of polyoma-virus VP2 (containing amino acids Glu307-Leu318) as the NLS of this protein.

  9. Identification of novel residues involved in nuclear localization of a baculovirus polyhedrin protein.

    PubMed

    Katsuma, S; Deng, D X; Zhou, C L; Iwanaga, M; Noguchi, Y; Kobayashi, M; Maeda, S

    2000-10-01

    A baculovirus polyhedrin protein has proven to possess a nuclear localization signal (NLS) sequence and a domain required for supramolecular assembly. Here we investigated five Bombyx mori nucleopolyhedrovirus (BmNPV) mutants that did not produce polyhedra. Two of five mutants were generated during routine baculoviral expression vector screening, and three were isolated by treatment with the mutagen 5-bromo-2'-deoxyuridine (BrdU). Marker rescue mapping and nucleotide sequence analysis showed that mutations in the polyhedrin gene caused the altered phenotype of these mutants. Biochemical fractionation indicated that cells infected with these mutants exhibited polyhedrin protein in both the nucleus and the cytoplasm. Electron microscopic observation revealed that polyhedrin produced by these mutants ocurred in both the nucleus and the cytoplasm, but did not form a crystalline lattice. Despite the incompleteness of polyhedrin nuclear localization, the NLSs of the five mutants were unchanged, although some of the mutations occurred within residues just outside of the domain reported to be required for polyhedron assembly (4). This result suggests that (a) the polyhedrin NLS directs polyhedrin to the nucleus, but the efficiency of this localization is regulated by regions other than the NLS (probably, polyhedrin conformation and its association with the nucleus are also involved), and (b) formation of a crystalline lattice may also be determined by several domains within polyhedrin. PMID:11129641

  10. TransgeneOmics - A transgenic platform for protein localization based function exploration.

    PubMed

    Hasse, Susanne; Hyman, Anthony A; Sarov, Mihail

    2016-03-01

    The localization of a protein is intrinsically linked to its role in the structural and functional organization of the cell. Advances in transgenic technology have streamlined the use of protein localization as a function discovery tool. Here we review the use of large genomic DNA constructs such as bacterial artificial chromosomes as a transgenic platform for systematic tag-based protein function exploration. PMID:26475212

  11. Functional localization of the auditory thalamus in individual human subjects

    PubMed Central

    Jiang, Fang; Stecker, G. Christopher; Fine, Ione

    2013-01-01

    Here we describe an easily implemented protocol based on sparse MR acquisition and a scrambled ‘music’ auditory stimulus that allows for reliable measurement of functional activity within the medial geniculate body (MGB, the primary auditory thalamic nucleus) in individual subjects. We find that our method is equally accurate and reliable as previously developed structural methods, and offers significantly more accuracy in identifying the MGB than group based methods. We also find that lateralization and binaural summation within the MGB resembles that found in auditory cortex. PMID:23603350

  12. Glycolytic Enzymes Localize to Synapses under Energy Stress to Support Synaptic Function.

    PubMed

    Jang, SoRi; Nelson, Jessica C; Bend, Eric G; Rodríguez-Laureano, Lucelenie; Tueros, Felipe G; Cartagenova, Luis; Underwood, Katherine; Jorgensen, Erik M; Colón-Ramos, Daniel A

    2016-04-20

    Changes in neuronal activity create local and transient changes in energy demands at synapses. Here we discover a metabolic compartment that forms in vivo near synapses to meet local energy demands and support synaptic function in Caenorhabditis elegans neurons. Under conditions of energy stress, glycolytic enzymes redistribute from a diffuse localization in the cytoplasm to a punctate localization adjacent to synapses. Glycolytic enzymes colocalize, suggesting the ad hoc formation of a glycolysis compartment, or a "glycolytic metabolon," that can maintain local levels of ATP. Local formation of the glycolytic metabolon is dependent on presynaptic scaffolding proteins, and disruption of the glycolytic metabolon blocks the synaptic vesicle cycle, impairs synaptic recovery, and affects locomotion. Our studies indicate that under energy stress conditions, energy demands in C. elegans synapses are met locally through the assembly of a glycolytic metabolon to sustain synaptic function and behavior. VIDEO ABSTRACT. PMID:27068791

  13. Functional Effect of Pim1 Depends upon Intracellular Localization in Human Cardiac Progenitor Cells.

    PubMed

    Samse, Kaitlen; Emathinger, Jacqueline; Hariharan, Nirmala; Quijada, Pearl; Ilves, Kelli; Völkers, Mirko; Ormachea, Lucia; De La Torre, Andrea; Orogo, Amabel M; Alvarez, Roberto; Din, Shabana; Mohsin, Sadia; Monsanto, Megan; Fischer, Kimberlee M; Dembitsky, Walter P; Gustafsson, Åsa B; Sussman, Mark A

    2015-05-29

    Human cardiac progenitor cells (hCPC) improve heart function after autologous transfer in heart failure patients. Regenerative potential of hCPCs is severely limited with age, requiring genetic modification to enhance therapeutic potential. A legacy of work from our laboratory with Pim1 kinase reveals effects on proliferation, survival, metabolism, and rejuvenation of hCPCs in vitro and in vivo. We demonstrate that subcellular targeting of Pim1 bolsters the distinct cardioprotective effects of this kinase in hCPCs to increase proliferation and survival, and antagonize cellular senescence. Adult hCPCs isolated from patients undergoing left ventricular assist device implantation were engineered to overexpress Pim1 throughout the cell (PimWT) or targeted to either mitochondrial (Mito-Pim1) or nuclear (Nuc-Pim1) compartments. Nuc-Pim1 enhances stem cell youthfulness associated with decreased senescence-associated β-galactosidase activity, preserved telomere length, reduced expression of p16 and p53, and up-regulation of nucleostemin relative to PimWT hCPCs. Alternately, Mito-Pim1 enhances survival by increasing expression of Bcl-2 and Bcl-XL and decreasing cell death after H2O2 treatment, thereby preserving mitochondrial integrity superior to PimWT. Mito-Pim1 increases the proliferation rate by up-regulation of cell cycle modulators Cyclin D, CDK4, and phospho-Rb. Optimal stem cell traits such as proliferation, survival, and increased youthful properties of aged hCPCs are enhanced after targeted Pim1 localization to mitochondrial or nuclear compartments. Targeted Pim1 overexpression in hCPCs allows for selection of the desired phenotypic properties to overcome patient variability and improve specific stem cell characteristics. PMID:25882843

  14. Functional Effect of Pim1 Depends upon Intracellular Localization in Human Cardiac Progenitor Cells

    PubMed Central

    Samse, Kaitlen; Emathinger, Jacqueline; Hariharan, Nirmala; Quijada, Pearl; Ilves, Kelli; Völkers, Mirko; Ormachea, Lucia; De La Torre, Andrea; Orogo, Amabel M.; Alvarez, Roberto; Din, Shabana; Mohsin, Sadia; Monsanto, Megan; Fischer, Kimberlee M.; Dembitsky, Walter P.; Gustafsson, Åsa B.; Sussman, Mark A.

    2015-01-01

    Human cardiac progenitor cells (hCPC) improve heart function after autologous transfer in heart failure patients. Regenerative potential of hCPCs is severely limited with age, requiring genetic modification to enhance therapeutic potential. A legacy of work from our laboratory with Pim1 kinase reveals effects on proliferation, survival, metabolism, and rejuvenation of hCPCs in vitro and in vivo. We demonstrate that subcellular targeting of Pim1 bolsters the distinct cardioprotective effects of this kinase in hCPCs to increase proliferation and survival, and antagonize cellular senescence. Adult hCPCs isolated from patients undergoing left ventricular assist device implantation were engineered to overexpress Pim1 throughout the cell (PimWT) or targeted to either mitochondrial (Mito-Pim1) or nuclear (Nuc-Pim1) compartments. Nuc-Pim1 enhances stem cell youthfulness associated with decreased senescence-associated β-galactosidase activity, preserved telomere length, reduced expression of p16 and p53, and up-regulation of nucleostemin relative to PimWT hCPCs. Alternately, Mito-Pim1 enhances survival by increasing expression of Bcl-2 and Bcl-XL and decreasing cell death after H2O2 treatment, thereby preserving mitochondrial integrity superior to PimWT. Mito-Pim1 increases the proliferation rate by up-regulation of cell cycle modulators Cyclin D, CDK4, and phospho-Rb. Optimal stem cell traits such as proliferation, survival, and increased youthful properties of aged hCPCs are enhanced after targeted Pim1 localization to mitochondrial or nuclear compartments. Targeted Pim1 overexpression in hCPCs allows for selection of the desired phenotypic properties to overcome patient variability and improve specific stem cell characteristics. PMID:25882843

  15. An impact source localization technique for a nuclear power plant by using sensors of different types.

    PubMed

    Choi, Young-Chul; Park, Jin-Ho; Choi, Kyoung-Sik

    2011-01-01

    In a nuclear power plant, a loose part monitoring system (LPMS) provides information on the location and the mass of a loosened or detached metal impacted onto the inner surface of the primary pressure boundary. Typically, accelerometers are mounted on the surface of a reactor vessel to localize the impact location caused by the impact of metallic substances on the reactor system. However, in some cases, the number of accelerometers is not sufficient to estimate the impact location precisely. In such a case, one of useful methods is to utilize other types of sensor that can measure the vibration of the reactor structure. For example, acoustic emission (AE) sensors are installed on the reactor structure to detect leakage or cracks on the primary pressure boundary. However, accelerometers and AE sensors have a different frequency range. The frequency of interest of AE sensors is higher than that of accelerometers. In this paper, we propose a method of impact source localization by using both accelerometer signals and AE signals, simultaneously. The main concept of impact location estimation is based on the arrival time difference of the impact stress wave between different sensor locations. However, it is difficult to find the arrival time difference between sensors, because the primary frequency ranges of accelerometers and AE sensors are different. To overcome the problem, we used phase delays of an envelope of impact signals. This is because the impact signals from the accelerometer and the AE sensor are similar in the whole shape (envelope). To verify the proposed method, we have performed experiments for a reactor mock-up model and a real nuclear power plant. The experimental results demonstrate that we can enhance the reliability and precision of the impact source localization. Therefore, if the proposed method is applied to a nuclear power plant, we can obtain the effect of additional installed sensors. PMID:20851393

  16. Nuclear receptors CAR and PXR: Molecular, functional, and biomedical aspects.

    PubMed

    di Masi, Alessandra; De Marinis, Elisabetta; Ascenzi, Paolo; Marino, Maria

    2009-10-01

    Nuclear receptors (NRs) are ligand-activated transcription factors sharing a common evolutionary history and having similar sequence features at the protein level. Selective ligand(s) for some NRs is not known, therefore these NRs have been named "orphan receptors". Whenever ligands have been recognized for any of the orphan receptor, it has been categorized and grouped as "adopted" orphan receptor. This group includes the constitutive androstane receptor (CAR) and the pregnane X receptor (PXR). They function as sensors of toxic byproducts derived from endogenous metabolites and of exogenous chemicals, in order to enhance their elimination. This unique function of CAR and PXR sets them apart from the steroid hormone receptors. The broad response profile has established that CAR and PXR are xenobiotic sensors that coordinately regulate xenobiotic clearance in the liver and intestine via induction of genes involved in drug and xenobiotic metabolism. In the past few years, research has revealed new and mostly unsuspected roles for CAR and PXR in modulating hormone, lipid, and energy homeostasis as well as cancer and liver steatosis. The purpose of this review is to highlight the structural and molecular bases of CAR and PXR impact on human health, providing information on mechanisms through which diet, chemical exposure, and environment ultimately impact health and disease. PMID:19427329

  17. Molecular mechanism by which acyclic retinoid induces nuclear localization of transglutaminase 2 in human hepatocellular carcinoma cells

    PubMed Central

    Shrestha, R; Tatsukawa, H; Shrestha, R; Ishibashi, N; Matsuura, T; Kagechika, H; Kose, S; Hitomi, K; Imamoto, N; Kojima, S

    2015-01-01

    Nuclear accumulation of transglutaminase 2 (TG2) is an important step in TG2-dependent cell death. However, the underlying molecular mechanisms for nuclear translocation of TG2 are still poorly understood. In this study, we demonstrated that acyclic retinoid (ACR) induced nuclear accumulation of TG2 in JHH-7 cells, a hepatocellular carcinoma (HCC) leading to their apoptosis. We further demonstrated molecular mechanism in nuclear-cytoplasmic trafficking of TG2 and an effect of ACR on it. We identified a novel 14-amino acid nuclear localization signal (NLS) 466AEKEETGMAMRIRV479 in the ‘C' domain and a leucine-rich nuclear export signal (NES) 657LHMGLHKL664 in the ‘D' domain that allowed TG2 to shuttle between the nuclear and cytosolic milieu. Increased nuclear import of GAPDH myc-HIS fused with the identified NLS was observed, confirming its nuclear import ability. Leptomycin B, an inhibitor of exportin-1 as well as point mutation of all leucine residues to glutamine residues in the NES of TG2 demolished its nuclear export. TG2 formed a trimeric complex with importin-α and importin-β independently from transamidase activity which strongly suggested the involvement of a NLS-based translocation of TG2 to the nucleus. ACR accelerated the formation of the trimeric complex and that may be at least in part responsible for enhanced nuclear localization of TG2 in HCC cells treated with ACR. PMID:26633708

  18. Isotropic proton-detected local-field nuclear magnetic resonancein solids

    SciTech Connect

    Havlin, Robert H.; Walls, Jamie D.; Pines, Alexander

    2004-08-04

    A new nuclear magnetic resonance (NMR) method is presented which produces linear, isotropic proton-detected local-field spectra for InS spin systems in powdered samples. The method, HETeronuclear Isotropic Evolution (HETIE), refocuses the anisotropic portion of the heteronuclear dipolar coupling frequencies by evolving the system under a series of specially designed Hamiltonians and evolution pathways. The theory behind HETIE is represented along with experimental studies conducted on a powdered sample of ferrocene, demonstrating the methodology outlined in this paper. Applications of HETIE for structural determination in solid-state NMR are discussed.

  19. Nonmyofilament-Associated Troponin T3 Nuclear and Nucleolar Localization Sequence and Leucine Zipper Domain Mediate Muscle Cell Apoptosis

    PubMed Central

    Zhang, Tan; Birbrair, Alexander; Delbono, Osvaldo

    2013-01-01

    Troponin T (TnT) plays a major role in striated muscle contraction. We recently demonstrated that the fast skeletal muscle TnT3 isoform is localized in the muscle nucleus, and either its full-length or COOH-terminus leads to muscle cell apoptosis. Here, we further explored the mechanism by which it enters the nucleus and promotes cytotoxicity. Amino acid truncation and substitution showed that its COOH-terminus contains a dominant nuclear/nucleolar localization sequence (KLKRQK) and the basic lysine and arginine residues might play an important role in the nuclear retention and nucleolar enrichment of KLKRQK-DsRed fusion proteins. Deleting this domain or substituting lysine and arginine residues (KLAAQK) resulted in a dramatic loss of TnT3 nuclear and nucleolar localization. In contrast, the GATAKGKVGGRWK domain-DsRed construct localized exclusively in the cytoplasm, indicating that a nuclear exporting sequence is possibly localized in this region. Additionally, we identified a classical DNA-binding Leucine Zipper Domain (LZD) which is conserved among TnT isoforms and species. Deletion of LZD or KLKRQK sequence significantly reduced cell apoptosis compared to full-length TnT3. We conclude that TnT3 contains both a nuclear localization signal and a DNA binding domain, which may mediate nuclear/nucleolar signaling and muscle cell apoptosis. PMID:23378072

  20. Local Analysis via the Real Space GREEN’S Function Method

    NASA Astrophysics Data System (ADS)

    Wu, Shi-Yu; Jayanthi, Chakram S.

    A complete account of the development of the method of real space Green’s function is given in this review. The emphasis is placed on the calculation of the local Green’s function in a real space representation. The discussion is centered on a list of issues particularly relevant to the study of properties of complex systems with reduced symmetry.They include: (i) the convergence procedure for calculating the local Green’s function of infinite systems without any boundary effects associated with an arbitrary truncation of the system; (ii) a general recursive relation which streamlines the calculation of the local Green’s function; (iii) the calculation of the eigenvector of selected eigenvalues directly from the Green’s function. An example of the application of the method to carry out a local analysis of dynamics of the Au(511) surface is also presented.

  1. Scanning tunneling microscopy current from localized basis orbital density functional theory

    NASA Astrophysics Data System (ADS)

    Gustafsson, Alexander; Paulsson, Magnus

    2016-03-01

    We present a method capable of calculating elastic scanning tunneling microscopy (STM) currents from localized atomic orbital density functional theory (DFT). To overcome the poor accuracy of the localized orbital description of the wave functions far away from the atoms, we propagate the wave functions, using the total DFT potential. From the propagated wave functions, the Bardeen's perturbative approach provides the tunneling current. To illustrate the method we investigate carbon monoxide adsorbed on a Cu(111) surface and recover the depression/protrusion observed experimentally with normal/CO-functionalized STM tips. The theory furthermore allows us to discuss the significance of s - and p -wave tips.

  2. Nuclear/cytoplasmic localization of the von Hippel-Lindau tumor suppressor gene product is determined by cell density.

    PubMed Central

    Lee, S; Chen, D Y; Humphrey, J S; Gnarra, J R; Linehan, W M; Klausner, R D

    1996-01-01

    The product of the von Hippel-Lindau (VHL) tumor suppressor gene, the gene inactivated in VHL disease and in sporadic clear-cell renal carcinomas, has recently been shown to have as a functional target the transcription elongation complex, elongin (also called SIII). Here it is shown that there is a tightly regulated, cell-density-dependent transport of VHL into and/or out of the nucleus. In densely grown cells, the VHL protein is predominantly in the cytoplasm, whereas in sparse cultures, most of the protein can be detected in the nucleus. We have identified a putative nuclear localization signal in the first 60 and first 28 amino acids of the human and rat VHL protein, respectively. Sequences in the C-terminal region of the VHL protein may also be required for localization to the cytosol. These findings provide the initial indication of a novel cell density-dependent pathway that is responsible for the regulation of VHL cellular localization. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8700833

  3. Passive localization in the deep ocean based on cross-correlation function matching.

    PubMed

    Lei, Zhixiong; Yang, Kunde; Ma, Yuanliang

    2016-06-01

    Passive localization of a sound source in the deep ocean is investigated in this study. The source can be localized by taking advantage of a cross-correlation function matching technique. When a two-sensor vertical array is used in the deep ocean, two types of side lobe curves appear in the ambiguity surface of the localization. The side lobe curves are analytically expressed and they are then used as indicators of the localization result instead of the scanning point with the maximum power. Simulation and experiment demonstrate the performance of the proposed passive localization method. PMID:27369172

  4. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity.

    PubMed

    Görner, W; Durchschlag, E; Martinez-Pastor, M T; Estruch, F; Ammerer, G; Hamilton, B; Ruis, H; Schüller, C

    1998-02-15

    Msn2p and the partially redundant factor Msn4p are key regulators of stress-responsive gene expression in Saccharomyces cerevisiae. They are required for the transcription of a number of genes coding for proteins with stress-protective functions. Both Msn2p and Msn4p are Cys2His2 zinc finger proteins and bind to the stress response element (STRE). In vivo footprinting studies show that the occupation of STREs is enhanced in stressed cells and dependent on the presence of Msn2p and Msn4p. Both factors accumulate in the nucleus under stress conditions, such as heat shock, osmotic stress, carbon-source starvation, and in the presence of ethanol or sorbate. Stress-induced nuclear localization was found to be rapid, reversible, and independent of protein synthesis. Nuclear localization of Msn2p and Msn4p was shown to be correlated inversely to cAMP levels and protein kinase A (PKA) activity. A region with significant homologies shared between Msn2p and Msn4p is sufficient to confer stress-regulated localization to a SV40-NLS-GFP fusion protein. Serine to alanine or aspartate substitutions in a conserved PKA consensus site abolished cAMP-driven nuclear export and cytoplasmic localization in unstressed cells. We propose stress and cAMP-regulated intracellular localization of Msn2p to be a key step in STRE-dependent transcription and in the general stress response. PMID:9472026

  5. Austromegabalanus psittacus barnacle shell structure and proteoglycan localization and functionality.

    PubMed

    Fernández, M S; Arias, J I; Neira-Carrillo, A; Arias, J L

    2015-09-01

    Comparative analyzes of biomineralization models have being crucial for the understanding of the functional properties of biominerals and the elucidation of the processes through which biomacromolecules control the synthesis and structural organization of inorganic mineral-based biomaterials. Among calcium carbonate-containing bioceramics, egg, mollusk and echinoderm shells, and crustacean carapaces, have being fairly well characterized. However, Thoraceca barnacles, although being crustacea, showing molting cycle, build a quite stable and heavily mineralized shell that completely surround the animal, which is for life firmly cemented to the substratum. This makes barnacles an interesting model for studying processes of biomineralization. Here we studied the main microstructural and ultrastructural features of Austromegabalanus psittacus barnacle shell, characterize the occurrence of specific proteoglycans (keratan-, dermatan- and chondroitin-6-sulfate proteoglycans) in different soluble and insoluble organic fractions extracted from the shell, and tested them for their ability to crystallize calcium carbonate in vitro. Our results indicate that, in the barnacle model, proteoglycans are good candidates for the modification of the calcite crystal morphology, although the cooperative effect of some additional proteins in the shell could not be excluded. PMID:26276577

  6. DPP6 Domains Responsible for Its Localization and Function*

    PubMed Central

    Lin, Lin; Long, Laura K.; Hatch, Michael M.; Hoffman, Dax A.

    2014-01-01

    Dipeptidyl peptidase-like protein 6 (DPP6) is an auxiliary subunit of the Kv4 family of voltage-gated K+ channels known to enhance channel surface expression and potently accelerate their kinetics. DPP6 is a single transmembrane protein, which is structurally remarkable for its large extracellular domain. Included in this domain is a cysteine-rich motif, the function of which is unknown. Here we show that this cysteine-rich domain of DPP6 is required for its export from the ER and expression on the cell surface. Disulfide bridges formed at C349/C356 and C465/C468 of the cysteine-rich domain are necessary for the enhancement of Kv4.2 channel surface expression but not its interaction with Kv4.2 subunits. The short intracellular N-terminal and transmembrane domains of DPP6 associates with and accelerates the recovery from inactivation of Kv4.2, but the entire extracellular domain is necessary to enhance Kv4.2 surface expression and stabilization. Our findings show that the cysteine-rich domain of DPP6 plays an important role in protein folding of DPP6 that is required for transport of DPP6/Kv4.2 complexes out of the ER. PMID:25190807

  7. DPP6 domains responsible for its localization and function.

    PubMed

    Lin, Lin; Long, Laura K; Hatch, Michael M; Hoffman, Dax A

    2014-11-14

    Dipeptidyl peptidase-like protein 6 (DPP6) is an auxiliary subunit of the Kv4 family of voltage-gated K(+) channels known to enhance channel surface expression and potently accelerate their kinetics. DPP6 is a single transmembrane protein, which is structurally remarkable for its large extracellular domain. Included in this domain is a cysteine-rich motif, the function of which is unknown. Here we show that this cysteine-rich domain of DPP6 is required for its export from the ER and expression on the cell surface. Disulfide bridges formed at C349/C356 and C465/C468 of the cysteine-rich domain are necessary for the enhancement of Kv4.2 channel surface expression but not its interaction with Kv4.2 subunits. The short intracellular N-terminal and transmembrane domains of DPP6 associates with and accelerates the recovery from inactivation of Kv4.2, but the entire extracellular domain is necessary to enhance Kv4.2 surface expression and stabilization. Our findings show that the cysteine-rich domain of DPP6 plays an important role in protein folding of DPP6 that is required for transport of DPP6/Kv4.2 complexes out of the ER. PMID:25190807

  8. An alternative domain containing a leucine-rich sequence regulates nuclear cytoplasmic localization of protein 4.1R.

    PubMed

    Luque, Carlos M; Pérez-Ferreiro, Carmen M; Pérez-Gonzalez, Alicia; Englmeier, Ludwig; Koffa, Maria D; Correas, Isabel

    2003-01-24

    In red blood cells, protein 4.1 (4.1R) is an 80-kDa protein that stabilizes the spectrin-actin network and anchors it to the plasma membrane. The picture is more complex in nucleated cells, in which many 4.1R isoforms, varying in size and intracellular location, have been identified. To contribute to the characterization of signals involved in differential intracellular localization of 4.1R, we have analyzed the role the exon 5-encoded sequence plays in 4.1R distribution. We show that exon 5 encodes a leucine-rich sequence that shares key features with nuclear export signals (NESs). This sequence adopts the topology employed for NESs of other proteins and conserves two hydrophobic residues that are shown to be critical for NES function. A 4.1R isoform expressing the leucine-rich sequence binds to the export receptor CRM1 in a RanGTP-dependent fashion, whereas this does not occur in a mutant whose two conserved hydrophobic residues are substituted. These two residues are also essential for 4.1R intracellular distribution, because the 4.1R protein containing the leucine-rich sequence localizes in the cytoplasm, whereas the mutant protein predominantly accumulates in the nucleus. We hypothesize that the leucine-rich sequence in 4.1R controls distribution and concomitantly function of a specific set of 4.1R isoforms. PMID:12427749

  9. Local analyses of Planck maps with Minkowski functionals

    NASA Astrophysics Data System (ADS)

    Novaes, C. P.; Bernui, A.; Marques, G. A.; Ferreira, I. S.

    2016-09-01

    Minkowski functionals (MF) are excellent tools to investigate the statistical properties of the cosmic background radiation (CMB) maps. Between their notorious advantages is the possibility to use them efficiently in patches of the CMB sphere, which allow studies in masked skies, inclusive analyses of small sky regions. Then, possible deviations from Gaussianity are investigated by comparison with MF obtained from a set of Gaussian isotropic simulated CMB maps to which are applied the same cut-sky masks. These analyses are sensitive enough to detect contaminations of small intensity like primary and secondary CMB anisotropies. Our methodology uses the MF, widely employed to study non-Gaussianities in CMB data, and asserts Gaussian deviations only when all of them points out an exceptional χ2 value, at more than 2.2σ confidence level, in a given sky patch. Following this rigorous procedure, we find 13 regions in the foreground-cleaned Planck maps that evince such high levels of non-Gaussian deviations. According to our results, these non-Gaussian contributions show signatures that can be associated to the presence of hot or cold spots in such regions. Moreover, some of these non-Gaussian deviations signals suggest the presence of foreground residuals in those regions located near the Galactic plane. Additionally, we confirm that most of the regions revealed in our analyses, but not all, have been recently reported in studies done by the Planck collaboration. Furthermore, we also investigate whether these non-Gaussian deviations can be possibly sourced by systematics, like inhomogeneous noise and beam effect in the released Planck data, or perhaps due to residual Galactic foregrounds.

  10. Towards improved local hybrid functionals by calibration of exchange-energy densities

    SciTech Connect

    Arbuznikov, Alexei V. E-mail: martin.kaupp@tu-berlin.de; Kaupp, Martin E-mail: martin.kaupp@tu-berlin.de

    2014-11-28

    A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.

  11. Towards improved local hybrid functionals by calibration of exchange-energy densities

    NASA Astrophysics Data System (ADS)

    Arbuznikov, Alexei V.; Kaupp, Martin

    2014-11-01

    A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.

  12. Metallicity Distribution Functions of Four Local Group Dwarf Galaxies

    NASA Astrophysics Data System (ADS)

    Ross, Teresa L.; Holtzman, Jon; Saha, Abhijit; Anthony-Twarog, Barbara J.

    2015-06-01

    We present stellar metallicities in Leo I, Leo II, IC 1613, and Phoenix dwarf galaxies derived from medium (F390M) and broad (F555W, F814W) band photometry using the Wide Field Camera 3 instrument on board the Hubble Space Telescope. We measured metallicity distribution functions (MDFs) in two ways, (1) matching stars to isochrones in color-color diagrams and (2) solving for the best linear combination of synthetic populations to match the observed color-color diagram. The synthetic technique reduces the effect of photometric scatter and produces MDFs 30%-50% narrower than the MDFs produced from individually matched stars. We fit the synthetic and individual MDFs to analytical chemical evolution models (CEMs) to quantify the enrichment and the effect of gas flows within the galaxies. Additionally, we measure stellar metallicity gradients in Leo I and II. For IC 1613 and Phoenix our data do not have the radial extent to confirm a metallicity gradient for either galaxy. We find the MDF of Leo I (dwarf spheroidal) to be very peaked with a steep metal-rich cutoff and an extended metal-poor tail, while Leo II (dwarf spheroidal), Phoenix (dwarf transition), and IC 1613 (dwarf irregular) have wider, less peaked MDFs than Leo I. A simple CEM is not the best fit for any of our galaxies; therefore we also fit the “Best Accretion Model” of Lynden-Bell. For Leo II, IC 1613, and Phoenix we find similar accretion parameters for the CEM even though they all have different effective yields, masses, star formation histories, and morphologies. We suggest that the dynamical history of a galaxy is reflected in the MDF, where broad MDFs are seen in galaxies that have chemically evolved in relative isolation and narrowly peaked MDFs are seen in galaxies that have experienced more complicated dynamical interactions concurrent with their chemical evolution. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is

  13. Local electric dipole moments for periodic systems via density functional theory embedding.

    PubMed

    Luber, Sandra

    2014-12-21

    We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange-correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries. PMID:25527922

  14. Local electric dipole moments for periodic systems via density functional theory embedding

    NASA Astrophysics Data System (ADS)

    Luber, Sandra

    2014-12-01

    We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange-correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

  15. Local electric dipole moments for periodic systems via density functional theory embedding

    SciTech Connect

    Luber, Sandra

    2014-12-21

    We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange–correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

  16. The nuclear localization of low risk HPV11 E7 protein mediated by its zinc binding domain is independent of nuclear import receptors

    SciTech Connect

    Piccioli, Zachary; McKee, Courtney H.; Leszczynski, Anna; Onder, Zeynep; Hannah, Erin C.; Mamoor, Shahan; Crosby, Lauren; Moroianu, Junona

    2010-11-10

    We investigated the nuclear import of low risk HPV11 E7 protein using 1) transfection assays in HeLa cells with EGFP fusion plasmids containing 11E7 and its domains and 2) nuclear import assays in digitonin-permeabilized HeLa cells with GST fusion proteins containing 11E7 and its domains. The EGFP-11E7 and EGFP-11cE7{sub 39-98} localized mostly to the nucleus. The GST-11E7 and GST-11cE7{sub 39-98} were imported into the nuclei in the presence of either Ran-GDP or RanG19V-GTP mutant and in the absence of nuclear import receptors. This suggests that 11E7 enters the nucleus via a Ran-dependent pathway, independent of nuclear import receptors, mediated by a nuclear localization signal located in its C-terminal domain (cNLS). This cNLS contains the zinc binding domain consisting of two copies of Cys-X-X-Cys motif. Mutagenesis of Cys residues in these motifs changed the localization of the EGFP-11cE7/-11E7 mutants to cytoplasmic, suggesting that the zinc binding domain is essential for nuclear localization of 11E7.

  17. Inhibitors of oxygen sensing prolyl hydroxylases regulate nuclear localization of the transcription factors Smad2 and YAP/TAZ involved in CTGF synthesis.

    PubMed

    Preisser, Felix; Giehl, Klaudia; Rehm, Margot; Goppelt-Struebe, Margarete

    2016-08-01

    Pharmacological inhibition of oxygen sensing prolyl hydroxylase domain enzymes (PHDs) has been shown to preserve renal structure and function in various models of kidney disease. Since transforming growth factor β-1 (TGFβ-1) is one of the major mediators of kidney injury, we investigated if inhibition of PHDs with subsequent stabilization of hypoxia inducible transcription factors (HIF) might interfere with TGFβ-1 signaling with special emphasis on its target gene connective tissue growth factor (CTGF). Overnight incubation of human renal tubular cells, primary cells and cell lines, with the PDH inhibitor DMOG increased Smad3 expression, but barely affected Smad2. Both Smads were translocated into the nucleus upon activation of the cells with TGFβ-1. Interestingly, Smad3 nuclear localization was enhanced upon pretreatment of the cells with DMOG for several hours, whereas nuclear Smad2 was reduced. This differential localization was independent of Smad2/3 phosphorylation. Reduced nuclear Smad2 correlated with impaired CTGF secretion in DMOG-treated cells and transient downregulation of Smad2 interfered with TGFβ-1-induced CTGF synthesis. Furthermore, YAP was confirmed as indispensable transcription factor involved in CTGF synthesis. Nuclear localization of YAP and TAZ was reduced in DMOG-treated cells. Our data thus provide evidence for DMOG-mediated reduction of CTGF expression by regulating the nuclear localization of the transcription factors Smad2, YAP and TAZ. Prolonged inhibition of PHDs was necessary to achieve alterations in cellular localization suggesting an indirect HIF-mediated effect. This mechanism might be extended to other transcription factors and target genes, and may thus represent a novel mechanism of negative regulation of gene expression by PHD inhibition. PMID:27155083

  18. Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA

    PubMed Central

    Wang, Shunfang; Liu, Shuhui

    2015-01-01

    An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one. PMID:26703574

  19. Subcellular localization of calcium and Ca-ATPase activity during nuclear maturation in Bufo arenarum oocytes.

    PubMed

    Ramos, Inés; Cisint, Susana B; Crespo, Claudia A; Medina, Marcela F; Fernández, Silvia N

    2009-08-01

    The localization of calcium and Ca-ATPase activity in Bufo arenarum oocytes was investigated by ultracytochemical techniques during progesterone-induced nuclear maturation, under in vitro conditions. No Ca2+ deposits were detected in either control oocytes or progesterone-treated ones for 1-2 h. At the time when nuclear migration started, electron dense deposits of Ca2+ were visible in vesicles, endoplasmic reticulum cisternae and in the space between the annulate lamellae membranes. Furthermore, Ca-ATPase activity was also detected in these membrane structures. As maturation progressed, the cation deposits were observed in the cytomembrane structures, which underwent an important reorganization and redistribution. Thus, they moved from the subcortex and became located predominantly in the oocyte cortex area when nuclear maturation ended. Ca2+ stores were observed in vesicles surrounding or between the cortical granules, which are aligned close to the plasma membrane. The positive Ca-ATPase reaction in these membrane structures could indicate that the calcium deposit is an ATP-dependent process. Our results suggest that during oocyte maturation calcium would be stored in membrane structures where it remains available for release at the time of fertilization. Data obtained under our experimental conditions indicate that calcium from the extracellular medium would be important for the oocyte maturation process. PMID:19397840

  20. Nuclear localization of Lyn tyrosine kinase mediated by inhibition of its kinase activity

    SciTech Connect

    Ikeda, Kikuko; Nakayama, Yuji; Togashi, Yuuki; Obata, Yuuki; Kuga, Takahisa; Kasahara, Kousuke; Fukumoto, Yasunori; Yamaguchi, Naoto

    2008-11-01

    Src-family kinases, cytoplasmic enzymes that participate in various signaling events, are found at not only the plasma membrane but also subcellular compartments, such as the nucleus, the Golgi apparatus and late endosomes/lysosomes. Lyn, a member of the Src-family kinases, is known to play a role in DNA damage response and cell cycle control in the nucleus. However, it is still unclear how the localization of Lyn to the nucleus is regulated. Here, we investigated the mechanism of the distribution of Lyn between the cytoplasm and the nucleus in epitheloid HeLa cells and hematopoietic THP-1 cells. Lyn was definitely detected in purified nuclei by immunofluorescence and immunoblotting analyses. Nuclear accumulation of Lyn was enhanced upon treatment of cells with leptomycin B (LMB), an inhibitor of Crm1-mediated nuclear export. Moreover, Lyn mutants lacking the sites for lipid modification were highly accumulated in the nucleus upon LMB treatment. Intriguingly, inhibition of the kinase activity of Lyn by SU6656, Csk overexpression, or point mutation in the ATP-binding site induced an increase in nuclear Lyn levels. These results suggest that Lyn being imported into and rapidly exported from the nucleus preferentially accumulates in the nucleus by inhibition of the kinase activity and lipid modification.

  1. Nuclear localization of TEF3-1 promotes cell cycle progression and angiogenesis in cancer

    PubMed Central

    Xu, Jie; Men, Qiuxu; Lei, Tao; Di, Da; Liu, Ting; Li, Wenhua; Liu, Xin

    2016-01-01

    TEF3-1 (transcriptional enhancer factor 3 isoform 1), also known as TEAD4 (TEA domain family member 4), was recently revealed as an oncogenic character in cancer development. However, the underlying molecular pathogenic mechanisms remain undefined. In this paper, we investigated nuclear TEF3-1 could promote G1/S transition in HUVECs, and the expression levels of cyclins and CDKs were upregulated. Additionally, if TEF3-1 was knocked down, the expression of cyclins and CDKs was downregulated while the expression of P21, a negative regulator of the cell cycle, was upregulated. A microarray analysis also confirmed that TEF3-1 overexpression upregulates genes that are related to cell cycle progression and the promotion of angiogenesis. Moreover, we observed that nuclear TEF3-1 was highly expressed during the formation of vascular structures in gastric cancer (GC). Finally, tumor xenograft experiments indicated that, when TEF3-1 was knocked down, tumor growth and angiogenesis were also suppressed. Taken together, these results demonstrate for the first time that TEF3-1 localization to the nucleus stimulates the cell cycle progression in HUVECs and specifically contributes to tumor angiogenesis. Nuclear TEF3-1 in HUVECs may serve as an oncogenic biomarker, and the suppression of TEF3-1 may be a potential target in anti-tumor therapy. PMID:26885617

  2. Nuclear localization of TEF3-1 promotes cell cycle progression and angiogenesis in cancer.

    PubMed

    Teng, Kaixuan; Deng, Cuilan; Xu, Jie; Men, Qiuxu; Lei, Tao; Di, Da; Liu, Ting; Li, Wenhua; Liu, Xin

    2016-03-22

    TEF3-1 (transcriptional enhancer factor 3 isoform 1), also known as TEAD4 (TEA domain family member 4), was recently revealed as an oncogenic character in cancer development. However, the underlying molecular pathogenic mechanisms remain undefined. In this paper, we investigated nuclear TEF3-1 could promote G1/S transition in HUVECs, and the expression levels of cyclins and CDKs were upregulated. Additionally, if TEF3-1 was knocked down, the expression of cyclins and CDKs was downregulated while the expression of P21, a negative regulator of the cell cycle, was upregulated. A microarray analysis also confirmed that TEF3-1 overexpression upregulates genes that are related to cell cycle progression and the promotion of angiogenesis. Moreover, we observed that nuclear TEF3-1 was highly expressed during the formation of vascular structures in gastric cancer (GC). Finally, tumor xenograft experiments indicated that, when TEF3-1 was knocked down, tumor growth and angiogenesis were also suppressed. Taken together, these results demonstrate for the first time that TEF3-1 localization to the nucleus stimulates the cell cycle progression in HUVECs and specifically contributes to tumor angiogenesis. Nuclear TEF3-1 in HUVECs may serve as an oncogenic biomarker, and the suppression of TEF3-1 may be a potential target in anti-tumor therapy. PMID:26885617

  3. Relationship Between Nutrient Enrichment and Benthic Function: Local Effects and Spatial Patterns

    EPA Science Inventory

    Eutrophication-induced changes to benthic structure and function are problems of enormous ecological and economic significance. Understanding the relationships between nutrient enrichment and effects, modifying factors such as localized transport time, and symptoms of eutrophica...

  4. Membrane Transporters for Sulfated Steroids in the Human Testis - Cellular Localization, Expression Pattern and Functional Analysis

    PubMed Central

    Wapelhorst, Britta; Grosser, Gary; Günther, Sabine; Alber, Jörg; Döring, Barbara; Kliesch, Sabine; Weidner, Wolfgang; Galuska, Christina E.; Hartmann, Michaela F.; Wudy, Stefan A.; Bergmann, Martin; Geyer, Joachim

    2013-01-01

    Sulfated steroid hormones are commonly considered to be biologically inactive metabolites, but may be reactivated by the steroid sulfatase into biologically active free steroids, thereby having regulatory function via nuclear androgen and estrogen receptors which are widespread in the testis. However, a prerequisite for this mode of action would be a carrier-mediated import of the hydrophilic steroid sulfate molecules into specific target cells in reproductive tissues such as the testis. In the present study we detected predominant expression of the Sodium-dependent Organic Anion Transporter (SOAT), the Organic Anion Transporting Polypeptide 6A1, and the Organic Solute Carrier Partner 1 in human testis biopsies. All of these showed significantly lower or even absent mRNA expression in severe disorders of spermatogenesis (arrest at the level of spermatocytes or spermatogonia, Sertoli cell only syndrome). Only SOAT was significantly lower expressed in biopsies showing hypospermatogenesis. By use of immunohistochemistry SOAT was localized to germ cells at various stages in human testis biopsies showing normal spermatogenesis. SOAT immunoreactivity was detected in zygotene primary spermatocytes of stage V, pachytene spermatocytes of all stages (I–V), secondary spermatocytes of stage VI, and round spermatids (step 1 and step 2) in stages I and II. Furthermore, SOAT transport function for steroid sulfates was analyzed with a novel liquid chromatography tandem mass spectrometry procedure capable of profiling steroid sulfate molecules from cell lysates. With this technique, the cellular inward-directed SOAT transport was verified for the established substrates dehydroepiandrosterone sulfate and estrone-3-sulfate. Additionally, β-estradiol-3-sulfate and androstenediol-3-sulfate were identified as novel SOAT substrates. PMID:23667501

  5. Lamin A precursor induces barrier-to-autointegration factor nuclear localization.

    PubMed

    Capanni, Cristina; Cenni, Vittoria; Haraguchi, Tokuko; Squarzoni, Stefano; Schüchner, Stefan; Ogris, Egon; Novelli, Giuseppe; Maraldi, Nadir; Lattanzi, Giovanna

    2010-07-01

    Lamin A, a protein component of the nuclear lamina, is synthesized as a precursor named prelamin A, whose multi-step maturation process involves different protein intermediates. As demonstrated in laminopathies such as familial partial lipodystrophy, mandibuloacral dysplasia, Werner syndrome, Hutchinson-Gilford progeria syndrome and restrictive dermopathy, failure of prelamin A processing results in the accumulation of lamin A protein precursors inside the nucleus which dominantly produces aberrant chromatin structure. To understand if nuclear lamina components may be involved in prelamin A chromatin remodeling effects, we investigated barrier-to-autointegration factor (BAF) localization and expression in prelamin A accumulating cells. BAF is a DNA-binding protein that interacts directly with histones, lamins and LEM-domain proteins and has roles in chromatin structure, mitosis and gene regulation. In this study, we show that the BAF heterogeneous localization between nucleus and cytoplasm observed in HEK293 cycling cells changes in response to prelamin A accumulation. In particular, we observed that the accumulation of lamin A, non-farnesylated prelamin A and farnesylated carboxymethylated lamin A precursors induce BAF nuclear translocation. Moreover, we show that the treatment of human fibroblasts with prelamin A interfering drugs results in similar changes. Finally, we report that the accumulation of progerin, a truncated form of farnesylated and carboxymethylated prelamin A identified in Hutchinson-Gilford progeria syndrome cells, induces BAF recruitment in the nucleus. These findings are supported by coimmunoprecipitation of prelamin A or progerin with BAF in vivo and suggest that BAF could mediate prelamin A-induced chromatin effects. PMID:20581439

  6. Nuclear APC.

    PubMed

    Neufeld, Kristi L

    2009-01-01

    Mutational inactivation of the tumor suppressor gene APC (Adenomatous polyposis coli) is thought to be an initiating step in the progression of the vast majority ofcolorectal cancers. Attempts to understand APC function have revealed more than a dozen binding partners as well as several subcellular localizations including at cell-cell junctions, associated with microtubules at the leading edge of migrating cells, at the apical membrane, in the cytoplasm and in the nucleus. The present chapter focuses on APC localization and functions in the nucleus. APC contains two classical nuclear localization signals, with a third domain that can enhance nuclear import. Along with two sets of nuclear export signals, the nuclear localization signals enable the large APC protein to shuttle between the nucleus and cytoplasm. Nuclear APC can oppose beta-catenin-mediated transcription. This down-regulation of nuclear beta-catenin activity by APC most likely involves nuclear sequestration of beta-catenin from the transcription complex as well as interaction of APC with transcription corepressor CtBP. Additional nuclear binding partners for APC include transcription factor activator protein AP-2alpha, nuclear export factor Crm1, protein tyrosine phosphatase PTP-BL and perhaps DNA itself. Interaction of APC with polymerase beta and PCNA, suggests a role for APC in DNA repair. The observation that increases in the cytoplasmic distribution of APC correlate with colon cancer progression suggests that disruption of these nuclear functions of APC plays an important role in cancer progression. APC prevalence in the cytoplasm of quiescent cells points to a potential function for nuclear APC in control of cell proliferation. Clear definition of APC's nuclear function(s) will expand the possibilities for early colorectal cancer diagnostics and therapeutics targeted to APC. PMID:19928349

  7. The BARD1 BRCT domain contributes to p53 binding, cytoplasmic and mitochondrial localization, and apoptotic function.

    PubMed

    Tembe, Varsha; Martino-Echarri, Estefania; Marzec, Kamila A; Mok, Myth T S; Brodie, Kirsty M; Mills, Kate; Lei, Ying; DeFazio, Anna; Rizos, Helen; Kettle, Emma; Boadle, Ross; Henderson, Beric R

    2015-09-01

    BARD1 is a breast cancer tumor suppressor with multiple domains and functions. BARD1 comprises a tandem BRCT domain at the C-terminus, and this sequence has been reported to target BARD1 to distinct subcellular locations such as nuclear DNA breakage sites and the centrosome through binding to regulatory proteins such as HP1 and OLA1, respectively. We now identify the BRCT domain as a binding site for p53. We first confirmed previous reports that endogenous BARD1 binds to p53 by immunoprecipitation assay, and further show that BARD1/p53 complexes locate at mitochondria suggesting a cellular location for p53 regulation of BARD1 apoptotic activity. We used a proximity ligation assay to map three distinct p53 binding sequences in human BARD1, ranging from weak (425-525) and modest (525-567) to strong (551-777 comprising BRCT domains). Deletion of the BRCT sequence caused major defects in the ability of BARD1 to (1) bind p53, (2) localize to the cytoplasm and mitochondria, and (3) induce Bax oligomerization and apoptosis. Our data suggest that BARD1 can move to mitochondria independent of p53, but subsequently associates with p53 to induce Bax clustering in part by decreasing mitochondrial Bcl-2 levels. We therefore identify a role for the BRCT domain in stimulating BARD1 nuclear export and mitochondrial localization, and in assembling mitochondrial BARD1/p53 complexes to regulate specific activities such as apoptotic function. PMID:26022179

  8. In Situ Characterization of the Local Work Function along Individual Free Standing Nanowire by Electrostatic Deflection

    PubMed Central

    Chen, Yicong; Zhao, Chengchun; Huang, Feng; Zhan, Runze; Deng, Shaozhi; Xu, Ningsheng; Chen, Jun

    2016-01-01

    In situ characterization of the work function of quasi one dimensional nanomaterials is essential for exploring their applications. Here we proposed to use the electrostatic deflection induced by work function difference between nanoprobe and nanowire for in situ measuring the local work function along a free standing nanowire. The physical mechanism for the measurement was discussed in details and a parabolic relationship between the deflection and the potential difference was derived. As a demonstration, measurement of the local work functions on the tip and the sidewall of a ZnO nanowire with Au catalyst at its end and a LaB6 nanowire have been achieved with good accuracy. PMID:26882827

  9. Structural information content of networks: graph entropy based on local vertex functionals.

    PubMed

    Dehmer, Matthias; Emmert-Streib, Frank

    2008-04-01

    In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating j-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties. PMID:18243802

  10. Library of sophisticated functions for analysis of nuclear spectra

    NASA Astrophysics Data System (ADS)

    Morháč, Miroslav; Matoušek, Vladislav

    2009-10-01

    In the paper we present compact library for analysis of nuclear spectra. The library consists of sophisticated functions for background elimination, smoothing, peak searching, deconvolution, and peak fitting. The functions can process one- and two-dimensional spectra. The software described in the paper comprises a number of conventional as well as newly developed methods needed to analyze experimental data. Program summaryProgram title: SpecAnalysLib 1.1 Catalogue identifier: AEDZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 42 154 No. of bytes in distributed program, including test data, etc.: 2 379 437 Distribution format: tar.gz Programming language: C++ Computer: Pentium 3 PC 2.4 GHz or higher, Borland C++ Builder v. 6. A precompiled Windows version is included in the distribution package Operating system: Windows 32 bit versions RAM: 10 MB Word size: 32 bits Classification: 17.6 Nature of problem: The demand for advanced highly effective experimental data analysis functions is enormous. The library package represents one approach to give the physicists the possibility to use the advanced routines simply by calling them from their own programs. SpecAnalysLib is a collection of functions for analysis of one- and two-parameter γ-ray spectra, but they can be used for other types of data as well. The library consists of sophisticated functions for background elimination, smoothing, peak searching, deconvolution, and peak fitting. Solution method: The algorithms of background estimation are based on Sensitive Non-linear Iterative Peak (SNIP) clipping algorithm. The smoothing algorithms are based on the convolution of the original data with several types of filters and algorithms based on discrete

  11. A study of nuclear effect in F{sub 3} structure function in the deep inelastic v(v-bar) reactions in nuclei

    SciTech Connect

    Athar, M. Sajjad; Singh, S. K.; Simo, I. Ruiz; Vacas, M. J. Vicente

    2009-11-25

    We study nuclear effect in the F{sub 3}{sup A}(x) structure function in the deep inelastic neutrino reactions on iron by taking into account Fermi motion, binding, target mass correction, shadowing and anti-shadowing corrections. Calculations have been done in a local density approximation using relativistic nuclear spectral functions which include nucleon correlations for nuclear matter. Results for F{sub 3}{sup A}(x) have been compared with the results reported at NuTeV and also with some of the older experiments reported in the literature.

  12. LRP130, a single-stranded DNA/RNA-binding protein, localizes at the outer nuclear and endoplasmic reticulum membrane, and interacts with mRNA in vivo.

    PubMed

    Tsuchiya, Naoto; Fukuda, Hirokazu; Nakashima, Katsuhiko; Nagao, Minako; Sugimura, Takashi; Nakagama, Hitoshi

    2004-05-01

    LRP130 (also known as a LRPPRC) is an RNA and single-stranded DNA-binding protein, and recently identified as a candidate gene responsible for the Leigh syndrome, a French-Canadian type cytochrome c oxidase deficiency. However, the biological function of LRP130 still remains largely unresolved. In the present study, we found that the C-terminal half of the mouse LRP130 located within a 120 amino acid sequence (a.a. 845-964) binds to synthetic RNA homopolymers, poly(G), poly(U), and poly(C), as well as r(CUGCC)(6). Assessment of the subcellular localization indicated both nuclear/endoplasmic reticulum (ER) and mitochondrial fractions to be positive. To further analyze the subcellular localization of LRP130, a nuclear/ER fraction was fractionated into the nucleoplasm (NP) and nuclear envelope (NE)/ER, and the latter was further separated into outer nuclear membrane (ONM)/ER and inner nuclear membrane (INM) by treatment with Triton X-100. LRP130 was detectable in all three fractions, and the distribution pattern was in good accordance with that known for ONM/ER proteins. Interestingly, immunostaining of HeLa cells demonstrated nuclear rim staining of LRP130, specifically at the outside of the NE and also at ER, and association of LRP130 with poly(A)(+) RNA was restricted only to the ONM/ER fraction. Overexpression of full-length mouse LRP130 fused with EGFP resulted in nuclear accumulation of poly(A)(+) RNA in HeLa cells. Taking all these results together, it is suggested that LRP130, a novel type of RNA-binding protein, associates with mRNA/mRNP complexes at the outside of NE and ER, and plays a role in control of mRNA metabolisms. PMID:15081402

  13. Identification of a functional nuclear export signal in the green fluorescent protein asFP499

    SciTech Connect

    Mustafa, Huseyin . E-mail: huseyinm@hotmail.com; Strasser, Bernd; Rauth, Sabine; Irving, Robert A.; Wark, Kim L.

    2006-04-21

    The green fluorescent protein (GFP) asFP499 from Anemonia sulcata is a distant homologue of the GFP from Aequorea victoria. We cloned the asFP499 gene into a mammalian expression vector and showed that this protein was expressed in the human lymphoblast cell line Ramos RA1 and in the embryonic kidney 293T cell line (HEK 293T). In HEK 293T cells, asFP499 was localized mainly in the cytoplasm, suggesting that the protein was excluded from the nucleus. We identified {sub 194}LRMEKLNI{sub 201} as a candidate nuclear export signal in asFP499 and mutated the isoleucine at position 201 to an alanine. Unlike the wildtype form, the mutant protein was distributed throughout the cytoplasm and nucleus. This is First report of a GFP that contains a functional NES.

  14. The methylation of the C-terminal region of hnRNPQ (NSAP1) is important for its nuclear localization

    SciTech Connect

    Passos, Dario O.; Quaresma, Alexandre J.C.; Kobarg, Joerg . E-mail: jkobarg@lnls.br

    2006-07-28

    Protein arginine methylation is an irreversible post-translational protein modification catalyzed by a family of at least nine different enzymes entitled PRMTs (protein arginine methyl transferases). Although PRMT1 is responsible for 85% of the protein methylation in human cells, its substrate spectrum has not yet been fully characterized nor are the functional consequences of methylation for the protein substrates well understood. Therefore, we set out to employ the yeast two-hybrid system in order to identify new substrate proteins for human PRMT1. We were able to identify nine different PRMT1 interacting proteins involved in different aspects of RNA metabolism, five of which had been previously described either as substrates for PRMT1 or as functionally associated with PRMT1. Among the four new identified possible protein substrates was hnRNPQ3 (NSAP1), a protein whose function has been implicated in diverse steps of mRNA maturation, including splicing, editing, and degradation. By in vitro methylation assays we were able to show that hnRNPQ3 is a substrate for PRMT1 and that its C-terminal RGG box domain is the sole target for methylation. By further studies with the inhibitor of methylation Adox we provide evidence that hnRNPQ1-3 are methylated in vivo. Finally, we demonstrate by immunofluorescence analysis of HeLa cells that the methylation of hnRNPQ is important for its nuclear localization, since Adox treatment causes its re-distribution from the nucleus to the cytoplasm.

  15. Increased EID1 nuclear translocation impairs synaptic plasticity and memory function associated with pathogenesis of Alzheimer's disease.

    PubMed

    Liu, Rugao; Lei, Joy X; Luo, Chun; Lan, Xun; Chi, Liying; Deng, Panyue; Lei, Saobo; Ghribi, Othman; Liu, Qing Yan

    2012-03-01

    Though loss of function in CBP/p300, a family of CREB-binding proteins, has been causally associated with a variety of human neurological disorders, such as Rubinstein-Taybi syndrome, Huntington's disease and drug addiction, the role of EP300 interacting inhibitor of differentiation 1 (EID1), a CBP/p300 inhibitory protein, in modulating neurological functions remains completely unknown. Through the examination of EID1 expression and cellular distribution, we discovered that there is a significant increase of EID1 nuclear translocation in the cortical neurons of Alzheimer's disease (AD) patient brains compared to that of control brains. To study the potential effects of EID1 on neurological functions associated with learning and memory, we generated a transgenic mouse model with a neuron-specific expression of human EID1 gene in the brain. Overexpression of EID1 led to an increase in its nuclear localization in neurons mimicking that seen in human AD brains. The transgenic mice had a disrupted neurofilament organization and increase of astrogliosis in the cortex and hippocampus. Furthermore, we demonstrated that overexpression of EID1 reduced hippocampal long-term potentiation and impaired spatial learning and memory function in the transgenic mice. Our results indicated that the negative effects of extra nuclear EID1 in transgenic mouse brains are likely due to its inhibitory function on CBP/p300 mediated histone and p53 acetylation, thus affecting the expression of downstream genes involved in the maintenance of neuronal structure and function. Together, our data raise the possibility that alteration of EID1 expression, particularly the increase of EID1 nuclear localization that inhibits CBP/p300 activity in neuronal cells, may play an important role in AD pathogenesis. PMID:22186421

  16. Applying and assessing some semi-local density functionals for condensed matter physics and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Hao, Pan

    Density functional theory (DFT) is a widely used quantum mechanical method for the simulation of the electronic structure of atoms, molecules, and solids. The only part that needs to be approximated is the exchange-correlation energy as a functional of the electron density. After many-year development, there is a huge variety of exchange-correlation functionals. According to the ingredients, an exchange-correlation functional can be classified as a semi-local functional or beyond. A semi-local functional can be nonempirical or empirical and only uses locality information, such as electron density, gradient of the density, Laplacian of the density, and kinetic energy density. Unlike a non-local functional that uses non-locality information, a semi-local functional is computationally efficient and can be applied to large systems. The meta-generalized gradient approximation (meta-GGA), which is the highest-level semi-local functional, has the potential to give a good description for condensed matter physics and quantum chemistry. We built the self-consistent revised Tao-Perdew-Staroverov-Scuseria (revTPSS) meta-GGA into the band-structure program BAND to test the performances of some self-consistent semi-local functionals on lattice constant with a 58-solid test set. The self-consistent effect of revTPSS was also discussed. The vibration of a crystal has a contribution to the ground state energy of a system, which is the zero-point energy at zero temperature. It has anharmonicity at the equilibrium geometry. The standard DFT doesn't consider the zero-point energy of a crystal. We used density functional perturbation theory (DFPT), which is a powerful and flexible theoretical technique within the density functional framework, to study the zero-point energy and make a correction to the lattice constant. The method was compared to a traditional zero-point anharmonic expansion method that is based on the Debye and Dugdale-MacDonald approximations. We also tested some new

  17. Cross-species sequence analysis reveals multiple charged residue-rich domains that regulate nuclear/cytoplasmic partitioning and membrane localization of a kinase anchoring protein 12 (SSeCKS/Gravin).

    PubMed

    Streb, Jeffrey W; Miano, Joseph M

    2005-07-29

    A kinase anchoring proteins (AKAPs) assemble and compartmentalize multiprotein signaling complexes at discrete subcellular locales and thus confer specificity to transduction cascades using ubiquitous signaling enzymes, such as protein kinase A. Intrinsic targeting domains in each AKAP determine the subcellular localization of these complexes and, along with protein-protein interaction domains, form the core of AKAP function. As a foundational step toward elucidating the relationship between location and function, we have used cross-species sequence analysis and deletion mapping to facilitate the identification of the targeting determinants of AKAP12 (also known as SSeCKS or Gravin). Three charged residue-rich regions were identified that regulate two aspects of AKAP12 localization, nuclear/cytoplasmic partitioning and perinuclear/cell periphery targeting. Using deletion mapping and green fluorescent protein chimeras, we uncovered a heretofore unrecognized nuclear localization potential. Five nuclear localization signals, including a novel class of this type of signal termed X2-NLS, are found in the central region of AKAP12 and are important for nuclear targeting. However, this nuclear localization is suppressed by the negatively charged C terminus that mediates nuclear exclusion. In this condition, the distribution of AKAP12 is regulated by an N-terminal targeting domain that simultaneously directs perinuclear and peripheral AKAP12 localization. Three basic residue-rich regions in the N-terminal targeting region have similarity to the MARCKS proteins and were found to control AKAP12 localization to ganglioside-rich regions at the cell periphery. Our data suggest that AKAP12 localization is regulated by a hierarchy of targeting domains and that the localization of AKAP12-assembled signaling complexes may be dynamically regulated. PMID:15923193

  18. Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity.

    PubMed

    Darricarrère, Nicole; Liu, Na; Watanabe, Toshiaki; Lin, Haifan

    2013-01-22

    The Piwi protein subfamily is essential for Piwi-interacting RNA (piRNA) biogenesis, transposon silencing, and germ-line development, all of which have been proposed to require Piwi endonuclease activity, as validated for two cytoplasmic Piwi proteins in mice. However, recent evidence has led to questioning of the generality of this mechanism for the Piwi members that reside in the nucleus. Drosophila offers a distinct opportunity to study the function of nuclear Piwi proteins because, among three Drosophila Piwi proteins--called Piwi, Aubergine, and Argonaute 3--Piwi is the only member of this subfamily that is localized in the nucleus and expressed in both germ-line and somatic cells in the gonad, where it is responsible for piRNA biogenesis and regulatory functions essential for fertility. In this study, we demonstrate beyond doubt that the slicer activity of Piwi is not required for any known functions in vivo. We show that, in transgenic flies with the DDX catalytic triad of PIWI mutated, neither primary nor secondary piRNA biogenesis is detectably affected, transposons remain repressed, and fertility is normal. Our observations demonstrate that the mechanism of Piwi is independent of its in vitro endonuclease activity. Instead, it is consistent with the alternative mode of Piwi function as a molecule involved in the piRNA-directed guidance of epigenetic factors to chromatin. PMID:23297219

  19. The effect of local and large-scale environments on nuclear activity and star formation

    NASA Astrophysics Data System (ADS)

    Argudo-Fernández, M.; Shen, S.; Sabater, J.; Duarte Puertas, S.; Verley, S.; Yang, X.

    2016-07-01

    Context. Active galactic nuclei (AGN) are one of the main drivers for the transition from star-forming disk to passive spheroidal galaxies, however, the role of large-scale environment versus one-on-one interactions in triggering different types of AGN is still uncertain. We present a statistical study of the prevalence of the nuclear activity in isolated galaxies and physically bound isolated pairs. Aims: For the purpose of this study we considered optically and radio selected nuclear activity types. We aim to assess the effect of one-on-one interaction on the fraction of AGN and the role of their large-scale environment. Methods: To study the effect of one-on-one interaction on the fraction of AGN in isolated galaxy pairs, we compare these AGN with a sample of isolated galaxies homogeneously selected under the same isolation criterion. We examine the effect of the large-scale environment by comparing isolated systems with control samples of single galaxies and galaxy pairs. We use the tidal strength parameter to quantify the effects of local and large-scale environments. Results: In general we found no difference in the prevalence of optical AGN for the considered samples. For massive galaxies, the fraction of optical AGN in isolated galaxies is slightly higher than that in the control samples. Also, the fraction of passives in high mass isolated galaxies is smaller than in any other sample. Generally, there is no dependence on optical nuclear activity with local environment. On the other hand, we found evidence that radio AGN are strongly affected by the local environment. Conclusions: The optical AGN phenomenon is related to cold gas accretion, while radio AGN are related to hot gas accretion. In this context, there is more cold gas, fuelling the central optical AGN, in isolated systems. Our results are in agreement with a scenario where cold gas accretion by secular evolution is the main driver of optical AGN, while hot gas accretion and one

  20. Source functions of nuclear explosions from spectral synthesis and inversion. Scientific report No. 1

    SciTech Connect

    Puster, P.; Jordan, T.H.

    1996-11-20

    We apply methods for the recovery of the frequency dependent moment rate tensor, M(w), to the study of Lop Nor nuclear explosions. This approach encompasses many source parameter diagnostics that have been traditionally used to discriminate nuclear explosions from chemical explosions and earthquakes and has the potential to provide new discrimination tools. We parameterize the source as M(w) = M1(a) + MD(a), where M1(co) and MD(O) are isotropic and deviatoric components, respectively. Our goal is to quantify both isotropic and deviatoric components, and investigate the different contributions to MD(a), in particular the tectonic release. Since tectonic release can bias estimates of M1(o) and may limit discrimination capabilities of sparse networks, it is important to be able to characterize the amount of tectonic release - in particular as a function of frequency. Our approach uses synthetic seismograms to improve the localization of signal measurements in both time and frequency domains. We adapt our earthquake-source inversion algorithms to account for isotropic sources at very shallow depths. We test our algorithms using a synthetic case with a known moment-tensor source composed in equal parts of isotropic and deviatoric sources; we successfully recover both MD and M using body waves and surface waves on horizontal and vertical components. We apply our methods to a data set containing both SH and Love waves as well as the body-wave portion between P and R1 and the minor-arc Rayleigh waves from the 92/5/21 Chinese nuclear test. We recover a significant tectonic release component for this event; the deviatoric moment tensor is a dip-slip reverse fault with a scalar moment MD = 1.9 +/- 0.2 x 10(17) Nm. The strike of the best-fitting double-couple is 320 deg. The source-time function derived from SH-polarized waves shows some complexity, with a sharp pulse i.

  1. Co-localization of the amyloid precursor protein and the Notch intracellular domains in nuclear transcription factories

    PubMed Central

    Konietzko, Uwe; Goodger, Zoë V.; Meyer, Michelle; Kohli, Bernhard M.; Bosset, Jérôme; Lahiri, Debomoy K.; Nitsch, Roger M.

    2009-01-01

    The β-amyloid precursor protein (APP) plays a major role in Alzheimer’s disease. The APP intracellular domain (AICD), together with Fe65 and Tip60, localizes to spherical nuclear AFT complexes that might represent sites of transcription. We now show that endogenous AICD is targeted to similar nuclear spots. AFT complexes were closely associated with Cajal and PML bodies but did not localize to nucleoli or splicing speckles. Live imaging revealed that AFT complexes were highly mobile within nuclei. Following pharmacological inhibition of transcription AFT complexes merged into a few large assemblies. We have previously shown that AICD regulates the expression of its own precursor APP. Transfection of APP promoter plasmids as substrates resulted in cytosolic AFT complex formation at the labeled APP promoter plasmids. In addition, identification of chromosomal APP or KAI1 gene loci by fluorescence in situ hybridization showed their close association with nuclear AFT complexes. The transcriptional activator Notch intracellular domain (NICD) localized to the same nuclear spots as occupied by AFT complexes, suggesting that these nuclear compartments correspond to transcription factories. Fe65 and Tip60 also co-localized with APP in the neurites of primary neurons. Pre-assembled AFT complexes may serve to assist fast nuclear signaling upon endoproteolytic APP cleavage. PMID:18403052

  2. KAOS/LIB-V: A library of nuclear response functions generated by KAOS-V code from ENDF/B-V and other data files

    SciTech Connect

    Farawila, Y.; Gohar, Y.; Maynard, C.

    1989-04-01

    KAOS/LIB-V: A library of processed nuclear responses for neutronics analyses of nuclear systems has been generated. The library was prepared using the KAOS-V code and nuclear data from ENDF/B-V. The library includes kerma (kinetic energy released in materials) factors and other nuclear response functions for all materials presently of interest in fusion and fission applications for 43 nonfissionable and 15 fissionable isotopes and elements. The nuclear response functions include gas production and tritium-breeding functions, and all important reaction cross sections. KAOS/LIB-V employs the VITAMIN-E weighting function and energy group structure of 174 neutron groups. Auxiliary nuclear data bases, e.g., the Japanese evaluated nuclear data library JENDL-2 were used as a source of isotopic cross sections when these data are not provided in ENDF/B-V files for a natural element. These are needed mainly to estimate average quantities such as effective Q-values for the natural element. This analysis of local energy deposition was instrumental in detecting and understanding energy balance deficiencies and other problems in the ENDF/B-V data. Pertinent information about the library and a graphical display of the main nuclear response functions for all materials in the library are given. 35 refs.

  3. Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal

    PubMed Central

    Dreyer, Thiago R.; Freitas, Fernanda Z.; Bertolini, Maria Célia; Fontes, Marcos R. M.

    2015-01-01

    Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site. PMID:26091498

  4. The method of local linear approximation in the theory of nonlinear functional-differential equations

    SciTech Connect

    Slyusarchuk, Vasilii E

    2010-10-06

    Conditions for the existence of solutions to the nonlinear functional-differential equation (d{sup m}x(t))/dt{sup m} + (fx)(t)=h(t), t element of R in the space of functions bounded on the axes are obtained by using local linear approximation to the operator F. Bibliography: 21 items.

  5. Extension of local-type inequality for the higher order correlation functions

    SciTech Connect

    Suyama, Teruaki; Yokoyama, Shuichiro E-mail: shu@a.phys.nagoya-u.ac.jp

    2011-07-01

    For the local-type primordial perturbation, it is known that there is an inequality between the bispectrum and the trispectrum. By using the diagrammatic method, we develop a general formalism to systematically construct the similar inequalities up to any order correlation function. As an application, we explicitly derive all the inequalities up to six and eight-point functions.

  6. A functional equivalent of endoplasmic reticulum and Golgi in axons for secretion of locally synthesized proteins

    PubMed Central

    Merianda, Tanuja T.; Lin, Andrew C.; Lam, Joyce S.Y.; Vuppalanchi, Deepika; Willis, Dianna E.; Karin, Norman; Holt, Christine E.; Twiss, Jeffery L.

    2013-01-01

    Subcellular localization of protein synthesis provides a means to regulate the protein composition in far reaches of a cell. This localized protein synthesis gives neuronal processes autonomy to rapidly respond to extracellular stimuli. Locally synthesized axonal proteins enable neurons to respond to guidance cues and can help to initiate regeneration after injury. Most studies of axonal mRNA translation have concentrated on cytoplasmic proteins. While ultrastructural studies suggest that axons do not have rough endoplasmic reticulum or Golgi apparatus, mRNAs for transmembrane and secreted proteins localize to axons. Here, we show that growing axons with protein synthetic activity contain ER and Golgi components needed for classical protein synthesis and secretion. Isolated axons have the capacity to traffic locally synthesized proteins into secretory pathways and inhibition of Golgi function attenuates translation-dependent axonal growth responses. Finally, the capacity for secreting locally synthesized proteins in axons appears to be increased by injury. PMID:19022387

  7. Anomalous organic magnetoresistance from competing carrier-spin-dependent interactions with localized electronic and nuclear spins

    NASA Astrophysics Data System (ADS)

    Flatté, Michael E.

    Transport of carriers through disordered electronic energy landscapes occurs via hopping or tunneling through various sites, and can enhance the effects of carrier spin dynamics on the transport. When incoherent hopping preserves the spin orientation of carriers, the magnetic-field-dependent correlations between pairs of spins influence the charge conductivity of the material. Examples of these phenomena have been identified in hopping transport in organic semiconductors and colloidal quantum dots, as well as tunneling through oxide barriers in complex oxide devices, among other materials. The resulting room-temperature magnetic field effects on the conductivity or electroluminescence require external fields of only a few milliTesla. These magnetic field effects can be dramatically modified by changes in the local spin environment. Recent theoretical and experimental work has identified a regime for low-field magnetoresistance in organic semiconductors in which the spin-relaxing effects of localized nuclear spins and electronic spins interfere1. The regime is studied experimentally by the controlled addition of localized electronic spins, through the addition of a stable free radical (galvinoxyl) to a material (MEH-PPV) that exhibits substantial room-temperature magnetoresistance (20 initially suppressed by the doping, as the localized electronic spin mixes one of the two spins whose correlation controls the transport. At intermediate doping, when one spin is fully decohered but the other is not, there is a regime where the magnetoresistance is insensitive to the doping level. For much greater doping concentrations the magnetoresistance is fully suppressed as both spins that control the charge conductivity of the material are mixed. The behavior is described within a theoretical model describing the effect of carrier spin dynamics on the current. Generalizations to amorphous and other disordered crystalline semiconductors will also be described. This work was

  8. Local work function and STM tip-induced distortion of graphene on Ir(111)

    NASA Astrophysics Data System (ADS)

    Altenburg, S. J.; Berndt, R.

    2014-05-01

    The contact conductance and the apparent barrier height ϕ of graphene on Ir(111) are measured with a cryogenic scanning tunneling microscope. A strong dependence of ϕ on the tip-sample distance is found and explained by a local lifting of the graphene film by van-der-Waals forces. Variations of ϕ observed within the moiré unit cell of the graphene layer are interpreted in terms of differences in the local work function and the buckling of the graphene film. Comparison to results based on density functional theory indicates that a modulation of the charge transfer between graphene and Ir(111) is the origin of the work function variations.

  9. NuMA localization, stability, and function in spindle orientation involve 4.1 and Cdk1 interactions

    PubMed Central

    Seldin, Lindsey; Poulson, Nicholas D.; Foote, Henry P.; Lechler, Terry

    2013-01-01

    The epidermis is a multilayered epithelium that requires asymmetric divisions for stratification. A conserved cortical protein complex, including LGN, nuclear mitotic apparatus (NuMA), and dynein/dynactin, plays a key role in establishing proper spindle orientation during asymmetric divisions. The requirements for the cortical recruitment of these proteins, however, remain unclear. In this work, we show that NuMA is required to recruit dynactin to the cell cortex of keratinocytes. NuMA's cortical recruitment requires LGN; however, LGN interactions are not sufficient for this localization. Using fluorescence recovery after photobleaching, we find that the 4.1-binding domain of NuMA is important for stabilizing its interaction with the cell cortex. This is functionally important, as loss of 4.1/NuMA interaction results in spindle orientation defects, using two distinct assays. Furthermore, we observe an increase in cortical NuMA localization as cells enter anaphase. Inhibition of Cdk1 or mutation of a single residue in NuMA mimics this effect. NuMA's anaphase localization is independent of LGN and 4.1 interactions, revealing two distinct mechanisms responsible for NuMA cortical recruitment at different stages of mitosis. This work highlights the complexity of NuMA localization and reveals the importance of NuMA cortical stability for productive force generation during spindle orientation. PMID:24109598

  10. Nuclear Trafficking of the Rabies Virus Interferon Antagonist P-Protein Is Regulated by an Importin-Binding Nuclear Localization Sequence in the C-Terminal Domain

    PubMed Central

    Rowe, Caitlin L.; Wagstaff, Kylie M.; Oksayan, Sibil; Glover, Dominic J.

    2016-01-01

    Rabies virus P-protein is expressed as five isoforms (P1-P5) which undergo nucleocytoplasmic trafficking important to roles in immune evasion. Although nuclear import of P3 is known to be mediated by an importin (IMP)-recognised nuclear localization sequence in the N-terminal region (N-NLS), the mechanisms underlying nuclear import of other P isoforms in which the N-NLS is inactive or has been deleted have remained unresolved. Based on the previous observation that mutation of basic residues K214/R260 of the P-protein C-terminal domain (P-CTD) can result in nuclear exclusion of P3, we used live cell imaging, protein interaction analysis and in vitro nuclear transport assays to examine in detail the nuclear trafficking properties of this domain. We find that the effect of mutation of K214/R260 on P3 is largely dependent on nuclear export, suggesting that nuclear exclusion of mutated P3 involves the P-CTD-localized nuclear export sequence (C-NES). However, assays using cells in which nuclear export is pharmacologically inhibited indicate that these mutations significantly inhibit P3 nuclear accumulation and, importantly, prevent nuclear accumulation of P1, suggestive of effects on NLS-mediated import activity in these isoforms. Consistent with this, molecular binding and transport assays indicate that the P-CTD mediates IMPα2/IMPβ1-dependent nuclear import by conferring direct binding to the IMPα2/IMPβ1 heterodimer, as well as to a truncated form of IMPα2 lacking the IMPβ-binding autoinhibitory domain (ΔIBB-IMPα2), and IMPβ1 alone. These properties are all dependent on K214 and R260. This provides the first evidence that P-CTD contains a genuine IMP-binding NLS, and establishes the mechanism by which P-protein isoforms other than P3 can be imported to the nucleus. These data underpin a refined model for P-protein trafficking that involves the concerted action of multiple NESs and IMP-binding NLSs, and highlight the intricate regulation of P

  11. Nuclear Trafficking of the Rabies Virus Interferon Antagonist P-Protein Is Regulated by an Importin-Binding Nuclear Localization Sequence in the C-Terminal Domain.

    PubMed

    Rowe, Caitlin L; Wagstaff, Kylie M; Oksayan, Sibil; Glover, Dominic J; Jans, David A; Moseley, Gregory W

    2016-01-01

    Rabies virus P-protein is expressed as five isoforms (P1-P5) which undergo nucleocytoplasmic trafficking important to roles in immune evasion. Although nuclear import of P3 is known to be mediated by an importin (IMP)-recognised nuclear localization sequence in the N-terminal region (N-NLS), the mechanisms underlying nuclear import of other P isoforms in which the N-NLS is inactive or has been deleted have remained unresolved. Based on the previous observation that mutation of basic residues K214/R260 of the P-protein C-terminal domain (P-CTD) can result in nuclear exclusion of P3, we used live cell imaging, protein interaction analysis and in vitro nuclear transport assays to examine in detail the nuclear trafficking properties of this domain. We find that the effect of mutation of K214/R260 on P3 is largely dependent on nuclear export, suggesting that nuclear exclusion of mutated P3 involves the P-CTD-localized nuclear export sequence (C-NES). However, assays using cells in which nuclear export is pharmacologically inhibited indicate that these mutations significantly inhibit P3 nuclear accumulation and, importantly, prevent nuclear accumulation of P1, suggestive of effects on NLS-mediated import activity in these isoforms. Consistent with this, molecular binding and transport assays indicate that the P-CTD mediates IMPα2/IMPβ1-dependent nuclear import by conferring direct binding to the IMPα2/IMPβ1 heterodimer, as well as to a truncated form of IMPα2 lacking the IMPβ-binding autoinhibitory domain (ΔIBB-IMPα2), and IMPβ1 alone. These properties are all dependent on K214 and R260. This provides the first evidence that P-CTD contains a genuine IMP-binding NLS, and establishes the mechanism by which P-protein isoforms other than P3 can be imported to the nucleus. These data underpin a refined model for P-protein trafficking that involves the concerted action of multiple NESs and IMP-binding NLSs, and highlight the intricate regulation of P

  12. [GnRH analogues containing SV-40 virus T-antigen nuclear localization sequence].

    PubMed

    Burov, S V; Iablokova, T V; Dorosh, M Iu; Kriviziuk, E V; Efremov, A M; Orlov, S V

    2010-01-01

    To improve the efficiency of anticancer drugs due to their delivery to intracellular targets a set of GnRH analogues containing nuclear localization signal (NLS) of SV-40 virus large T-antigen have been synthesized. NLS was attached to the parent molecule via ε-amino group of D-Lysine in position 1 or 6 of peptide sequence using orthogonal protection strategy. The biological activity studies revealed that incorporation of NLS moiety significantly increases cytotoxic activity of palmitoyl-containing GnRH analogues in vitro. The influence of tested peptides on tumor cells does not accompanied by the destruction of cell membrane, as confirmed in experiments with normal fibroblasts, used as a control. PMID:21063449

  13. GD3 nuclear localization after apoptosis induction in HUT-78 cells.

    PubMed

    Tempera, Italo; Buchetti, Barbara; Lococo, Emanuela; Gradini, Roberto; Mastronardi, Annalisa; Mascellino, Maria Teresa; Sale, Patrizio; Mosca, Luciana; d'Erme, Maria; Lenti, Luisa

    2008-04-11

    Glycosphingolipids are essential components of plasma membrane and act as antigens, mediators of cell adhesion, and modulators of signal transduction. Following activation of the Fas receptor, gangliosides are recuited in various intracellular compartments. We have evaluated whether the pro-apoptotic anti-CD95 antibody induces a nuclear localization of GD3 in HUT-78 cells. Our data shows that GD3 translocation from cytosol to nuclei is strongly correlated to concomitant rapid phosphorylation of histone H1 shortly after induction of apoptosis. This work advances the hypothesis that GD3 induces a post-translational modification of histone H1 thus influencing the apoptosis process through transcriptional activation/repression of specific genes. PMID:18261989

  14. GD3 nuclear localization after apoptosis induction in HUT-78 cells

    SciTech Connect

    Tempera, Italo; Buchetti, Barbara; Lococo, Emanuela; Gradini, Roberto; Mastronardi, Annalisa; Mascellino, Maria Teresa; Sale, Patrizio; Mosca, Luciana; D'Erme, Maria Lenti, Luisa

    2008-04-11

    Glycosphingolipids are essential components of plasma membrane and act as antigens, mediators of cell adhesion, and modulators of signal transduction. Following activation of the Fas receptor, gangliosides are recuited in various intracellular compartments. We have evaluated whether the pro-apoptotic anti-CD95 antibody induces a nuclear localization of GD3 in HUT-78 cells. Our data shows that GD3 translocation from cytosol to nuclei is strongly correlated to concomitant rapid phosphorylation of histone H1 shortly after induction of apoptosis. This work advances the hypothesis that GD3 induces a post-translational modification of histone H1 thus influencing the apoptosis process through transcriptional activation/repression of specific genes.

  15. Effect of nuclear mass on carrier-envelope-phase-controlled electron localization in dissociating molecules

    NASA Astrophysics Data System (ADS)

    Xu, Han; Xu, Tian-Yu; He, Feng; Kielpinski, D.; Sang, R. T.; Litvinyuk, I. V.

    2014-04-01

    We explore the effect of nuclear mass on the laser-driven electron localization process. We dissociate a mixed H2 and D2 target with intense, carrier-envelope-phase (CEP) stable 6 fs laser pulses and detect the products in a reaction microscope. We observe a very strong CEP-dependent asymmetry in proton and deuteron emission for low dissociation energy channels. This asymmetry is stronger for H2 than for D2. We also observe a large CEP offset between the asymmetry spectra for H2 and D2. Our theoretical simulations, based on a one-dimensional two-channel model, agree very well with the asymmetry spectra, but fail to account properly for the phase difference between the two isotopes.

  16. Tissue-Specific Signals Control Reversible Program of Localization and Functional Polarization of Macrophages

    PubMed Central

    Okabe, Yasutaka; Medzhitov, Ruslan

    2014-01-01

    SUMMARY Tissue-resident macrophages are highly heterogeneous in terms of their functions and phenotypes as a consequence of adaptation to different tissue environments. Local tissue-derived signals are thought to control functional polarization of resident macrophages; however, the identity of these signals remains largely unknown. It is also unknown whether functional heterogeneity is a result of irreversible lineage-specific differentiation or a consequence of continuous but reversible induction of diverse functional programs. Here, we identified retinoic acid as a signal that induces tissue-specific localization and functional polarization of peritoneal macrophages through the reversible induction of transcription factor GATA6. We further found that GATA6 in macrophages regulates gut IgA production through peritoneal B-1 cells. These results provide insight into the regulation of tissue-resident macrophage functional specialization by tissue-derived signals. PMID:24792964

  17. New approaches for the calibration of exchange-energy densities in local hybrid functionals.

    PubMed

    Maier, Toni M; Haasler, Matthias; Arbuznikov, Alexei V; Kaupp, Martin

    2016-08-21

    The ambiguity of exchange-energy densities is a fundamental challenge for the development of local hybrid functionals, or of other functionals based on a local mixing of exchange-energy densities. In this work, a systematic construction of semi-local calibration functions (CFs) for adjusting the exchange-energy densities in local hybrid functionals is provided, which directly links a given CF to an underlying semi-local exchange functional, as well as to the second-order gradient expansion of the exchange hole. Using successive steps of integration by parts allows the derivation of correction terms of increasing order, resulting in more and more complicated but also more flexible CFs. We derive explicit first- and second-order CFs (pig1 and pig2) based on B88 generalized-gradient approximation (GGA) exchange, and a first-order CF (tpig1) based on τ-dependent B98 meta-GGA exchange. We combine these CFs with different long-range damping functions and evaluate them for calibration of LDA, B88 GGA, and TPSS meta-GGA exchange-energy densities. Based on a minimization of unphysical nondynamical correlation contributions in three noble-gas dimer potential-energy curves, free parameters in the CFs are optimized, and performance of various approaches in the calibration of different exchange-energy densities is compared. Most notably, the second-order pig2 CF provides the largest flexibility with respect to the diffuseness of the damping function. This suggests that higher-order CFs based on the present integration-by-parts scheme may be particularly suitable for the flexible construction of local hybrid functionals. PMID:27080804

  18. ALS mutant FUS disrupts nuclear localization and sequesters wild-type FUS within cytoplasmic stress granules

    PubMed Central

    Vance, Caroline; Scotter, Emma L.; Nishimura, Agnes L.; Troakes, Claire; Mitchell, Jacqueline C.; Kathe, Claudia; Urwin, Hazel; Manser, Catherine; Miller, Christopher C.; Hortobágyi, Tibor; Dragunow, Mike; Rogelj, Boris; Shaw, Christopher E.

    2013-01-01

    Mutations in the gene encoding Fused in Sarcoma (FUS) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. FUS is a predominantly nuclear DNA- and RNA-binding protein that is involved in RNA processing. Large FUS-immunoreactive inclusions fill the perikaryon of surviving motor neurons of ALS patients carrying mutations at post-mortem. This sequestration of FUS is predicted to disrupt RNA processing and initiate neurodegeneration. Here, we demonstrate that C-terminal ALS mutations disrupt the nuclear localizing signal (NLS) of FUS resulting in cytoplasmic accumulation in transfected cells and patient fibroblasts. FUS mislocalization is rescued by the addition of the wild-type FUS NLS to mutant proteins. We also show that oxidative stress recruits mutant FUS to cytoplasmic stress granules where it is able to bind and sequester wild-type FUS. While FUS interacts with itself directly by protein–protein interaction, the recruitment of FUS to stress granules and interaction with PABP are RNA dependent. These findings support a two-hit hypothesis, whereby cytoplasmic mislocalization of FUS protein, followed by cellular stress, contributes to the formation of cytoplasmic aggregates that may sequester FUS, disrupt RNA processing and initiate motor neuron degeneration. PMID:23474818

  19. ALS mutant FUS disrupts nuclear localization and sequesters wild-type FUS within cytoplasmic stress granules.

    PubMed

    Vance, Caroline; Scotter, Emma L; Nishimura, Agnes L; Troakes, Claire; Mitchell, Jacqueline C; Kathe, Claudia; Urwin, Hazel; Manser, Catherine; Miller, Christopher C; Hortobágyi, Tibor; Dragunow, Mike; Rogelj, Boris; Shaw, Christopher E

    2013-07-01

    Mutations in the gene encoding Fused in Sarcoma (FUS) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. FUS is a predominantly nuclear DNA- and RNA-binding protein that is involved in RNA processing. Large FUS-immunoreactive inclusions fill the perikaryon of surviving motor neurons of ALS patients carrying mutations at post-mortem. This sequestration of FUS is predicted to disrupt RNA processing and initiate neurodegeneration. Here, we demonstrate that C-terminal ALS mutations disrupt the nuclear localizing signal (NLS) of FUS resulting in cytoplasmic accumulation in transfected cells and patient fibroblasts. FUS mislocalization is rescued by the addition of the wild-type FUS NLS to mutant proteins. We also show that oxidative stress recruits mutant FUS to cytoplasmic stress granules where it is able to bind and sequester wild-type FUS. While FUS interacts with itself directly by protein-protein interaction, the recruitment of FUS to stress granules and interaction with PABP are RNA dependent. These findings support a two-hit hypothesis, whereby cytoplasmic mislocalization of FUS protein, followed by cellular stress, contributes to the formation of cytoplasmic aggregates that may sequester FUS, disrupt RNA processing and initiate motor neuron degeneration. PMID:23474818

  20. Modulation of nuclear localization of the influenza virus nucleoprotein through interaction with actin filaments.

    PubMed

    Digard, P; Elton, D; Bishop, K; Medcalf, E; Weeds, A; Pope, B

    1999-03-01

    The influenza virus genome is transcribed in the nuclei of infected cells but assembled into progeny virions in the cytoplasm. This is reflected in the cellular distribution of the virus nucleoprotein (NP), a protein which encapsidates genomic RNA to form ribonucleoprotein structures. At early times postinfection NP is found in the nucleus, but at later times it is found predominantly in the cytoplasm. NP contains several sequences proposed to act as nuclear localization signals (NLSs), and it is not clear how these are overridden to allow cytoplasmic accumulation of the protein. We find that NP binds tightly to filamentous actin in vitro and have identified a cluster of residues in NP essential for the interaction. Complexes containing RNA, NP, and actin could be formed, suggesting that viral ribonucleoproteins also bind actin. In cells, exogenously expressed NP when expressed at a high level partitioned to the cytoplasm, where it associated with F-actin stress fibers. In contrast, mutants unable to bind F-actin efficiently were imported into the nucleus even under conditions of high-level expression. Similarly, nuclear import of NLS-deficient NP molecules was restored by concomitant disruption of F-actin binding. We propose that the interaction of NP with F-actin causes the cytoplasmic retention of influenza virus ribonucleoproteins. PMID:9971805

  1. Distinct nuclear localization patterns of DNA methyltransferases in developing and mature mammalian retina.

    PubMed

    Nasonkin, Igor O; Lazo, Kevin; Hambright, Dustin; Brooks, Matthew; Fariss, Robert; Swaroop, Anand

    2011-07-01

    DNA methyltransferases--DNMT1, DNMT3a, and DNMT3b--produce methylation patterns that dynamically regulate chromatin remodeling and gene expression. The vertebrate retina provides an ideal model to elucidate molecular control of neurogenesis as all neuronal cell types and Müller glia are generated in a conserved order from common pools of progenitor cells. As a prelude to exploring epigenetic regulation of mammalian retinal development, we investigated the expression of Dnmt1, Dnmt3a, and Dnmt3b in the mouse retina from embryonic day (E) 10.5 to 10 months of age. High levels of transcripts for all three Dnmt genes were observed in early stages of retinal differentiation, with significantly reduced expression after birth. Although DNMT1 protein is abundant in retinal progenitors at E10.5, it becomes restricted to postmitotic cells by E15.5. Most cells in the postnatal retina show nuclear immunostaining of DNMT1; however, the photoreceptors exhibit distinctive patterns. In rods, weak expression of DNMT1 is detected in perinuclear region and in the nucleus, whereas a strong nuclear labeling is evident in cones. DNMT3a and DNMT3b show a discrete pattern in developing retina with high expression at E11.5, little or no immunostaining by E15.5, and then postnatal expression overlapping with DNMT1 in early born neurons (ganglion, amacrine and horizontal cells, and cones). Robust nuclear localization of DNMTs in cones compared to rods suggests a potential role of DNA methylation in differential remodeling of chromatin in these two specialized neurons. Our studies indicate that DNA methyltransferases contribute to the establishment and maturation of cell fates during retinal development. PMID:21452232

  2. Midkine-a Protein Localization in the Developing and Adult Retina of the Zebrafish and Its Function During Photoreceptor Regeneration

    PubMed Central

    Taylor, Scott; Thummel, Ryan; Hitchcock, Peter F.

    2015-01-01

    Midkine is a heparin binding growth factor with important functions in neuronal development and survival, but little is known about its function in the retina. Previous studies show that in the developing zebrafish, Midkine-a (Mdka) regulates cell cycle kinetics in retinal progenitors, and following injury to the adult zebrafish retina, mdka is strongly upregulated in Müller glia and the injury-induced photoreceptor progenitors. Here we provide the first data describing Mdka protein localization during different stages of retinal development and during the regeneration of photoreceptors in adults. We also experimentally test the role of Mdka during photoreceptor regeneration. The immuno-localization of Mdka reflects the complex spatiotemporal pattern of gene expression and also reveals the apparent secretion and extracellular trafficking of this protein. During embryonic retinal development the Mdka antibodies label all mitotically active cells, but at the onset of neuronal differentiation, immunostaining is also localized to the nascent inner plexiform layer. Starting at five days post fertilization through the juvenile stage, Mdka immunostaining labels the cytoplasm of horizontal cells and the overlying somata of rod photoreceptors. Double immunolabeling shows that in adult horizontal cells, Mdka co-localizes with markers of the Golgi complex. Together, these data are interpreted to show that Mdka is synthesized in horizontal cells and secreted into the outer nuclear layer. In adults, Mdka is also present in the end feet of Müller glia. Similar to mdka gene expression, Mdka in horizontal cells is regulated by circadian rhythms. After the light-induced death of photoreceptors, Mdka immuonolabeling is localized to Müller glia, the intrinsic stem cells of the zebrafish retina, and proliferating photoreceptor progenitors. Knockdown of Mdka during photoreceptor regeneration results in less proliferation and diminished regeneration of rod photoreceptors. These data

  3. p27 Nuclear localization and growth arrest caused by perlecan knockdown in human endothelial cells

    SciTech Connect

    Sakai, Katsuya; Oka, Kiyomasa; Matsumoto, Kunio; Nakamura, Toshikazu

    2010-02-12

    Perlecan, a secreted heparan sulfate proteoglycan, is a major component of the vascular basement membrane and participates in angiogenesis. Here, we used small interference RNA-mediated knockdown of perlecan expression to investigate the regulatory function of perlecan in the growth of human vascular endothelial cells. Basic fibroblast growth factor (bFGF)-induced ERK phosphorylation and cyclin D1 expression were unchanged by perlecan deficiency in endothelial cells; however, perlecan deficiency inhibited the Rb protein phosphorylation and DNA synthesis induced by bFGF. By contrast to cytoplasmic localization of the cyclin-dependent kinase inhibitor p27 in control endothelial cells, p27 was localized in the nucleus and its expression increased in perlecan-deficient cells, which suggests that p27 mediates inhibition of Rb phosphorylation. In addition to the well-characterized function of perlecan as a co-receptor for heparin-binding growth factors such as bFGF, our results suggest that perlecan plays an indispensible role in endothelial cell proliferation and acts through a mechanism that involves subcellular localization of p27.

  4. One- and many-electron self-interaction error in local and global hybrid functionals

    NASA Astrophysics Data System (ADS)

    Schmidt, Tobias; Kümmel, Stephan

    2016-04-01

    Electronic self-interaction poses a fundamental challenge in density-functional theory. It greatly limits, e.g., the physical interpretation of eigenvalues as electron removal energies. We here investigate whether local hybrid functionals that are designed to be free from one-electron self-interaction lead to occupied Kohn-Sham eigenvalues and orbitals that approximate photoemission observables well. We compare the local hybrid results to the ones from global hybrid functionals that only partially counteract the self-interaction, and to the results that are obtained with a Perdew-Zunger-type self-interaction correction. Furthermore, we check whether being nominally free from one-electron self-interaction translates into a reduced many-electron self-interaction error. Our findings show that this is not the case for the local hybrid functionals that we studied: In practice they are similar to global hybrids in many respects, despite being formally superior. This finding indicates that there is a conceptual difference between the Perdew-Zunger way and the local hybrid way of translating the one-electron condition to a many-electron system. We also point out and solve some difficulties that occur when using local hybrid functionals in combination with pseudopotentials.

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

    SciTech Connect

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

    2011-08-12

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

  6. AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region.

    PubMed

    Morisawa, G; Han-Yama, A; Moda, I; Tamai, A; Iwabuchi, M; Meshi, T

    2000-10-01

    Interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) have been implicated in various nuclear functions. We have identified a novel protein from wheat, AT hook-containing MAR binding protein1 (AHM1), that binds preferentially to MARs. A multidomain protein, AHM1 has the special combination of a J domain-homologous region and a Zn finger-like motif (a J-Z array) and an AT hook. For MAR binding, the AT hook at the C terminus was essential, and an internal portion containing the Zn finger-like motif was additionally required in vivo. AHM1 was found in the nuclear matrix fraction and was localized in the nucleoplasm. AHM1 fused to green fluorescent protein had a speckled distribution pattern inside the nucleus. AHM1 is most likely a nuclear matrix component that functions between intranuclear framework and MARs. J-Z arrays can be found in a group of (hypothetical) proteins in plants, which may share some functions, presumably to recruit specific Hsp70 partners as co-chaperones. PMID:11041885

  7. Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants.

    PubMed

    Zhou, Xiao; Graumann, Katja; Wirthmueller, Lennart; Jones, Jonathan D G; Meier, Iris

    2014-06-01

    Although a plethora of nuclear envelope (NE) transmembrane proteins (NETs) have been identified in opisthokonts, plant NETs are largely unknown. The only known NET homologues in plants are Sad1/UNC-84 (SUN) proteins, which bind Klarsicht/ANC-1/Syne-1 homology (KASH) proteins. Therefore, de novo identification of plant NETs is necessary. Based on similarities between opisthokont KASH proteins and the only known plant KASH proteins, WPP domain-interacting proteins, we used a computational method to identify the KASH subset of plant NETs. Ten potential plant KASH protein families were identified, and five candidates from four of these families were verified for their NE localization, depending on SUN domain interaction. Of those, Arabidopsis thaliana SINE1 is involved in actin-dependent nuclear positioning in guard cells, whereas its paralogue SINE2 contributes to innate immunity against an oomycete pathogen. This study dramatically expands our knowledge of plant KASH proteins and suggests that plants and opisthokonts have recruited different KASH proteins to perform NE regulatory functions. PMID:24891605

  8. The nuclear factor SPBP contains different functional domains and stimulates the activity of various transcriptional activators.

    PubMed

    Rekdal, C; Sjøttem, E; Johansen, T

    2000-12-22

    SPBP (stromelysin-1 platelet-derived growth factor-responsive element binding protein) was originally cloned from a cDNA expression library by virtue of its ability to bind to a platelet-derived growth factor-responsive element in the human stromelysin-1 promoter. A 937-amino acid-long protein was deduced from a 3995-nucleotide murine cDNA sequence. By analyses of both human and murine cDNAs, we now show that SPBP is twice as large as originally found. The human SPBP gene contains six exons and is located on chromosome 22q13.1-13.3. Two isoforms differing in their C termini are expressed due to alternative splicing. PCR analyses of multitissue cDNA panels showed that SPBP is expressed in most tissues except for ovary and prostate. Functional mapping revealed that SPBP is a nuclear, multidomain protein containing an N-terminal region with transactivating ability, a novel type of DNA-binding domain containing an AT hook motif, and a bipartite nuclear localization signal as well as a C-terminal zinc finger domain. This type of zinc finger domain is also found in the trithorax family of chromatin-based transcriptional regulator proteins. Using cotransfection experiments, we find that SPBP enhances the transcriptional activity of various transcription factors such as c-Jun, Ets1, Sp1, and Pax6. Hence, SPBP seems to act as a transcriptional coactivator. PMID:10995766

  9. Local, Regional and National Responses for Medical Management of a Radiological/Nuclear Incident

    PubMed Central

    Dainiak, Nicholas; Skudlarska, Beata; Albanese, Joseph

    2013-01-01

    Radiological and nuclear devices may be used by terrorists or may be the source of accidental exposure. A tiered approach has been recommended for response to a terrorist event wherein local, regional, state and federal assets become involved sequentially, as the magnitude in severity of the incident increases. State-wide hospital plans have been developed and published for Connecticut, New York and California. These plans address delineation of responsibilities of various categories of health professionals, protection of healthcare providers, identification and classification of individuals who might have been exposed to and/or contaminated by radiation and, in the case of Connecticut response plan, early management of victims. Regional response programs such as the New England Regional Health Compact (consisting of 6 member states) have been developed to manage consequences of radiation injury. The Department of Homeland Security is ultimately responsible for managing both health consequences and the crisis. Multiple US national response assets may be called upon for use in radiological incidents. These include agencies and programs that have been developed by the Department of Energy, the Environmental Protection Agency and the Department of Defense. Coordination of national, regional and state assets with local response efforts is necessary to provide a timely and efficient response. PMID:23447742

  10. Expression and localization of heterogeneous nuclear ribonucleoprotein K in mouse ovaries and preimplantation embryos.

    PubMed

    Zhang, Ping; Wang, Ningling; Lin, Xianhua; Jin, Li; Xu, Hong; Li, Rong; Huang, Hefeng

    2016-02-26

    Heterogeneous nuclear ribonucleoprotein K (hnRNP K), an evolutionarily conserved protein, is involved in several important cellular processes that are relevant to cell proliferation, differentiation, apoptosis, and cancer development. However, details of hnRNP K expression during mammalian oogenesis and preimplantation embryo development are lacking. The present study investigates the expression and cellular localization of K protein in the mouse ovaries and preimplantation embryos using immunostaining. We demonstrate, for the first time, that hnRNP K is abundantly expressed in the nuclei of mouse oocytes in primordial, primary and secondary follicles. In germ vesicle (GV)-stage oocytes, hnRNP K accumulates in the germinal vesicle in a spot distribution manner. After germinal vesicle breakdown, speckled hnRNP K is diffusely distributed in the cytoplasm. However, after fertilization, the K protein relocates into the female and male pronucleus and persists in the blastomere nuclei. Localization of K protein in the human ovary and ovarian granulosa cell tumor (GCT) was also investigated. Overall, this study provides important morphological evidence to better understand the possible roles of hnRNP K in mammalian oogenesis and early embryo development. PMID:26850853

  11. Local, regional and national responses for medical management of a radiological/nuclear incident.

    PubMed

    Dainiak, Nicholas; Skudlarska, Beata; Albanese, Joseph

    2013-01-01

    Radiological and nuclear devices may be used by terrorists or may be the source of accidental exposure. A tiered approach has been recommended for response to a terrorist event wherein local, regional, state and federal assets become involved sequentially, as the magnitude in severity of the incident increases. State-wide hospital plans have been developed and published for Connecticut, New York and California. These plans address delineation of responsibilities of various categories of health professionals, protection of healthcare providers, identification and classification of individuals who might have been exposed to and/or contaminated by radiation and, in the case of Connecticut response plan, early management of victims. Regional response programs such as the New England Regional Health Compact (consisting of 6 member states) have been developed to manage consequences of radiation injury. The Department of Homeland Security is ultimately responsible for managing both health consequences and the crisis. Multiple US national response assets may be called upon for use in radiological incidents. These include agencies and programs that have been developed by the Department of Energy, the Environmental Protection Agency and the Department of Defense. Coordination of national, regional and state assets with local response efforts is necessary to provide a timely and efficient response. PMID:23447742

  12. Quasi-particle energy spectra in local reduced density matrix functional theory.

    PubMed

    Lathiotakis, Nektarios N; Helbig, Nicole; Rubio, Angel; Gidopoulos, Nikitas I

    2014-10-28

    Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C20 isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids. PMID:25362285

  13. Quasi-particle energy spectra in local reduced density matrix functional theory

    SciTech Connect

    Lathiotakis, Nektarios N.; Helbig, Nicole; Rubio, Angel

    2014-10-28

    Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C{sub 20} isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.

  14. Nuclear Safety Functions of ITER Gas Injection System Instrumentation and Control and the Concept Design

    NASA Astrophysics Data System (ADS)

    Yang, Yu; Maruyama, S.; Fossen, A.; Villers, F.; Kiss, G.; Zhang, Bo; Li, Bo; Jiang, Tao; Huang, Xiangmei

    2016-08-01

    The ITER Gas Injection System (GIS) plays an important role on fueling, wall conditioning and distribution for plasma operation. Besides that, to support the safety function of ITER, GIS needs to implement three nuclear safety Instrumentation and Control (I&C) functions. In this paper, these three functions are introduced with the emphasis on their latest safety classifications. The nuclear I&C design concept is briefly discussed at the end.

  15. Aurora B–mediated localized delays in nuclear envelope formation facilitate inclusion of late-segregating chromosome fragments

    PubMed Central

    Karg, Travis; Warecki, Brandt; Sullivan, William

    2015-01-01

    To determine how chromosome segregation is coordinated with nuclear envelope formation (NEF), we examined the dynamics of NEF in the presence of lagging acentric chromosomes in Drosophila neuroblasts. Acentric chromosomes often exhibit delayed but ultimately successful segregation and incorporation into daughter nuclei. However, it is unknown whether these late-segregating acentric fragments influence NEF to ensure their inclusion in daughter nuclei. Through live analysis, we show that acentric chromosomes induce highly localized delays in the reassembly of the nuclear envelope. These delays result in a gap in the nuclear envelope that facilitates the inclusion of lagging acentrics into telophase daughter nuclei. Localized delays of nuclear envelope reassembly require Aurora B kinase activity. In cells with reduced Aurora B activity, there is a decrease in the frequency of local nuclear envelope reassembly delays, resulting in an increase in the frequency of acentric-bearing, lamin-coated micronuclei. These studies reveal a novel role of Aurora B in maintaining genomic integrity by promoting the formation of a passageway in the nuclear envelope through which late-segregating acentric chromosomes enter the telophase daughter nucleus. PMID:25877868

  16. Fundamental limitations of the local approximation for electron distribution function and fluid model in bounded plasmas

    SciTech Connect

    Krasilnikov, M. B. Kudryavtsev, A. A.; Kapustin, K. D.

    2014-12-15

    It is shown that the local approximation for computing the electron distribution function depends both on the ratio between the energy relaxation length and a characteristic plasma length and on the ratio between heating and ambipolar electric fields. In particular, the local approximation is not valid at the discharge periphery even at high pressure due to the fact that the ambipolar electric field practically always is larger than the heating electric field.

  17. Local Release of Highly Loaded Antibodies from Functionalized Nanoporous Support for Cancer Immunotherapy

    SciTech Connect

    Lei, Chenghong; Liu, P.; Chen, Baowei; Mao, Yumeng; Engelmann, Heather E.; Shin, Yongsoon; Jaffar, Jade; Hellstrom, Ingegerd; Liu, Jun; Hellstrom, Karl E.

    2010-05-26

    We report that antibodies can be loaded in functionalized mesoporous silica (FMS) with super-high density to provide long-lasting local release at a given site. Preliminary data indicate that FMS-antibody injected directly into a mouse melanoma induces a greater inhibition of tumor growth than seen in various controls, including the antibody injected intraperitoneally. Our findings introduce a novel approach for local delivery of therapeutically active proteins to tumors and potentially, other diseases.

  18. Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology.

    PubMed

    Sommer, Felix; Bäckhed, Fredrik

    2016-05-01

    Interactions between the host and its associated microbiota differ spatially and the local cross talk determines organ function and physiology. Animals and their organs are not uniform but contain several functional and cellular compartments and gradients. In the intestinal tract, different parts of the gut carry out different functions, tissue structure varies accordingly, epithelial cells are differentially distributed and gradients exist for several physicochemical parameters such as nutrients, pH, or oxygen. Consequently, the microbiota composition also differs along the length of the gut, but also between lumen and mucosa of the same intestinal segment, and even along the crypt-villus axis in the epithelium. Thus, host-microbiota interactions are highly site-specific and the local cross talk determines intestinal function and physiology. Here we review recent advances in our understanding of site-specific host-microbiota interactions and discuss their functional relevance for host physiology. PMID:26990415

  19. DAYSLEEPER: a nuclear and vesicular-localized protein that is expressed in proliferating tissues

    PubMed Central

    2013-01-01

    Background DAYSLEEPER is a domesticated transposase that is essential for development in Arabidopsis thaliana [Nature, 436:282–284, 2005]. It is derived from a hAT-superfamily transposon and contains many of the features found in the coding sequence of these elements [Nature, 436:282–284, 2005, Genetics, 158:949–957, 2001]. This work sheds light on the expression of this gene and localization of its product in protoplasts and in planta. Using deletion constructs, important domains in the protein were identified. Results DAYSLEEPER is predominantly expressed in meristems, developing flowers and siliques. The protein is mainly localized in the nucleus, but can also be seen in discrete foci in the cytoplasm. Using several vesicular markers, we found that these foci belong to vesicular structures of the trans-golgi network, multivesicular bodies (MVB’s) and late endosomes. The central region as well as both the N- and the C-terminus are essential to DAYSLEEPER function, since versions of DAYSLEEPER deleted for these regions are not able to complement the daysleeper phenotype. Like hAT-transposases, we show that DAYSLEEPER has a functionally conserved dimerization domain [J Biol Chem, 282:7563–7575, 2007]. Conclusions DAYSLEEPER has retained the global structure of hAT transposases and it seems that most of these conserved features are essential to DAYSLEEPER’s cellular function. Although structurally similar, DAYSLEEPER seems to have broadened its range of action beyond the nucleus in comparison to transposases. PMID:24330683

  20. Quantifying local exciton, charge resonance, and multiexciton character in correlated wave functions of multichromophoric systems

    NASA Astrophysics Data System (ADS)

    Casanova, David; Krylov, Anna I.

    2016-01-01

    A new method for quantifying the contributions of local excitation, charge resonance, and multiexciton configurations in correlated wave functions of multichromophoric systems is presented. The approach relies on fragment-localized orbitals and employs spin correlators. Its utility is illustrated by calculations on model clusters of hydrogen, ethylene, and tetracene molecules using adiabatic restricted-active-space configuration interaction wave functions. In addition to the wave function analysis, this approach provides a basis for a simple state-specific energy correction accounting for insufficient description of electron correlation. The decomposition scheme also allows one to compute energies of the diabatic states of the local excitonic, charge-resonance, and multi-excitonic character. The new method provides insight into electronic structure of multichromophoric systems and delivers valuable reference data for validating excitonic models.

  1. Nuclear localization of the Hermes transposase depends on basic amino acid residues at the N-terminus of the protein.

    PubMed

    Michel, K; Atkinson, P W

    2003-07-01

    For the Hermes transposable element to be mobilized in its eukaryotic host, the transposase, encoded by the element, must make contact with its DNA. After synthesis in the cytoplasm, the transposase has to be actively imported into the nucleus because its size of 70.1 kDa prevents passive diffusion through the nuclear pore. Studies in vitro using transient expression of a Hermes-EGFP fusion protein in Drosophila melanogaster Schneider 2 cells showed the transposase was located predominantly in the nucleus. In silico sequence analysis, however, did not reveal any nuclear localization signal (NLS). To identify the sequence(s) responsible for localization of Hermes transposase in the nucleus, truncated or mutated forms of the transposase were examined for their influence on sub-cellular localization of marker proteins fused to the transposase. Using the same expression system and a GFP-GUS fusion double marker, residues 1-110 were recognized as sufficient, and residues 1-32 as necessary, for nuclear localization. Amino acid K25 greatly facilitated nuclear localization, indicating that at least this basic amino acid plays a significant role in this process. This sequence overlaps the proposed DNA binding region of the Hermes transposase and is not necessarily conserved in all members of the hAT transposable element family. PMID:12858343

  2. Exchange–Correlation Functionals via Local Interpolation along the Adiabatic Connection

    PubMed Central

    2016-01-01

    The construction of density-functional approximations is explored by modeling the adiabatic connection locally, using energy densities defined in terms of the electrostatic potential of the exchange–correlation hole. These local models are more amenable to the construction of size-consistent approximations than their global counterparts. In this work we use accurate input local ingredients to assess the accuracy of a range of local interpolation models against accurate exchange–correlation energy densities. The importance of the strictly correlated electrons (SCE) functional describing the strong coupling limit is emphasized, enabling the corresponding interpolated functionals to treat strong correlation effects. In addition to exploring the performance of such models numerically for the helium and beryllium isoelectronic series and the dissociation of the hydrogen molecule, an approximate analytic model is presented for the initial slope of the local adiabatic connection. Comparisons are made with approaches based on global models, and prospects for future approximations based on the local adiabatic connection are discussed. PMID:27116427

  3. Exchange-Correlation Functionals via Local Interpolation along the Adiabatic Connection.

    PubMed

    Vuckovic, Stefan; Irons, Tom J P; Savin, Andreas; Teale, Andrew M; Gori-Giorgi, Paola

    2016-06-14

    The construction of density-functional approximations is explored by modeling the adiabatic connection locally, using energy densities defined in terms of the electrostatic potential of the exchange-correlation hole. These local models are more amenable to the construction of size-consistent approximations than their global counterparts. In this work we use accurate input local ingredients to assess the accuracy of a range of local interpolation models against accurate exchange-correlation energy densities. The importance of the strictly correlated electrons (SCE) functional describing the strong coupling limit is emphasized, enabling the corresponding interpolated functionals to treat strong correlation effects. In addition to exploring the performance of such models numerically for the helium and beryllium isoelectronic series and the dissociation of the hydrogen molecule, an approximate analytic model is presented for the initial slope of the local adiabatic connection. Comparisons are made with approaches based on global models, and prospects for future approximations based on the local adiabatic connection are discussed. PMID:27116427

  4. Cortical localization of cognitive function by regression of performance on event-related potentials

    NASA Technical Reports Server (NTRS)

    Montgomery, R. W.; Montgomery, L. D.; Guisado, R.

    1992-01-01

    This paper demonstrates a new method of mapping cortical localization of cognitive function, using electroencephalographic data. Cross-subject regression analyses are used to identify cortical sites and post-stimulus latencies where there is a high correlation between subjects' performance and their cognitive event-related potential amplitude. The procedure was tested using a mental arithmetic task and was found to identify essentially the same cortical regions that have been associated with such tasks on the basis of research with patients suffering localized cortical lesions. Thus, it appears to offer an inexpensive, noninvasive tool for exploring the dynamics of localization in neurologically normal subjects.

  5. Structural determination of importin alpha in complex with beak and feather disease virus capsid nuclear localization signal

    SciTech Connect

    Patterson, Edward I.; Dombrovski, Andrew K.; Swarbrick, Crystall M.D.; Raidal, Shane R.; Forwood, Jade K.

    2013-09-06

    Highlights: •Circovirus capsid proteins contain large nuclear localization signals (NLS). •A method of nuclear import has not been elucidated. •Beak and feather disease virus (BFDV) capsid NLS was crystallized with importin α. •The structure showed BFDV NLS binding to the major site of importin α. •Result shows implications for mechanism of nuclear transport for all circoviruses. -- Abstract: Circoviruses represent a rapidly increasing genus of viruses that infect a variety of vertebrates. Replication requires shuttling viral molecules into the host cell nucleus, a process facilitated by capsid-associated protein (Cap). Whilst a nuclear localization signal (NLS) has been shown to mediate nuclear translocation, the mode of nuclear transport remains to be elucidated. To better understand this process, beak and feather disease virus (BFDV) Cap NLS was crystallized with nuclear import receptor importin-α (Impα). Diffraction yielded structural data to 2.9 Å resolution, and the binding site on both Impα and BFDV Cap NLS were well resolved. The binding mechanism for the major site is likely conserved across circoviruses as supported by the similarity of NLSs in circovirus Caps. This finding illuminates a crucial step for infection of host cells by this viral family, and provides a platform for rational drug design against the binding interface.

  6. Localization of function in anterior cingulate cortex: from psychosurgery to functional neuroimaging.

    PubMed

    Gasquoine, Philip Gerard

    2013-03-01

    Early localizationists linked anterior cingulate cortex (ACC: Brodmann's area 24 and adjacent regions) with emotional behavior, paving the way for bilateral cingulotomy psychosurgery in severe, treatment resistant, cases of obsessive-compulsive disorder, chronic pain, depression, and substance abuse. Neuropsychological follow-up of such cases demonstrated executive function impairment. Abnormal neuroimaged activity in ACC has been found in many psychiatric conditions, including obsessive-compulsive disorder, chronic pain, substance abuse, and schizophrenia. With healthy participants, increased neuroimaged activity in ACC has been linked with challenging executive function tasks, homeostatically incongruous physical states, and the encoding of the pleasant/averseness of stimuli. There is disagreement on the cortical substrate subsumed by the term ACC, the existence of functionally distinct ACC subregions (e.g., dorsal: cognitive vs. ventral: emotion), and the interpretation of functional neuroimaging studies. Synthesis of neuropsychological and functional neuroimaging studies suggests ACC contributes to behavior by modifying responses especially in reaction to challenging cognitive and physical states that require additional effortful cognitive control. This is accomplished by monitoring the emotional salience of stimuli, exerting control over the autonomic nervous system, and modulating cognitive activity. PMID:23313645

  7. A Crowdsourced nucleus: Understanding nuclear organization in terms of dynamically networked protein function

    PubMed Central

    Wood, Ashley M.; Garza-Gongora, Arturo G.; Kosak, Steven T.

    2014-01-01

    The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. PMID:24412853

  8. Nuclear import, virion incorporation, and cell cycle arrest/differentiation are mediated by distinct functional domains of human immunodeficiency virus type 1 Vpr.

    PubMed Central

    Mahalingam, S; Ayyavoo, V; Patel, M; Kieber-Emmons, T; Weiner, D B

    1997-01-01

    The vpr gene product of human immunodeficiency virus type 1 (HIV-1) is a virion-associated protein that is essential for efficient viral replication in monocytes/macrophages. Vpr is primarily localized in the nucleus when expressed in the absence of other viral proteins. Vpr is packaged efficiently into viral particles through interactions with the p6 domain of the Gag precursor polyprotein p55gag. We developed a panel of expression vectors encoding Vpr molecules mutated in the amino-terminal helical domain, leucine-isoleucine (LR) domain, and carboxy-terminal domain to map the different functional domains and to define the interrelationships between virion incorporation, nuclear localization, cell cycle arrest, and differentiation functions of Vpr. We observed that substitution mutations in the N-terminal domain of Vpr impaired both nuclear localization and virion packaging, suggesting that the helical structure may play a vital role in modulating both of these biological properties. The LR domain was found to be involved in the nuclear localization of Vpr. In contrast, cell cycle arrest appears to be largely controlled by the C-terminal domain of Vpr. The LR and C-terminal domains do not appear to be essential for virion incorporation of Vpr. Interestingly, we found that two Vpr mutants harboring single amino acid substitutions (A30L and G75A) retained the ability to translocate to the nucleus but were impaired in the cell cycle arrest function. In contrast, mutation of Leu68 to Ser resulted in a protein that localizes in the cytoplasm while retaining the ability to arrest host cell proliferation. We speculate that the nuclear localization and cell cycle arrest functions of Vpr are not interrelated and that these functions are mediated by separable putative functional domains of Vpr. PMID:9261351

  9. Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin

    PubMed Central

    Dechat, Thomas; Pfleghaar, Katrin; Sengupta, Kaushik; Shimi, Takeshi; Shumaker, Dale K.; Solimando, Liliana; Goldman, Robert D.

    2008-01-01

    Over the past few years it has become evident that the intermediate filament proteins, the types A and B nuclear lamins, not only provide a structural framework for the nucleus, but are also essential for many aspects of normal nuclear function. Insights into lamin-related functions have been derived from studies of the remarkably large number of disease-causing mutations in the human lamin A gene. This review provides an up-to-date overview of the functions of nuclear lamins, emphasizing their roles in epigenetics, chromatin organization, DNA replication, transcription, and DNA repair. In addition, we discuss recent evidence supporting the importance of lamins in viral infections. PMID:18381888

  10. Meshless Local Petrov-Galerkin Euler-Bernoulli Beam Problems: A Radial Basis Function Approach

    NASA Technical Reports Server (NTRS)

    Raju, I. S.; Phillips, D. R.; Krishnamurthy, T.

    2003-01-01

    A radial basis function implementation of the meshless local Petrov-Galerkin (MLPG) method is presented to study Euler-Bernoulli beam problems. Radial basis functions, rather than generalized moving least squares (GMLS) interpolations, are used to develop the trial functions. This choice yields a computationally simpler method as fewer matrix inversions and multiplications are required than when GMLS interpolations are used. Test functions are chosen as simple weight functions as in the conventional MLPG method. Compactly and noncompactly supported radial basis functions are considered. The non-compactly supported cubic radial basis function is found to perform very well. Results obtained from the radial basis MLPG method are comparable to those obtained using the conventional MLPG method for mixed boundary value problems and problems with discontinuous loading conditions.

  11. Dual effect of local anesthetics on the function of excitable rod outer segment disk membrane

    SciTech Connect

    Mashimo, T.; Abe, K.; Yoshiya, I.

    1986-04-01

    The effects of local anesthetics and a divalent cation, Ca2+, on the function of rhodopsin were estimated from the measurements of light-induced proton uptake. The light-induced proton uptake by rhodopsin in the rod outer segment disk membrane was enhanced at lower pH (4) but depressed at higher pHs (6 to 8) by the tertiary amine local anesthetics lidocaine, bupivacaine, tetracaine, and dibucaine. The order of local anesthetic-induced depression of the proton uptake followed that of their clinical anesthetic potencies. The depression of the proton uptake versus the concentration of the uncharged form of local anesthetic nearly describes the same curve for small and large dose of added anesthetic. Furthermore, a neutral local anesthetic, benzocaine, depressed the proton uptake at all pHs between 4 and 7. These results indicate that the depression of the proton uptake is due to the effect of only the uncharged form. It is hypothesized that the uncharged form of local anesthetics interacts hydrophobically with the rhodopsin in the disk membrane. The dual effect of local anesthetics on the proton uptake, on the other hand, suggests that the activation of the function of rhodopsin may be caused by the charged form. There was no significant change in the light-induced proton uptake by rhodopsin when 1 mM of Ca2+ was introduced into the disk membrane at varying pHs in the absence or presence of local anesthetics. This fact indicates that Ca2+ ion does not influence the diprotonating process of metarhodopsin; neither does it interfere with the local anesthetic-induced changes in the rhodopsin molecule.

  12. Red-channel (6000-8000 Å) nuclear spectra of 376 local galaxies

    NASA Astrophysics Data System (ADS)

    Gavazzi, Giuseppe; Consolandi, Guido; Dotti, Massimo; Fossati, Matteo; Savorgnan, Giulia; Gualandi, Roberto; Bruni, Ivan

    2013-10-01

    We obtained long-slit optical spectra of the nuclear regions of 376 galaxies in the local Universe using the 1.5 m Cassini telescope of Bologna Observatory. Of these spectra, 164 were either never taken before by the Sloan Digital Sky Survey (SDSS), or given by the Nasa Extragalactic Database (NED). With these new spectra, we contribute investigating the occurrence of active galactic nuclei (AGNs). Nevertheless, we stress that the present sample is by no means complete, thus, it cannot be used to perform any demographic study. Following the method used in a previous work, we classify the nuclear spectra using a six bin scheme: SEY (Seyfert), sAGN (strong AGN), and wAGN (weak AGN) represent active galactic nuclei of different levels of activity; HII accounts for star-forming nuclei; RET (retired) and PAS (passive) refer to nuclei with poor or no star-formation activity. The spectral classification is performed using the ratio of λ 6584 [NII] to Hα lines and the equivalent width (EW) of Hα versus [NII] /Hα (WHAN diagnostic introduced by Cid Fernandes and collaborators) after correcting Hα for underlying absorption. The obtained spectra are made available in machine readable format via the Strasbourg Astronomical Data Center (CDS) and NED. Full Tables 3 and 4 and Fig. 4 (in FITS format) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/558/A68

  13. An absence of nuclear lamins in keratinocytes leads to ichthyosis, defective epidermal barrier function, and intrusion of nuclear membranes and endoplasmic reticulum into the nuclear chromatin.

    PubMed

    Jung, Hea-Jin; Tatar, Angelica; Tu, Yiping; Nobumori, Chika; Yang, Shao H; Goulbourne, Chris N; Herrmann, Harald; Fong, Loren G; Young, Stephen G

    2014-12-01

    B-type lamins (lamins B1 and B2) have been considered to be essential for many crucial functions in the cell nucleus (e.g., DNA replication and mitotic spindle formation). However, this view has been challenged by the observation that an absence of both B-type lamins in keratinocytes had no effect on cell proliferation or the development of skin and hair. The latter findings raised the possibility that the functions of B-type lamins are subserved by lamins A and C. To explore that idea, we created mice lacking all nuclear lamins in keratinocytes. Those mice developed ichthyosis and a skin barrier defect, which led to death from dehydration within a few days after birth. Microscopy of nuclear-lamin-deficient skin revealed hyperkeratosis and a disordered stratum corneum with an accumulation of neutral lipid droplets; however, BrdU incorporation into keratinocytes was normal. Skin grafting experiments confirmed the stratum corneum abnormalities and normal BrdU uptake. Interestingly, the absence of nuclear lamins in keratinocytes resulted in an interspersion of nuclear/endoplasmic reticulum membranes with the chromatin. Thus, a key function of the nuclear lamina is to serve as a "fence" and prevent the incursion of cytoplasmic organelles into the nuclear chromatin. PMID:25312645

  14. An Absence of Nuclear Lamins in Keratinocytes Leads to Ichthyosis, Defective Epidermal Barrier Function, and Intrusion of Nuclear Membranes and Endoplasmic Reticulum into the Nuclear Chromatin

    PubMed Central

    Jung, Hea-Jin; Tatar, Angelica; Tu, Yiping; Nobumori, Chika; Yang, Shao H.; Goulbourne, Chris N.; Herrmann, Harald

    2014-01-01

    B-type lamins (lamins B1 and B2) have been considered to be essential for many crucial functions in the cell nucleus (e.g., DNA replication and mitotic spindle formation). However, this view has been challenged by the observation that an absence of both B-type lamins in keratinocytes had no effect on cell proliferation or the development of skin and hair. The latter findings raised the possibility that the functions of B-type lamins are subserved by lamins A and C. To explore that idea, we created mice lacking all nuclear lamins in keratinocytes. Those mice developed ichthyosis and a skin barrier defect, which led to death from dehydration within a few days after birth. Microscopy of nuclear-lamin-deficient skin revealed hyperkeratosis and a disordered stratum corneum with an accumulation of neutral lipid droplets; however, BrdU incorporation into keratinocytes was normal. Skin grafting experiments confirmed the stratum corneum abnormalities and normal BrdU uptake. Interestingly, the absence of nuclear lamins in keratinocytes resulted in an interspersion of nuclear/endoplasmic reticulum membranes with the chromatin. Thus, a key function of the nuclear lamina is to serve as a “fence” and prevent the incursion of cytoplasmic organelles into the nuclear chromatin. PMID:25312645

  15. Development and Implementation of a High-Throughput High-Content Screening Assay to Identify Inhibitors of Androgen Receptor Nuclear Localization in Castration-Resistant Prostate Cancer Cells.

    PubMed

    Johnston, Paul A; Nguyen, Minh M; Dar, Javid A; Ai, Junkui; Wang, Yujuan; Masoodi, Khalid Z; Shun, Tongying; Shinde, Sunita; Camarco, Daniel P; Hua, Yun; Huryn, Donna M; Wilson, Gabriela Mustata; Lazo, John S; Nelson, Joel B; Wipf, Peter; Wang, Zhou

    2016-05-01

    Patients with castration-resistant prostate cancer (CRPC) can be treated with abiraterone, a potent inhibitor of androgen synthesis, or enzalutamide, a second-generation androgen receptor (AR) antagonist, both targeting AR signaling. However, most patients relapse after several months of therapy and a majority of patients with relapsed CRPC tumors express the AR target gene prostate-specific antigen (PSA), suggesting that AR signaling is reactivated and can be targeted again to inhibit the relapsed tumors. Novel small molecules capable of inhibiting AR function may lead to urgently needed therapies for patients resistant to abiraterone, enzalutamide, and/or other previously approved antiandrogen therapies. Here, we describe a high-throughput high-content screening (HCS) campaign to identify small-molecule inhibitors of AR nuclear localization in the C4-2 CRPC cell line stably transfected with GFP-AR-GFP (2GFP-AR). The implementation of this HCS assay to screen a National Institutes of Health library of 219,055 compounds led to the discovery of 3 small molecules capable of inhibiting AR nuclear localization and function in C4-2 cells, demonstrating the feasibility of using this cell-based phenotypic assay to identify small molecules targeting the subcellular localization of AR. Furthermore, the three hit compounds provide opportunities to develop novel AR drugs with potential for therapeutic intervention in CRPC patients who have relapsed after treatment with antiandrogens, such as abiraterone and/or enzalutamide. PMID:27187604

  16. Symmetry energy from nuclear masses and neutron-star observations using generalised Skyrme functionals

    NASA Astrophysics Data System (ADS)

    Chamel, N.; Fantina, A. F.; Pearson, J. M.; Goriely, S.

    2016-01-01

    We study the constraints imposed by nuclear mass measurements and neutron-star observations on the symmetry energy. For this purpose, we use a family of unified equations of state of neutron-star interiors, based on generalised Skyrme functionals that were fitted to essentially all the experimental nuclear mass data while ensuring a realistic neutron-matter equation of state.

  17. Testing for parity violation in nuclei using spin density matrices for nuclear density functionals

    NASA Astrophysics Data System (ADS)

    Barrett, B. R.; Giraud, B. G.

    2015-06-01

    The spin density matrix (SDM) used in atomic and molecular physics is revisited for nuclear physics, in the context of the radial density functional theory. The vector part of the SDM defines a ‘hedgehog’ situation, which exists only if nuclear states contain some amount of parity violation. A toy model is given as an illustrative example.

  18. Quantitative cw Overhauser Dynamic Nuclear Polarization for the Analysis of Local Water Dynamics

    PubMed Central

    Franck, John M.; Pavlova, Anna; Scott, John A.; Han, Songi

    2013-01-01

    Liquid state Overhauser Effect Dynamic Nuclear Polarization (ODNP) has experienced a recent resurgence of interest. The ODNP technique described here relies on the double resonance of electron spin resonance (ESR) at the most common, i.e. X-band (~ 10 GHz), frequency and 1H nuclear magnetic resonance (NMR) at ~ 15 MHz. It requires only a standard continuous wave (cw) ESR spectrometer with an NMR probe inserted or built into an X-band cavity. Our focus lies on reviewing a new and powerful manifestation of ODNP as a high frequency NMR relaxometry tool that probes dipolar cross relaxation between the electron spins and the 1H nuclear spins at X-band frequencies. This technique selectively measures the translational mobility of water within a volume extending 0.5–1.5 nm outward from a nitroxide radical spin probe that is attached to a targeted site of a macromolecule. This method has been applied to study the dynamics of water that hydrates or permeates the surface or interior of proteins, polymers, and lipid membrane vesicles. We begin by reviewing the recent advances that have helped develop ODNP into a tool for mapping the dynamic landscape of hydration water with sub-nanometer locality. In order to bind this work coherently together, and to place it in the context of the extensive body of research in the field of NMR relaxometry, we then rephrase the analytical model and extend the description of the ODNP-derived NMR signal enhancements. This extended model highlights several aspects of ODNP data analysis, including the importance of considering all possible effects of microwave sample heating, the need to consider the error associated with various relaxation rates, and the unique ability of ODNP to probe the electron–1H cross-relaxation process, which is uniquely sensitive to fast (tens of ps) dynamical processes. By implementing the relevant corrections in a stepwise fashion, this paper draws a consensus result from previous ODNP procedures, and then shows

  19. Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles

    PubMed Central

    Miyagawa, Ryu; Tano, Keiko; Mizuno, Rie; Nakamura, Yo; Ijiri, Kenichi; Rakwal, Randeep; Shibato, Junko; Masuo, Yoshinori; Mayeda, Akila; Hirose, Tetsuro; Akimitsu, Nobuyoshi

    2012-01-01

    MALAT-1 noncoding RNA is localized to nuclear speckles despite its mRNA-like characteristics. Here, we report the identification of several key factors that promote the localization of MALAT-1 to nuclear speckles and also provide evidence that MALAT-1 is involved in the regulation of gene expression. Heterokaryon assays revealed that MALAT-1 does not shuttle between the nucleus and cytoplasm. RNAi-mediated repression of the nuclear speckle proteins, RNPS1, SRm160, or IBP160, which are well-known mRNA processing factors, resulted in the diffusion of MALAT-1 to the nucleoplasm. We demonstrated that MALAT-1 contains two distinct elements directing transcripts to nuclear speckles, which were also capable of binding to RNPS1 in vitro. Depletion of MALAT-1 represses the expression of several genes. Taken together, our results suggest that RNPS1, SRm160, and IBP160 contribute to the localization of MALAT-1 to nuclear speckles, where MALAT-1 could be involved in regulating gene expression. PMID:22355166

  20. Approaches to local connectivity in autism using resting state functional connectivity MRI.

    PubMed

    Maximo, Jose O; Keown, Christopher L; Nair, Aarti; Müller, Ralph-Axel

    2013-01-01

    While the literature on aberrant long-distance connectivity in autism spectrum disorder (ASD) has grown fast over the past decade, little is known about local connectivity. We used regional homogeneity and local density approaches at different spatial scales to exami